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Diff for /imach/src/imach.c between versions 1.106 and 1.131

version 1.106, 2006/01/19 13:24:36	version 1.131, 2009/06/20 16:22:47
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	Revision 1.131 2009/06/20 16:22:47 brouard
	Some dimensions resccaled

	Revision 1.130 2009/05/26 06:44:34 brouard
	(Module): Max Covariate is now set to 20 instead of 8. A
	lot of cleaning with variables initialized to 0. Trying to make
	V2+V3age+V1+V4 strb=V3age+V1+V4 working better.

	Revision 1.129 2007/08/31 13:49:27 lievre
	Modification of the way of exiting when the covariate is not binary in order to see on the window the error message before exiting

	Revision 1.128 2006/06/30 13:02:05 brouard
	(Module): Clarifications on computing e.j

	Revision 1.127 2006/04/28 18:11:50 brouard
	(Module): Yes the sum of survivors was wrong since
	imach-114 because nhstepm was no more computed in the age
	loop. Now we define nhstepma in the age loop.
	(Module): In order to speed up (in case of numerous covariates) we
	compute health expectancies (without variances) in a first step
	and then all the health expectancies with variances or standard
	deviation (needs data from the Hessian matrices) which slows the
	computation.
	In the future we should be able to stop the program is only health
	expectancies and graph are needed without standard deviations.

	Revision 1.126 2006/04/28 17:23:28 brouard
	(Module): Yes the sum of survivors was wrong since
	imach-114 because nhstepm was no more computed in the age
	loop. Now we define nhstepma in the age loop.
	Version 0.98h

	Revision 1.125 2006/04/04 15:20:31 lievre
	Errors in calculation of health expectancies. Age was not initialized.
	Forecasting file added.

	Revision 1.124 2006/03/22 17:13:53 lievre
	Parameters are printed with %lf instead of %f (more numbers after the comma).
	The log-likelihood is printed in the log file

	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	Revision 1.106 2006/01/19 13:24:36 brouard
Some cleaning and links added in html output	Some cleaning and links added in html output

Line 173	Line 299
hPijx.	hPijx.

Also this programme outputs the covariance matrix of the parameters but also	Also this programme outputs the covariance matrix of the parameters but also
of the life expectancies. It also computes the stable prevalence.	of the life expectancies. It also computes the period (stable) prevalence.

Authors: Nicolas Brouard (brouard@ined.fr) and Agn�s Li�vre (lievre@ined.fr).	Authors: Nicolas Brouard (brouard@ined.fr) and Agn�s Li�vre (lievre@ined.fr).
Institut national d'�tudes d�mographiques, Paris.	Institut national d'�tudes d�mographiques, Paris.
Line 202	Line 328
begin-prev-date,...	begin-prev-date,...
open gnuplot file	open gnuplot file
open html file	open html file
stable prevalence	period (stable) prevalence
for age prevalim()	for age prevalim()
h Pij x	h Pij x
variance of p varprob	variance of p varprob
Line 214	Line 340
varevsij()	varevsij()
if popbased==1 varevsij(,popbased)	if popbased==1 varevsij(,popbased)
total life expectancies	total life expectancies
Variance of stable prevalence	Variance of period (stable) prevalence
end	end
*/	*/

Line 227	Line 353
#include <string.h>	#include <string.h>
#include <unistd.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 <sys/time.h> */
#include <time.h>	#include <time.h>
#include "timeval.h"	#include "timeval.h"
Line 235	Line 367
/* #define _(String) gettext (String) */	/* #define _(String) gettext (String) */

#define MAXLINE 256	#define MAXLINE 256

#define GNUPLOTPROGRAM "gnuplot"	#define GNUPLOTPROGRAM "gnuplot"
/#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"/	/#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"/
#define FILENAMELENGTH 132	#define FILENAMELENGTH 132
/#define DEBUG/
/#define windows/
#define GLOCK_ERROR_NOPATH -1 /* empty path */	#define GLOCK_ERROR_NOPATH -1 /* empty path */
#define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */	#define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */

#define MAXPARM 30 /* Maximum number of parameters for the optimization */	#define MAXPARM 128 /* Maximum number of parameters for the optimization */
#define NPARMAX 64 /* (nlstate+ndeath-1)nlstatencovmodel */	#define NPARMAX 64 /* (nlstate+ndeath-1)nlstatencovmodel */

#define NINTERVMAX 8	#define NINTERVMAX 8
#define NLSTATEMAX 8 /* Maximum number of live states (for func) */	#define NLSTATEMAX 8 /* Maximum number of live states (for func) */
#define NDEATHMAX 8 /* Maximum number of dead states (for func) */	#define NDEATHMAX 8 /* Maximum number of dead states (for func) */
#define NCOVMAX 8 /* Maximum number of covariates */	#define NCOVMAX 20 /* Maximum number of covariates */
#define MAXN 20000	#define MAXN 20000
#define YEARM 12. /* Number of months per year */	#define YEARM 12. /* Number of months per year */
#define AGESUP 130	#define AGESUP 130
Line 257	Line 389
#define AGEGOMP 10. /* Minimal age for Gompertz adjustment */	#define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
#ifdef UNIX	#ifdef UNIX
#define DIRSEPARATOR '/'	#define DIRSEPARATOR '/'
	#define CHARSEPARATOR "/"
#define ODIRSEPARATOR '\\'	#define ODIRSEPARATOR '\\'
#else	#else
#define DIRSEPARATOR '\\'	#define DIRSEPARATOR '\\'
	#define CHARSEPARATOR "\\"
#define ODIRSEPARATOR '/'	#define ODIRSEPARATOR '/'
#endif	#endif

/* $Id$ */	/* $Id$ */
/* $State$ */	/* $State$ */

char version[]="Imach version 0.98a, January 2006, INED-EUROREVES ";	char version[]="Imach version 0.98k, June 2006, INED-EUROREVES-Institut de longevite ";
char fullversion[]="$Revision$ $Date$";	char fullversion[]="$Revision$ $Date$";
int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */	char strstart[80];
int nvar;	char optionfilext[10], optionfilefiname[FILENAMELENGTH];
int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;	int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
	int nvar=0;
	int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov=0; /* Number of covariates, of covariates with 'age' /
int npar=NPARMAX;	int npar=NPARMAX;
int nlstate=2; /* Number of live states */	int nlstate=2; /* Number of live states */
int ndeath=1; /* Number of dead states */	int ndeath=1; /* Number of dead states */
int ncovmodel, ncovcol; /* Total number of covariables including constant a121 +b12x ncovmodel=2 */	int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a121 +b12x ncovmodel=2 */
int popbased=0;	int popbased=0;

int wav; / Number of waves for this individuual 0 is possible */	int wav; / Number of waves for this individuual 0 is possible */
int maxwav; /* Maxim number of waves */	int maxwav=0; /* Maxim number of waves */
int jmin, jmax; /* min, max spacing between 2 waves */	int jmin=0, jmax=0; /* min, max spacing between 2 waves */
int gipmx, gsw; /* Global variables on the number of contributions	int ijmin=0, ijmax=0; /* Individuals having jmin and jmax */
	int gipmx=0, gsw=0; /* Global variables on the number of contributions
to the likelihood and the sum of weights (done by funcone)*/	to the likelihood and the sum of weights (done by funcone)*/
int mle, weightopt;	int mle=1, weightopt=0;
int *mw; / mw[mi][i] is number of the mi wave for this individual */	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 *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	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. */	* wave mi and wave mi+1 is not an exact multiple of stepm. */
double jmean; /* Mean space between 2 waves */	double jmean=1; /* Mean space between 2 waves */
double oldm, newm, *savm; / Working pointers to matrices */	double oldm, newm, *savm; / Working pointers to matrices */
double oldms, newms, *savms; / Fixed working pointers to matrices */	double oldms, newms, *savms; / Fixed working pointers to matrices */
FILE fic,ficpar, ficparo,ficres, ficrespl, ficrespij, ficrest,ficresf,*ficrespop;	FILE fic,ficpar, ficparo,ficres, ficresp, ficrespl, ficrespij, ficrest,ficresf,ficrespop;
FILE ficlog, ficrespow;	FILE ficlog, ficrespow;
int globpr; /* Global variable for printing or not */	int globpr=0; /* Global variable for printing or not */
double fretone; /* Only one call to likelihood */	double fretone; /* Only one call to likelihood */
long ipmx; /* Number of contributions */	long ipmx=0; /* Number of contributions */
double sw; /* Sum of weights */	double sw; /* Sum of weights */
char filerespow[FILENAMELENGTH];	char filerespow[FILENAMELENGTH];
char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */	char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
Line 304 FILE *ficresprobmorprev;	Line 441 FILE *ficresprobmorprev;
FILE fichtm, fichtmcov; /* Html File */	FILE fichtm, fichtmcov; /* Html File */
FILE *ficreseij;	FILE *ficreseij;
char filerese[FILENAMELENGTH];	char filerese[FILENAMELENGTH];
	FILE *ficresstdeij;
	char fileresstde[FILENAMELENGTH];
	FILE *ficrescveij;
	char filerescve[FILENAMELENGTH];
FILE *ficresvij;	FILE *ficresvij;
char fileresv[FILENAMELENGTH];	char fileresv[FILENAMELENGTH];
FILE *ficresvpl;	FILE *ficresvpl;
char fileresvpl[FILENAMELENGTH];	char fileresvpl[FILENAMELENGTH];
char title[MAXLINE];	char title[MAXLINE];
char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];	char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];	char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];	char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
char command[FILENAMELENGTH];	char command[FILENAMELENGTH];
int outcmd=0;	int outcmd=0;
Line 332 long time_value;	Line 473 long time_value;
extern long time();	extern long time();
char strcurr[80], strfor[80];	char strcurr[80], strfor[80];

	char *endptr;
	long lval;
	double dval;

