-/* $Id$
- $State$
- $Log$
- Revision 1.123 2006/03/20 10:52:43 brouard
- * imach.c (Module): <title> changed, corresponds to .htm file
- name. <head> headers where missing.
-
- * imach.c (Module): Weights can have a decimal point as for
- English (a comma might work with a correct LC_NUMERIC environment,
- otherwise the weight is truncated).
- Modification of warning when the covariates values are not 0 or
- 1.
- Version 0.98g
-
- Revision 1.122 2006/03/20 09:45:41 brouard
- (Module): Weights can have a decimal point as for
- English (a comma might work with a correct LC_NUMERIC environment,
- otherwise the weight is truncated).
- Modification of warning when the covariates values are not 0 or
- 1.
- Version 0.98g
-
- Revision 1.121 2006/03/16 17:45:01 lievre
- * imach.c (Module): Comments concerning covariates added
-
- * imach.c (Module): refinements in the computation of lli if
- status=-2 in order to have more reliable computation if stepm is
- not 1 month. Version 0.98f
-
- Revision 1.120 2006/03/16 15:10:38 lievre
- (Module): refinements in the computation of lli if
- status=-2 in order to have more reliable computation if stepm is
- not 1 month. Version 0.98f
-
- Revision 1.119 2006/03/15 17:42:26 brouard
- (Module): Bug if status = -2, the loglikelihood was
- computed as likelihood omitting the logarithm. Version O.98e
-
- Revision 1.118 2006/03/14 18:20:07 brouard
- (Module): varevsij Comments added explaining the second
- table of variances if popbased=1 .
- (Module): Covariances of eij, ekl added, graphs fixed, new html link.
- (Module): Function pstamp added
- (Module): Version 0.98d
-
- Revision 1.117 2006/03/14 17:16:22 brouard
- (Module): varevsij Comments added explaining the second
- table of variances if popbased=1 .
- (Module): Covariances of eij, ekl added, graphs fixed, new html link.
- (Module): Function pstamp added
- (Module): Version 0.98d
-
- Revision 1.116 2006/03/06 10:29:27 brouard
- (Module): Variance-covariance wrong links and
- varian-covariance of ej. is needed (Saito).
-
- Revision 1.115 2006/02/27 12:17:45 brouard
- (Module): One freematrix added in mlikeli! 0.98c
-
- Revision 1.114 2006/02/26 12:57:58 brouard
- (Module): Some improvements in processing parameter
- filename with strsep.
-
- Revision 1.113 2006/02/24 14:20:24 brouard
- (Module): Memory leaks checks with valgrind and:
- datafile was not closed, some imatrix were not freed and on matrix
- allocation too.
-
- Revision 1.112 2006/01/30 09:55:26 brouard
- (Module): Back to gnuplot.exe instead of wgnuplot.exe
-
- Revision 1.111 2006/01/25 20:38:18 brouard
- (Module): Lots of cleaning and bugs added (Gompertz)
- (Module): Comments can be added in data file. Missing date values
- can be a simple dot '.'.
-
- Revision 1.110 2006/01/25 00:51:50 brouard
- (Module): Lots of cleaning and bugs added (Gompertz)
-
- Revision 1.109 2006/01/24 19:37:15 brouard
- (Module): Comments (lines starting with a #) are allowed in data.
-
- Revision 1.108 2006/01/19 18:05:42 lievre
- Gnuplot problem appeared...
- To be fixed
-
- Revision 1.107 2006/01/19 16:20:37 brouard
- Test existence of gnuplot in imach path
-
- Revision 1.106 2006/01/19 13:24:36 brouard
- Some cleaning and links added in html output
-
- Revision 1.105 2006/01/05 20:23:19 lievre
- *** empty log message ***
-
- Revision 1.104 2005/09/30 16:11:43 lievre
- (Module): sump fixed, loop imx fixed, and simplifications.
- (Module): If the status is missing at the last wave but we know
- that the person is alive, then we can code his/her status as -2
- (instead of missing=-1 in earlier versions) and his/her
- contributions to the likelihood is 1 - Prob of dying from last
- health status (= 1-p13= p11+p12 in the easiest case of somebody in
- the healthy state at last known wave). Version is 0.98
-
- Revision 1.103 2005/09/30 15:54:49 lievre
- (Module): sump fixed, loop imx fixed, and simplifications.
-
- Revision 1.102 2004/09/15 17:31:30 brouard
- Add the possibility to read data file including tab characters.
-
- Revision 1.101 2004/09/15 10:38:38 brouard
- Fix on curr_time
-
- Revision 1.100 2004/07/12 18:29:06 brouard
- Add version for Mac OS X. Just define UNIX in Makefile
-
- Revision 1.99 2004/06/05 08:57:40 brouard
- *** empty log message ***
-
- Revision 1.98 2004/05/16 15:05:56 brouard
- New version 0.97 . First attempt to estimate force of mortality
- directly from the data i.e. without the need of knowing the health
- state at each age, but using a Gompertz model: log u =a + b*age .
- This is the basic analysis of mortality and should be done before any
- other analysis, in order to test if the mortality estimated from the
- cross-longitudinal survey is different from the mortality estimated
- from other sources like vital statistic data.
-
- The same imach parameter file can be used but the option for mle should be -3.
-
- Agnès, who wrote this part of the code, tried to keep most of the
- former routines in order to include the new code within the former code.
-
- The output is very simple: only an estimate of the intercept and of
- the slope with 95% confident intervals.
-
- Current limitations:
- A) Even if you enter covariates, i.e. with the
- model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
- B) There is no computation of Life Expectancy nor Life Table.
-
- Revision 1.97 2004/02/20 13:25:42 lievre
- Version 0.96d. Population forecasting command line is (temporarily)
- suppressed.
-
- Revision 1.96 2003/07/15 15:38:55 brouard
- * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
- rewritten within the same printf. Workaround: many printfs.
-
- Revision 1.95 2003/07/08 07:54:34 brouard
- * imach.c (Repository):
- (Repository): Using imachwizard code to output a more meaningful covariance
- matrix (cov(a12,c31) instead of numbers.
-
- Revision 1.94 2003/06/27 13:00:02 brouard
- Just cleaning
-
- Revision 1.93 2003/06/25 16:33:55 brouard
- (Module): On windows (cygwin) function asctime_r doesn't
- exist so I changed back to asctime which exists.
- (Module): Version 0.96b
-
- Revision 1.92 2003/06/25 16:30:45 brouard
- (Module): On windows (cygwin) function asctime_r doesn't
- exist so I changed back to asctime which exists.
-
- Revision 1.91 2003/06/25 15:30:29 brouard
- * imach.c (Repository): Duplicated warning errors corrected.
- (Repository): Elapsed time after each iteration is now output. It
- helps to forecast when convergence will be reached. Elapsed time
- is stamped in powell. We created a new html file for the graphs
- concerning matrix of covariance. It has extension -cov.htm.
-
- Revision 1.90 2003/06/24 12:34:15 brouard
- (Module): Some bugs corrected for windows. Also, when
- mle=-1 a template is output in file "or"mypar.txt with the design
- of the covariance matrix to be input.
-
- Revision 1.89 2003/06/24 12:30:52 brouard
- (Module): Some bugs corrected for windows. Also, when
- mle=-1 a template is output in file "or"mypar.txt with the design
- of the covariance matrix to be input.
-
- Revision 1.88 2003/06/23 17:54:56 brouard
- * 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.
-
- Revision 1.87 2003/06/18 12:26:01 brouard
- Version 0.96
-
- Revision 1.86 2003/06/17 20:04:08 brouard
- (Module): Change position of html and gnuplot routines and added
- routine fileappend.
-
- Revision 1.85 2003/06/17 13:12:43 brouard
- * imach.c (Repository): Check when date of death was earlier that
- current date of interview. It may happen when the death was just
- prior to the death. In this case, dh was negative and likelihood
- was wrong (infinity). We still send an "Error" but patch by
- assuming that the date of death was just one stepm after the
- interview.
- (Repository): Because some people have very long ID (first column)
- we changed int to long in num[] and we added a new lvector for
- memory allocation. But we also truncated to 8 characters (left
- truncation)
- (Repository): No more line truncation errors.
-
- Revision 1.84 2003/06/13 21:44:43 brouard
- * imach.c (Repository): Replace "freqsummary" at a correct
- place. It differs from routine "prevalence" which may be called
- many times. Probs is memory consuming and must be used with
- parcimony.
- Version 0.95a3 (should output exactly the same maximization than 0.8a2)
-
- Revision 1.83 2003/06/10 13:39:11 lievre
- *** empty log message ***
-
- Revision 1.82 2003/06/05 15:57:20 brouard
- Add log in imach.c and fullversion number is now printed.
-
-*/
-/*
- Interpolated Markov Chain
-
- Short summary of the programme:
-
- This program computes Healthy Life Expectancies from
- cross-longitudinal data. Cross-longitudinal data consist in: -1- a
- first survey ("cross") where individuals from different ages are
- interviewed on their health status or degree of disability (in the
- case of a health survey which is our main interest) -2- at least a
- second wave of interviews ("longitudinal") which measure each change
- (if any) in individual health status. Health expectancies are
- computed from the time spent in each health state according to a
- model. More health states you consider, more time is necessary to reach the
- Maximum Likelihood of the parameters involved in the model. The
- simplest model is the multinomial logistic model where pij is the
- probability to be observed in state j at the second wave
- conditional to be observed in state i at the first wave. Therefore
- the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
- 'age' is age and 'sex' is a covariate. If you want to have a more
- complex model than "constant and age", you should modify the program
- where the markup *Covariates have to be included here again* invites
- you to do it. More covariates you add, slower the
- convergence.
-
- The advantage of this computer programme, compared to a simple
- multinomial logistic model, is clear when the delay between waves is not
- identical for each individual. Also, if a individual missed an
- intermediate interview, the information is lost, but taken into
- account using an interpolation or extrapolation.
-
- hPijx is the probability to be observed in state i at age x+h
- conditional to the observed state i at age x. The delay 'h' can be
- split into an exact number (nh*stepm) of unobserved intermediate
- states. This elementary transition (by month, quarter,
- semester or year) is modelled as a multinomial logistic. The hPx
- matrix is simply the matrix product of nh*stepm elementary matrices
- and the contribution of each individual to the likelihood is simply
- hPijx.
-
- Also this programme outputs the covariance matrix of the parameters but also
- of the life expectancies. It also computes the period (stable) prevalence.
-
- Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
- Institut national d'études démographiques, Paris.
- This software have been partly granted by Euro-REVES, a concerted action
- from the European Union.
- It is copyrighted identically to a GNU software product, ie programme and
- software can be distributed freely for non commercial use. Latest version
- can be accessed at http://euroreves.ined.fr/imach .
-
- Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
- or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
-
- **********************************************************************/
-/*
- main
- read parameterfile
- read datafile
- concatwav
- freqsummary
- if (mle >= 1)
- mlikeli
- print results files
- if mle==1
- computes hessian
- read end of parameter file: agemin, agemax, bage, fage, estepm
- begin-prev-date,...
- open gnuplot file
- open html file
- period (stable) prevalence
- for age prevalim()
- h Pij x
- variance of p varprob
- forecasting if prevfcast==1 prevforecast call prevalence()
- health expectancies
- Variance-covariance of DFLE
- prevalence()
- movingaverage()
- varevsij()
- if popbased==1 varevsij(,popbased)
- total life expectancies
- Variance of period (stable) prevalence
- end
-*/
-
-
-
-
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <unistd.h>
-
-#include <limits.h>
-#include <sys/types.h>
-#include <sys/stat.h>
-#include <errno.h>
-extern int errno;
-
-/* #include <sys/time.h> */
-#include <time.h>
-#include "timeval.h"
-
-/* #include <libintl.h> */
-/* #define _(String) gettext (String) */
-
-#define MAXLINE 256
-
-#define GNUPLOTPROGRAM "gnuplot"
-/*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
-#define FILENAMELENGTH 132
-
-#define GLOCK_ERROR_NOPATH -1 /* empty path */
-#define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
-
-#define MAXPARM 30 /* Maximum number of parameters for the optimization */
-#define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
-
-#define NINTERVMAX 8
-#define NLSTATEMAX 8 /* Maximum number of live states (for func) */
-#define NDEATHMAX 8 /* Maximum number of dead states (for func) */
-#define NCOVMAX 8 /* Maximum number of covariates */
-#define MAXN 20000
-#define YEARM 12. /* Number of months per year */
-#define AGESUP 130
-#define AGEBASE 40
-#define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
-#ifdef UNIX
-#define DIRSEPARATOR '/'
-#define CHARSEPARATOR "/"
-#define ODIRSEPARATOR '\\'
-#else
-#define DIRSEPARATOR '\\'
-#define CHARSEPARATOR "\\"
-#define ODIRSEPARATOR '/'
-#endif
-
-/* $Id$ */
-/* $State$ */
-
-char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";
-char fullversion[]="$Revision$ $Date$";
-char strstart[80];
-char optionfilext[10], optionfilefiname[FILENAMELENGTH];
-int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
-int nvar;
-int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
-int npar=NPARMAX;
-int nlstate=2; /* Number of live states */
-int ndeath=1; /* Number of dead states */
-int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
-int popbased=0;
-
-int *wav; /* Number of waves for this individuual 0 is possible */
-int maxwav; /* Maxim number of waves */
-int jmin, jmax; /* min, max spacing between 2 waves */
-int ijmin, ijmax; /* Individuals having jmin and jmax */
-int gipmx, gsw; /* Global variables on the number of contributions
- to the likelihood and the sum of weights (done by funcone)*/
-int mle, weightopt;
-int **mw; /* mw[mi][i] is number of the mi wave for this individual */
-int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
-int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
- * wave mi and wave mi+1 is not an exact multiple of stepm. */
-double jmean; /* Mean space between 2 waves */
-double **oldm, **newm, **savm; /* Working pointers to matrices */
-double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
-FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
-FILE *ficlog, *ficrespow;
-int globpr; /* Global variable for printing or not */
-double fretone; /* Only one call to likelihood */
-long ipmx; /* Number of contributions */
-double sw; /* Sum of weights */
-char filerespow[FILENAMELENGTH];
-char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
-FILE *ficresilk;
-FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
-FILE *ficresprobmorprev;
-FILE *fichtm, *fichtmcov; /* Html File */
-FILE *ficreseij;
-char filerese[FILENAMELENGTH];
-FILE *ficresstdeij;
-char fileresstde[FILENAMELENGTH];
-FILE *ficrescveij;
-char filerescve[FILENAMELENGTH];
-FILE *ficresvij;
-char fileresv[FILENAMELENGTH];
-FILE *ficresvpl;
-char fileresvpl[FILENAMELENGTH];
-char title[MAXLINE];
-char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
-char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
-char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
-char command[FILENAMELENGTH];
-int outcmd=0;
-
-char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
-
-char filelog[FILENAMELENGTH]; /* Log file */
-char filerest[FILENAMELENGTH];
-char fileregp[FILENAMELENGTH];
-char popfile[FILENAMELENGTH];
-
-char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
-
-struct timeval start_time, end_time, curr_time, last_time, forecast_time;
-struct timezone tzp;
-extern int gettimeofday();
-struct tm tmg, tm, tmf, *gmtime(), *localtime();
-long time_value;
-extern long time();
-char strcurr[80], strfor[80];
-
-char *endptr;
-long lval;
-double dval;
-
-#define NR_END 1
-#define FREE_ARG char*
-#define FTOL 1.0e-10
-
-#define NRANSI
-#define ITMAX 200
-
-#define TOL 2.0e-4
-
-#define CGOLD 0.3819660
-#define ZEPS 1.0e-10
-#define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);
-
-#define GOLD 1.618034
-#define GLIMIT 100.0
-#define TINY 1.0e-20
-
-static double maxarg1,maxarg2;
-#define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
-#define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
-
-#define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
-#define rint(a) floor(a+0.5)
-
-static double sqrarg;
-#define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
-#define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
-int agegomp= AGEGOMP;
-
-int imx;
-int stepm=1;
-/* Stepm, step in month: minimum step interpolation*/
-
-int estepm;
-/* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
-
-int m,nb;
-long *num;
-int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
-double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
-double **pmmij, ***probs;
-double *ageexmed,*agecens;
-double dateintmean=0;
-
-double *weight;
-int **s; /* Status */
-double *agedc, **covar, idx;
-int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
-double *lsurv, *lpop, *tpop;
-
-double ftol=FTOL; /* Tolerance for computing Max Likelihood */
-double ftolhess; /* Tolerance for computing hessian */
-
-/**************** split *************************/
-static int split( char *path, char *dirc, char *name, char *ext, char *finame )
-{
- /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
- the name of the file (name), its extension only (ext) and its first part of the name (finame)
- */
- char *ss; /* pointer */
- int l1, l2; /* length counters */
-
- l1 = strlen(path ); /* length of path */
- if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
- ss= strrchr( path, DIRSEPARATOR ); /* find last / */
- if ( ss == NULL ) { /* no directory, so determine current directory */
- strcpy( name, path ); /* we got the fullname name because no directory */
- /*if(strrchr(path, ODIRSEPARATOR )==NULL)
- printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
- /* get current working directory */
- /* extern char* getcwd ( char *buf , int len);*/
- if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
- return( GLOCK_ERROR_GETCWD );
- }
- /* got dirc from getcwd*/
- printf(" DIRC = %s \n",dirc);
- } else { /* strip direcotry from path */
- ss++; /* after this, the filename */
- l2 = strlen( ss ); /* length of filename */
- if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
- strcpy( name, ss ); /* save file name */
- strncpy( dirc, path, l1 - l2 ); /* now the directory */
- dirc[l1-l2] = 0; /* add zero */
- printf(" DIRC2 = %s \n",dirc);
- }
- /* We add a separator at the end of dirc if not exists */
- l1 = strlen( dirc ); /* length of directory */
- if( dirc[l1-1] != DIRSEPARATOR ){
- dirc[l1] = DIRSEPARATOR;
- dirc[l1+1] = 0;
- printf(" DIRC3 = %s \n",dirc);
- }
- ss = strrchr( name, '.' ); /* find last / */
- if (ss >0){
- ss++;
- strcpy(ext,ss); /* save extension */
- l1= strlen( name);
- l2= strlen(ss)+1;
- strncpy( finame, name, l1-l2);
- finame[l1-l2]= 0;
- }
-
- return( 0 ); /* we're done */
-}
-
-
-/******************************************/
-
-void replace_back_to_slash(char *s, char*t)
-{
- int i;
- int lg=0;
- i=0;
- lg=strlen(t);
- for(i=0; i<= lg; i++) {
- (s[i] = t[i]);
- if (t[i]== '\\') s[i]='/';
- }
-}
-
-int nbocc(char *s, char occ)
-{
- int i,j=0;
- int lg=20;
- i=0;
- lg=strlen(s);
- for(i=0; i<= lg; i++) {
- if (s[i] == occ ) j++;
- }
- return j;
-}
-
-void cutv(char *u,char *v, char*t, char occ)
-{
- /* cuts string t into u and v where u ends before first occurence of char 'occ'
- and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
- gives u="abcedf" and v="ghi2j" */
- int i,lg,j,p=0;
- i=0;
- for(j=0; j<=strlen(t)-1; j++) {
- if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
- }
-
- lg=strlen(t);
- for(j=0; j<p; j++) {
- (u[j] = t[j]);
- }
- u[p]='\0';
-
- for(j=0; j<= lg; j++) {
- if (j>=(p+1))(v[j-p-1] = t[j]);
- }
-}
-
-/********************** nrerror ********************/
-
-void nrerror(char error_text[])
-{
- fprintf(stderr,"ERREUR ...\n");
- fprintf(stderr,"%s\n",error_text);
- exit(EXIT_FAILURE);
-}
-/*********************** vector *******************/
-double *vector(int nl, int nh)
-{
- double *v;
- v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
- if (!v) nrerror("allocation failure in vector");
- return v-nl+NR_END;
-}
-
-/************************ free vector ******************/
-void free_vector(double*v, int nl, int nh)
-{
- free((FREE_ARG)(v+nl-NR_END));
-}
-
-/************************ivector *******************************/
-int *ivector(long nl,long nh)
-{
- int *v;
- v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
- if (!v) nrerror("allocation failure in ivector");
- return v-nl+NR_END;
-}
-
-/******************free ivector **************************/
-void free_ivector(int *v, long nl, long nh)
-{
- free((FREE_ARG)(v+nl-NR_END));
-}
-
-/************************lvector *******************************/
-long *lvector(long nl,long nh)
-{
- long *v;
- v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
- if (!v) nrerror("allocation failure in ivector");
- return v-nl+NR_END;
-}
-
-/******************free lvector **************************/
-void free_lvector(long *v, long nl, long nh)
-{
- free((FREE_ARG)(v+nl-NR_END));
-}
-
-/******************* imatrix *******************************/
-int **imatrix(long nrl, long nrh, long ncl, long nch)
- /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
-{
- long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;
- int **m;
-
- /* allocate pointers to rows */
- m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));
- if (!m) nrerror("allocation failure 1 in matrix()");
- m += NR_END;
- m -= nrl;
-
-
- /* allocate rows and set pointers to them */
- m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));
- if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
- m[nrl] += NR_END;
- m[nrl] -= ncl;
-
- for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;
-
- /* return pointer to array of pointers to rows */
- return m;
-}
-
-/****************** free_imatrix *************************/
-void free_imatrix(m,nrl,nrh,ncl,nch)
- int **m;
- long nch,ncl,nrh,nrl;
- /* free an int matrix allocated by imatrix() */
-{
- free((FREE_ARG) (m[nrl]+ncl-NR_END));
- free((FREE_ARG) (m+nrl-NR_END));
-}
-
-/******************* matrix *******************************/
-double **matrix(long nrl, long nrh, long ncl, long nch)
-{
- long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
- double **m;
-
- m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
- if (!m) nrerror("allocation failure 1 in matrix()");
- m += NR_END;
- m -= nrl;
-
- m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
- if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
- m[nrl] += NR_END;
- m[nrl] -= ncl;
-
- for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
- return m;
- /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
- */
-}
-
-/*************************free matrix ************************/
-void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
-{
- free((FREE_ARG)(m[nrl]+ncl-NR_END));
- free((FREE_ARG)(m+nrl-NR_END));
-}
-
-/******************* ma3x *******************************/
-double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
-{
- long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
- double ***m;
-
- m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
- if (!m) nrerror("allocation failure 1 in matrix()");
- m += NR_END;
- m -= nrl;
-
- m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
- if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
- m[nrl] += NR_END;
- m[nrl] -= ncl;
-
- for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
-
- m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
- if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
- m[nrl][ncl] += NR_END;
- m[nrl][ncl] -= nll;
- for (j=ncl+1; j<=nch; j++)
- m[nrl][j]=m[nrl][j-1]+nlay;
-
- for (i=nrl+1; i<=nrh; i++) {
- m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
- for (j=ncl+1; j<=nch; j++)
- m[i][j]=m[i][j-1]+nlay;
- }
- return m;
- /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
- &(m[i][j][k]) <=> *((*(m+i) + j)+k)
- */
-}
-
-/*************************free ma3x ************************/
-void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
-{
- free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
- free((FREE_ARG)(m[nrl]+ncl-NR_END));
- free((FREE_ARG)(m+nrl-NR_END));
-}
-
-/*************** function subdirf ***********/
-char *subdirf(char fileres[])
-{
- /* Caution optionfilefiname is hidden */
- strcpy(tmpout,optionfilefiname);
- strcat(tmpout,"/"); /* Add to the right */
- strcat(tmpout,fileres);
- return tmpout;
-}
-
-/*************** function subdirf2 ***********/
-char *subdirf2(char fileres[], char *preop)
-{
-
- /* Caution optionfilefiname is hidden */
- strcpy(tmpout,optionfilefiname);
- strcat(tmpout,"/");
- strcat(tmpout,preop);
- strcat(tmpout,fileres);
- return tmpout;
-}
-
-/*************** function subdirf3 ***********/
-char *subdirf3(char fileres[], char *preop, char *preop2)
-{
-
- /* Caution optionfilefiname is hidden */
- strcpy(tmpout,optionfilefiname);
- strcat(tmpout,"/");
- strcat(tmpout,preop);
- strcat(tmpout,preop2);
- strcat(tmpout,fileres);
- return tmpout;
-}
-
-/***************** f1dim *************************/
-extern int ncom;
-extern double *pcom,*xicom;
-extern double (*nrfunc)(double []);
-
-double f1dim(double x)
-{
- int j;
- double f;
- double *xt;
-
- xt=vector(1,ncom);
- for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];
- f=(*nrfunc)(xt);
- free_vector(xt,1,ncom);
- return f;
-}
-
-/*****************brent *************************/
-double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin)
-{
- int iter;
- double a,b,d,etemp;
- double fu,fv,fw,fx;
- double ftemp;
- double p,q,r,tol1,tol2,u,v,w,x,xm;
- double e=0.0;
-
- a=(ax < cx ? ax : cx);
- b=(ax > cx ? ax : cx);
- x=w=v=bx;
- fw=fv=fx=(*f)(x);
- for (iter=1;iter<=ITMAX;iter++) {
- xm=0.5*(a+b);
- tol2=2.0*(tol1=tol*fabs(x)+ZEPS);
- /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
- printf(".");fflush(stdout);
- fprintf(ficlog,".");fflush(ficlog);
-#ifdef DEBUG
- 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);
- 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);
- /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
-#endif
- if (fabs(x-xm) <= (tol2-0.5*(b-a))){
- *xmin=x;
- return fx;
- }
- ftemp=fu;
- if (fabs(e) > tol1) {
- r=(x-w)*(fx-fv);
- q=(x-v)*(fx-fw);
- p=(x-v)*q-(x-w)*r;
- q=2.0*(q-r);
- if (q > 0.0) p = -p;
- q=fabs(q);
- etemp=e;
- e=d;
- if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))
- d=CGOLD*(e=(x >= xm ? a-x : b-x));
- else {
- d=p/q;
- u=x+d;
- if (u-a < tol2 || b-u < tol2)
- d=SIGN(tol1,xm-x);
- }
- } else {
- d=CGOLD*(e=(x >= xm ? a-x : b-x));
- }
- u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));
- fu=(*f)(u);
- if (fu <= fx) {
- if (u >= x) a=x; else b=x;
- SHFT(v,w,x,u)
- SHFT(fv,fw,fx,fu)
- } else {
- if (u < x) a=u; else b=u;
- if (fu <= fw || w == x) {
- v=w;
- w=u;
- fv=fw;
- fw=fu;
- } else if (fu <= fv || v == x || v == w) {
- v=u;
- fv=fu;
- }
- }
- }
- nrerror("Too many iterations in brent");
- *xmin=x;
- return fx;
-}
-
-/****************** mnbrak ***********************/
-
-void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,
- double (*func)(double))
-{
- double ulim,u,r,q, dum;
- double fu;
-
- *fa=(*func)(*ax);
- *fb=(*func)(*bx);
- if (*fb > *fa) {
- SHFT(dum,*ax,*bx,dum)
- SHFT(dum,*fb,*fa,dum)
- }
- *cx=(*bx)+GOLD*(*bx-*ax);
- *fc=(*func)(*cx);
- while (*fb > *fc) {
- r=(*bx-*ax)*(*fb-*fc);
- q=(*bx-*cx)*(*fb-*fa);
- u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/
- (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));
- ulim=(*bx)+GLIMIT*(*cx-*bx);
- if ((*bx-u)*(u-*cx) > 0.0) {
- fu=(*func)(u);
- } else if ((*cx-u)*(u-ulim) > 0.0) {
- fu=(*func)(u);
- if (fu < *fc) {
- SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))
- SHFT(*fb,*fc,fu,(*func)(u))
- }
- } else if ((u-ulim)*(ulim-*cx) >= 0.0) {
- u=ulim;
- fu=(*func)(u);
- } else {
- u=(*cx)+GOLD*(*cx-*bx);
- fu=(*func)(u);
- }
- SHFT(*ax,*bx,*cx,u)
- SHFT(*fa,*fb,*fc,fu)
- }
-}
-
-/*************** linmin ************************/
-
-int ncom;
-double *pcom,*xicom;
-double (*nrfunc)(double []);
-
-void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))
-{
- double brent(double ax, double bx, double cx,
- double (*f)(double), double tol, double *xmin);
- double f1dim(double x);
- void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,
- double *fc, double (*func)(double));
- int j;
- double xx,xmin,bx,ax;
- double fx,fb,fa;
-
- ncom=n;
- pcom=vector(1,n);
- xicom=vector(1,n);
- nrfunc=func;
- for (j=1;j<=n;j++) {
- pcom[j]=p[j];
- xicom[j]=xi[j];
- }
- ax=0.0;
- xx=1.0;
- mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);
- *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
-#ifdef DEBUG
- printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
- fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
-#endif
- for (j=1;j<=n;j++) {
- xi[j] *= xmin;
- p[j] += xi[j];
- }
- free_vector(xicom,1,n);
- free_vector(pcom,1,n);
-}
-
-char *asc_diff_time(long time_sec, char ascdiff[])
-{
- long sec_left, days, hours, minutes;
- days = (time_sec) / (60*60*24);
- sec_left = (time_sec) % (60*60*24);
- hours = (sec_left) / (60*60) ;
- sec_left = (sec_left) %(60*60);
- minutes = (sec_left) /60;
- sec_left = (sec_left) % (60);
- sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);
- return ascdiff;
-}
-
-/*************** powell ************************/
-void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,
- double (*func)(double []))
-{
- void linmin(double p[], double xi[], int n, double *fret,
- double (*func)(double []));
- int i,ibig,j;
- double del,t,*pt,*ptt,*xit;
- double fp,fptt;
- double *xits;
- int niterf, itmp;
-
- pt=vector(1,n);
- ptt=vector(1,n);
- xit=vector(1,n);
- xits=vector(1,n);
- *fret=(*func)(p);
- for (j=1;j<=n;j++) pt[j]=p[j];
- for (*iter=1;;++(*iter)) {
- fp=(*fret);
- ibig=0;
- del=0.0;
- last_time=curr_time;
- (void) gettimeofday(&curr_time,&tzp);
- 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);
- 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); fflush(ficlog);
-/* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
- for (i=1;i<=n;i++) {
- printf(" %d %.12f",i, p[i]);
- fprintf(ficlog," %d %.12lf",i, p[i]);
- fprintf(ficrespow," %.12lf", p[i]);
- }
- printf("\n");
- fprintf(ficlog,"\n");
- fprintf(ficrespow,"\n");fflush(ficrespow);
- if(*iter <=3){
- tm = *localtime(&curr_time.tv_sec);
- strcpy(strcurr,asctime(&tm));
-/* asctime_r(&tm,strcurr); */
- forecast_time=curr_time;
- itmp = strlen(strcurr);
- if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
- strcurr[itmp-1]='\0';
- printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
- fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
- for(niterf=10;niterf<=30;niterf+=10){
- forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
- tmf = *localtime(&forecast_time.tv_sec);
-/* asctime_r(&tmf,strfor); */
- strcpy(strfor,asctime(&tmf));
- itmp = strlen(strfor);
- if(strfor[itmp-1]=='\n')
- strfor[itmp-1]='\0';
- 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);
- 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);
- }
- }
- for (i=1;i<=n;i++) {
- for (j=1;j<=n;j++) xit[j]=xi[j][i];
- fptt=(*fret);
-#ifdef DEBUG
- printf("fret=%lf \n",*fret);
- fprintf(ficlog,"fret=%lf \n",*fret);
-#endif
- printf("%d",i);fflush(stdout);
- fprintf(ficlog,"%d",i);fflush(ficlog);
- linmin(p,xit,n,fret,func);
- if (fabs(fptt-(*fret)) > del) {
- del=fabs(fptt-(*fret));
- ibig=i;
- }
-#ifdef DEBUG
- printf("%d %.12e",i,(*fret));
- fprintf(ficlog,"%d %.12e",i,(*fret));
- for (j=1;j<=n;j++) {
- xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
- printf(" x(%d)=%.12e",j,xit[j]);
- fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
- }
- for(j=1;j<=n;j++) {
- printf(" p=%.12e",p[j]);
- fprintf(ficlog," p=%.12e",p[j]);
- }
- printf("\n");
- fprintf(ficlog,"\n");
-#endif
- }
- if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
-#ifdef DEBUG
- int k[2],l;
- k[0]=1;
- k[1]=-1;
- printf("Max: %.12e",(*func)(p));
- fprintf(ficlog,"Max: %.12e",(*func)(p));
- for (j=1;j<=n;j++) {
- printf(" %.12e",p[j]);
- fprintf(ficlog," %.12e",p[j]);
- }
- printf("\n");
- fprintf(ficlog,"\n");
- for(l=0;l<=1;l++) {
- for (j=1;j<=n;j++) {
- ptt[j]=p[j]+(p[j]-pt[j])*k[l];
- printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
- fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
- }
- printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
- fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
- }
-#endif
-
-
- free_vector(xit,1,n);
- free_vector(xits,1,n);
- free_vector(ptt,1,n);
- free_vector(pt,1,n);
- return;
- }
- if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");
- for (j=1;j<=n;j++) {
- ptt[j]=2.0*p[j]-pt[j];
- xit[j]=p[j]-pt[j];
- pt[j]=p[j];
- }
- fptt=(*func)(ptt);
- if (fptt < fp) {
- t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);
- if (t < 0.0) {
- linmin(p,xit,n,fret,func);
- for (j=1;j<=n;j++) {
- xi[j][ibig]=xi[j][n];
- xi[j][n]=xit[j];
- }
-#ifdef DEBUG
- printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
- fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
- for(j=1;j<=n;j++){
- printf(" %.12e",xit[j]);
- fprintf(ficlog," %.12e",xit[j]);
- }
- printf("\n");
- fprintf(ficlog,"\n");
-#endif
- }
- }
- }
-}
-
-/**** Prevalence limit (stable or period prevalence) ****************/
-
-double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
-{
- /* Computes the prevalence limit in each live state at age x by left multiplying the unit
- matrix by transitions matrix until convergence is reached */
-
- int i, ii,j,k;
- double min, max, maxmin, maxmax,sumnew=0.;
- double **matprod2();
- double **out, cov[NCOVMAX], **pmij();
- double **newm;
- double agefin, delaymax=50 ; /* Max number of years to converge */
-
- for (ii=1;ii<=nlstate+ndeath;ii++)
- for (j=1;j<=nlstate+ndeath;j++){
- oldm[ii][j]=(ii==j ? 1.0 : 0.0);
- }
-
- cov[1]=1.;
-
- /* Even if hstepm = 1, at least one multiplication by the unit matrix */
- for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
- newm=savm;
- /* Covariates have to be included here again */
- cov[2]=agefin;
-
- for (k=1; k<=cptcovn;k++) {
- cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
- /* 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]]);*/
- }
- for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
- for (k=1; k<=cptcovprod;k++)
- cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-
- /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
- /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
- /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
- out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
-
- savm=oldm;
- oldm=newm;
- maxmax=0.;
- for(j=1;j<=nlstate;j++){
- min=1.;
- max=0.;
- for(i=1; i<=nlstate; i++) {
- sumnew=0;
- for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
- prlim[i][j]= newm[i][j]/(1-sumnew);
- max=FMAX(max,prlim[i][j]);
- min=FMIN(min,prlim[i][j]);
- }
- maxmin=max-min;
- maxmax=FMAX(maxmax,maxmin);
- }
- if(maxmax < ftolpl){
- return prlim;
- }
- }
-}
-
-/*************** transition probabilities ***************/
-
-double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
-{
- double s1, s2;
- /*double t34;*/
- int i,j,j1, nc, ii, jj;
-
- for(i=1; i<= nlstate; i++){
- for(j=1; j<i;j++){
- for (nc=1, s2=0.;nc <=ncovmodel; nc++){
- /*s2 += param[i][j][nc]*cov[nc];*/
- s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
-/* printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
- }
- ps[i][j]=s2;
-/* printf("s1=%.17e, s2=%.17e\n",s1,s2); */
- }
- for(j=i+1; j<=nlstate+ndeath;j++){
- for (nc=1, s2=0.;nc <=ncovmodel; nc++){
- s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
-/* printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
- }
- ps[i][j]=s2;
- }
- }
- /*ps[3][2]=1;*/
-
- for(i=1; i<= nlstate; i++){
- s1=0;
- for(j=1; j<i; j++)
- s1+=exp(ps[i][j]);
- for(j=i+1; j<=nlstate+ndeath; j++)
- s1+=exp(ps[i][j]);
- ps[i][i]=1./(s1+1.);
- for(j=1; j<i; j++)
- ps[i][j]= exp(ps[i][j])*ps[i][i];
- for(j=i+1; j<=nlstate+ndeath; j++)
- ps[i][j]= exp(ps[i][j])*ps[i][i];
- /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
- } /* end i */
-
- for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
- for(jj=1; jj<= nlstate+ndeath; jj++){
- ps[ii][jj]=0;
- ps[ii][ii]=1;
- }
- }
-
-
-/* for(ii=1; ii<= nlstate+ndeath; ii++){ */
-/* for(jj=1; jj<= nlstate+ndeath; jj++){ */
-/* printf("ddd %lf ",ps[ii][jj]); */
-/* } */
-/* printf("\n "); */
-/* } */
-/* printf("\n ");printf("%lf ",cov[2]); */
- /*
- for(i=1; i<= npar; i++) printf("%f ",x[i]);
- goto end;*/
- return ps;
-}
-
-/**************** Product of 2 matrices ******************/
-
-double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
-{
- /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
- b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
- /* in, b, out are matrice of pointers which should have been initialized
- before: only the contents of out is modified. The function returns
- a pointer to pointers identical to out */
- long i, j, k;
- for(i=nrl; i<= nrh; i++)
- for(k=ncolol; k<=ncoloh; k++)
- for(j=ncl,out[i][k]=0.; j<=nch; j++)
- out[i][k] +=in[i][j]*b[j][k];
-
- return out;
-}
-
-
-/************* Higher Matrix Product ***************/
-
-double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
-{
- /* Computes the transition matrix starting at age 'age' over
- 'nhstepm*hstepm*stepm' months (i.e. until
- age (in years) age+nhstepm*hstepm*stepm/12) by multiplying
- nhstepm*hstepm matrices.
- Output is stored in matrix po[i][j][h] for h every 'hstepm' step
- (typically every 2 years instead of every month which is too big
- for the memory).
- Model is determined by parameters x and covariates have to be
- included manually here.
-
- */
-
- int i, j, d, h, k;
- double **out, cov[NCOVMAX];
- double **newm;
-
- /* Hstepm could be zero and should return the unit matrix */
- for (i=1;i<=nlstate+ndeath;i++)
- for (j=1;j<=nlstate+ndeath;j++){
- oldm[i][j]=(i==j ? 1.0 : 0.0);
- po[i][j][0]=(i==j ? 1.0 : 0.0);
- }
- /* Even if hstepm = 1, at least one multiplication by the unit matrix */
- for(h=1; h <=nhstepm; h++){
- for(d=1; d <=hstepm; d++){
- newm=savm;
- /* Covariates have to be included here again */
- cov[1]=1.;
- cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
- for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
- for (k=1; k<=cptcovage;k++)
- cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
- for (k=1; k<=cptcovprod;k++)
- cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-
-
- /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
- /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
- out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
- pmij(pmmij,cov,ncovmodel,x,nlstate));
- savm=oldm;
- oldm=newm;
- }
- for(i=1; i<=nlstate+ndeath; i++)
- for(j=1;j<=nlstate+ndeath;j++) {
- po[i][j][h]=newm[i][j];
- /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
- */
- }
- } /* end h */
- return po;
-}
-
-
-/*************** log-likelihood *************/
-double func( double *x)
-{
- int i, ii, j, k, mi, d, kk;
- double l, ll[NLSTATEMAX], cov[NCOVMAX];
- double **out;
- double sw; /* Sum of weights */
- double lli; /* Individual log likelihood */
- int s1, s2;
- double bbh, survp;
- long ipmx;
- /*extern weight */
- /* We are differentiating ll according to initial status */
- /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
- /*for(i=1;i<imx;i++)
- printf(" %d\n",s[4][i]);
- */
- cov[1]=1.;
-
- for(k=1; k<=nlstate; k++) ll[k]=0.;
-
- if(mle==1){
- for (i=1,ipmx=0, sw=0.; i<=imx; i++){
- for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
- for(mi=1; mi<= wav[i]-1; mi++){
- for (ii=1;ii<=nlstate+ndeath;ii++)
- for (j=1;j<=nlstate+ndeath;j++){
- oldm[ii][j]=(ii==j ? 1.0 : 0.0);
- savm[ii][j]=(ii==j ? 1.0 : 0.0);
- }
- for(d=0; d<dh[mi][i]; d++){
- newm=savm;
- cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
- for (kk=1; kk<=cptcovage;kk++) {
- cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
- }
- out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
- 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
- savm=oldm;
- oldm=newm;
- } /* end mult */
-
- /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
- /* But now since version 0.9 we anticipate for bias at large stepm.
- * If stepm is larger than one month (smallest stepm) and if the exact delay
- * (in months) between two waves is not a multiple of stepm, we rounded to
- * the nearest (and in case of equal distance, to the lowest) interval but now
- * we keep into memory the bias bh[mi][i] and also the previous matrix product
- * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
- * probability in order to take into account the bias as a fraction of the way
- * from savm to out if bh is negative or even beyond if bh is positive. bh varies
- * -stepm/2 to stepm/2 .
- * For stepm=1 the results are the same as for previous versions of Imach.
- * For stepm > 1 the results are less biased than in previous versions.
- */
- s1=s[mw[mi][i]][i];
- s2=s[mw[mi+1][i]][i];
- bbh=(double)bh[mi][i]/(double)stepm;
- /* bias bh is positive if real duration
- * is higher than the multiple of stepm and negative otherwise.
- */
- /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
- if( s2 > nlstate){
- /* i.e. if s2 is a death state and if the date of death is known
- then the contribution to the likelihood is the probability to
- die between last step unit time and current step unit time,
- which is also equal to probability to die before dh
- minus probability to die before dh-stepm .
- In version up to 0.92 likelihood was computed
- as if date of death was unknown. Death was treated as any other
- health state: the date of the interview describes the actual state
- and not the date of a change in health state. The former idea was
- to consider that at each interview the state was recorded
- (healthy, disable or death) and IMaCh was corrected; but when we
- introduced the exact date of death then we should have modified
- the contribution of an exact death to the likelihood. This new
- contribution is smaller and very dependent of the step unit
- stepm. It is no more the probability to die between last interview
- and month of death but the probability to survive from last
- interview up to one month before death multiplied by the
- probability to die within a month. Thanks to Chris
- Jackson for correcting this bug. Former versions increased
- mortality artificially. The bad side is that we add another loop
- which slows down the processing. The difference can be up to 10%
- lower mortality.
- */
- lli=log(out[s1][s2] - savm[s1][s2]);
-
-
- } else if (s2==-2) {
- for (j=1,survp=0. ; j<=nlstate; j++)
- survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
- /*survp += out[s1][j]; */
- lli= log(survp);
- }
-
- else if (s2==-4) {
- for (j=3,survp=0. ; j<=nlstate; j++)
- survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
- lli= log(survp);
- }
-
- else if (s2==-5) {
- for (j=1,survp=0. ; j<=2; j++)
- survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
- lli= log(survp);
- }
-
- else{
- lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
- /* 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 */
- }
- /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
- /*if(lli ==000.0)*/
- /*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); */
- ipmx +=1;
- sw += weight[i];
- ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
- } /* end of wave */
- } /* end of individual */
- } else if(mle==2){
- for (i=1,ipmx=0, sw=0.; i<=imx; i++){
- for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
- for(mi=1; mi<= wav[i]-1; mi++){
- for (ii=1;ii<=nlstate+ndeath;ii++)
- for (j=1;j<=nlstate+ndeath;j++){
- oldm[ii][j]=(ii==j ? 1.0 : 0.0);
- savm[ii][j]=(ii==j ? 1.0 : 0.0);
- }
- for(d=0; d<=dh[mi][i]; d++){
- newm=savm;
- cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
- for (kk=1; kk<=cptcovage;kk++) {
- cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
- }
- out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
- 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
- savm=oldm;
- oldm=newm;
- } /* end mult */
-
- s1=s[mw[mi][i]][i];
- s2=s[mw[mi+1][i]][i];
- bbh=(double)bh[mi][i]/(double)stepm;
- 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 */
- ipmx +=1;
- sw += weight[i];
- ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
- } /* end of wave */
- } /* end of individual */
- } else if(mle==3){ /* exponential inter-extrapolation */
- for (i=1,ipmx=0, sw=0.; i<=imx; i++){
- for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
- for(mi=1; mi<= wav[i]-1; mi++){
- for (ii=1;ii<=nlstate+ndeath;ii++)
- for (j=1;j<=nlstate+ndeath;j++){
- oldm[ii][j]=(ii==j ? 1.0 : 0.0);
- savm[ii][j]=(ii==j ? 1.0 : 0.0);
- }
- for(d=0; d<dh[mi][i]; d++){
- newm=savm;
- cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
- for (kk=1; kk<=cptcovage;kk++) {
- cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
- }
- out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
- 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
- savm=oldm;
- oldm=newm;
- } /* end mult */
-
- s1=s[mw[mi][i]][i];
- s2=s[mw[mi+1][i]][i];
- bbh=(double)bh[mi][i]/(double)stepm;
- 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 */
- ipmx +=1;
- sw += weight[i];
- ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
- } /* end of wave */
- } /* end of individual */
- }else if (mle==4){ /* ml=4 no inter-extrapolation */
- for (i=1,ipmx=0, sw=0.; i<=imx; i++){
- for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
- for(mi=1; mi<= wav[i]-1; mi++){
- for (ii=1;ii<=nlstate+ndeath;ii++)
- for (j=1;j<=nlstate+ndeath;j++){
- oldm[ii][j]=(ii==j ? 1.0 : 0.0);
- savm[ii][j]=(ii==j ? 1.0 : 0.0);
- }
- for(d=0; d<dh[mi][i]; d++){
- newm=savm;
- cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
- for (kk=1; kk<=cptcovage;kk++) {
- cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
- }
-
- out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
- 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
- savm=oldm;
- oldm=newm;
- } /* end mult */
-
- s1=s[mw[mi][i]][i];
- s2=s[mw[mi+1][i]][i];
- if( s2 > nlstate){
- lli=log(out[s1][s2] - savm[s1][s2]);
- }else{
- lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
- }
- ipmx +=1;
- sw += weight[i];
- ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-/* 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]); */
- } /* end of wave */
- } /* end of individual */
- }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
- for (i=1,ipmx=0, sw=0.; i<=imx; i++){
- for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
- for(mi=1; mi<= wav[i]-1; mi++){
- for (ii=1;ii<=nlstate+ndeath;ii++)
- for (j=1;j<=nlstate+ndeath;j++){
- oldm[ii][j]=(ii==j ? 1.0 : 0.0);
- savm[ii][j]=(ii==j ? 1.0 : 0.0);
- }
- for(d=0; d<dh[mi][i]; d++){
- newm=savm;
- cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
- for (kk=1; kk<=cptcovage;kk++) {
- cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
- }
-
- out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
- 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
- savm=oldm;
- oldm=newm;
- } /* end mult */
-
- s1=s[mw[mi][i]][i];
- s2=s[mw[mi+1][i]][i];
- lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
- ipmx +=1;
- sw += weight[i];
- ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
- /*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]);*/
- } /* end of wave */
- } /* end of individual */
- } /* End of if */
- for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
- /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
- l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
- return -l;
-}
-
-/*************** log-likelihood *************/
-double funcone( double *x)
-{
- /* Same as likeli but slower because of a lot of printf and if */
- int i, ii, j, k, mi, d, kk;
- double l, ll[NLSTATEMAX], cov[NCOVMAX];
- double **out;
- double lli; /* Individual log likelihood */
- double llt;
- int s1, s2;
- double bbh, survp;
- /*extern weight */
- /* We are differentiating ll according to initial status */
- /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
- /*for(i=1;i<imx;i++)
- printf(" %d\n",s[4][i]);
- */
- cov[1]=1.;
-
- for(k=1; k<=nlstate; k++) ll[k]=0.;
-
- for (i=1,ipmx=0, sw=0.; i<=imx; i++){
- for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
- for(mi=1; mi<= wav[i]-1; mi++){
- for (ii=1;ii<=nlstate+ndeath;ii++)
- for (j=1;j<=nlstate+ndeath;j++){
- oldm[ii][j]=(ii==j ? 1.0 : 0.0);
- savm[ii][j]=(ii==j ? 1.0 : 0.0);
- }
- for(d=0; d<dh[mi][i]; d++){
- newm=savm;
- cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
- for (kk=1; kk<=cptcovage;kk++) {
- cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
- }
- out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
- 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
- savm=oldm;
- oldm=newm;
- } /* end mult */
-
- s1=s[mw[mi][i]][i];
- s2=s[mw[mi+1][i]][i];
- bbh=(double)bh[mi][i]/(double)stepm;
- /* bias is positive if real duration
- * is higher than the multiple of stepm and negative otherwise.
