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Diff for /imach/src/imach.c between versions 1.106 and 1.124

version 1.106, 2006/01/19 13:24:36	version 1.124, 2006/03/22 17:13:53
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	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 263
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 Agnès Lièvre (lievre@ined.fr).	Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
Institut national d'études démographiques, Paris.	Institut national d'études démographiques, Paris.
Line 202	Line 292
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 304
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 317
#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 331
/* #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 */

Line 257	Line 353
#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 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";
char fullversion[]="$Revision$ $Date$";	char fullversion[]="$Revision$ $Date$";
	char strstart[80];
	char optionfilext[10], optionfilefiname[FILENAMELENGTH];
int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */	int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
int nvar;	int nvar;
int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;	int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
Line 280 int popbased=0;	Line 380 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; /* Maxim number of waves */
int jmin, jmax; /* min, max spacing between 2 waves */	int jmin, jmax; /* min, max spacing between 2 waves */
	int ijmin, ijmax; /* Individuals having jmin and jmax */
int gipmx, gsw; /* Global variables on the number of contributions	int gipmx, gsw; /* 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, weightopt;
Line 290 int *bh; / bh[mi][i] is the bias (+ or	Line 391 int *bh; / bh[mi][i] is the bias (+ or
double jmean; /* Mean space between 2 waves */	double jmean; /* 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; /* Global variable for printing or not */
double fretone; /* Only one call to likelihood */	double fretone; /* Only one call to likelihood */
Line 304 FILE *ficresprobmorprev;	Line 405 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 437 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 388 double ftolhess; /* Tolerance for comput	Line 497 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 506 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 515 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 524 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 542 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 1005 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 1128 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 1309 double func( double *x)	Line 1421 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) {
for (j=3,survp=0. ; j<=nlstate; j++)
survp += out[s1][j];
lli= survp;
}	}

else if (s2==-5) {	else if (s2==-4) {
for (j=1,survp=0. ; j<=2; 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 += (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 1520 double funcone( double *x)	Line 1632 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 1536 double funcone( double *x)	Line 1652 double funcone( double *x)
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 1738 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 2006 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 */
Line 1898 void freqsummary(char fileres[], int ia	Line 2020 void freqsummary(char fileres[], int ia
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 2084 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 1976 fprintf(ficresp, "#Local time at start:	Line 2097 fprintf(ficresp, "#Local time at start:
for(i=iagemin; i <= iagemax+3; i++){	for(i=iagemin; i <= iagemax+3; i++){
if(i==iagemax+3){	if(i==iagemax+3){
fprintf(ficlog,"Total");	fprintf(ficlog,"Total");
	fprintf(fichtm,"<br>Total<br>");
}else{	}else{
if(first==1){	if(first==1){
first=0;	first=0;
Line 2176 void concatwav(int wav[], int **dh, int	Line 2298 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 2325 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 2343 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 2393 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 **************************/
Line 2324 void tricode(int Tvar, int *nbcode, in	Line 2458 void tricode(int Tvar, int *nbcode, in

/********* 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(char fileres[], double *eij, double x[], int nlstate, int stepm, int bage, int fage, double oldm, double **savm, int cij, int estepm,char strstart[] )

{	{
/* Health expectancies */	/* 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;
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;
	/* nhstepm age range expressed in number of stepm */
	nstepm=(int) rint((agelim-age)*YEARM/stepm);
	/* 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 ++){ /* If stepm=6 months */
	/* Computed by stepm unit matrices, product of hstepm matrices, stored
	in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */

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

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

	{
	/* Covariances of health expectancies eij and of total life expectancies according
	to initial status i, ei. .
	*/
	int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
	double age, agelim, hf;
	double *p3matp, p3matm, **varhe;
double dnewm,doldm;	double 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 2632 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-age)*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;*/
/* Typically if 20 years nstepm = 2012/6=40 stepm /	nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
/* 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);
p3mat=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);	gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
gp=matrix(0,nhstepm,1,nlstate*nlstate);	trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
gm=matrix(0,nhstepm,1,nlstate*nlstate);	gp=matrix(0,nhstepm,1,nlstate*nlstate);
	gm=matrix(0,nhstepm,1,nlstate*nlstate);

	for (age=bage; age<=fage; age ++){

/* Computed by stepm unit matrices, product of hstepm matrices, stored	/* Computed by stepm unit matrices, product of hstepm matrices, stored
in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */	in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);


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 2697 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 2811 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 2826 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 in the population i.e cross-sectionally\n in each health state (popbased=1)");
	else
	fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
fprintf(ficresvij,"# Age");	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 2811 void varprevlim(char fileres[], double *	Line 3076 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 3192 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 3185 To be simple, these graphs help to under	Line 3451 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 3471 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, (b) health expectancies by health status at initial age: ei., eij . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
<a href=\"%s\">%s</a> <br>\n</li>",	<a href=\"%s\">%s</a> <br>\n</li>",
estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));	estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));


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

m=cptcoveff;	m=cptcoveff;
Line 3236 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 3505 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 3526 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 3539 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), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences (i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));	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: <a href=\"%s\">%s</a> <br>\n",
subdirf2(fileres,"t"),subdirf2(fileres,"t"));	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 3348 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 3625 plot [%.f:%.f] \"%s\" every :::%d::%d u
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 3673 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 3688 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 4251 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 4264 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 4333 void printinggnuplotmort(char fileres[],




/***********************************************/	/***********************************************/
/************** Main Program ***************/	/************** Main Program ***************/
/***********************************************/	/***********************************************/
Line 4059 int main(int argc, char *argv[])	Line 4342 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;

