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version 1.62, 2002/11/20 07:56:21	version 1.86, 2003/06/17 20:04:08
Line 1	Line 1
/* $Id$	/* $Id$
	$State$
	$Log$
	Revision 1.86 2003/06/17 20:04:08 brouard
	(Module): Change position of html and gnuplot routines and added
	routine fileappend.

	Revision 1.85 2003/06/17 13:12:43 brouard
	* imach.c (Repository): Check when date of death was earlier that
	current date of interview. It may happen when the death was just
	prior to the death. In this case, dh was negative and likelihood
	was wrong (infinity). We still send an "Error" but patch by
	assuming that the date of death was just one stepm after the
	interview.
	(Repository): Because some people have very long ID (first column)
	we changed int to long in num[] and we added a new lvector for
	memory allocation. But we also truncated to 8 characters (left
	truncation)
	(Repository): No more line truncation errors.

	Revision 1.84 2003/06/13 21:44:43 brouard
	* imach.c (Repository): Replace "freqsummary" at a correct
	place. It differs from routine "prevalence" which may be called
	many times. Probs is memory consuming and must be used with
	parcimony.
	Version 0.95a3 (should output exactly the same maximization than 0.8a2)

	Revision 1.83 2003/06/10 13:39:11 lievre
	* empty log message *

	Revision 1.82 2003/06/05 15:57:20 brouard
	Add log in imach.c and fullversion number is now printed.

	*/
	/*
Interpolated Markov Chain	Interpolated Markov Chain

Short summary of the programme:	Short summary of the programme:
Line 32	Line 66
hPijx is the probability to be observed in state i at age x+h	hPijx is the probability to be observed in state i at age x+h
conditional to the observed state i at age x. The delay 'h' can be	conditional to the observed state i at age x. The delay 'h' can be
split into an exact number (nh*stepm) of unobserved intermediate	split into an exact number (nh*stepm) of unobserved intermediate
states. This elementary transition (by month or quarter trimester,	states. This elementary transition (by month, quarter,
semester or year) is model as a multinomial logistic. The hPx	semester or year) is modelled as a multinomial logistic. The hPx
matrix is simply the matrix product of nh*stepm elementary matrices	matrix is simply the matrix product of nh*stepm elementary matrices
and the contribution of each individual to the likelihood is simply	and the contribution of each individual to the likelihood is simply
hPijx.	hPijx.
Line 48	Line 82
It is copyrighted identically to a GNU software product, ie programme and	It is copyrighted identically to a GNU software product, ie programme and
software can be distributed freely for non commercial use. Latest version	software can be distributed freely for non commercial use. Latest version
can be accessed at http://euroreves.ined.fr/imach .	can be accessed at http://euroreves.ined.fr/imach .

	Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
	or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so

**********************************************************************/	**********************************************************************/
	/*
	main
	read parameterfile
	read datafile
	concatwav
	freqsummary
	if (mle >= 1)
	mlikeli
	print results files
	if mle==1
	computes hessian
	read end of parameter file: agemin, agemax, bage, fage, estepm
	begin-prev-date,...
	open gnuplot file
	open html file
	stable prevalence
	for age prevalim()
	h Pij x
	variance of p varprob
	forecasting if prevfcast==1 prevforecast call prevalence()
	health expectancies
	Variance-covariance of DFLE
	prevalence()
	movingaverage()
	varevsij()
	if popbased==1 varevsij(,popbased)
	total life expectancies
	Variance of stable prevalence
	end
	*/




#include <math.h>	#include <math.h>
#include <stdio.h>	#include <stdio.h>
#include <stdlib.h>	#include <stdlib.h>
#include <unistd.h>	#include <unistd.h>

	#include <sys/time.h>
	#include <time.h>
	#include "timeval.h"

#define MAXLINE 256	#define MAXLINE 256
#define GNUPLOTPROGRAM "gnuplot"	#define GNUPLOTPROGRAM "gnuplot"
/#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"/	/#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"/
#define FILENAMELENGTH 80	#define FILENAMELENGTH 132
/#define DEBUG/	/#define DEBUG/
#define windows	/#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 75	Line 150
#define YEARM 12. /* Number of months per year */	#define YEARM 12. /* Number of months per year */
#define AGESUP 130	#define AGESUP 130
#define AGEBASE 40	#define AGEBASE 40
#ifdef windows	#ifdef unix
#define DIRSEPARATOR '\\'
#define ODIRSEPARATOR '/'
#else
#define DIRSEPARATOR '/'	#define DIRSEPARATOR '/'
#define ODIRSEPARATOR '\\'	#define ODIRSEPARATOR '\\'
	#else
	#define DIRSEPARATOR '\\'
	#define ODIRSEPARATOR '/'
#endif	#endif

char version[80]="Imach version 0.9, November 2002, INED-EUROREVES ";	/* $Id$ */
	/* $State$ */

	char version[]="Imach version 0.95a2, June 2003, INED-EUROREVES ";
	char fullversion[]="$Revision$ $Date$";
int erreur; /* Error number */	int erreur; /* Error number */
int nvar;	int nvar;
int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;	int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
Line 105 double jmean; /* Mean space between 2 wa	Line 184 double jmean; /* Mean space between 2 wa
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, ficrespl, ficrespij, ficrest,ficresf,*ficrespop;
FILE *ficlog;	FILE ficlog, ficrespow;
	int globpr; /* Global variable for printing or not */
	double fretone; /* Only one call to likelihood */
	long ipmx; /* Number of contributions */
	double sw; /* Sum of weights */
	char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
	FILE *ficresilk;
FILE ficgp,ficresprob,ficpop, ficresprobcov, *ficresprobcor;	FILE ficgp,ficresprob,ficpop, ficresprobcov, *ficresprobcor;
FILE *ficresprobmorprev;	FILE *ficresprobmorprev;
FILE fichtm; / Html File */	FILE fichtm; / Html File */
Line 163 int estepm;	Line 248 int estepm;
/* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/	/* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/

int m,nb;	int m,nb;
int num, firstpass=0, lastpass=4,cod, ncodemax, Tage;	long *num;
	int firstpass=0, lastpass=4,cod, ncodemax, *Tage;
double *agev,moisnais, annais, moisdc, andc,mint, *anint;	double *agev,moisnais, annais, moisdc, andc,mint, *anint;
double pmmij, *probs;	double pmmij, *probs;
double dateintmean=0;	double dateintmean=0;
Line 188 static int split( char path, char dirc	Line 274 static int split( char path, char dirc
if ( ss == NULL ) { /* no directory, so use current */	if ( ss == NULL ) { /* no directory, so use current */
/*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);*/
#if defined(__bsd__) /* get current working directory */	/* get current working directory */
extern char *getwd( );	/* extern char* getcwd ( char buf , int len);/

if ( getwd( dirc ) == NULL ) {
#else
extern char *getcwd( );

if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {	if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
#endif
return( GLOCK_ERROR_GETCWD );	return( GLOCK_ERROR_GETCWD );
}	}
strcpy( name, path ); /* we've got it */	strcpy( name, path ); /* we've got it */
Line 209 static int split( char path, char dirc	Line 289 static int split( char path, char dirc
dirc[l1-l2] = 0; /* add zero */	dirc[l1-l2] = 0; /* add zero */
}	}
l1 = strlen( dirc ); /* length of directory */	l1 = strlen( dirc ); /* length of directory */
#ifdef windows	/*#ifdef windows
if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }	if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
#else	#else
if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }	if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
#endif	#endif
	*/
ss = strrchr( name, '.' ); /* find last / */	ss = strrchr( name, '.' ); /* find last / */
ss++;	ss++;
strcpy(ext,ss); /* save extension */	strcpy(ext,ss); /* save extension */
Line 311 void free_ivector(int *v, long nl, long	Line 392 void free_ivector(int *v, long nl, long
free((FREE_ARG)(v+nl-NR_END));	free((FREE_ARG)(v+nl-NR_END));
}	}