- */
- if( s2 > nlstate && (mle <5) ){ /* Jackson */
- lli=log(out[s1][s2] - savm[s1][s2]);
- } else if (s2==-2) {
- for (j=1,survp=0. ; j<=nlstate; j++)
- survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
- lli= log(survp);
- }else if (mle==1){
- lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
- } else if(mle==2){
- 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 */
- } else if(mle==3){ /* exponential inter-extrapolation */
- 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 */
- } else if (mle==4){ /* mle=4 no inter-extrapolation */
- lli=log(out[s1][s2]); /* Original formula */
- } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
- lli=log(out[s1][s2]); /* Original formula */
- } /* End of if */
- ipmx +=1;
- sw += weight[i];
- ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
-/* 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]); */
- if(globpr){
- fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
- %11.6f %11.6f %11.6f ", \
- num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
- 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
- for(k=1,llt=0.,l=0.; k<=nlstate; k++){
- llt +=ll[k]*gipmx/gsw;
- fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
- }
- fprintf(ficresilk," %10.6f\n", -llt);
- }
- } /* end of wave */
- } /* end of individual */
- for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
- /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
- l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
- if(globpr==0){ /* First time we count the contributions and weights */
- gipmx=ipmx;
- gsw=sw;
- }
- return -l;
-}
-
-
-/*************** function likelione ***********/
-void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
-{
- /* This routine should help understanding what is done with
- the selection of individuals/waves and
- to check the exact contribution to the likelihood.
- Plotting could be done.
- */
- int k;
-
- if(*globpri !=0){ /* Just counts and sums, no printings */
- strcpy(fileresilk,"ilk");
- strcat(fileresilk,fileres);
- if((ficresilk=fopen(fileresilk,"w"))==NULL) {
- printf("Problem with resultfile: %s\n", fileresilk);
- fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
- }
- 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");
- fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
- /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
- for(k=1; k<=nlstate; k++)
- fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
- fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
- }
-
- *fretone=(*funcone)(p);
- if(*globpri !=0){
- fclose(ficresilk);
- fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
- fflush(fichtm);
- }
- return;
-}
-
-
-/*********** Maximum Likelihood Estimation ***************/
-
-void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
-{
- int i,j, iter;
- double **xi;
- double fret;
- double fretone; /* Only one call to likelihood */
- /* char filerespow[FILENAMELENGTH];*/
- xi=matrix(1,npar,1,npar);
- for (i=1;i<=npar;i++)
- for (j=1;j<=npar;j++)
- xi[i][j]=(i==j ? 1.0 : 0.0);
- printf("Powell\n"); fprintf(ficlog,"Powell\n");
- strcpy(filerespow,"pow");
- strcat(filerespow,fileres);
- if((ficrespow=fopen(filerespow,"w"))==NULL) {
- printf("Problem with resultfile: %s\n", filerespow);
- fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
- }
- fprintf(ficrespow,"# Powell\n# iter -2*LL");
- for (i=1;i<=nlstate;i++)
- for(j=1;j<=nlstate+ndeath;j++)
- if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
- fprintf(ficrespow,"\n");
-
- powell(p,xi,npar,ftol,&iter,&fret,func);
-
- free_matrix(xi,1,npar,1,npar);
- fclose(ficrespow);
- printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
- fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
- fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
-
-}
-
-/**** Computes Hessian and covariance matrix ***/
-void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
-{
- double **a,**y,*x,pd;
- double **hess;
- int i, j,jk;
- int *indx;
-
- double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
- double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
- void lubksb(double **a, int npar, int *indx, double b[]) ;
- void ludcmp(double **a, int npar, int *indx, double *d) ;
- double gompertz(double p[]);
- hess=matrix(1,npar,1,npar);
-
- printf("\nCalculation of the hessian matrix. Wait...\n");
- fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
- for (i=1;i<=npar;i++){
- printf("%d",i);fflush(stdout);
- fprintf(ficlog,"%d",i);fflush(ficlog);
-
- hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
-
- /* printf(" %f ",p[i]);
- printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
- }
-
- for (i=1;i<=npar;i++) {
- for (j=1;j<=npar;j++) {
- if (j>i) {
- printf(".%d%d",i,j);fflush(stdout);
- fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
- hess[i][j]=hessij(p,delti,i,j,func,npar);
-
- hess[j][i]=hess[i][j];
- /*printf(" %lf ",hess[i][j]);*/
- }
- }
- }
- printf("\n");
- fprintf(ficlog,"\n");
-
- printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
- fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
-
- a=matrix(1,npar,1,npar);
- y=matrix(1,npar,1,npar);
- x=vector(1,npar);
- indx=ivector(1,npar);
- for (i=1;i<=npar;i++)
- for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
- ludcmp(a,npar,indx,&pd);
-
- for (j=1;j<=npar;j++) {
- for (i=1;i<=npar;i++) x[i]=0;
- x[j]=1;
- lubksb(a,npar,indx,x);
- for (i=1;i<=npar;i++){
- matcov[i][j]=x[i];
- }
- }
-
- printf("\n#Hessian matrix#\n");
- fprintf(ficlog,"\n#Hessian matrix#\n");
- for (i=1;i<=npar;i++) {
- for (j=1;j<=npar;j++) {
- printf("%.3e ",hess[i][j]);
- fprintf(ficlog,"%.3e ",hess[i][j]);
- }
- printf("\n");
- fprintf(ficlog,"\n");
- }
-
- /* Recompute Inverse */
- for (i=1;i<=npar;i++)
- for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
- ludcmp(a,npar,indx,&pd);
-
- /* printf("\n#Hessian matrix recomputed#\n");
-
- for (j=1;j<=npar;j++) {
- for (i=1;i<=npar;i++) x[i]=0;
- x[j]=1;
- lubksb(a,npar,indx,x);
- for (i=1;i<=npar;i++){
- y[i][j]=x[i];
- printf("%.3e ",y[i][j]);
- fprintf(ficlog,"%.3e ",y[i][j]);
- }
- printf("\n");
- fprintf(ficlog,"\n");
- }
- */
-
- free_matrix(a,1,npar,1,npar);
- free_matrix(y,1,npar,1,npar);
- free_vector(x,1,npar);
- free_ivector(indx,1,npar);
- free_matrix(hess,1,npar,1,npar);
-
-
-}
-
-/*************** hessian matrix ****************/
-double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
-{
- int i;
- int l=1, lmax=20;
- double k1,k2;
- double p2[NPARMAX+1];
- double res;
- double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
- double fx;
- int k=0,kmax=10;
- double l1;
-
- fx=func(x);
- for (i=1;i<=npar;i++) p2[i]=x[i];
- for(l=0 ; l <=lmax; l++){
- l1=pow(10,l);
- delts=delt;
- for(k=1 ; k <kmax; k=k+1){
- delt = delta*(l1*k);
- p2[theta]=x[theta] +delt;
- k1=func(p2)-fx;
- p2[theta]=x[theta]-delt;
- k2=func(p2)-fx;
- /*res= (k1-2.0*fx+k2)/delt/delt; */
- res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
-
-#ifdef DEBUG
- 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);
- 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);
-#endif
- /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
- if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
- k=kmax;
- }
- else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
- k=kmax; l=lmax*10.;
- }
- else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){
- delts=delt;
- }
- }
- }
- delti[theta]=delts;
- return res;
-
-}
-
-double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
-{
- int i;
- int l=1, l1, lmax=20;
- double k1,k2,k3,k4,res,fx;
- double p2[NPARMAX+1];
- int k;
-
- fx=func(x);
- for (k=1; k<=2; k++) {
- for (i=1;i<=npar;i++) p2[i]=x[i];
- p2[thetai]=x[thetai]+delti[thetai]/k;
- p2[thetaj]=x[thetaj]+delti[thetaj]/k;
- k1=func(p2)-fx;
-
- p2[thetai]=x[thetai]+delti[thetai]/k;
- p2[thetaj]=x[thetaj]-delti[thetaj]/k;
- k2=func(p2)-fx;
-
- p2[thetai]=x[thetai]-delti[thetai]/k;
- p2[thetaj]=x[thetaj]+delti[thetaj]/k;
- k3=func(p2)-fx;
-
- p2[thetai]=x[thetai]-delti[thetai]/k;
- p2[thetaj]=x[thetaj]-delti[thetaj]/k;
- k4=func(p2)-fx;
- res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
-#ifdef DEBUG
- 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);
- 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);
-#endif
- }
- return res;
-}
-
-/************** Inverse of matrix **************/
-void ludcmp(double **a, int n, int *indx, double *d)
-{
- int i,imax,j,k;
- double big,dum,sum,temp;
- double *vv;
-
- vv=vector(1,n);
- *d=1.0;
- for (i=1;i<=n;i++) {
- big=0.0;
- for (j=1;j<=n;j++)
- if ((temp=fabs(a[i][j])) > big) big=temp;
- if (big == 0.0) nrerror("Singular matrix in routine ludcmp");
- vv[i]=1.0/big;
- }
- for (j=1;j<=n;j++) {
- for (i=1;i<j;i++) {
- sum=a[i][j];
- for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];
- a[i][j]=sum;
- }
- big=0.0;
- for (i=j;i<=n;i++) {
- sum=a[i][j];
- for (k=1;k<j;k++)
- sum -= a[i][k]*a[k][j];
- a[i][j]=sum;
- if ( (dum=vv[i]*fabs(sum)) >= big) {
- big=dum;
- imax=i;
- }
- }
- if (j != imax) {
- for (k=1;k<=n;k++) {
- dum=a[imax][k];
- a[imax][k]=a[j][k];
- a[j][k]=dum;
- }
- *d = -(*d);
- vv[imax]=vv[j];
- }
- indx[j]=imax;
- if (a[j][j] == 0.0) a[j][j]=TINY;
- if (j != n) {
- dum=1.0/(a[j][j]);
- for (i=j+1;i<=n;i++) a[i][j] *= dum;
- }
- }
- free_vector(vv,1,n); /* Doesn't work */
-;
-}
-
-void lubksb(double **a, int n, int *indx, double b[])
-{
- int i,ii=0,ip,j;
- double sum;
-
- for (i=1;i<=n;i++) {
- ip=indx[i];
- sum=b[ip];
- b[ip]=b[i];
- if (ii)
- for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];
- else if (sum) ii=i;
- b[i]=sum;
- }
- for (i=n;i>=1;i--) {
- sum=b[i];
- for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];
- b[i]=sum/a[i][i];
- }
-}
-
-void pstamp(FILE *fichier)
-{
- fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
-}
-
-/************ Frequencies ********************/
-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[])
-{ /* Some frequencies */
-
- int i, m, jk, k1,i1, j1, bool, z1,z2,j;
- int first;
- double ***freq; /* Frequencies */
- double *pp, **prop;
- double pos,posprop, k2, dateintsum=0,k2cpt=0;
- char fileresp[FILENAMELENGTH];
-
- pp=vector(1,nlstate);
- prop=matrix(1,nlstate,iagemin,iagemax+3);
- strcpy(fileresp,"p");
- strcat(fileresp,fileres);
- if((ficresp=fopen(fileresp,"w"))==NULL) {
- printf("Problem with prevalence resultfile: %s\n", fileresp);
- fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
- exit(0);
- }
- freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
- j1=0;
-
- j=cptcoveff;
- if (cptcovn<1) {j=1;ncodemax[1]=1;}
-
- first=1;
-
- for(k1=1; k1<=j;k1++){
- for(i1=1; i1<=ncodemax[k1];i1++){
- j1++;
- /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
- scanf("%d", i);*/
- for (i=-5; i<=nlstate+ndeath; i++)
- for (jk=-5; jk<=nlstate+ndeath; jk++)
- for(m=iagemin; m <= iagemax+3; m++)
- freq[i][jk][m]=0;
-
- for (i=1; i<=nlstate; i++)
- for(m=iagemin; m <= iagemax+3; m++)
- prop[i][m]=0;
-
- dateintsum=0;
- k2cpt=0;
- for (i=1; i<=imx; i++) {
- bool=1;
- if (cptcovn>0) {
- for (z1=1; z1<=cptcoveff; z1++)
- if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
- bool=0;
- }
- if (bool==1){
- for(m=firstpass; m<=lastpass; m++){
- k2=anint[m][i]+(mint[m][i]/12.);
- /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
- if(agev[m][i]==0) agev[m][i]=iagemax+1;
- if(agev[m][i]==1) agev[m][i]=iagemax+2;
- if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
- if (m<lastpass) {
- freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
- freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
- }
-
- if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
- dateintsum=dateintsum+k2;
- k2cpt++;
- }
- /*}*/
- }
- }
- }
-
- /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
- pstamp(ficresp);
- if (cptcovn>0) {
- fprintf(ficresp, "\n#********** Variable ");
- for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
- fprintf(ficresp, "**********\n#");
- }
- for(i=1; i<=nlstate;i++)
- fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
- fprintf(ficresp, "\n");
-
- for(i=iagemin; i <= iagemax+3; i++){
- if(i==iagemax+3){
- fprintf(ficlog,"Total");
- fprintf(fichtm,"<br>Total<br>");
- }else{
- if(first==1){
- first=0;
- printf("See log file for details...\n");
- }
- fprintf(ficlog,"Age %d", i);
- }
- for(jk=1; jk <=nlstate ; jk++){
- for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
- pp[jk] += freq[jk][m][i];
- }
- for(jk=1; jk <=nlstate ; jk++){
- for(m=-1, pos=0; m <=0 ; m++)
- pos += freq[jk][m][i];
- if(pp[jk]>=1.e-10){
- if(first==1){
- printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
- }
- fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
- }else{
- if(first==1)
- printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
- fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
- }
- }
-
- for(jk=1; jk <=nlstate ; jk++){
- for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
- pp[jk] += freq[jk][m][i];
- }
- for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
- pos += pp[jk];
- posprop += prop[jk][i];
- }
- for(jk=1; jk <=nlstate ; jk++){
- if(pos>=1.e-5){
- if(first==1)
- printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
- fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
- }else{
- if(first==1)
- printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
- fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
- }
- if( i <= iagemax){
- if(pos>=1.e-5){
- fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
- /*probs[i][jk][j1]= pp[jk]/pos;*/
- /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
- }
- else
- fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
- }
- }
-
- for(jk=-1; jk <=nlstate+ndeath; jk++)
- for(m=-1; m <=nlstate+ndeath; m++)
- if(freq[jk][m][i] !=0 ) {
- if(first==1)
- printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
- fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
- }
- if(i <= iagemax)
- fprintf(ficresp,"\n");
- if(first==1)
- printf("Others in log...\n");
- fprintf(ficlog,"\n");
- }
- }
- }
- dateintmean=dateintsum/k2cpt;
-
- fclose(ficresp);
- free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
- free_vector(pp,1,nlstate);
- free_matrix(prop,1,nlstate,iagemin, iagemax+3);
- /* End of Freq */
-}
-
-/************ Prevalence ********************/
-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)
-{
- /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
- in each health status at the date of interview (if between dateprev1 and dateprev2).
- We still use firstpass and lastpass as another selection.
- */
-
- int i, m, jk, k1, i1, j1, bool, z1,z2,j;
- double ***freq; /* Frequencies */
- double *pp, **prop;
- double pos,posprop;
- double y2; /* in fractional years */
- int iagemin, iagemax;
-
- iagemin= (int) agemin;
- iagemax= (int) agemax;
- /*pp=vector(1,nlstate);*/
- prop=matrix(1,nlstate,iagemin,iagemax+3);
- /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
- j1=0;
-
- j=cptcoveff;
- if (cptcovn<1) {j=1;ncodemax[1]=1;}
-
- for(k1=1; k1<=j;k1++){
- for(i1=1; i1<=ncodemax[k1];i1++){
- j1++;
-
- for (i=1; i<=nlstate; i++)
- for(m=iagemin; m <= iagemax+3; m++)
- prop[i][m]=0.0;
-
- for (i=1; i<=imx; i++) { /* Each individual */
- bool=1;
- if (cptcovn>0) {
- for (z1=1; z1<=cptcoveff; z1++)
- if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
- bool=0;
- }
- if (bool==1) {
- for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
- y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
- if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
- if(agev[m][i]==0) agev[m][i]=iagemax+1;
- if(agev[m][i]==1) agev[m][i]=iagemax+2;
- 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);
- if (s[m][i]>0 && s[m][i]<=nlstate) {
- /*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]]);*/
- prop[s[m][i]][(int)agev[m][i]] += weight[i];
- prop[s[m][i]][iagemax+3] += weight[i];
- }
- }
- } /* end selection of waves */
- }
- }
- for(i=iagemin; i <= iagemax+3; i++){
-
- for(jk=1,posprop=0; jk <=nlstate ; jk++) {
- posprop += prop[jk][i];
- }
-
- for(jk=1; jk <=nlstate ; jk++){
- if( i <= iagemax){
- if(posprop>=1.e-5){
- probs[i][jk][j1]= prop[jk][i]/posprop;
- }
- }
- }/* end jk */
- }/* end i */
- } /* end i1 */
- } /* end k1 */
-
- /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
- /*free_vector(pp,1,nlstate);*/
- free_matrix(prop,1,nlstate, iagemin,iagemax+3);
-} /* End of prevalence */
-
-/************* Waves Concatenation ***************/
-
-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)
-{
- /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
- Death is a valid wave (if date is known).
- mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
- dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
- and mw[mi+1][i]. dh depends on stepm.
- */
-
- int i, mi, m;
- /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
- double sum=0., jmean=0.;*/
- int first;
- int j, k=0,jk, ju, jl;
- double sum=0.;
- first=0;
- jmin=1e+5;
- jmax=-1;
- jmean=0.;
- for(i=1; i<=imx; i++){
- mi=0;
- m=firstpass;
- while(s[m][i] <= nlstate){
- if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
- mw[++mi][i]=m;
- if(m >=lastpass)
- break;
- else
- m++;
- }/* end while */
- if (s[m][i] > nlstate){
- mi++; /* Death is another wave */
- /* if(mi==0) never been interviewed correctly before death */
- /* Only death is a correct wave */
- mw[mi][i]=m;
- }
-
- wav[i]=mi;
- if(mi==0){
- nbwarn++;
- if(first==0){
- printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
- first=1;
- }
- if(first==1){
- fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
- }
- } /* end mi==0 */
- } /* End individuals */
-
- for(i=1; i<=imx; i++){
- for(mi=1; mi<wav[i];mi++){
- if (stepm <=0)
- dh[mi][i]=1;
- else{
- if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
- if (agedc[i] < 2*AGESUP) {
- j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);
- if(j==0) j=1; /* Survives at least one month after exam */
- else if(j<0){
- nberr++;
- 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]);
- j=1; /* Temporary Dangerous patch */
- 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);
- 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]);
- 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);
- }
- k=k+1;
- if (j >= jmax){
- jmax=j;
- ijmax=i;
- }
- if (j <= jmin){
- jmin=j;
- ijmin=i;
- }
- sum=sum+j;
- /*if (j<0) printf("j=%d num=%d \n",j,i);*/
- /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
- }
- }
- else{
- j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
-/* 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]); */
-
- k=k+1;
- if (j >= jmax) {
- jmax=j;
- ijmax=i;
- }
- else if (j <= jmin){
- jmin=j;
- ijmin=i;
- }
- /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
- /*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]);*/
- if(j<0){
- nberr++;
- 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]);
- 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]);
- }
- sum=sum+j;
- }
- jk= j/stepm;
- jl= j -jk*stepm;
- ju= j -(jk+1)*stepm;
- if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
- if(jl==0){
- dh[mi][i]=jk;
- bh[mi][i]=0;
- }else{ /* We want a negative bias in order to only have interpolation ie
- * at the price of an extra matrix product in likelihood */
- dh[mi][i]=jk+1;
- bh[mi][i]=ju;
- }
- }else{
- if(jl <= -ju){
- dh[mi][i]=jk;
- bh[mi][i]=jl; /* bias is positive if real duration
- * is higher than the multiple of stepm and negative otherwise.
- */
- }
- else{
- dh[mi][i]=jk+1;
- bh[mi][i]=ju;
- }
- if(dh[mi][i]==0){
- dh[mi][i]=1; /* At least one step */
- bh[mi][i]=ju; /* At least one step */
- /* 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);*/
- }
- } /* end if mle */
- }
- } /* end wave */
- }
- jmean=sum/k;
- 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);
- 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);
- }
-
-/*********** Tricode ****************************/
-void tricode(int *Tvar, int **nbcode, int imx)
-{
-
- int Ndum[20],ij=1, k, j, i, maxncov=19;
- int cptcode=0;
- cptcoveff=0;
-
- for (k=0; k<maxncov; k++) Ndum[k]=0;
- for (k=1; k<=7; k++) ncodemax[k]=0;
-
- for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
- for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
- modality*/
- ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
- Ndum[ij]++; /*store the modality */
- /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
- if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable
- Tvar[j]. If V=sex and male is 0 and
- female is 1, then cptcode=1.*/
- }
-
- for (i=0; i<=cptcode; i++) {
- 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 */
- }
-
- ij=1;
- for (i=1; i<=ncodemax[j]; i++) {
- for (k=0; k<= maxncov; k++) {
- if (Ndum[k] != 0) {
- nbcode[Tvar[j]][ij]=k;
- /* 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; */
-
- ij++;
- }
- if (ij > ncodemax[j]) break;
- }
- }
- }
-
- for (k=0; k< maxncov; k++) Ndum[k]=0;
-
- for (i=1; i<=ncovmodel-2; i++) {
- /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
- ij=Tvar[i];
- Ndum[ij]++;
- }
-
- ij=1;
- for (i=1; i<= maxncov; i++) {
- if((Ndum[i]!=0) && (i<=ncovcol)){
- Tvaraff[ij]=i; /*For printing */
- ij++;
- }
- }
-
- cptcoveff=ij-1; /*Number of simple covariates*/
-}
-
-/*********** Health Expectancies ****************/
-
-void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
-
-{
- /* Health expectancies, no variances */
- int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
- double age, agelim, hf;
- double ***p3mat;
- double eip;
-
- pstamp(ficreseij);
- fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
- fprintf(ficreseij,"# Age");
- for(i=1; i<=nlstate;i++){
- for(j=1; j<=nlstate;j++){
- fprintf(ficreseij," e%1d%1d ",i,j);
- }
- fprintf(ficreseij," e%1d. ",i);
- }
- fprintf(ficreseij,"\n");
-
-
- if(estepm < stepm){
- printf ("Problem %d lower than %d\n",estepm, stepm);
- }
- else hstepm=estepm;
- /* We compute the life expectancy from trapezoids spaced every estepm months
- * This is mainly to measure the difference between two models: for example
- * if stepm=24 months pijx are given only every 2 years and by summing them
- * we are calculating an estimate of the Life Expectancy assuming a linear
- * progression in between and thus overestimating or underestimating according
- * to the curvature of the survival function. If, for the same date, we
- * estimate the model with stepm=1 month, we can keep estepm to 24 months
- * to compare the new estimate of Life expectancy with the same linear
- * hypothesis. A more precise result, taking into account a more precise
- * curvature will be obtained if estepm is as small as stepm. */
-
- /* For example we decided to compute the life expectancy with the smallest unit */
- /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
- nhstepm is the number of hstepm from age to agelim
- nstepm is the number of stepm from age to agelin.
- Look at hpijx to understand the reason of that which relies in memory size
- and note for a fixed period like estepm months */
- /* We decided (b) to get a life expectancy respecting the most precise curvature of the
- survival function given by stepm (the optimization length). Unfortunately it
- means that if the survival funtion is printed only each two years of age and if
- you sum them up and add 1 year (area under the trapezoids) you won't get the same
- results. So we changed our mind and took the option of the best precision.
- */
- hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-
- agelim=AGESUP;
- /* nhstepm age range expressed in number of stepm */
- nstepm=(int) rint((agelim-age)*YEARM/stepm);
- /* Typically if 20 years nstepm = 20*12/6=40 stepm */
- /* if (stepm >= YEARM) hstepm=1;*/
- nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
- p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
-
- for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
- /* Computed by stepm unit matrices, product of hstepm matrices, stored
- in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
-
- hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
-
- hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
-
- printf("%d|",(int)age);fflush(stdout);
- fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
-
- /* Computing expectancies */
- for(i=1; i<=nlstate;i++)
- for(j=1; j<=nlstate;j++)
- for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
- eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
-
- /* 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]);*/
-
- }
-
- fprintf(ficreseij,"%3.0f",age );
- for(i=1; i<=nlstate;i++){
- eip=0;
- for(j=1; j<=nlstate;j++){
- eip +=eij[i][j][(int)age];
- fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
- }
- fprintf(ficreseij,"%9.4f", eip );
- }
- fprintf(ficreseij,"\n");
-
- }
- free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- printf("\n");
- fprintf(ficlog,"\n");
-
-}
-
-void cvevsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
-
-{
- /* Covariances of health expectancies eij and of total life expectancies according
- to initial status i, ei. .
- */
- int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
- double age, agelim, hf;
- double ***p3matp, ***p3matm, ***varhe;
- double **dnewm,**doldm;
- double *xp, *xm;
- double **gp, **gm;
- double ***gradg, ***trgradg;
- int theta;
-
- double eip, vip;
-
- varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
- xp=vector(1,npar);
- xm=vector(1,npar);
- dnewm=matrix(1,nlstate*nlstate,1,npar);
- doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
-
- pstamp(ficresstdeij);
- fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
- fprintf(ficresstdeij,"# Age");
- for(i=1; i<=nlstate;i++){
- for(j=1; j<=nlstate;j++)
- fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
- fprintf(ficresstdeij," e%1d. ",i);
- }
- fprintf(ficresstdeij,"\n");
-
- pstamp(ficrescveij);
- fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
- fprintf(ficrescveij,"# Age");
- for(i=1; i<=nlstate;i++)
- for(j=1; j<=nlstate;j++){
- cptj= (j-1)*nlstate+i;
- for(i2=1; i2<=nlstate;i2++)
- for(j2=1; j2<=nlstate;j2++){
- cptj2= (j2-1)*nlstate+i2;
- if(cptj2 <= cptj)
- fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
- }
- }
- fprintf(ficrescveij,"\n");
-
- if(estepm < stepm){
- printf ("Problem %d lower than %d\n",estepm, stepm);
- }
- else hstepm=estepm;
- /* We compute the life expectancy from trapezoids spaced every estepm months
- * This is mainly to measure the difference between two models: for example
- * if stepm=24 months pijx are given only every 2 years and by summing them
- * we are calculating an estimate of the Life Expectancy assuming a linear
- * progression in between and thus overestimating or underestimating according
- * to the curvature of the survival function. If, for the same date, we
- * estimate the model with stepm=1 month, we can keep estepm to 24 months
- * to compare the new estimate of Life expectancy with the same linear
- * hypothesis. A more precise result, taking into account a more precise
- * curvature will be obtained if estepm is as small as stepm. */
-
- /* For example we decided to compute the life expectancy with the smallest unit */
- /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
- nhstepm is the number of hstepm from age to agelim
- nstepm is the number of stepm from age to agelin.
- Look at hpijx to understand the reason of that which relies in memory size
- and note for a fixed period like estepm months */
- /* We decided (b) to get a life expectancy respecting the most precise curvature of the
- survival function given by stepm (the optimization length). Unfortunately it
- means that if the survival funtion is printed only each two years of age and if
- you sum them up and add 1 year (area under the trapezoids) you won't get the same
- results. So we changed our mind and took the option of the best precision.
- */
- hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
-
- /* If stepm=6 months */
- /* nhstepm age range expressed in number of stepm */
- agelim=AGESUP;
- nstepm=(int) rint((agelim-age)*YEARM/stepm);
- /* Typically if 20 years nstepm = 20*12/6=40 stepm */
- /* if (stepm >= YEARM) hstepm=1;*/
- nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
-
- p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
- trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
- gp=matrix(0,nhstepm,1,nlstate*nlstate);
- gm=matrix(0,nhstepm,1,nlstate*nlstate);
-
- for (age=bage; age<=fage; age ++){
-
- /* Computed by stepm unit matrices, product of hstepm matrices, stored
- in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
-
- hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
-
- /* Computing Variances of health expectancies */
- /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
- decrease memory allocation */
- for(theta=1; theta <=npar; theta++){
- for(i=1; i<=npar; i++){
- xp[i] = x[i] + (i==theta ?delti[theta]:0);
- xm[i] = x[i] - (i==theta ?delti[theta]:0);
- }
- hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
- hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
-
- for(j=1; j<= nlstate; j++){
- for(i=1; i<=nlstate; i++){
- for(h=0; h<=nhstepm-1; h++){
- gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
- gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
- }
- }
- }
-
- for(ij=1; ij<= nlstate*nlstate; ij++)
- for(h=0; h<=nhstepm-1; h++){
- gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
- }
- }/* End theta */
-
-
- for(h=0; h<=nhstepm-1; h++)
- for(j=1; j<=nlstate*nlstate;j++)
- for(theta=1; theta <=npar; theta++)
- trgradg[h][j][theta]=gradg[h][theta][j];
-
-
- for(ij=1;ij<=nlstate*nlstate;ij++)
- for(ji=1;ji<=nlstate*nlstate;ji++)
- varhe[ij][ji][(int)age] =0.;
-
- printf("%d|",(int)age);fflush(stdout);
- fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
- for(h=0;h<=nhstepm-1;h++){
- for(k=0;k<=nhstepm-1;k++){
- matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
- matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
- for(ij=1;ij<=nlstate*nlstate;ij++)
- for(ji=1;ji<=nlstate*nlstate;ji++)
- varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
- }
- }
- /* Computing expectancies */
- hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
- for(i=1; i<=nlstate;i++)
- for(j=1; j<=nlstate;j++)
- for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
- eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
-
- /* 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]);*/
-
- }
-
- fprintf(ficresstdeij,"%3.0f",age );
- for(i=1; i<=nlstate;i++){
- eip=0.;
- vip=0.;
- for(j=1; j<=nlstate;j++){
- eip += eij[i][j][(int)age];
- for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
- vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
- fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
- }
- fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
- }
- fprintf(ficresstdeij,"\n");
-
- fprintf(ficrescveij,"%3.0f",age );
- for(i=1; i<=nlstate;i++)
- for(j=1; j<=nlstate;j++){
- cptj= (j-1)*nlstate+i;
- for(i2=1; i2<=nlstate;i2++)
- for(j2=1; j2<=nlstate;j2++){
- cptj2= (j2-1)*nlstate+i2;
- if(cptj2 <= cptj)
- fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
- }
- }
- fprintf(ficrescveij,"\n");
-
- }
- free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
- free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
- free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
- free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
- free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- printf("\n");
- fprintf(ficlog,"\n");
-
- free_vector(xm,1,npar);
- free_vector(xp,1,npar);
- free_matrix(dnewm,1,nlstate*nlstate,1,npar);
- free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
- free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
-}
-
-/************ Variance ******************/
-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[])
-{
- /* Variance of health expectancies */
- /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
- /* double **newm;*/
- double **dnewm,**doldm;
- double **dnewmp,**doldmp;
- int i, j, nhstepm, hstepm, h, nstepm ;
- int k, cptcode;
- double *xp;
- double **gp, **gm; /* for var eij */
- double ***gradg, ***trgradg; /*for var eij */
- double **gradgp, **trgradgp; /* for var p point j */
- double *gpp, *gmp; /* for var p point j */
- double **varppt; /* for var p point j nlstate to nlstate+ndeath */
- double ***p3mat;
- double age,agelim, hf;
- double ***mobaverage;
- int theta;
- char digit[4];
- char digitp[25];
-
- char fileresprobmorprev[FILENAMELENGTH];
-
- if(popbased==1){
- if(mobilav!=0)
- strcpy(digitp,"-populbased-mobilav-");
- else strcpy(digitp,"-populbased-nomobil-");
- }
- else
- strcpy(digitp,"-stablbased-");
-
- if (mobilav!=0) {
- mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
- if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
- fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
- printf(" Error in movingaverage mobilav=%d\n",mobilav);
- }
- }
-
- strcpy(fileresprobmorprev,"prmorprev");
- sprintf(digit,"%-d",ij);
- /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
- strcat(fileresprobmorprev,digit); /* Tvar to be done */
- strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
- strcat(fileresprobmorprev,fileres);
- if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
- printf("Problem with resultfile: %s\n", fileresprobmorprev);
- fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
- }
- printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
-
- fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
- pstamp(ficresprobmorprev);
- 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);
- fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
- for(j=nlstate+1; j<=(nlstate+ndeath);j++){
- fprintf(ficresprobmorprev," p.%-d SE",j);
- for(i=1; i<=nlstate;i++)
- fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
- }
- fprintf(ficresprobmorprev,"\n");
- fprintf(ficgp,"\n# Routine varevsij");
- /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
- 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");
- fprintf(fichtm,"\n<br>%s <br>\n",digitp);
-/* } */
- varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
- pstamp(ficresvij);
- fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
- if(popbased==1)
- fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
- else
- fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
- fprintf(ficresvij,"# Age");
- for(i=1; i<=nlstate;i++)
- for(j=1; j<=nlstate;j++)
- fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
- fprintf(ficresvij,"\n");
-
- xp=vector(1,npar);
- dnewm=matrix(1,nlstate,1,npar);
- doldm=matrix(1,nlstate,1,nlstate);
- dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
- doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
-
- gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
- gpp=vector(nlstate+1,nlstate+ndeath);
- gmp=vector(nlstate+1,nlstate+ndeath);
- trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
-
- if(estepm < stepm){
- printf ("Problem %d lower than %d\n",estepm, stepm);
- }
- else hstepm=estepm;
- /* For example we decided to compute the life expectancy with the smallest unit */
- /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
- nhstepm is the number of hstepm from age to agelim
- nstepm is the number of stepm from age to agelin.
- Look at hpijx to understand the reason of that which relies in memory size
- and note for a fixed period like k years */
- /* We decided (b) to get a life expectancy respecting the most precise curvature of the
- survival function given by stepm (the optimization length). Unfortunately it
- means that if the survival funtion is printed every two years of age and if
- you sum them up and add 1 year (area under the trapezoids) you won't get the same
- results. So we changed our mind and took the option of the best precision.
- */
- hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
- agelim = AGESUP;
- for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
- nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
- nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
- p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
- gp=matrix(0,nhstepm,1,nlstate);
- gm=matrix(0,nhstepm,1,nlstate);
-
-
- for(theta=1; theta <=npar; theta++){
- for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
- xp[i] = x[i] + (i==theta ?delti[theta]:0);
- }
- hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
- prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-
- if (popbased==1) {
- if(mobilav ==0){
- for(i=1; i<=nlstate;i++)
- prlim[i][i]=probs[(int)age][i][ij];
- }else{ /* mobilav */
- for(i=1; i<=nlstate;i++)
- prlim[i][i]=mobaverage[(int)age][i][ij];
- }
- }
-
- for(j=1; j<= nlstate; j++){
- for(h=0; h<=nhstepm; h++){
- for(i=1, gp[h][j]=0.;i<=nlstate;i++)
- gp[h][j] += prlim[i][i]*p3mat[i][j][h];
- }
- }
- /* This for computing probability of death (h=1 means
- computed over hstepm matrices product = hstepm*stepm months)
- as a weighted average of prlim.
- */
- for(j=nlstate+1;j<=nlstate+ndeath;j++){
- for(i=1,gpp[j]=0.; i<= nlstate; i++)
- gpp[j] += prlim[i][i]*p3mat[i][j][1];
- }
- /* end probability of death */
-
- for(i=1; i<=npar; i++) /* Computes gradient x - delta */
- xp[i] = x[i] - (i==theta ?delti[theta]:0);
- hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
- prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
-
- if (popbased==1) {
- if(mobilav ==0){
- for(i=1; i<=nlstate;i++)
- prlim[i][i]=probs[(int)age][i][ij];
- }else{ /* mobilav */
- for(i=1; i<=nlstate;i++)
- prlim[i][i]=mobaverage[(int)age][i][ij];
- }
- }
-
- for(j=1; j<= nlstate; j++){
- for(h=0; h<=nhstepm; h++){
- for(i=1, gm[h][j]=0.;i<=nlstate;i++)
- gm[h][j] += prlim[i][i]*p3mat[i][j][h];
- }
- }
- /* This for computing probability of death (h=1 means
- computed over hstepm matrices product = hstepm*stepm months)
- as a weighted average of prlim.
- */
- for(j=nlstate+1;j<=nlstate+ndeath;j++){
- for(i=1,gmp[j]=0.; i<= nlstate; i++)
- gmp[j] += prlim[i][i]*p3mat[i][j][1];
- }
- /* end probability of death */
-
- for(j=1; j<= nlstate; j++) /* vareij */
- for(h=0; h<=nhstepm; h++){
- gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
- }
-
- for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
- gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
- }
-
- } /* End theta */
-
- trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
-
- for(h=0; h<=nhstepm; h++) /* veij */
- for(j=1; j<=nlstate;j++)
- for(theta=1; theta <=npar; theta++)
- trgradg[h][j][theta]=gradg[h][theta][j];
-
- for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
- for(theta=1; theta <=npar; theta++)
- trgradgp[j][theta]=gradgp[theta][j];
-
-
- hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
- for(i=1;i<=nlstate;i++)
- for(j=1;j<=nlstate;j++)
- vareij[i][j][(int)age] =0.;
-
- for(h=0;h<=nhstepm;h++){
- for(k=0;k<=nhstepm;k++){
- matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
- matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
- for(i=1;i<=nlstate;i++)
- for(j=1;j<=nlstate;j++)
- vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
- }
- }
-
- /* pptj */
- matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
- matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
- for(j=nlstate+1;j<=nlstate+ndeath;j++)
- for(i=nlstate+1;i<=nlstate+ndeath;i++)
- varppt[j][i]=doldmp[j][i];
- /* end ppptj */
- /* x centered again */
- hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
- prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
-
- if (popbased==1) {
- if(mobilav ==0){
- for(i=1; i<=nlstate;i++)
- prlim[i][i]=probs[(int)age][i][ij];
- }else{ /* mobilav */
- for(i=1; i<=nlstate;i++)
- prlim[i][i]=mobaverage[(int)age][i][ij];
- }
- }
-
- /* This for computing probability of death (h=1 means
- computed over hstepm (estepm) matrices product = hstepm*stepm months)
- as a weighted average of prlim.