#define NR_END 1	#define NR_END 1
#define FREE_ARG char*	#define FREE_ARG char*
#define FTOL 1.0e-10	#define FTOL 1.0e-10
Line 379 double dateintmean=0;	Line 524 double dateintmean=0;
double *weight;	double *weight;
int *s; / Status */	int *s; / Status */
double agedc, *covar, idx;	double agedc, *covar, idx;
int *nbcode, Tcode, Tvar, codtab, Tvard, Tprod, cptcovprod, *Tvaraff;	int *nbcode, Tvar, codtab, Tvard, Tprod, cptcovprod, Tvaraff;
double lsurv, lpop, *tpop;	double lsurv, lpop, *tpop;

double ftol=FTOL; /* Tolerance for computing Max Likelihood */	double ftol=FTOL; /* Tolerance for computing Max Likelihood */
Line 388 double ftolhess; /* Tolerance for comput	Line 533 double ftolhess; /* Tolerance for comput
/************** split ***********************/	/************** split ***********************/
static int split( char path, char dirc, char name, char ext, char *finame )	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)	/* 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)	the name of the file (name), its extension only (ext) and its first part of the name (finame)
*/	*/
char ss; / pointer */	char ss; / pointer */
Line 397 static int split( char path, char dirc	Line 542 static int split( char path, char dirc
l1 = strlen(path ); /* length of path */	l1 = strlen(path ); /* length of path */
if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );	if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
ss= strrchr( path, DIRSEPARATOR ); /* find last / */	ss= strrchr( path, DIRSEPARATOR ); /* find last / */
if ( ss == NULL ) { /* no directory, so use current */	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)	/*if(strrchr(path, ODIRSEPARATOR )==NULL)
printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/	printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
/* get current working directory */	/* get current working directory */
Line 405 static int split( char path, char dirc	Line 551 static int split( char path, char dirc
if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {	if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
return( GLOCK_ERROR_GETCWD );	return( GLOCK_ERROR_GETCWD );
}	}
strcpy( name, path ); /* we've got it */	/* got dirc from getcwd*/
	printf(" DIRC = %s \n",dirc);
} else { /* strip direcotry from path */	} else { /* strip direcotry from path */
ss++; /* after this, the filename */	ss++; /* after this, the filename */
l2 = strlen( ss ); /* length of filename */	l2 = strlen( ss ); /* length of filename */
Line 413 static int split( char path, char dirc	Line 560 static int split( char path, char dirc
strcpy( name, ss ); /* save file name */	strcpy( name, ss ); /* save file name */
strncpy( dirc, path, l1 - l2 ); /* now the directory */	strncpy( dirc, path, l1 - l2 ); /* now the directory */
dirc[l1-l2] = 0; /* add zero */	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 */	l1 = strlen( dirc ); /* length of directory */
/*#ifdef windows	if( dirc[l1-1] != DIRSEPARATOR ){
if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }	dirc[l1] = DIRSEPARATOR;
#else	dirc[l1+1] = 0;
if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }	printf(" DIRC3 = %s \n",dirc);
#endif	}
*/
ss = strrchr( name, '.' ); /* find last / */	ss = strrchr( name, '.' ); /* find last / */
if (ss >0){	if (ss >0){
ss++;	ss++;
Line 430 static int split( char path, char dirc	Line 578 static int split( char path, char dirc
strncpy( finame, name, l1-l2);	strncpy( finame, name, l1-l2);
finame[l1-l2]= 0;	finame[l1-l2]= 0;
}	}

return( 0 ); /* we're done */	return( 0 ); /* we're done */
}	}

Line 892 void powell(double p[], double **xi, int	Line 1041 void powell(double p[], double **xi, int
last_time=curr_time;	last_time=curr_time;
(void) gettimeofday(&curr_time,&tzp);	(void) gettimeofday(&curr_time,&tzp);
printf("\nPowell iter=%d -2LL=%.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);	printf("\nPowell iter=%d -2LL=%.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 -2LL=%.12f %ld sec. %ld sec.",iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);	fprintf(ficlog,"\nPowell iter=%d -2LL=%.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);	/* fprintf(ficrespow,"%d %.12f %ld",iter,fret,curr_time.tv_sec-start_time.tv_sec); */
*/
for (i=1;i<=n;i++) {	for (i=1;i<=n;i++) {
printf(" %d %.12f",i, p[i]);	printf(" %d %.12f",i, p[i]);
fprintf(ficlog," %d %.12lf",i, p[i]);	fprintf(ficlog," %d %.12lf",i, p[i]);
Line 1016 void powell(double p[], double **xi, int	Line 1164 void powell(double p[], double **xi, int
}	}
}	}

/** Prevalence limit (stable prevalence) **************/	/** Prevalence limit (stable or period prevalence) **************/

double prevalim(double prlim, int nlstate, double x[], double age, double oldm, double savm, double ftolpl, int ij)	double prevalim(double prlim, int nlstate, double x[], double age, double oldm, double savm, double ftolpl, int ij)
{	{
Line 1026 double prevalim(double prlim, int nl	Line 1174 double prevalim(double prlim, int nl
int i, ii,j,k;	int i, ii,j,k;
double min, max, maxmin, maxmax,sumnew=0.;	double min, max, maxmin, maxmax,sumnew=0.;
double **matprod2();	double **matprod2();
double out, cov[NCOVMAX], pmij();	double out, cov[NCOVMAX+1], pmij();
double **newm;	double **newm;
double agefin, delaymax=50 ; /* Max number of years to converge */	double agefin, delaymax=50 ; /* Max number of years to converge */

Line 1108 double pmij(double ps, double *cov,	Line 1256 double pmij(double ps, double *cov,

for(i=1; i<= nlstate; i++){	for(i=1; i<= nlstate; i++){
s1=0;	s1=0;
for(j=1; j<i; j++)	for(j=1; j<i; j++){
s1+=exp(ps[i][j]);	s1+=exp(ps[i][j]);
for(j=i+1; j<=nlstate+ndeath; j++)	/printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); /
	}
	for(j=i+1; j<=nlstate+ndeath; j++){
s1+=exp(ps[i][j]);	s1+=exp(ps[i][j]);
	/printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); /
	}
ps[i][i]=1./(s1+1.);	ps[i][i]=1./(s1+1.);
for(j=1; j<i; j++)	for(j=1; j<i; j++)
ps[i][j]= exp(ps[i][j])*ps[i][i];	ps[i][j]= exp(ps[i][j])*ps[i][i];
Line 1177 double *hpxij(double *po, int nhstep	Line 1329 double *hpxij(double *po, int nhstep
*/	*/

int i, j, d, h, k;	int i, j, d, h, k;
double **out, cov[NCOVMAX];	double **out, cov[NCOVMAX+1];
double **newm;	double **newm;

/* Hstepm could be zero and should return the unit matrix */	/* Hstepm could be zero and should return the unit matrix */
Line 1193 double *hpxij(double *po, int nhstep	Line 1345 double *hpxij(double *po, int nhstep
/* Covariates have to be included here again */	/* Covariates have to be included here again */
cov[1]=1.;	cov[1]=1.;
cov[2]=age+((h-1)hstepm + (d-1))stepm/YEARM;	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<=cptcovn;k++)
	cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
for (k=1; k<=cptcovage;k++)	for (k=1; k<=cptcovage;k++)
cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];	cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
for (k=1; k<=cptcovprod;k++)	for (k=1; k<=cptcovprod;k++)
Line 1210 double *hpxij(double *po, int nhstep	Line 1363 double *hpxij(double *po, int nhstep
for(i=1; i<=nlstate+ndeath; i++)	for(i=1; i<=nlstate+ndeath; i++)
for(j=1;j<=nlstate+ndeath;j++) {	for(j=1;j<=nlstate+ndeath;j++) {
po[i][j][h]=newm[i][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]);	/if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);/
*/
}	}
	/printf("h=%d ",h);/
} /* end h */	} /* end h */
	/* printf("\n H=%d \n",h); */
return po;	return po;
}	}

Line 1222 double *hpxij(double *po, int nhstep	Line 1376 double *hpxij(double *po, int nhstep
double func( double *x)	double func( double *x)
{	{
int i, ii, j, k, mi, d, kk;	int i, ii, j, k, mi, d, kk;
double l, ll[NLSTATEMAX], cov[NCOVMAX];	double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
double **out;	double **out;
double sw; /* Sum of weights */	double sw; /* Sum of weights */
double lli; /* Individual log likelihood */	double lli; /* Individual log likelihood */
Line 1309 double func( double *x)	Line 1463 double func( double *x)

} else if (s2==-2) {	} else if (s2==-2) {
for (j=1,survp=0. ; j<=nlstate; j++)	for (j=1,survp=0. ; j<=nlstate; j++)
survp += out[s1][j];	survp += (1.+bbh)out[s1][j]- bbhsavm[s1][j];
lli= survp;	/survp += out[s1][j]; /
	lli= log(survp);
}	}

else if (s2==-4) {	else if (s2==-4) {
for (j=3,survp=0. ; j<=nlstate; j++)	for (j=3,survp=0. ; j<=nlstate; j++)
survp += out[s1][j];	survp += (1.+bbh)out[s1][j]- bbhsavm[s1][j];
lli= survp;	lli= log(survp);
}	}

else if (s2==-5) {
for (j=1,survp=0. ; j<=2; j++)
survp += out[s1][j];
lli= survp;
}


	else if (s2==-5) {
	for (j=1,survp=0. ; j<=2; j++)
	survp += (1.+bbh)out[s1][j]- bbhsavm[s1][j];
	lli= log(survp);
	}

else{	else{
lli= log((1.+bbh)out[s1][s2]- bbhsavm[s1][s2]); /* linear interpolation */	lli= log((1.+bbh)out[s1][s2]- bbhsavm[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= (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 */
Line 1476 double funcone( double *x)	Line 1630 double funcone( double *x)
{	{
/* Same as likeli but slower because of a lot of printf and if */	/* Same as likeli but slower because of a lot of printf and if */
int i, ii, j, k, mi, d, kk;	int i, ii, j, k, mi, d, kk;
double l, ll[NLSTATEMAX], cov[NCOVMAX];	double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
double **out;	double **out;
double lli; /* Individual log likelihood */	double lli; /* Individual log likelihood */
double llt;	double llt;
Line 1520 double funcone( double *x)	Line 1674 double funcone( double *x)
*/	*/
if( s2 > nlstate && (mle <5) ){ /* Jackson */	if( s2 > nlstate && (mle <5) ){ /* Jackson */
lli=log(out[s1][s2] - savm[s1][s2]);	lli=log(out[s1][s2] - savm[s1][s2]);
} else if (mle==1){	} else if (s2==-2) {
	for (j=1,survp=0. ; j<=nlstate; j++)
	survp += (1.+bbh)out[s1][j]- bbhsavm[s1][j];
	lli= log(survp);
	}else if (mle==1){
lli= log((1.+bbh)out[s1][s2]- bbhsavm[s1][s2]); /* linear interpolation */	lli= log((1.+bbh)out[s1][s2]- bbhsavm[s1][s2]); /* linear interpolation */
} else if(mle==2){	} else if(mle==2){
lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)out[s1][s2]- bbhsavm[s1][s2]):log((1.+bbh)out[s1][s2])); / linear interpolation */	lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)out[s1][s2]- bbhsavm[s1][s2]):log((1.+bbh)out[s1][s2])); / linear interpolation */
Line 1534 double funcone( double *x)	Line 1692 double funcone( double *x)
ipmx +=1;	ipmx +=1;
sw += weight[i];	sw += weight[i];
ll[s[mw[mi][i]][i]] += 2weight[i]lli;	ll[s[mw[mi][i]][i]] += 2weight[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]); */	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){	if(globpr){
fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\	fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
%10.6f %10.6f %10.6f ", \	%11.6f %11.6f %11.6f ", \
num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],	num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2weight[i]lli,out[s1][s2],savm[s1][s2]);	2weight[i]lli,out[s1][s2],savm[s1][s2]);
for(k=1,llt=0.,l=0.; k<=nlstate; k++){	for(k=1,llt=0.,l=0.; k<=nlstate; k++){
Line 1622 void mlikeli(FILE *ficres,double p[], in	Line 1780 void mlikeli(FILE *ficres,double p[], in

powell(p,xi,npar,ftol,&iter,&fret,func);	powell(p,xi,npar,ftol,&iter,&fret,func);

	free_matrix(xi,1,npar,1,npar);
fclose(ficrespow);	fclose(ficrespow);
printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));	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(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
Line 1889 void lubksb(double *a, int n, int indx	Line 2048 void lubksb(double *a, int n, int indx
}	}
}	}

	void pstamp(FILE *fichier)
	{
	fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
	}