	/**********************lvector *****************************/
	long *lvector(long nl,long nh)
	{
	long *v;
	v=(long ) malloc((size_t)((nh-nl+1+NR_END)sizeof(long)));
	if (!v) nrerror("allocation failure in ivector");
	return v-nl+NR_END;
	}

	/****************free lvector ************************/
	void free_lvector(long *v, long nl, long nh)
	{
	free((FREE_ARG)(v+nl-NR_END));
	}

/***************** imatrix *****************************/	/***************** imatrix *****************************/
int **imatrix(long nrl, long nrh, long ncl, long nch)	int **imatrix(long nrl, long nrh, long ncl, long nch)
/* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */	/* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */
Line 365 double **matrix(long nrl, long nrh, long	Line 461 double **matrix(long nrl, long nrh, long

for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;	for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
return m;	return m;
	/* print ((m+1)+70) or print m[1][70]; print m+1 or print &(m[1])
	*/
}	}

/***********************free matrix **********************/	/***********************free matrix **********************/
Line 404 double ***ma3x(long nrl, long nrh, long	Line 502 double ***ma3x(long nrl, long nrh, long
for (j=ncl+1; j<=nch; j++)	for (j=ncl+1; j<=nch; j++)
m[i][j]=m[i][j-1]+nlay;	m[i][j]=m[i][j-1]+nlay;
}	}
return m;	return m;
	/* gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
	&(m[i][j][k]) <=> (((m+i) + j)+k)
	*/
}	}

/***********************free ma3x **********************/	/***********************free ma3x **********************/
Line 612 void powell(double p[], double **xi, int	Line 713 void powell(double p[], double **xi, int
del=0.0;	del=0.0;
printf("\nPowell iter=%d -2LL=%.12f",iter,*fret);	printf("\nPowell iter=%d -2LL=%.12f",iter,*fret);
fprintf(ficlog,"\nPowell iter=%d -2LL=%.12f",iter,*fret);	fprintf(ficlog,"\nPowell iter=%d -2LL=%.12f",iter,*fret);
for (i=1;i<=n;i++)	fprintf(ficrespow,"%d %.12f",iter,fret);
	for (i=1;i<=n;i++) {
printf(" %d %.12f",i, p[i]);	printf(" %d %.12f",i, p[i]);
fprintf(ficlog," %d %.12f",i, p[i]);	fprintf(ficlog," %d %.12lf",i, p[i]);
	fprintf(ficrespow," %.12lf", p[i]);
	}
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
	fprintf(ficrespow,"\n");
for (i=1;i<=n;i++) {	for (i=1;i<=n;i++) {
for (j=1;j<=n;j++) xit[j]=xi[j][i];	for (j=1;j<=n;j++) xit[j]=xi[j][i];
fptt=(*fret);	fptt=(*fret);
Line 856 double matprod2(double out, double *	Line 961 double matprod2(double out, double *

double *hpxij(double po, int nhstepm, double age, int hstepm, double x, int nlstate, int stepm, double oldm, double savm, int ij )	double *hpxij(double po, int nhstepm, double age, int hstepm, double x, int nlstate, int stepm, double oldm, double savm, int ij )
{	{
/* Computes the transition matrix starting at age 'age' over 'nhstepmhstepmstepm' month	/* Computes the transition matrix starting at age 'age' over
duration (i.e. until	'nhstepmhstepmstepm' months (i.e. until
age (in years) age+nhstepmstepm/12) by multiplying nhstepmhstepm matrices.	age (in years) age+nhstepmhstepmstepm/12) by multiplying
	nhstepm*hstepm matrices.
Output is stored in matrix po[i][j][h] for h every 'hstepm' step	Output is stored in matrix po[i][j][h] for h every 'hstepm' step
(typically every 2 years instead of every month which is too big).	(typically every 2 years instead of every month which is too big
	for the memory).
Model is determined by parameters x and covariates have to be	Model is determined by parameters x and covariates have to be
included manually here.	included manually here.

Line 917 double func( double *x)	Line 1024 double func( double *x)
double sw; /* Sum of weights */	double sw; /* Sum of weights */
double lli; /* Individual log likelihood */	double lli; /* Individual log likelihood */
int s1, s2;	int s1, s2;
double bbh;	double bbh, survp;
long ipmx;	long ipmx;
/extern weight /	/extern weight /
/* We are differentiating ll according to initial status */	/* We are differentiating ll according to initial status */
Line 944 double func( double *x)	Line 1051 double func( double *x)
for (kk=1; kk<=cptcovage;kk++) {	for (kk=1; kk<=cptcovage;kk++) {
cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];	cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
}	}

out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));	1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
savm=oldm;	savm=oldm;
oldm=newm;	oldm=newm;


} /* end mult */	} /* end mult */

/lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);/ /* Original formula */	/lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);/ /* Original formula */
Line 968 double func( double *x)	Line 1072 double func( double *x)
*/	*/
s1=s[mw[mi][i]][i];	s1=s[mw[mi][i]][i];
s2=s[mw[mi+1][i]][i];	s2=s[mw[mi+1][i]][i];
bbh=(double)bh[mi][i]/(double)stepm;	bbh=(double)bh[mi][i]/(double)stepm;
lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));	/* bias is positive if real duration
/lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]):log((1.-bbh)out[s1][s2]));*/	* is higher than the multiple of stepm and negative otherwise.
	*/
	/* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]):log((1.+bbh)out[s1][s2]));/
	if( s2 > nlstate){
	/* i.e. if s2 is a death state and if the date of death is known then the contribution
	to the likelihood is the probability to die between last step unit time and current
	step unit time, which is also the differences between probability to die before dh
	and probability to die before dh-stepm .
	In version up to 0.92 likelihood was computed
	as if date of death was unknown. Death was treated as any other
	health state: the date of the interview describes the actual state
	and not the date of a change in health state. The former idea was
	to consider that at each interview the state was recorded
	(healthy, disable or death) and IMaCh was corrected; but when we
	introduced the exact date of death then we should have modified
	the contribution of an exact death to the likelihood. This new
	contribution is smaller and very dependent of the step unit
	stepm. It is no more the probability to die between last interview
	and month of death but the probability to survive from last
	interview up to one month before death multiplied by the
	probability to die within a month. Thanks to Chris
	Jackson for correcting this bug. Former versions increased
	mortality artificially. The bad side is that we add another loop
	which slows down the processing. The difference can be up to 10%
	lower mortality.
	*/
	lli=log(out[s1][s2] - savm[s1][s2]);
	}else{
	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=(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]);/
	/if(lli ==000.0)/
	/printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); /
	ipmx +=1;
	sw += weight[i];
	ll[s[mw[mi][i]][i]] += 2weight[i]lli;
	} /* end of wave */
	} /* end of individual */
	} else if(mle==2){
	for (i=1,ipmx=0, sw=0.; i<=imx; i++){
	for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
	for(mi=1; mi<= wav[i]-1; mi++){
	for (ii=1;ii<=nlstate+ndeath;ii++)
	for (j=1;j<=nlstate+ndeath;j++){
	oldm[ii][j]=(ii==j ? 1.0 : 0.0);
	savm[ii][j]=(ii==j ? 1.0 : 0.0);
	}
	for(d=0; d<=dh[mi][i]; d++){
	newm=savm;
	cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
	for (kk=1; kk<=cptcovage;kk++) {
	cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
	}
	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
	1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
	savm=oldm;
	oldm=newm;
	} /* end mult */