- */
- for(j=nlstate+1;j<=nlstate+ndeath;j++){
- for(i=1,gmp[j]=0.;i<= nlstate; i++)
- gmp[j] += prlim[i][i]*p3mat[i][j][1];
- }
- /* end probability of death */
-
- fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
- for(j=nlstate+1; j<=(nlstate+ndeath);j++){
- fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
- for(i=1; i<=nlstate;i++){
- fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
- }
- }
- fprintf(ficresprobmorprev,"\n");
-
- fprintf(ficresvij,"%.0f ",age );
- for(i=1; i<=nlstate;i++)
- for(j=1; j<=nlstate;j++){
- fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
- }
- fprintf(ficresvij,"\n");
- free_matrix(gp,0,nhstepm,1,nlstate);
- free_matrix(gm,0,nhstepm,1,nlstate);
- free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
- free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
- free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- } /* End age */
- free_vector(gpp,nlstate+1,nlstate+ndeath);
- free_vector(gmp,nlstate+1,nlstate+ndeath);
- free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
- free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
- fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
- /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
- fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
-/* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
-/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
-/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
- fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
- fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
- fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
- fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
- 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);
- /* 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);
-*/
-/* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
- fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
-
- free_vector(xp,1,npar);
- free_matrix(doldm,1,nlstate,1,nlstate);
- free_matrix(dnewm,1,nlstate,1,npar);
- free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
- free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
- free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
- if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
- fclose(ficresprobmorprev);
- fflush(ficgp);
- fflush(fichtm);
-} /* end varevsij */
-
-/************ Variance of prevlim ******************/
-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[])
-{
- /* Variance of prevalence limit */
- /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
- double **newm;
- double **dnewm,**doldm;
- int i, j, nhstepm, hstepm;
- int k, cptcode;
- double *xp;
- double *gp, *gm;
- double **gradg, **trgradg;
- double age,agelim;
- int theta;
-
- pstamp(ficresvpl);
- fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
- fprintf(ficresvpl,"# Age");
- for(i=1; i<=nlstate;i++)
- fprintf(ficresvpl," %1d-%1d",i,i);
- fprintf(ficresvpl,"\n");
-
- xp=vector(1,npar);
- dnewm=matrix(1,nlstate,1,npar);
- doldm=matrix(1,nlstate,1,nlstate);
-
- hstepm=1*YEARM; /* Every year of age */
- hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
- agelim = AGESUP;
- for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
- nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
- if (stepm >= YEARM) hstepm=1;
- nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
- gradg=matrix(1,npar,1,nlstate);
- gp=vector(1,nlstate);
- gm=vector(1,nlstate);
-
- for(theta=1; theta <=npar; theta++){
- for(i=1; i<=npar; i++){ /* Computes gradient */
- xp[i] = x[i] + (i==theta ?delti[theta]:0);
- }
- prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
- for(i=1;i<=nlstate;i++)
- gp[i] = prlim[i][i];
-
- for(i=1; i<=npar; i++) /* Computes gradient */
- xp[i] = x[i] - (i==theta ?delti[theta]:0);
- prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
- for(i=1;i<=nlstate;i++)
- gm[i] = prlim[i][i];
-
- for(i=1;i<=nlstate;i++)
- gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
- } /* End theta */
-
- trgradg =matrix(1,nlstate,1,npar);
-
- for(j=1; j<=nlstate;j++)
- for(theta=1; theta <=npar; theta++)
- trgradg[j][theta]=gradg[theta][j];
-
- for(i=1;i<=nlstate;i++)
- varpl[i][(int)age] =0.;
- matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
- matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
- for(i=1;i<=nlstate;i++)
- varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
-
- fprintf(ficresvpl,"%.0f ",age );
- for(i=1; i<=nlstate;i++)
- fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
- fprintf(ficresvpl,"\n");
- free_vector(gp,1,nlstate);
- free_vector(gm,1,nlstate);
- free_matrix(gradg,1,npar,1,nlstate);
- free_matrix(trgradg,1,nlstate,1,npar);
- } /* End age */
-
- free_vector(xp,1,npar);
- free_matrix(doldm,1,nlstate,1,npar);
- free_matrix(dnewm,1,nlstate,1,nlstate);
-
-}
-
-/************ Variance of one-step probabilities ******************/
-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[])
-{
- int i, j=0, i1, k1, l1, t, tj;
- int k2, l2, j1, z1;
- int k=0,l, cptcode;
- int first=1, first1;
- double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
- double **dnewm,**doldm;
- double *xp;
- double *gp, *gm;
- double **gradg, **trgradg;
- double **mu;
- double age,agelim, cov[NCOVMAX];
- double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
- int theta;
- char fileresprob[FILENAMELENGTH];
- char fileresprobcov[FILENAMELENGTH];
- char fileresprobcor[FILENAMELENGTH];
-
- double ***varpij;
-
- strcpy(fileresprob,"prob");
- strcat(fileresprob,fileres);
- if((ficresprob=fopen(fileresprob,"w"))==NULL) {
- printf("Problem with resultfile: %s\n", fileresprob);
- fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
- }
- strcpy(fileresprobcov,"probcov");
- strcat(fileresprobcov,fileres);
- if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
- printf("Problem with resultfile: %s\n", fileresprobcov);
- fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
- }
- strcpy(fileresprobcor,"probcor");
- strcat(fileresprobcor,fileres);
- if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
- printf("Problem with resultfile: %s\n", fileresprobcor);
- fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
- }
- printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
- fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
- printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
- fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
- printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
- fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
- pstamp(ficresprob);
- fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
- fprintf(ficresprob,"# Age");
- pstamp(ficresprobcov);
- fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
- fprintf(ficresprobcov,"# Age");
- pstamp(ficresprobcor);
- fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
- fprintf(ficresprobcor,"# Age");
-
-
- for(i=1; i<=nlstate;i++)
- for(j=1; j<=(nlstate+ndeath);j++){
- fprintf(ficresprob," p%1d-%1d (SE)",i,j);
- fprintf(ficresprobcov," p%1d-%1d ",i,j);
- fprintf(ficresprobcor," p%1d-%1d ",i,j);
- }
- /* fprintf(ficresprob,"\n");
- fprintf(ficresprobcov,"\n");
- fprintf(ficresprobcor,"\n");
- */
- xp=vector(1,npar);
- dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
- doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
- mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
- varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
- first=1;
- fprintf(ficgp,"\n# Routine varprob");
- fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
- fprintf(fichtm,"\n");
-
- fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
- fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
- file %s<br>\n",optionfilehtmcov);
- fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
-and drawn. It helps understanding how is the covariance between two incidences.\
- They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
- 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. \
-It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
-would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
-standard deviations wide on each axis. <br>\
- Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
- and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
-To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
-
- cov[1]=1;
- tj=cptcoveff;
- if (cptcovn<1) {tj=1;ncodemax[1]=1;}
- j1=0;
- for(t=1; t<=tj;t++){
- for(i1=1; i1<=ncodemax[t];i1++){
- j1++;
- if (cptcovn>0) {
- fprintf(ficresprob, "\n#********** Variable ");
- for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
- fprintf(ficresprob, "**********\n#\n");
- fprintf(ficresprobcov, "\n#********** Variable ");
- for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
- fprintf(ficresprobcov, "**********\n#\n");
-
- fprintf(ficgp, "\n#********** Variable ");
- for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
- fprintf(ficgp, "**********\n#\n");
-
-
- fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
- for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
- fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
-
- fprintf(ficresprobcor, "\n#********** Variable ");
- for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
- fprintf(ficresprobcor, "**********\n#");
- }
-
- for (age=bage; age<=fage; age ++){
- cov[2]=age;
- for (k=1; k<=cptcovn;k++) {
- cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
- }
- for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
- for (k=1; k<=cptcovprod;k++)
- cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
-
- gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
- trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
- gp=vector(1,(nlstate)*(nlstate+ndeath));
- gm=vector(1,(nlstate)*(nlstate+ndeath));
-
- for(theta=1; theta <=npar; theta++){
- for(i=1; i<=npar; i++)
- xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
-
- pmij(pmmij,cov,ncovmodel,xp,nlstate);
-
- k=0;
- for(i=1; i<= (nlstate); i++){
- for(j=1; j<=(nlstate+ndeath);j++){
- k=k+1;
- gp[k]=pmmij[i][j];
- }
- }
-
- for(i=1; i<=npar; i++)
- xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
-
- pmij(pmmij,cov,ncovmodel,xp,nlstate);
- k=0;
- for(i=1; i<=(nlstate); i++){
- for(j=1; j<=(nlstate+ndeath);j++){
- k=k+1;
- gm[k]=pmmij[i][j];
- }
- }
-
- for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
- gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
- }
-
- for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
- for(theta=1; theta <=npar; theta++)
- trgradg[j][theta]=gradg[theta][j];
-
- matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
- matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
- free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
- free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
- free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
- free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
-
- pmij(pmmij,cov,ncovmodel,x,nlstate);
-
- k=0;
- for(i=1; i<=(nlstate); i++){
- for(j=1; j<=(nlstate+ndeath);j++){
- k=k+1;
- mu[k][(int) age]=pmmij[i][j];
- }
- }
- for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
- for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
- varpij[i][j][(int)age] = doldm[i][j];
-
- /*printf("\n%d ",(int)age);
- for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
- printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
- fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
- }*/
-
- fprintf(ficresprob,"\n%d ",(int)age);
- fprintf(ficresprobcov,"\n%d ",(int)age);
- fprintf(ficresprobcor,"\n%d ",(int)age);
-
- for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
- fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
- for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
- fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
- fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
- }
- i=0;
- for (k=1; k<=(nlstate);k++){
- for (l=1; l<=(nlstate+ndeath);l++){
- i=i++;
- fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
- fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
- for (j=1; j<=i;j++){
- fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
- fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
- }
- }
- }/* end of loop for state */
- } /* end of loop for age */
-
- /* Confidence intervalle of pij */
- /*
- fprintf(ficgp,"\nset noparametric;unset label");
- fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
- fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
- 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);
- fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
- fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
- fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
- */
-
- /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
- first1=1;
- for (k2=1; k2<=(nlstate);k2++){
- for (l2=1; l2<=(nlstate+ndeath);l2++){
- if(l2==k2) continue;
- j=(k2-1)*(nlstate+ndeath)+l2;
- for (k1=1; k1<=(nlstate);k1++){
- for (l1=1; l1<=(nlstate+ndeath);l1++){
- if(l1==k1) continue;
- i=(k1-1)*(nlstate+ndeath)+l1;
- if(i<=j) continue;
- for (age=bage; age<=fage; age ++){
- if ((int)age %5==0){
- v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
- v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
- cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
- mu1=mu[i][(int) age]/stepm*YEARM ;
- mu2=mu[j][(int) age]/stepm*YEARM;
- c12=cv12/sqrt(v1*v2);
- /* Computing eigen value of matrix of covariance */
- lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
- lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
- /* Eigen vectors */
- v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
- /*v21=sqrt(1.-v11*v11); *//* error */
- v21=(lc1-v1)/cv12*v11;
- v12=-v21;
- v22=v11;
- tnalp=v21/v11;
- if(first1==1){
- first1=0;
- 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);
- }
- 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);
- /*printf(fignu*/
- /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
- /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
- if(first==1){
- first=0;
- fprintf(ficgp,"\nset parametric;unset label");
- 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);
- fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
- fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
- :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
-%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
- subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
- subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
- fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
- fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
- fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
- fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
- fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
- 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",\
- mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
- mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
- }else{
- first=0;
- fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
- fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
- fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
- 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",\
- mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
- mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
- }/* if first */
- } /* age mod 5 */
- } /* end loop age */
- fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
- first=1;
- } /*l12 */
- } /* k12 */
- } /*l1 */
- }/* k1 */
- } /* loop covariates */
- }
- free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
- free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
- free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
- free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
- free_vector(xp,1,npar);
- fclose(ficresprob);
- fclose(ficresprobcov);
- fclose(ficresprobcor);
- fflush(ficgp);
- fflush(fichtmcov);
-}
-
-
-/******************* Printing html file ***********/
-void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
- int lastpass, int stepm, int weightopt, char model[],\
- int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
- int popforecast, int estepm ,\
- double jprev1, double mprev1,double anprev1, \
- double jprev2, double mprev2,double anprev2){
- int jj1, k1, i1, cpt;
-
- fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
- <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
-</ul>");
- fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
- - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
- jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
- fprintf(fichtm,"\
- - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
- stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
- fprintf(fichtm,"\
- - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
- subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
- fprintf(fichtm,"\
- - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age: ei., eij . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
- <a href=\"%s\">%s</a> <br>\n</li>",
- estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
-
-
-fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
-
- m=cptcoveff;
- if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-
- jj1=0;
- for(k1=1; k1<=m;k1++){
- for(i1=1; i1<=ncodemax[k1];i1++){
- jj1++;
- if (cptcovn > 0) {
- fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
- for (cpt=1; cpt<=cptcoveff;cpt++)
- fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
- fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
- }
- /* Pij */
- fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
-<img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
- /* Quasi-incidences */
- fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
- before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
-<img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
- /* Period (stable) prevalence in each health state */
- for(cpt=1; cpt<nlstate;cpt++){
- fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
-<img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
- }
- for(cpt=1; cpt<=nlstate;cpt++) {
- fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
-<img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
- }
- } /* end i1 */
- }/* End k1 */
- fprintf(fichtm,"</ul>");
-
-
- fprintf(fichtm,"\
-\n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
- - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
-
- fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
- subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
- fprintf(fichtm,"\
- - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
- subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
-
- fprintf(fichtm,"\
- - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
- subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
- fprintf(fichtm,"\
- - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
- <a href=\"%s\">%s</a> <br>\n</li>",
- estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
- fprintf(fichtm,"\
- - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
- <a href=\"%s\">%s</a> <br>\n</li>",
- estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
- fprintf(fichtm,"\
- - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences (i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
- estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
- fprintf(fichtm,"\
- - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <a href=\"%s\">%s</a> <br>\n",
- subdirf2(fileres,"t"),subdirf2(fileres,"t"));
- fprintf(fichtm,"\
- - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
- subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
-
-/* if(popforecast==1) fprintf(fichtm,"\n */
-/* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
-/* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
-/* <br>",fileres,fileres,fileres,fileres); */
-/* else */
-/* 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); */
- fflush(fichtm);
- fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
-
- m=cptcoveff;
- if (cptcovn < 1) {m=1;ncodemax[1]=1;}
-
- jj1=0;
- for(k1=1; k1<=m;k1++){
- for(i1=1; i1<=ncodemax[k1];i1++){
- jj1++;
- if (cptcovn > 0) {
- fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
- for (cpt=1; cpt<=cptcoveff;cpt++)
- fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
- fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
- }
- for(cpt=1; cpt<=nlstate;cpt++) {
- fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
-prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
-<img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
- }
- fprintf(fichtm,"\n<br>- Total life expectancy by age and \
-health expectancies in states (1) and (2): %s%d.png<br>\
-<img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
- } /* end i1 */
- }/* End k1 */
- fprintf(fichtm,"</ul>");
- fflush(fichtm);
-}
-
-/******************* Gnuplot file **************/
-void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-
- char dirfileres[132],optfileres[132];
- int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
- int ng;
-/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
-/* printf("Problem with file %s",optionfilegnuplot); */
-/* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
-/* } */
-
- /*#ifdef windows */
- fprintf(ficgp,"cd \"%s\" \n",pathc);
- /*#endif */
- m=pow(2,cptcoveff);
-
- strcpy(dirfileres,optionfilefiname);
- strcpy(optfileres,"vpl");
- /* 1eme*/
- for (cpt=1; cpt<= nlstate ; cpt ++) {
- for (k1=1; k1<= m ; k1 ++) {
- fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
- fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
- fprintf(ficgp,"set xlabel \"Age\" \n\
-set ylabel \"Probability\" \n\
-set ter png small\n\
-set size 0.65,0.65\n\
-plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
-
- for (i=1; i<= nlstate ; i ++) {
- if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
- else fprintf(ficgp," \%%*lf (\%%*lf)");
- }
- fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
- for (i=1; i<= nlstate ; i ++) {
- if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
- else fprintf(ficgp," \%%*lf (\%%*lf)");
- }
- fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
- for (i=1; i<= nlstate ; i ++) {
- if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
- else fprintf(ficgp," \%%*lf (\%%*lf)");
- }
- fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
- }
- }
- /*2 eme*/
-
- for (k1=1; k1<= m ; k1 ++) {
- fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
- fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
-
- for (i=1; i<= nlstate+1 ; i ++) {
- k=2*i;
- fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
- for (j=1; j<= nlstate+1 ; j ++) {
- if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
- else fprintf(ficgp," \%%*lf (\%%*lf)");
- }
- if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
- else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
- fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
- for (j=1; j<= nlstate+1 ; j ++) {
- if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
- else fprintf(ficgp," \%%*lf (\%%*lf)");
- }
- fprintf(ficgp,"\" t\"\" w l 0,");
- fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
- for (j=1; j<= nlstate+1 ; j ++) {
- if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
- else fprintf(ficgp," \%%*lf (\%%*lf)");
- }
- if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
- else fprintf(ficgp,"\" t\"\" w l 0,");
- }
- }
-
- /*3eme*/
-
- for (k1=1; k1<= m ; k1 ++) {
- for (cpt=1; cpt<= nlstate ; cpt ++) {
- /* k=2+nlstate*(2*cpt-2); */
- k=2+(nlstate+1)*(cpt-1);
- fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
- fprintf(ficgp,"set ter png small\n\
-set size 0.65,0.65\n\
-plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
- /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
- for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
- fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
- fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
- for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
- fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
-
- */
- for (i=1; i< nlstate ; i ++) {
- fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
- /* 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);*/
-
- }
- fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
- }
- }
-
- /* CV preval stable (period) */
- for (k1=1; k1<= m ; k1 ++) {
- for (cpt=1; cpt<=nlstate ; cpt ++) {
- k=3;
- fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
- fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
-set ter png small\nset size 0.65,0.65\n\
-unset log y\n\
-plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
-
- for (i=1; i< nlstate ; i ++)
- fprintf(ficgp,"+$%d",k+i+1);
- fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
-
- l=3+(nlstate+ndeath)*cpt;
- fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
- for (i=1; i< nlstate ; i ++) {
- l=3+(nlstate+ndeath)*cpt;
- fprintf(ficgp,"+$%d",l+i+1);
- }
- fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
- }
- }
-
- /* proba elementaires */
- for(i=1,jk=1; i <=nlstate; i++){
- for(k=1; k <=(nlstate+ndeath); k++){
- if (k != i) {
- for(j=1; j <=ncovmodel; j++){
- fprintf(ficgp,"p%d=%f ",jk,p[jk]);
- jk++;
- fprintf(ficgp,"\n");
- }
- }
- }
- }
-
- for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
- for(jk=1; jk <=m; jk++) {
- fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng);
- if (ng==2)
- fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
- else
- fprintf(ficgp,"\nset title \"Probability\"\n");
- fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
- i=1;
- for(k2=1; k2<=nlstate; k2++) {
- k3=i;
- for(k=1; k<=(nlstate+ndeath); k++) {
- if (k != k2){
- if(ng==2)
- fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
- else
- fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
- ij=1;
- for(j=3; j <=ncovmodel; j++) {
- if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
- fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
- ij++;
- }
- else
- fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
- }
- fprintf(ficgp,")/(1");
-
- for(k1=1; k1 <=nlstate; k1++){
- fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
- ij=1;
- for(j=3; j <=ncovmodel; j++){
- if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
- fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
- ij++;
- }
- else
- fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
- }
- fprintf(ficgp,")");
- }
- fprintf(ficgp,") t \"p%d%d\" ", k2,k);
- if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
- i=i+ncovmodel;
- }
- } /* end k */
- } /* end k2 */
- } /* end jk */
- } /* end ng */
- fflush(ficgp);
-} /* end gnuplot */
-
-
-/*************** Moving average **************/
-int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
-
- int i, cpt, cptcod;
- int modcovmax =1;
- int mobilavrange, mob;
- double age;
-
- modcovmax=2*cptcoveff;/* Max number of modalities. We suppose
- a covariate has 2 modalities */
- if (cptcovn<1) modcovmax=1; /* At least 1 pass */
-
- if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
- if(mobilav==1) mobilavrange=5; /* default */
- else mobilavrange=mobilav;
- for (age=bage; age<=fage; age++)
- for (i=1; i<=nlstate;i++)
- for (cptcod=1;cptcod<=modcovmax;cptcod++)
- mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
- /* We keep the original values on the extreme ages bage, fage and for
- fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
- we use a 5 terms etc. until the borders are no more concerned.
- */
- for (mob=3;mob <=mobilavrange;mob=mob+2){
- for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
- for (i=1; i<=nlstate;i++){
- for (cptcod=1;cptcod<=modcovmax;cptcod++){
- mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
- for (cpt=1;cpt<=(mob-1)/2;cpt++){
- mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
- mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
- }
- mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
- }
- }
- }/* end age */
- }/* end mob */
- }else return -1;
- return 0;
-}/* End movingaverage */
-
-
-/************** Forecasting ******************/
-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){
- /* proj1, year, month, day of starting projection
- agemin, agemax range of age
- dateprev1 dateprev2 range of dates during which prevalence is computed
- anproj2 year of en of projection (same day and month as proj1).
- */
- int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
- int *popage;
- double agec; /* generic age */
- double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
- double *popeffectif,*popcount;
- double ***p3mat;
- double ***mobaverage;
- char fileresf[FILENAMELENGTH];
-
- agelim=AGESUP;
- prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-
- strcpy(fileresf,"f");
- strcat(fileresf,fileres);
- if((ficresf=fopen(fileresf,"w"))==NULL) {
- printf("Problem with forecast resultfile: %s\n", fileresf);
- fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
- }
- printf("Computing forecasting: result on file '%s' \n", fileresf);
- fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
-
- if (cptcoveff==0) ncodemax[cptcoveff]=1;
-
- if (mobilav!=0) {
- mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
- if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
- fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
- printf(" Error in movingaverage mobilav=%d\n",mobilav);
- }
- }
-
- stepsize=(int) (stepm+YEARM-1)/YEARM;
- if (stepm<=12) stepsize=1;
- if(estepm < stepm){
- printf ("Problem %d lower than %d\n",estepm, stepm);
- }
- else hstepm=estepm;
-
- hstepm=hstepm/stepm;
- yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
- fractional in yp1 */
- anprojmean=yp;
- yp2=modf((yp1*12),&yp);
- mprojmean=yp;
- yp1=modf((yp2*30.5),&yp);
- jprojmean=yp;
- if(jprojmean==0) jprojmean=1;
- if(mprojmean==0) jprojmean=1;
-
- i1=cptcoveff;
- if (cptcovn < 1){i1=1;}
-
- fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);
-
- fprintf(ficresf,"#****** Routine prevforecast **\n");
-
-/* if (h==(int)(YEARM*yearp)){ */
- for(cptcov=1, k=0;cptcov<=i1;cptcov++){
- for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
- k=k+1;
- fprintf(ficresf,"\n#******");
- for(j=1;j<=cptcoveff;j++) {
- 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]]);
- }
- fprintf(ficresf,"******\n");
- fprintf(ficresf,"# Covariate valuofcovar yearproj age");
- for(j=1; j<=nlstate+ndeath;j++){
- for(i=1; i<=nlstate;i++)
- fprintf(ficresf," p%d%d",i,j);
- fprintf(ficresf," p.%d",j);
- }
- for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
- fprintf(ficresf,"\n");
- fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
-
- for (agec=fage; agec>=(ageminpar-1); agec--){
- nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
- nhstepm = nhstepm/hstepm;
- p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- oldm=oldms;savm=savms;
- hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);
-
- for (h=0; h<=nhstepm; h++){
- if (h*hstepm/YEARM*stepm ==yearp) {
- fprintf(ficresf,"\n");
- for(j=1;j<=cptcoveff;j++)
- fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
- }
- for(j=1; j<=nlstate+ndeath;j++) {
- ppij=0.;
- for(i=1; i<=nlstate;i++) {
- if (mobilav==1)
- ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
- else {
- ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
- }
- if (h*hstepm/YEARM*stepm== yearp) {
- fprintf(ficresf," %.3f", p3mat[i][j][h]);
- }
- } /* end i */
- if (h*hstepm/YEARM*stepm==yearp) {
- fprintf(ficresf," %.3f", ppij);
- }
- }/* end j */
- } /* end h */
- free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- } /* end agec */
- } /* end yearp */
- } /* end cptcod */
- } /* end cptcov */
-
- if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-
- fclose(ficresf);
-}
-
-/************** Forecasting *****not tested NB*************/
-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){
-
- int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
- int *popage;
- double calagedatem, agelim, kk1, kk2;
- double *popeffectif,*popcount;
- double ***p3mat,***tabpop,***tabpopprev;
- double ***mobaverage;
- char filerespop[FILENAMELENGTH];
-
- tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
- tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
- agelim=AGESUP;
- calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
-
- prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
-
-
- strcpy(filerespop,"pop");
- strcat(filerespop,fileres);
- if((ficrespop=fopen(filerespop,"w"))==NULL) {
- printf("Problem with forecast resultfile: %s\n", filerespop);
- fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
- }
- printf("Computing forecasting: result on file '%s' \n", filerespop);
- fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
-
- if (cptcoveff==0) ncodemax[cptcoveff]=1;
-
- if (mobilav!=0) {
- mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
- if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
- fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
- printf(" Error in movingaverage mobilav=%d\n",mobilav);
- }
- }
-
- stepsize=(int) (stepm+YEARM-1)/YEARM;
- if (stepm<=12) stepsize=1;
-
- agelim=AGESUP;
-
- hstepm=1;
- hstepm=hstepm/stepm;
-
- if (popforecast==1) {
- if((ficpop=fopen(popfile,"r"))==NULL) {
- printf("Problem with population file : %s\n",popfile);exit(0);
- fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
- }
- popage=ivector(0,AGESUP);
- popeffectif=vector(0,AGESUP);
- popcount=vector(0,AGESUP);
-
- i=1;
- while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
-
- imx=i;
- for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
- }
-
- for(cptcov=1,k=0;cptcov<=i2;cptcov++){
- for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
- k=k+1;
- fprintf(ficrespop,"\n#******");
- for(j=1;j<=cptcoveff;j++) {
- fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- }
- fprintf(ficrespop,"******\n");
- fprintf(ficrespop,"# Age");
- for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
- if (popforecast==1) fprintf(ficrespop," [Population]");
-
- for (cpt=0; cpt<=0;cpt++) {
- fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
-
- for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
- nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
- nhstepm = nhstepm/hstepm;
-
- p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- oldm=oldms;savm=savms;
- hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
-
- for (h=0; h<=nhstepm; h++){
- if (h==(int) (calagedatem+YEARM*cpt)) {
- fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
- }
- for(j=1; j<=nlstate+ndeath;j++) {
- kk1=0.;kk2=0;
- for(i=1; i<=nlstate;i++) {
- if (mobilav==1)
- kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
- else {
- kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
- }
- }
- if (h==(int)(calagedatem+12*cpt)){
- tabpop[(int)(agedeb)][j][cptcod]=kk1;
- /*fprintf(ficrespop," %.3f", kk1);
- if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
- }
- }
- for(i=1; i<=nlstate;i++){
- kk1=0.;
- for(j=1; j<=nlstate;j++){
- kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
- }
- tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
- }
-
- if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
- fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
- }
- free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- }
- }
-
- /******/
-
- for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
- fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
- for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
- nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
- nhstepm = nhstepm/hstepm;
-
- p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- oldm=oldms;savm=savms;
- hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
- for (h=0; h<=nhstepm; h++){
- if (h==(int) (calagedatem+YEARM*cpt)) {
- fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
- }
- for(j=1; j<=nlstate+ndeath;j++) {
- kk1=0.;kk2=0;
- for(i=1; i<=nlstate;i++) {
- kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
- }
- if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
- }
- }
- free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- }
- }
- }
- }
-
- if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
-
- if (popforecast==1) {
- free_ivector(popage,0,AGESUP);
- free_vector(popeffectif,0,AGESUP);
- free_vector(popcount,0,AGESUP);
- }
- free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
- free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
- fclose(ficrespop);
-} /* End of popforecast */
-
-int fileappend(FILE *fichier, char *optionfich)
-{
- if((fichier=fopen(optionfich,"a"))==NULL) {
- printf("Problem with file: %s\n", optionfich);
- fprintf(ficlog,"Problem with file: %s\n", optionfich);
- return (0);
- }
- fflush(fichier);
- return (1);
-}
-
-
-/**************** function prwizard **********************/
-void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)
-{
-
- /* Wizard to print covariance matrix template */
-
- char ca[32], cb[32], cc[32];
- int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
- int numlinepar;
-
- printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
- fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
- for(i=1; i <=nlstate; i++){
- jj=0;
- for(j=1; j <=nlstate+ndeath; j++){
- if(j==i) continue;
- jj++;
- /*ca[0]= k+'a'-1;ca[1]='\0';*/
- printf("%1d%1d",i,j);
- fprintf(ficparo,"%1d%1d",i,j);
- for(k=1; k<=ncovmodel;k++){
- /* printf(" %lf",param[i][j][k]); */
- /* fprintf(ficparo," %lf",param[i][j][k]); */
- printf(" 0.");
- fprintf(ficparo," 0.");
- }
- printf("\n");
- fprintf(ficparo,"\n");
- }
- }
- printf("# Scales (for hessian or gradient estimation)\n");
- fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
- npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
- for(i=1; i <=nlstate; i++){
- jj=0;
- for(j=1; j <=nlstate+ndeath; j++){
- if(j==i) continue;
- jj++;
- fprintf(ficparo,"%1d%1d",i,j);
- printf("%1d%1d",i,j);
- fflush(stdout);
- for(k=1; k<=ncovmodel;k++){
- /* printf(" %le",delti3[i][j][k]); */
- /* fprintf(ficparo," %le",delti3[i][j][k]); */
- printf(" 0.");
- fprintf(ficparo," 0.");
- }
- numlinepar++;
- printf("\n");
- fprintf(ficparo,"\n");
- }
- }
- printf("# Covariance matrix\n");
-/* # 121 Var(a12)\n\ */
-/* # 122 Cov(b12,a12) Var(b12)\n\ */
-/* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
-/* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
-/* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
-/* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
-/* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
-/* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
- fflush(stdout);
- fprintf(ficparo,"# 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" */
-
- for(itimes=1;itimes<=2;itimes++){
- jj=0;
- for(i=1; i <=nlstate; i++){
- for(j=1; j <=nlstate+ndeath; j++){
- if(j==i) continue;
- for(k=1; k<=ncovmodel;k++){
- jj++;
- ca[0]= k+'a'-1;ca[1]='\0';
- if(itimes==1){
- printf("#%1d%1d%d",i,j,k);
- fprintf(ficparo,"#%1d%1d%d",i,j,k);
- }else{
- printf("%1d%1d%d",i,j,k);
- fprintf(ficparo,"%1d%1d%d",i,j,k);
- /* printf(" %.5le",matcov[i][j]); */
- }
- ll=0;
- for(li=1;li <=nlstate; li++){
- for(lj=1;lj <=nlstate+ndeath; lj++){
- if(lj==li) continue;
- for(lk=1;lk<=ncovmodel;lk++){
- ll++;
- if(ll<=jj){
- cb[0]= lk +'a'-1;cb[1]='\0';
- if(ll<jj){
- if(itimes==1){
- printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
- fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
- }else{
- printf(" 0.");
- fprintf(ficparo," 0.");
- }
- }else{
- if(itimes==1){
- printf(" Var(%s%1d%1d)",ca,i,j);
- fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
- }else{
- printf(" 0.");
- fprintf(ficparo," 0.");
- }
- }
- }
- } /* end lk */
- } /* end lj */
- } /* end li */
- printf("\n");
- fprintf(ficparo,"\n");
- numlinepar++;
- } /* end k*/
- } /*end j */
- } /* end i */
- } /* end itimes */
-
-} /* end of prwizard */
-/******************* Gompertz Likelihood ******************************/
-double gompertz(double x[])
-{
- double A,B,L=0.0,sump=0.,num=0.;
- int i,n=0; /* n is the size of the sample */
-
- for (i=0;i<=imx-1 ; i++) {
- sump=sump+weight[i];
- /* sump=sump+1;*/
- num=num+1;
- }
-
-
- /* for (i=0; i<=imx; i++)
- 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]);*/
-
- for (i=1;i<=imx ; i++)
- {
- if (cens[i] == 1 && wav[i]>1)
- A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
-
- if (cens[i] == 0 && wav[i]>1)
- A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
- +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
-
- /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
- if (wav[i] > 1 ) { /* ??? */
- L=L+A*weight[i];
- /* 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]);*/
- }
- }
-
- /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
-
- return -2*L*num/sump;
-}
-
-/******************* Printing html file ***********/
-void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
- int lastpass, int stepm, int weightopt, char model[],\
- int imx, double p[],double **matcov,double agemortsup){
- int i,k;
-
- fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
- fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
- for (i=1;i<=2;i++)
- 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]));
- fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
- fprintf(fichtm,"</ul>");
-
-fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
-
- 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>");
-
- for (k=agegomp;k<(agemortsup-2);k++)
- 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]);
-
-
- fflush(fichtm);
-}
-
-/******************* Gnuplot file **************/
-void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
-
- char dirfileres[132],optfileres[132];
- int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
- int ng;
-
-
- /*#ifdef windows */
- fprintf(ficgp,"cd \"%s\" \n",pathc);
- /*#endif */
-
-
- strcpy(dirfileres,optionfilefiname);
- strcpy(optfileres,"vpl");
- fprintf(ficgp,"set out \"graphmort.png\"\n ");
- fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n ");
- fprintf(ficgp, "set ter png small\n set log y\n");
- fprintf(ficgp, "set size 0.65,0.65\n");
- fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
-
-}
-
-
-
-
-
-/***********************************************/
-/**************** Main Program *****************/
-/***********************************************/
-
-int main(int argc, char *argv[])
-{
- int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
- int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
- int linei, month, year,iout;
- int jj, ll, li, lj, lk, imk;
- int numlinepar=0; /* Current linenumber of parameter file */
- int itimes;
- int NDIM=2;
-
- char ca[32], cb[32], cc[32];
- char dummy[]=" ";
- /* FILE *fichtm; *//* Html File */
- /* FILE *ficgp;*/ /*Gnuplot File */
- struct stat info;
- double agedeb, agefin,hf;
- double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
-
- double fret;
- double **xi,tmp,delta;
-
- double dum; /* Dummy variable */
- double ***p3mat;
- double ***mobaverage;
- int *indx;
- char line[MAXLINE], linepar[MAXLINE];
- char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
- char pathr[MAXLINE], pathimach[MAXLINE];
- char **bp, *tok, *val; /* pathtot */
- int firstobs=1, lastobs=10;
- int sdeb, sfin; /* Status at beginning and end */
- int c, h , cpt,l;
- int ju,jl, mi;
- int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
- int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;
- int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
- int mobilav=0,popforecast=0;
- int hstepm, nhstepm;
- int agemortsup;
- float sumlpop=0.;
- double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
- double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
-
- double bage, fage, age, agelim, agebase;
- double ftolpl=FTOL;
- double **prlim;
- double *severity;
- double ***param; /* Matrix of parameters */
- double *p;
- double **matcov; /* Matrix of covariance */
- double ***delti3; /* Scale */
- double *delti; /* Scale */
- double ***eij, ***vareij;
- double **varpl; /* Variances of prevalence limits by age */
- double *epj, vepp;
- double kk1, kk2;
- double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
- double **ximort;
- char *alph[]={"a","a","b","c","d","e"}, str[4];
- int *dcwave;
-
- char z[1]="c", occ;
-
- char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
- char *strt, strtend[80];
- char *stratrunc;
- int lstra;
-
- long total_usecs;
-
-/* setlocale (LC_ALL, ""); */
-/* bindtextdomain (PACKAGE, LOCALEDIR); */
-/* textdomain (PACKAGE); */
-/* setlocale (LC_CTYPE, ""); */
-/* setlocale (LC_MESSAGES, ""); */
-
- /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
- (void) gettimeofday(&start_time,&tzp);
- curr_time=start_time;
- tm = *localtime(&start_time.tv_sec);
- tmg = *gmtime(&start_time.tv_sec);
- strcpy(strstart,asctime(&tm));
-
-/* printf("Localtime (at start)=%s",strstart); */
-/* tp.tv_sec = tp.tv_sec +86400; */
-/* tm = *localtime(&start_time.tv_sec); */
-/* tmg.tm_year=tmg.tm_year +dsign*dyear; */
-/* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
-/* tmg.tm_hour=tmg.tm_hour + 1; */
-/* tp.tv_sec = mktime(&tmg); */
-/* strt=asctime(&tmg); */
-/* printf("Time(after) =%s",strstart); */
-/* (void) time (&time_value);
-* printf("time=%d,t-=%d\n",time_value,time_value-86400);
-* tm = *localtime(&time_value);
-* strstart=asctime(&tm);
-* printf("tim_value=%d,asctime=%s\n",time_value,strstart);
-*/
-
- nberr=0; /* Number of errors and warnings */
- nbwarn=0;
- getcwd(pathcd, size);
-
- printf("\n%s\n%s",version,fullversion);
- if(argc <=1){
- printf("\nEnter the parameter file name: ");
- fgets(pathr,FILENAMELENGTH,stdin);
- i=strlen(pathr);
- if(pathr[i-1]=='\n')
- pathr[i-1]='\0';
- for (tok = pathr; tok != NULL; ){
- printf("Pathr |%s|\n",pathr);
- while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
- printf("val= |%s| pathr=%s\n",val,pathr);
- strcpy (pathtot, val);
- if(pathr[0] == '\0') break; /* Dirty */
- }
- }
- else{
- strcpy(pathtot,argv[1]);
- }
- /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
- /*cygwin_split_path(pathtot,path,optionfile);
- printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
- /* cutv(path,optionfile,pathtot,'\\');*/
-
- /* Split argv[0], imach program to get pathimach */
- printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
- split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
- printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
- /* strcpy(pathimach,argv[0]); */
- /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
- split(pathtot,path,optionfile,optionfilext,optionfilefiname);
- printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
- chdir(path); /* Can be a relative path */
- if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
- printf("Current directory %s!\n",pathcd);
- strcpy(command,"mkdir ");
- strcat(command,optionfilefiname);
- if((outcmd=system(command)) != 0){
- printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
- /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
- /* fclose(ficlog); */
-/* exit(1); */
- }
-/* if((imk=mkdir(optionfilefiname))<0){ */
-/* perror("mkdir"); */
-/* } */
-
- /*-------- arguments in the command line --------*/
-
- /* Log file */
- strcat(filelog, optionfilefiname);
- strcat(filelog,".log"); /* */
- if((ficlog=fopen(filelog,"w"))==NULL) {
- printf("Problem with logfile %s\n",filelog);
- goto end;
- }
- fprintf(ficlog,"Log filename:%s\n",filelog);
- fprintf(ficlog,"\n%s\n%s",version,fullversion);
- fprintf(ficlog,"\nEnter the parameter file name: \n");
- fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
- path=%s \n\
- optionfile=%s\n\
- optionfilext=%s\n\
- optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
-
- printf("Local time (at start):%s",strstart);
- fprintf(ficlog,"Local time (at start): %s",strstart);
- fflush(ficlog);