/********** Frequencies ******************/	/********** 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[])	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 */	{ /* Some frequencies */

int i, m, jk, k1,i1, j1, bool, z1,z2,j;	int i, m, jk, k1,i1, j1, bool, z1,j;
int first;	int first;
double **freq; / Frequencies */	double **freq; / Frequencies */
double pp, *prop;	double pp, *prop;
double pos,posprop, k2, dateintsum=0,k2cpt=0;	double pos,posprop, k2, dateintsum=0,k2cpt=0;
FILE *ficresp;
char fileresp[FILENAMELENGTH];	char fileresp[FILENAMELENGTH];

pp=vector(1,nlstate);	pp=vector(1,nlstate);
Line 1963 void freqsummary(char fileres[], int ia	Line 2126 void freqsummary(char fileres[], int ia
}	}

/* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/	/* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
fprintf(ficresp, "#Local time at start: %s", strstart);	pstamp(ficresp);
if (cptcovn>0) {	if (cptcovn>0) {
fprintf(ficresp, "\n#********** Variable ");	fprintf(ficresp, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
Line 2063 void prevalence(double ***probs, double	Line 2226 void prevalence(double ***probs, double
We still use firstpass and lastpass as another selection.	We still use firstpass and lastpass as another selection.
*/	*/

int i, m, jk, k1, i1, j1, bool, z1,z2,j;	int i, m, jk, k1, i1, j1, bool, z1,j;
double **freq; / Frequencies */	double **freq; / Frequencies */
double pp, *prop;	double pp, *prop;
double pos,posprop;	double pos,posprop;
Line 2121 void prevalence(double ***probs, double	Line 2284 void prevalence(double ***probs, double
if( i <= iagemax){	if( i <= iagemax){
if(posprop>=1.e-5){	if(posprop>=1.e-5){
probs[i][jk][j1]= prop[jk][i]/posprop;	probs[i][jk][j1]= prop[jk][i]/posprop;
}	} else
	printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
}	}
}/* end jk */	}/* end jk */
}/* end i */	}/* end i */
Line 2176 void concatwav(int wav[], int **dh, int	Line 2340 void concatwav(int wav[], int **dh, int
if(mi==0){	if(mi==0){
nbwarn++;	nbwarn++;
if(first==0){	if(first==0){
printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);	printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
first=1;	first=1;
}	}
if(first==1){	if(first==1){
fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);	fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
}	}
} /* end mi==0 */	} /* end mi==0 */
} /* End individuals */	} /* End individuals */
Line 2203 void concatwav(int wav[], int **dh, int	Line 2367 void concatwav(int wav[], int **dh, int
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);	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;	k=k+1;
if (j >= jmax) jmax=j;	if (j >= jmax){
if (j <= jmin) jmin=j;	jmax=j;
	ijmax=i;
	}
	if (j <= jmin){
	jmin=j;
	ijmin=i;
	}
sum=sum+j;	sum=sum+j;
/if (j<0) printf("j=%d num=%d \n",j,i);/	/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);*/	/* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
Line 2215 void concatwav(int wav[], int **dh, int	Line 2385 void concatwav(int wav[], int **dh, int
/* 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]); */	/* 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;	k=k+1;
if (j >= jmax) jmax=j;	if (j >= jmax) {
else if (j <= jmin)jmin=j;	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); */	/* 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]);/	/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){	if(j<0){
Line 2259 void concatwav(int wav[], int **dh, int	Line 2435 void concatwav(int wav[], int **dh, int
} /* end wave */	} /* end wave */
}	}
jmean=sum/k;	jmean=sum/k;
printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);	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 Max=%d Mean=%f\n\n ",jmin, jmax,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 **************************/	/********* Tricode **************************/
void tricode(int Tvar, int *nbcode, int imx)	void tricode(int Tvar, int *nbcode, int imx)
{	{

int Ndum[20],ij=1, k, j, i, maxncov=19;	/* Tvar[i]=atoi(stre); /* find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1 */

	int Ndum[20],ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
int cptcode=0;	int cptcode=0;
cptcoveff=0;	cptcoveff=0;

for (k=0; k<maxncov; k++) Ndum[k]=0;	for (k=0; k<maxncov; k++) Ndum[k]=0;
for (k=1; k<=7; k++) ncodemax[k]=0;	for (k=1; k<=7; k++) ncodemax[k]=0; /* Horrible constant again */

for (j=1; j<=(cptcovn+2*cptcovprod); j++) {	for (j=1; j<=(cptcovn+2cptcovprod); j++) { / For each covariate */
for (i=1; i<=imx; i++) { /*reads the data file to get the maximum	for (i=1; i<=imx; i++) { /*reads the data file to get the maximum
modality*/	modality*/
ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/	ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual, might be -1*/
Ndum[ij]++; /store the modality /	Ndum[ij]++; /counts the occurence of this modality /
/printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);/	/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	if (ij > cptcode) cptcode=ij; /* getting the maximum value of the modality of the covariate (should be 0 or 1 now)
Tvar[j]. If V=sex and male is 0 and	Tvar[j]. If V=sex and male is 0 and
female is 1, then cptcode=1.*/	female is 1, then cptcode=1.*/
}	}

for (i=0; i<=cptcode; i++) {	for (i=0; i<=cptcode; i++) { /* i=-1 ?*/
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 */	if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariate. In fact ncodemax[j]=2 (dichotom. variables only) but it can be more */
}	} /* Ndum[-1] number of undefined modalities */

ij=1;	ij=1;
for (i=1; i<=ncodemax[j]; i++) {	for (i=1; i<=ncodemax[j]; i++) { /* i= 1 to 2 */
for (k=0; k<= maxncov; k++) {	for (k=0; k<= maxncov; k++) { /* k=-1 ?*/
if (Ndum[k] != 0) {	if (Ndum[k] != 0) { /* If at least one individual responded to this modality k */
nbcode[Tvar[j]][ij]=k;	nbcode[Tvar[j]][ij]=k; /* stores the modality in an array nbcode.
/* store the modality in an array. k is a modality. If we have model=V1+V1sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; /	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++;	ij++;
}	}
if (ij > ncodemax[j]) break;	if (ij > ncodemax[j]) break;
Line 2305 void tricode(int Tvar, int *nbcode, in	Line 2483 void tricode(int Tvar, int *nbcode, in

for (k=0; k< maxncov; k++) Ndum[k]=0;	for (k=0; k< maxncov; k++) Ndum[k]=0;

for (i=1; i<=ncovmodel-2; i++) {	for (i=1; i<=ncovmodel-2; i++) { /* -2, cste and age */
/* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1V2./	/* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1V2./
ij=Tvar[i];	ij=Tvar[i]; /* Tvar might be -1 if status was unknown */
Ndum[ij]++;	Ndum[ij]++;
}	}

Line 2318 void tricode(int Tvar, int *nbcode, in	Line 2496 void tricode(int Tvar, int *nbcode, in
ij++;	ij++;
}	}
}	}
	ij--;
cptcoveff=ij-1; /Number of simple covariates/	cptcoveff=ij; /Number of simple covariates/
}	}

/********* Health Expectancies **************/	/********* Health Expectancies **************/

void evsij(char fileres[], double *eij, double x[], int nlstate, int stepm, int bage, int fage, double oldm, double savm, int ij, int estepm,double delti[],double matcov,char strstart[] )	void evsij(double *eij, double x[], int nlstate, int stepm, int bage, int fage, double oldm, double **savm, int cij, int estepm,char strstart[] )

{	{
/* Health expectancies */	/* Health expectancies, no variances */
int i, j, nhstepm, hstepm, h, nstepm, k, cptj;	int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
	int nhstepma, nstepma; /* Decreasing with age */
double age, agelim, hf;	double age, agelim, hf;
double *p3mat,*varhe;	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;
	/* 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 */

	/* nhstepm age range expressed in number of stepm */
	nstepm=(int) rint((agelim-bage)YEARM/stepm); / Biggest nstepm */
	/* Typically if 20 years nstepm = 2012/6=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 ++){
	nstepma=(int) rint((agelim-bage)YEARM/stepm); / Biggest nstepm */
	/* Typically if 20 years nstepm = 2012/6=40 stepm /
	/* if (stepm >= YEARM) hstepm=1;*/
	nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */

	/* If stepm=6 months */
	/* Computed by stepm unit matrices, product of hstepma matrices, stored
	in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */

	hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);

	hf=hstepmstepm/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(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;
	int nhstepma, nstepma; /* Decreasing with age */
	double age, agelim, hf;
	double *p3matp, p3matm, **varhe;
double dnewm,doldm;	double dnewm,doldm;
double *xp;	double xp, xm;
double gp, gm;	double gp, gm;
double *gradg, *trgradg;	double *gradg, *trgradg;
int theta;	int theta;

	double eip, vip;

varhe=ma3x(1,nlstatenlstate,1,nlstatenlstate,(int) bage, (int) fage);	varhe=ma3x(1,nlstatenlstate,1,nlstatenlstate,(int) bage, (int) fage);
xp=vector(1,npar);	xp=vector(1,npar);
	xm=vector(1,npar);
dnewm=matrix(1,nlstate*nlstate,1,npar);	dnewm=matrix(1,nlstate*nlstate,1,npar);
doldm=matrix(1,nlstatenlstate,1,nlstatenlstate);	doldm=matrix(1,nlstatenlstate,1,nlstatenlstate);

fprintf(ficreseij,"# Local time at start: %s", strstart);	pstamp(ficresstdeij);
fprintf(ficreseij,"# Health expectancies\n");	fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
fprintf(ficreseij,"# Age");	fprintf(ficresstdeij,"# Age");
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++){
for(j=1; j<=nlstate;j++)	for(j=1; j<=nlstate;j++)
fprintf(ficreseij," %1d-%1d (SE)",i,j);	fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
fprintf(ficreseij,"\n");	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){	if(estepm < stepm){
printf ("Problem %d lower than %d\n",estepm, stepm);	printf ("Problem %d lower than %d\n",estepm, stepm);
}	}
Line 2379 void evsij(char fileres[], double ***eij	Line 2688 void evsij(char fileres[], double ***eij
*/	*/
hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */	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;	agelim=AGESUP;
for (age=bage; age<=fage; age ++){ /* If stepm=6 months */	nstepm=(int) rint((agelim-bage)*YEARM/stepm);
/* nhstepm age range expressed in number of stepm */	/* Typically if 20 years nstepm = 2012/6=40 stepm /
nstepm=(int) rint((agelim-age)*YEARM/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 ++){
	nstepma=(int) rint((agelim-bage)YEARM/stepm); / Biggest nstepm */
/* Typically if 20 years nstepm = 2012/6=40 stepm /	/* Typically if 20 years nstepm = 2012/6=40 stepm /
/* if (stepm >= YEARM) hstepm=1;*/	/* if (stepm >= YEARM) hstepm=1;*/
nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */	nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
gp=matrix(0,nhstepm,1,nlstate*nlstate);
gm=matrix(0,nhstepm,1,nlstate*nlstate);