	/lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);/ /* Original formula */
	/* But now since version 0.9 we anticipate for bias and large stepm.
	* If stepm is larger than one month (smallest stepm) and if the exact delay
	* (in months) between two waves is not a multiple of stepm, we rounded to
	* the nearest (and in case of equal distance, to the lowest) interval but now
	* we keep into memory the bias bh[mi][i] and also the previous matrix product
	* (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
	* probability in order to take into account the bias as a fraction of the way
	* from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
	* -stepm/2 to stepm/2 .
	* For stepm=1 the results are the same as for previous versions of Imach.
	* For stepm > 1 the results are less biased than in previous versions.
	*/
	s1=s[mw[mi][i]][i];
	s2=s[mw[mi+1][i]][i];
	bbh=(double)bh[mi][i]/(double)stepm;
	/* bias is positive if real duration
	* is higher than the multiple of stepm and negative otherwise.
	*/
	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]>1.e-8 ?(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]):log((1.+bbh)out[s1][s2]));/
	/lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]):log((1.-+bh)out[s1][s2])); / / exponential interpolation */
	/lli=(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]);/
	/if(lli ==000.0)/
	/printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); /
	ipmx +=1;
	sw += weight[i];
	ll[s[mw[mi][i]][i]] += 2weight[i]lli;
	} /* end of wave */
	} /* end of individual */
	} else if(mle==3){ /* exponential inter-extrapolation */
	for (i=1,ipmx=0, sw=0.; i<=imx; i++){
	for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
	for(mi=1; mi<= wav[i]-1; mi++){
	for (ii=1;ii<=nlstate+ndeath;ii++)
	for (j=1;j<=nlstate+ndeath;j++){
	oldm[ii][j]=(ii==j ? 1.0 : 0.0);
	savm[ii][j]=(ii==j ? 1.0 : 0.0);
	}
	for(d=0; d<dh[mi][i]; d++){
	newm=savm;
	cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
	for (kk=1; kk<=cptcovage;kk++) {
	cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
	}
	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
	1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
	savm=oldm;
	oldm=newm;
	} /* end mult */

	/lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);/ /* Original formula */
	/* But now since version 0.9 we anticipate for bias and large stepm.
	* If stepm is larger than one month (smallest stepm) and if the exact delay
	* (in months) between two waves is not a multiple of stepm, we rounded to
	* the nearest (and in case of equal distance, to the lowest) interval but now
	* we keep into memory the bias bh[mi][i] and also the previous matrix product
	* (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
	* probability in order to take into account the bias as a fraction of the way
	* from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
	* -stepm/2 to stepm/2 .
	* For stepm=1 the results are the same as for previous versions of Imach.
	* For stepm > 1 the results are less biased than in previous versions.
	*/
	s1=s[mw[mi][i]][i];
	s2=s[mw[mi+1][i]][i];
	bbh=(double)bh[mi][i]/(double)stepm;
	/* bias is positive if real duration
	* is higher than the multiple of stepm and negative otherwise.
	*/
	/* 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]>1.e-8 ?(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]):log((1.+bbh)out[s1][s2])); / exponential inter-extrapolation */
/lli=(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]);/	/lli=(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]);/
/if(lli ==000.0)/	/if(lli ==000.0)/
/printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); /	/printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); /
Line 979 double func( double *x)	Line 1214 double func( double *x)
ll[s[mw[mi][i]][i]] += 2weight[i]lli;	ll[s[mw[mi][i]][i]] += 2weight[i]lli;
} /* end of wave */	} /* end of wave */
} /* end of individual */	} /* end of individual */
} else{	}else if (mle==4){ /* ml=4 no inter-extrapolation */
for (i=1,ipmx=0, sw=0.; i<=imx; i++){	for (i=1,ipmx=0, sw=0.; i<=imx; i++){
for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];	for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
for(mi=1; mi<= wav[i]-1; mi++){	for(mi=1; mi<= wav[i]-1; mi++){
Line 1001 double func( double *x)	Line 1236 double func( double *x)
oldm=newm;	oldm=newm;
} /* end mult */	} /* end mult */

	s1=s[mw[mi][i]][i];
	s2=s[mw[mi+1][i]][i];
	if( s2 > nlstate){
	lli=log(out[s1][s2] - savm[s1][s2]);
	}else{
	lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
	}
	ipmx +=1;
	sw += weight[i];
	ll[s[mw[mi][i]][i]] += 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]); */
	} /* end of wave */
	} /* end of individual */
	}else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
	for (i=1,ipmx=0, sw=0.; i<=imx; i++){
	for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
	for(mi=1; mi<= wav[i]-1; mi++){
	for (ii=1;ii<=nlstate+ndeath;ii++)
	for (j=1;j<=nlstate+ndeath;j++){
	oldm[ii][j]=(ii==j ? 1.0 : 0.0);
	savm[ii][j]=(ii==j ? 1.0 : 0.0);
	}
	for(d=0; d<dh[mi][i]; d++){
	newm=savm;
	cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
	for (kk=1; kk<=cptcovage;kk++) {
	cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
	}

	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
	1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
	savm=oldm;
	oldm=newm;
	} /* end mult */

	s1=s[mw[mi][i]][i];
	s2=s[mw[mi+1][i]][i];
lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */	lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
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]);/
} /* end of wave */	} /* end of wave */
} /* end of individual */	} /* end of individual */
} /* End of if */	} /* End of if */
Line 1014 double func( double *x)	Line 1287 double func( double *x)
return -l;	return -l;
}	}

	/************* log-likelihood ***********/
	double funcone( double *x)
	{
	int i, ii, j, k, mi, d, kk;
	double l, ll[NLSTATEMAX], cov[NCOVMAX];
	double **out;
	double lli; /* Individual log likelihood */
	int s1, s2;
	double bbh, survp;
	/extern weight /
	/* We are differentiating ll according to initial status */
	/* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
	/*for(i=1;i<imx;i++)
	printf(" %d\n",s[4][i]);
	*/
	cov[1]=1.;

	for(k=1; k<=nlstate; k++) ll[k]=0.;

	for (i=1,ipmx=0, sw=0.; i<=imx; i++){
	for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
	for(mi=1; mi<= wav[i]-1; mi++){
	for (ii=1;ii<=nlstate+ndeath;ii++)
	for (j=1;j<=nlstate+ndeath;j++){
	oldm[ii][j]=(ii==j ? 1.0 : 0.0);
	savm[ii][j]=(ii==j ? 1.0 : 0.0);
	}
	for(d=0; d<dh[mi][i]; d++){
	newm=savm;
	cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
	for (kk=1; kk<=cptcovage;kk++) {
	cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
	}
	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
	1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
	savm=oldm;
	oldm=newm;
	} /* end mult */