-/* (void) gettimeofday(&curr_time,&tzp); */
-/* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
-
- /* */
- strcpy(fileres,"r");
- strcat(fileres, optionfilefiname);
- strcat(fileres,".txt"); /* Other files have txt extension */
-
- /*---------arguments file --------*/
-
- if((ficpar=fopen(optionfile,"r"))==NULL) {
- printf("Problem with optionfile %s\n",optionfile);
- fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
- fflush(ficlog);
- goto end;
- }
-
-
-
- strcpy(filereso,"o");
- strcat(filereso,fileres);
- if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
- printf("Problem with Output resultfile: %s\n", filereso);
- fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
- fflush(ficlog);
- goto end;
- }
-
- /* Reads comments: lines beginning with '#' */
- numlinepar=0;
- while((c=getc(ficpar))=='#' && c!= EOF){
- ungetc(c,ficpar);
- fgets(line, MAXLINE, ficpar);
- numlinepar++;
- puts(line);
- fputs(line,ficparo);
- fputs(line,ficlog);
- }
- ungetc(c,ficpar);
-
- 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);
- numlinepar++;
- 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);
- 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);
- 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);
- fflush(ficlog);
- while((c=getc(ficpar))=='#' && c!= EOF){
- ungetc(c,ficpar);
- fgets(line, MAXLINE, ficpar);
- numlinepar++;
- puts(line);
- fputs(line,ficparo);
- fputs(line,ficlog);
- }
- ungetc(c,ficpar);
-
-
- covar=matrix(0,NCOVMAX,1,n);
- cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
- if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
-
- ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
- nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
- npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
-
- delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
- delti=delti3[1][1];
- /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
- if(mle==-1){ /* Print a wizard for help writing covariance matrix */
- prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
- printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
- fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
- free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
- fclose (ficparo);
- fclose (ficlog);
- goto end;
- exit(0);
- }
- else if(mle==-3) {
- prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
- printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
- fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
- param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
- matcov=matrix(1,npar,1,npar);
- }
- else{
- /* Read guess parameters */
- /* Reads comments: lines beginning with '#' */
- while((c=getc(ficpar))=='#' && c!= EOF){
- ungetc(c,ficpar);
- fgets(line, MAXLINE, ficpar);
- numlinepar++;
- puts(line);
- fputs(line,ficparo);
- fputs(line,ficlog);
- }
- ungetc(c,ficpar);
-
- param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
- for(i=1; i <=nlstate; i++){
- j=0;
- for(jj=1; jj <=nlstate+ndeath; jj++){
- if(jj==i) continue;
- j++;
- fscanf(ficpar,"%1d%1d",&i1,&j1);
- if ((i1 != i) && (j1 != j)){
- printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
-It might be a problem of design; if ncovcol and the model are correct\n \
-run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
- exit(1);
- }
- fprintf(ficparo,"%1d%1d",i1,j1);
- if(mle==1)
- printf("%1d%1d",i,j);
- fprintf(ficlog,"%1d%1d",i,j);
- for(k=1; k<=ncovmodel;k++){
- fscanf(ficpar," %lf",¶m[i][j][k]);
- if(mle==1){
- printf(" %lf",param[i][j][k]);
- fprintf(ficlog," %lf",param[i][j][k]);
- }
- else
- fprintf(ficlog," %lf",param[i][j][k]);
- fprintf(ficparo," %lf",param[i][j][k]);
- }
- fscanf(ficpar,"\n");
- numlinepar++;
- if(mle==1)
- printf("\n");
- fprintf(ficlog,"\n");
- fprintf(ficparo,"\n");
- }
- }
- fflush(ficlog);
-
- p=param[1][1];
-
- /* Reads comments: lines beginning with '#' */
- while((c=getc(ficpar))=='#' && c!= EOF){
- ungetc(c,ficpar);
- fgets(line, MAXLINE, ficpar);
- numlinepar++;
- puts(line);
- fputs(line,ficparo);
- fputs(line,ficlog);
- }
- ungetc(c,ficpar);
-
- for(i=1; i <=nlstate; i++){
- for(j=1; j <=nlstate+ndeath-1; j++){
- fscanf(ficpar,"%1d%1d",&i1,&j1);
- if ((i1-i)*(j1-j)!=0){
- printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
- exit(1);
- }
- printf("%1d%1d",i,j);
- fprintf(ficparo,"%1d%1d",i1,j1);
- fprintf(ficlog,"%1d%1d",i1,j1);
- for(k=1; k<=ncovmodel;k++){
- fscanf(ficpar,"%le",&delti3[i][j][k]);
- printf(" %le",delti3[i][j][k]);
- fprintf(ficparo," %le",delti3[i][j][k]);
- fprintf(ficlog," %le",delti3[i][j][k]);
- }
- fscanf(ficpar,"\n");
- numlinepar++;
- printf("\n");
- fprintf(ficparo,"\n");
- fprintf(ficlog,"\n");
- }
- }
- fflush(ficlog);
-
- delti=delti3[1][1];
-
-
- /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
-
- /* Reads comments: lines beginning with '#' */
- while((c=getc(ficpar))=='#' && c!= EOF){
- ungetc(c,ficpar);
- fgets(line, MAXLINE, ficpar);
- numlinepar++;
- puts(line);
- fputs(line,ficparo);
- fputs(line,ficlog);
- }
- ungetc(c,ficpar);
-
- matcov=matrix(1,npar,1,npar);
- for(i=1; i <=npar; i++){
- fscanf(ficpar,"%s",&str);
- if(mle==1)
- printf("%s",str);
- fprintf(ficlog,"%s",str);
- fprintf(ficparo,"%s",str);
- for(j=1; j <=i; j++){
- fscanf(ficpar," %le",&matcov[i][j]);
- if(mle==1){
- printf(" %.5le",matcov[i][j]);
- }
- fprintf(ficlog," %.5le",matcov[i][j]);
- fprintf(ficparo," %.5le",matcov[i][j]);
- }
- fscanf(ficpar,"\n");
- numlinepar++;
- if(mle==1)
- printf("\n");
- fprintf(ficlog,"\n");
- fprintf(ficparo,"\n");
- }
- for(i=1; i <=npar; i++)
- for(j=i+1;j<=npar;j++)
- matcov[i][j]=matcov[j][i];
-
- if(mle==1)
- printf("\n");
- fprintf(ficlog,"\n");
-
- fflush(ficlog);
-
- /*-------- Rewriting parameter file ----------*/
- strcpy(rfileres,"r"); /* "Rparameterfile */
- strcat(rfileres,optionfilefiname); /* Parameter file first name*/
- strcat(rfileres,"."); /* */
- strcat(rfileres,optionfilext); /* Other files have txt extension */
- if((ficres =fopen(rfileres,"w"))==NULL) {
- printf("Problem writing new parameter file: %s\n", fileres);goto end;
- fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
- }
- fprintf(ficres,"#%s\n",version);
- } /* End of mle != -3 */
-
- /*-------- data file ----------*/
- if((fic=fopen(datafile,"r"))==NULL) {
- printf("Problem while opening datafile: %s\n", datafile);goto end;
- fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
- }
-
- n= lastobs;
- severity = vector(1,maxwav);
- outcome=imatrix(1,maxwav+1,1,n);
- num=lvector(1,n);
- moisnais=vector(1,n);
- annais=vector(1,n);
- moisdc=vector(1,n);
- andc=vector(1,n);
- agedc=vector(1,n);
- cod=ivector(1,n);
- weight=vector(1,n);
- for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
- mint=matrix(1,maxwav,1,n);
- anint=matrix(1,maxwav,1,n);
- s=imatrix(1,maxwav+1,1,n);
- tab=ivector(1,NCOVMAX);
- ncodemax=ivector(1,8);
-
- i=1;
- linei=0;
- while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
- linei=linei+1;
- for(j=strlen(line); j>=0;j--){ /* Untabifies line */
- if(line[j] == '\t')
- line[j] = ' ';
- }
- for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
- ;
- };
- line[j+1]=0; /* Trims blanks at end of line */
- if(line[0]=='#'){
- fprintf(ficlog,"Comment line\n%s\n",line);
- printf("Comment line\n%s\n",line);
- continue;
- }
-
- for (j=maxwav;j>=1;j--){
- cutv(stra, strb,line,' ');
- errno=0;
- lval=strtol(strb,&endptr,10);
- /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
- if( strb[0]=='\0' || (*endptr != '\0')){
- 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);
- exit(1);
- }
- s[j][i]=lval;
-
- strcpy(line,stra);
- cutv(stra, strb,line,' ');
- if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
- }
- else if(iout=sscanf(strb,"%s.") != 0){
- month=99;
- year=9999;
- }else{
- 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);
- exit(1);
- }
- anint[j][i]= (double) year;
- mint[j][i]= (double)month;
- strcpy(line,stra);
- } /* ENd Waves */
-
- cutv(stra, strb,line,' ');
- if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
- }
- else if(iout=sscanf(strb,"%s.",dummy) != 0){
- month=99;
- year=9999;
- }else{
- 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);
- exit(1);
- }
- andc[i]=(double) year;
- moisdc[i]=(double) month;
- strcpy(line,stra);
-
- cutv(stra, strb,line,' ');
- if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
- }
- else if(iout=sscanf(strb,"%s.") != 0){
- month=99;
- year=9999;
- }else{
- 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);
- exit(1);
- }
- annais[i]=(double)(year);
- moisnais[i]=(double)(month);
- strcpy(line,stra);
-
- cutv(stra, strb,line,' ');
- errno=0;
- dval=strtod(strb,&endptr);
- if( strb[0]=='\0' || (*endptr != '\0')){
- printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
- exit(1);
- }
- weight[i]=dval;
- strcpy(line,stra);
-
- for (j=ncovcol;j>=1;j--){
- cutv(stra, strb,line,' ');
- errno=0;
- lval=strtol(strb,&endptr,10);
- if( strb[0]=='\0' || (*endptr != '\0')){
- 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);
- exit(1);
- }
- if(lval <-1 || lval >1){
- printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
- Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
- for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
- For example, for multinomial values like 1, 2 and 3,\n \
- build V1=0 V2=0 for the reference value (1),\n \
- V1=1 V2=0 for (2) \n \
- and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
- output of IMaCh is often meaningless.\n \
- Exiting.\n",lval,linei, i,line,j);
- exit(1);
- }
- covar[j][i]=(double)(lval);
- strcpy(line,stra);
- }
- lstra=strlen(stra);
-
- if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
- stratrunc = &(stra[lstra-9]);
- num[i]=atol(stratrunc);
- }
- else
- num[i]=atol(stra);
- /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
- 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;}*/
-
- i=i+1;
- } /* End loop reading data */
- fclose(fic);
- /* printf("ii=%d", ij);
- scanf("%d",i);*/
- imx=i-1; /* Number of individuals */
-
- /* for (i=1; i<=imx; i++){
- if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
- if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
- if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
- }*/
- /* for (i=1; i<=imx; i++){
- if (s[4][i]==9) s[4][i]=-1;
- 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]));}*/
-
- /* for (i=1; i<=imx; i++) */
-
- /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
- else weight[i]=1;*/
-
- /* Calculation of the number of parameters from char model */
- Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
- Tprod=ivector(1,15);
- Tvaraff=ivector(1,15);
- Tvard=imatrix(1,15,1,2);
- Tage=ivector(1,15);
-
- if (strlen(model) >1){ /* If there is at least 1 covariate */
- j=0, j1=0, k1=1, k2=1;
- j=nbocc(model,'+'); /* j=Number of '+' */
- j1=nbocc(model,'*'); /* j1=Number of '*' */
- cptcovn=j+1;
- cptcovprod=j1; /*Number of products */
-
- strcpy(modelsav,model);
- if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
- printf("Error. Non available option model=%s ",model);
- fprintf(ficlog,"Error. Non available option model=%s ",model);
- goto end;
- }
-
- /* This loop fills the array Tvar from the string 'model'.*/
-
- for(i=(j+1); i>=1;i--){
- cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
- if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
- /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
- /*scanf("%d",i);*/
- if (strchr(strb,'*')) { /* Model includes a product */
- cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/
- if (strcmp(strc,"age")==0) { /* Vn*age */
- cptcovprod--;
- cutv(strb,stre,strd,'V');
- Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
- cptcovage++;
- Tage[cptcovage]=i;
- /*printf("stre=%s ", stre);*/
- }
- else if (strcmp(strd,"age")==0) { /* or age*Vn */
- cptcovprod--;
- cutv(strb,stre,strc,'V');
- Tvar[i]=atoi(stre);
- cptcovage++;
- Tage[cptcovage]=i;
- }
- else { /* Age is not in the model */
- cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
- Tvar[i]=ncovcol+k1;
- cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
- Tprod[k1]=i;
- Tvard[k1][1]=atoi(strc); /* m*/
- Tvard[k1][2]=atoi(stre); /* n */
- Tvar[cptcovn+k2]=Tvard[k1][1];
- Tvar[cptcovn+k2+1]=Tvard[k1][2];
- for (k=1; k<=lastobs;k++)
- covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
- k1++;
- k2=k2+2;
- }
- }
- else { /* no more sum */
- /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
- /* scanf("%d",i);*/
- cutv(strd,strc,strb,'V');
- Tvar[i]=atoi(strc);
- }
- strcpy(modelsav,stra);
- /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
- scanf("%d",i);*/
- } /* end of loop + */
- } /* end model */
-
- /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
- If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
-
- /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
- printf("cptcovprod=%d ", cptcovprod);
- fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
-
- scanf("%d ",i);*/
-
- /* if(mle==1){*/
- if (weightopt != 1) { /* Maximisation without weights*/
- for(i=1;i<=n;i++) weight[i]=1.0;
- }
- /*-calculation of age at interview from date of interview and age at death -*/
- agev=matrix(1,maxwav,1,imx);
-
- for (i=1; i<=imx; i++) {
- for(m=2; (m<= maxwav); m++) {
- if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
- anint[m][i]=9999;
- s[m][i]=-1;
- }
- if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
- nberr++;
- 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);
- 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);
- s[m][i]=-1;
- }
- if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
- nberr++;
- 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]);
- 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]);
- s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
- }
- }
- }
-
- for (i=1; i<=imx; i++) {
- agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
- for(m=firstpass; (m<= lastpass); m++){
- if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
- if (s[m][i] >= nlstate+1) {
- if(agedc[i]>0)
- if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
- agev[m][i]=agedc[i];
- /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
- else {
- if ((int)andc[i]!=9999){
- nbwarn++;
- printf("Warning negative age at death: %ld line:%d\n",num[i],i);
- fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
- agev[m][i]=-1;
- }
- }
- }
- else if(s[m][i] !=9){ /* Standard case, age in fractional
- years but with the precision of a month */
- agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
- if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
- agev[m][i]=1;
- else if(agev[m][i] <agemin){
- agemin=agev[m][i];
- /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
- }
- else if(agev[m][i] >agemax){
- agemax=agev[m][i];
- /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
- }
- /*agev[m][i]=anint[m][i]-annais[i];*/
- /* agev[m][i] = age[i]+2*m;*/
- }
- else { /* =9 */
- agev[m][i]=1;
- s[m][i]=-1;
- }
- }
- else /*= 0 Unknown */
- agev[m][i]=1;
- }
-
- }
- for (i=1; i<=imx; i++) {
- for(m=firstpass; (m<=lastpass); m++){
- if (s[m][i] > (nlstate+ndeath)) {
- nberr++;
- 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);
- 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);
- goto end;
- }
- }
- }
-
- /*for (i=1; i<=imx; i++){
- for (m=firstpass; (m<lastpass); m++){
- printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
-}
-
-}*/
-
-
- printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
- fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
-
- agegomp=(int)agemin;
- free_vector(severity,1,maxwav);
- free_imatrix(outcome,1,maxwav+1,1,n);
- free_vector(moisnais,1,n);
- free_vector(annais,1,n);
- /* free_matrix(mint,1,maxwav,1,n);
- free_matrix(anint,1,maxwav,1,n);*/
- free_vector(moisdc,1,n);
- free_vector(andc,1,n);
-
-
- wav=ivector(1,imx);
- dh=imatrix(1,lastpass-firstpass+1,1,imx);
- bh=imatrix(1,lastpass-firstpass+1,1,imx);
- mw=imatrix(1,lastpass-firstpass+1,1,imx);
-
- /* Concatenates waves */
- concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
-
- /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
-
- Tcode=ivector(1,100);
- nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
- ncodemax[1]=1;
- if (cptcovn > 0) tricode(Tvar,nbcode,imx);
-
- codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
- the estimations*/
- h=0;
- m=pow(2,cptcoveff);
-
- for(k=1;k<=cptcoveff; k++){
- for(i=1; i <=(m/pow(2,k));i++){
- for(j=1; j <= ncodemax[k]; j++){
- for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
- h++;
- if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
- /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
- }
- }
- }
- }
- /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
- codtab[1][2]=1;codtab[2][2]=2; */
- /* for(i=1; i <=m ;i++){
- for(k=1; k <=cptcovn; k++){
- printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
- }
- printf("\n");
- }
- scanf("%d",i);*/
-
- /*------------ gnuplot -------------*/
- strcpy(optionfilegnuplot,optionfilefiname);
- if(mle==-3)
- strcat(optionfilegnuplot,"-mort");
- strcat(optionfilegnuplot,".gp");
-
- if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
- printf("Problem with file %s",optionfilegnuplot);
- }
- else{
- fprintf(ficgp,"\n# %s\n", version);
- fprintf(ficgp,"# %s\n", optionfilegnuplot);
- fprintf(ficgp,"set missing 'NaNq'\n");
- }
- /* fclose(ficgp);*/
- /*--------- index.htm --------*/
-
- strcpy(optionfilehtm,optionfilefiname); /* Main html file */
- if(mle==-3)
- strcat(optionfilehtm,"-mort");
- strcat(optionfilehtm,".htm");
- if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
- printf("Problem with %s \n",optionfilehtm), exit(0);
- }
-
- strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
- strcat(optionfilehtmcov,"-cov.htm");
- if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {
- printf("Problem with %s \n",optionfilehtmcov), exit(0);
- }
- else{
- fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
-<hr size=\"2\" color=\"#EC5E5E\"> \n\
-Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
- optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
- }
-
- fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
-<hr size=\"2\" color=\"#EC5E5E\"> \n\
-Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
-\n\
-<hr size=\"2\" color=\"#EC5E5E\">\
- <ul><li><h4>Parameter files</h4>\n\
- - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
- - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
- - Log file of the run: <a href=\"%s\">%s</a><br>\n\
- - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
- - Date and time at start: %s</ul>\n",\
- optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
- optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
- fileres,fileres,\
- filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
- fflush(fichtm);
-
- strcpy(pathr,path);
- strcat(pathr,optionfilefiname);
- chdir(optionfilefiname); /* Move to directory named optionfile */
-
- /* Calculates basic frequencies. Computes observed prevalence at single age
- and prints on file fileres'p'. */
- freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
-
- fprintf(fichtm,"\n");
- fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
-Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
-Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
- imx,agemin,agemax,jmin,jmax,jmean);
- pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
- oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
- newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
- savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
- oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
-
-
- /* For Powell, parameters are in a vector p[] starting at p[1]
- so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
- p=param[1][1]; /* *(*(*(param +1)+1)+0) */
-
- globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
-
- if (mle==-3){
- ximort=matrix(1,NDIM,1,NDIM);
- cens=ivector(1,n);
- ageexmed=vector(1,n);
- agecens=vector(1,n);
- dcwave=ivector(1,n);
-
- for (i=1; i<=imx; i++){
- dcwave[i]=-1;
- for (m=firstpass; m<=lastpass; m++)
- if (s[m][i]>nlstate) {
- dcwave[i]=m;
- /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
- break;
- }
- }
-
- for (i=1; i<=imx; i++) {
- if (wav[i]>0){
- ageexmed[i]=agev[mw[1][i]][i];
- j=wav[i];
- agecens[i]=1.;
-
- if (ageexmed[i]> 1 && wav[i] > 0){
- agecens[i]=agev[mw[j][i]][i];
- cens[i]= 1;
- }else if (ageexmed[i]< 1)
- cens[i]= -1;
- if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
- cens[i]=0 ;
- }
- else cens[i]=-1;
- }
-
- for (i=1;i<=NDIM;i++) {
- for (j=1;j<=NDIM;j++)
- ximort[i][j]=(i == j ? 1.0 : 0.0);
- }
-
- p[1]=0.0268; p[NDIM]=0.083;
- /*printf("%lf %lf", p[1], p[2]);*/
-
-
- printf("Powell\n"); fprintf(ficlog,"Powell\n");
- strcpy(filerespow,"pow-mort");
- strcat(filerespow,fileres);
- if((ficrespow=fopen(filerespow,"w"))==NULL) {
- printf("Problem with resultfile: %s\n", filerespow);
- fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
- }
- fprintf(ficrespow,"# Powell\n# iter -2*LL");
- /* for (i=1;i<=nlstate;i++)
- for(j=1;j<=nlstate+ndeath;j++)
- if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
- */
- fprintf(ficrespow,"\n");
-
- powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
- fclose(ficrespow);
-
- hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
-
- for(i=1; i <=NDIM; i++)
- for(j=i+1;j<=NDIM;j++)
- matcov[i][j]=matcov[j][i];
-
- printf("\nCovariance matrix\n ");
- for(i=1; i <=NDIM; i++) {
- for(j=1;j<=NDIM;j++){
- printf("%f ",matcov[i][j]);
- }
- printf("\n ");
- }
-
- printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
- for (i=1;i<=NDIM;i++)
- printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
-
- lsurv=vector(1,AGESUP);
- lpop=vector(1,AGESUP);
- tpop=vector(1,AGESUP);
- lsurv[agegomp]=100000;
-
- for (k=agegomp;k<=AGESUP;k++) {
- agemortsup=k;
- if (p[1]*exp(p[2]*(k-agegomp))>1) break;
- }
-
- for (k=agegomp;k<agemortsup;k++)
- lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
-
- for (k=agegomp;k<agemortsup;k++){
- lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
- sumlpop=sumlpop+lpop[k];
- }
-
- tpop[agegomp]=sumlpop;
- for (k=agegomp;k<(agemortsup-3);k++){
- /* tpop[k+1]=2;*/
- tpop[k+1]=tpop[k]-lpop[k];
- }
-
-
- printf("\nAge lx qx dx Lx Tx e(x)\n");
- for (k=agegomp;k<(agemortsup-2);k++)
- 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]);
-
-
- replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
- printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
-
- printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
- stepm, weightopt,\
- model,imx,p,matcov,agemortsup);
-
- free_vector(lsurv,1,AGESUP);
- free_vector(lpop,1,AGESUP);
- free_vector(tpop,1,AGESUP);
- } /* Endof if mle==-3 */
-
- else{ /* For mle >=1 */
-
- likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
- printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
- for (k=1; k<=npar;k++)
- printf(" %d %8.5f",k,p[k]);
- printf("\n");
- globpr=1; /* to print the contributions */
- likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
- printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
- for (k=1; k<=npar;k++)
- printf(" %d %8.5f",k,p[k]);
- printf("\n");
- if(mle>=1){ /* Could be 1 or 2 */
- mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
- }
-
- /*--------- results files --------------*/
- 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);
-
-
- fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
- printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
- fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
- for(i=1,jk=1; i <=nlstate; i++){
- for(k=1; k <=(nlstate+ndeath); k++){
- if (k != i) {
- printf("%d%d ",i,k);
- fprintf(ficlog,"%d%d ",i,k);
- fprintf(ficres,"%1d%1d ",i,k);
- for(j=1; j <=ncovmodel; j++){
- printf("%lf ",p[jk]);
- fprintf(ficlog,"%lf ",p[jk]);
- fprintf(ficres,"%lf ",p[jk]);
- jk++;
- }
- printf("\n");
- fprintf(ficlog,"\n");
- fprintf(ficres,"\n");
- }
- }
- }
- if(mle!=0){
- /* Computing hessian and covariance matrix */
- ftolhess=ftol; /* Usually correct */
- hesscov(matcov, p, npar, delti, ftolhess, func);
- }
- fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
- printf("# Scales (for hessian or gradient estimation)\n");
- fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
- for(i=1,jk=1; i <=nlstate; i++){
- for(j=1; j <=nlstate+ndeath; j++){
- if (j!=i) {
- fprintf(ficres,"%1d%1d",i,j);
- printf("%1d%1d",i,j);
- fprintf(ficlog,"%1d%1d",i,j);
- for(k=1; k<=ncovmodel;k++){
- printf(" %.5e",delti[jk]);
- fprintf(ficlog," %.5e",delti[jk]);
- fprintf(ficres," %.5e",delti[jk]);
- jk++;
- }
- printf("\n");
- fprintf(ficlog,"\n");
- fprintf(ficres,"\n");
- }
- }
- }
-
- 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");
- if(mle>=1)
- 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");
- 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");
- /* # 121 Var(a12)\n\ */
- /* # 122 Cov(b12,a12) Var(b12)\n\ */
- /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
- /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
- /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
- /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
- /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
- /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
-
-
- /* Just to have a covariance matrix which will be more understandable
- even is we still don't want to manage dictionary of variables
- */
- for(itimes=1;itimes<=2;itimes++){
- jj=0;
- for(i=1; i <=nlstate; i++){
- for(j=1; j <=nlstate+ndeath; j++){
- if(j==i) continue;
- for(k=1; k<=ncovmodel;k++){
- jj++;
- ca[0]= k+'a'-1;ca[1]='\0';
- if(itimes==1){
- if(mle>=1)
- printf("#%1d%1d%d",i,j,k);
- fprintf(ficlog,"#%1d%1d%d",i,j,k);
- fprintf(ficres,"#%1d%1d%d",i,j,k);
- }else{
- if(mle>=1)
- printf("%1d%1d%d",i,j,k);
- fprintf(ficlog,"%1d%1d%d",i,j,k);
- fprintf(ficres,"%1d%1d%d",i,j,k);
- }
- ll=0;
- for(li=1;li <=nlstate; li++){
- for(lj=1;lj <=nlstate+ndeath; lj++){
- if(lj==li) continue;
- for(lk=1;lk<=ncovmodel;lk++){
- ll++;
- if(ll<=jj){
- cb[0]= lk +'a'-1;cb[1]='\0';
- if(ll<jj){
- if(itimes==1){
- if(mle>=1)
- printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
- fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
- fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
- }else{
- if(mle>=1)
- printf(" %.5e",matcov[jj][ll]);
- fprintf(ficlog," %.5e",matcov[jj][ll]);
- fprintf(ficres," %.5e",matcov[jj][ll]);
- }
- }else{
- if(itimes==1){
- if(mle>=1)
- printf(" Var(%s%1d%1d)",ca,i,j);
- fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
- fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
- }else{
- if(mle>=1)
- printf(" %.5e",matcov[jj][ll]);
- fprintf(ficlog," %.5e",matcov[jj][ll]);
- fprintf(ficres," %.5e",matcov[jj][ll]);
- }
- }
- }
- } /* end lk */
- } /* end lj */
- } /* end li */
- if(mle>=1)
- printf("\n");
- fprintf(ficlog,"\n");
- fprintf(ficres,"\n");
- numlinepar++;
- } /* end k*/
- } /*end j */
- } /* end i */
- } /* end itimes */
-
- fflush(ficlog);
- fflush(ficres);
-
- while((c=getc(ficpar))=='#' && c!= EOF){
- ungetc(c,ficpar);
- fgets(line, MAXLINE, ficpar);
- puts(line);
- fputs(line,ficparo);
- }
- ungetc(c,ficpar);
-
- estepm=0;
- fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
- if (estepm==0 || estepm < stepm) estepm=stepm;
- if (fage <= 2) {
- bage = ageminpar;
- fage = agemaxpar;
- }
-
- fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
- fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
- fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
-
- while((c=getc(ficpar))=='#' && c!= EOF){
- ungetc(c,ficpar);
- fgets(line, MAXLINE, ficpar);
- puts(line);
- fputs(line,ficparo);
- }
- ungetc(c,ficpar);
-
- 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);
- 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);
- 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);
- printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
- 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);
-
- while((c=getc(ficpar))=='#' && c!= EOF){
- ungetc(c,ficpar);
- fgets(line, MAXLINE, ficpar);
- puts(line);
- fputs(line,ficparo);
- }
- ungetc(c,ficpar);
-
-
- dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
- dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
-
- fscanf(ficpar,"pop_based=%d\n",&popbased);
- fprintf(ficparo,"pop_based=%d\n",popbased);
- fprintf(ficres,"pop_based=%d\n",popbased);
-
- while((c=getc(ficpar))=='#' && c!= EOF){
- ungetc(c,ficpar);
- fgets(line, MAXLINE, ficpar);
- puts(line);
- fputs(line,ficparo);
- }
- ungetc(c,ficpar);
-
- 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);
- 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);
- 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);
- 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);
- 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);
- /* day and month of proj2 are not used but only year anproj2.*/
-
-
-
- /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
- /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-
- replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
- printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
-
- printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
- model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
- jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
-
- /*------------ free_vector -------------*/
- /* chdir(path); */
-
- free_ivector(wav,1,imx);
- free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
- free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
- free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
- free_lvector(num,1,n);
- free_vector(agedc,1,n);
- /*free_matrix(covar,0,NCOVMAX,1,n);*/
- /*free_matrix(covar,1,NCOVMAX,1,n);*/
- fclose(ficparo);
- fclose(ficres);
-
-
- /*--------------- Prevalence limit (period or stable prevalence) --------------*/
-
- strcpy(filerespl,"pl");
- strcat(filerespl,fileres);
- if((ficrespl=fopen(filerespl,"w"))==NULL) {
- printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
- fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
- }
- printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
- fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
- pstamp(ficrespl);
- fprintf(ficrespl,"# Period (stable) prevalence \n");
- fprintf(ficrespl,"#Age ");
- for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
- fprintf(ficrespl,"\n");
-
- prlim=matrix(1,nlstate,1,nlstate);
-
- agebase=ageminpar;
- agelim=agemaxpar;
- ftolpl=1.e-10;
- i1=cptcoveff;
- if (cptcovn < 1){i1=1;}
-
- for(cptcov=1,k=0;cptcov<=i1;cptcov++){
- for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
- k=k+1;
- /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
- fprintf(ficrespl,"\n#******");
- printf("\n#******");
- fprintf(ficlog,"\n#******");
- for(j=1;j<=cptcoveff;j++) {
- fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- }
- fprintf(ficrespl,"******\n");
- printf("******\n");
- fprintf(ficlog,"******\n");
-
- for (age=agebase; age<=agelim; age++){
- prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
- fprintf(ficrespl,"%.0f ",age );
- for(j=1;j<=cptcoveff;j++)
- fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- for(i=1; i<=nlstate;i++)
- fprintf(ficrespl," %.5f", prlim[i][i]);
- fprintf(ficrespl,"\n");
- }
- }
- }
- fclose(ficrespl);
-
- /*------------- h Pij x at various ages ------------*/
-
- strcpy(filerespij,"pij"); strcat(filerespij,fileres);
- if((ficrespij=fopen(filerespij,"w"))==NULL) {
- printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
- fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
- }
- printf("Computing pij: result on file '%s' \n", filerespij);
- fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
-
- stepsize=(int) (stepm+YEARM-1)/YEARM;
- /*if (stepm<=24) stepsize=2;*/
-
- agelim=AGESUP;
- hstepm=stepsize*YEARM; /* Every year of age */
- hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
-
- /* hstepm=1; aff par mois*/
- pstamp(ficrespij);
- fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
- for(cptcov=1,k=0;cptcov<=i1;cptcov++){
- for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
- k=k+1;
- fprintf(ficrespij,"\n#****** ");
- for(j=1;j<=cptcoveff;j++)
- fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- fprintf(ficrespij,"******\n");
-
- for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
- nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */
- nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
-
- /* nhstepm=nhstepm*YEARM; aff par mois*/
-
- p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- oldm=oldms;savm=savms;
- hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
- fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
- for(i=1; i<=nlstate;i++)
- for(j=1; j<=nlstate+ndeath;j++)
- fprintf(ficrespij," %1d-%1d",i,j);
- fprintf(ficrespij,"\n");
- for (h=0; h<=nhstepm; h++){
- fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
- for(i=1; i<=nlstate;i++)
- for(j=1; j<=nlstate+ndeath;j++)
- fprintf(ficrespij," %.5f", p3mat[i][j][h]);
- fprintf(ficrespij,"\n");
- }
- free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- fprintf(ficrespij,"\n");
- }
- }
- }
-
- varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
-
- fclose(ficrespij);
-
- probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
- for(i=1;i<=AGESUP;i++)
- for(j=1;j<=NCOVMAX;j++)
- for(k=1;k<=NCOVMAX;k++)
- probs[i][j][k]=0.;
-
- /*---------- Forecasting ------------------*/
- /*if((stepm == 1) && (strcmp(model,".")==0)){*/
- if(prevfcast==1){
- /* if(stepm ==1){*/
- prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
- /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
- /* } */
- /* else{ */
- /* erreur=108; */
- /* 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); */
- /* 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); */
- /* } */
- }
-
-
- /*---------- Health expectancies and variances ------------*/
-
- strcpy(filerest,"t");
- strcat(filerest,fileres);
- if((ficrest=fopen(filerest,"w"))==NULL) {
- printf("Problem with total LE resultfile: %s\n", filerest);goto end;
- fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
- }
- printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
- fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
-
-
- strcpy(filerese,"e");
- strcat(filerese,fileres);
- if((ficreseij=fopen(filerese,"w"))==NULL) {
- printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
- fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
- }
- printf("Computing Health Expectancies: result on file '%s' \n", filerese);
- fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
-
- strcpy(fileresstde,"stde");
- strcat(fileresstde,fileres);
- if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
- printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
- fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
- }
- printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
- fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
-
- strcpy(filerescve,"cve");
- strcat(filerescve,fileres);
- if((ficrescveij=fopen(filerescve,"w"))==NULL) {
- printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
- fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
- }
- printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
- fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
-
- strcpy(fileresv,"v");
- strcat(fileresv,fileres);
- if((ficresvij=fopen(fileresv,"w"))==NULL) {
- printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
- fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
- }
- printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
- fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
-
- /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
- prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
- /* 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",\
- ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
- */
-
- if (mobilav!=0) {
- mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
- if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
- fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
- printf(" Error in movingaverage mobilav=%d\n",mobilav);
- }
- }
-
- for(cptcov=1,k=0;cptcov<=i1;cptcov++){
- for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
- k=k+1;
- fprintf(ficrest,"\n#****** ");
- for(j=1;j<=cptcoveff;j++)
- fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- fprintf(ficrest,"******\n");
-
- fprintf(ficreseij,"\n#****** ");
- fprintf(ficresstdeij,"\n#****** ");
- fprintf(ficrescveij,"\n#****** ");
- for(j=1;j<=cptcoveff;j++) {
- fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- }
- fprintf(ficreseij,"******\n");
- fprintf(ficresstdeij,"******\n");
- fprintf(ficrescveij,"******\n");
-
- fprintf(ficresvij,"\n#****** ");
- for(j=1;j<=cptcoveff;j++)
- fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- fprintf(ficresvij,"******\n");
-
- eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
- oldm=oldms;savm=savms;
- evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
- cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
-
- vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
- oldm=oldms;savm=savms;
- varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
- if(popbased==1){
- varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
- }
-
- pstamp(ficrest);
- fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
- for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
- fprintf(ficrest,"\n");
-
- epj=vector(1,nlstate+1);
- for(age=bage; age <=fage ;age++){
- prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
- if (popbased==1) {
- if(mobilav ==0){
- for(i=1; i<=nlstate;i++)
- prlim[i][i]=probs[(int)age][i][k];
- }else{ /* mobilav */
- for(i=1; i<=nlstate;i++)
- prlim[i][i]=mobaverage[(int)age][i][k];
- }
- }
-
- fprintf(ficrest," %4.0f",age);
- for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
- for(i=1, epj[j]=0.;i <=nlstate;i++) {
- epj[j] += prlim[i][i]*eij[i][j][(int)age];
- /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
- }
- epj[nlstate+1] +=epj[j];
- }
-
- for(i=1, vepp=0.;i <=nlstate;i++)
- for(j=1;j <=nlstate;j++)
- vepp += vareij[i][j][(int)age];
- fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
- for(j=1;j <=nlstate;j++){
- fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
- }
- fprintf(ficrest,"\n");
- }
- free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
- free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
- free_vector(epj,1,nlstate+1);
- }
- }
- free_vector(weight,1,n);
- free_imatrix(Tvard,1,15,1,2);
- free_imatrix(s,1,maxwav+1,1,n);
- free_matrix(anint,1,maxwav,1,n);
- free_matrix(mint,1,maxwav,1,n);
- free_ivector(cod,1,n);
- free_ivector(tab,1,NCOVMAX);
- fclose(ficreseij);
- fclose(ficresstdeij);
- fclose(ficrescveij);
- fclose(ficresvij);
- fclose(ficrest);
- fclose(ficpar);
-
- /*------- Variance of period (stable) prevalence------*/
-
- strcpy(fileresvpl,"vpl");
- strcat(fileresvpl,fileres);
- if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
- printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
- exit(0);
- }
- printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
-
- for(cptcov=1,k=0;cptcov<=i1;cptcov++){
- for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
- k=k+1;
- fprintf(ficresvpl,"\n#****** ");
- for(j=1;j<=cptcoveff;j++)
- fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
- fprintf(ficresvpl,"******\n");
-
- varpl=matrix(1,nlstate,(int) bage, (int) fage);
- oldm=oldms;savm=savms;
- varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
- free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
- }
- }
-
- fclose(ficresvpl);
-
- /*---------- End : free ----------------*/
- if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
- free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
-
- } /* mle==-3 arrives here for freeing */
- free_matrix(prlim,1,nlstate,1,nlstate);
- free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
- free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
- free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
- free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
- free_matrix(covar,0,NCOVMAX,1,n);
- free_matrix(matcov,1,npar,1,npar);
- /*free_vector(delti,1,npar);*/
- free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
- free_matrix(agev,1,maxwav,1,imx);
- free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
-
- free_ivector(ncodemax,1,8);
- free_ivector(Tvar,1,15);
- free_ivector(Tprod,1,15);
- free_ivector(Tvaraff,1,15);
- free_ivector(Tage,1,15);
- free_ivector(Tcode,1,100);
-
- free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
- free_imatrix(codtab,1,100,1,10);
- fflush(fichtm);
- fflush(ficgp);
-
-
- if((nberr >0) || (nbwarn>0)){
- printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
- fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
- }else{
- printf("End of Imach\n");
- fprintf(ficlog,"End of Imach\n");
- }
- printf("See log file on %s\n",filelog);
- /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */
- (void) gettimeofday(&end_time,&tzp);
- tm = *localtime(&end_time.tv_sec);
- tmg = *gmtime(&end_time.tv_sec);
- strcpy(strtend,asctime(&tm));
- printf("Local time at start %s\nLocal time at end %s",strstart, strtend);
- fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend);
- printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
-
- printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
- fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
- fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
- /* printf("Total time was %d uSec.\n", total_usecs);*/
-/* if(fileappend(fichtm,optionfilehtm)){ */
- fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
- fclose(fichtm);
- fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
- fclose(fichtmcov);
- fclose(ficgp);
- fclose(ficlog);
- /*------ End -----------*/
-
-
- printf("Before Current directory %s!\n",pathcd);
- if(chdir(pathcd) != 0)
- printf("Can't move to directory %s!\n",path);
- if(getcwd(pathcd,MAXLINE) > 0)
- printf("Current directory %s!\n",pathcd);
- /*strcat(plotcmd,CHARSEPARATOR);*/
- sprintf(plotcmd,"gnuplot");
-#ifndef UNIX
- sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
-#endif
- if(!stat(plotcmd,&info)){
- printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
- if(!stat(getenv("GNUPLOTBIN"),&info)){
- printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
- }else
- strcpy(pplotcmd,plotcmd);
-#ifdef UNIX
- strcpy(plotcmd,GNUPLOTPROGRAM);
- if(!stat(plotcmd,&info)){
- printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
- }else
- strcpy(pplotcmd,plotcmd);
-#endif
- }else
- strcpy(pplotcmd,plotcmd);
-
- sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
- printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
-
- if((outcmd=system(plotcmd)) != 0){
- printf("\n Problem with gnuplot\n");
- }
- printf(" Wait...");
- while (z[0] != 'q') {
- /* chdir(path); */
- printf("\nType e to edit output files, g to graph again and q for exiting: ");
- scanf("%s",z);
-/* if (z[0] == 'c') system("./imach"); */
- if (z[0] == 'e') {
- printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
- system(optionfilehtm);
- }
- else if (z[0] == 'g') system(plotcmd);
- else if (z[0] == 'q') exit(0);
- }
- end:
- while (z[0] != 'q') {
- printf("\nType q for exiting: ");
- scanf("%s",z);
- }
-}
-
-
-
+/* $Id$\r
+ $State$\r
+ $Log$\r
+ Revision 1.124 2006/03/22 17:13:53 lievre\r
+ Parameters are printed with %lf instead of %f (more numbers after the comma).\r
+ The log-likelihood is printed in the log file\r
+\r
+ Revision 1.123 2006/03/20 10:52:43 brouard\r
+ * imach.c (Module): <title> changed, corresponds to .htm file\r
+ name. <head> headers where missing.\r
+\r
+ * imach.c (Module): Weights can have a decimal point as for\r
+ English (a comma might work with a correct LC_NUMERIC environment,\r
+ otherwise the weight is truncated).\r
+ Modification of warning when the covariates values are not 0 or\r
+ 1.\r
+ Version 0.98g\r
+\r
+ Revision 1.122 2006/03/20 09:45:41 brouard\r
+ (Module): Weights can have a decimal point as for\r
+ English (a comma might work with a correct LC_NUMERIC environment,\r
+ otherwise the weight is truncated).\r
+ Modification of warning when the covariates values are not 0 or\r
+ 1.\r
+ Version 0.98g\r
+\r
+ Revision 1.121 2006/03/16 17:45:01 lievre\r
+ * imach.c (Module): Comments concerning covariates added\r
+\r
+ * imach.c (Module): refinements in the computation of lli if\r
+ status=-2 in order to have more reliable computation if stepm is\r
+ not 1 month. Version 0.98f\r
+\r
+ Revision 1.120 2006/03/16 15:10:38 lievre\r
+ (Module): refinements in the computation of lli if\r
+ status=-2 in order to have more reliable computation if stepm is\r
+ not 1 month. Version 0.98f\r
+\r
+ Revision 1.119 2006/03/15 17:42:26 brouard\r
+ (Module): Bug if status = -2, the loglikelihood was\r
+ computed as likelihood omitting the logarithm. Version O.98e\r
+\r
+ Revision 1.118 2006/03/14 18:20:07 brouard\r
+ (Module): varevsij Comments added explaining the second\r
+ table of variances if popbased=1 .\r
+ (Module): Covariances of eij, ekl added, graphs fixed, new html link.\r
+ (Module): Function pstamp added\r
+ (Module): Version 0.98d\r
+\r
+ Revision 1.117 2006/03/14 17:16:22 brouard\r
+ (Module): varevsij Comments added explaining the second\r
+ table of variances if popbased=1 .\r
+ (Module): Covariances of eij, ekl added, graphs fixed, new html link.\r
+ (Module): Function pstamp added\r
+ (Module): Version 0.98d\r
+\r
+ Revision 1.116 2006/03/06 10:29:27 brouard\r
+ (Module): Variance-covariance wrong links and\r
+ varian-covariance of ej. is needed (Saito).\r
+\r
+ Revision 1.115 2006/02/27 12:17:45 brouard\r
+ (Module): One freematrix added in mlikeli! 0.98c\r
+\r
+ Revision 1.114 2006/02/26 12:57:58 brouard\r
+ (Module): Some improvements in processing parameter\r
+ filename with strsep.\r
+\r
+ Revision 1.113 2006/02/24 14:20:24 brouard\r
+ (Module): Memory leaks checks with valgrind and:\r
+ datafile was not closed, some imatrix were not freed and on matrix\r
+ allocation too.\r
+\r
+ Revision 1.112 2006/01/30 09:55:26 brouard\r
+ (Module): Back to gnuplot.exe instead of wgnuplot.exe\r
+\r
+ Revision 1.111 2006/01/25 20:38:18 brouard\r
+ (Module): Lots of cleaning and bugs added (Gompertz)\r
+ (Module): Comments can be added in data file. Missing date values\r
+ can be a simple dot '.'.\r
+\r
+ Revision 1.110 2006/01/25 00:51:50 brouard\r
+ (Module): Lots of cleaning and bugs added (Gompertz)\r
+\r
+ Revision 1.109 2006/01/24 19:37:15 brouard\r
+ (Module): Comments (lines starting with a #) are allowed in data.\r
+\r
+ Revision 1.108 2006/01/19 18:05:42 lievre\r
+ Gnuplot problem appeared...\r
+ To be fixed\r
+\r
+ Revision 1.107 2006/01/19 16:20:37 brouard\r
+ Test existence of gnuplot in imach path\r
+\r
+ Revision 1.106 2006/01/19 13:24:36 brouard\r
+ Some cleaning and links added in html output\r
+\r
+ Revision 1.105 2006/01/05 20:23:19 lievre\r
+ *** empty log message ***\r
+\r
+ Revision 1.104 2005/09/30 16:11:43 lievre\r
+ (Module): sump fixed, loop imx fixed, and simplifications.\r
+ (Module): If the status is missing at the last wave but we know\r
+ that the person is alive, then we can code his/her status as -2\r
+ (instead of missing=-1 in earlier versions) and his/her\r
+ contributions to the likelihood is 1 - Prob of dying from last\r
+ health status (= 1-p13= p11+p12 in the easiest case of somebody in\r
+ the healthy state at last known wave). Version is 0.98\r
+\r
+ Revision 1.103 2005/09/30 15:54:49 lievre\r
+ (Module): sump fixed, loop imx fixed, and simplifications.\r
+\r
+ Revision 1.102 2004/09/15 17:31:30 brouard\r
+ Add the possibility to read data file including tab characters.\r
+\r
+ Revision 1.101 2004/09/15 10:38:38 brouard\r
+ Fix on curr_time\r
+\r
+ Revision 1.100 2004/07/12 18:29:06 brouard\r