/* 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, ij);


	/* If stepm=6 months */
	/* Computed by stepm unit matrices, product of hstepma matrices, stored
	in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */

hf=hstepmstepm/YEARM; / Duration of hstepm expressed in year unit. */	hf=hstepmstepm/YEARM; / Duration of hstepm expressed in year unit. */

/* Computing Variances of health expectancies */	/* Computing Variances of health expectancies */
	/* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
for(theta=1; theta <=npar; theta++){	decrease memory allocation */
	for(theta=1; theta <=npar; theta++){
for(i=1; i<=npar; i++){	for(i=1; i<=npar; i++){
xp[i] = x[i] + (i==theta ?delti[theta]:0);	xp[i] = x[i] + (i==theta ?delti[theta]:0);
	xm[i] = x[i] - (i==theta ?delti[theta]:0);
}	}
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);	hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
	hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);

cptj=0;
for(j=1; j<= nlstate; j++){	for(j=1; j<= nlstate; j++){
for(i=1; i<=nlstate; i++){	for(i=1; i<=nlstate; i++){
cptj=cptj+1;	for(h=0; h<=nhstepm-1; h++){
for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){	gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
gp[h][cptj] = (p3mat[i][j][h]+p3mat[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(i=1; i<=npar; i++)
xp[i] = x[i] - (i==theta ?delti[theta]:0);
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);

cptj=0;
for(j=1; j<= nlstate; j++){
for(i=1;i<=nlstate;i++){
cptj=cptj+1;
for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){

gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
}
}
}
for(j=1; j<= nlstate*nlstate; j++)
for(h=0; h<=nhstepm-1; h++){	for(h=0; h<=nhstepm-1; h++){
gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];	gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
}	}
}	}/* End theta */

/* End theta */
	for(h=0; h<=nhstepm-1; h++)
trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);

for(h=0; h<=nhstepm-1; h++)
for(j=1; j<=nlstate*nlstate;j++)	for(j=1; j<=nlstate*nlstate;j++)
for(theta=1; theta <=npar; theta++)	for(theta=1; theta <=npar; theta++)
trgradg[h][j][theta]=gradg[h][theta][j];	trgradg[h][j][theta]=gradg[h][theta][j];


for(i=1;i<=nlstate*nlstate;i++)	for(ij=1;ij<=nlstate*nlstate;ij++)
for(j=1;j<=nlstate*nlstate;j++)	for(ji=1;ji<=nlstate*nlstate;ji++)
varhe[i][j][(int)age] =0.;	varhe[ij][ji][(int)age] =0.;

printf("%d\|",(int)age);fflush(stdout);	printf("%d\|",(int)age);fflush(stdout);
fprintf(ficlog,"%d\|",(int)age);fflush(ficlog);	fprintf(ficlog,"%d\|",(int)age);fflush(ficlog);
Line 2457 void evsij(char fileres[], double ***eij	Line 2758 void evsij(char fileres[], double ***eij
for(k=0;k<=nhstepm-1;k++){	for(k=0;k<=nhstepm-1;k++){
matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);	matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
matprod2(doldm,dnewm,1,nlstatenlstate,1,npar,1,nlstatenlstate,gradg[k]);	matprod2(doldm,dnewm,1,nlstatenlstate,1,npar,1,nlstatenlstate,gradg[k]);
for(i=1;i<=nlstate*nlstate;i++)	for(ij=1;ij<=nlstate*nlstate;ij++)
for(j=1;j<=nlstate*nlstate;j++)	for(ji=1;ji<=nlstate*nlstate;ji++)
varhe[i][j][(int)age] += doldm[i][j]hfhf;	varhe[ij][ji][(int)age] += doldm[ij][ji]hfhf;
}	}
}	}

/* Computing expectancies */	/* Computing expectancies */
	hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++)	for(j=1; j<=nlstate;j++)
for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){	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;	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]);*/	/* 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 );	fprintf(ficresstdeij,"%3.0f",age );
cptj=0;	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(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++){	for(j=1; j<=nlstate;j++){
cptj++;	cptj= (j-1)*nlstate+i;
fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );	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(ficreseij,"\n");	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(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
}	}
	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");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");

	free_vector(xm,1,npar);
free_vector(xp,1,npar);	free_vector(xp,1,npar);
free_matrix(dnewm,1,nlstate*nlstate,1,npar);	free_matrix(dnewm,1,nlstate*nlstate,1,npar);
free_matrix(doldm,1,nlstatenlstate,1,nlstatenlstate);	free_matrix(doldm,1,nlstatenlstate,1,nlstatenlstate);
Line 2550 void varevsij(char optionfilefiname[], d	Line 2873 void varevsij(char optionfilefiname[], d
printf("Computing total mortality p.j=w1p1j+w2p2j+..: result on file '%s' \n",fileresprobmorprev);	printf("Computing total mortality p.j=w1p1j+w2p2j+..: result on file '%s' \n",fileresprobmorprev);

fprintf(ficlog,"Computing total mortality p.j=w1p1j+w2p2j+..: result on file '%s' \n",fileresprobmorprev);	fprintf(ficlog,"Computing total mortality p.j=w1p1j+w2p2j+..: result on file '%s' \n",fileresprobmorprev);
fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);	pstamp(ficresprobmorprev);
fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1p1j+w2p2j+... stand dev in()\n",estepm);	fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1p1j+w2p2j+... stand dev in()\n",estepm);
fprintf(ficresprobmorprev,"# Age cov=%-d",ij);	fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
for(j=nlstate+1; j<=(nlstate+ndeath);j++){	for(j=nlstate+1; j<=(nlstate+ndeath);j++){
Line 2565 void varevsij(char optionfilefiname[], d	Line 2888 void varevsij(char optionfilefiname[], d
fprintf(fichtm,"\n<br>%s <br>\n",digitp);	fprintf(fichtm,"\n<br>%s <br>\n",digitp);
/* } */	/* } */
varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);	varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
fprintf(ficresvij, "#Local time at start: %s", strstart);	pstamp(ficresvij);
fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are the stable prevalence in health states i\n");	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 (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d\n",mobilav);
	else
	fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
fprintf(ficresvij,"# Age");	fprintf(ficresvij,"# Age");
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++)	for(j=1; j<=nlstate;j++)
fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);	fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
fprintf(ficresvij,"\n");	fprintf(ficresvij,"\n");

xp=vector(1,npar);	xp=vector(1,npar);
Line 2592 void varevsij(char optionfilefiname[], d	Line 2919 void varevsij(char optionfilefiname[], d
/* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.	/* 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	nhstepm is the number of hstepm from age to agelim
nstepm is the number of stepm from age to agelin.	nstepm is the number of stepm from age to agelin.
Look at hpijx to understand the reason of that which relies in memory size	Look at function hpijx to understand why (it is linked to memory size questions) */
and note for a fixed period like k years */
/* We decided (b) to get a life expectancy respecting the most precise curvature of the	/* 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	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	means that if the survival funtion is printed every two years of age and if
Line 2659 void varevsij(char optionfilefiname[], d	Line 2985 void varevsij(char optionfilefiname[], d
}	}
}	}

for(j=1; j<= nlstate; j++){	for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
for(h=0; h<=nhstepm; h++){	for(h=0; h<=nhstepm; h++){
for(i=1, gm[h][j]=0.;i<=nlstate;i++)	for(i=1, gm[h][j]=0.;i<=nlstate;i++)
gm[h][j] += prlim[i][i]*p3mat[i][j][h];	gm[h][j] += prlim[i][i]*p3mat[i][j][h];
Line 2769 void varevsij(char optionfilefiname[], d	Line 3095 void varevsij(char optionfilefiname[], d
free_vector(gmp,nlstate+1,nlstate+ndeath);	free_vector(gmp,nlstate+1,nlstate+ndeath);
free_matrix(gradgp,1,npar,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*/	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");	fprintf(ficgp,"\nunset parametric;unset label; set ter png small;set size 0.65, 0.65");
/* for(j=nlstate+1; j<= nlstate+ndeath; j++){ // Only the first actually */	/* 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 set log y; unset log 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 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) 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 replot \"%s\" u 1:(($3-1.96$4)%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
Line 2811 void varprevlim(char fileres[], double *	Line 3137 void varprevlim(char fileres[], double *
double gradg, trgradg;	double gradg, trgradg;
double age,agelim;	double age,agelim;
int theta;	int theta;
fprintf(ficresvpl, "#Local time at start: %s", strstart);
fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");	pstamp(ficresvpl);
	fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
fprintf(ficresvpl,"# Age");	fprintf(ficresvpl,"# Age");
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
fprintf(ficresvpl," %1d-%1d",i,i);	fprintf(ficresvpl," %1d-%1d",i,i);
Line 2926 void varprob(char optionfilefiname[], do	Line 3253 void varprob(char optionfilefiname[], do
fprintf(ficlog,"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);	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);	fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
fprintf(ficresprob, "#Local time at start: %s", strstart);	pstamp(ficresprob);
fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");	fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
fprintf(ficresprob,"# Age");	fprintf(ficresprob,"# Age");
fprintf(ficresprobcov, "#Local time at start: %s", strstart);	pstamp(ficresprobcov);
fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");	fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
fprintf(ficresprobcov,"# Age");	fprintf(ficresprobcov,"# Age");
fprintf(ficresprobcor, "#Local time at start: %s", strstart);	pstamp(ficresprobcor);
fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");	fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
fprintf(ficresprobcov,"# Age");	fprintf(ficresprobcor,"# Age");


for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
Line 2947 void varprob(char optionfilefiname[], do	Line 3274 void varprob(char optionfilefiname[], do
fprintf(ficresprobcov,"\n");	fprintf(ficresprobcov,"\n");
fprintf(ficresprobcor,"\n");	fprintf(ficresprobcor,"\n");
*/	*/
xp=vector(1,npar);	xp=vector(1,npar);
dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);	dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
doldm=matrix(1,(nlstate)(nlstate+ndeath),1,(nlstate)(nlstate+ndeath));	doldm=matrix(1,(nlstate)(nlstate+ndeath),1,(nlstate)(nlstate+ndeath));
mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);	mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
Line 3100 To be simple, these graphs help to under	Line 3427 To be simple, these graphs help to under

/* Confidence intervalle of pij */	/* Confidence intervalle of pij */
/*	/*
fprintf(ficgp,"\nset noparametric;unset label");	fprintf(ficgp,"\nunset parametric;unset label");
fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");	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(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>Probability with confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
Line 3185 To be simple, these graphs help to under	Line 3512 To be simple, these graphs help to under
}	}
free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);	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(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);	free_vector(xp,1,npar);
fclose(ficresprob);	fclose(ficresprob);
fclose(ficresprobcov);	fclose(ficresprobcov);
Line 3203 void printinghtml(char fileres[], char t	Line 3532 void printinghtml(char fileres[], char t
double jprev2, double mprev2,double anprev2){	double jprev2, double mprev2,double anprev2){
int jj1, k1, i1, cpt;	int jj1, k1, i1, cpt;

fprintf(fichtm,"<ul><li><a> href="#firstorder">Result files (first order: no variance)</a>\n \	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 \	<li><a href='#secondorder'>Result files (second order (variance)</a>\n \
</ul>");	</ul>");
fprintf(fichtm,"<ul><li><h4><a name="firstorder">Result files (first order: no variance)</a></h4>\n \	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 ",	- 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"));	jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",	- Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));	stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",	- Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));	subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Life expectancies by age and initial health status (estepm=%2d months): \	- (a) Life expectancies by health status at initial age, ei. (b) health expectancies by health status at initial age, eij . If one or more covariates 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>",	<a href=\"%s\">%s</a> <br>\n",
estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));	estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
	fprintf(fichtm,"\
	- Population projections by age and states: \
	<a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));

fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");	fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");