	s1=s[mw[mi][i]][i];
	s2=s[mw[mi+1][i]][i];
	bbh=(double)bh[mi][i]/(double)stepm;
	/* bias is positive if real duration
	* is higher than the multiple of stepm and negative otherwise.
	*/
	if( s2 > nlstate && (mle <5) ){ /* Jackson */
	lli=log(out[s1][s2] - savm[s1][s2]);
	} else if (mle==1){
	lli= log((1.+bbh)out[s1][s2]- bbhsavm[s1][s2]); /* linear interpolation */
	} 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 */
	} else if(mle==3){ /* exponential inter-extrapolation */
	lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]):log((1.+bbh)out[s1][s2])); / exponential inter-extrapolation */
	} else if (mle==4){ /* mle=4 no inter-extrapolation */
	lli=log(out[s1][s2]); /* Original formula */
	} else{ /* ml>=5 no inter-extrapolation no jackson =0.8a */
	lli=log(out[s1][s2]); /* Original formula */
	} /* End of if */
	ipmx +=1;
	sw += weight[i];
	ll[s[mw[mi][i]][i]] += 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]); */
	if(globpr){
	fprintf(ficresilk,"%ld %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
	%10.6f %10.6f %10.6f ", \
	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]);
	for(k=1,l=0.; k<=nlstate; k++)
	fprintf(ficresilk," %10.6f",ll[k]);
	fprintf(ficresilk,"\n");
	}
	} /* end of wave */
	} /* end of individual */
	for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
	/* printf("l1=%f l2=%f ",ll[1],ll[2]); */
	l= lipmx/sw; / To get the same order of magnitude as if weight=1 for every body */
	return -l;
	}


	void likelione(FILE ficres,double p[], int npar, int nlstate, int globpr, long ipmx, double sw, double fretone, double (funcone)(double []))
	{
	/* This routine should help understanding what is done with the selection of individuals/waves and
	to check the exact contribution to the likelihood.
	Plotting could be done.
	*/
	int k;
	if(globpr !=0){ /* Just counts and sums no printings */
	strcpy(fileresilk,"ilk");
	strcat(fileresilk,fileres);
	if((ficresilk=fopen(fileresilk,"w"))==NULL) {
	printf("Problem with resultfile: %s\n", fileresilk);
	fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
	}
	fprintf(ficresilk, "#individual(line's record) s1 s2 wave# effective_wave# number_of_product_matrix pij weight 2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state\n");
	fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight out sav ");
	/* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2weight[i]lli,out[s1][s2],savm[s1][s2]); */
	for(k=1; k<=nlstate; k++)
	fprintf(ficresilk," ll[%d]",k);
	fprintf(ficresilk,"\n");
	}

	fretone=(funcone)(p);
	if(globpr !=0){
	fclose(ficresilk);
	if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
	printf("Problem with html file: %s\n", optionfilehtm);
	fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
	exit(0);
	}
	else{
	fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",fileresilk);
	fclose(fichtm);
	}
	}
	return;
	}

/********* Maximum Likelihood Estimation *************/	/********* Maximum Likelihood Estimation *************/

void mlikeli(FILE ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (func)(double []))	void mlikeli(FILE ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (func)(double []))
{	{
int i,j, iter;	int i,j, iter;
double *xi,delti;	double **xi;
double fret;	double fret;
	double fretone; /* Only one call to likelihood */
	char filerespow[FILENAMELENGTH];
xi=matrix(1,npar,1,npar);	xi=matrix(1,npar,1,npar);
for (i=1;i<=npar;i++)	for (i=1;i<=npar;i++)
for (j=1;j<=npar;j++)	for (j=1;j<=npar;j++)
xi[i][j]=(i==j ? 1.0 : 0.0);	xi[i][j]=(i==j ? 1.0 : 0.0);
printf("Powell\n"); fprintf(ficlog,"Powell\n");	printf("Powell\n"); fprintf(ficlog,"Powell\n");
	strcpy(filerespow,"pow");
	strcat(filerespow,fileres);
	if((ficrespow=fopen(filerespow,"w"))==NULL) {
	printf("Problem with resultfile: %s\n", filerespow);
	fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
	}
	fprintf(ficrespow,"# Powell\n# iter -2*LL");
	for (i=1;i<=nlstate;i++)
	for(j=1;j<=nlstate+ndeath;j++)
	if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
	fprintf(ficrespow,"\n");

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

printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));	fclose(ficrespow);
fprintf(ficlog,"#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(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));	fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));

}	}
Line 1293 void lubksb(double *a, int n, int indx	Line 1698 void lubksb(double *a, int n, int indx
}	}

/********** Frequencies ******************/	/********** Frequencies ******************/
void freqsummary(char fileres[], int agemin, int agemax, int s, double agev, int nlstate, int imx, int Tvaraff, int nbcode, int ncodemax,double mint,double anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)	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)
{ /* Some frequencies */	{ /* Some frequencies */

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

pp=vector(1,nlstate);	pp=vector(1,nlstate);
probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);	prop=matrix(1,nlstate,iagemin,iagemax+3);
strcpy(fileresp,"p");	strcpy(fileresp,"p");
strcat(fileresp,fileres);	strcat(fileresp,fileres);
if((ficresp=fopen(fileresp,"w"))==NULL) {	if((ficresp=fopen(fileresp,"w"))==NULL) {
Line 1313 void freqsummary(char fileres[], int ag	Line 1718 void freqsummary(char fileres[], int ag
fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);	fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
exit(0);	exit(0);
}	}
freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);	freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
j1=0;	j1=0;

j=cptcoveff;	j=cptcoveff;
Line 1328 void freqsummary(char fileres[], int ag	Line 1733 void freqsummary(char fileres[], int ag
scanf("%d", i);*/	scanf("%d", i);*/
for (i=-1; i<=nlstate+ndeath; i++)	for (i=-1; i<=nlstate+ndeath; i++)
for (jk=-1; jk<=nlstate+ndeath; jk++)	for (jk=-1; jk<=nlstate+ndeath; jk++)
for(m=agemin; m <= agemax+3; m++)	for(m=iagemin; m <= iagemax+3; m++)
freq[i][jk][m]=0;	freq[i][jk][m]=0;

	for (i=1; i<=nlstate; i++)
	for(m=iagemin; m <= iagemax+3; m++)
	prop[i][m]=0;

dateintsum=0;	dateintsum=0;
k2cpt=0;	k2cpt=0;
Line 1343 void freqsummary(char fileres[], int ag	Line 1752 void freqsummary(char fileres[], int ag
if (bool==1){	if (bool==1){
for(m=firstpass; m<=lastpass; m++){	for(m=firstpass; m<=lastpass; m++){
k2=anint[m][i]+(mint[m][i]/12.);	k2=anint[m][i]+(mint[m][i]/12.);
if ((k2>=dateprev1) && (k2<=dateprev2)) {	/if ((k2>=dateprev1) && (k2<=dateprev2)) {/
if(agev[m][i]==0) agev[m][i]=agemax+1;	if(agev[m][i]==0) agev[m][i]=iagemax+1;
if(agev[m][i]==1) agev[m][i]=agemax+2;	if(agev[m][i]==1) agev[m][i]=iagemax+2;
	if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
if (m<lastpass) {	if (m<lastpass) {
freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];	freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];	freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
}	}

if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {	if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
dateintsum=dateintsum+k2;	dateintsum=dateintsum+k2;
k2cpt++;	k2cpt++;
}	}
}	/}/
}	}
}	}
}	}