+ Add version for Mac OS X. Just define UNIX in Makefile\r
+\r
+ Revision 1.99 2004/06/05 08:57:40 brouard\r
+ *** empty log message ***\r
+\r
+ Revision 1.98 2004/05/16 15:05:56 brouard\r
+ New version 0.97 . First attempt to estimate force of mortality\r
+ directly from the data i.e. without the need of knowing the health\r
+ state at each age, but using a Gompertz model: log u =a + b*age .\r
+ This is the basic analysis of mortality and should be done before any\r
+ other analysis, in order to test if the mortality estimated from the\r
+ cross-longitudinal survey is different from the mortality estimated\r
+ from other sources like vital statistic data.\r
+\r
+ The same imach parameter file can be used but the option for mle should be -3.\r
+\r
+ Agnès, who wrote this part of the code, tried to keep most of the\r
+ former routines in order to include the new code within the former code.\r
+\r
+ The output is very simple: only an estimate of the intercept and of\r
+ the slope with 95% confident intervals.\r
+\r
+ Current limitations:\r
+ A) Even if you enter covariates, i.e. with the\r
+ model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.\r
+ B) There is no computation of Life Expectancy nor Life Table.\r
+\r
+ Revision 1.97 2004/02/20 13:25:42 lievre\r
+ Version 0.96d. Population forecasting command line is (temporarily)\r
+ suppressed.\r
+\r
+ Revision 1.96 2003/07/15 15:38:55 brouard\r
+ * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is\r
+ rewritten within the same printf. Workaround: many printfs.\r
+\r
+ Revision 1.95 2003/07/08 07:54:34 brouard\r
+ * imach.c (Repository):\r
+ (Repository): Using imachwizard code to output a more meaningful covariance\r
+ matrix (cov(a12,c31) instead of numbers.\r
+\r
+ Revision 1.94 2003/06/27 13:00:02 brouard\r
+ Just cleaning\r
+\r
+ Revision 1.93 2003/06/25 16:33:55 brouard\r
+ (Module): On windows (cygwin) function asctime_r doesn't\r
+ exist so I changed back to asctime which exists.\r
+ (Module): Version 0.96b\r
+\r
+ Revision 1.92 2003/06/25 16:30:45 brouard\r
+ (Module): On windows (cygwin) function asctime_r doesn't\r
+ exist so I changed back to asctime which exists.\r
+\r
+ Revision 1.91 2003/06/25 15:30:29 brouard\r
+ * imach.c (Repository): Duplicated warning errors corrected.\r
+ (Repository): Elapsed time after each iteration is now output. It\r
+ helps to forecast when convergence will be reached. Elapsed time\r
+ is stamped in powell. We created a new html file for the graphs\r
+ concerning matrix of covariance. It has extension -cov.htm.\r
+\r
+ Revision 1.90 2003/06/24 12:34:15 brouard\r
+ (Module): Some bugs corrected for windows. Also, when\r
+ mle=-1 a template is output in file "or"mypar.txt with the design\r
+ of the covariance matrix to be input.\r
+\r
+ Revision 1.89 2003/06/24 12:30:52 brouard\r
+ (Module): Some bugs corrected for windows. Also, when\r
+ mle=-1 a template is output in file "or"mypar.txt with the design\r
+ of the covariance matrix to be input.\r
+\r
+ Revision 1.88 2003/06/23 17:54:56 brouard\r
+ * 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.\r
+\r
+ Revision 1.87 2003/06/18 12:26:01 brouard\r
+ Version 0.96\r
+\r
+ Revision 1.86 2003/06/17 20:04:08 brouard\r
+ (Module): Change position of html and gnuplot routines and added\r
+ routine fileappend.\r
+\r
+ Revision 1.85 2003/06/17 13:12:43 brouard\r
+ * imach.c (Repository): Check when date of death was earlier that\r
+ current date of interview. It may happen when the death was just\r
+ prior to the death. In this case, dh was negative and likelihood\r
+ was wrong (infinity). We still send an "Error" but patch by\r
+ assuming that the date of death was just one stepm after the\r
+ interview.\r
+ (Repository): Because some people have very long ID (first column)\r
+ we changed int to long in num[] and we added a new lvector for\r
+ memory allocation. But we also truncated to 8 characters (left\r
+ truncation)\r
+ (Repository): No more line truncation errors.\r
+\r
+ Revision 1.84 2003/06/13 21:44:43 brouard\r
+ * imach.c (Repository): Replace "freqsummary" at a correct\r
+ place. It differs from routine "prevalence" which may be called\r
+ many times. Probs is memory consuming and must be used with\r
+ parcimony.\r
+ Version 0.95a3 (should output exactly the same maximization than 0.8a2)\r
+\r
+ Revision 1.83 2003/06/10 13:39:11 lievre\r
+ *** empty log message ***\r
+\r
+ Revision 1.82 2003/06/05 15:57:20 brouard\r
+ Add log in imach.c and fullversion number is now printed.\r
+\r
+*/\r
+/*\r
+ Interpolated Markov Chain\r
+\r
+ Short summary of the programme:\r
+ \r
+ This program computes Healthy Life Expectancies from\r
+ cross-longitudinal data. Cross-longitudinal data consist in: -1- a\r
+ first survey ("cross") where individuals from different ages are\r
+ interviewed on their health status or degree of disability (in the\r
+ case of a health survey which is our main interest) -2- at least a\r
+ second wave of interviews ("longitudinal") which measure each change\r
+ (if any) in individual health status. Health expectancies are\r
+ computed from the time spent in each health state according to a\r
+ model. More health states you consider, more time is necessary to reach the\r
+ Maximum Likelihood of the parameters involved in the model. The\r
+ simplest model is the multinomial logistic model where pij is the\r
+ probability to be observed in state j at the second wave\r
+ conditional to be observed in state i at the first wave. Therefore\r
+ the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where\r
+ 'age' is age and 'sex' is a covariate. If you want to have a more\r
+ complex model than "constant and age", you should modify the program\r
+ where the markup *Covariates have to be included here again* invites\r
+ you to do it. More covariates you add, slower the\r
+ convergence.\r
+\r
+ The advantage of this computer programme, compared to a simple\r
+ multinomial logistic model, is clear when the delay between waves is not\r
+ identical for each individual. Also, if a individual missed an\r
+ intermediate interview, the information is lost, but taken into\r
+ account using an interpolation or extrapolation. \r
+\r
+ hPijx is the probability to be observed in state i at age x+h\r
+ conditional to the observed state i at age x. The delay 'h' can be\r
+ split into an exact number (nh*stepm) of unobserved intermediate\r
+ states. This elementary transition (by month, quarter,\r
+ semester or year) is modelled as a multinomial logistic. The hPx\r
+ matrix is simply the matrix product of nh*stepm elementary matrices\r
+ and the contribution of each individual to the likelihood is simply\r
+ hPijx.\r
+\r
+ Also this programme outputs the covariance matrix of the parameters but also\r
+ of the life expectancies. It also computes the period (stable) prevalence. \r
+ \r
+ Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).\r
+ Institut national d'études démographiques, Paris.\r
+ This software have been partly granted by Euro-REVES, a concerted action\r
+ from the European Union.\r
+ It is copyrighted identically to a GNU software product, ie programme and\r
+ software can be distributed freely for non commercial use. Latest version\r
+ can be accessed at http://euroreves.ined.fr/imach .\r
+\r
+ Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach\r
+ or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so\r
+ \r
+ **********************************************************************/\r
+/*\r
+ main\r
+ read parameterfile\r
+ read datafile\r
+ concatwav\r
+ freqsummary\r
+ if (mle >= 1)\r
+ mlikeli\r
+ print results files\r
+ if mle==1 \r
+ computes hessian\r
+ read end of parameter file: agemin, agemax, bage, fage, estepm\r
+ begin-prev-date,...\r
+ open gnuplot file\r
+ open html file\r
+ period (stable) prevalence\r
+ for age prevalim()\r
+ h Pij x\r
+ variance of p varprob\r
+ forecasting if prevfcast==1 prevforecast call prevalence()\r
+ health expectancies\r
+ Variance-covariance of DFLE\r
+ prevalence()\r
+ movingaverage()\r
+ varevsij() \r
+ if popbased==1 varevsij(,popbased)\r
+ total life expectancies\r
+ Variance of period (stable) prevalence\r
+ end\r
+*/\r
+\r
+\r
+\r
+ \r
+#include <math.h>\r
+#include <stdio.h>\r
+#include <stdlib.h>\r
+#include <string.h>\r
+#include <unistd.h>\r
+\r
+#include <limits.h>\r
+#include <sys/types.h>\r
+#include <sys/stat.h>\r
+#include <errno.h>\r
+extern int errno;\r
+\r
+/* #include <sys/time.h> */\r
+#include <time.h>\r
+#include "timeval.h"\r
+\r
+/* #include <libintl.h> */\r
+/* #define _(String) gettext (String) */\r
+\r
+#define MAXLINE 256\r
+\r
+#define GNUPLOTPROGRAM "gnuplot"\r
+/*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/\r
+#define FILENAMELENGTH 132\r
+\r
+#define GLOCK_ERROR_NOPATH -1 /* empty path */\r
+#define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */\r
+\r
+#define MAXPARM 30 /* Maximum number of parameters for the optimization */\r
+#define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */\r
+\r
+#define NINTERVMAX 8\r
+#define NLSTATEMAX 8 /* Maximum number of live states (for func) */\r
+#define NDEATHMAX 8 /* Maximum number of dead states (for func) */\r
+#define NCOVMAX 8 /* Maximum number of covariates */\r
+#define MAXN 20000\r
+#define YEARM 12. /* Number of months per year */\r
+#define AGESUP 130\r
+#define AGEBASE 40\r
+#define AGEGOMP 10. /* Minimal age for Gompertz adjustment */\r
+#ifdef UNIX\r
+#define DIRSEPARATOR '/'\r
+#define CHARSEPARATOR "/"\r
+#define ODIRSEPARATOR '\\'\r
+#else\r
+#define DIRSEPARATOR '\\'\r
+#define CHARSEPARATOR "\\"\r
+#define ODIRSEPARATOR '/'\r
+#endif\r
+\r
+/* $Id$ */\r
+/* $State$ */\r
+\r
+char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";\r
+char fullversion[]="$Revision$ $Date$"; \r
+char strstart[80];\r
+char optionfilext[10], optionfilefiname[FILENAMELENGTH];\r
+int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */\r
+int nvar;\r
+int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;\r
+int npar=NPARMAX;\r
+int nlstate=2; /* Number of live states */\r
+int ndeath=1; /* Number of dead states */\r
+int ncovmodel, ncovcol; /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */\r
+int popbased=0;\r
+\r
+int *wav; /* Number of waves for this individuual 0 is possible */\r
+int maxwav; /* Maxim number of waves */\r
+int jmin, jmax; /* min, max spacing between 2 waves */\r
+int ijmin, ijmax; /* Individuals having jmin and jmax */ \r
+int gipmx, gsw; /* Global variables on the number of contributions \r
+ to the likelihood and the sum of weights (done by funcone)*/\r
+int mle, weightopt;\r
+int **mw; /* mw[mi][i] is number of the mi wave for this individual */\r
+int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */\r
+int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between\r
+ * wave mi and wave mi+1 is not an exact multiple of stepm. */\r
+double jmean; /* Mean space between 2 waves */\r
+double **oldm, **newm, **savm; /* Working pointers to matrices */\r
+double **oldms, **newms, **savms; /* Fixed working pointers to matrices */\r
+FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;\r
+FILE *ficlog, *ficrespow;\r
+int globpr; /* Global variable for printing or not */\r
+double fretone; /* Only one call to likelihood */\r
+long ipmx; /* Number of contributions */\r
+double sw; /* Sum of weights */\r
+char filerespow[FILENAMELENGTH];\r
+char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */\r
+FILE *ficresilk;\r
+FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;\r
+FILE *ficresprobmorprev;\r
+FILE *fichtm, *fichtmcov; /* Html File */\r
+FILE *ficreseij;\r
+char filerese[FILENAMELENGTH];\r
+FILE *ficresstdeij;\r
+char fileresstde[FILENAMELENGTH];\r
+FILE *ficrescveij;\r
+char filerescve[FILENAMELENGTH];\r
+FILE *ficresvij;\r
+char fileresv[FILENAMELENGTH];\r
+FILE *ficresvpl;\r
+char fileresvpl[FILENAMELENGTH];\r
+char title[MAXLINE];\r
+char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];\r
+char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];\r
+char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH]; \r
+char command[FILENAMELENGTH];\r
+int outcmd=0;\r
+\r
+char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];\r
+\r
+char filelog[FILENAMELENGTH]; /* Log file */\r
+char filerest[FILENAMELENGTH];\r
+char fileregp[FILENAMELENGTH];\r
+char popfile[FILENAMELENGTH];\r
+\r
+char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;\r
+\r
+struct timeval start_time, end_time, curr_time, last_time, forecast_time;\r
+struct timezone tzp;\r
+extern int gettimeofday();\r
+struct tm tmg, tm, tmf, *gmtime(), *localtime();\r
+long time_value;\r
+extern long time();\r
+char strcurr[80], strfor[80];\r
+\r
+char *endptr;\r
+long lval;\r
+double dval;\r
+\r
+#define NR_END 1\r
+#define FREE_ARG char*\r
+#define FTOL 1.0e-10\r
+\r
+#define NRANSI \r
+#define ITMAX 200 \r
+\r
+#define TOL 2.0e-4 \r
+\r
+#define CGOLD 0.3819660 \r
+#define ZEPS 1.0e-10 \r
+#define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); \r
+\r
+#define GOLD 1.618034 \r
+#define GLIMIT 100.0 \r
+#define TINY 1.0e-20 \r
+\r
+static double maxarg1,maxarg2;\r
+#define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))\r
+#define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))\r
+ \r
+#define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))\r
+#define rint(a) floor(a+0.5)\r
+\r
+static double sqrarg;\r
+#define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)\r
+#define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} \r
+int agegomp= AGEGOMP;\r
+\r
+int imx; \r
+int stepm=1;\r
+/* Stepm, step in month: minimum step interpolation*/\r
+\r
+int estepm;\r
+/* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/\r
+\r
+int m,nb;\r
+long *num;\r
+int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;\r
+double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;\r
+double **pmmij, ***probs;\r
+double *ageexmed,*agecens;\r
+double dateintmean=0;\r
+\r
+double *weight;\r
+int **s; /* Status */\r
+double *agedc, **covar, idx;\r
+int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;\r
+double *lsurv, *lpop, *tpop;\r
+\r
+double ftol=FTOL; /* Tolerance for computing Max Likelihood */\r
+double ftolhess; /* Tolerance for computing hessian */\r
+\r
+/**************** split *************************/\r
+static int split( char *path, char *dirc, char *name, char *ext, char *finame )\r
+{\r
+ /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)\r
+ the name of the file (name), its extension only (ext) and its first part of the name (finame)\r
+ */ \r
+ char *ss; /* pointer */\r
+ int l1, l2; /* length counters */\r
+\r
+ l1 = strlen(path ); /* length of path */\r
+ if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );\r
+ ss= strrchr( path, DIRSEPARATOR ); /* find last / */\r
+ if ( ss == NULL ) { /* no directory, so determine current directory */\r
+ strcpy( name, path ); /* we got the fullname name because no directory */\r
+ /*if(strrchr(path, ODIRSEPARATOR )==NULL)\r
+ printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/\r
+ /* get current working directory */\r
+ /* extern char* getcwd ( char *buf , int len);*/\r
+ if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {\r
+ return( GLOCK_ERROR_GETCWD );\r
+ }\r
+ /* got dirc from getcwd*/\r
+ printf(" DIRC = %s \n",dirc);\r
+ } else { /* strip direcotry from path */\r
+ ss++; /* after this, the filename */\r
+ l2 = strlen( ss ); /* length of filename */\r
+ if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );\r
+ strcpy( name, ss ); /* save file name */\r
+ strncpy( dirc, path, l1 - l2 ); /* now the directory */\r
+ dirc[l1-l2] = 0; /* add zero */\r
+ printf(" DIRC2 = %s \n",dirc);\r
+ }\r
+ /* We add a separator at the end of dirc if not exists */\r
+ l1 = strlen( dirc ); /* length of directory */\r
+ if( dirc[l1-1] != DIRSEPARATOR ){\r
+ dirc[l1] = DIRSEPARATOR;\r
+ dirc[l1+1] = 0; \r
+ printf(" DIRC3 = %s \n",dirc);\r
+ }\r
+ ss = strrchr( name, '.' ); /* find last / */\r
+ if (ss >0){\r
+ ss++;\r
+ strcpy(ext,ss); /* save extension */\r
+ l1= strlen( name);\r
+ l2= strlen(ss)+1;\r
+ strncpy( finame, name, l1-l2);\r
+ finame[l1-l2]= 0;\r
+ }\r
+\r
+ return( 0 ); /* we're done */\r
+}\r
+\r
+\r
+/******************************************/\r
+\r
+void replace_back_to_slash(char *s, char*t)\r
+{\r
+ int i;\r
+ int lg=0;\r
+ i=0;\r
+ lg=strlen(t);\r
+ for(i=0; i<= lg; i++) {\r
+ (s[i] = t[i]);\r
+ if (t[i]== '\\') s[i]='/';\r
+ }\r
+}\r
+\r
+int nbocc(char *s, char occ)\r
+{\r
+ int i,j=0;\r
+ int lg=20;\r
+ i=0;\r
+ lg=strlen(s);\r
+ for(i=0; i<= lg; i++) {\r
+ if (s[i] == occ ) j++;\r
+ }\r
+ return j;\r
+}\r
+\r
+void cutv(char *u,char *v, char*t, char occ)\r
+{\r
+ /* cuts string t into u and v where u ends before first occurence of char 'occ' \r
+ and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')\r
+ gives u="abcedf" and v="ghi2j" */\r
+ int i,lg,j,p=0;\r
+ i=0;\r
+ for(j=0; j<=strlen(t)-1; j++) {\r
+ if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;\r
+ }\r
+\r
+ lg=strlen(t);\r
+ for(j=0; j<p; j++) {\r
+ (u[j] = t[j]);\r
+ }\r
+ u[p]='\0';\r
+\r
+ for(j=0; j<= lg; j++) {\r
+ if (j>=(p+1))(v[j-p-1] = t[j]);\r
+ }\r
+}\r
+\r
+/********************** nrerror ********************/\r
+\r
+void nrerror(char error_text[])\r
+{\r
+ fprintf(stderr,"ERREUR ...\n");\r
+ fprintf(stderr,"%s\n",error_text);\r
+ exit(EXIT_FAILURE);\r
+}\r
+/*********************** vector *******************/\r
+double *vector(int nl, int nh)\r
+{\r
+ double *v;\r
+ v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));\r
+ if (!v) nrerror("allocation failure in vector");\r
+ return v-nl+NR_END;\r
+}\r
+\r
+/************************ free vector ******************/\r
+void free_vector(double*v, int nl, int nh)\r
+{\r
+ free((FREE_ARG)(v+nl-NR_END));\r
+}\r
+\r
+/************************ivector *******************************/\r
+int *ivector(long nl,long nh)\r
+{\r
+ int *v;\r
+ v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));\r
+ if (!v) nrerror("allocation failure in ivector");\r
+ return v-nl+NR_END;\r
+}\r
+\r
+/******************free ivector **************************/\r
+void free_ivector(int *v, long nl, long nh)\r
+{\r
+ free((FREE_ARG)(v+nl-NR_END));\r
+}\r
+\r
+/************************lvector *******************************/\r
+long *lvector(long nl,long nh)\r
+{\r
+ long *v;\r
+ v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));\r
+ if (!v) nrerror("allocation failure in ivector");\r
+ return v-nl+NR_END;\r
+}\r
+\r
+/******************free lvector **************************/\r
+void free_lvector(long *v, long nl, long nh)\r
+{\r
+ free((FREE_ARG)(v+nl-NR_END));\r
+}\r
+\r
+/******************* imatrix *******************************/\r
+int **imatrix(long nrl, long nrh, long ncl, long nch) \r
+ /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ \r
+{ \r
+ long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; \r
+ int **m; \r
+ \r
+ /* allocate pointers to rows */ \r
+ m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); \r
+ if (!m) nrerror("allocation failure 1 in matrix()"); \r
+ m += NR_END; \r
+ m -= nrl; \r
+ \r
+ \r
+ /* allocate rows and set pointers to them */ \r
+ m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); \r
+ if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); \r
+ m[nrl] += NR_END; \r
+ m[nrl] -= ncl; \r
+ \r
+ for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; \r
+ \r
+ /* return pointer to array of pointers to rows */ \r
+ return m; \r
+} \r
+\r
+/****************** free_imatrix *************************/\r
+void free_imatrix(m,nrl,nrh,ncl,nch)\r
+ int **m;\r
+ long nch,ncl,nrh,nrl; \r
+ /* free an int matrix allocated by imatrix() */ \r
+{ \r
+ free((FREE_ARG) (m[nrl]+ncl-NR_END)); \r
+ free((FREE_ARG) (m+nrl-NR_END)); \r
+} \r
+\r
+/******************* matrix *******************************/\r
+double **matrix(long nrl, long nrh, long ncl, long nch)\r
+{\r
+ long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;\r
+ double **m;\r
+\r
+ m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));\r
+ if (!m) nrerror("allocation failure 1 in matrix()");\r
+ m += NR_END;\r
+ m -= nrl;\r
+\r
+ m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));\r
+ if (!m[nrl]) nrerror("allocation failure 2 in matrix()");\r
+ m[nrl] += NR_END;\r
+ m[nrl] -= ncl;\r
+\r
+ for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;\r
+ return m;\r
+ /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) \r
+ */\r
+}\r
+\r
+/*************************free matrix ************************/\r
+void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)\r
+{\r
+ free((FREE_ARG)(m[nrl]+ncl-NR_END));\r
+ free((FREE_ARG)(m+nrl-NR_END));\r
+}\r
+\r
+/******************* ma3x *******************************/\r
+double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)\r
+{\r
+ long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;\r
+ double ***m;\r
+\r
+ m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));\r
+ if (!m) nrerror("allocation failure 1 in matrix()");\r
+ m += NR_END;\r
+ m -= nrl;\r
+\r
+ m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));\r
+ if (!m[nrl]) nrerror("allocation failure 2 in matrix()");\r
+ m[nrl] += NR_END;\r
+ m[nrl] -= ncl;\r
+\r
+ for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;\r
+\r
+ m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));\r
+ if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");\r
+ m[nrl][ncl] += NR_END;\r
+ m[nrl][ncl] -= nll;\r
+ for (j=ncl+1; j<=nch; j++) \r
+ m[nrl][j]=m[nrl][j-1]+nlay;\r
+ \r
+ for (i=nrl+1; i<=nrh; i++) {\r
+ m[i][ncl]=m[i-1l][ncl]+ncol*nlay;\r
+ for (j=ncl+1; j<=nch; j++) \r
+ m[i][j]=m[i][j-1]+nlay;\r
+ }\r
+ return m; \r
+ /* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])\r
+ &(m[i][j][k]) <=> *((*(m+i) + j)+k)\r
+ */\r
+}\r
+\r
+/*************************free ma3x ************************/\r
+void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)\r
+{\r
+ free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));\r
+ free((FREE_ARG)(m[nrl]+ncl-NR_END));\r
+ free((FREE_ARG)(m+nrl-NR_END));\r
+}\r
+\r
+/*************** function subdirf ***********/\r
+char *subdirf(char fileres[])\r
+{\r
+ /* Caution optionfilefiname is hidden */\r
+ strcpy(tmpout,optionfilefiname);\r
+ strcat(tmpout,"/"); /* Add to the right */\r
+ strcat(tmpout,fileres);\r
+ return tmpout;\r
+}\r
+\r
+/*************** function subdirf2 ***********/\r
+char *subdirf2(char fileres[], char *preop)\r
+{\r
+ \r
+ /* Caution optionfilefiname is hidden */\r
+ strcpy(tmpout,optionfilefiname);\r
+ strcat(tmpout,"/");\r
+ strcat(tmpout,preop);\r
+ strcat(tmpout,fileres);\r
+ return tmpout;\r
+}\r
+\r
+/*************** function subdirf3 ***********/\r
+char *subdirf3(char fileres[], char *preop, char *preop2)\r
+{\r
+ \r
+ /* Caution optionfilefiname is hidden */\r
+ strcpy(tmpout,optionfilefiname);\r
+ strcat(tmpout,"/");\r
+ strcat(tmpout,preop);\r
+ strcat(tmpout,preop2);\r
+ strcat(tmpout,fileres);\r
+ return tmpout;\r
+}\r
+\r
+/***************** f1dim *************************/\r
+extern int ncom; \r
+extern double *pcom,*xicom;\r
+extern double (*nrfunc)(double []); \r
+ \r
+double f1dim(double x) \r
+{ \r
+ int j; \r
+ double f;\r
+ double *xt; \r
+ \r
+ xt=vector(1,ncom); \r
+ for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; \r
+ f=(*nrfunc)(xt); \r
+ free_vector(xt,1,ncom); \r
+ return f; \r
+} \r
+\r
+/*****************brent *************************/\r
+double brent(double ax, double bx, double cx, double (*f)(double), double tol, double *xmin) \r
+{ \r
+ int iter; \r
+ double a,b,d,etemp;\r
+ double fu,fv,fw,fx;\r
+ double ftemp;\r
+ double p,q,r,tol1,tol2,u,v,w,x,xm; \r
+ double e=0.0; \r
+ \r
+ a=(ax < cx ? ax : cx); \r
+ b=(ax > cx ? ax : cx); \r
+ x=w=v=bx; \r
+ fw=fv=fx=(*f)(x); \r
+ for (iter=1;iter<=ITMAX;iter++) { \r
+ xm=0.5*(a+b); \r
+ tol2=2.0*(tol1=tol*fabs(x)+ZEPS); \r
+ /* if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/\r
+ printf(".");fflush(stdout);\r
+ fprintf(ficlog,".");fflush(ficlog);\r
+#ifdef DEBUG\r
+ 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);\r
+ 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);\r
+ /* if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */\r
+#endif\r
+ if (fabs(x-xm) <= (tol2-0.5*(b-a))){ \r
+ *xmin=x; \r
+ return fx; \r
+ } \r
+ ftemp=fu;\r
+ if (fabs(e) > tol1) { \r
+ r=(x-w)*(fx-fv); \r
+ q=(x-v)*(fx-fw); \r
+ p=(x-v)*q-(x-w)*r; \r
+ q=2.0*(q-r); \r
+ if (q > 0.0) p = -p; \r
+ q=fabs(q); \r
+ etemp=e; \r
+ e=d; \r
+ if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) \r
+ d=CGOLD*(e=(x >= xm ? a-x : b-x)); \r
+ else { \r
+ d=p/q; \r
+ u=x+d; \r
+ if (u-a < tol2 || b-u < tol2) \r
+ d=SIGN(tol1,xm-x); \r
+ } \r
+ } else { \r
+ d=CGOLD*(e=(x >= xm ? a-x : b-x)); \r
+ } \r
+ u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); \r
+ fu=(*f)(u); \r
+ if (fu <= fx) { \r
+ if (u >= x) a=x; else b=x; \r
+ SHFT(v,w,x,u) \r
+ SHFT(fv,fw,fx,fu) \r
+ } else { \r
+ if (u < x) a=u; else b=u; \r
+ if (fu <= fw || w == x) { \r
+ v=w; \r
+ w=u; \r
+ fv=fw; \r
+ fw=fu; \r
+ } else if (fu <= fv || v == x || v == w) { \r
+ v=u; \r
+ fv=fu; \r
+ } \r
+ } \r
+ } \r
+ nrerror("Too many iterations in brent"); \r
+ *xmin=x; \r
+ return fx; \r
+} \r
+\r
+/****************** mnbrak ***********************/\r
+\r
+void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, \r
+ double (*func)(double)) \r
+{ \r
+ double ulim,u,r,q, dum;\r
+ double fu; \r
+ \r
+ *fa=(*func)(*ax); \r
+ *fb=(*func)(*bx); \r
+ if (*fb > *fa) { \r
+ SHFT(dum,*ax,*bx,dum) \r
+ SHFT(dum,*fb,*fa,dum) \r
+ } \r
+ *cx=(*bx)+GOLD*(*bx-*ax); \r
+ *fc=(*func)(*cx); \r
+ while (*fb > *fc) { \r
+ r=(*bx-*ax)*(*fb-*fc); \r
+ q=(*bx-*cx)*(*fb-*fa); \r
+ u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ \r
+ (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); \r
+ ulim=(*bx)+GLIMIT*(*cx-*bx); \r
+ if ((*bx-u)*(u-*cx) > 0.0) { \r
+ fu=(*func)(u); \r
+ } else if ((*cx-u)*(u-ulim) > 0.0) { \r
+ fu=(*func)(u); \r
+ if (fu < *fc) { \r
+ SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) \r
+ SHFT(*fb,*fc,fu,(*func)(u)) \r
+ } \r
+ } else if ((u-ulim)*(ulim-*cx) >= 0.0) { \r
+ u=ulim; \r
+ fu=(*func)(u); \r
+ } else { \r
+ u=(*cx)+GOLD*(*cx-*bx); \r
+ fu=(*func)(u); \r
+ } \r
+ SHFT(*ax,*bx,*cx,u) \r
+ SHFT(*fa,*fb,*fc,fu) \r
+ } \r
+} \r
+\r
+/*************** linmin ************************/\r
+\r
+int ncom; \r
+double *pcom,*xicom;\r
+double (*nrfunc)(double []); \r
+ \r
+void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) \r
+{ \r
+ double brent(double ax, double bx, double cx, \r
+ double (*f)(double), double tol, double *xmin); \r
+ double f1dim(double x); \r
+ void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, \r
+ double *fc, double (*func)(double)); \r
+ int j; \r
+ double xx,xmin,bx,ax; \r
+ double fx,fb,fa;\r
+ \r
+ ncom=n; \r
+ pcom=vector(1,n); \r
+ xicom=vector(1,n); \r
+ nrfunc=func; \r
+ for (j=1;j<=n;j++) { \r
+ pcom[j]=p[j]; \r
+ xicom[j]=xi[j]; \r
+ } \r
+ ax=0.0; \r
+ xx=1.0; \r
+ mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); \r
+ *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); \r
+#ifdef DEBUG\r
+ printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);\r
+ fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);\r
+#endif\r
+ for (j=1;j<=n;j++) { \r
+ xi[j] *= xmin; \r
+ p[j] += xi[j]; \r
+ } \r
+ free_vector(xicom,1,n); \r
+ free_vector(pcom,1,n); \r
+} \r
+\r
+char *asc_diff_time(long time_sec, char ascdiff[])\r
+{\r
+ long sec_left, days, hours, minutes;\r
+ days = (time_sec) / (60*60*24);\r
+ sec_left = (time_sec) % (60*60*24);\r
+ hours = (sec_left) / (60*60) ;\r
+ sec_left = (sec_left) %(60*60);\r
+ minutes = (sec_left) /60;\r
+ sec_left = (sec_left) % (60);\r
+ sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left); \r
+ return ascdiff;\r
+}\r
+\r
+/*************** powell ************************/\r
+void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, \r
+ double (*func)(double [])) \r
+{ \r
+ void linmin(double p[], double xi[], int n, double *fret, \r
+ double (*func)(double [])); \r
+ int i,ibig,j; \r
+ double del,t,*pt,*ptt,*xit;\r
+ double fp,fptt;\r
+ double *xits;\r
+ int niterf, itmp;\r
+\r
+ pt=vector(1,n); \r
+ ptt=vector(1,n); \r
+ xit=vector(1,n); \r
+ xits=vector(1,n); \r
+ *fret=(*func)(p); \r
+ for (j=1;j<=n;j++) pt[j]=p[j]; \r
+ for (*iter=1;;++(*iter)) { \r
+ fp=(*fret); \r
+ ibig=0; \r
+ del=0.0; \r
+ last_time=curr_time;\r
+ (void) gettimeofday(&curr_time,&tzp);\r
+ 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);\r
+ 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); fflush(ficlog);\r
+/* fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */\r
+ for (i=1;i<=n;i++) {\r
+ printf(" %d %.12f",i, p[i]);\r
+ fprintf(ficlog," %d %.12lf",i, p[i]);\r
+ fprintf(ficrespow," %.12lf", p[i]);\r
+ }\r
+ printf("\n");\r
+ fprintf(ficlog,"\n");\r
+ fprintf(ficrespow,"\n");fflush(ficrespow);\r
+ if(*iter <=3){\r
+ tm = *localtime(&curr_time.tv_sec);\r
+ strcpy(strcurr,asctime(&tm));\r
+/* asctime_r(&tm,strcurr); */\r
+ forecast_time=curr_time; \r
+ itmp = strlen(strcurr);\r
+ if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */\r
+ strcurr[itmp-1]='\0';\r
+ printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);\r
+ fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);\r
+ for(niterf=10;niterf<=30;niterf+=10){\r
+ forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);\r
+ tmf = *localtime(&forecast_time.tv_sec);\r
+/* asctime_r(&tmf,strfor); */\r
+ strcpy(strfor,asctime(&tmf));\r
+ itmp = strlen(strfor);\r
+ if(strfor[itmp-1]=='\n')\r
+ strfor[itmp-1]='\0';\r
+ 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);\r
+ 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);\r
+ }\r
+ }\r
+ for (i=1;i<=n;i++) { \r
+ for (j=1;j<=n;j++) xit[j]=xi[j][i]; \r
+ fptt=(*fret); \r
+#ifdef DEBUG\r
+ printf("fret=%lf \n",*fret);\r
+ fprintf(ficlog,"fret=%lf \n",*fret);\r
+#endif\r
+ printf("%d",i);fflush(stdout);\r
+ fprintf(ficlog,"%d",i);fflush(ficlog);\r
+ linmin(p,xit,n,fret,func); \r
+ if (fabs(fptt-(*fret)) > del) { \r
+ del=fabs(fptt-(*fret)); \r
+ ibig=i; \r
+ } \r
+#ifdef DEBUG\r
+ printf("%d %.12e",i,(*fret));\r
+ fprintf(ficlog,"%d %.12e",i,(*fret));\r
+ for (j=1;j<=n;j++) {\r
+ xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);\r
+ printf(" x(%d)=%.12e",j,xit[j]);\r
+ fprintf(ficlog," x(%d)=%.12e",j,xit[j]);\r
+ }\r
+ for(j=1;j<=n;j++) {\r
+ printf(" p=%.12e",p[j]);\r
+ fprintf(ficlog," p=%.12e",p[j]);\r
+ }\r
+ printf("\n");\r
+ fprintf(ficlog,"\n");\r
+#endif\r
+ } \r
+ if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {\r
+#ifdef DEBUG\r
+ int k[2],l;\r
+ k[0]=1;\r
+ k[1]=-1;\r
+ printf("Max: %.12e",(*func)(p));\r
+ fprintf(ficlog,"Max: %.12e",(*func)(p));\r
+ for (j=1;j<=n;j++) {\r
+ printf(" %.12e",p[j]);\r
+ fprintf(ficlog," %.12e",p[j]);\r
+ }\r
+ printf("\n");\r
+ fprintf(ficlog,"\n");\r
+ for(l=0;l<=1;l++) {\r
+ for (j=1;j<=n;j++) {\r
+ ptt[j]=p[j]+(p[j]-pt[j])*k[l];\r
+ printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);\r
+ fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);\r
+ }\r
+ printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));\r
+ fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));\r
+ }\r
+#endif\r
+\r
+\r
+ free_vector(xit,1,n); \r
+ free_vector(xits,1,n); \r
+ free_vector(ptt,1,n); \r
+ free_vector(pt,1,n); \r
+ return; \r
+ } \r
+ if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); \r
+ for (j=1;j<=n;j++) { \r
+ ptt[j]=2.0*p[j]-pt[j]; \r
+ xit[j]=p[j]-pt[j]; \r
+ pt[j]=p[j]; \r
+ } \r
+ fptt=(*func)(ptt); \r
+ if (fptt < fp) { \r
+ t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); \r
+ if (t < 0.0) { \r
+ linmin(p,xit,n,fret,func); \r
+ for (j=1;j<=n;j++) { \r
+ xi[j][ibig]=xi[j][n]; \r
+ xi[j][n]=xit[j]; \r
+ }\r
+#ifdef DEBUG\r
+ printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);\r
+ fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);\r
+ for(j=1;j<=n;j++){\r
+ printf(" %.12e",xit[j]);\r
+ fprintf(ficlog," %.12e",xit[j]);\r
+ }\r
+ printf("\n");\r
+ fprintf(ficlog,"\n");\r
+#endif\r
+ }\r
+ } \r
+ } \r
+} \r
+\r
+/**** Prevalence limit (stable or period prevalence) ****************/\r
+\r
+double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)\r
+{\r
+ /* Computes the prevalence limit in each live state at age x by left multiplying the unit\r
+ matrix by transitions matrix until convergence is reached */\r
+\r
+ int i, ii,j,k;\r
+ double min, max, maxmin, maxmax,sumnew=0.;\r
+ double **matprod2();\r
+ double **out, cov[NCOVMAX], **pmij();\r
+ double **newm;\r
+ double agefin, delaymax=50 ; /* Max number of years to converge */\r
+\r
+ for (ii=1;ii<=nlstate+ndeath;ii++)\r
+ for (j=1;j<=nlstate+ndeath;j++){\r
+ oldm[ii][j]=(ii==j ? 1.0 : 0.0);\r
+ }\r
+\r
+ cov[1]=1.;\r
+ \r
+ /* Even if hstepm = 1, at least one multiplication by the unit matrix */\r
+ for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){\r
+ newm=savm;\r
+ /* Covariates have to be included here again */\r
+ cov[2]=agefin;\r
+ \r
+ for (k=1; k<=cptcovn;k++) {\r
+ cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];\r
+ /* 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]]);*/\r
+ }\r
+ for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];\r
+ for (k=1; k<=cptcovprod;k++)\r
+ cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];\r
+\r
+ /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/\r
+ /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/\r
+ /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/\r
+ out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);\r
+\r
+ savm=oldm;\r
+ oldm=newm;\r
+ maxmax=0.;\r
+ for(j=1;j<=nlstate;j++){\r
+ min=1.;\r
+ max=0.;\r
+ for(i=1; i<=nlstate; i++) {\r
+ sumnew=0;\r
+ for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];\r
+ prlim[i][j]= newm[i][j]/(1-sumnew);\r
+ max=FMAX(max,prlim[i][j]);\r
+ min=FMIN(min,prlim[i][j]);\r
+ }\r
+ maxmin=max-min;\r
+ maxmax=FMAX(maxmax,maxmin);\r
+ }\r
+ if(maxmax < ftolpl){\r
+ return prlim;\r
+ }\r
+ }\r
+}\r
+\r
+/*************** transition probabilities ***************/ \r
+\r
+double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )\r
+{\r
+ double s1, s2;\r
+ /*double t34;*/\r
+ int i,j,j1, nc, ii, jj;\r
+\r
+ for(i=1; i<= nlstate; i++){\r
+ for(j=1; j<i;j++){\r
+ for (nc=1, s2=0.;nc <=ncovmodel; nc++){\r
+ /*s2 += param[i][j][nc]*cov[nc];*/\r
+ s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];\r
+/* printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */\r
+ }\r
+ ps[i][j]=s2;\r
+/* printf("s1=%.17e, s2=%.17e\n",s1,s2); */\r
+ }\r
+ for(j=i+1; j<=nlstate+ndeath;j++){\r
+ for (nc=1, s2=0.;nc <=ncovmodel; nc++){\r
+ s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];\r
+/* printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */\r
+ }\r
+ ps[i][j]=s2;\r
+ }\r
+ }\r
+ /*ps[3][2]=1;*/\r
+ \r
+ for(i=1; i<= nlstate; i++){\r
+ s1=0;\r
+ for(j=1; j<i; j++)\r
+ s1+=exp(ps[i][j]);\r
+ for(j=i+1; j<=nlstate+ndeath; j++)\r
+ s1+=exp(ps[i][j]);\r
+ ps[i][i]=1./(s1+1.);\r
+ for(j=1; j<i; j++)\r
+ ps[i][j]= exp(ps[i][j])*ps[i][i];\r
+ for(j=i+1; j<=nlstate+ndeath; j++)\r
+ ps[i][j]= exp(ps[i][j])*ps[i][i];\r
+ /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */\r
+ } /* end i */\r
+ \r
+ for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){\r
+ for(jj=1; jj<= nlstate+ndeath; jj++){\r
+ ps[ii][jj]=0;\r
+ ps[ii][ii]=1;\r
+ }\r
+ }\r
+ \r
+\r
+/* for(ii=1; ii<= nlstate+ndeath; ii++){ */\r
+/* for(jj=1; jj<= nlstate+ndeath; jj++){ */\r
+/* printf("ddd %lf ",ps[ii][jj]); */\r
+/* } */\r
+/* printf("\n "); */\r
+/* } */\r
+/* printf("\n ");printf("%lf ",cov[2]); */\r
+ /*\r
+ for(i=1; i<= npar; i++) printf("%f ",x[i]);\r
+ goto end;*/\r
+ return ps;\r
+}\r
+\r
+/**************** Product of 2 matrices ******************/\r
+\r
+double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)\r
+{\r
+ /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times\r
+ b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */\r
+ /* in, b, out are matrice of pointers which should have been initialized \r
+ before: only the contents of out is modified. The function returns\r
+ a pointer to pointers identical to out */\r
+ long i, j, k;\r
+ for(i=nrl; i<= nrh; i++)\r
+ for(k=ncolol; k<=ncoloh; k++)\r
+ for(j=ncl,out[i][k]=0.; j<=nch; j++)\r
+ out[i][k] +=in[i][j]*b[j][k];\r
+\r
+ return out;\r
+}\r
+\r
+\r
+/************* Higher Matrix Product ***************/\r
+\r
+double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )\r
+{\r
+ /* Computes the transition matrix starting at age 'age' over \r
+ 'nhstepm*hstepm*stepm' months (i.e. until\r
+ age (in years) age+nhstepm*hstepm*stepm/12) by multiplying \r
+ nhstepm*hstepm matrices. \r
+ Output is stored in matrix po[i][j][h] for h every 'hstepm' step \r
+ (typically every 2 years instead of every month which is too big \r
+ for the memory).\r
+ Model is determined by parameters x and covariates have to be \r
+ included manually here. \r
+\r
+ */\r
+\r
+ int i, j, d, h, k;\r
+ double **out, cov[NCOVMAX];\r
+ double **newm;\r
+\r
+ /* Hstepm could be zero and should return the unit matrix */\r
+ for (i=1;i<=nlstate+ndeath;i++)\r
+ for (j=1;j<=nlstate+ndeath;j++){\r
+ oldm[i][j]=(i==j ? 1.0 : 0.0);\r
+ po[i][j][0]=(i==j ? 1.0 : 0.0);\r
+ }\r
+ /* Even if hstepm = 1, at least one multiplication by the unit matrix */\r
+ for(h=1; h <=nhstepm; h++){\r
+ for(d=1; d <=hstepm; d++){\r
+ newm=savm;\r
+ /* Covariates have to be included here again */\r
+ cov[1]=1.;\r
+ cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;\r
+ for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];\r
+ for (k=1; k<=cptcovage;k++)\r
+ cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];\r
+ for (k=1; k<=cptcovprod;k++)\r
+ cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];\r
+\r
+\r
+ /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/\r
+ /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/\r
+ out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, \r
+ pmij(pmmij,cov,ncovmodel,x,nlstate));\r
+ savm=oldm;\r
+ oldm=newm;\r
+ }\r
+ for(i=1; i<=nlstate+ndeath; i++)\r
+ for(j=1;j<=nlstate+ndeath;j++) {\r
+ po[i][j][h]=newm[i][j];\r
+ /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);\r
+ */\r
+ }\r
+ } /* end h */\r
+ return po;\r
+}\r
+\r
+\r
+/*************** log-likelihood *************/\r
+double func( double *x)\r
+{\r
+ int i, ii, j, k, mi, d, kk;\r
+ double l, ll[NLSTATEMAX], cov[NCOVMAX];\r
+ double **out;\r
+ double sw; /* Sum of weights */\r
+ double lli; /* Individual log likelihood */\r
+ int s1, s2;\r
+ double bbh, survp;\r
+ long ipmx;\r
+ /*extern weight */\r
+ /* We are differentiating ll according to initial status */\r
+ /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/\r
+ /*for(i=1;i<imx;i++) \r
+ printf(" %d\n",s[4][i]);\r
+ */\r
+ cov[1]=1.;\r
+\r
+ for(k=1; k<=nlstate; k++) ll[k]=0.;\r
+\r
+ if(mle==1){\r
+ for (i=1,ipmx=0, sw=0.; i<=imx; i++){\r
+ for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];\r
+ for(mi=1; mi<= wav[i]-1; mi++){\r
+ for (ii=1;ii<=nlstate+ndeath;ii++)\r
+ for (j=1;j<=nlstate+ndeath;j++){\r
+ oldm[ii][j]=(ii==j ? 1.0 : 0.0);\r
+ savm[ii][j]=(ii==j ? 1.0 : 0.0);\r
+ }\r
+ for(d=0; d<dh[mi][i]; d++){\r
+ newm=savm;\r
+ cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;\r
+ for (kk=1; kk<=cptcovage;kk++) {\r
+ cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];\r
+ }\r
+ out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,\r
+ 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));\r
+ savm=oldm;\r
+ oldm=newm;\r
+ } /* end mult */\r
+ \r
+ /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */\r
+ /* But now since version 0.9 we anticipate for bias at large stepm.\r
+ * If stepm is larger than one month (smallest stepm) and if the exact delay \r
+ * (in months) between two waves is not a multiple of stepm, we rounded to \r
+ * the nearest (and in case of equal distance, to the lowest) interval but now\r
+ * we keep into memory the bias bh[mi][i] and also the previous matrix product\r
+ * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the\r
+ * probability in order to take into account the bias as a fraction of the way\r
+ * from savm to out if bh is negative or even beyond if bh is positive. bh varies\r
+ * -stepm/2 to stepm/2 .\r
+ * For stepm=1 the results are the same as for previous versions of Imach.\r
+ * For stepm > 1 the results are less biased than in previous versions. \r
+ */\r
+ s1=s[mw[mi][i]][i];\r
+ s2=s[mw[mi+1][i]][i];\r
+ bbh=(double)bh[mi][i]/(double)stepm; \r
+ /* bias bh is positive if real duration\r
+ * is higher than the multiple of stepm and negative otherwise.\r
+ */\r
+ /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/\r
+ if( s2 > nlstate){ \r
+ /* i.e. if s2 is a death state and if the date of death is known \r
+ then the contribution to the likelihood is the probability to \r
+ die between last step unit time and current step unit time, \r
+ which is also equal to probability to die before dh \r
+ minus probability to die before dh-stepm . \r
+ In version up to 0.92 likelihood was computed\r
+ as if date of death was unknown. Death was treated as any other\r
+ health state: the date of the interview describes the actual state\r
+ and not the date of a change in health state. The former idea was\r
+ to consider that at each interview the state was recorded\r
+ (healthy, disable or death) and IMaCh was corrected; but when we\r
+ introduced the exact date of death then we should have modified\r
+ the contribution of an exact death to the likelihood. This new\r
+ contribution is smaller and very dependent of the step unit\r
+ stepm. It is no more the probability to die between last interview\r
+ and month of death but the probability to survive from last\r
+ interview up to one month before death multiplied by the\r
+ probability to die within a month. Thanks to Chris\r
+ Jackson for correcting this bug. Former versions increased\r
+ mortality artificially. The bad side is that we add another loop\r
+ which slows down the processing. The difference can be up to 10%\r
+ lower mortality.\r
+ */\r
+ lli=log(out[s1][s2] - savm[s1][s2]);\r
+\r
+\r
+ } else if (s2==-2) {\r
+ for (j=1,survp=0. ; j<=nlstate; j++) \r
+ survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];\r
+ /*survp += out[s1][j]; */\r
+ lli= log(survp);\r
+ }\r
+ \r
+ else if (s2==-4) { \r
+ for (j=3,survp=0. ; j<=nlstate; j++) \r
+ survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];\r
+ lli= log(survp); \r
+ } \r
+\r
+ else if (s2==-5) { \r
+ for (j=1,survp=0. ; j<=2; j++) \r
+ survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];\r
+ lli= log(survp); \r
+ } \r
+ \r
+ else{\r
+ lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */\r
+ /* 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 */\r
+ } \r
+ /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/\r
+ /*if(lli ==000.0)*/\r
+ /*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); */\r
+ ipmx +=1;\r
+ sw += weight[i];\r
+ ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;\r
+ } /* end of wave */\r
+ } /* end of individual */\r
+ } else if(mle==2){\r
+ for (i=1,ipmx=0, sw=0.; i<=imx; i++){\r
+ for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];\r
+ for(mi=1; mi<= wav[i]-1; mi++){\r
+ for (ii=1;ii<=nlstate+ndeath;ii++)\r
+ for (j=1;j<=nlstate+ndeath;j++){\r
+ oldm[ii][j]=(ii==j ? 1.0 : 0.0);\r
+ savm[ii][j]=(ii==j ? 1.0 : 0.0);\r
+ }\r
+ for(d=0; d<=dh[mi][i]; d++){\r
+ newm=savm;\r
+ cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;\r
+ for (kk=1; kk<=cptcovage;kk++) {\r
+ cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];\r
+ }\r
+ out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,\r
+ 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));\r
+ savm=oldm;\r
+ oldm=newm;\r
+ } /* end mult */\r
+ \r
+ s1=s[mw[mi][i]][i];\r
+ s2=s[mw[mi+1][i]][i];\r
+ bbh=(double)bh[mi][i]/(double)stepm; \r
+ 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 */\r
+ ipmx +=1;\r
+ sw += weight[i];\r
+ ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;\r
+ } /* end of wave */\r
+ } /* end of individual */\r
+ } else if(mle==3){ /* exponential inter-extrapolation */\r
+ for (i=1,ipmx=0, sw=0.; i<=imx; i++){\r
+ for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];\r
+ for(mi=1; mi<= wav[i]-1; mi++){\r
+ for (ii=1;ii<=nlstate+ndeath;ii++)\r
+ for (j=1;j<=nlstate+ndeath;j++){\r
+ oldm[ii][j]=(ii==j ? 1.0 : 0.0);\r
+ savm[ii][j]=(ii==j ? 1.0 : 0.0);\r
+ }\r
+ for(d=0; d<dh[mi][i]; d++){\r
+ newm=savm;\r
+ cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;\r
+ for (kk=1; kk<=cptcovage;kk++) {\r
+ cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];\r
+ }\r
+ out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,\r
+ 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));\r
+ savm=oldm;\r
+ oldm=newm;\r
+ } /* end mult */\r
+ \r
+ s1=s[mw[mi][i]][i];\r
+ s2=s[mw[mi+1][i]][i];\r
+ bbh=(double)bh[mi][i]/(double)stepm; \r
+ 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 */\r
+ ipmx +=1;\r
+ sw += weight[i];\r
+ ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;\r
+ } /* end of wave */\r
+ } /* end of individual */\r
+ }else if (mle==4){ /* ml=4 no inter-extrapolation */\r
+ for (i=1,ipmx=0, sw=0.; i<=imx; i++){\r
+ for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];\r
+ for(mi=1; mi<= wav[i]-1; mi++){\r
+ for (ii=1;ii<=nlstate+ndeath;ii++)\r
+ for (j=1;j<=nlstate+ndeath;j++){\r
+ oldm[ii][j]=(ii==j ? 1.0 : 0.0);\r
+ savm[ii][j]=(ii==j ? 1.0 : 0.0);\r
+ }\r
+ for(d=0; d<dh[mi][i]; d++){\r
+ newm=savm;\r
+ cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;\r
+ for (kk=1; kk<=cptcovage;kk++) {\r
+ cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];\r
+ }\r
+ \r
+ out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,\r
+ 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));\r
+ savm=oldm;\r
+ oldm=newm;\r
+ } /* end mult */\r
+ \r
+ s1=s[mw[mi][i]][i];\r
+ s2=s[mw[mi+1][i]][i];\r
+ if( s2 > nlstate){ \r
+ lli=log(out[s1][s2] - savm[s1][s2]);\r
+ }else{\r
+ lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */\r
+ }\r
+ ipmx +=1;\r
+ sw += weight[i];\r
+ ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;\r
+/* 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]); */\r
+ } /* end of wave */\r
+ } /* end of individual */\r
+ }else{ /* ml=5 no inter-extrapolation no jackson =0.8a */\r
+ for (i=1,ipmx=0, sw=0.; i<=imx; i++){\r
+ for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];\r
+ for(mi=1; mi<= wav[i]-1; mi++){\r
+ for (ii=1;ii<=nlstate+ndeath;ii++)\r
+ for (j=1;j<=nlstate+ndeath;j++){\r
+ oldm[ii][j]=(ii==j ? 1.0 : 0.0);\r
+ savm[ii][j]=(ii==j ? 1.0 : 0.0);\r
+ }\r
+ for(d=0; d<dh[mi][i]; d++){\r
+ newm=savm;\r
+ cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;\r
+ for (kk=1; kk<=cptcovage;kk++) {\r
+ cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];\r
+ }\r
+ \r
+ out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,\r
+ 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));\r
+ savm=oldm;\r
+ oldm=newm;\r
+ } /* end mult */\r
+ \r
+ s1=s[mw[mi][i]][i];\r
+ s2=s[mw[mi+1][i]][i];\r
+ lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */\r
+ ipmx +=1;\r
+ sw += weight[i];\r
+ ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;\r
+ /*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]);*/\r
+ } /* end of wave */\r
+ } /* end of individual */\r
+ } /* End of if */\r
+ for(k=1,l=0.; k<=nlstate; k++) l += ll[k];\r
+ /* printf("l1=%f l2=%f ",ll[1],ll[2]); */\r
+ l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */\r
+ return -l;\r
+}\r
+\r
+/*************** log-likelihood *************/\r
+double funcone( double *x)\r
+{\r
+ /* Same as likeli but slower because of a lot of printf and if */\r
+ int i, ii, j, k, mi, d, kk;\r
+ double l, ll[NLSTATEMAX], cov[NCOVMAX];\r
+ double **out;\r
+ double lli; /* Individual log likelihood */\r