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 4366 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 4402 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 4444 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 4464 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 4280 int main(int argc, char *argv[])	Line 4583 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 4614 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 4643 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 4438 int main(int argc, char *argv[])	Line 4743 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 4461 int main(int argc, char *argv[])	Line 4766 int main(int argc, char *argv[])
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,' ');
	errno=0;
	lval=strtol(strb,&endptr,10);
	/* if (errno == ERANGE && (lval == LONG_MAX \|\| lval == LONG_MIN))*/
	if( strb[0]=='\0' \|\| (*endptr != '\0')){
	printf("Error reading data around '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);
	exit(1);
}	}
	s[j][i]=lval;
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 %s 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);	exit(1);
if(lstra > 9){ /* More than 2*32 or max of what printf can write with %ld /	}
stratrunc = &(stra[lstra-9]);	anint[j][i]= (double) year;
num[i]=atol(stratrunc);	mint[j][i]= (double)month;
	strcpy(line,stra);
	} /* ENd Waves */

	cutv(stra, strb,line,' ');
	if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
	}
	else if(iout=sscanf(strb,"%s.",dummy) != 0){
	month=99;
	year=9999;
	}else{
	printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
	exit(1);
	}
	andc[i]=(double) year;
	moisdc[i]=(double) month;
	strcpy(line,stra);

	cutv(stra, strb,line,' ');
	if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
	}
	else if(iout=sscanf(strb,"%s.") != 0){
	month=99;
	year=9999;
	}else{
	printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line,j);
	exit(1);
	}
	annais[i]=(double)(year);
	moisnais[i]=(double)(month);
	strcpy(line,stra);

	cutv(stra, strb,line,' ');
	errno=0;
	dval=strtod(strb,&endptr);
	if( strb[0]=='\0' \|\| (*endptr != '\0')){
	printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
	exit(1);
	}
	weight[i]=dval;
	strcpy(line,stra);

	for (j=ncovcol;j>=1;j--){
	cutv(stra, strb,line,' ');
	errno=0;
	lval=strtol(strb,&endptr,10);
	if( strb[0]=='\0' \|\| (*endptr != '\0')){
	printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1). Exiting.\n",lval, linei,i, line);
	exit(1);
	}
	if(lval <-1 \|\| lval >1){
	printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
	Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
	for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
	For example, for multinomial values like 1, 2 and 3,\n \
	build V1=0 V2=0 for the reference value (1),\n \
	V1=1 V2=0 for (2) \n \
	and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
	output of IMaCh is often meaningless.\n \
	Exiting.\n",lval,linei, i,line,j);
	exit(1);
}	}
else	covar[j][i]=(double)(lval);
num[i]=atol(stra);	strcpy(line,stra);
	}
/*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){	lstra=strlen(stra);
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;}*/
	if(lstra > 9){ /* More than 2*32 or max of what printf can write with %ld /
i=i+1;	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 4595 int main(int argc, char *argv[])	Line 4982 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 5031 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 4776 int main(int argc, char *argv[])	Line 5161 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 5209 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 5219 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 5230 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 5248 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 5288 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 */	else{ /* For mle >=1 */

likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */	likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
Line 4969 lsurv=vector(1,AGESUP);	Line 5361 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 5555 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 5577 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 5256 lsurv=vector(1,AGESUP);	Line 5648 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 5326 lsurv=vector(1,AGESUP);	Line 5718 lsurv=vector(1,AGESUP);
printf("Problem with total LE resultfile: %s\n", filerest);goto end;	printf("Problem with total LE resultfile: %s\n", filerest);goto end;
fprintf(ficlog,"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 LEs with variances: file '%s' \n", filerest);	printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);	fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);


strcpy(filerese,"e");	strcpy(filerese,"e");
Line 5339 lsurv=vector(1,AGESUP);	Line 5731 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);

	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);
if((ficresvij=fopen(fileresv,"w"))==NULL) {	if((ficresvij=fopen(fileresv,"w"))==NULL) {
Line 5371 lsurv=vector(1,AGESUP);	Line 5781 lsurv=vector(1,AGESUP);
fprintf(ficrest,"******\n");	fprintf(ficrest,"******\n");

fprintf(ficreseij,"\n#****** ");	fprintf(ficreseij,"\n#****** ");
for(j=1;j<=cptcoveff;j++)	fprintf(ficresstdeij,"\n#****** ");
	fprintf(ficrescveij,"\n#****** ");
	for(j=1;j<=cptcoveff;j++) {
fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
	fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
	fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
	}
fprintf(ficreseij,"******\n");	fprintf(ficreseij,"******\n");
	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 5799 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);	evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);
	cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);

vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);	vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
oldm=oldms;savm=savms;	oldm=oldms;savm=savms;
Line 5391 lsurv=vector(1,AGESUP);	Line 5809 lsurv=vector(1,AGESUP);
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,popbased,mobilav, strstart);
}	}

fprintf(ficrest, "#Local time at start: %s", strstart);	pstamp(ficrest);
fprintf(ficrest,"#Total LEs with variances: e.. (std) ");	fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);	for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
fprintf(ficrest,"\n");	fprintf(ficrest,"\n");

Line 5440 lsurv=vector(1,AGESUP);	Line 5858 lsurv=vector(1,AGESUP);
free_ivector(cod,1,n);	free_ivector(cod,1,n);
free_ivector(tab,1,NCOVMAX);	free_ivector(tab,1,NCOVMAX);
fclose(ficreseij);	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 5896 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 */
	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 5495 lsurv=vector(1,AGESUP);	Line 5915 lsurv=vector(1,AGESUP);
free_ivector(Tage,1,15);	free_ivector(Tage,1,15);
free_ivector(Tcode,1,100);	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 5943 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.1.124