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);*/

if (cptcovn>0) {	if (cptcovn>0) {
fprintf(ficresp, "\n#********** Variable ");	fprintf(ficresp, "\n#********** Variable ");
Line 1371 void freqsummary(char fileres[], int ag	Line 1781 void freqsummary(char fileres[], int ag
fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);	fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
fprintf(ficresp, "\n");	fprintf(ficresp, "\n");

for(i=(int)agemin; i <= (int)agemax+3; i++){	for(i=iagemin; i <= iagemax+3; i++){
if(i==(int)agemax+3){	if(i==iagemax+3){
fprintf(ficlog,"Total");	fprintf(ficlog,"Total");
}else{	}else{
if(first==1){	if(first==1){
Line 1403 void freqsummary(char fileres[], int ag	Line 1813 void freqsummary(char fileres[], int ag
for(jk=1; jk <=nlstate ; jk++){	for(jk=1; jk <=nlstate ; jk++){
for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)	for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
pp[jk] += freq[jk][m][i];	pp[jk] += freq[jk][m][i];
}	}
	for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
for(jk=1,pos=0; jk <=nlstate ; jk++)
pos += pp[jk];	pos += pp[jk];
	posprop += prop[jk][i];
	}
for(jk=1; jk <=nlstate ; jk++){	for(jk=1; jk <=nlstate ; jk++){
if(pos>=1.e-5){	if(pos>=1.e-5){
if(first==1)	if(first==1)
Line 1417 void freqsummary(char fileres[], int ag	Line 1828 void freqsummary(char fileres[], int ag
printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);	printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);	fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
}	}
if( i <= (int) agemax){	if( i <= iagemax){
if(pos>=1.e-5){	if(pos>=1.e-5){
fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);	fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
probs[i][jk][j1]= pp[jk]/pos;	/probs[i][jk][j1]= pp[jk]/pos;/
/printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);/	/printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);/
}	}
else	else
fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);	fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
}	}
}	}

Line 1435 void freqsummary(char fileres[], int ag	Line 1846 void freqsummary(char fileres[], int ag
printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);	printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);	fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
}	}
if(i <= (int) agemax)	if(i <= iagemax)
fprintf(ficresp,"\n");	fprintf(ficresp,"\n");
if(first==1)	if(first==1)
printf("Others in log...\n");	printf("Others in log...\n");
Line 1446 void freqsummary(char fileres[], int ag	Line 1857 void freqsummary(char fileres[], int ag
dateintmean=dateintsum/k2cpt;	dateintmean=dateintsum/k2cpt;

fclose(ficresp);	fclose(ficresp);
free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);	free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
free_vector(pp,1,nlstate);	free_vector(pp,1,nlstate);
	free_matrix(prop,1,nlstate,iagemin, iagemax+3);
/* End of Freq */	/* End of Freq */
}	}

/********** Prevalence ******************/	/********** Prevalence ******************/
void prevalence(int agemin, float agemax, int s, double agev, int nlstate, int imx, int Tvar, int nbcode, int ncodemax,double mint,double anint, double dateprev1,double dateprev2, double calagedate)	void prevalence(double *probs, double agemin, double agemax, int s, double *agev, int nlstate, int imx, int Tvar, int *nbcode, int ncodemax,double mint,double anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
{ /* Some frequencies */	{
	/* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
	in each health status at the date of interview (if between dateprev1 and dateprev2).
	We still use firstpass and lastpass as another selection.
	*/

int i, m, jk, k1, i1, j1, bool, z1,z2,j;	int i, m, jk, k1, i1, j1, bool, z1,z2,j;
double **freq; / Frequencies */	double **freq; / Frequencies */
double *pp;	double pp, *prop;
double pos, k2;	double pos,posprop;
	double y2; /* in fractional years */
pp=vector(1,nlstate);	int iagemin, iagemax;

freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);	iagemin= (int) agemin;
	iagemax= (int) agemax;
	/pp=vector(1,nlstate);/
	prop=matrix(1,nlstate,iagemin,iagemax+3);
	/* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
j1=0;	j1=0;

j=cptcoveff;	j=cptcoveff;
Line 1473 void prevalence(int agemin, float agemax	Line 1892 void prevalence(int agemin, float agemax
for(i1=1; i1<=ncodemax[k1];i1++){	for(i1=1; i1<=ncodemax[k1];i1++){
j1++;	j1++;

for (i=-1; i<=nlstate+ndeath; i++)	for (i=1; i<=nlstate; i++)
for (jk=-1; jk<=nlstate+ndeath; jk++)	for(m=iagemin; m <= iagemax+3; m++)
for(m=agemin; m <= agemax+3; m++)	prop[i][m]=0.0;
freq[i][jk][m]=0;

for (i=1; i<=imx; i++) {	for (i=1; i<=imx; i++) { /* Each individual */
bool=1;	bool=1;
if (cptcovn>0) {	if (cptcovn>0) {
for (z1=1; z1<=cptcoveff; z1++)	for (z1=1; z1<=cptcoveff; z1++)
Line 1486 void prevalence(int agemin, float agemax	Line 1904 void prevalence(int agemin, float agemax
bool=0;	bool=0;
}	}
if (bool==1) {	if (bool==1) {
for(m=firstpass; m<=lastpass; m++){	for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
k2=anint[m][i]+(mint[m][i]/12.);	y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
if ((k2>=dateprev1) && (k2<=dateprev2)) {	if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
if(agev[m][i]==0) agev[m][i]=agemax+1;	if(agev[m][i]==0) agev[m][i]=iagemax+1;
if(agev[m][i]==1) agev[m][i]=agemax+2;	if(agev[m][i]==1) agev[m][i]=iagemax+2;
if (m<lastpass) {	if((int)agev[m][i] <iagemin \|\| (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m);
if (calagedate>0)	if (s[m][i]>0 && s[m][i]<=nlstate) {
freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];	/if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);/
else	prop[s[m][i]][(int)agev[m][i]] += weight[i];
freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];	prop[s[m][i]][iagemax+3] += weight[i];
freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];	}
}
}	}
}	} /* end selection of waves */
}	}
}	}
for(i=(int)agemin; i <= (int)agemax+3; i++){	for(i=iagemin; i <= iagemax+3; i++){
for(jk=1; jk <=nlstate ; jk++){
for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
pp[jk] += freq[jk][m][i];
}
for(jk=1; jk <=nlstate ; jk++){
for(m=-1, pos=0; m <=0 ; m++)
pos += freq[jk][m][i];
}

for(jk=1; jk <=nlstate ; jk++){
for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
pp[jk] += freq[jk][m][i];
}

for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];	for(jk=1,posprop=0; jk <=nlstate ; jk++) {
	posprop += prop[jk][i];
for(jk=1; jk <=nlstate ; jk++){	}
if( i <= (int) agemax){
if(pos>=1.e-5){	for(jk=1; jk <=nlstate ; jk++){
probs[i][jk][j1]= pp[jk]/pos;	if( i <= iagemax){
}	if(posprop>=1.e-5){
}	probs[i][jk][j1]= prop[jk][i]/posprop;
}/* end jk */	}
}/* end i */	}
	}/* end jk */
	}/* end i */
} /* end i1 */	} /* end i1 */
} /* end k1 */	} /* end k1 */


free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
free_vector(pp,1,nlstate);

} /* End of Freq */	/* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
	/free_vector(pp,1,nlstate);/
	free_matrix(prop,1,nlstate, iagemin,iagemax+3);
	} /* End of prevalence */

/*********** Waves Concatenation *************/	/*********** Waves Concatenation *************/