+ double llt;\r
+ int s1, s2;\r
+ double bbh, survp;\r
+ /*extern weight */\r
+ /* We are differentiating ll according to initial status */\r
+ /* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/\r
+ /*for(i=1;i<imx;i++) \r
+ printf(" %d\n",s[4][i]);\r
+ */\r
+ cov[1]=1.;\r
+\r
+ for(k=1; k<=nlstate; k++) ll[k]=0.;\r
+\r
+ for (i=1,ipmx=0, sw=0.; i<=imx; i++){\r
+ for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];\r
+ for(mi=1; mi<= wav[i]-1; mi++){\r
+ for (ii=1;ii<=nlstate+ndeath;ii++)\r
+ for (j=1;j<=nlstate+ndeath;j++){\r
+ oldm[ii][j]=(ii==j ? 1.0 : 0.0);\r
+ savm[ii][j]=(ii==j ? 1.0 : 0.0);\r
+ }\r
+ for(d=0; d<dh[mi][i]; d++){\r
+ newm=savm;\r
+ cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;\r
+ for (kk=1; kk<=cptcovage;kk++) {\r
+ cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];\r
+ }\r
+ out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,\r
+ 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));\r
+ savm=oldm;\r
+ oldm=newm;\r
+ } /* end mult */\r
+ \r
+ s1=s[mw[mi][i]][i];\r
+ s2=s[mw[mi+1][i]][i];\r
+ bbh=(double)bh[mi][i]/(double)stepm; \r
+ /* bias is positive if real duration\r
+ * is higher than the multiple of stepm and negative otherwise.\r
+ */\r
+ if( s2 > nlstate && (mle <5) ){ /* Jackson */\r
+ lli=log(out[s1][s2] - savm[s1][s2]);\r
+ } else if (s2==-2) {\r
+ for (j=1,survp=0. ; j<=nlstate; j++) \r
+ survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];\r
+ lli= log(survp);\r
+ }else if (mle==1){\r
+ lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */\r
+ } else if(mle==2){\r
+ 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 */\r
+ } else if(mle==3){ /* exponential inter-extrapolation */\r
+ 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 */\r
+ } else if (mle==4){ /* mle=4 no inter-extrapolation */\r
+ lli=log(out[s1][s2]); /* Original formula */\r
+ } else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */\r
+ lli=log(out[s1][s2]); /* Original formula */\r
+ } /* End of if */\r
+ ipmx +=1;\r
+ sw += weight[i];\r
+ ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;\r
+/* 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]); */\r
+ if(globpr){\r
+ fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\\r
+ %11.6f %11.6f %11.6f ", \\r
+ num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],\r
+ 2*weight[i]*lli,out[s1][s2],savm[s1][s2]);\r
+ for(k=1,llt=0.,l=0.; k<=nlstate; k++){\r
+ llt +=ll[k]*gipmx/gsw;\r
+ fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);\r
+ }\r
+ fprintf(ficresilk," %10.6f\n", -llt);\r
+ }\r
+ } /* end of wave */\r
+ } /* end of individual */\r
+ for(k=1,l=0.; k<=nlstate; k++) l += ll[k];\r
+ /* printf("l1=%f l2=%f ",ll[1],ll[2]); */\r
+ l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */\r
+ if(globpr==0){ /* First time we count the contributions and weights */\r
+ gipmx=ipmx;\r
+ gsw=sw;\r
+ }\r
+ return -l;\r
+}\r
+\r
+\r
+/*************** function likelione ***********/\r
+void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))\r
+{\r
+ /* This routine should help understanding what is done with \r
+ the selection of individuals/waves and\r
+ to check the exact contribution to the likelihood.\r
+ Plotting could be done.\r
+ */\r
+ int k;\r
+\r
+ if(*globpri !=0){ /* Just counts and sums, no printings */\r
+ strcpy(fileresilk,"ilk"); \r
+ strcat(fileresilk,fileres);\r
+ if((ficresilk=fopen(fileresilk,"w"))==NULL) {\r
+ printf("Problem with resultfile: %s\n", fileresilk);\r
+ fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);\r
+ }\r
+ 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");\r
+ fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");\r
+ /* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */\r
+ for(k=1; k<=nlstate; k++) \r
+ fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);\r
+ fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");\r
+ }\r
+\r
+ *fretone=(*funcone)(p);\r
+ if(*globpri !=0){\r
+ fclose(ficresilk);\r
+ fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));\r
+ fflush(fichtm); \r
+ } \r
+ return;\r
+}\r
+\r
+\r
+/*********** Maximum Likelihood Estimation ***************/\r
+\r
+void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))\r
+{\r
+ int i,j, iter;\r
+ double **xi;\r
+ double fret;\r
+ double fretone; /* Only one call to likelihood */\r
+ /* char filerespow[FILENAMELENGTH];*/\r
+ xi=matrix(1,npar,1,npar);\r
+ for (i=1;i<=npar;i++)\r
+ for (j=1;j<=npar;j++)\r
+ xi[i][j]=(i==j ? 1.0 : 0.0);\r
+ printf("Powell\n"); fprintf(ficlog,"Powell\n");\r
+ strcpy(filerespow,"pow"); \r
+ strcat(filerespow,fileres);\r
+ if((ficrespow=fopen(filerespow,"w"))==NULL) {\r
+ printf("Problem with resultfile: %s\n", filerespow);\r
+ fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);\r
+ }\r
+ fprintf(ficrespow,"# Powell\n# iter -2*LL");\r
+ for (i=1;i<=nlstate;i++)\r
+ for(j=1;j<=nlstate+ndeath;j++)\r
+ if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);\r
+ fprintf(ficrespow,"\n");\r
+\r
+ powell(p,xi,npar,ftol,&iter,&fret,func);\r
+\r
+ free_matrix(xi,1,npar,1,npar);\r
+ fclose(ficrespow);\r
+ printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));\r
+ fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));\r
+ fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));\r
+\r
+}\r
+\r
+/**** Computes Hessian and covariance matrix ***/\r
+void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))\r
+{\r
+ double **a,**y,*x,pd;\r
+ double **hess;\r
+ int i, j,jk;\r
+ int *indx;\r
+\r
+ double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);\r
+ double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);\r
+ void lubksb(double **a, int npar, int *indx, double b[]) ;\r
+ void ludcmp(double **a, int npar, int *indx, double *d) ;\r
+ double gompertz(double p[]);\r
+ hess=matrix(1,npar,1,npar);\r
+\r
+ printf("\nCalculation of the hessian matrix. Wait...\n");\r
+ fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");\r
+ for (i=1;i<=npar;i++){\r
+ printf("%d",i);fflush(stdout);\r
+ fprintf(ficlog,"%d",i);fflush(ficlog);\r
+ \r
+ hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);\r
+ \r
+ /* printf(" %f ",p[i]);\r
+ printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/\r
+ }\r
+ \r
+ for (i=1;i<=npar;i++) {\r
+ for (j=1;j<=npar;j++) {\r
+ if (j>i) { \r
+ printf(".%d%d",i,j);fflush(stdout);\r
+ fprintf(ficlog,".%d%d",i,j);fflush(ficlog);\r
+ hess[i][j]=hessij(p,delti,i,j,func,npar);\r
+ \r
+ hess[j][i]=hess[i][j]; \r
+ /*printf(" %lf ",hess[i][j]);*/\r
+ }\r
+ }\r
+ }\r
+ printf("\n");\r
+ fprintf(ficlog,"\n");\r
+\r
+ printf("\nInverting the hessian to get the covariance matrix. Wait...\n");\r
+ fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");\r
+ \r
+ a=matrix(1,npar,1,npar);\r
+ y=matrix(1,npar,1,npar);\r
+ x=vector(1,npar);\r
+ indx=ivector(1,npar);\r
+ for (i=1;i<=npar;i++)\r
+ for (j=1;j<=npar;j++) a[i][j]=hess[i][j];\r
+ ludcmp(a,npar,indx,&pd);\r
+\r
+ for (j=1;j<=npar;j++) {\r
+ for (i=1;i<=npar;i++) x[i]=0;\r
+ x[j]=1;\r
+ lubksb(a,npar,indx,x);\r
+ for (i=1;i<=npar;i++){ \r
+ matcov[i][j]=x[i];\r
+ }\r
+ }\r
+\r
+ printf("\n#Hessian matrix#\n");\r
+ fprintf(ficlog,"\n#Hessian matrix#\n");\r
+ for (i=1;i<=npar;i++) { \r
+ for (j=1;j<=npar;j++) { \r
+ printf("%.3e ",hess[i][j]);\r
+ fprintf(ficlog,"%.3e ",hess[i][j]);\r
+ }\r
+ printf("\n");\r
+ fprintf(ficlog,"\n");\r
+ }\r
+\r
+ /* Recompute Inverse */\r
+ for (i=1;i<=npar;i++)\r
+ for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];\r
+ ludcmp(a,npar,indx,&pd);\r
+\r
+ /* printf("\n#Hessian matrix recomputed#\n");\r
+\r
+ for (j=1;j<=npar;j++) {\r
+ for (i=1;i<=npar;i++) x[i]=0;\r
+ x[j]=1;\r
+ lubksb(a,npar,indx,x);\r
+ for (i=1;i<=npar;i++){ \r
+ y[i][j]=x[i];\r
+ printf("%.3e ",y[i][j]);\r
+ fprintf(ficlog,"%.3e ",y[i][j]);\r
+ }\r
+ printf("\n");\r
+ fprintf(ficlog,"\n");\r
+ }\r
+ */\r
+\r
+ free_matrix(a,1,npar,1,npar);\r
+ free_matrix(y,1,npar,1,npar);\r
+ free_vector(x,1,npar);\r
+ free_ivector(indx,1,npar);\r
+ free_matrix(hess,1,npar,1,npar);\r
+\r
+\r
+}\r
+\r
+/*************** hessian matrix ****************/\r
+double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)\r
+{\r
+ int i;\r
+ int l=1, lmax=20;\r
+ double k1,k2;\r
+ double p2[NPARMAX+1];\r
+ double res;\r
+ double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;\r
+ double fx;\r
+ int k=0,kmax=10;\r
+ double l1;\r
+\r
+ fx=func(x);\r
+ for (i=1;i<=npar;i++) p2[i]=x[i];\r
+ for(l=0 ; l <=lmax; l++){\r
+ l1=pow(10,l);\r
+ delts=delt;\r
+ for(k=1 ; k <kmax; k=k+1){\r
+ delt = delta*(l1*k);\r
+ p2[theta]=x[theta] +delt;\r
+ k1=func(p2)-fx;\r
+ p2[theta]=x[theta]-delt;\r
+ k2=func(p2)-fx;\r
+ /*res= (k1-2.0*fx+k2)/delt/delt; */\r
+ res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */\r
+ \r
+#ifdef DEBUG\r
+ 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);\r
+ 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);\r
+#endif\r
+ /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */\r
+ if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){\r
+ k=kmax;\r
+ }\r
+ else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */\r
+ k=kmax; l=lmax*10.;\r
+ }\r
+ else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ \r
+ delts=delt;\r
+ }\r
+ }\r
+ }\r
+ delti[theta]=delts;\r
+ return res; \r
+ \r
+}\r
+\r
+double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)\r
+{\r
+ int i;\r
+ int l=1, l1, lmax=20;\r
+ double k1,k2,k3,k4,res,fx;\r
+ double p2[NPARMAX+1];\r
+ int k;\r
+\r
+ fx=func(x);\r
+ for (k=1; k<=2; k++) {\r
+ for (i=1;i<=npar;i++) p2[i]=x[i];\r
+ p2[thetai]=x[thetai]+delti[thetai]/k;\r
+ p2[thetaj]=x[thetaj]+delti[thetaj]/k;\r
+ k1=func(p2)-fx;\r
+ \r
+ p2[thetai]=x[thetai]+delti[thetai]/k;\r
+ p2[thetaj]=x[thetaj]-delti[thetaj]/k;\r
+ k2=func(p2)-fx;\r
+ \r
+ p2[thetai]=x[thetai]-delti[thetai]/k;\r
+ p2[thetaj]=x[thetaj]+delti[thetaj]/k;\r
+ k3=func(p2)-fx;\r
+ \r
+ p2[thetai]=x[thetai]-delti[thetai]/k;\r
+ p2[thetaj]=x[thetaj]-delti[thetaj]/k;\r
+ k4=func(p2)-fx;\r
+ res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */\r
+#ifdef DEBUG\r
+ 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);\r
+ 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);\r
+#endif\r
+ }\r
+ return res;\r
+}\r
+\r
+/************** Inverse of matrix **************/\r
+void ludcmp(double **a, int n, int *indx, double *d) \r
+{ \r
+ int i,imax,j,k; \r
+ double big,dum,sum,temp; \r
+ double *vv; \r
+ \r
+ vv=vector(1,n); \r
+ *d=1.0; \r
+ for (i=1;i<=n;i++) { \r
+ big=0.0; \r
+ for (j=1;j<=n;j++) \r
+ if ((temp=fabs(a[i][j])) > big) big=temp; \r
+ if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); \r
+ vv[i]=1.0/big; \r
+ } \r
+ for (j=1;j<=n;j++) { \r
+ for (i=1;i<j;i++) { \r
+ sum=a[i][j]; \r
+ for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; \r
+ a[i][j]=sum; \r
+ } \r
+ big=0.0; \r
+ for (i=j;i<=n;i++) { \r
+ sum=a[i][j]; \r
+ for (k=1;k<j;k++) \r
+ sum -= a[i][k]*a[k][j]; \r
+ a[i][j]=sum; \r
+ if ( (dum=vv[i]*fabs(sum)) >= big) { \r
+ big=dum; \r
+ imax=i; \r
+ } \r
+ } \r
+ if (j != imax) { \r
+ for (k=1;k<=n;k++) { \r
+ dum=a[imax][k]; \r
+ a[imax][k]=a[j][k]; \r
+ a[j][k]=dum; \r
+ } \r
+ *d = -(*d); \r
+ vv[imax]=vv[j]; \r
+ } \r
+ indx[j]=imax; \r
+ if (a[j][j] == 0.0) a[j][j]=TINY; \r
+ if (j != n) { \r
+ dum=1.0/(a[j][j]); \r
+ for (i=j+1;i<=n;i++) a[i][j] *= dum; \r
+ } \r
+ } \r
+ free_vector(vv,1,n); /* Doesn't work */\r
+;\r
+} \r
+\r
+void lubksb(double **a, int n, int *indx, double b[]) \r
+{ \r
+ int i,ii=0,ip,j; \r
+ double sum; \r
+ \r
+ for (i=1;i<=n;i++) { \r
+ ip=indx[i]; \r
+ sum=b[ip]; \r
+ b[ip]=b[i]; \r
+ if (ii) \r
+ for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; \r
+ else if (sum) ii=i; \r
+ b[i]=sum; \r
+ } \r
+ for (i=n;i>=1;i--) { \r
+ sum=b[i]; \r
+ for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; \r
+ b[i]=sum/a[i][i]; \r
+ } \r
+} \r
+\r
+void pstamp(FILE *fichier)\r
+{\r
+ fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);\r
+}\r
+\r
+/************ Frequencies ********************/\r
+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[])\r
+{ /* Some frequencies */\r
+ \r
+ int i, m, jk, k1,i1, j1, bool, z1,z2,j;\r
+ int first;\r
+ double ***freq; /* Frequencies */\r
+ double *pp, **prop;\r
+ double pos,posprop, k2, dateintsum=0,k2cpt=0;\r
+ char fileresp[FILENAMELENGTH];\r
+ \r
+ pp=vector(1,nlstate);\r
+ prop=matrix(1,nlstate,iagemin,iagemax+3);\r
+ strcpy(fileresp,"p");\r
+ strcat(fileresp,fileres);\r
+ if((ficresp=fopen(fileresp,"w"))==NULL) {\r
+ printf("Problem with prevalence resultfile: %s\n", fileresp);\r
+ fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);\r
+ exit(0);\r
+ }\r
+ freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);\r
+ j1=0;\r
+ \r
+ j=cptcoveff;\r
+ if (cptcovn<1) {j=1;ncodemax[1]=1;}\r
+\r
+ first=1;\r
+\r
+ for(k1=1; k1<=j;k1++){\r
+ for(i1=1; i1<=ncodemax[k1];i1++){\r
+ j1++;\r
+ /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);\r
+ scanf("%d", i);*/\r
+ for (i=-5; i<=nlstate+ndeath; i++) \r
+ for (jk=-5; jk<=nlstate+ndeath; jk++) \r
+ for(m=iagemin; m <= iagemax+3; m++)\r
+ freq[i][jk][m]=0;\r
+\r
+ for (i=1; i<=nlstate; i++) \r
+ for(m=iagemin; m <= iagemax+3; m++)\r
+ prop[i][m]=0;\r
+ \r
+ dateintsum=0;\r
+ k2cpt=0;\r
+ for (i=1; i<=imx; i++) {\r
+ bool=1;\r
+ if (cptcovn>0) {\r
+ for (z1=1; z1<=cptcoveff; z1++) \r
+ if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) \r
+ bool=0;\r
+ }\r
+ if (bool==1){\r
+ for(m=firstpass; m<=lastpass; m++){\r
+ k2=anint[m][i]+(mint[m][i]/12.);\r
+ /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/\r
+ if(agev[m][i]==0) agev[m][i]=iagemax+1;\r
+ if(agev[m][i]==1) agev[m][i]=iagemax+2;\r
+ if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];\r
+ if (m<lastpass) {\r
+ freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];\r
+ freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];\r
+ }\r
+ \r
+ if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {\r
+ dateintsum=dateintsum+k2;\r
+ k2cpt++;\r
+ }\r
+ /*}*/\r
+ }\r
+ }\r
+ }\r
+ \r
+ /* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/\r
+ pstamp(ficresp);\r
+ if (cptcovn>0) {\r
+ fprintf(ficresp, "\n#********** Variable "); \r
+ for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);\r
+ fprintf(ficresp, "**********\n#");\r
+ }\r
+ for(i=1; i<=nlstate;i++) \r
+ fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);\r
+ fprintf(ficresp, "\n");\r
+ \r
+ for(i=iagemin; i <= iagemax+3; i++){\r
+ if(i==iagemax+3){\r
+ fprintf(ficlog,"Total");\r
+ }else{\r
+ if(first==1){\r
+ first=0;\r
+ printf("See log file for details...\n");\r
+ }\r
+ fprintf(ficlog,"Age %d", i);\r
+ }\r
+ for(jk=1; jk <=nlstate ; jk++){\r
+ for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)\r
+ pp[jk] += freq[jk][m][i]; \r
+ }\r
+ for(jk=1; jk <=nlstate ; jk++){\r
+ for(m=-1, pos=0; m <=0 ; m++)\r
+ pos += freq[jk][m][i];\r
+ if(pp[jk]>=1.e-10){\r
+ if(first==1){\r
+ printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);\r
+ }\r
+ fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);\r
+ }else{\r
+ if(first==1)\r
+ printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);\r
+ fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);\r
+ }\r
+ }\r
+\r
+ for(jk=1; jk <=nlstate ; jk++){\r
+ for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)\r
+ pp[jk] += freq[jk][m][i];\r
+ } \r
+ for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){\r
+ pos += pp[jk];\r
+ posprop += prop[jk][i];\r
+ }\r
+ for(jk=1; jk <=nlstate ; jk++){\r
+ if(pos>=1.e-5){\r
+ if(first==1)\r
+ printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);\r
+ fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);\r
+ }else{\r
+ if(first==1)\r
+ printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);\r
+ fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);\r
+ }\r
+ if( i <= iagemax){\r
+ if(pos>=1.e-5){\r
+ fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);\r
+ /*probs[i][jk][j1]= pp[jk]/pos;*/\r
+ /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/\r
+ }\r
+ else\r
+ fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);\r
+ }\r
+ }\r
+ \r
+ for(jk=-1; jk <=nlstate+ndeath; jk++)\r
+ for(m=-1; m <=nlstate+ndeath; m++)\r
+ if(freq[jk][m][i] !=0 ) {\r
+ if(first==1)\r
+ printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);\r
+ fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);\r
+ }\r
+ if(i <= iagemax)\r
+ fprintf(ficresp,"\n");\r
+ if(first==1)\r
+ printf("Others in log...\n");\r
+ fprintf(ficlog,"\n");\r
+ }\r
+ }\r
+ }\r
+ dateintmean=dateintsum/k2cpt; \r
+ \r
+ fclose(ficresp);\r
+ free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);\r
+ free_vector(pp,1,nlstate);\r
+ free_matrix(prop,1,nlstate,iagemin, iagemax+3);\r
+ /* End of Freq */\r
+}\r
+\r
+/************ Prevalence ********************/\r
+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)\r
+{ \r
+ /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people\r
+ in each health status at the date of interview (if between dateprev1 and dateprev2).\r
+ We still use firstpass and lastpass as another selection.\r
+ */\r
+ \r
+ int i, m, jk, k1, i1, j1, bool, z1,z2,j;\r
+ double ***freq; /* Frequencies */\r
+ double *pp, **prop;\r
+ double pos,posprop; \r
+ double y2; /* in fractional years */\r
+ int iagemin, iagemax;\r
+\r
+ iagemin= (int) agemin;\r
+ iagemax= (int) agemax;\r
+ /*pp=vector(1,nlstate);*/\r
+ prop=matrix(1,nlstate,iagemin,iagemax+3); \r
+ /* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/\r
+ j1=0;\r
+ \r
+ j=cptcoveff;\r
+ if (cptcovn<1) {j=1;ncodemax[1]=1;}\r
+ \r
+ for(k1=1; k1<=j;k1++){\r
+ for(i1=1; i1<=ncodemax[k1];i1++){\r
+ j1++;\r
+ \r
+ for (i=1; i<=nlstate; i++) \r
+ for(m=iagemin; m <= iagemax+3; m++)\r
+ prop[i][m]=0.0;\r
+ \r
+ for (i=1; i<=imx; i++) { /* Each individual */\r
+ bool=1;\r
+ if (cptcovn>0) {\r
+ for (z1=1; z1<=cptcoveff; z1++) \r
+ if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) \r
+ bool=0;\r
+ } \r
+ if (bool==1) { \r
+ for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/\r
+ y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */\r
+ if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */\r
+ if(agev[m][i]==0) agev[m][i]=iagemax+1;\r
+ if(agev[m][i]==1) agev[m][i]=iagemax+2;\r
+ 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); \r
+ if (s[m][i]>0 && s[m][i]<=nlstate) { \r
+ /*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]]);*/\r
+ prop[s[m][i]][(int)agev[m][i]] += weight[i];\r
+ prop[s[m][i]][iagemax+3] += weight[i]; \r
+ } \r
+ }\r
+ } /* end selection of waves */\r
+ }\r
+ }\r
+ for(i=iagemin; i <= iagemax+3; i++){ \r
+ \r
+ for(jk=1,posprop=0; jk <=nlstate ; jk++) { \r
+ posprop += prop[jk][i]; \r
+ } \r
+\r
+ for(jk=1; jk <=nlstate ; jk++){ \r
+ if( i <= iagemax){ \r
+ if(posprop>=1.e-5){ \r
+ probs[i][jk][j1]= prop[jk][i]/posprop;\r
+ } \r
+ } \r
+ }/* end jk */ \r
+ }/* end i */ \r
+ } /* end i1 */\r
+ } /* end k1 */\r
+ \r
+ /* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/\r
+ /*free_vector(pp,1,nlstate);*/\r
+ free_matrix(prop,1,nlstate, iagemin,iagemax+3);\r
+} /* End of prevalence */\r
+\r
+/************* Waves Concatenation ***************/\r
+\r
+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)\r
+{\r
+ /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.\r
+ Death is a valid wave (if date is known).\r
+ mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i\r
+ dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]\r
+ and mw[mi+1][i]. dh depends on stepm.\r
+ */\r
+\r
+ int i, mi, m;\r
+ /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;\r
+ double sum=0., jmean=0.;*/\r
+ int first;\r
+ int j, k=0,jk, ju, jl;\r
+ double sum=0.;\r
+ first=0;\r
+ jmin=1e+5;\r
+ jmax=-1;\r
+ jmean=0.;\r
+ for(i=1; i<=imx; i++){\r
+ mi=0;\r
+ m=firstpass;\r
+ while(s[m][i] <= nlstate){\r
+ if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)\r
+ mw[++mi][i]=m;\r
+ if(m >=lastpass)\r
+ break;\r
+ else\r
+ m++;\r
+ }/* end while */\r
+ if (s[m][i] > nlstate){\r
+ mi++; /* Death is another wave */\r
+ /* if(mi==0) never been interviewed correctly before death */\r
+ /* Only death is a correct wave */\r
+ mw[mi][i]=m;\r
+ }\r
+\r
+ wav[i]=mi;\r
+ if(mi==0){\r
+ nbwarn++;\r
+ if(first==0){\r
+ printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);\r
+ first=1;\r
+ }\r
+ if(first==1){\r
+ fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);\r
+ }\r
+ } /* end mi==0 */\r
+ } /* End individuals */\r
+\r
+ for(i=1; i<=imx; i++){\r
+ for(mi=1; mi<wav[i];mi++){\r
+ if (stepm <=0)\r
+ dh[mi][i]=1;\r
+ else{\r
+ if (s[mw[mi+1][i]][i] > nlstate) { /* A death */\r
+ if (agedc[i] < 2*AGESUP) {\r
+ j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); \r
+ if(j==0) j=1; /* Survives at least one month after exam */\r
+ else if(j<0){\r
+ nberr++;\r
+ 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]);\r
+ j=1; /* Temporary Dangerous patch */\r
+ 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);\r
+ 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]);\r
+ 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);\r
+ }\r
+ k=k+1;\r
+ if (j >= jmax){\r
+ jmax=j;\r
+ ijmax=i;\r
+ }\r
+ if (j <= jmin){\r
+ jmin=j;\r
+ ijmin=i;\r
+ }\r
+ sum=sum+j;\r
+ /*if (j<0) printf("j=%d num=%d \n",j,i);*/\r
+ /* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/\r
+ }\r
+ }\r
+ else{\r
+ j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));\r
+/* 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]); */\r
+\r
+ k=k+1;\r
+ if (j >= jmax) {\r
+ jmax=j;\r
+ ijmax=i;\r
+ }\r
+ else if (j <= jmin){\r
+ jmin=j;\r
+ ijmin=i;\r
+ }\r
+ /* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */\r
+ /*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]);*/\r
+ if(j<0){\r
+ nberr++;\r
+ 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]);\r
+ 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]);\r
+ }\r
+ sum=sum+j;\r
+ }\r
+ jk= j/stepm;\r
+ jl= j -jk*stepm;\r
+ ju= j -(jk+1)*stepm;\r
+ if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */\r
+ if(jl==0){\r
+ dh[mi][i]=jk;\r
+ bh[mi][i]=0;\r
+ }else{ /* We want a negative bias in order to only have interpolation ie\r
+ * at the price of an extra matrix product in likelihood */\r
+ dh[mi][i]=jk+1;\r
+ bh[mi][i]=ju;\r
+ }\r
+ }else{\r
+ if(jl <= -ju){\r
+ dh[mi][i]=jk;\r
+ bh[mi][i]=jl; /* bias is positive if real duration\r
+ * is higher than the multiple of stepm and negative otherwise.\r
+ */\r
+ }\r
+ else{\r
+ dh[mi][i]=jk+1;\r
+ bh[mi][i]=ju;\r
+ }\r
+ if(dh[mi][i]==0){\r
+ dh[mi][i]=1; /* At least one step */\r
+ bh[mi][i]=ju; /* At least one step */\r
+ /* 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);*/\r
+ }\r
+ } /* end if mle */\r
+ }\r
+ } /* end wave */\r
+ }\r
+ jmean=sum/k;\r
+ 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);\r
+ 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);\r
+ }\r
+\r
+/*********** Tricode ****************************/\r
+void tricode(int *Tvar, int **nbcode, int imx)\r
+{\r
+ \r
+ int Ndum[20],ij=1, k, j, i, maxncov=19;\r
+ int cptcode=0;\r
+ cptcoveff=0; \r
+ \r
+ for (k=0; k<maxncov; k++) Ndum[k]=0;\r
+ for (k=1; k<=7; k++) ncodemax[k]=0;\r
+\r
+ for (j=1; j<=(cptcovn+2*cptcovprod); j++) {\r
+ for (i=1; i<=imx; i++) { /*reads the data file to get the maximum \r
+ modality*/ \r
+ ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/\r
+ Ndum[ij]++; /*store the modality */\r
+ /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/\r
+ if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable \r
+ Tvar[j]. If V=sex and male is 0 and \r
+ female is 1, then cptcode=1.*/\r
+ }\r
+\r
+ for (i=0; i<=cptcode; i++) {\r
+ 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 */\r
+ }\r
+\r
+ ij=1; \r
+ for (i=1; i<=ncodemax[j]; i++) {\r
+ for (k=0; k<= maxncov; k++) {\r
+ if (Ndum[k] != 0) {\r
+ nbcode[Tvar[j]][ij]=k; \r
+ /* 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; */\r
+ \r
+ ij++;\r
+ }\r
+ if (ij > ncodemax[j]) break; \r
+ } \r
+ } \r
+ } \r
+\r
+ for (k=0; k< maxncov; k++) Ndum[k]=0;\r
+\r
+ for (i=1; i<=ncovmodel-2; i++) { \r
+ /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/\r
+ ij=Tvar[i];\r
+ Ndum[ij]++;\r
+ }\r
+\r
+ ij=1;\r
+ for (i=1; i<= maxncov; i++) {\r
+ if((Ndum[i]!=0) && (i<=ncovcol)){\r
+ Tvaraff[ij]=i; /*For printing */\r
+ ij++;\r
+ }\r
+ }\r
+ \r
+ cptcoveff=ij-1; /*Number of simple covariates*/\r
+}\r
+\r
+/*********** Health Expectancies ****************/\r
+\r
+void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )\r
+\r
+{\r
+ /* Health expectancies, no variances */\r
+ int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;\r
+ double age, agelim, hf;\r
+ double ***p3mat;\r
+ double eip;\r
+\r
+ pstamp(ficreseij);\r
+ fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");\r
+ fprintf(ficreseij,"# Age");\r
+ for(i=1; i<=nlstate;i++){\r
+ for(j=1; j<=nlstate;j++){\r
+ fprintf(ficreseij," e%1d%1d ",i,j);\r
+ }\r
+ fprintf(ficreseij," e%1d. ",i);\r
+ }\r
+ fprintf(ficreseij,"\n");\r
+\r
+ \r
+ if(estepm < stepm){\r
+ printf ("Problem %d lower than %d\n",estepm, stepm);\r
+ }\r
+ else hstepm=estepm; \r
+ /* We compute the life expectancy from trapezoids spaced every estepm months\r
+ * This is mainly to measure the difference between two models: for example\r
+ * if stepm=24 months pijx are given only every 2 years and by summing them\r
+ * we are calculating an estimate of the Life Expectancy assuming a linear \r
+ * progression in between and thus overestimating or underestimating according\r
+ * to the curvature of the survival function. If, for the same date, we \r
+ * estimate the model with stepm=1 month, we can keep estepm to 24 months\r
+ * to compare the new estimate of Life expectancy with the same linear \r
+ * hypothesis. A more precise result, taking into account a more precise\r
+ * curvature will be obtained if estepm is as small as stepm. */\r
+\r
+ /* For example we decided to compute the life expectancy with the smallest unit */\r
+ /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. \r
+ nhstepm is the number of hstepm from age to agelim \r
+ nstepm is the number of stepm from age to agelin. \r
+ Look at hpijx to understand the reason of that which relies in memory size\r
+ and note for a fixed period like estepm months */\r
+ /* We decided (b) to get a life expectancy respecting the most precise curvature of the\r
+ survival function given by stepm (the optimization length). Unfortunately it\r
+ means that if the survival funtion is printed only each two years of age and if\r
+ you sum them up and add 1 year (area under the trapezoids) you won't get the same \r
+ results. So we changed our mind and took the option of the best precision.\r
+ */\r
+ hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ \r
+\r
+ agelim=AGESUP;\r
+ /* If stepm=6 months */\r
+ /* Computed by stepm unit matrices, product of hstepm matrices, stored\r
+ in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */\r
+ \r
+/* nhstepm age range expressed in number of stepm */\r
+ nstepm=(int) rint((agelim-bage)*YEARM/stepm); \r
+ /* Typically if 20 years nstepm = 20*12/6=40 stepm */ \r
+ /* if (stepm >= YEARM) hstepm=1;*/\r
+ nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */\r
+ p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);\r
+\r
+ for (age=bage; age<=fage; age ++){ \r
+\r
+\r
+ hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij); \r
+ \r
+ hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */\r
+ \r
+ printf("%d|",(int)age);fflush(stdout);\r
+ fprintf(ficlog,"%d|",(int)age);fflush(ficlog);\r
+ \r
+\r
+ /* Computing expectancies */\r
+ for(i=1; i<=nlstate;i++)\r
+ for(j=1; j<=nlstate;j++)\r
+ for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){\r
+ eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;\r
+ \r
+ /*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]);*/\r
+\r
+ }\r
+ \r
+ fprintf(ficreseij,"%3.0f",age );\r
+ for(i=1; i<=nlstate;i++){\r
+ eip=0;\r
+ for(j=1; j<=nlstate;j++){\r
+ eip +=eij[i][j][(int)age];\r
+ fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );\r
+ }\r
+ fprintf(ficreseij,"%9.4f", eip );\r
+ }\r
+ fprintf(ficreseij,"\n");\r
+ \r
+ }\r
+ free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);\r
+ printf("\n");\r
+ fprintf(ficlog,"\n");\r
+ \r
+}\r
+\r
+void cvevsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )\r
+\r
+{\r
+ /* Covariances of health expectancies eij and of total life expectancies according\r
+ to initial status i, ei. .\r
+ */\r
+ int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;\r
+ double age, agelim, hf;\r
+ double ***p3matp, ***p3matm, ***varhe;\r
+ double **dnewm,**doldm;\r
+ double *xp, *xm;\r
+ double **gp, **gm;\r
+ double ***gradg, ***trgradg;\r
+ int theta;\r
+\r
+ double eip, vip;\r
+\r
+ varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);\r
+ xp=vector(1,npar);\r
+ xm=vector(1,npar);\r
+ dnewm=matrix(1,nlstate*nlstate,1,npar);\r
+ doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);\r
+ \r
+ pstamp(ficresstdeij);\r
+ fprintf(ficresstdeij,"# Health expectancies with standard errors\n");\r
+ fprintf(ficresstdeij,"# Age");\r
+ for(i=1; i<=nlstate;i++){\r
+ for(j=1; j<=nlstate;j++)\r
+ fprintf(ficresstdeij," e%1d%1d (SE)",i,j);\r
+ fprintf(ficresstdeij," e%1d. ",i);\r
+ }\r
+ fprintf(ficresstdeij,"\n");\r
+\r
+ pstamp(ficrescveij);\r
+ fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");\r
+ fprintf(ficrescveij,"# Age");\r
+ for(i=1; i<=nlstate;i++)\r
+ for(j=1; j<=nlstate;j++){\r
+ cptj= (j-1)*nlstate+i;\r
+ for(i2=1; i2<=nlstate;i2++)\r
+ for(j2=1; j2<=nlstate;j2++){\r
+ cptj2= (j2-1)*nlstate+i2;\r
+ if(cptj2 <= cptj)\r
+ fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);\r
+ }\r
+ }\r
+ fprintf(ficrescveij,"\n");\r
+ \r
+ if(estepm < stepm){\r
+ printf ("Problem %d lower than %d\n",estepm, stepm);\r
+ }\r
+ else hstepm=estepm; \r
+ /* We compute the life expectancy from trapezoids spaced every estepm months\r
+ * This is mainly to measure the difference between two models: for example\r
+ * if stepm=24 months pijx are given only every 2 years and by summing them\r
+ * we are calculating an estimate of the Life Expectancy assuming a linear \r
+ * progression in between and thus overestimating or underestimating according\r
+ * to the curvature of the survival function. If, for the same date, we \r
+ * estimate the model with stepm=1 month, we can keep estepm to 24 months\r
+ * to compare the new estimate of Life expectancy with the same linear \r
+ * hypothesis. A more precise result, taking into account a more precise\r
+ * curvature will be obtained if estepm is as small as stepm. */\r
+\r
+ /* For example we decided to compute the life expectancy with the smallest unit */\r
+ /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. \r
+ nhstepm is the number of hstepm from age to agelim \r
+ nstepm is the number of stepm from age to agelin. \r
+ Look at hpijx to understand the reason of that which relies in memory size\r
+ and note for a fixed period like estepm months */\r
+ /* We decided (b) to get a life expectancy respecting the most precise curvature of the\r
+ survival function given by stepm (the optimization length). Unfortunately it\r
+ means that if the survival funtion is printed only each two years of age and if\r
+ you sum them up and add 1 year (area under the trapezoids) you won't get the same \r
+ results. So we changed our mind and took the option of the best precision.\r
+ */\r
+ hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ \r
+\r
+ /* If stepm=6 months */\r
+ /* nhstepm age range expressed in number of stepm */\r
+ agelim=AGESUP;\r
+ nstepm=(int) rint((agelim-bage)*YEARM/stepm); \r
+ /* Typically if 20 years nstepm = 20*12/6=40 stepm */ \r
+ /* if (stepm >= YEARM) hstepm=1;*/\r
+ nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */\r
+ \r
+ p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);\r
+ p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);\r
+ gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);\r
+ trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);\r
+ gp=matrix(0,nhstepm,1,nlstate*nlstate);\r
+ gm=matrix(0,nhstepm,1,nlstate*nlstate);\r
+\r
+ for (age=bage; age<=fage; age ++){ \r
+\r
+ /* Computed by stepm unit matrices, product of hstepm matrices, stored\r
+ in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */\r
+ \r
+ hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */\r
+\r
+ /* Computing Variances of health expectancies */\r
+ /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to\r
+ decrease memory allocation */\r
+ for(theta=1; theta <=npar; theta++){\r
+ for(i=1; i<=npar; i++){ \r
+ xp[i] = x[i] + (i==theta ?delti[theta]:0);\r
+ xm[i] = x[i] - (i==theta ?delti[theta]:0);\r
+ }\r
+ hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij); \r
+ hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij); \r
+ \r
+ for(j=1; j<= nlstate; j++){\r
+ for(i=1; i<=nlstate; i++){\r
+ for(h=0; h<=nhstepm-1; h++){\r
+ gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;\r
+ gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;\r
+ }\r
+ }\r
+ }\r
+ \r
+ for(ij=1; ij<= nlstate*nlstate; ij++)\r
+ for(h=0; h<=nhstepm-1; h++){\r
+ gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];\r
+ }\r
+ }/* End theta */\r
+ \r
+ \r
+ for(h=0; h<=nhstepm-1; h++)\r
+ for(j=1; j<=nlstate*nlstate;j++)\r
+ for(theta=1; theta <=npar; theta++)\r
+ trgradg[h][j][theta]=gradg[h][theta][j];\r
+ \r
+\r
+ for(ij=1;ij<=nlstate*nlstate;ij++)\r
+ for(ji=1;ji<=nlstate*nlstate;ji++)\r
+ varhe[ij][ji][(int)age] =0.;\r
+\r
+ printf("%d|",(int)age);fflush(stdout);\r
+ fprintf(ficlog,"%d|",(int)age);fflush(ficlog);\r
+ for(h=0;h<=nhstepm-1;h++){\r
+ for(k=0;k<=nhstepm-1;k++){\r
+ matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);\r
+ matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);\r
+ for(ij=1;ij<=nlstate*nlstate;ij++)\r
+ for(ji=1;ji<=nlstate*nlstate;ji++)\r
+ varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;\r
+ }\r
+ }\r
+\r
+ /* Computing expectancies */\r
+ hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij); \r
+ for(i=1; i<=nlstate;i++)\r
+ for(j=1; j<=nlstate;j++)\r
+ for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){\r
+ eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;\r
+ \r
+ /* 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]);*/\r
+\r
+ }\r
+\r
+ fprintf(ficresstdeij,"%3.0f",age );\r
+ for(i=1; i<=nlstate;i++){\r
+ eip=0.;\r
+ vip=0.;\r
+ for(j=1; j<=nlstate;j++){\r
+ eip += eij[i][j][(int)age];\r
+ for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */\r
+ vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];\r
+ fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );\r
+ }\r
+ fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));\r
+ }\r
+ fprintf(ficresstdeij,"\n");\r
+\r
+ fprintf(ficrescveij,"%3.0f",age );\r
+ for(i=1; i<=nlstate;i++)\r
+ for(j=1; j<=nlstate;j++){\r
+ cptj= (j-1)*nlstate+i;\r
+ for(i2=1; i2<=nlstate;i2++)\r
+ for(j2=1; j2<=nlstate;j2++){\r
+ cptj2= (j2-1)*nlstate+i2;\r
+ if(cptj2 <= cptj)\r
+ fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);\r
+ }\r
+ }\r
+ fprintf(ficrescveij,"\n");\r
+ \r
+ }\r
+ free_matrix(gm,0,nhstepm,1,nlstate*nlstate);\r
+ free_matrix(gp,0,nhstepm,1,nlstate*nlstate);\r
+ free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);\r
+ free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);\r
+ free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);\r
+ free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);\r
+ printf("\n");\r
+ fprintf(ficlog,"\n");\r
+\r
+ free_vector(xm,1,npar);\r
+ free_vector(xp,1,npar);\r
+ free_matrix(dnewm,1,nlstate*nlstate,1,npar);\r
+ free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);\r
+ free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);\r
+}\r
+\r
+/************ Variance ******************/\r
+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[])\r
+{\r
+ /* Variance of health expectancies */\r
+ /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/\r
+ /* double **newm;*/\r
+ double **dnewm,**doldm;\r
+ double **dnewmp,**doldmp;\r
+ int i, j, nhstepm, hstepm, h, nstepm ;\r
+ int k, cptcode;\r
+ double *xp;\r
+ double **gp, **gm; /* for var eij */\r
+ double ***gradg, ***trgradg; /*for var eij */\r
+ double **gradgp, **trgradgp; /* for var p point j */\r
+ double *gpp, *gmp; /* for var p point j */\r
+ double **varppt; /* for var p point j nlstate to nlstate+ndeath */\r
+ double ***p3mat;\r
+ double age,agelim, hf;\r
+ double ***mobaverage;\r
+ int theta;\r
+ char digit[4];\r
+ char digitp[25];\r
+\r
+ char fileresprobmorprev[FILENAMELENGTH];\r
+\r
+ if(popbased==1){\r
+ if(mobilav!=0)\r
+ strcpy(digitp,"-populbased-mobilav-");\r
+ else strcpy(digitp,"-populbased-nomobil-");\r
+ }\r
+ else \r
+ strcpy(digitp,"-stablbased-");\r
+\r
+ if (mobilav!=0) {\r
+ mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);\r
+ if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){\r
+ fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);\r
+ printf(" Error in movingaverage mobilav=%d\n",mobilav);\r
+ }\r
+ }\r
+\r
+ strcpy(fileresprobmorprev,"prmorprev"); \r
+ sprintf(digit,"%-d",ij);\r
+ /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/\r
+ strcat(fileresprobmorprev,digit); /* Tvar to be done */\r
+ strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */\r
+ strcat(fileresprobmorprev,fileres);\r
+ if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {\r
+ printf("Problem with resultfile: %s\n", fileresprobmorprev);\r
+ fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);\r
+ }\r
+ printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);\r
+ \r
+ fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);\r
+ pstamp(ficresprobmorprev);\r
+ 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);\r
+ fprintf(ficresprobmorprev,"# Age cov=%-d",ij);\r
+ for(j=nlstate+1; j<=(nlstate+ndeath);j++){\r
+ fprintf(ficresprobmorprev," p.%-d SE",j);\r
+ for(i=1; i<=nlstate;i++)\r
+ fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);\r
+ } \r
+ fprintf(ficresprobmorprev,"\n");\r
+ fprintf(ficgp,"\n# Routine varevsij");\r
+ /* fprintf(fichtm, "#Local time at start: %s", strstart);*/\r
+ 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");\r
+ fprintf(fichtm,"\n<br>%s <br>\n",digitp);\r
+/* } */\r
+ varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);\r
+ pstamp(ficresvij);\r
+ fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");\r
+ if(popbased==1)\r
+ fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");\r
+ else\r
+ fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");\r
+ fprintf(ficresvij,"# Age");\r
+ for(i=1; i<=nlstate;i++)\r
+ for(j=1; j<=nlstate;j++)\r
+ fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);\r
+ fprintf(ficresvij,"\n");\r
+\r
+ xp=vector(1,npar);\r
+ dnewm=matrix(1,nlstate,1,npar);\r
+ doldm=matrix(1,nlstate,1,nlstate);\r
+ dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);\r
+ doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);\r
+\r
+ gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);\r
+ gpp=vector(nlstate+1,nlstate+ndeath);\r
+ gmp=vector(nlstate+1,nlstate+ndeath);\r
+ trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/\r
+ \r
+ if(estepm < stepm){\r
+ printf ("Problem %d lower than %d\n",estepm, stepm);\r
+ }\r
+ else hstepm=estepm; \r
+ /* For example we decided to compute the life expectancy with the smallest unit */\r
+ /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. \r
+ nhstepm is the number of hstepm from age to agelim \r
+ nstepm is the number of stepm from age to agelin. \r
+ Look at hpijx to understand the reason of that which relies in memory size\r
+ and note for a fixed period like k years */\r
+ /* We decided (b) to get a life expectancy respecting the most precise curvature of the\r
+ survival function given by stepm (the optimization length). Unfortunately it\r
+ means that if the survival funtion is printed every two years of age and if\r
+ you sum them up and add 1 year (area under the trapezoids) you won't get the same \r
+ results. So we changed our mind and took the option of the best precision.\r
+ */\r
+ hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ \r
+ agelim = AGESUP;\r
+ for (age=bage; age<=fage; age ++){ /* If stepm=6 months */\r
+ nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ \r
+ nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */\r
+ p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);\r
+ gradg=ma3x(0,nhstepm,1,npar,1,nlstate);\r
+ gp=matrix(0,nhstepm,1,nlstate);\r
+ gm=matrix(0,nhstepm,1,nlstate);\r
+\r
+\r
+ for(theta=1; theta <=npar; theta++){\r
+ for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/\r
+ xp[i] = x[i] + (i==theta ?delti[theta]:0);\r
+ }\r
+ hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); \r
+ prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);\r
+\r
+ if (popbased==1) {\r
+ if(mobilav ==0){\r
+ for(i=1; i<=nlstate;i++)\r
+ prlim[i][i]=probs[(int)age][i][ij];\r
+ }else{ /* mobilav */ \r
+ for(i=1; i<=nlstate;i++)\r
+ prlim[i][i]=mobaverage[(int)age][i][ij];\r
+ }\r
+ }\r
+ \r
+ for(j=1; j<= nlstate; j++){\r
+ for(h=0; h<=nhstepm; h++){\r
+ for(i=1, gp[h][j]=0.;i<=nlstate;i++)\r
+ gp[h][j] += prlim[i][i]*p3mat[i][j][h];\r
+ }\r
+ }\r
+ /* This for computing probability of death (h=1 means\r
+ computed over hstepm matrices product = hstepm*stepm months) \r
+ as a weighted average of prlim.\r
+ */\r
+ for(j=nlstate+1;j<=nlstate+ndeath;j++){\r
+ for(i=1,gpp[j]=0.; i<= nlstate; i++)\r
+ gpp[j] += prlim[i][i]*p3mat[i][j][1];\r
+ } \r
+ /* end probability of death */\r
+\r
+ for(i=1; i<=npar; i++) /* Computes gradient x - delta */\r
+ xp[i] = x[i] - (i==theta ?delti[theta]:0);\r
+ hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); \r
+ prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);\r
+ \r
+ if (popbased==1) {\r
+ if(mobilav ==0){\r
+ for(i=1; i<=nlstate;i++)\r
+ prlim[i][i]=probs[(int)age][i][ij];\r
+ }else{ /* mobilav */ \r
+ for(i=1; i<=nlstate;i++)\r
+ prlim[i][i]=mobaverage[(int)age][i][ij];\r
+ }\r
+ }\r
+\r
+ for(j=1; j<= nlstate; j++){\r
+ for(h=0; h<=nhstepm; h++){\r
+ for(i=1, gm[h][j]=0.;i<=nlstate;i++)\r
+ gm[h][j] += prlim[i][i]*p3mat[i][j][h];\r
+ }\r
+ }\r
+ /* This for computing probability of death (h=1 means\r
+ computed over hstepm matrices product = hstepm*stepm months) \r
+ as a weighted average of prlim.\r
+ */\r
+ for(j=nlstate+1;j<=nlstate+ndeath;j++){\r
+ for(i=1,gmp[j]=0.; i<= nlstate; i++)\r
+ gmp[j] += prlim[i][i]*p3mat[i][j][1];\r
+ } \r
+ /* end probability of death */\r
+\r
+ for(j=1; j<= nlstate; j++) /* vareij */\r
+ for(h=0; h<=nhstepm; h++){\r
+ gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];\r
+ }\r
+\r
+ for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */\r
+ gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];\r
+ }\r
+\r
+ } /* End theta */\r
+\r
+ trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */\r
+\r
+ for(h=0; h<=nhstepm; h++) /* veij */\r
+ for(j=1; j<=nlstate;j++)\r
+ for(theta=1; theta <=npar; theta++)\r
+ trgradg[h][j][theta]=gradg[h][theta][j];\r
+\r
+ for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */\r
+ for(theta=1; theta <=npar; theta++)\r
+ trgradgp[j][theta]=gradgp[theta][j];\r
+ \r
+\r
+ hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */\r
+ for(i=1;i<=nlstate;i++)\r
+ for(j=1;j<=nlstate;j++)\r
+ vareij[i][j][(int)age] =0.;\r
+\r
+ for(h=0;h<=nhstepm;h++){\r
+ for(k=0;k<=nhstepm;k++){\r
+ matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);\r
+ matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);\r
+ for(i=1;i<=nlstate;i++)\r
+ for(j=1;j<=nlstate;j++)\r
+ vareij[i][j][(int)age] += doldm[i][j]*hf*hf;\r
+ }\r
+ }\r
+ \r
+ /* pptj */\r
+ matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);\r
+ matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);\r
+ for(j=nlstate+1;j<=nlstate+ndeath;j++)\r
+ for(i=nlstate+1;i<=nlstate+ndeath;i++)\r
+ varppt[j][i]=doldmp[j][i];\r
+ /* end ppptj */\r
+ /* x centered again */\r
+ hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij); \r
+ prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);\r
+ \r
+ if (popbased==1) {\r
+ if(mobilav ==0){\r
+ for(i=1; i<=nlstate;i++)\r
+ prlim[i][i]=probs[(int)age][i][ij];\r
+ }else{ /* mobilav */ \r
+ for(i=1; i<=nlstate;i++)\r
+ prlim[i][i]=mobaverage[(int)age][i][ij];\r
+ }\r
+ }\r
+ \r
+ /* This for computing probability of death (h=1 means\r
+ computed over hstepm (estepm) matrices product = hstepm*stepm months) \r
+ as a weighted average of prlim.\r
+ */\r
+ for(j=nlstate+1;j<=nlstate+ndeath;j++){\r
+ for(i=1,gmp[j]=0.;i<= nlstate; i++) \r
+ gmp[j] += prlim[i][i]*p3mat[i][j][1]; \r
+ } \r
+ /* end probability of death */\r
+\r
+ fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);\r
+ for(j=nlstate+1; j<=(nlstate+ndeath);j++){\r
+ fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));\r
+ for(i=1; i<=nlstate;i++){\r
+ fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);\r
+ }\r
+ } \r
+ fprintf(ficresprobmorprev,"\n");\r
+\r
+ fprintf(ficresvij,"%.0f ",age );\r
+ for(i=1; i<=nlstate;i++)\r
+ for(j=1; j<=nlstate;j++){\r
+ fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);\r
+ }\r
+ fprintf(ficresvij,"\n");\r
+ free_matrix(gp,0,nhstepm,1,nlstate);\r
+ free_matrix(gm,0,nhstepm,1,nlstate);\r
+ free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);\r
+ free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);\r
+ free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);\r
+ } /* End age */\r
+ free_vector(gpp,nlstate+1,nlstate+ndeath);\r
+ free_vector(gmp,nlstate+1,nlstate+ndeath);\r
+ free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);\r
+ free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/\r
+ fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");\r
+ /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */\r
+ fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");\r
+/* fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */\r
+/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */\r
+/* fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */\r
+ fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));\r
+ fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));\r
+ fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));\r
+ fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));\r
+ 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);\r
+ /* 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);\r
+*/\r
+/* fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */\r
+ fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);\r
+\r
+ free_vector(xp,1,npar);\r
+ free_matrix(doldm,1,nlstate,1,nlstate);\r
+ free_matrix(dnewm,1,nlstate,1,npar);\r
+ free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);\r
+ free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);\r
+ free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);\r
+ if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);\r
+ fclose(ficresprobmorprev);\r
+ fflush(ficgp);\r
+ fflush(fichtm); \r
+} /* end varevsij */\r
+\r
+/************ Variance of prevlim ******************/\r
+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[])\r
+{\r
+ /* Variance of prevalence limit */\r
+ /* double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/\r
+ double **newm;\r
+ double **dnewm,**doldm;\r
+ int i, j, nhstepm, hstepm;\r
+ int k, cptcode;\r
+ double *xp;\r
+ double *gp, *gm;\r
+ double **gradg, **trgradg;\r
+ double age,agelim;\r
+ int theta;\r
+ \r
+ pstamp(ficresvpl);\r
+ fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");\r
+ fprintf(ficresvpl,"# Age");\r
+ for(i=1; i<=nlstate;i++)\r
+ fprintf(ficresvpl," %1d-%1d",i,i);\r
+ fprintf(ficresvpl,"\n");\r
+\r
+ xp=vector(1,npar);\r
+ dnewm=matrix(1,nlstate,1,npar);\r
+ doldm=matrix(1,nlstate,1,nlstate);\r
+ \r
+ hstepm=1*YEARM; /* Every year of age */\r
+ hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ \r
+ agelim = AGESUP;\r