Line 3236 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 3568 fprintf(fichtm," \n<ul><li><b>Graphs</b>
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");	fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
}	}
/* Pij */	/* Pij */
fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \	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);	<img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
/* Quasi-incidences */	/* Quasi-incidences */
fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\	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: %s%d2.png<br> \	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);	<img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
/* Stable prevalence in each health state */	/* Period (stable) prevalence in each health state */
for(cpt=1; cpt<nlstate;cpt++){	for(cpt=1; cpt<nlstate;cpt++){
fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \	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);	<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++) {	for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \	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);	<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 i1 */
}/* End k1 */	}/* End k1 */
Line 3257 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 3589 fprintf(fichtm," \n<ul><li><b>Graphs</b>


fprintf(fichtm,"\	fprintf(fichtm,"\
\n<br><li><h4> <a name="secondorder">Result files (second order: variances)</a></h4>\n\	\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);	- 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",	fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
Line 3270 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 3602 fprintf(fichtm," \n<ul><li><b>Graphs</b>
- Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",	- Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));	subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",	- 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), e<sup>ij</sup> 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"));	estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",	- Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (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",
subdirf2(fileres,"t"),subdirf2(fileres,"t"));	estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\	- Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));	subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));

/* if(popforecast==1) fprintf(fichtm,"\n */	/* if(popforecast==1) fprintf(fichtm,"\n */
Line 3307 prevalence (with 95%% confidence interva	Line 3647 prevalence (with 95%% confidence interva
<img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);	<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 \	fprintf(fichtm,"\n<br>- Total life expectancy by age and \
health expectancies in states (1) and (2): %s%d.png<br>\	health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
	true period expectancies (those weighted with period prevalences are also\
	drawn in addition to the population based expectancies computed using\
	observed and cahotic prevalences: %s%d.png<br>\
<img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);	<img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
} /* end i1 */	} /* end i1 */
}/* End k1 */	}/* End k1 */
Line 3319 health expectancies in states (1) and (2	Line 3662 health expectancies in states (1) and (2
void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){	void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){

char dirfileres[132],optfileres[132];	char dirfileres[132],optfileres[132];
int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;	int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
int ng;	int ng=0;
/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */	/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
/* printf("Problem with file %s",optionfilegnuplot); */	/* printf("Problem with file %s",optionfilegnuplot); */
/* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */	/* fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
Line 3346 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 3689 plot [%.f:%.f] \"%s\" every :::%d::%d u

for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");	if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
else fprintf(ficgp," \%%lf (\%%lf)");	else fprintf(ficgp," \%%lf (\%%lf)");
}	}
fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);	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 ++) {	for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");	if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
else fprintf(ficgp," \%%lf (\%%lf)");	else fprintf(ficgp," \%%lf (\%%lf)");
Line 3396 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 3739 plot [%.f:%.f] \"%s\" every :::%d::%d u

for (k1=1; k1<= m ; k1 ++) {	for (k1=1; k1<= m ; k1 ++) {
for (cpt=1; cpt<= nlstate ; cpt ++) {	for (cpt=1; cpt<= nlstate ; cpt ++) {
k=2+nlstate(2cpt-2);	/* k=2+nlstate(2cpt-2); */
	k=2+(nlstate+1)*(cpt-1);
fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);	fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
fprintf(ficgp,"set ter png small\n\	fprintf(ficgp,"set ter png small\n\
set size 0.65,0.65\n\	set size 0.65,0.65\n\
Line 3410 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 3754 plot [%.f:%.f] \"%s\" every :::%d::%d u

*/	*/
for (i=1; i< nlstate ; i ++) {	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+2*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+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+2i,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);
}	}
}	}

Line 3971 double gompertz(double x[])	Line 4317 double gompertz(double x[])
{	{
double A,B,L=0.0,sump=0.,num=0.;	double A,B,L=0.0,sump=0.,num=0.;
int i,n=0; /* n is the size of the sample */	int i,n=0; /* n is the size of the sample */

for (i=0;i<=imx-1 ; i++) {	for (i=0;i<=imx-1 ; i++) {
sump=sump+weight[i];	sump=sump+weight[i];
/* sump=sump+1;*/	/* sump=sump+1;*/
Line 3983 double gompertz(double x[])	Line 4330 double gompertz(double x[])

for (i=1;i<=imx ; i++)	for (i=1;i<=imx ; i++)
{	{
if (cens[i]==1 & wav[i]>1)	if (cens[i] == 1 && wav[i]>1)
A=-x[1]/(x[2])(exp(x[2](agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));	A=-x[1]/(x[2])(exp(x[2](agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));

if (cens[i]==0 & wav[i]>1)	if (cens[i] == 0 && wav[i]>1)
A=-x[1]/(x[2])(exp(x[2](agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))	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);	+log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);

if (wav[i]>1 & agecens[i]>15) {	/if (wav[i] > 1 && agecens[i] > 15) {/ /* ??? */
	if (wav[i] > 1 ) { /* ??? */
L=L+A*weight[i];	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("\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]);/
}	}
Line 4051 void printinggnuplotmort(char fileres[],	Line 4399 void printinggnuplotmort(char fileres[],




/***********************************************/	/***********************************************/
/************** Main Program ***************/	/************** Main Program ***************/
/***********************************************/	/***********************************************/
Line 4059 int main(int argc, char *argv[])	Line 4408 int main(int argc, char *argv[])
{	{
int movingaverage(double *probs, double bage,double fage, double *mobaverage, int mobilav);	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 i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
	int linei, month, year,iout;
int jj, ll, li, lj, lk, imk;	int jj, ll, li, lj, lk, imk;
int numlinepar=0; /* Current linenumber of parameter file */	int numlinepar=0; /* Current linenumber of parameter file */
int itimes;	int itimes;
int NDIM=2;	int NDIM=2;
	int vpopbased=0;

char ca[32], cb[32], cc[32];	char ca[32], cb[32], cc[32];
	char dummy[]=" ";
/* FILE fichtm; //* Html File */	/* FILE fichtm; //* Html File */
/* FILE ficgp;/ /Gnuplot File /	/* FILE ficgp;/ /Gnuplot File /
	struct stat info;
double agedeb, agefin,hf;	double agedeb, agefin,hf;
double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;	double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;

Line 4080 int main(int argc, char *argv[])	Line 4433 int main(int argc, char *argv[])
char line[MAXLINE], linepar[MAXLINE];	char line[MAXLINE], linepar[MAXLINE];
char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];	char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
char pathr[MAXLINE], pathimach[MAXLINE];	char pathr[MAXLINE], pathimach[MAXLINE];
	char *bp, tok, val; / pathtot */
int firstobs=1, lastobs=10;	int firstobs=1, lastobs=10;
int sdeb, sfin; /* Status at beginning and end */	int sdeb, sfin; /* Status at beginning and end */
int c, h , cpt,l;	int c, h , cpt,l;
Line 4115 int main(int argc, char *argv[])	Line 4469 int main(int argc, char *argv[])
char z[1]="c", occ;	char z[1]="c", occ;

char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];	char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
char strstart[80], *strt, strtend[80];	char *strt, strtend[80];
char *stratrunc;	char *stratrunc;
int lstra;	int lstra;

Line 4157 int main(int argc, char *argv[])	Line 4511 int main(int argc, char *argv[])
printf("\n%s\n%s",version,fullversion);	printf("\n%s\n%s",version,fullversion);
if(argc <=1){	if(argc <=1){
printf("\nEnter the parameter file name: ");	printf("\nEnter the parameter file name: ");
scanf("%s",pathtot);	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{	else{
strcpy(pathtot,argv[1]);	strcpy(pathtot,argv[1]);
Line 4167 int main(int argc, char *argv[])	Line 4531 int main(int argc, char *argv[])
printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/	printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
/* cutv(path,optionfile,pathtot,'\\');*/	/* 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);	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]); */	/* strcpy(pathimach,argv[0]); */
	/* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
split(pathtot,path,optionfile,optionfilext,optionfilefiname);	split(pathtot,path,optionfile,optionfilext,optionfilefiname);
printf("pathimach=%s, pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);	printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
chdir(path);	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 ");	strcpy(command,"mkdir ");
strcat(command,optionfilefiname);	strcat(command,optionfilefiname);
if((outcmd=system(command)) != 0){	if((outcmd=system(command)) != 0){
Line 4269 int main(int argc, char *argv[])	Line 4639 int main(int argc, char *argv[])
ncovmodel=2+cptcovn; /Number of variables = cptcovn + intercept + age /	ncovmodel=2+cptcovn; /Number of variables = cptcovn + intercept + age /
nvar=ncovmodel-1; /* Suppressing age as a basic covariate */	nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
npar= (nlstate+ndeath-1)nlstatencovmodel; /* Number of parameters*/	npar= (nlstate+ndeath-1)nlstatencovmodel; /* Number of parameters*/
	if(npar >MAXPARM \|\| nlstate >NLSTATEMAX \|\| ndeath >NDEATHMAX \|\| ncovmodel>NCOVMAX){
	printf("Too complex model for current IMaCh: npar=(nlstate+ndeath-1)nlstatencovmodel=%d >= %d(MAXPARM) or nlstate=%d >= %d(NLSTATEMAX) or ndeath=%d >= %d(NDEATHMAX) or ncovmodel=(k+age+#of+signs)=%d(NCOVMAX) >= %d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
	fprintf(ficlog,"Too complex model for current IMaCh: %d >=%d(MAXPARM) or %d >=%d(NLSTATEMAX) or %d >=%d(NDEATHMAX) or %d(NCOVMAX) >=%d\n",npar, MAXPARM, nlstate, NLSTATEMAX, ndeath, NDEATHMAX, ncovmodel, NCOVMAX);
	fflush(stdout);
	fclose (ficlog);
	goto end;
	}
delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);	delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
delti=delti3[1][1];	delti=delti3[1][1];
/delti=vector(1,npar); //* Scale of each paramater (output from hesscov)*/	/delti=vector(1,npar); //* Scale of each paramater (output from hesscov)*/
Line 4280 int main(int argc, char *argv[])	Line 4656 int main(int argc, char *argv[])
free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);	free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
fclose (ficparo);	fclose (ficparo);
fclose (ficlog);	fclose (ficlog);
	goto end;
exit(0);	exit(0);
}	}
else if(mle==-3) {	else if(mle==-3) {
Line 4310 int main(int argc, char *argv[])	Line 4687 int main(int argc, char *argv[])
j++;	j++;
fscanf(ficpar,"%1d%1d",&i1,&j1);	fscanf(ficpar,"%1d%1d",&i1,&j1);
if ((i1 != i) && (j1 != j)){	if ((i1 != i) && (j1 != j)){
printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);	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);	exit(1);
}	}
fprintf(ficparo,"%1d%1d",i1,j1);	fprintf(ficparo,"%1d%1d",i1,j1);
Line 4337 int main(int argc, char *argv[])	Line 4716 int main(int argc, char *argv[])
}	}
fflush(ficlog);	fflush(ficlog);


p=param[1][1];	p=param[1][1];