Line 1578 void concatwav(int wav[], int **dh, int	Line 1983 void concatwav(int wav[], int **dh, int
wav[i]=mi;	wav[i]=mi;
if(mi==0){	if(mi==0){
if(first==0){	if(first==0){
printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);	printf("Warning! None valid information for:%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, no any valid information for:%d line=%d\n",num[i],i);	fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
}	}
} /* end mi==0 */	} /* end mi==0 */
}	} /* End individuals */

for(i=1; i<=imx; i++){	for(i=1; i<=imx; i++){
for(mi=1; mi<wav[i];mi++){	for(mi=1; mi<wav[i];mi++){
if (stepm <=0)	if (stepm <=0)
dh[mi][i]=1;	dh[mi][i]=1;
else{	else{
if (s[mw[mi+1][i]][i] > nlstate) {	if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
if (agedc[i] < 2*AGESUP) {	if (agedc[i] < 2*AGESUP) {
j= rint(agedc[i]12-agev[mw[mi][i]][i]12);	j= rint(agedc[i]12-agev[mw[mi][i]][i]12);
if(j==0) j=1; /* Survives at least one month after exam */	if(j==0) j=1; /* Survives at least one month after exam */
k=k+1;	else if(j<0){
if (j >= jmax) jmax=j;	printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
if (j <= jmin) jmin=j;	j=1; /* Careful Patch */
sum=sum+j;	printf(" We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n You MUST fix the contradiction between dates.\n",stepm);
/if (j<0) printf("j=%d num=%d \n",j,i); /	printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
	fprintf(ficlog," We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n You MUST fix the contradiction between dates.\n",stepm);
	}
	k=k+1;
	if (j >= jmax) jmax=j;
	if (j <= jmin) jmin=j;
	sum=sum+j;
	/if (j<0) printf("j=%d num=%d \n",j,i);/
	/* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
}	}
}	}
else{	else{
j= rint( (agev[mw[mi+1][i]][i]12 - agev[mw[mi][i]][i]12));	j= rint( (agev[mw[mi+1][i]][i]12 - agev[mw[mi][i]][i]12));
	/* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
k=k+1;	k=k+1;
if (j >= jmax) jmax=j;	if (j >= jmax) jmax=j;
else if (j <= jmin)jmin=j;	else if (j <= jmin)jmin=j;
/* 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]);/
	if(j<0){
	printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
	fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
	}
sum=sum+j;	sum=sum+j;
}	}
jk= j/stepm;	jk= j/stepm;
jl= j -jk*stepm;	jl= j -jk*stepm;
ju= j -(jk+1)*stepm;	ju= j -(jk+1)*stepm;
if(jl <= -ju){	if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
dh[mi][i]=jk;	if(jl==0){
bh[mi][i]=jl;	dh[mi][i]=jk;
}	bh[mi][i]=0;
else{	}else{ /* We want a negative bias in order to only have interpolation ie
dh[mi][i]=jk+1;	* at the price of an extra matrix product in likelihood */
bh[mi][i]=ju;	dh[mi][i]=jk+1;
}	bh[mi][i]=ju;
if(dh[mi][i]==0){	}
dh[mi][i]=1; /* At least one step */	}else{
bh[mi][i]=ju; /* At least one step */	if(jl <= -ju){
printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);	dh[mi][i]=jk;
}	bh[mi][i]=jl; /* bias is positive if real duration
if(i==298 \|\| i==287 \|\| i==763 \|\|i==1061)printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d",bh[mi][i],ju,jl,dh[mi][i],jk,stepm);	* is higher than the multiple of stepm and negative otherwise.
	*/
	}
	else{
	dh[mi][i]=jk+1;
	bh[mi][i]=ju;
	}
	if(dh[mi][i]==0){
	dh[mi][i]=1; /* At least one step */
	bh[mi][i]=ju; /* At least one step */
	/* printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
	}
	} /* end if mle */
}	}
}	} /* end wave */
}	}
jmean=sum/k;	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 Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
Line 1710 void evsij(char fileres[], double ***eij	Line 2141 void evsij(char fileres[], double ***eij
double *gradg, *trgradg;	double *gradg, *trgradg;
int theta;	int theta;

varhe=ma3x(1,nlstate2,1,nlstate2,(int) bage, (int) fage);	varhe=ma3x(1,nlstatenlstate,1,nlstatenlstate,(int) bage, (int) fage);
xp=vector(1,npar);	xp=vector(1,npar);
dnewm=matrix(1,nlstate*2,1,npar);	dnewm=matrix(1,nlstate*nlstate,1,npar);
doldm=matrix(1,nlstate2,1,nlstate2);	doldm=matrix(1,nlstatenlstate,1,nlstatenlstate);

fprintf(ficreseij,"# Health expectancies\n");	fprintf(ficreseij,"# Health expectancies\n");
fprintf(ficreseij,"# Age");	fprintf(ficreseij,"# Age");
Line 1730 void evsij(char fileres[], double ***eij	Line 2161 void evsij(char fileres[], double ***eij
* This is mainly to measure the difference between two models: for example	* 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	* 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	* we are calculating an estimate of the Life Expectancy assuming a linear
* progression inbetween and thus overestimating or underestimating according	* progression in between and thus overestimating or underestimating according
* to the curvature of the survival function. If, for the same date, we	* 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	* 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	* to compare the new estimate of Life expectancy with the same linear
Line 1759 void evsij(char fileres[], double ***eij	Line 2190 void evsij(char fileres[], double ***eij
/* if (stepm >= YEARM) hstepm=1;*/	/* if (stepm >= YEARM) hstepm=1;*/
nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */	nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);	gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
gp=matrix(0,nhstepm,1,nlstate*2);	gp=matrix(0,nhstepm,1,nlstate*nlstate);
gm=matrix(0,nhstepm,1,nlstate*2);	gm=matrix(0,nhstepm,1,nlstate*nlstate);

/* 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 */
Line 1798 void evsij(char fileres[], double ***eij	Line 2229 void evsij(char fileres[], double ***eij
for(i=1;i<=nlstate;i++){	for(i=1;i<=nlstate;i++){
cptj=cptj+1;	cptj=cptj+1;
for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){	for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){

gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;	gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
}	}
}	}
}	}
for(j=1; j<= nlstate*2; j++)	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][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
}	}
Line 1810 void evsij(char fileres[], double ***eij	Line 2242 void evsij(char fileres[], double ***eij

/* End theta */	/* End theta */

trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);	trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);

for(h=0; h<=nhstepm-1; h++)	for(h=0; h<=nhstepm-1; h++)
for(j=1; j<=nlstate*2;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*2;i++)	for(i=1;i<=nlstate*nlstate;i++)
for(j=1;j<=nlstate*2;j++)	for(j=1;j<=nlstate*nlstate;j++)
varhe[i][j][(int)age] =0.;	varhe[i][j][(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);
for(h=0;h<=nhstepm-1;h++){	for(h=0;h<=nhstepm-1;h++){
for(k=0;k<=nhstepm-1;k++){	for(k=0;k<=nhstepm-1;k++){
matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);	matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
matprod2(doldm,dnewm,1,nlstate2,1,npar,1,nlstate2,gradg[k]);	matprod2(doldm,dnewm,1,nlstatenlstate,1,npar,1,nlstatenlstate,gradg[k]);
for(i=1;i<=nlstate*2;i++)	for(i=1;i<=nlstate*nlstate;i++)
for(j=1;j<=nlstate*2;j++)	for(j=1;j<=nlstate*nlstate;j++)
varhe[i][j][(int)age] += doldm[i][j]hfhf;	varhe[i][j][(int)age] += doldm[i][j]hfhf;
}	}
}	}
Line 1852 void evsij(char fileres[], double ***eij	Line 2284 void evsij(char fileres[], double ***eij
}	}
fprintf(ficreseij,"\n");	fprintf(ficreseij,"\n");

free_matrix(gm,0,nhstepm,1,nlstate*2);	free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
free_matrix(gp,0,nhstepm,1,nlstate*2);	free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);	free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);	free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
}	}
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");

free_vector(xp,1,npar);	free_vector(xp,1,npar);
free_matrix(dnewm,1,nlstate*2,1,npar);	free_matrix(dnewm,1,nlstate*nlstate,1,npar);
free_matrix(doldm,1,nlstate2,1,nlstate2);	free_matrix(doldm,1,nlstatenlstate,1,nlstatenlstate);
free_ma3x(varhe,1,nlstate2,1,nlstate2,(int) bage, (int)fage);	free_ma3x(varhe,1,nlstatenlstate,1,nlstatenlstate,(int) bage, (int)fage);
}	}