+ for (age=bage; age<=fage; age ++){ /* If stepm=6 months */\r
+ nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ \r
+ if (stepm >= YEARM) hstepm=1;\r
+ nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */\r
+ gradg=matrix(1,npar,1,nlstate);\r
+ gp=vector(1,nlstate);\r
+ gm=vector(1,nlstate);\r
+\r
+ for(theta=1; theta <=npar; theta++){\r
+ for(i=1; i<=npar; i++){ /* Computes gradient */\r
+ xp[i] = x[i] + (i==theta ?delti[theta]:0);\r
+ }\r
+ prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);\r
+ for(i=1;i<=nlstate;i++)\r
+ gp[i] = prlim[i][i];\r
+ \r
+ for(i=1; i<=npar; i++) /* Computes gradient */\r
+ xp[i] = x[i] - (i==theta ?delti[theta]:0);\r
+ prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);\r
+ for(i=1;i<=nlstate;i++)\r
+ gm[i] = prlim[i][i];\r
+\r
+ for(i=1;i<=nlstate;i++)\r
+ gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];\r
+ } /* End theta */\r
+\r
+ trgradg =matrix(1,nlstate,1,npar);\r
+\r
+ for(j=1; j<=nlstate;j++)\r
+ for(theta=1; theta <=npar; theta++)\r
+ trgradg[j][theta]=gradg[theta][j];\r
+\r
+ for(i=1;i<=nlstate;i++)\r
+ varpl[i][(int)age] =0.;\r
+ matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);\r
+ matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);\r
+ for(i=1;i<=nlstate;i++)\r
+ varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */\r
+\r
+ fprintf(ficresvpl,"%.0f ",age );\r
+ for(i=1; i<=nlstate;i++)\r
+ fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));\r
+ fprintf(ficresvpl,"\n");\r
+ free_vector(gp,1,nlstate);\r
+ free_vector(gm,1,nlstate);\r
+ free_matrix(gradg,1,npar,1,nlstate);\r
+ free_matrix(trgradg,1,nlstate,1,npar);\r
+ } /* End age */\r
+\r
+ free_vector(xp,1,npar);\r
+ free_matrix(doldm,1,nlstate,1,npar);\r
+ free_matrix(dnewm,1,nlstate,1,nlstate);\r
+\r
+}\r
+\r
+/************ Variance of one-step probabilities ******************/\r
+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[])\r
+{\r
+ int i, j=0, i1, k1, l1, t, tj;\r
+ int k2, l2, j1, z1;\r
+ int k=0,l, cptcode;\r
+ int first=1, first1;\r
+ double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;\r
+ double **dnewm,**doldm;\r
+ double *xp;\r
+ double *gp, *gm;\r
+ double **gradg, **trgradg;\r
+ double **mu;\r
+ double age,agelim, cov[NCOVMAX];\r
+ double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */\r
+ int theta;\r
+ char fileresprob[FILENAMELENGTH];\r
+ char fileresprobcov[FILENAMELENGTH];\r
+ char fileresprobcor[FILENAMELENGTH];\r
+\r
+ double ***varpij;\r
+\r
+ strcpy(fileresprob,"prob"); \r
+ strcat(fileresprob,fileres);\r
+ if((ficresprob=fopen(fileresprob,"w"))==NULL) {\r
+ printf("Problem with resultfile: %s\n", fileresprob);\r
+ fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);\r
+ }\r
+ strcpy(fileresprobcov,"probcov"); \r
+ strcat(fileresprobcov,fileres);\r
+ if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {\r
+ printf("Problem with resultfile: %s\n", fileresprobcov);\r
+ fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);\r
+ }\r
+ strcpy(fileresprobcor,"probcor"); \r
+ strcat(fileresprobcor,fileres);\r
+ if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {\r
+ printf("Problem with resultfile: %s\n", fileresprobcor);\r
+ fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);\r
+ }\r
+ printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);\r
+ fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);\r
+ printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);\r
+ fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);\r
+ printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);\r
+ fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);\r
+ pstamp(ficresprob);\r
+ fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");\r
+ fprintf(ficresprob,"# Age");\r
+ pstamp(ficresprobcov);\r
+ fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");\r
+ fprintf(ficresprobcov,"# Age");\r
+ pstamp(ficresprobcor);\r
+ fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");\r
+ fprintf(ficresprobcor,"# Age");\r
+\r
+\r
+ for(i=1; i<=nlstate;i++)\r
+ for(j=1; j<=(nlstate+ndeath);j++){\r
+ fprintf(ficresprob," p%1d-%1d (SE)",i,j);\r
+ fprintf(ficresprobcov," p%1d-%1d ",i,j);\r
+ fprintf(ficresprobcor," p%1d-%1d ",i,j);\r
+ } \r
+ /* fprintf(ficresprob,"\n");\r
+ fprintf(ficresprobcov,"\n");\r
+ fprintf(ficresprobcor,"\n");\r
+ */\r
+ xp=vector(1,npar);\r
+ dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);\r
+ doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));\r
+ mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);\r
+ varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);\r
+ first=1;\r
+ fprintf(ficgp,"\n# Routine varprob");\r
+ fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");\r
+ fprintf(fichtm,"\n");\r
+\r
+ fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);\r
+ fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\\r
+ file %s<br>\n",optionfilehtmcov);\r
+ fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\\r
+and drawn. It helps understanding how is the covariance between two incidences.\\r
+ They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");\r
+ 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. \\r
+It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \\r
+would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \\r
+standard deviations wide on each axis. <br>\\r
+ Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\\r
+ and made the appropriate rotation to look at the uncorrelated principal directions.<br>\\r
+To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");\r
+\r
+ cov[1]=1;\r
+ tj=cptcoveff;\r
+ if (cptcovn<1) {tj=1;ncodemax[1]=1;}\r
+ j1=0;\r
+ for(t=1; t<=tj;t++){\r
+ for(i1=1; i1<=ncodemax[t];i1++){ \r
+ j1++;\r
+ if (cptcovn>0) {\r
+ fprintf(ficresprob, "\n#********** Variable "); \r
+ for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);\r
+ fprintf(ficresprob, "**********\n#\n");\r
+ fprintf(ficresprobcov, "\n#********** Variable "); \r
+ for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);\r
+ fprintf(ficresprobcov, "**********\n#\n");\r
+ \r
+ fprintf(ficgp, "\n#********** Variable "); \r
+ for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);\r
+ fprintf(ficgp, "**********\n#\n");\r
+ \r
+ \r
+ fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable "); \r
+ for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);\r
+ fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");\r
+ \r
+ fprintf(ficresprobcor, "\n#********** Variable "); \r
+ for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);\r
+ fprintf(ficresprobcor, "**********\n#"); \r
+ }\r
+ \r
+ for (age=bage; age<=fage; age ++){ \r
+ cov[2]=age;\r
+ for (k=1; k<=cptcovn;k++) {\r
+ cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];\r
+ }\r
+ for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];\r
+ for (k=1; k<=cptcovprod;k++)\r
+ cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];\r
+ \r
+ gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));\r
+ trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);\r
+ gp=vector(1,(nlstate)*(nlstate+ndeath));\r
+ gm=vector(1,(nlstate)*(nlstate+ndeath));\r
+ \r
+ for(theta=1; theta <=npar; theta++){\r
+ for(i=1; i<=npar; i++)\r
+ xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);\r
+ \r
+ pmij(pmmij,cov,ncovmodel,xp,nlstate);\r
+ \r
+ k=0;\r
+ for(i=1; i<= (nlstate); i++){\r
+ for(j=1; j<=(nlstate+ndeath);j++){\r
+ k=k+1;\r
+ gp[k]=pmmij[i][j];\r
+ }\r
+ }\r
+ \r
+ for(i=1; i<=npar; i++)\r
+ xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);\r
+ \r
+ pmij(pmmij,cov,ncovmodel,xp,nlstate);\r
+ k=0;\r
+ for(i=1; i<=(nlstate); i++){\r
+ for(j=1; j<=(nlstate+ndeath);j++){\r
+ k=k+1;\r
+ gm[k]=pmmij[i][j];\r
+ }\r
+ }\r
+ \r
+ for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) \r
+ gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta]; \r
+ }\r
+\r
+ for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)\r
+ for(theta=1; theta <=npar; theta++)\r
+ trgradg[j][theta]=gradg[theta][j];\r
+ \r
+ matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); \r
+ matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);\r
+ free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));\r
+ free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));\r
+ free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);\r
+ free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);\r
+\r
+ pmij(pmmij,cov,ncovmodel,x,nlstate);\r
+ \r
+ k=0;\r
+ for(i=1; i<=(nlstate); i++){\r
+ for(j=1; j<=(nlstate+ndeath);j++){\r
+ k=k+1;\r
+ mu[k][(int) age]=pmmij[i][j];\r
+ }\r
+ }\r
+ for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)\r
+ for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)\r
+ varpij[i][j][(int)age] = doldm[i][j];\r
+\r
+ /*printf("\n%d ",(int)age);\r
+ for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){\r
+ printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));\r
+ fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));\r
+ }*/\r
+\r
+ fprintf(ficresprob,"\n%d ",(int)age);\r
+ fprintf(ficresprobcov,"\n%d ",(int)age);\r
+ fprintf(ficresprobcor,"\n%d ",(int)age);\r
+\r
+ for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)\r
+ fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));\r
+ for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){\r
+ fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);\r
+ fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);\r
+ }\r
+ i=0;\r
+ for (k=1; k<=(nlstate);k++){\r
+ for (l=1; l<=(nlstate+ndeath);l++){ \r
+ i=i++;\r
+ fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);\r
+ fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);\r
+ for (j=1; j<=i;j++){\r
+ fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);\r
+ fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));\r
+ }\r
+ }\r
+ }/* end of loop for state */\r
+ } /* end of loop for age */\r
+\r
+ /* Confidence intervalle of pij */\r
+ /*\r
+ fprintf(ficgp,"\nset noparametric;unset label");\r
+ fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");\r
+ fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");\r
+ 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);\r
+ fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);\r
+ fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);\r
+ fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);\r
+ */\r
+\r
+ /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/\r
+ first1=1;\r
+ for (k2=1; k2<=(nlstate);k2++){\r
+ for (l2=1; l2<=(nlstate+ndeath);l2++){ \r
+ if(l2==k2) continue;\r
+ j=(k2-1)*(nlstate+ndeath)+l2;\r
+ for (k1=1; k1<=(nlstate);k1++){\r
+ for (l1=1; l1<=(nlstate+ndeath);l1++){ \r
+ if(l1==k1) continue;\r
+ i=(k1-1)*(nlstate+ndeath)+l1;\r
+ if(i<=j) continue;\r
+ for (age=bage; age<=fage; age ++){ \r
+ if ((int)age %5==0){\r
+ v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;\r
+ v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;\r
+ cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;\r
+ mu1=mu[i][(int) age]/stepm*YEARM ;\r
+ mu2=mu[j][(int) age]/stepm*YEARM;\r
+ c12=cv12/sqrt(v1*v2);\r
+ /* Computing eigen value of matrix of covariance */\r
+ lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;\r
+ lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;\r
+ /* Eigen vectors */\r
+ v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));\r
+ /*v21=sqrt(1.-v11*v11); *//* error */\r
+ v21=(lc1-v1)/cv12*v11;\r
+ v12=-v21;\r
+ v22=v11;\r
+ tnalp=v21/v11;\r
+ if(first1==1){\r
+ first1=0;\r
+ 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);\r
+ }\r
+ 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);\r
+ /*printf(fignu*/\r
+ /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */\r
+ /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */\r
+ if(first==1){\r
+ first=0;\r
+ fprintf(ficgp,"\nset parametric;unset label");\r
+ 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);\r
+ fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");\r
+ fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\\r
+ :<a href=\"%s%d%1d%1d-%1d%1d.png\">\\r
+%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\\r
+ subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\\r
+ subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);\r
+ fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);\r
+ fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);\r
+ fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);\r
+ fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);\r
+ fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);\r
+ 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",\\r
+ mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\\r
+ mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));\r
+ }else{\r
+ first=0;\r
+ fprintf(fichtmcov," %d (%.3f),",(int) age, c12);\r
+ fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);\r
+ fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);\r
+ 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",\\r
+ mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\\r
+ mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));\r
+ }/* if first */\r
+ } /* age mod 5 */\r
+ } /* end loop age */\r
+ fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);\r
+ first=1;\r
+ } /*l12 */\r
+ } /* k12 */\r
+ } /*l1 */\r
+ }/* k1 */\r
+ } /* loop covariates */\r
+ }\r
+ free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);\r
+ free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);\r
+ free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));\r
+ free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);\r
+ free_vector(xp,1,npar);\r
+ fclose(ficresprob);\r
+ fclose(ficresprobcov);\r
+ fclose(ficresprobcor);\r
+ fflush(ficgp);\r
+ fflush(fichtmcov);\r
+}\r
+\r
+\r
+/******************* Printing html file ***********/\r
+void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \\r
+ int lastpass, int stepm, int weightopt, char model[],\\r
+ int imx,int jmin, int jmax, double jmeanint,char rfileres[],\\r
+ int popforecast, int estepm ,\\r
+ double jprev1, double mprev1,double anprev1, \\r
+ double jprev2, double mprev2,double anprev2){\r
+ int jj1, k1, i1, cpt;\r
+\r
+ fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \\r
+ <li><a href='#secondorder'>Result files (second order (variance)</a>\n \\r
+</ul>");\r
+ fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \\r
+ - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",\r
+ jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));\r
+ fprintf(fichtm,"\\r
+ - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",\r
+ stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));\r
+ fprintf(fichtm,"\\r
+ - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",\r
+ subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));\r
+ fprintf(fichtm,"\\r
+ - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age: ei., eij . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \\r
+ <a href=\"%s\">%s</a> <br>\n",\r
+ estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));\r
+ fprintf(fichtm,"\\r
+ - Population projections by age and states: \\r
+ <a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));\r
+\r
+fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");\r
+\r
+ m=cptcoveff;\r
+ if (cptcovn < 1) {m=1;ncodemax[1]=1;}\r
+\r
+ jj1=0;\r
+ for(k1=1; k1<=m;k1++){\r
+ for(i1=1; i1<=ncodemax[k1];i1++){\r
+ jj1++;\r
+ if (cptcovn > 0) {\r
+ fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");\r
+ for (cpt=1; cpt<=cptcoveff;cpt++) \r
+ fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);\r
+ fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");\r
+ }\r
+ /* Pij */\r
+ fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \\r
+<img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); \r
+ /* Quasi-incidences */\r
+ fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\\r
+ before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \\r
+<img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); \r
+ /* Period (stable) prevalence in each health state */\r
+ for(cpt=1; cpt<nlstate;cpt++){\r
+ fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \\r
+<img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);\r
+ }\r
+ for(cpt=1; cpt<=nlstate;cpt++) {\r
+ fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \\r
+<img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);\r
+ }\r
+ } /* end i1 */\r
+ }/* End k1 */\r
+ fprintf(fichtm,"</ul>");\r
+\r
+\r
+ fprintf(fichtm,"\\r
+\n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\\r
+ - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);\r
+\r
+ fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",\r
+ subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));\r
+ fprintf(fichtm,"\\r
+ - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",\r
+ subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));\r
+\r
+ fprintf(fichtm,"\\r
+ - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",\r
+ subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));\r
+ fprintf(fichtm,"\\r
+ - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \\r
+ <a href=\"%s\">%s</a> <br>\n</li>",\r
+ estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));\r
+ fprintf(fichtm,"\\r
+ - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \\r
+ <a href=\"%s\">%s</a> <br>\n</li>",\r
+ estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));\r
+ fprintf(fichtm,"\\r
+ - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences (i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",\r
+ estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));\r
+ fprintf(fichtm,"\\r
+ - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <a href=\"%s\">%s</a> <br>\n",\r
+ subdirf2(fileres,"t"),subdirf2(fileres,"t"));\r
+ fprintf(fichtm,"\\r
+ - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\\r
+ subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));\r
+\r
+/* if(popforecast==1) fprintf(fichtm,"\n */\r
+/* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */\r
+/* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */\r
+/* <br>",fileres,fileres,fileres,fileres); */\r
+/* else */\r
+/* 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); */\r
+ fflush(fichtm);\r
+ fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");\r
+\r
+ m=cptcoveff;\r
+ if (cptcovn < 1) {m=1;ncodemax[1]=1;}\r
+\r
+ jj1=0;\r
+ for(k1=1; k1<=m;k1++){\r
+ for(i1=1; i1<=ncodemax[k1];i1++){\r
+ jj1++;\r
+ if (cptcovn > 0) {\r
+ fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");\r
+ for (cpt=1; cpt<=cptcoveff;cpt++) \r
+ fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);\r
+ fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");\r
+ }\r
+ for(cpt=1; cpt<=nlstate;cpt++) {\r
+ fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \\r
+prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\\r
+<img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1); \r
+ }\r
+ fprintf(fichtm,"\n<br>- Total life expectancy by age and \\r
+health expectancies in states (1) and (2): %s%d.png<br>\\r
+<img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);\r
+ } /* end i1 */\r
+ }/* End k1 */\r
+ fprintf(fichtm,"</ul>");\r
+ fflush(fichtm);\r
+}\r
+\r
+/******************* Gnuplot file **************/\r
+void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){\r
+\r
+ char dirfileres[132],optfileres[132];\r
+ int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;\r
+ int ng;\r
+/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */\r
+/* printf("Problem with file %s",optionfilegnuplot); */\r
+/* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */\r
+/* } */\r
+\r
+ /*#ifdef windows */\r
+ fprintf(ficgp,"cd \"%s\" \n",pathc);\r
+ /*#endif */\r
+ m=pow(2,cptcoveff);\r
+\r
+ strcpy(dirfileres,optionfilefiname);\r
+ strcpy(optfileres,"vpl");\r
+ /* 1eme*/\r
+ for (cpt=1; cpt<= nlstate ; cpt ++) {\r
+ for (k1=1; k1<= m ; k1 ++) {\r
+ fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);\r
+ fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);\r
+ fprintf(ficgp,"set xlabel \"Age\" \n\\r
+set ylabel \"Probability\" \n\\r
+set ter png small\n\\r
+set size 0.65,0.65\n\\r
+plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);\r
+\r
+ for (i=1; i<= nlstate ; i ++) {\r
+ if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");\r
+ else fprintf(ficgp," \%%*lf (\%%*lf)");\r
+ }\r
+ fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);\r
+ for (i=1; i<= nlstate ; i ++) {\r
+ if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");\r
+ else fprintf(ficgp," \%%*lf (\%%*lf)");\r
+ } \r
+ fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); \r
+ for (i=1; i<= nlstate ; i ++) {\r
+ if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");\r
+ else fprintf(ficgp," \%%*lf (\%%*lf)");\r
+ } \r
+ fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));\r
+ }\r
+ }\r
+ /*2 eme*/\r
+ \r
+ for (k1=1; k1<= m ; k1 ++) { \r
+ fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);\r
+ fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);\r
+ \r
+ for (i=1; i<= nlstate+1 ; i ++) {\r
+ k=2*i;\r
+ fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);\r
+ for (j=1; j<= nlstate+1 ; j ++) {\r
+ if (j==i) fprintf(ficgp," \%%lf (\%%lf)");\r
+ else fprintf(ficgp," \%%*lf (\%%*lf)");\r
+ } \r
+ if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");\r
+ else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);\r
+ fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);\r
+ for (j=1; j<= nlstate+1 ; j ++) {\r
+ if (j==i) fprintf(ficgp," \%%lf (\%%lf)");\r
+ else fprintf(ficgp," \%%*lf (\%%*lf)");\r
+ } \r
+ fprintf(ficgp,"\" t\"\" w l 0,");\r
+ fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);\r
+ for (j=1; j<= nlstate+1 ; j ++) {\r
+ if (j==i) fprintf(ficgp," \%%lf (\%%lf)");\r
+ else fprintf(ficgp," \%%*lf (\%%*lf)");\r
+ } \r
+ if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");\r
+ else fprintf(ficgp,"\" t\"\" w l 0,");\r
+ }\r
+ }\r
+ \r
+ /*3eme*/\r
+ \r
+ for (k1=1; k1<= m ; k1 ++) { \r
+ for (cpt=1; cpt<= nlstate ; cpt ++) {\r
+ /* k=2+nlstate*(2*cpt-2); */\r
+ k=2+(nlstate+1)*(cpt-1);\r
+ fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);\r
+ fprintf(ficgp,"set ter png small\n\\r
+set size 0.65,0.65\n\\r
+plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);\r
+ /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);\r
+ for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");\r
+ fprintf(ficgp,"\" t \"e%d1\" w l",cpt);\r
+ fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);\r
+ for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");\r
+ fprintf(ficgp,"\" t \"e%d1\" w l",cpt);\r
+ \r
+ */\r
+ for (i=1; i< nlstate ; i ++) {\r
+ fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);\r
+ /* 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);*/\r
+ \r
+ } \r
+ fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);\r
+ }\r
+ }\r
+ \r
+ /* CV preval stable (period) */\r
+ for (k1=1; k1<= m ; k1 ++) { \r
+ for (cpt=1; cpt<=nlstate ; cpt ++) {\r
+ k=3;\r
+ fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);\r
+ fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\\r
+set ter png small\nset size 0.65,0.65\n\\r
+unset log y\n\\r
+plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);\r
+ \r
+ for (i=1; i< nlstate ; i ++)\r
+ fprintf(ficgp,"+$%d",k+i+1);\r
+ fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);\r
+ \r
+ l=3+(nlstate+ndeath)*cpt;\r
+ fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);\r
+ for (i=1; i< nlstate ; i ++) {\r
+ l=3+(nlstate+ndeath)*cpt;\r
+ fprintf(ficgp,"+$%d",l+i+1);\r
+ }\r
+ fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1); \r
+ } \r
+ } \r
+ \r
+ /* proba elementaires */\r
+ for(i=1,jk=1; i <=nlstate; i++){\r
+ for(k=1; k <=(nlstate+ndeath); k++){\r
+ if (k != i) {\r
+ for(j=1; j <=ncovmodel; j++){\r
+ fprintf(ficgp,"p%d=%f ",jk,p[jk]);\r
+ jk++; \r
+ fprintf(ficgp,"\n");\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/\r
+ for(jk=1; jk <=m; jk++) {\r
+ fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); \r
+ if (ng==2)\r
+ fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");\r
+ else\r
+ fprintf(ficgp,"\nset title \"Probability\"\n");\r
+ fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);\r
+ i=1;\r
+ for(k2=1; k2<=nlstate; k2++) {\r
+ k3=i;\r
+ for(k=1; k<=(nlstate+ndeath); k++) {\r
+ if (k != k2){\r
+ if(ng==2)\r
+ fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);\r
+ else\r
+ fprintf(ficgp," exp(p%d+p%d*x",i,i+1);\r
+ ij=1;\r
+ for(j=3; j <=ncovmodel; j++) {\r
+ if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {\r
+ fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);\r
+ ij++;\r
+ }\r
+ else\r
+ fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);\r
+ }\r
+ fprintf(ficgp,")/(1");\r
+ \r
+ for(k1=1; k1 <=nlstate; k1++){ \r
+ fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);\r
+ ij=1;\r
+ for(j=3; j <=ncovmodel; j++){\r
+ if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {\r
+ fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);\r
+ ij++;\r
+ }\r
+ else\r
+ fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);\r
+ }\r
+ fprintf(ficgp,")");\r
+ }\r
+ fprintf(ficgp,") t \"p%d%d\" ", k2,k);\r
+ if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");\r
+ i=i+ncovmodel;\r
+ }\r
+ } /* end k */\r
+ } /* end k2 */\r
+ } /* end jk */\r
+ } /* end ng */\r
+ fflush(ficgp); \r
+} /* end gnuplot */\r
+\r
+\r
+/*************** Moving average **************/\r
+int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){\r
+\r
+ int i, cpt, cptcod;\r
+ int modcovmax =1;\r
+ int mobilavrange, mob;\r
+ double age;\r
+\r
+ modcovmax=2*cptcoveff;/* Max number of modalities. We suppose \r
+ a covariate has 2 modalities */\r
+ if (cptcovn<1) modcovmax=1; /* At least 1 pass */\r
+\r
+ if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){\r
+ if(mobilav==1) mobilavrange=5; /* default */\r
+ else mobilavrange=mobilav;\r
+ for (age=bage; age<=fage; age++)\r
+ for (i=1; i<=nlstate;i++)\r
+ for (cptcod=1;cptcod<=modcovmax;cptcod++)\r
+ mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];\r
+ /* We keep the original values on the extreme ages bage, fage and for \r
+ fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2\r
+ we use a 5 terms etc. until the borders are no more concerned. \r
+ */ \r
+ for (mob=3;mob <=mobilavrange;mob=mob+2){\r
+ for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){\r
+ for (i=1; i<=nlstate;i++){\r
+ for (cptcod=1;cptcod<=modcovmax;cptcod++){\r
+ mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];\r
+ for (cpt=1;cpt<=(mob-1)/2;cpt++){\r
+ mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];\r
+ mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];\r
+ }\r
+ mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;\r
+ }\r
+ }\r
+ }/* end age */\r
+ }/* end mob */\r
+ }else return -1;\r
+ return 0;\r
+}/* End movingaverage */\r
+\r
+\r
+/************** Forecasting ******************/\r
+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){\r
+ /* proj1, year, month, day of starting projection \r
+ agemin, agemax range of age\r
+ dateprev1 dateprev2 range of dates during which prevalence is computed\r
+ anproj2 year of en of projection (same day and month as proj1).\r
+ */\r
+ int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;\r
+ int *popage;\r
+ double agec; /* generic age */\r
+ double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;\r
+ double *popeffectif,*popcount;\r
+ double ***p3mat;\r
+ double ***mobaverage;\r
+ char fileresf[FILENAMELENGTH];\r
+\r
+ agelim=AGESUP;\r
+ prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);\r
+ \r
+ strcpy(fileresf,"f"); \r
+ strcat(fileresf,fileres);\r
+ if((ficresf=fopen(fileresf,"w"))==NULL) {\r
+ printf("Problem with forecast resultfile: %s\n", fileresf);\r
+ fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);\r
+ }\r
+ printf("Computing forecasting: result on file '%s' \n", fileresf);\r
+ fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);\r
+\r
+ if (cptcoveff==0) ncodemax[cptcoveff]=1;\r
+\r
+ if (mobilav!=0) {\r
+ mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);\r
+ if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){\r
+ fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);\r
+ printf(" Error in movingaverage mobilav=%d\n",mobilav);\r
+ }\r
+ }\r
+\r
+ stepsize=(int) (stepm+YEARM-1)/YEARM;\r
+ if (stepm<=12) stepsize=1;\r
+ if(estepm < stepm){\r
+ printf ("Problem %d lower than %d\n",estepm, stepm);\r
+ }\r
+ else hstepm=estepm; \r
+\r
+ hstepm=hstepm/stepm; \r
+ yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and\r
+ fractional in yp1 */\r
+ anprojmean=yp;\r
+ yp2=modf((yp1*12),&yp);\r
+ mprojmean=yp;\r
+ yp1=modf((yp2*30.5),&yp);\r
+ jprojmean=yp;\r
+ if(jprojmean==0) jprojmean=1;\r
+ if(mprojmean==0) jprojmean=1;\r
+\r
+ i1=cptcoveff;\r
+ if (cptcovn < 1){i1=1;}\r
+ \r
+ fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); \r
+ \r
+ fprintf(ficresf,"#****** Routine prevforecast **\n");\r
+\r
+/* if (h==(int)(YEARM*yearp)){ */\r
+ for(cptcov=1, k=0;cptcov<=i1;cptcov++){\r
+ for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){\r
+ k=k+1;\r
+ fprintf(ficresf,"\n#******");\r
+ for(j=1;j<=cptcoveff;j++) {\r
+ 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]]);\r
+ }\r
+ fprintf(ficresf,"******\n");\r
+ fprintf(ficresf,"# Covariate valuofcovar yearproj age");\r
+ for(j=1; j<=nlstate+ndeath;j++){ \r
+ for(i=1; i<=nlstate;i++) \r
+ fprintf(ficresf," p%d%d",i,j);\r
+ fprintf(ficresf," p.%d",j);\r
+ }\r
+ for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { \r
+ fprintf(ficresf,"\n");\r
+ fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp); \r
+\r
+ for (agec=fage; agec>=(ageminpar-1); agec--){ \r
+ nhstepm=(int) rint((agelim-agec)*YEARM/stepm); \r
+ nhstepm = nhstepm/hstepm; \r
+ p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);\r
+ oldm=oldms;savm=savms;\r
+ hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k); \r
+ \r
+ for (h=0; h<=nhstepm; h++){\r
+ if (h*hstepm/YEARM*stepm ==yearp) {\r
+ fprintf(ficresf,"\n");\r
+ for(j=1;j<=cptcoveff;j++) \r
+ fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);\r
+ fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);\r
+ } \r
+ for(j=1; j<=nlstate+ndeath;j++) {\r
+ ppij=0.;\r
+ for(i=1; i<=nlstate;i++) {\r
+ if (mobilav==1) \r
+ ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];\r
+ else {\r
+ ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];\r
+ }\r
+ if (h*hstepm/YEARM*stepm== yearp) {\r
+ fprintf(ficresf," %.3f", p3mat[i][j][h]);\r
+ }\r
+ } /* end i */\r
+ if (h*hstepm/YEARM*stepm==yearp) {\r
+ fprintf(ficresf," %.3f", ppij);\r
+ }\r
+ }/* end j */\r
+ } /* end h */\r
+ free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);\r
+ } /* end agec */\r
+ } /* end yearp */\r
+ } /* end cptcod */\r
+ } /* end cptcov */\r
+ \r
+ if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);\r
+\r
+ fclose(ficresf);\r
+}\r
+\r
+/************** Forecasting *****not tested NB*************/\r
+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){\r
+ \r
+ int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;\r
+ int *popage;\r
+ double calagedatem, agelim, kk1, kk2;\r
+ double *popeffectif,*popcount;\r
+ double ***p3mat,***tabpop,***tabpopprev;\r
+ double ***mobaverage;\r
+ char filerespop[FILENAMELENGTH];\r
+\r
+ tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);\r
+ tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);\r
+ agelim=AGESUP;\r
+ calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;\r
+ \r
+ prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);\r
+ \r
+ \r
+ strcpy(filerespop,"pop"); \r
+ strcat(filerespop,fileres);\r
+ if((ficrespop=fopen(filerespop,"w"))==NULL) {\r
+ printf("Problem with forecast resultfile: %s\n", filerespop);\r
+ fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);\r
+ }\r
+ printf("Computing forecasting: result on file '%s' \n", filerespop);\r
+ fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);\r
+\r
+ if (cptcoveff==0) ncodemax[cptcoveff]=1;\r
+\r
+ if (mobilav!=0) {\r
+ mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);\r
+ if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){\r
+ fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);\r
+ printf(" Error in movingaverage mobilav=%d\n",mobilav);\r
+ }\r
+ }\r
+\r
+ stepsize=(int) (stepm+YEARM-1)/YEARM;\r
+ if (stepm<=12) stepsize=1;\r
+ \r
+ agelim=AGESUP;\r
+ \r
+ hstepm=1;\r
+ hstepm=hstepm/stepm; \r
+ \r
+ if (popforecast==1) {\r
+ if((ficpop=fopen(popfile,"r"))==NULL) {\r
+ printf("Problem with population file : %s\n",popfile);exit(0);\r
+ fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);\r
+ } \r
+ popage=ivector(0,AGESUP);\r
+ popeffectif=vector(0,AGESUP);\r
+ popcount=vector(0,AGESUP);\r
+ \r
+ i=1; \r
+ while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;\r
+ \r
+ imx=i;\r
+ for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];\r
+ }\r
+\r
+ for(cptcov=1,k=0;cptcov<=i2;cptcov++){\r
+ for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){\r
+ k=k+1;\r
+ fprintf(ficrespop,"\n#******");\r
+ for(j=1;j<=cptcoveff;j++) {\r
+ fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);\r
+ }\r
+ fprintf(ficrespop,"******\n");\r
+ fprintf(ficrespop,"# Age");\r
+ for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);\r
+ if (popforecast==1) fprintf(ficrespop," [Population]");\r
+ \r
+ for (cpt=0; cpt<=0;cpt++) { \r
+ fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); \r
+ \r
+ for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ \r
+ nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); \r
+ nhstepm = nhstepm/hstepm; \r
+ \r
+ p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);\r
+ oldm=oldms;savm=savms;\r
+ hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); \r
+ \r
+ for (h=0; h<=nhstepm; h++){\r
+ if (h==(int) (calagedatem+YEARM*cpt)) {\r
+ fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);\r
+ } \r
+ for(j=1; j<=nlstate+ndeath;j++) {\r
+ kk1=0.;kk2=0;\r
+ for(i=1; i<=nlstate;i++) { \r
+ if (mobilav==1) \r
+ kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];\r
+ else {\r
+ kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];\r
+ }\r
+ }\r
+ if (h==(int)(calagedatem+12*cpt)){\r
+ tabpop[(int)(agedeb)][j][cptcod]=kk1;\r
+ /*fprintf(ficrespop," %.3f", kk1);\r
+ if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/\r
+ }\r
+ }\r
+ for(i=1; i<=nlstate;i++){\r
+ kk1=0.;\r
+ for(j=1; j<=nlstate;j++){\r
+ kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; \r
+ }\r
+ tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];\r
+ }\r
+\r
+ if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) \r
+ fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);\r
+ }\r
+ free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);\r
+ }\r
+ }\r
+ \r
+ /******/\r
+\r
+ for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { \r
+ fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt); \r
+ for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ \r
+ nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); \r
+ nhstepm = nhstepm/hstepm; \r
+ \r
+ p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);\r
+ oldm=oldms;savm=savms;\r
+ hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); \r
+ for (h=0; h<=nhstepm; h++){\r
+ if (h==(int) (calagedatem+YEARM*cpt)) {\r
+ fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);\r
+ } \r
+ for(j=1; j<=nlstate+ndeath;j++) {\r
+ kk1=0.;kk2=0;\r
+ for(i=1; i<=nlstate;i++) { \r
+ kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod]; \r
+ }\r
+ if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1); \r
+ }\r
+ }\r
+ free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);\r
+ }\r
+ }\r
+ } \r
+ }\r
+ \r
+ if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);\r
+\r
+ if (popforecast==1) {\r
+ free_ivector(popage,0,AGESUP);\r
+ free_vector(popeffectif,0,AGESUP);\r
+ free_vector(popcount,0,AGESUP);\r
+ }\r
+ free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);\r
+ free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);\r
+ fclose(ficrespop);\r
+} /* End of popforecast */\r
+\r
+int fileappend(FILE *fichier, char *optionfich)\r
+{\r
+ if((fichier=fopen(optionfich,"a"))==NULL) {\r
+ printf("Problem with file: %s\n", optionfich);\r
+ fprintf(ficlog,"Problem with file: %s\n", optionfich);\r
+ return (0);\r
+ }\r
+ fflush(fichier);\r
+ return (1);\r
+}\r
+\r
+\r
+/**************** function prwizard **********************/\r
+void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo)\r
+{\r
+\r
+ /* Wizard to print covariance matrix template */\r
+\r
+ char ca[32], cb[32], cc[32];\r
+ int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;\r
+ int numlinepar;\r
+\r
+ printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");\r
+ fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");\r
+ for(i=1; i <=nlstate; i++){\r
+ jj=0;\r
+ for(j=1; j <=nlstate+ndeath; j++){\r
+ if(j==i) continue;\r
+ jj++;\r
+ /*ca[0]= k+'a'-1;ca[1]='\0';*/\r
+ printf("%1d%1d",i,j);\r
+ fprintf(ficparo,"%1d%1d",i,j);\r
+ for(k=1; k<=ncovmodel;k++){\r
+ /* printf(" %lf",param[i][j][k]); */\r
+ /* fprintf(ficparo," %lf",param[i][j][k]); */\r
+ printf(" 0.");\r
+ fprintf(ficparo," 0.");\r
+ }\r
+ printf("\n");\r
+ fprintf(ficparo,"\n");\r
+ }\r
+ }\r
+ printf("# Scales (for hessian or gradient estimation)\n");\r
+ fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");\r
+ npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ \r
+ for(i=1; i <=nlstate; i++){\r
+ jj=0;\r
+ for(j=1; j <=nlstate+ndeath; j++){\r
+ if(j==i) continue;\r
+ jj++;\r
+ fprintf(ficparo,"%1d%1d",i,j);\r
+ printf("%1d%1d",i,j);\r
+ fflush(stdout);\r
+ for(k=1; k<=ncovmodel;k++){\r
+ /* printf(" %le",delti3[i][j][k]); */\r
+ /* fprintf(ficparo," %le",delti3[i][j][k]); */\r
+ printf(" 0.");\r
+ fprintf(ficparo," 0.");\r
+ }\r
+ numlinepar++;\r
+ printf("\n");\r
+ fprintf(ficparo,"\n");\r
+ }\r
+ }\r
+ printf("# Covariance matrix\n");\r
+/* # 121 Var(a12)\n\ */\r
+/* # 122 Cov(b12,a12) Var(b12)\n\ */\r
+/* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */\r
+/* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */\r
+/* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */\r
+/* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */\r
+/* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */\r
+/* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */\r
+ fflush(stdout);\r
+ fprintf(ficparo,"# Covariance matrix\n");\r
+ /* # 121 Var(a12)\n\ */\r
+ /* # 122 Cov(b12,a12) Var(b12)\n\ */\r
+ /* # ...\n\ */\r
+ /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */\r
+ \r
+ for(itimes=1;itimes<=2;itimes++){\r
+ jj=0;\r
+ for(i=1; i <=nlstate; i++){\r
+ for(j=1; j <=nlstate+ndeath; j++){\r
+ if(j==i) continue;\r
+ for(k=1; k<=ncovmodel;k++){\r
+ jj++;\r
+ ca[0]= k+'a'-1;ca[1]='\0';\r
+ if(itimes==1){\r
+ printf("#%1d%1d%d",i,j,k);\r
+ fprintf(ficparo,"#%1d%1d%d",i,j,k);\r
+ }else{\r
+ printf("%1d%1d%d",i,j,k);\r
+ fprintf(ficparo,"%1d%1d%d",i,j,k);\r
+ /* printf(" %.5le",matcov[i][j]); */\r
+ }\r
+ ll=0;\r
+ for(li=1;li <=nlstate; li++){\r
+ for(lj=1;lj <=nlstate+ndeath; lj++){\r
+ if(lj==li) continue;\r
+ for(lk=1;lk<=ncovmodel;lk++){\r
+ ll++;\r
+ if(ll<=jj){\r
+ cb[0]= lk +'a'-1;cb[1]='\0';\r
+ if(ll<jj){\r
+ if(itimes==1){\r
+ printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);\r
+ fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);\r
+ }else{\r
+ printf(" 0.");\r
+ fprintf(ficparo," 0.");\r
+ }\r
+ }else{\r
+ if(itimes==1){\r
+ printf(" Var(%s%1d%1d)",ca,i,j);\r
+ fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);\r
+ }else{\r
+ printf(" 0.");\r
+ fprintf(ficparo," 0.");\r
+ }\r
+ }\r
+ }\r
+ } /* end lk */\r
+ } /* end lj */\r
+ } /* end li */\r
+ printf("\n");\r
+ fprintf(ficparo,"\n");\r
+ numlinepar++;\r
+ } /* end k*/\r
+ } /*end j */\r
+ } /* end i */\r
+ } /* end itimes */\r
+\r
+} /* end of prwizard */\r
+/******************* Gompertz Likelihood ******************************/\r
+double gompertz(double x[])\r
+{ \r
+ double A,B,L=0.0,sump=0.,num=0.;\r
+ int i,n=0; /* n is the size of the sample */\r
+\r
+ for (i=0;i<=imx-1 ; i++) {\r
+ sump=sump+weight[i];\r
+ /* sump=sump+1;*/\r
+ num=num+1;\r
+ }\r
+ \r
+ \r
+ /* for (i=0; i<=imx; i++) \r
+ 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]);*/\r
+\r
+ for (i=1;i<=imx ; i++)\r
+ {\r
+ if (cens[i] == 1 && wav[i]>1)\r
+ A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));\r
+ \r
+ if (cens[i] == 0 && wav[i]>1)\r
+ A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))\r
+ +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM); \r
+ \r
+ /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */\r
+ if (wav[i] > 1 ) { /* ??? */\r
+ L=L+A*weight[i];\r
+ /* 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]);*/\r
+ }\r
+ }\r
+\r
+ /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/\r
+ \r
+ return -2*L*num/sump;\r
+}\r
+\r
+/******************* Printing html file ***********/\r
+void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \\r
+ int lastpass, int stepm, int weightopt, char model[],\\r
+ int imx, double p[],double **matcov,double agemortsup){\r
+ int i,k;\r
+\r
+ fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");\r
+ fprintf(fichtm," mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);\r
+ for (i=1;i<=2;i++) \r
+ 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]));\r
+ fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");\r
+ fprintf(fichtm,"</ul>");\r
+\r
+fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");\r
+\r
+ 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>");\r
+\r
+ for (k=agegomp;k<(agemortsup-2);k++) \r
+ 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]);\r
+\r
+ \r
+ fflush(fichtm);\r
+}\r
+\r
+/******************* Gnuplot file **************/\r
+void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){\r
+\r
+ char dirfileres[132],optfileres[132];\r
+ int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;\r
+ int ng;\r
+\r
+\r
+ /*#ifdef windows */\r
+ fprintf(ficgp,"cd \"%s\" \n",pathc);\r
+ /*#endif */\r
+\r
+\r
+ strcpy(dirfileres,optionfilefiname);\r
+ strcpy(optfileres,"vpl");\r
+ fprintf(ficgp,"set out \"graphmort.png\"\n "); \r
+ fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); \r
+ fprintf(ficgp, "set ter png small\n set log y\n"); \r
+ fprintf(ficgp, "set size 0.65,0.65\n");\r
+ fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);\r
+\r
+} \r
+\r
+\r
+\r
+\r
+\r
+/***********************************************/\r
+/**************** Main Program *****************/\r
+/***********************************************/\r
+\r
+int main(int argc, char *argv[])\r
+{\r
+ int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);\r
+ int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;\r
+ int linei, month, year,iout;\r
+ int jj, ll, li, lj, lk, imk;\r
+ int numlinepar=0; /* Current linenumber of parameter file */\r
+ int itimes;\r
+ int NDIM=2;\r
+\r
+ char ca[32], cb[32], cc[32];\r
+ char dummy[]=" ";\r
+ /* FILE *fichtm; *//* Html File */\r
+ /* FILE *ficgp;*/ /*Gnuplot File */\r
+ struct stat info;\r
+ double agedeb, agefin,hf;\r
+ double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;\r
+\r
+ double fret;\r
+ double **xi,tmp,delta;\r
+\r
+ double dum; /* Dummy variable */\r
+ double ***p3mat;\r
+ double ***mobaverage;\r
+ int *indx;\r
+ char line[MAXLINE], linepar[MAXLINE];\r
+ char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];\r
+ char pathr[MAXLINE], pathimach[MAXLINE]; \r
+ char **bp, *tok, *val; /* pathtot */\r
+ int firstobs=1, lastobs=10;\r
+ int sdeb, sfin; /* Status at beginning and end */\r
+ int c, h , cpt,l;\r
+ int ju,jl, mi;\r
+ int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;\r
+ int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; \r
+ int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */\r
+ int mobilav=0,popforecast=0;\r
+ int hstepm, nhstepm;\r
+ int agemortsup;\r
+ float sumlpop=0.;\r
+ double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;\r
+ double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;\r
+\r
+ double bage, fage, age, agelim, agebase;\r
+ double ftolpl=FTOL;\r
+ double **prlim;\r
+ double *severity;\r
+ double ***param; /* Matrix of parameters */\r
+ double *p;\r
+ double **matcov; /* Matrix of covariance */\r
+ double ***delti3; /* Scale */\r
+ double *delti; /* Scale */\r
+ double ***eij, ***vareij;\r
+ double **varpl; /* Variances of prevalence limits by age */\r
+ double *epj, vepp;\r
+ double kk1, kk2;\r
+ double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;\r
+ double **ximort;\r
+ char *alph[]={"a","a","b","c","d","e"}, str[4];\r
+ int *dcwave;\r
+\r
+ char z[1]="c", occ;\r
+\r
+ char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];\r
+ char *strt, strtend[80];\r
+ char *stratrunc;\r
+ int lstra;\r
+\r
+ long total_usecs;\r
+ \r
+/* setlocale (LC_ALL, ""); */\r
+/* bindtextdomain (PACKAGE, LOCALEDIR); */\r
+/* textdomain (PACKAGE); */\r
+/* setlocale (LC_CTYPE, ""); */\r
+/* setlocale (LC_MESSAGES, ""); */\r
+\r
+ /* gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */\r
+ (void) gettimeofday(&start_time,&tzp);\r
+ curr_time=start_time;\r
+ tm = *localtime(&start_time.tv_sec);\r
+ tmg = *gmtime(&start_time.tv_sec);\r
+ strcpy(strstart,asctime(&tm));\r
+\r
+/* printf("Localtime (at start)=%s",strstart); */\r
+/* tp.tv_sec = tp.tv_sec +86400; */\r
+/* tm = *localtime(&start_time.tv_sec); */\r
+/* tmg.tm_year=tmg.tm_year +dsign*dyear; */\r
+/* tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */\r
+/* tmg.tm_hour=tmg.tm_hour + 1; */\r
+/* tp.tv_sec = mktime(&tmg); */\r
+/* strt=asctime(&tmg); */\r
+/* printf("Time(after) =%s",strstart); */\r
+/* (void) time (&time_value);\r
+* printf("time=%d,t-=%d\n",time_value,time_value-86400);\r
+* tm = *localtime(&time_value);\r
+* strstart=asctime(&tm);\r
+* printf("tim_value=%d,asctime=%s\n",time_value,strstart); \r
+*/\r
+\r
+ nberr=0; /* Number of errors and warnings */\r
+ nbwarn=0;\r
+ getcwd(pathcd, size);\r
+\r
+ printf("\n%s\n%s",version,fullversion);\r
+ if(argc <=1){\r
+ printf("\nEnter the parameter file name: ");\r
+ fgets(pathr,FILENAMELENGTH,stdin);\r
+ i=strlen(pathr);\r
+ if(pathr[i-1]=='\n')\r
+ pathr[i-1]='\0';\r
+ for (tok = pathr; tok != NULL; ){\r
+ printf("Pathr |%s|\n",pathr);\r
+ while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');\r
+ printf("val= |%s| pathr=%s\n",val,pathr);\r
+ strcpy (pathtot, val);\r
+ if(pathr[0] == '\0') break; /* Dirty */\r
+ }\r
+ }\r
+ else{\r
+ strcpy(pathtot,argv[1]);\r
+ }\r
+ /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/\r
+ /*cygwin_split_path(pathtot,path,optionfile);\r
+ printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/\r
+ /* cutv(path,optionfile,pathtot,'\\');*/\r
+\r
+ /* Split argv[0], imach program to get pathimach */\r
+ printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);\r
+ split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);\r
+ printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);\r
+ /* strcpy(pathimach,argv[0]); */\r
+ /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */\r
+ split(pathtot,path,optionfile,optionfilext,optionfilefiname);\r
+ printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);\r
+ chdir(path); /* Can be a relative path */\r
+ if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */\r
+ printf("Current directory %s!\n",pathcd);\r
+ strcpy(command,"mkdir ");\r
+ strcat(command,optionfilefiname);\r
+ if((outcmd=system(command)) != 0){\r
+ printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);\r
+ /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */\r
+ /* fclose(ficlog); */\r
+/* exit(1); */\r
+ }\r
+/* if((imk=mkdir(optionfilefiname))<0){ */\r
+/* perror("mkdir"); */\r
+/* } */\r
+\r
+ /*-------- arguments in the command line --------*/\r
+\r