/* Reads comments: lines beginning with '#' */	/* Reads comments: lines beginning with '#' */
Line 4393 int main(int argc, char *argv[])	Line 4771 int main(int argc, char *argv[])
ungetc(c,ficpar);	ungetc(c,ficpar);

matcov=matrix(1,npar,1,npar);	matcov=matrix(1,npar,1,npar);
	for(i=1; i <=npar; i++)
	for(j=1; j <=npar; j++) matcov[i][j]=0.;

for(i=1; i <=npar; i++){	for(i=1; i <=npar; i++){
fscanf(ficpar,"%s",&str);	fscanf(ficpar,"%s",&str);
if(mle==1)	if(mle==1)
Line 4438 int main(int argc, char *argv[])	Line 4819 int main(int argc, char *argv[])

/-------- data file ----------/	/-------- data file ----------/
if((fic=fopen(datafile,"r"))==NULL) {	if((fic=fopen(datafile,"r"))==NULL) {
printf("Problem with datafile: %s\n", datafile);goto end;	printf("Problem while opening datafile: %s\n", datafile);goto end;
fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;	fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
}	}

n= lastobs;	n= lastobs;
Line 4456 int main(int argc, char *argv[])	Line 4837 int main(int argc, char *argv[])
for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */	for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
mint=matrix(1,maxwav,1,n);	mint=matrix(1,maxwav,1,n);
anint=matrix(1,maxwav,1,n);	anint=matrix(1,maxwav,1,n);
s=imatrix(1,maxwav+1,1,n);	s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
tab=ivector(1,NCOVMAX);	tab=ivector(1,NCOVMAX);
ncodemax=ivector(1,8);	ncodemax=ivector(1,8);

i=1;	i=1;
while (fgets(line, MAXLINE, fic) != NULL) {	linei=0;
if ((i >= firstobs) && (i <=lastobs)) {	while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
for(j=0; line[j] != '\n';j++){ /* Untabifies line */	linei=linei+1;
if(line[j] == '\t')	for(j=strlen(line); j>=0;j--){ /* Untabifies line */
line[j] = ' ';	if(line[j] == '\t')
}	line[j] = ' ';
for (j=maxwav;j>=1;j--){	}
cutv(stra, strb,line,' '); s[j][i]=atoi(strb);	for(j=strlen(line)-1; (line[j]==' ')\|\|(line[j]==10)\|\|(line[j]==13);j--){
strcpy(line,stra);	;
cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);	};
cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);	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,' ');
	if(strb[0]=='.') { /* Missing status */
	lval=-1;
	}else{
	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 '%s' at line number %ld 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);
	fprintf(ficlog,"Error reading data around '%s' at line number %ld 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);fflush(ficlog);
	goto end;
	}
}	}
	s[j][i]=lval;
cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);	strcpy(line,stra);
	cutv(stra, strb,line,' ');
cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);	if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);	}
	else if(iout=sscanf(strb,"%s.") != 0){
cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);	month=99;
for (j=ncovcol;j>=1;j--){	year=9999;
cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);	}else{
}	printf("Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);
lstra=strlen(stra);	fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);fflush(ficlog);
if(lstra > 9){ /* More than 2*32 or max of what printf can write with %ld /	goto end;
stratrunc = &(stra[lstra-9]);
num[i]=atol(stratrunc);
}	}
else	anint[j][i]= (double) year;
num[i]=atol(stra);	mint[j][i]= (double)month;
	strcpy(line,stra);
/*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){	} /* ENd Waves */
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;}*/
	cutv(stra, strb,line,' ');
i=i+1;	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 for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
	fprintf(ficlog,"Error reading data around '%s' at line number %ld for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);fflush(ficlog);
	goto end;
}	}
}	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);
	fprintf(ficlog,"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);fflush(ficlog);
	goto end;
	}
	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);
	fprintf(ficlog,"Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
	fflush(ficlog);
	goto end;
	}
	weight[i]=dval;
	strcpy(line,stra);

	for (j=ncovcol;j>=1;j--){
	cutv(stra, strb,line,' ');
	if(strb[0]=='.') { /* Missing status */
	lval=-1;
	}else{
	errno=0;
	lval=strtol(strb,&endptr,10);
	if( strb[0]=='\0' \|\| (*endptr != '\0')){
	printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);
	fprintf(ficlog,"Error reading data around '%d' at line number %ld for individual %d, '%s'\nShould be a covariate value (=0 for the reference or 1 for alternative). Exiting.\n",lval, linei,i, line);fflush(ficlog);
	goto end;
	}
	}
	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);
	fprintf(ficlog,"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);fflush(ficlog);
	goto end;
	}
	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);	/* printf("ii=%d", ij);
scanf("%d",i);*/	scanf("%d",i);*/
imx=i-1; /* Number of individuals */	imx=i-1; /* Number of individuals */
Line 4517 int main(int argc, char *argv[])	Line 5004 int main(int argc, char *argv[])
else weight[i]=1;*/	else weight[i]=1;*/

/* Calculation of the number of parameters from char model */	/* 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 */	Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. Stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
Tprod=ivector(1,15);	Tprod=ivector(1,15);
Tvaraff=ivector(1,15);	Tvaraff=ivector(1,15);
Tvard=imatrix(1,15,1,2);	Tvard=imatrix(1,15,1,2);
Line 4527 int main(int argc, char *argv[])	Line 5014 int main(int argc, char *argv[])
j=0, j1=0, k1=1, k2=1;	j=0, j1=0, k1=1, k2=1;
j=nbocc(model,'+'); /* j=Number of '+' */	j=nbocc(model,'+'); /* j=Number of '+' */
j1=nbocc(model,''); / j1=Number of '' /	j1=nbocc(model,''); / j1=Number of '' /
cptcovn=j+1;	cptcovn=j+1; /* Number of covariates V1+V2+V3 =>2+1=3 */
cptcovprod=j1; /Number of products /	cptcovprod=j1; /Number of products V1V2 =1 */

strcpy(modelsav,model);	strcpy(modelsav,model);
if ((strcmp(model,"age")==0) \|\| (strcmp(model,"age*age")==0)){	if ((strcmp(model,"age")==0) \|\| (strcmp(model,"age*age")==0)){
printf("Error. Non available option model=%s ",model);	printf("Error. Non available option model=%s ",model);
fprintf(ficlog,"Error. Non available option model=%s ",model);	fprintf(ficlog,"Error. Non available option model=%s ",model);fflush(ficlog);
goto end;	goto end;
}	}

/* This loop fills the array Tvar from the string 'model'.*/	/* This loop fills the array Tvar from the string 'model'.*/
	/* j is the number of + signs in the model V1+V2+V3 j=2 i=3 to 1 */
for(i=(j+1); i>=1;i--){	for(i=(j+1); i>=1;i--){
cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */	cutv(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
	modelsav=V2+V3age+V1+V4 strb=V3age+V1+V4
	stra=V2
	*/
if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */	if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
/* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/	/* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
/scanf("%d",i);/	/scanf("%d",i);/
if (strchr(strb,'')) { / Model includes a product */	if (strchr(strb,'')) { / Model includes a product V1+V3age+V2 strb=V3age*/
cutv(strd,strc,strb,''); / strdstrc VmVn (if not age)/	cutv(strd,strc,strb,''); / strdstrc VmVn: V3age strc=age strd=V3 ; V3V2 strc=V2, strd=V3 */
if (strcmp(strc,"age")==0) { /* Vnage /	if (strcmp(strc,"age")==0) { /* Vnage /
cptcovprod--;	cptcovprod--;
cutv(strb,stre,strd,'V');	cutv(strb,stre,strd,'V');
Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/	Tvar[i]=atoi(stre); /* V1+V3age+V2 Tvar[2]=3 /
cptcovage++;	cptcovage++; /* Sum the number of covariates including ages as a product */
Tage[cptcovage]=i;	Tage[cptcovage]=i; /* Tage[1] =2 */
/printf("stre=%s ", stre);/	/printf("stre=%s ", stre);/
}	}
else if (strcmp(strd,"age")==0) { /* or ageVn /	else if (strcmp(strd,"age")==0) { /* or ageVn /
cptcovprod--;	cptcovprod--;
Line 4561 int main(int argc, char *argv[])	Line 5051 int main(int argc, char *argv[])
cptcovage++;	cptcovage++;
Tage[cptcovage]=i;	Tage[cptcovage]=i;
}	}
else { /* Age is not in the model */	else { /* Age is not in the model V1+V3V2+V2 strb=V3V2*/
cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/	cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n; strb=V3V2 stre=3 strc=/
Tvar[i]=ncovcol+k1;	Tvar[i]=ncovcol+k1; /* find 'n' in Vn and stores in Tvar.
	If already ncovcol=2 and model=V2V1 Tvar[1]=2+1 and Tvar[2]=2+2 etc /
cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */	cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
Tprod[k1]=i;	Tprod[k1]=i; /* Tprod[1] */
Tvard[k1][1]=atoi(strc); /* m*/	Tvard[k1][1]=atoi(strc); /* m*/
Tvard[k1][2]=atoi(stre); /* n */	Tvard[k1][2]=atoi(stre); /* n */
Tvar[cptcovn+k2]=Tvard[k1][1];	Tvar[cptcovn+k2]=Tvard[k1][1];
Line 4582 int main(int argc, char *argv[])	Line 5073 int main(int argc, char *argv[])
cutv(strd,strc,strb,'V');	cutv(strd,strc,strb,'V');
Tvar[i]=atoi(strc);	Tvar[i]=atoi(strc);
}	}
strcpy(modelsav,stra);	strcpy(modelsav,stra); /* modelsav=V2+V3age+V1+V4 strb=V3age+V1+V4 */
/*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);	/*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
scanf("%d",i);*/	scanf("%d",i);*/
} /* end of loop + */	} /* end of loop + */
Line 4595 int main(int argc, char *argv[])	Line 5086 int main(int argc, char *argv[])
printf("cptcovprod=%d ", cptcovprod);	printf("cptcovprod=%d ", cptcovprod);
fprintf(ficlog,"cptcovprod=%d ", cptcovprod);	fprintf(ficlog,"cptcovprod=%d ", cptcovprod);

scanf("%d ",i);	scanf("%d ",i);*/
fclose(fic);*/

/* if(mle==1){*/	/* if(mle==1){*/
if (weightopt != 1) { /* Maximisation without weights*/	if (weightopt != 1) { /* Maximisation without weights*/
Line 4645 int main(int argc, char *argv[])	Line 5135 int main(int argc, char *argv[])
}	}
}	}
else if(s[m][i] !=9){ /* Standard case, age in fractional	else if(s[m][i] !=9){ /* Standard case, age in fractional
years but with the precision of a	years but with the precision of a month */
month */
agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);	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)	if((int)mint[m][i]==99 \|\| (int)anint[m][i]==9999)
agev[m][i]=1;	agev[m][i]=1;
Line 4714 int main(int argc, char *argv[])	Line 5203 int main(int argc, char *argv[])

/* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */	/* 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);	nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
ncodemax[1]=1;	ncodemax[1]=1;
if (cptcovn > 0) tricode(Tvar,nbcode,imx);	if (cptcovn > 0) tricode(Tvar,nbcode,imx);
Line 4724 int main(int argc, char *argv[])	Line 5212 int main(int argc, char *argv[])
h=0;	h=0;
m=pow(2,cptcoveff);	m=pow(2,cptcoveff);

for(k=1;k<=cptcoveff; k++){	for(k=1;k<=cptcoveff; k++){ /* scans any effective covariate */
for(i=1; i <=(m/pow(2,k));i++){	for(i=1; i <=(m/pow(2,k));i++){ /* i=1 to 8/1=8; i=1 to 8/2=4; i=1 to 8/8=1 */
for(j=1; j <= ncodemax[k]; j++){	for(j=1; j <= ncodemax[k]; j++){ /* For each modality of this covariate */
for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){	for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){ /* cpt=1 to 8/2*(3+1-1 or 3+1-3) =1 or 4 /
h++;	h++;
if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;	if (h>m)
/* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/	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 codtab[h][Tvar[k]]=%d \n",h, k,j,codtab[h][k],Tvar[k],codtab[h][Tvar[k]]);
}	}
}	}
}	}
Line 4739 int main(int argc, char *argv[])	Line 5228 int main(int argc, char *argv[])
codtab[1][2]=1;codtab[2][2]=2; */	codtab[1][2]=1;codtab[2][2]=2; */
/* for(i=1; i <=m ;i++){	/* for(i=1; i <=m ;i++){
for(k=1; k <=cptcovn; k++){	for(k=1; k <=cptcovn; k++){
printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);	printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
}	}
printf("\n");	printf("\n");
}	}
Line 4767 int main(int argc, char *argv[])	Line 5256 int main(int argc, char *argv[])
strcat(optionfilehtm,"-mort");	strcat(optionfilehtm,"-mort");
strcat(optionfilehtm,".htm");	strcat(optionfilehtm,".htm");
if((fichtm=fopen(optionfilehtm,"w"))==NULL) {	if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
printf("Problem with %s \n",optionfilehtm), exit(0);	printf("Problem with %s \n",optionfilehtm);
	exit(0);
}	}

strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */	strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
Line 4776 int main(int argc, char *argv[])	Line 5266 int main(int argc, char *argv[])
printf("Problem with %s \n",optionfilehtmcov), exit(0);	printf("Problem with %s \n",optionfilehtmcov), exit(0);
}	}
else{	else{
fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \	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\	<hr size=\"2\" color=\"#EC5E5E\"> \n\
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\	Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);	optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
}	}

fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \	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\	<hr size=\"2\" color=\"#EC5E5E\"> \n\
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\	Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
\n\	\n\
<hr size=\"2\" color=\"#EC5E5E\">\	<hr size=\"2\" color=\"#EC5E5E\">\
<ul><li><h4>Parameter files</h4>\n\	<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\	- 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\	- Log file of the run: <a href=\"%s\">%s</a><br>\n\
- Gnuplot file name: <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",\	- Date and time at start: %s</ul>\n",\
fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\	optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
	optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
fileres,fileres,\	fileres,fileres,\
filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);	filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
fflush(fichtm);	fflush(fichtm);
Line 4822 Interval (in months) between two waves:	Line 5314 Interval (in months) between two waves:
p=param[1][1]; /* (((param +1)+1)+0) /	p=param[1][1]; /* (((param +1)+1)+0) /

globpr=0; /* To get the number ipmx of contributions and the sum of weights*/	globpr=0; /* To get the number ipmx of contributions and the sum of weights*/

if (mle==-3){	if (mle==-3){
ximort=matrix(1,NDIM,1,NDIM);	ximort=matrix(1,NDIM,1,NDIM);
cens=ivector(1,n);	cens=ivector(1,n);
Line 4831 Interval (in months) between two waves:	Line 5324 Interval (in months) between two waves:

for (i=1; i<=imx; i++){	for (i=1; i<=imx; i++){
dcwave[i]=-1;	dcwave[i]=-1;
for (j=1; j<=lastpass; j++)	for (m=firstpass; m<=lastpass; m++)
if (s[j][i]>nlstate) {	if (s[m][i]>nlstate) {
dcwave[i]=j;	dcwave[i]=m;
/* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/	/* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
break;	break;
}	}
Line 4842 Interval (in months) between two waves:	Line 5335 Interval (in months) between two waves:
for (i=1; i<=imx; i++) {	for (i=1; i<=imx; i++) {
if (wav[i]>0){	if (wav[i]>0){
ageexmed[i]=agev[mw[1][i]][i];	ageexmed[i]=agev[mw[1][i]][i];
j=wav[i];agecens[i]=1.;	j=wav[i];
if (ageexmed[i]>1 & wav[i]>0) agecens[i]=agev[mw[j][i]][i];	agecens[i]=1.;
cens[i]=1;
	if (ageexmed[i]> 1 && wav[i] > 0){
if (ageexmed[i]<1) cens[i]=-1;	agecens[i]=agev[mw[j][i]][i];
if (agedc[i]< AGESUP & agedc[i]>1 & dcwave[i]>firstpass & dcwave[i]<=lastpass) cens[i]=0 ;	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;	else cens[i]=-1;
}	}
Line 4856 Interval (in months) between two waves:	Line 5353 Interval (in months) between two waves:
for (j=1;j<=NDIM;j++)	for (j=1;j<=NDIM;j++)
ximort[i][j]=(i == j ? 1.0 : 0.0);	ximort[i][j]=(i == j ? 1.0 : 0.0);
}	}

p[1]=0.1; p[2]=0.1;	p[1]=0.0268; p[NDIM]=0.083;
/printf("%lf %lf", p[1], p[2]);/	/printf("%lf %lf", p[1], p[2]);/


printf("Powell\n"); fprintf(ficlog,"Powell\n");	printf("Powell\n"); fprintf(ficlog,"Powell\n");
strcpy(filerespow,"pow-mort");	strcpy(filerespow,"pow-mort");
strcat(filerespow,fileres);	strcat(filerespow,fileres);
if((ficrespow=fopen(filerespow,"w"))==NULL) {	if((ficrespow=fopen(filerespow,"w"))==NULL) {
printf("Problem with resultfile: %s\n", filerespow);	printf("Problem with resultfile: %s\n", filerespow);
fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);	fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
}	}
fprintf(ficrespow,"# Powell\n# iter -2*LL");	fprintf(ficrespow,"# Powell\n# iter -2*LL");
/* for (i=1;i<=nlstate;i++)	/* for (i=1;i<=nlstate;i++)
for(j=1;j<=nlstate+ndeath;j++)	for(j=1;j<=nlstate+ndeath;j++)
if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);	if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
*/	*/
fprintf(ficrespow,"\n");	fprintf(ficrespow,"\n");

powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);	powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
fclose(ficrespow);	fclose(ficrespow);

hesscov(matcov, p, NDIM,delti, 1e-4, gompertz);	hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);

for(i=1; i <=NDIM; i++)	for(i=1; i <=NDIM; i++)
for(j=i+1;j<=NDIM;j++)	for(j=i+1;j<=NDIM;j++)
Line 4896 Interval (in months) between two waves:	Line 5393 Interval (in months) between two waves:
for (i=1;i<=NDIM;i++)	for (i=1;i<=NDIM;i++)
printf("%f [%f ; %f]\n",p[i],p[i]-2sqrt(matcov[i][i]),p[i]+2sqrt(matcov[i][i]));	printf("%f [%f ; %f]\n",p[i],p[i]-2sqrt(matcov[i][i]),p[i]+2sqrt(matcov[i][i]));

lsurv=vector(1,AGESUP);	lsurv=vector(1,AGESUP);
lpop=vector(1,AGESUP);	lpop=vector(1,AGESUP);
tpop=vector(1,AGESUP);	tpop=vector(1,AGESUP);
lsurv[agegomp]=100000;	lsurv[agegomp]=100000;

for (k=agegomp;k<=AGESUP;k++) {	for (k=agegomp;k<=AGESUP;k++) {
agemortsup=k;	agemortsup=k;
if (p[1]exp(p[2](k-agegomp))>1) break;	if (p[1]exp(p[2](k-agegomp))>1) break;
}	}

for (k=agegomp;k<agemortsup;k++)	for (k=agegomp;k<agemortsup;k++)
lsurv[k+1]=lsurv[k]-lsurv[k](p[1]exp(p[2]*(k-agegomp)));	lsurv[k+1]=lsurv[k]-lsurv[k](p[1]exp(p[2]*(k-agegomp)));

for (k=agegomp;k<agemortsup;k++){	for (k=agegomp;k<agemortsup;k++){
lpop[k]=(lsurv[k]+lsurv[k+1])/2.;	lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
sumlpop=sumlpop+lpop[k];	sumlpop=sumlpop+lpop[k];
}	}

tpop[agegomp]=sumlpop;	tpop[agegomp]=sumlpop;
for (k=agegomp;k<(agemortsup-3);k++){	for (k=agegomp;k<(agemortsup-3);k++){
/* tpop[k+1]=2;*/	/* tpop[k+1]=2;*/
tpop[k+1]=tpop[k]-lpop[k];	tpop[k+1]=tpop[k]-lpop[k];
}	}


printf("\nAge lx qx dx Lx Tx e(x)\n");	printf("\nAge lx qx dx Lx Tx e(x)\n");
for (k=agegomp;k<(agemortsup-2);k++)	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]);	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,path); /* Even gnuplot wants a / */	replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);	printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);

printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \	printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
stepm, weightopt,\	stepm, weightopt,\
model,imx,p,matcov,agemortsup);	model,imx,p,matcov,agemortsup);

free_vector(lsurv,1,AGESUP);	free_vector(lsurv,1,AGESUP);
free_vector(lpop,1,AGESUP);	free_vector(lpop,1,AGESUP);
free_vector(tpop,1,AGESUP);	free_vector(tpop,1,AGESUP);
} /* Endof if mle==-3 */	} /* Endof if mle==-3 */

else{ /* For mle >=1 */

likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */	else{ /* For mle >=1 */
	globpr=1;/* debug */
	/* 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);	printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
for (k=1; k<=npar;k++)	for (k=1; k<=npar;k++)
printf(" %d %8.5f",k,p[k]);	printf(" %d %8.5f",k,p[k]);
Line 4969 lsurv=vector(1,AGESUP);	Line 5466 lsurv=vector(1,AGESUP);
fprintf(ficlog,"%d%d ",i,k);	fprintf(ficlog,"%d%d ",i,k);
fprintf(ficres,"%1d%1d ",i,k);	fprintf(ficres,"%1d%1d ",i,k);
for(j=1; j <=ncovmodel; j++){	for(j=1; j <=ncovmodel; j++){
printf("%f ",p[jk]);	printf("%lf ",p[jk]);
fprintf(ficlog,"%f ",p[jk]);	fprintf(ficlog,"%lf ",p[jk]);
fprintf(ficres,"%f ",p[jk]);	fprintf(ficres,"%lf ",p[jk]);
jk++;	jk++;
}	}
printf("\n");	printf("\n");
Line 5163 lsurv=vector(1,AGESUP);	Line 5660 lsurv=vector(1,AGESUP);
/* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/	/* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
/,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);/	/,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);/

replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */	replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);	printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);

printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\	printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
Line 5185 lsurv=vector(1,AGESUP);	Line 5682 lsurv=vector(1,AGESUP);
fclose(ficres);	fclose(ficres);