/********** Variance ****************/	/********** Variance ****************/
Line 1920 void varevsij(char optionfilefiname[], d	Line 2352 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,"# probabilities of dying during a year and weighted mean w1p1j+w2p2j+... stand dev in()\n");	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++){
fprintf(ficresprobmorprev," p.%-d SE",j);	fprintf(ficresprobmorprev," p.%-d SE",j);
Line 1942 void varevsij(char optionfilefiname[], d	Line 2374 void varevsij(char optionfilefiname[], d
exit(0);	exit(0);
}	}
else{	else{
fprintf(fichtm,"\n<li><h4> Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");	fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
fprintf(fichtm,"\n<br>%s (� revoir) <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);

Line 1977 void varevsij(char optionfilefiname[], d	Line 2409 void varevsij(char optionfilefiname[], d
and note for a fixed period like k years */	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 only each two years of age and if	means that if the survival funtion is printed every two years of age and if
you sum them up and add 1 year (area under the trapezoids) you won't get the same	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.	results. So we changed our mind and took the option of the best precision.
*/	*/
Line 1993 void varevsij(char optionfilefiname[], d	Line 2425 void varevsij(char optionfilefiname[], d


for(theta=1; theta <=npar; theta++){	for(theta=1; theta <=npar; theta++){
for(i=1; i<=npar; i++){ /* Computes gradient */	for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
xp[i] = x[i] + (i==theta ?delti[theta]:0);	xp[i] = x[i] + (i==theta ?delti[theta]:0);
}	}
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);	hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
Line 2015 void varevsij(char optionfilefiname[], d	Line 2447 void varevsij(char optionfilefiname[], d
gp[h][j] += prlim[i][i]*p3mat[i][j][h];	gp[h][j] += prlim[i][i]*p3mat[i][j][h];
}	}
}	}
/* This for computing forces of mortality (h=1)as a weighted average */	/* This for computing probability of death (h=1 means
for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){	computed over hstepm matrices product = hstepm*stepm months)
for(i=1; i<= nlstate; i++)	as a weighted average of prlim.
	*/
	for(j=nlstate+1;j<=nlstate+ndeath;j++){
	for(i=1,gpp[j]=0.; i<= nlstate; i++)
gpp[j] += prlim[i][i]*p3mat[i][j][1];	gpp[j] += prlim[i][i]*p3mat[i][j][1];
}	}
/* end force of mortality */	/* end probability of death */

for(i=1; i<=npar; i++) /* Computes gradient */	for(i=1; i<=npar; i++) /* Computes gradient x - delta */
xp[i] = x[i] - (i==theta ?delti[theta]:0);	xp[i] = x[i] - (i==theta ?delti[theta]:0);
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);	hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);	prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
Line 2043 void varevsij(char optionfilefiname[], d	Line 2478 void varevsij(char optionfilefiname[], d
gm[h][j] += prlim[i][i]*p3mat[i][j][h];	gm[h][j] += prlim[i][i]*p3mat[i][j][h];
}	}
}	}
/* This for computing force of mortality (h=1)as a weighted average */	/* This for computing probability of death (h=1 means
for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){	computed over hstepm matrices product = hstepm*stepm months)
for(i=1; i<= nlstate; i++)	as a weighted average of prlim.
gmp[j] += prlim[i][i]*p3mat[i][j][1];	*/
	for(j=nlstate+1;j<=nlstate+ndeath;j++){
	for(i=1,gmp[j]=0.; i<= nlstate; i++)
	gmp[j] += prlim[i][i]*p3mat[i][j][1];
}	}
/* end force of mortality */	/* end probability of death */

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

for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */	for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];	gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
}	}
Line 2070 void varevsij(char optionfilefiname[], d	Line 2509 void varevsij(char optionfilefiname[], d
for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */	for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
for(theta=1; theta <=npar; theta++)	for(theta=1; theta <=npar; theta++)
trgradgp[j][theta]=gradgp[theta][j];	trgradgp[j][theta]=gradgp[theta][j];


hf=hstepmstepm/YEARM; / Duration of hstepm expressed in year unit. */	hf=hstepmstepm/YEARM; / Duration of hstepm expressed in year unit. */
for(i=1;i<=nlstate;i++)	for(i=1;i<=nlstate;i++)
Line 2085 void varevsij(char optionfilefiname[], d	Line 2525 void varevsij(char optionfilefiname[], d
vareij[i][j][(int)age] += doldm[i][j]hfhf;	vareij[i][j][(int)age] += doldm[i][j]hfhf;
}	}
}	}

/* pptj */	/* pptj */
matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);	matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);	matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
Line 2093 void varevsij(char optionfilefiname[], d	Line 2533 void varevsij(char optionfilefiname[], d
for(i=nlstate+1;i<=nlstate+ndeath;i++)	for(i=nlstate+1;i<=nlstate+ndeath;i++)
varppt[j][i]=doldmp[j][i];	varppt[j][i]=doldmp[j][i];
/* end ppptj */	/* end ppptj */
	/* x centered again */
hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);	hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);	prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);

Line 2105 void varevsij(char optionfilefiname[], d	Line 2546 void varevsij(char optionfilefiname[], d
prlim[i][i]=mobaverage[(int)age][i][ij];	prlim[i][i]=mobaverage[(int)age][i][ij];
}	}
}	}

/* This for computing force of mortality (h=1)as a weighted average */	/* This for computing probability of death (h=1 means
for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){	computed over hstepm (estepm) matrices product = hstepm*stepm months)
for(i=1; i<= nlstate; i++)	as a weighted average of prlim.
	*/
	for(j=nlstate+1;j<=nlstate+ndeath;j++){
	for(i=1,gmp[j]=0.;i<= nlstate; i++)
gmp[j] += prlim[i][i]*p3mat[i][j][1];	gmp[j] += prlim[i][i]*p3mat[i][j][1];
}	}
/* end force of mortality */	/* end probability of death */

fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);	fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
for(j=nlstate+1; j<=(nlstate+ndeath);j++){	for(j=nlstate+1; j<=(nlstate+ndeath);j++){
Line 2141 void varevsij(char optionfilefiname[], d	Line 2585 void varevsij(char optionfilefiname[], d
fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");	fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
/* for(j=nlstate+1; j<= nlstate+ndeath; j++){ // Only the first actually */	/* 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; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);	/* fprintf(ficgp,"\n 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); */
	fprintf(ficgp,"\n plot \"%s\" u 1:($3) not w l 1 ",fileresprobmorprev);
	fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
	fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);	fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);	fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
/* fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);	/* fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
*/	*/
fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);	fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);

free_vector(xp,1,npar);	free_vector(xp,1,npar);
free_matrix(doldm,1,nlstate,1,nlstate);	free_matrix(doldm,1,nlstate,1,nlstate);
Line 2160 void varevsij(char optionfilefiname[], d	Line 2607 void varevsij(char optionfilefiname[], d
fclose(ficresprobmorprev);	fclose(ficresprobmorprev);
fclose(ficgp);	fclose(ficgp);
fclose(fichtm);	fclose(fichtm);
}	} /* end varevsij */