+ /* Log file */\r
+ strcat(filelog, optionfilefiname);\r
+ strcat(filelog,".log"); /* */\r
+ if((ficlog=fopen(filelog,"w"))==NULL) {\r
+ printf("Problem with logfile %s\n",filelog);\r
+ goto end;\r
+ }\r
+ fprintf(ficlog,"Log filename:%s\n",filelog);\r
+ fprintf(ficlog,"\n%s\n%s",version,fullversion);\r
+ fprintf(ficlog,"\nEnter the parameter file name: \n");\r
+ fprintf(ficlog,"pathimach=%s\npathtot=%s\n\\r
+ path=%s \n\\r
+ optionfile=%s\n\\r
+ optionfilext=%s\n\\r
+ optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);\r
+\r
+ printf("Local time (at start):%s",strstart);\r
+ fprintf(ficlog,"Local time (at start): %s",strstart);\r
+ fflush(ficlog);\r
+/* (void) gettimeofday(&curr_time,&tzp); */\r
+/* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */\r
+\r
+ /* */\r
+ strcpy(fileres,"r");\r
+ strcat(fileres, optionfilefiname);\r
+ strcat(fileres,".txt"); /* Other files have txt extension */\r
+\r
+ /*---------arguments file --------*/\r
+\r
+ if((ficpar=fopen(optionfile,"r"))==NULL) {\r
+ printf("Problem with optionfile %s\n",optionfile);\r
+ fprintf(ficlog,"Problem with optionfile %s\n",optionfile);\r
+ fflush(ficlog);\r
+ goto end;\r
+ }\r
+\r
+\r
+\r
+ strcpy(filereso,"o");\r
+ strcat(filereso,fileres);\r
+ if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */\r
+ printf("Problem with Output resultfile: %s\n", filereso);\r
+ fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);\r
+ fflush(ficlog);\r
+ goto end;\r
+ }\r
+\r
+ /* Reads comments: lines beginning with '#' */\r
+ numlinepar=0;\r
+ while((c=getc(ficpar))=='#' && c!= EOF){\r
+ ungetc(c,ficpar);\r
+ fgets(line, MAXLINE, ficpar);\r
+ numlinepar++;\r
+ puts(line);\r
+ fputs(line,ficparo);\r
+ fputs(line,ficlog);\r
+ }\r
+ ungetc(c,ficpar);\r
+\r
+ 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);\r
+ numlinepar++;\r
+ 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);\r
+ 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);\r
+ 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);\r
+ fflush(ficlog);\r
+ while((c=getc(ficpar))=='#' && c!= EOF){\r
+ ungetc(c,ficpar);\r
+ fgets(line, MAXLINE, ficpar);\r
+ numlinepar++;\r
+ puts(line);\r
+ fputs(line,ficparo);\r
+ fputs(line,ficlog);\r
+ }\r
+ ungetc(c,ficpar);\r
+\r
+ \r
+ covar=matrix(0,NCOVMAX,1,n); \r
+ cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/\r
+ if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;\r
+\r
+ ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */\r
+ nvar=ncovmodel-1; /* Suppressing age as a basic covariate */\r
+ npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/\r
+\r
+ delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);\r
+ delti=delti3[1][1];\r
+ /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/\r
+ if(mle==-1){ /* Print a wizard for help writing covariance matrix */\r
+ prwizard(ncovmodel, nlstate, ndeath, model, ficparo);\r
+ printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);\r
+ fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);\r
+ free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); \r
+ fclose (ficparo);\r
+ fclose (ficlog);\r
+ goto end;\r
+ exit(0);\r
+ }\r
+ else if(mle==-3) {\r
+ prwizard(ncovmodel, nlstate, ndeath, model, ficparo);\r
+ printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);\r
+ fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);\r
+ param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);\r
+ matcov=matrix(1,npar,1,npar);\r
+ }\r
+ else{\r
+ /* Read guess parameters */\r
+ /* Reads comments: lines beginning with '#' */\r
+ while((c=getc(ficpar))=='#' && c!= EOF){\r
+ ungetc(c,ficpar);\r
+ fgets(line, MAXLINE, ficpar);\r
+ numlinepar++;\r
+ puts(line);\r
+ fputs(line,ficparo);\r
+ fputs(line,ficlog);\r
+ }\r
+ ungetc(c,ficpar);\r
+ \r
+ param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);\r
+ for(i=1; i <=nlstate; i++){\r
+ j=0;\r
+ for(jj=1; jj <=nlstate+ndeath; jj++){\r
+ if(jj==i) continue;\r
+ j++;\r
+ fscanf(ficpar,"%1d%1d",&i1,&j1);\r
+ if ((i1 != i) && (j1 != j)){\r
+ printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \\r
+It might be a problem of design; if ncovcol and the model are correct\n \\r
+run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);\r
+ exit(1);\r
+ }\r
+ fprintf(ficparo,"%1d%1d",i1,j1);\r
+ if(mle==1)\r
+ printf("%1d%1d",i,j);\r
+ fprintf(ficlog,"%1d%1d",i,j);\r
+ for(k=1; k<=ncovmodel;k++){\r
+ fscanf(ficpar," %lf",¶m[i][j][k]);\r
+ if(mle==1){\r
+ printf(" %lf",param[i][j][k]);\r
+ fprintf(ficlog," %lf",param[i][j][k]);\r
+ }\r
+ else\r
+ fprintf(ficlog," %lf",param[i][j][k]);\r
+ fprintf(ficparo," %lf",param[i][j][k]);\r
+ }\r
+ fscanf(ficpar,"\n");\r
+ numlinepar++;\r
+ if(mle==1)\r
+ printf("\n");\r
+ fprintf(ficlog,"\n");\r
+ fprintf(ficparo,"\n");\r
+ }\r
+ } \r
+ fflush(ficlog);\r
+\r
+ p=param[1][1];\r
+ \r
+ /* Reads comments: lines beginning with '#' */\r
+ while((c=getc(ficpar))=='#' && c!= EOF){\r
+ ungetc(c,ficpar);\r
+ fgets(line, MAXLINE, ficpar);\r
+ numlinepar++;\r
+ puts(line);\r
+ fputs(line,ficparo);\r
+ fputs(line,ficlog);\r
+ }\r
+ ungetc(c,ficpar);\r
+\r
+ for(i=1; i <=nlstate; i++){\r
+ for(j=1; j <=nlstate+ndeath-1; j++){\r
+ fscanf(ficpar,"%1d%1d",&i1,&j1);\r
+ if ((i1-i)*(j1-j)!=0){\r
+ printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);\r
+ exit(1);\r
+ }\r
+ printf("%1d%1d",i,j);\r
+ fprintf(ficparo,"%1d%1d",i1,j1);\r
+ fprintf(ficlog,"%1d%1d",i1,j1);\r
+ for(k=1; k<=ncovmodel;k++){\r
+ fscanf(ficpar,"%le",&delti3[i][j][k]);\r
+ printf(" %le",delti3[i][j][k]);\r
+ fprintf(ficparo," %le",delti3[i][j][k]);\r
+ fprintf(ficlog," %le",delti3[i][j][k]);\r
+ }\r
+ fscanf(ficpar,"\n");\r
+ numlinepar++;\r
+ printf("\n");\r
+ fprintf(ficparo,"\n");\r
+ fprintf(ficlog,"\n");\r
+ }\r
+ }\r
+ fflush(ficlog);\r
+\r
+ delti=delti3[1][1];\r
+\r
+\r
+ /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */\r
+ \r
+ /* Reads comments: lines beginning with '#' */\r
+ while((c=getc(ficpar))=='#' && c!= EOF){\r
+ ungetc(c,ficpar);\r
+ fgets(line, MAXLINE, ficpar);\r
+ numlinepar++;\r
+ puts(line);\r
+ fputs(line,ficparo);\r
+ fputs(line,ficlog);\r
+ }\r
+ ungetc(c,ficpar);\r
+ \r
+ matcov=matrix(1,npar,1,npar);\r
+ for(i=1; i <=npar; i++){\r
+ fscanf(ficpar,"%s",&str);\r
+ if(mle==1)\r
+ printf("%s",str);\r
+ fprintf(ficlog,"%s",str);\r
+ fprintf(ficparo,"%s",str);\r
+ for(j=1; j <=i; j++){\r
+ fscanf(ficpar," %le",&matcov[i][j]);\r
+ if(mle==1){\r
+ printf(" %.5le",matcov[i][j]);\r
+ }\r
+ fprintf(ficlog," %.5le",matcov[i][j]);\r
+ fprintf(ficparo," %.5le",matcov[i][j]);\r
+ }\r
+ fscanf(ficpar,"\n");\r
+ numlinepar++;\r
+ if(mle==1)\r
+ printf("\n");\r
+ fprintf(ficlog,"\n");\r
+ fprintf(ficparo,"\n");\r
+ }\r
+ for(i=1; i <=npar; i++)\r
+ for(j=i+1;j<=npar;j++)\r
+ matcov[i][j]=matcov[j][i];\r
+ \r
+ if(mle==1)\r
+ printf("\n");\r
+ fprintf(ficlog,"\n");\r
+ \r
+ fflush(ficlog);\r
+ \r
+ /*-------- Rewriting parameter file ----------*/\r
+ strcpy(rfileres,"r"); /* "Rparameterfile */\r
+ strcat(rfileres,optionfilefiname); /* Parameter file first name*/\r
+ strcat(rfileres,"."); /* */\r
+ strcat(rfileres,optionfilext); /* Other files have txt extension */\r
+ if((ficres =fopen(rfileres,"w"))==NULL) {\r
+ printf("Problem writing new parameter file: %s\n", fileres);goto end;\r
+ fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;\r
+ }\r
+ fprintf(ficres,"#%s\n",version);\r
+ } /* End of mle != -3 */\r
+\r
+ /*-------- data file ----------*/\r
+ if((fic=fopen(datafile,"r"))==NULL) {\r
+ printf("Problem while opening datafile: %s\n", datafile);goto end;\r
+ fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;\r
+ }\r
+\r
+ n= lastobs;\r
+ severity = vector(1,maxwav);\r
+ outcome=imatrix(1,maxwav+1,1,n);\r
+ num=lvector(1,n);\r
+ moisnais=vector(1,n);\r
+ annais=vector(1,n);\r
+ moisdc=vector(1,n);\r
+ andc=vector(1,n);\r
+ agedc=vector(1,n);\r
+ cod=ivector(1,n);\r
+ weight=vector(1,n);\r
+ for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */\r
+ mint=matrix(1,maxwav,1,n);\r
+ anint=matrix(1,maxwav,1,n);\r
+ s=imatrix(1,maxwav+1,1,n);\r
+ tab=ivector(1,NCOVMAX);\r
+ ncodemax=ivector(1,8);\r
+\r
+ i=1;\r
+ linei=0;\r
+ while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {\r
+ linei=linei+1;\r
+ for(j=strlen(line); j>=0;j--){ /* Untabifies line */\r
+ if(line[j] == '\t')\r
+ line[j] = ' ';\r
+ }\r
+ for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){\r
+ ;\r
+ };\r
+ line[j+1]=0; /* Trims blanks at end of line */\r
+ if(line[0]=='#'){\r
+ fprintf(ficlog,"Comment line\n%s\n",line);\r
+ printf("Comment line\n%s\n",line);\r
+ continue;\r
+ }\r
+\r
+ for (j=maxwav;j>=1;j--){\r
+ cutv(stra, strb,line,' '); \r
+ errno=0;\r
+ lval=strtol(strb,&endptr,10); \r
+ /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/\r
+ if( strb[0]=='\0' || (*endptr != '\0')){\r
+ 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);\r
+ exit(1);\r
+ }\r
+ s[j][i]=lval;\r
+ \r
+ strcpy(line,stra);\r
+ cutv(stra, strb,line,' ');\r
+ if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){\r
+ }\r
+ else if(iout=sscanf(strb,"%s.") != 0){\r
+ month=99;\r
+ year=9999;\r
+ }else{\r
+ 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);\r
+ exit(1);\r
+ }\r
+ anint[j][i]= (double) year; \r
+ mint[j][i]= (double)month; \r
+ strcpy(line,stra);\r
+ } /* ENd Waves */\r
+ \r
+ cutv(stra, strb,line,' '); \r
+ if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){\r
+ }\r
+ else if(iout=sscanf(strb,"%s.",dummy) != 0){\r
+ month=99;\r
+ year=9999;\r
+ }else{\r
+ 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);\r
+ exit(1);\r
+ }\r
+ andc[i]=(double) year; \r
+ moisdc[i]=(double) month; \r
+ strcpy(line,stra);\r
+ \r
+ cutv(stra, strb,line,' '); \r
+ if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){\r
+ }\r
+ else if(iout=sscanf(strb,"%s.") != 0){\r
+ month=99;\r
+ year=9999;\r
+ }else{\r
+ 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);\r
+ exit(1);\r
+ }\r
+ annais[i]=(double)(year);\r
+ moisnais[i]=(double)(month); \r
+ strcpy(line,stra);\r
+ \r
+ cutv(stra, strb,line,' '); \r
+ errno=0;\r
+ dval=strtod(strb,&endptr); \r
+ if( strb[0]=='\0' || (*endptr != '\0')){\r
+ printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);\r
+ exit(1);\r
+ }\r
+ weight[i]=dval; \r
+ strcpy(line,stra);\r
+ \r
+ for (j=ncovcol;j>=1;j--){\r
+ cutv(stra, strb,line,' '); \r
+ errno=0;\r
+ lval=strtol(strb,&endptr,10); \r
+ if( strb[0]=='\0' || (*endptr != '\0')){\r
+ 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);\r
+ exit(1);\r
+ }\r
+ if(lval <-1 || lval >1){\r
+ printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \\r
+ Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \\r
+ for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \\r
+ For example, for multinomial values like 1, 2 and 3,\n \\r
+ build V1=0 V2=0 for the reference value (1),\n \\r
+ V1=1 V2=0 for (2) \n \\r
+ and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \\r
+ output of IMaCh is often meaningless.\n \\r
+ Exiting.\n",lval,linei, i,line,j);\r
+ exit(1);\r
+ }\r
+ covar[j][i]=(double)(lval);\r
+ strcpy(line,stra);\r
+ } \r
+ lstra=strlen(stra);\r
+ \r
+ if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */\r
+ stratrunc = &(stra[lstra-9]);\r
+ num[i]=atol(stratrunc);\r
+ }\r
+ else\r
+ num[i]=atol(stra);\r
+ /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){\r
+ 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;}*/\r
+ \r
+ i=i+1;\r
+ } /* End loop reading data */\r
+ fclose(fic);\r
+ /* printf("ii=%d", ij);\r
+ scanf("%d",i);*/\r
+ imx=i-1; /* Number of individuals */\r
+\r
+ /* for (i=1; i<=imx; i++){\r
+ if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;\r
+ if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;\r
+ if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;\r
+ }*/\r
+ /* for (i=1; i<=imx; i++){\r
+ if (s[4][i]==9) s[4][i]=-1; \r
+ 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]));}*/\r
+ \r
+ /* for (i=1; i<=imx; i++) */\r
+ \r
+ /*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;\r
+ else weight[i]=1;*/\r
+\r
+ /* Calculation of the number of parameters from char model */\r
+ Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */\r
+ Tprod=ivector(1,15); \r
+ Tvaraff=ivector(1,15); \r
+ Tvard=imatrix(1,15,1,2);\r
+ Tage=ivector(1,15); \r
+ \r
+ if (strlen(model) >1){ /* If there is at least 1 covariate */\r
+ j=0, j1=0, k1=1, k2=1;\r
+ j=nbocc(model,'+'); /* j=Number of '+' */\r
+ j1=nbocc(model,'*'); /* j1=Number of '*' */\r
+ cptcovn=j+1; \r
+ cptcovprod=j1; /*Number of products */\r
+ \r
+ strcpy(modelsav,model); \r
+ if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){\r
+ printf("Error. Non available option model=%s ",model);\r
+ fprintf(ficlog,"Error. Non available option model=%s ",model);\r
+ goto end;\r
+ }\r
+ \r
+ /* This loop fills the array Tvar from the string 'model'.*/\r
+\r
+ for(i=(j+1); i>=1;i--){\r
+ cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ \r
+ if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */\r
+ /* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/\r
+ /*scanf("%d",i);*/\r
+ if (strchr(strb,'*')) { /* Model includes a product */\r
+ cutv(strd,strc,strb,'*'); /* strd*strc Vm*Vn (if not *age)*/\r
+ if (strcmp(strc,"age")==0) { /* Vn*age */\r
+ cptcovprod--;\r
+ cutv(strb,stre,strd,'V');\r
+ Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/\r
+ cptcovage++;\r
+ Tage[cptcovage]=i;\r
+ /*printf("stre=%s ", stre);*/\r
+ }\r
+ else if (strcmp(strd,"age")==0) { /* or age*Vn */\r
+ cptcovprod--;\r
+ cutv(strb,stre,strc,'V');\r
+ Tvar[i]=atoi(stre);\r
+ cptcovage++;\r
+ Tage[cptcovage]=i;\r
+ }\r
+ else { /* Age is not in the model */\r
+ cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/\r
+ Tvar[i]=ncovcol+k1;\r
+ cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */\r
+ Tprod[k1]=i;\r
+ Tvard[k1][1]=atoi(strc); /* m*/\r
+ Tvard[k1][2]=atoi(stre); /* n */\r
+ Tvar[cptcovn+k2]=Tvard[k1][1];\r
+ Tvar[cptcovn+k2+1]=Tvard[k1][2]; \r
+ for (k=1; k<=lastobs;k++) \r
+ covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];\r
+ k1++;\r
+ k2=k2+2;\r
+ }\r
+ }\r
+ else { /* no more sum */\r
+ /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/\r
+ /* scanf("%d",i);*/\r
+ cutv(strd,strc,strb,'V');\r
+ Tvar[i]=atoi(strc);\r
+ }\r
+ strcpy(modelsav,stra); \r
+ /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);\r
+ scanf("%d",i);*/\r
+ } /* end of loop + */\r
+ } /* end model */\r
+ \r
+ /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.\r
+ If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/\r
+\r
+ /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);\r
+ printf("cptcovprod=%d ", cptcovprod);\r
+ fprintf(ficlog,"cptcovprod=%d ", cptcovprod);\r
+\r
+ scanf("%d ",i);*/\r
+\r
+ /* if(mle==1){*/\r
+ if (weightopt != 1) { /* Maximisation without weights*/\r
+ for(i=1;i<=n;i++) weight[i]=1.0;\r
+ }\r
+ /*-calculation of age at interview from date of interview and age at death -*/\r
+ agev=matrix(1,maxwav,1,imx);\r
+\r
+ for (i=1; i<=imx; i++) {\r
+ for(m=2; (m<= maxwav); m++) {\r
+ if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){\r
+ anint[m][i]=9999;\r
+ s[m][i]=-1;\r
+ }\r
+ if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){\r
+ nberr++;\r
+ 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);\r
+ 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);\r
+ s[m][i]=-1;\r
+ }\r
+ if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){\r
+ nberr++;\r
+ 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]); \r
+ 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]); \r
+ s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */\r
+ }\r
+ }\r
+ }\r
+\r
+ for (i=1; i<=imx; i++) {\r
+ agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);\r
+ for(m=firstpass; (m<= lastpass); m++){\r
+ if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){\r
+ if (s[m][i] >= nlstate+1) {\r
+ if(agedc[i]>0)\r
+ if((int)moisdc[i]!=99 && (int)andc[i]!=9999)\r
+ agev[m][i]=agedc[i];\r
+ /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/\r
+ else {\r
+ if ((int)andc[i]!=9999){\r
+ nbwarn++;\r
+ printf("Warning negative age at death: %ld line:%d\n",num[i],i);\r
+ fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);\r
+ agev[m][i]=-1;\r
+ }\r
+ }\r
+ }\r
+ else if(s[m][i] !=9){ /* Standard case, age in fractional\r
+ years but with the precision of a month */\r
+ agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);\r
+ if((int)mint[m][i]==99 || (int)anint[m][i]==9999)\r
+ agev[m][i]=1;\r
+ else if(agev[m][i] <agemin){ \r
+ agemin=agev[m][i];\r
+ /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/\r
+ }\r
+ else if(agev[m][i] >agemax){\r
+ agemax=agev[m][i];\r
+ /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/\r
+ }\r
+ /*agev[m][i]=anint[m][i]-annais[i];*/\r
+ /* agev[m][i] = age[i]+2*m;*/\r
+ }\r
+ else { /* =9 */\r
+ agev[m][i]=1;\r
+ s[m][i]=-1;\r
+ }\r
+ }\r
+ else /*= 0 Unknown */\r
+ agev[m][i]=1;\r
+ }\r
+ \r
+ }\r
+ for (i=1; i<=imx; i++) {\r
+ for(m=firstpass; (m<=lastpass); m++){\r
+ if (s[m][i] > (nlstate+ndeath)) {\r
+ nberr++;\r
+ 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); \r
+ 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); \r
+ goto end;\r
+ }\r
+ }\r
+ }\r
+\r
+ /*for (i=1; i<=imx; i++){\r
+ for (m=firstpass; (m<lastpass); m++){\r
+ printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);\r
+}\r
+\r
+}*/\r
+\r
+\r
+ printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);\r
+ fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); \r
+\r
+ agegomp=(int)agemin;\r
+ free_vector(severity,1,maxwav);\r
+ free_imatrix(outcome,1,maxwav+1,1,n);\r
+ free_vector(moisnais,1,n);\r
+ free_vector(annais,1,n);\r
+ /* free_matrix(mint,1,maxwav,1,n);\r
+ free_matrix(anint,1,maxwav,1,n);*/\r
+ free_vector(moisdc,1,n);\r
+ free_vector(andc,1,n);\r
+\r
+ \r
+ wav=ivector(1,imx);\r
+ dh=imatrix(1,lastpass-firstpass+1,1,imx);\r
+ bh=imatrix(1,lastpass-firstpass+1,1,imx);\r
+ mw=imatrix(1,lastpass-firstpass+1,1,imx);\r
+ \r
+ /* Concatenates waves */\r
+ concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);\r
+\r
+ /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */\r
+\r
+ Tcode=ivector(1,100);\r
+ nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); \r
+ ncodemax[1]=1;\r
+ if (cptcovn > 0) tricode(Tvar,nbcode,imx);\r
+ \r
+ codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of \r
+ the estimations*/\r
+ h=0;\r
+ m=pow(2,cptcoveff);\r
+ \r
+ for(k=1;k<=cptcoveff; k++){\r
+ for(i=1; i <=(m/pow(2,k));i++){\r
+ for(j=1; j <= ncodemax[k]; j++){\r
+ for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){\r
+ h++;\r
+ if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;\r
+ /* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/\r
+ } \r
+ }\r
+ }\r
+ } \r
+ /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); \r
+ codtab[1][2]=1;codtab[2][2]=2; */\r
+ /* for(i=1; i <=m ;i++){ \r
+ for(k=1; k <=cptcovn; k++){\r
+ printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);\r
+ }\r
+ printf("\n");\r
+ }\r
+ scanf("%d",i);*/\r
+ \r
+ /*------------ gnuplot -------------*/\r
+ strcpy(optionfilegnuplot,optionfilefiname);\r
+ if(mle==-3)\r
+ strcat(optionfilegnuplot,"-mort");\r
+ strcat(optionfilegnuplot,".gp");\r
+\r
+ if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {\r
+ printf("Problem with file %s",optionfilegnuplot);\r
+ }\r
+ else{\r
+ fprintf(ficgp,"\n# %s\n", version); \r
+ fprintf(ficgp,"# %s\n", optionfilegnuplot); \r
+ fprintf(ficgp,"set missing 'NaNq'\n");\r
+ }\r
+ /* fclose(ficgp);*/\r
+ /*--------- index.htm --------*/\r
+\r
+ strcpy(optionfilehtm,optionfilefiname); /* Main html file */\r
+ if(mle==-3)\r
+ strcat(optionfilehtm,"-mort");\r
+ strcat(optionfilehtm,".htm");\r
+ if((fichtm=fopen(optionfilehtm,"w"))==NULL) {\r
+ printf("Problem with %s \n",optionfilehtm), exit(0);\r
+ }\r
+\r
+ strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */\r
+ strcat(optionfilehtmcov,"-cov.htm");\r
+ if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL) {\r
+ printf("Problem with %s \n",optionfilehtmcov), exit(0);\r
+ }\r
+ else{\r
+ fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \\r
+<hr size=\"2\" color=\"#EC5E5E\"> \n\\r
+Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\\r
+ optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);\r
+ }\r
+\r
+ fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \\r
+<hr size=\"2\" color=\"#EC5E5E\"> \n\\r
+Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\\r
+\n\\r
+<hr size=\"2\" color=\"#EC5E5E\">\\r
+ <ul><li><h4>Parameter files</h4>\n\\r
+ - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\\r
+ - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\\r
+ - Log file of the run: <a href=\"%s\">%s</a><br>\n\\r
+ - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\\r
+ - Date and time at start: %s</ul>\n",\\r
+ optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\\r
+ optionfilefiname,optionfilext,optionfilefiname,optionfilext,\\r
+ fileres,fileres,\\r
+ filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);\r
+ fflush(fichtm);\r
+\r
+ strcpy(pathr,path);\r
+ strcat(pathr,optionfilefiname);\r
+ chdir(optionfilefiname); /* Move to directory named optionfile */\r
+ \r
+ /* Calculates basic frequencies. Computes observed prevalence at single age\r
+ and prints on file fileres'p'. */\r
+ freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);\r
+\r
+ fprintf(fichtm,"\n");\r
+ fprintf(fichtm,"<br>Total number of observations=%d <br>\n\\r
+Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\\r
+Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\\r
+ imx,agemin,agemax,jmin,jmax,jmean);\r
+ pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */\r
+ oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */\r
+ newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */\r
+ savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */\r
+ oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */\r
+ \r
+ \r
+ /* For Powell, parameters are in a vector p[] starting at p[1]\r
+ so we point p on param[1][1] so that p[1] maps on param[1][1][1] */\r
+ p=param[1][1]; /* *(*(*(param +1)+1)+0) */\r
+\r
+ globpr=0; /* To get the number ipmx of contributions and the sum of weights*/\r
+\r
+ if (mle==-3){\r
+ ximort=matrix(1,NDIM,1,NDIM);\r
+ cens=ivector(1,n);\r
+ ageexmed=vector(1,n);\r
+ agecens=vector(1,n);\r
+ dcwave=ivector(1,n);\r
+ \r
+ for (i=1; i<=imx; i++){\r
+ dcwave[i]=-1;\r
+ for (m=firstpass; m<=lastpass; m++)\r
+ if (s[m][i]>nlstate) {\r
+ dcwave[i]=m;\r
+ /* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/\r
+ break;\r
+ }\r
+ }\r
+\r
+ for (i=1; i<=imx; i++) {\r
+ if (wav[i]>0){\r
+ ageexmed[i]=agev[mw[1][i]][i];\r
+ j=wav[i];\r
+ agecens[i]=1.; \r
+\r
+ if (ageexmed[i]> 1 && wav[i] > 0){\r
+ agecens[i]=agev[mw[j][i]][i];\r
+ cens[i]= 1;\r
+ }else if (ageexmed[i]< 1) \r
+ cens[i]= -1;\r
+ if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)\r
+ cens[i]=0 ;\r
+ }\r
+ else cens[i]=-1;\r
+ }\r
+ \r
+ for (i=1;i<=NDIM;i++) {\r
+ for (j=1;j<=NDIM;j++)\r
+ ximort[i][j]=(i == j ? 1.0 : 0.0);\r
+ }\r
+ \r
+ p[1]=0.0268; p[NDIM]=0.083;\r
+ /*printf("%lf %lf", p[1], p[2]);*/\r
+ \r
+ \r
+ printf("Powell\n"); fprintf(ficlog,"Powell\n");\r
+ strcpy(filerespow,"pow-mort"); \r
+ strcat(filerespow,fileres);\r
+ if((ficrespow=fopen(filerespow,"w"))==NULL) {\r
+ printf("Problem with resultfile: %s\n", filerespow);\r
+ fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);\r
+ }\r
+ fprintf(ficrespow,"# Powell\n# iter -2*LL");\r
+ /* for (i=1;i<=nlstate;i++)\r
+ for(j=1;j<=nlstate+ndeath;j++)\r
+ if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);\r
+ */\r
+ fprintf(ficrespow,"\n");\r
+ \r
+ powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);\r
+ fclose(ficrespow);\r
+ \r
+ hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); \r
+\r
+ for(i=1; i <=NDIM; i++)\r
+ for(j=i+1;j<=NDIM;j++)\r
+ matcov[i][j]=matcov[j][i];\r
+ \r
+ printf("\nCovariance matrix\n ");\r
+ for(i=1; i <=NDIM; i++) {\r
+ for(j=1;j<=NDIM;j++){ \r
+ printf("%f ",matcov[i][j]);\r
+ }\r
+ printf("\n ");\r
+ }\r
+ \r
+ printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);\r
+ for (i=1;i<=NDIM;i++) \r
+ printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));\r
+\r
+ lsurv=vector(1,AGESUP);\r
+ lpop=vector(1,AGESUP);\r
+ tpop=vector(1,AGESUP);\r
+ lsurv[agegomp]=100000;\r
+ \r
+ for (k=agegomp;k<=AGESUP;k++) {\r
+ agemortsup=k;\r
+ if (p[1]*exp(p[2]*(k-agegomp))>1) break;\r
+ }\r
+ \r
+ for (k=agegomp;k<agemortsup;k++)\r
+ lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));\r
+ \r
+ for (k=agegomp;k<agemortsup;k++){\r
+ lpop[k]=(lsurv[k]+lsurv[k+1])/2.;\r
+ sumlpop=sumlpop+lpop[k];\r
+ }\r
+ \r
+ tpop[agegomp]=sumlpop;\r
+ for (k=agegomp;k<(agemortsup-3);k++){\r
+ /* tpop[k+1]=2;*/\r
+ tpop[k+1]=tpop[k]-lpop[k];\r
+ }\r
+ \r
+ \r
+ printf("\nAge lx qx dx Lx Tx e(x)\n");\r
+ for (k=agegomp;k<(agemortsup-2);k++) \r
+ 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]);\r
+ \r
+ \r
+ replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */\r
+ printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);\r
+ \r
+ printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \\r
+ stepm, weightopt,\\r
+ model,imx,p,matcov,agemortsup);\r
+ \r
+ free_vector(lsurv,1,AGESUP);\r
+ free_vector(lpop,1,AGESUP);\r
+ free_vector(tpop,1,AGESUP);\r
+ } /* Endof if mle==-3 */\r
+ \r
+ else{ /* For mle >=1 */\r
+ \r
+ likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */\r
+ printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);\r
+ for (k=1; k<=npar;k++)\r
+ printf(" %d %8.5f",k,p[k]);\r
+ printf("\n");\r
+ globpr=1; /* to print the contributions */\r
+ likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */\r
+ printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);\r
+ for (k=1; k<=npar;k++)\r
+ printf(" %d %8.5f",k,p[k]);\r
+ printf("\n");\r
+ if(mle>=1){ /* Could be 1 or 2 */\r
+ mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);\r
+ }\r
+ \r
+ /*--------- results files --------------*/\r
+ 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);\r
+ \r
+ \r
+ fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");\r
+ printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");\r
+ fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");\r
+ for(i=1,jk=1; i <=nlstate; i++){\r
+ for(k=1; k <=(nlstate+ndeath); k++){\r
+ if (k != i) {\r
+ printf("%d%d ",i,k);\r
+ fprintf(ficlog,"%d%d ",i,k);\r
+ fprintf(ficres,"%1d%1d ",i,k);\r
+ for(j=1; j <=ncovmodel; j++){\r
+ printf("%lf ",p[jk]);\r
+ fprintf(ficlog,"%lf ",p[jk]);\r
+ fprintf(ficres,"%lf ",p[jk]);\r
+ jk++; \r
+ }\r
+ printf("\n");\r
+ fprintf(ficlog,"\n");\r
+ fprintf(ficres,"\n");\r
+ }\r
+ }\r
+ }\r
+ if(mle!=0){\r
+ /* Computing hessian and covariance matrix */\r
+ ftolhess=ftol; /* Usually correct */\r
+ hesscov(matcov, p, npar, delti, ftolhess, func);\r
+ }\r
+ fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");\r
+ printf("# Scales (for hessian or gradient estimation)\n");\r
+ fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");\r
+ for(i=1,jk=1; i <=nlstate; i++){\r
+ for(j=1; j <=nlstate+ndeath; j++){\r
+ if (j!=i) {\r
+ fprintf(ficres,"%1d%1d",i,j);\r
+ printf("%1d%1d",i,j);\r
+ fprintf(ficlog,"%1d%1d",i,j);\r
+ for(k=1; k<=ncovmodel;k++){\r
+ printf(" %.5e",delti[jk]);\r
+ fprintf(ficlog," %.5e",delti[jk]);\r
+ fprintf(ficres," %.5e",delti[jk]);\r
+ jk++;\r
+ }\r
+ printf("\n");\r
+ fprintf(ficlog,"\n");\r
+ fprintf(ficres,"\n");\r
+ }\r
+ }\r
+ }\r
+ \r
+ 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");\r
+ if(mle>=1)\r
+ 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");\r
+ 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");\r
+ /* # 121 Var(a12)\n\ */\r
+ /* # 122 Cov(b12,a12) Var(b12)\n\ */\r
+ /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */\r
+ /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */\r
+ /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */\r
+ /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */\r
+ /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */\r
+ /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */\r
+ \r
+ \r
+ /* Just to have a covariance matrix which will be more understandable\r
+ even is we still don't want to manage dictionary of variables\r
+ */\r
+ for(itimes=1;itimes<=2;itimes++){\r
+ jj=0;\r
+ for(i=1; i <=nlstate; i++){\r
+ for(j=1; j <=nlstate+ndeath; j++){\r
+ if(j==i) continue;\r
+ for(k=1; k<=ncovmodel;k++){\r
+ jj++;\r
+ ca[0]= k+'a'-1;ca[1]='\0';\r
+ if(itimes==1){\r
+ if(mle>=1)\r
+ printf("#%1d%1d%d",i,j,k);\r
+ fprintf(ficlog,"#%1d%1d%d",i,j,k);\r
+ fprintf(ficres,"#%1d%1d%d",i,j,k);\r
+ }else{\r
+ if(mle>=1)\r
+ printf("%1d%1d%d",i,j,k);\r
+ fprintf(ficlog,"%1d%1d%d",i,j,k);\r
+ fprintf(ficres,"%1d%1d%d",i,j,k);\r
+ }\r
+ ll=0;\r
+ for(li=1;li <=nlstate; li++){\r
+ for(lj=1;lj <=nlstate+ndeath; lj++){\r
+ if(lj==li) continue;\r
+ for(lk=1;lk<=ncovmodel;lk++){\r
+ ll++;\r
+ if(ll<=jj){\r
+ cb[0]= lk +'a'-1;cb[1]='\0';\r
+ if(ll<jj){\r
+ if(itimes==1){\r
+ if(mle>=1)\r
+ printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);\r
+ fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);\r
+ fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);\r
+ }else{\r
+ if(mle>=1)\r
+ printf(" %.5e",matcov[jj][ll]); \r
+ fprintf(ficlog," %.5e",matcov[jj][ll]); \r
+ fprintf(ficres," %.5e",matcov[jj][ll]); \r
+ }\r
+ }else{\r
+ if(itimes==1){\r
+ if(mle>=1)\r
+ printf(" Var(%s%1d%1d)",ca,i,j);\r
+ fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);\r
+ fprintf(ficres," Var(%s%1d%1d)",ca,i,j);\r
+ }else{\r
+ if(mle>=1)\r
+ printf(" %.5e",matcov[jj][ll]); \r
+ fprintf(ficlog," %.5e",matcov[jj][ll]); \r
+ fprintf(ficres," %.5e",matcov[jj][ll]); \r
+ }\r
+ }\r
+ }\r
+ } /* end lk */\r
+ } /* end lj */\r
+ } /* end li */\r
+ if(mle>=1)\r
+ printf("\n");\r
+ fprintf(ficlog,"\n");\r
+ fprintf(ficres,"\n");\r
+ numlinepar++;\r
+ } /* end k*/\r
+ } /*end j */\r
+ } /* end i */\r
+ } /* end itimes */\r
+ \r
+ fflush(ficlog);\r
+ fflush(ficres);\r
+ \r
+ while((c=getc(ficpar))=='#' && c!= EOF){\r
+ ungetc(c,ficpar);\r
+ fgets(line, MAXLINE, ficpar);\r
+ puts(line);\r
+ fputs(line,ficparo);\r
+ }\r
+ ungetc(c,ficpar);\r
+ \r
+ estepm=0;\r
+ fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);\r
+ if (estepm==0 || estepm < stepm) estepm=stepm;\r
+ if (fage <= 2) {\r
+ bage = ageminpar;\r
+ fage = agemaxpar;\r
+ }\r
+ \r
+ fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");\r
+ fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);\r
+ fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);\r
+ \r
+ while((c=getc(ficpar))=='#' && c!= EOF){\r
+ ungetc(c,ficpar);\r
+ fgets(line, MAXLINE, ficpar);\r
+ puts(line);\r
+ fputs(line,ficparo);\r
+ }\r
+ ungetc(c,ficpar);\r
+ \r
+ 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);\r
+ 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);\r
+ 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);\r
+ printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);\r
+ 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);\r
+ \r
+ while((c=getc(ficpar))=='#' && c!= EOF){\r
+ ungetc(c,ficpar);\r
+ fgets(line, MAXLINE, ficpar);\r
+ puts(line);\r
+ fputs(line,ficparo);\r
+ }\r
+ ungetc(c,ficpar);\r
+ \r
+ \r
+ dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;\r
+ dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;\r
+ \r
+ fscanf(ficpar,"pop_based=%d\n",&popbased);\r
+ fprintf(ficparo,"pop_based=%d\n",popbased); \r
+ fprintf(ficres,"pop_based=%d\n",popbased); \r
+ \r
+ while((c=getc(ficpar))=='#' && c!= EOF){\r
+ ungetc(c,ficpar);\r
+ fgets(line, MAXLINE, ficpar);\r
+ puts(line);\r
+ fputs(line,ficparo);\r
+ }\r
+ ungetc(c,ficpar);\r
+ \r
+ 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);\r
+ 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);\r
+ 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);\r
+ 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);\r
+ 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);\r
+ /* day and month of proj2 are not used but only year anproj2.*/\r
+ \r
+ \r
+ \r
+ /* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/\r
+ /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/\r
+ \r
+ replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */\r
+ printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);\r
+ \r
+ printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\\r
+ model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\\r
+ jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);\r
+ \r
+ /*------------ free_vector -------------*/\r
+ /* chdir(path); */\r
+ \r
+ free_ivector(wav,1,imx);\r
+ free_imatrix(dh,1,lastpass-firstpass+1,1,imx);\r
+ free_imatrix(bh,1,lastpass-firstpass+1,1,imx);\r
+ free_imatrix(mw,1,lastpass-firstpass+1,1,imx); \r
+ free_lvector(num,1,n);\r
+ free_vector(agedc,1,n);\r
+ /*free_matrix(covar,0,NCOVMAX,1,n);*/\r
+ /*free_matrix(covar,1,NCOVMAX,1,n);*/\r
+ fclose(ficparo);\r
+ fclose(ficres);\r
+\r
+\r
+ /*--------------- Prevalence limit (period or stable prevalence) --------------*/\r
+ \r
+ strcpy(filerespl,"pl");\r
+ strcat(filerespl,fileres);\r
+ if((ficrespl=fopen(filerespl,"w"))==NULL) {\r
+ printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;\r
+ fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;\r
+ }\r
+ printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);\r
+ fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);\r
+ pstamp(ficrespl);\r
+ fprintf(ficrespl,"# Period (stable) prevalence \n");\r
+ fprintf(ficrespl,"#Age ");\r
+ for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);\r
+ fprintf(ficrespl,"\n");\r
+ \r
+ prlim=matrix(1,nlstate,1,nlstate);\r
+\r
+ agebase=ageminpar;\r
+ agelim=agemaxpar;\r
+ ftolpl=1.e-10;\r
+ i1=cptcoveff;\r
+ if (cptcovn < 1){i1=1;}\r
+\r
+ for(cptcov=1,k=0;cptcov<=i1;cptcov++){\r
+ for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){\r
+ k=k+1;\r
+ /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/\r
+ fprintf(ficrespl,"\n#******");\r
+ printf("\n#******");\r
+ fprintf(ficlog,"\n#******");\r
+ for(j=1;j<=cptcoveff;j++) {\r
+ fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);\r
+ printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);\r
+ fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);\r
+ }\r
+ fprintf(ficrespl,"******\n");\r
+ printf("******\n");\r
+ fprintf(ficlog,"******\n");\r
+ \r
+ for (age=agebase; age<=agelim; age++){\r
+ prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);\r
+ fprintf(ficrespl,"%.0f ",age );\r
+ for(j=1;j<=cptcoveff;j++)\r
+ fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);\r
+ for(i=1; i<=nlstate;i++)\r
+ fprintf(ficrespl," %.5f", prlim[i][i]);\r
+ fprintf(ficrespl,"\n");\r
+ }\r
+ }\r
+ }\r
+ fclose(ficrespl);\r
+\r
+ /*------------- h Pij x at various ages ------------*/\r
+ \r
+ strcpy(filerespij,"pij"); strcat(filerespij,fileres);\r
+ if((ficrespij=fopen(filerespij,"w"))==NULL) {\r
+ printf("Problem with Pij resultfile: %s\n", filerespij);goto end;\r
+ fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;\r
+ }\r
+ printf("Computing pij: result on file '%s' \n", filerespij);\r
+ fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);\r
+ \r
+ stepsize=(int) (stepm+YEARM-1)/YEARM;\r
+ /*if (stepm<=24) stepsize=2;*/\r
+\r
+ agelim=AGESUP;\r
+ hstepm=stepsize*YEARM; /* Every year of age */\r
+ hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ \r
+\r
+ /* hstepm=1; aff par mois*/\r
+ pstamp(ficrespij);\r
+ fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");\r
+ for(cptcov=1,k=0;cptcov<=i1;cptcov++){\r
+ for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){\r
+ k=k+1;\r
+ fprintf(ficrespij,"\n#****** ");\r
+ for(j=1;j<=cptcoveff;j++) \r
+ fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);\r
+ fprintf(ficrespij,"******\n");\r
+ \r
+ for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */\r
+ nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ \r
+ nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */\r
+\r
+ /* nhstepm=nhstepm*YEARM; aff par mois*/\r
+\r
+ p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);\r
+ oldm=oldms;savm=savms;\r
+ hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); \r
+ fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");\r
+ for(i=1; i<=nlstate;i++)\r
+ for(j=1; j<=nlstate+ndeath;j++)\r
+ fprintf(ficrespij," %1d-%1d",i,j);\r
+ fprintf(ficrespij,"\n");\r
+ for (h=0; h<=nhstepm; h++){\r
+ fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );\r
+ for(i=1; i<=nlstate;i++)\r
+ for(j=1; j<=nlstate+ndeath;j++)\r
+ fprintf(ficrespij," %.5f", p3mat[i][j][h]);\r
+ fprintf(ficrespij,"\n");\r
+ }\r
+ free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);\r
+ fprintf(ficrespij,"\n");\r
+ }\r
+ }\r
+ }\r
+\r
+ varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);\r
+\r
+ fclose(ficrespij);\r
+\r
+ probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);\r
+ for(i=1;i<=AGESUP;i++)\r
+ for(j=1;j<=NCOVMAX;j++)\r
+ for(k=1;k<=NCOVMAX;k++)\r
+ probs[i][j][k]=0.;\r
+\r
+ /*---------- Forecasting ------------------*/\r
+ /*if((stepm == 1) && (strcmp(model,".")==0)){*/\r
+ if(prevfcast==1){\r
+ /* if(stepm ==1){*/\r
+ prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);\r
+ /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/\r
+ /* } */\r
+ /* else{ */\r
+ /* erreur=108; */\r
+ /* 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); */\r
+ /* 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); */\r
+ /* } */\r
+ }\r
+ \r
+\r
+ /*---------- Health expectancies and variances ------------*/\r
+\r
+ strcpy(filerest,"t");\r
+ strcat(filerest,fileres);\r
+ if((ficrest=fopen(filerest,"w"))==NULL) {\r
+ printf("Problem with total LE resultfile: %s\n", filerest);goto end;\r
+ fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;\r
+ }\r
+ printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); \r
+ fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); \r
+\r
+\r
+ strcpy(filerese,"e");\r
+ strcat(filerese,fileres);\r
+ if((ficreseij=fopen(filerese,"w"))==NULL) {\r
+ printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);\r
+ fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);\r
+ }\r
+ printf("Computing Health Expectancies: result on file '%s' \n", filerese);\r
+ fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);\r
+\r
+ strcpy(fileresstde,"stde");\r
+ strcat(fileresstde,fileres);\r
+ if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {\r
+ printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);\r
+ fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);\r
+ }\r
+ printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);\r
+ fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);\r
+\r
+ strcpy(filerescve,"cve");\r
+ strcat(filerescve,fileres);\r
+ if((ficrescveij=fopen(filerescve,"w"))==NULL) {\r
+ printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);\r
+ fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);\r
+ }\r
+ printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);\r
+ fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);\r
+\r
+ strcpy(fileresv,"v");\r
+ strcat(fileresv,fileres);\r
+ if((ficresvij=fopen(fileresv,"w"))==NULL) {\r
+ printf("Problem with variance resultfile: %s\n", fileresv);exit(0);\r
+ fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);\r
+ }\r
+ printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);\r
+ fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);\r
+\r
+ /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */\r
+ prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);\r
+ /* 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",\\r
+ ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);\r
+ */\r
+\r
+ if (mobilav!=0) {\r
+ mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);\r
+ if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){\r
+ fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);\r
+ printf(" Error in movingaverage mobilav=%d\n",mobilav);\r
+ }\r
+ }\r
+\r
+ for(cptcov=1,k=0;cptcov<=i1;cptcov++){\r
+ for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){\r
+ k=k+1; \r
+ fprintf(ficrest,"\n#****** ");\r
+ for(j=1;j<=cptcoveff;j++) \r
+ fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);\r
+ fprintf(ficrest,"******\n");\r
+\r
+ fprintf(ficreseij,"\n#****** ");\r
+ fprintf(ficresstdeij,"\n#****** ");\r
+ fprintf(ficrescveij,"\n#****** ");\r
+ for(j=1;j<=cptcoveff;j++) {\r
+ fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);\r
+ fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);\r
+ fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);\r
+ }\r
+ fprintf(ficreseij,"******\n");\r
+ fprintf(ficresstdeij,"******\n");\r
+ fprintf(ficrescveij,"******\n");\r
+\r
+ fprintf(ficresvij,"\n#****** ");\r
+ for(j=1;j<=cptcoveff;j++) \r
+ fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);\r
+ fprintf(ficresvij,"******\n");\r
+\r
+ eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);\r
+ oldm=oldms;savm=savms;\r
+ evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart); \r
+ cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart); \r
+ \r
+ vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);\r
+ oldm=oldms;savm=savms;\r
+ varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);\r
+ if(popbased==1){\r
+ varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);\r
+ }\r
+\r
+ pstamp(ficrest);\r
+ fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");\r
+ for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);\r
+ fprintf(ficrest,"\n");\r
+\r
+ epj=vector(1,nlstate+1);\r
+ for(age=bage; age <=fage ;age++){\r
+ prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);\r
+ if (popbased==1) {\r
+ if(mobilav ==0){\r
+ for(i=1; i<=nlstate;i++)\r
+ prlim[i][i]=probs[(int)age][i][k];\r
+ }else{ /* mobilav */ \r
+ for(i=1; i<=nlstate;i++)\r
+ prlim[i][i]=mobaverage[(int)age][i][k];\r
+ }\r
+ }\r
+ \r
+ fprintf(ficrest," %4.0f",age);\r
+ for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){\r
+ for(i=1, epj[j]=0.;i <=nlstate;i++) {\r
+ epj[j] += prlim[i][i]*eij[i][j][(int)age];\r
+ /* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/\r
+ }\r
+ epj[nlstate+1] +=epj[j];\r
+ }\r
+\r
+ for(i=1, vepp=0.;i <=nlstate;i++)\r
+ for(j=1;j <=nlstate;j++)\r
+ vepp += vareij[i][j][(int)age];\r
+ fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));\r
+ for(j=1;j <=nlstate;j++){\r
+ fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));\r
+ }\r
+ fprintf(ficrest,"\n");\r
+ }\r
+ free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);\r
+ free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);\r
+ free_vector(epj,1,nlstate+1);\r
+ }\r
+ }\r
+ free_vector(weight,1,n);\r
+ free_imatrix(Tvard,1,15,1,2);\r
+ free_imatrix(s,1,maxwav+1,1,n);\r
+ free_matrix(anint,1,maxwav,1,n); \r
+ free_matrix(mint,1,maxwav,1,n);\r
+ free_ivector(cod,1,n);\r
+ free_ivector(tab,1,NCOVMAX);\r
+ fclose(ficreseij);\r
+ fclose(ficresstdeij);\r
+ fclose(ficrescveij);\r
+ fclose(ficresvij);\r
+ fclose(ficrest);\r
+ fclose(ficpar);\r
+ \r
+ /*------- Variance of period (stable) prevalence------*/ \r
+\r
+ strcpy(fileresvpl,"vpl");\r
+ strcat(fileresvpl,fileres);\r
+ if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {\r
+ printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);\r
+ exit(0);\r
+ }\r
+ printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);\r
+\r
+ for(cptcov=1,k=0;cptcov<=i1;cptcov++){\r
+ for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){\r
+ k=k+1;\r
+ fprintf(ficresvpl,"\n#****** ");\r
+ for(j=1;j<=cptcoveff;j++) \r
+ fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);\r
+ fprintf(ficresvpl,"******\n");\r
+ \r
+ varpl=matrix(1,nlstate,(int) bage, (int) fage);\r
+ oldm=oldms;savm=savms;\r
+ varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);\r
+ free_matrix(varpl,1,nlstate,(int) bage, (int)fage);\r
+ }\r
+ }\r
+\r
+ fclose(ficresvpl);\r
+\r
+ /*---------- End : free ----------------*/\r
+ if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);\r
+ free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);\r
+\r
+ } /* mle==-3 arrives here for freeing */\r
+ free_matrix(prlim,1,nlstate,1,nlstate);\r
+ free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);\r
+ free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);\r
+ free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);\r
+ free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);\r
+ free_matrix(covar,0,NCOVMAX,1,n);\r
+ free_matrix(matcov,1,npar,1,npar);\r
+ /*free_vector(delti,1,npar);*/\r
+ free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); \r
+ free_matrix(agev,1,maxwav,1,imx);\r
+ free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);\r
+\r
+ free_ivector(ncodemax,1,8);\r
+ free_ivector(Tvar,1,15);\r
+ free_ivector(Tprod,1,15);\r
+ free_ivector(Tvaraff,1,15);\r
+ free_ivector(Tage,1,15);\r
+ free_ivector(Tcode,1,100);\r
+\r
+ free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);\r
+ free_imatrix(codtab,1,100,1,10);\r
+ fflush(fichtm);\r
+ fflush(ficgp);\r
+ \r
+\r
+ if((nberr >0) || (nbwarn>0)){\r
+ printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);\r
+ fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);\r
+ }else{\r
+ printf("End of Imach\n");\r
+ fprintf(ficlog,"End of Imach\n");\r
+ }\r
+ printf("See log file on %s\n",filelog);\r
+ /* gettimeofday(&end_time, (struct timezone*)0);*/ /* after time */\r
+ (void) gettimeofday(&end_time,&tzp);\r
+ tm = *localtime(&end_time.tv_sec);\r
+ tmg = *gmtime(&end_time.tv_sec);\r
+ strcpy(strtend,asctime(&tm));\r
+ printf("Local time at start %s\nLocal time at end %s",strstart, strtend); \r
+ fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend); \r
+ printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));\r
+\r
+ printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);\r
+ fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));\r
+ fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);\r
+ /* printf("Total time was %d uSec.\n", total_usecs);*/\r
+/* if(fileappend(fichtm,optionfilehtm)){ */\r
+ fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);\r
+ fclose(fichtm);\r
+ fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);\r
+ fclose(fichtmcov);\r
+ fclose(ficgp);\r
+ fclose(ficlog);\r
+ /*------ End -----------*/\r
+\r
+\r
+ printf("Before Current directory %s!\n",pathcd);\r
+ if(chdir(pathcd) != 0)\r
+ printf("Can't move to directory %s!\n",path);\r
+ if(getcwd(pathcd,MAXLINE) > 0)\r
+ printf("Current directory %s!\n",pathcd);\r
+ /*strcat(plotcmd,CHARSEPARATOR);*/\r
+ sprintf(plotcmd,"gnuplot");\r
+#ifndef UNIX\r
+ sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);\r
+#endif\r
+ if(!stat(plotcmd,&info)){\r
+ printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);\r
+ if(!stat(getenv("GNUPLOTBIN"),&info)){\r
+ printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);\r
+ }else\r
+ strcpy(pplotcmd,plotcmd);\r
+#ifdef UNIX\r
+ strcpy(plotcmd,GNUPLOTPROGRAM);\r
+ if(!stat(plotcmd,&info)){\r
+ printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);\r
+ }else\r
+ strcpy(pplotcmd,plotcmd);\r
+#endif\r
+ }else\r
+ strcpy(pplotcmd,plotcmd);\r
+ \r
+ sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);\r
+ printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);\r
+\r
+ if((outcmd=system(plotcmd)) != 0){\r
+ printf("\n Problem with gnuplot\n");\r
+ }\r
+ printf(" Wait...");\r
+ while (z[0] != 'q') {\r
+ /* chdir(path); */\r
+ printf("\nType e to edit output files, g to graph again and q for exiting: ");\r
+ scanf("%s",z);\r
+/* if (z[0] == 'c') system("./imach"); */\r
+ if (z[0] == 'e') {\r
+ printf("Starting browser with: %s",optionfilehtm);fflush(stdout);\r
+ system(optionfilehtm);\r
+ }\r
+ else if (z[0] == 'g') system(plotcmd);\r
+ else if (z[0] == 'q') exit(0);\r
+ }\r
+ end:\r
+ while (z[0] != 'q') {\r
+ printf("\nType q for exiting: ");\r
+ scanf("%s",z);\r
+ }\r
+}\r
+\r
+\r
+\r
git://henry.ined.fr / .git / commitdiff