/--------------- Prevalence limit (stable prevalence) --------------/	/--------------- Prevalence limit (period or stable prevalence) --------------/

strcpy(filerespl,"pl");	strcpy(filerespl,"pl");
strcat(filerespl,fileres);	strcat(filerespl,fileres);
if((ficrespl=fopen(filerespl,"w"))==NULL) {	if((ficrespl=fopen(filerespl,"w"))==NULL) {
printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;	printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;	fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
}	}
printf("Computing stable prevalence: result on file '%s' \n", filerespl);	printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);	fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
fprintf(ficrespl, "#Local time at start: %s", strstart);	pstamp(ficrespl);
fprintf(ficrespl,"#Stable prevalence \n");	fprintf(ficrespl,"# Period (stable) prevalence \n");
fprintf(ficrespl,"#Age ");	fprintf(ficrespl,"#Age ");
for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);	for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
fprintf(ficrespl,"\n");	fprintf(ficrespl,"\n");
Line 5212 lsurv=vector(1,AGESUP);	Line 5709 lsurv=vector(1,AGESUP);
for(cptcov=1,k=0;cptcov<=i1;cptcov++){	for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){	for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
k=k+1;	k=k+1;
/printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);/	/* to clean */
	printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,codtab[cptcod][cptcov],nbcode);
fprintf(ficrespl,"\n#******");	fprintf(ficrespl,"\n#******");
printf("\n#******");	printf("\n#******");
fprintf(ficlog,"\n#******");	fprintf(ficlog,"\n#******");
Line 5256 lsurv=vector(1,AGESUP);	Line 5754 lsurv=vector(1,AGESUP);
hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */	hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */

/* hstepm=1; aff par mois*/	/* hstepm=1; aff par mois*/
fprintf(ficrespij, "#Local time at start: %s", strstart);	pstamp(ficrespij);
fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");	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(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){	for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
Line 5318 lsurv=vector(1,AGESUP);	Line 5816 lsurv=vector(1,AGESUP);
}	}


/---------- Health expectancies and variances ------------/	/* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */

strcpy(filerest,"t");	prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
strcat(filerest,fileres);	/* 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",\
if((ficrest=fopen(filerest,"w"))==NULL) {	ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
printf("Problem with total LE resultfile: %s\n", filerest);goto end;	*/
fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
	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);
	}
}	}
printf("Computing Total LEs with variances: file '%s' \n", filerest);
fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);


	/---------- Health expectancies, no variances ------------/

strcpy(filerese,"e");	strcpy(filerese,"e");
strcat(filerese,fileres);	strcat(filerese,fileres);
if((ficreseij=fopen(filerese,"w"))==NULL) {	if((ficreseij=fopen(filerese,"w"))==NULL) {
Line 5338 lsurv=vector(1,AGESUP);	Line 5842 lsurv=vector(1,AGESUP);
}	}
printf("Computing Health Expectancies: result on file '%s' \n", filerese);	printf("Computing Health Expectancies: result on file '%s' \n", filerese);
fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);	fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
	for(cptcov=1,k=0;cptcov<=i1;cptcov++){
	for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
	k=k+1;
	fprintf(ficreseij,"\n#****** ");
	for(j=1;j<=cptcoveff;j++) {
	fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
	}
	fprintf(ficreseij,"******\n");

	eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
	oldm=oldms;savm=savms;
	evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);

	free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
	}
	}
	fclose(ficreseij);


	/---------- 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(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");	strcpy(fileresv,"v");
strcat(fileresv,fileres);	strcat(fileresv,fileres);
Line 5348 lsurv=vector(1,AGESUP);	Line 5901 lsurv=vector(1,AGESUP);
printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);	printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
fprintf(ficlog,"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(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){	for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
k=k+1;	k=k+1;
Line 5370 lsurv=vector(1,AGESUP);	Line 5909 lsurv=vector(1,AGESUP);
fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
fprintf(ficrest,"******\n");	fprintf(ficrest,"******\n");

fprintf(ficreseij,"\n#****** ");	fprintf(ficresstdeij,"\n#****** ");
for(j=1;j<=cptcoveff;j++)	fprintf(ficrescveij,"\n#****** ");
fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	for(j=1;j<=cptcoveff;j++) {
fprintf(ficreseij,"******\n");	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(ficresstdeij,"******\n");
	fprintf(ficrescveij,"******\n");

fprintf(ficresvij,"\n#****** ");	fprintf(ficresvij,"\n#****** ");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
Line 5382 lsurv=vector(1,AGESUP);	Line 5925 lsurv=vector(1,AGESUP);

eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);	eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
oldm=oldms;savm=savms;	oldm=oldms;savm=savms;
evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);	cvevsij(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);	vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
oldm=oldms;savm=savms;	pstamp(ficrest);
varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);	for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
if(popbased==1){	oldm=oldms;savm=savms;
varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);	varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are ");
}	if(vpopbased==1)
	fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
fprintf(ficrest, "#Local time at start: %s", strstart);	else
fprintf(ficrest,"#Total LEs with variances: e.. (std) ");	fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);	fprintf(ficrest,"# Age e.. (std) ");
fprintf(ficrest,"\n");	for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
	fprintf(ficrest,"\n");

epj=vector(1,nlstate+1);	epj=vector(1,nlstate+1);
for(age=bage; age <=fage ;age++){	for(age=bage; age <=fage ;age++){
prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);	prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
if (popbased==1) {	if (vpopbased==1) {
if(mobilav ==0){	if(mobilav ==0){
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
prlim[i][i]=probs[(int)age][i][k];	prlim[i][i]=probs[(int)age][i][k];
}else{ /* mobilav */	}else{ /* mobilav */
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
prlim[i][i]=mobaverage[(int)age][i][k];	prlim[i][i]=mobaverage[(int)age][i][k];
	}
}	}
}

fprintf(ficrest," %4.0f",age);	fprintf(ficrest," %4.0f",age);
for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){	for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
for(i=1, epj[j]=0.;i <=nlstate;i++) {	for(i=1, epj[j]=0.;i <=nlstate;i++) {
epj[j] += prlim[i][i]*eij[i][j][(int)age];	epj[j] += prlim[i][i]*eij[i][j][(int)age];
/* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/	/* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
	}
	epj[nlstate+1] +=epj[j];
}	}
epj[nlstate+1] +=epj[j];
}

for(i=1, vepp=0.;i <=nlstate;i++)	for(i=1, vepp=0.;i <=nlstate;i++)
for(j=1;j <=nlstate;j++)	for(j=1;j <=nlstate;j++)
vepp += vareij[i][j][(int)age];	vepp += vareij[i][j][(int)age];
fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));	fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
for(j=1;j <=nlstate;j++){	for(j=1;j <=nlstate;j++){
fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));	fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
	}
	fprintf(ficrest,"\n");
}	}
fprintf(ficrest,"\n");
}	}
free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);	free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);	free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
Line 5439 lsurv=vector(1,AGESUP);	Line 5984 lsurv=vector(1,AGESUP);
free_matrix(mint,1,maxwav,1,n);	free_matrix(mint,1,maxwav,1,n);
free_ivector(cod,1,n);	free_ivector(cod,1,n);
free_ivector(tab,1,NCOVMAX);	free_ivector(tab,1,NCOVMAX);
fclose(ficreseij);	fclose(ficresstdeij);
	fclose(ficrescveij);
fclose(ficresvij);	fclose(ficresvij);
fclose(ficrest);	fclose(ficrest);
fclose(ficpar);	fclose(ficpar);

/------- Variance of stable prevalence------/	/------- Variance of period (stable) prevalence------/

strcpy(fileresvpl,"vpl");	strcpy(fileresvpl,"vpl");
strcat(fileresvpl,fileres);	strcat(fileresvpl,fileres);
if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {	if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);	printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
exit(0);	exit(0);
}	}
printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);	printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);

for(cptcov=1,k=0;cptcov<=i1;cptcov++){	for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){	for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
Line 5476 lsurv=vector(1,AGESUP);	Line 6022 lsurv=vector(1,AGESUP);
free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);	free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);

} /* mle==-3 arrives here for freeing */	} /* mle==-3 arrives here for freeing */
	endfree:
	free_matrix(prlim,1,nlstate,1,nlstate);
free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);	free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
free_matrix(oldms, 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(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);	free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);

free_matrix(covar,0,NCOVMAX,1,n);	free_matrix(covar,0,NCOVMAX,1,n);
free_matrix(matcov,1,npar,1,npar);	free_matrix(matcov,1,npar,1,npar);
/free_vector(delti,1,npar);/	/free_vector(delti,1,npar);/
Line 5493 lsurv=vector(1,AGESUP);	Line 6040 lsurv=vector(1,AGESUP);
free_ivector(Tprod,1,15);	free_ivector(Tprod,1,15);
free_ivector(Tvaraff,1,15);	free_ivector(Tvaraff,1,15);
free_ivector(Tage,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(fichtm);
fflush(ficgp);	fflush(ficgp);

Line 5522 lsurv=vector(1,AGESUP);	Line 6069 lsurv=vector(1,AGESUP);
fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);	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);*/	/* printf("Total time was %d uSec.\n", total_usecs);*/
/* if(fileappend(fichtm,optionfilehtm)){ */	/* if(fileappend(fichtm,optionfilehtm)){ */
fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>",strstart, strtend);	fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
fclose(fichtm);	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(fichtmcov);
fclose(ficgp);	fclose(ficgp);
fclose(ficlog);	fclose(ficlog);
/------ End -----------/	/------ End -----------/

chdir(path);
strcpy(plotcmd,"\"");	printf("Before Current directory %s!\n",pathcd);
strcat(plotcmd,pathimach);	if(chdir(pathcd) != 0)
strcat(plotcmd,GNUPLOTPROGRAM);	printf("Can't move to directory %s!\n",path);
strcat(plotcmd,"\"");	if(getcwd(pathcd,MAXLINE) > 0)
strcat(plotcmd," ");	printf("Current directory %s!\n",pathcd);
strcat(plotcmd,optionfilegnuplot);	/strcat(plotcmd,CHARSEPARATOR);/
printf("Starting graphs with: %s",plotcmd);fflush(stdout);	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){	if((outcmd=system(plotcmd)) != 0){
printf(" Problem with gnuplot\n");	printf("\n Problem with gnuplot\n");
}	}
printf(" Wait...");	printf(" Wait...");
while (z[0] != 'q') {	while (z[0] != 'q') {

FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>

Removed from v.1.106
changed lines
	Added in v.1.131