/********** Variance of prevlim ****************/	/********** Variance of prevlim ****************/
void varprevlim(char fileres[], double varpl, double matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double oldm, double savm, double **prlim, double ftolpl, int ij)	void varprevlim(char fileres[], double varpl, double matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double oldm, double savm, double **prlim, double ftolpl, int ij)
Line 2306 void varprob(char optionfilefiname[], do	Line 2753 void varprob(char optionfilefiname[], do
fprintf(ficresprobcov," p%1d-%1d ",i,j);	fprintf(ficresprobcov," p%1d-%1d ",i,j);
fprintf(ficresprobcor," p%1d-%1d ",i,j);	fprintf(ficresprobcor," p%1d-%1d ",i,j);
}	}
fprintf(ficresprob,"\n");	/* fprintf(ficresprob,"\n");
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 2348 void varprob(char optionfilefiname[], do	Line 2796 void varprob(char optionfilefiname[], do
if (cptcovn>0) {	if (cptcovn>0) {
fprintf(ficresprob, "\n#********** Variable ");	fprintf(ficresprob, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
fprintf(ficresprob, "**********\n#");	fprintf(ficresprob, "**********\n#\n");
fprintf(ficresprobcov, "\n#********** Variable ");	fprintf(ficresprobcov, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
fprintf(ficresprobcov, "**********\n#");	fprintf(ficresprobcov, "**********\n#\n");

fprintf(ficgp, "\n#********** Variable ");	fprintf(ficgp, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
fprintf(ficgp, "**********\n#");	fprintf(ficgp, "**********\n#\n");


fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");	fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
Line 2364 void varprob(char optionfilefiname[], do	Line 2812 void varprob(char optionfilefiname[], do

fprintf(ficresprobcor, "\n#********** Variable ");	fprintf(ficresprobcor, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
fprintf(ficgp, "**********\n#");	fprintf(ficresprobcor, "**********\n#");
}	}

for (age=bage; age<=fage; age ++){	for (age=bage; age<=fage; age ++){
Line 2383 void varprob(char optionfilefiname[], do	Line 2831 void varprob(char optionfilefiname[], do

for(theta=1; theta <=npar; theta++){	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]:(double)0);

pmij(pmmij,cov,ncovmodel,xp,nlstate);	pmij(pmmij,cov,ncovmodel,xp,nlstate);

Line 2396 void varprob(char optionfilefiname[], do	Line 2844 void varprob(char optionfilefiname[], do
}	}

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]:(double)0);

pmij(pmmij,cov,ncovmodel,xp,nlstate);	pmij(pmmij,cov,ncovmodel,xp,nlstate);
k=0;	k=0;
Line 2408 void varprob(char optionfilefiname[], do	Line 2856 void varprob(char optionfilefiname[], do
}	}

for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)	for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];	gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];
}	}

for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)	for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
Line 2571 void printinghtml(char fileres[], char t	Line 3019 void printinghtml(char fileres[], char t
fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);	fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
}	}

fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n	fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
- Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n	- Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n \
- Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n	- Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n \
- Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n	- Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n \
- Life expectancies by age and initial health status (estepm=%2d months):	- Life expectancies by age and initial health status (estepm=%2d months): \
<a href=\"e%s\">e%s</a> <br>\n</li>", \	<a href=\"e%s\">e%s</a> <br>\n</li>", \
jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);	jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);

Line 2595 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 3043 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: pe%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: pe%s%d1.png<br> \
<img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);	<img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),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 before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>	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: pe%s%d2.png<br> \
<img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);	<img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
/* Stable prevalence in each health state */	/* 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>- Stable prevalence in each health state : p%s%d%d.png<br> \
<img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);	<img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),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): exp%s%d%d.png <br>	fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br> \
<img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);	<img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),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): e%s%d.png<br>	health expectancies in states (1) and (2): e%s%d.png<br>\
<img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);	<img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
} /* end i1 */	} /* end i1 */
}/* End k1 */	}/* End k1 */
fprintf(fichtm,"</ul>");	fprintf(fichtm,"</ul>");


fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n	fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
- Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n	- Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
- Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n	- Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n\
- Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n	- Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n\
- Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n	- Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n\
- Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n	- Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n\
- Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n	- Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n\
- Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);	- Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);

if(popforecast==1) fprintf(fichtm,"\n	/* if(popforecast==1) fprintf(fichtm,"\n */
- Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n	/* - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
- Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n	/* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
<br>",fileres,fileres,fileres,fileres);	/* <br>",fileres,fileres,fileres,fileres); */
else	/* else */
fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);	/* fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");	fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");

m=cptcoveff;	m=cptcoveff;
Line 2648 fprintf(fichtm," <ul><li><b>Graphs</b></	Line 3097 fprintf(fichtm," <ul><li><b>Graphs</b></
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");	fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
}	}
for(cpt=1; cpt<=nlstate;cpt++) {	for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident	fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
interval) in state (%d): v%s%d%d.png <br>	interval) in state (%d): v%s%d%d.png <br>\
<img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);	<img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
}	}
} /* end i1 */	} /* end i1 */
Line 2683 m=pow(2,cptcoveff);	Line 3132 m=pow(2,cptcoveff);
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,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);	fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,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)");
}	}
fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);	fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,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 2749 m=pow(2,cptcoveff);	Line 3198 m=pow(2,cptcoveff);
}	}
}	}

/* CV preval stat */	/* CV preval stable (period) */
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=3;	k=3;
fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);	fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
Line 2879 int movingaverage(double ***probs, doubl	Line 3328 int movingaverage(double ***probs, doubl


/************ Forecasting ****************/	/************ Forecasting ****************/
prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){	prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
	/* proj1, year, month, day of starting projection
int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;	agemin, agemax range of age
	dateprev1 dateprev2 range of dates during which prevalence is computed
	anproj2 year of en of projection (same day and month as proj1).
	*/
	int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
int *popage;	int *popage;
double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;	double agec; /* generic age */
	double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
double popeffectif,popcount;	double popeffectif,popcount;
double ***p3mat;	double ***p3mat;
double ***mobaverage;	double ***mobaverage;
char fileresf[FILENAMELENGTH];	char fileresf[FILENAMELENGTH];

agelim=AGESUP;	agelim=AGESUP;
calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;	prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);

prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);


strcpy(fileresf,"f");	strcpy(fileresf,"f");
strcat(fileresf,fileres);	strcat(fileresf,fileres);
Line 2916 prevforecast(char fileres[], double anpr	Line 3367 prevforecast(char fileres[], double anpr

stepsize=(int) (stepm+YEARM-1)/YEARM;	stepsize=(int) (stepm+YEARM-1)/YEARM;
if (stepm<=12) stepsize=1;	if (stepm<=12) stepsize=1;
	if(estepm < stepm){
agelim=AGESUP;	printf ("Problem %d lower than %d\n",estepm, stepm);
	}
hstepm=1;	else hstepm=estepm;

hstepm=hstepm/stepm;	hstepm=hstepm/stepm;
yp1=modf(dateintmean,&yp);	yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
	fractional in yp1 */
anprojmean=yp;	anprojmean=yp;
yp2=modf((yp1*12),&yp);	yp2=modf((yp1*12),&yp);
mprojmean=yp;	mprojmean=yp;
Line 2929 prevforecast(char fileres[], double anpr	Line 3382 prevforecast(char fileres[], double anpr
jprojmean=yp;	jprojmean=yp;
if(jprojmean==0) jprojmean=1;	if(jprojmean==0) jprojmean=1;
if(mprojmean==0) jprojmean=1;	if(mprojmean==0) jprojmean=1;

	i1=cptcoveff;
	if (cptcovn < 1){i1=1;}

fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);	fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);

for(cptcov=1;cptcov<=i2;cptcov++){	fprintf(ficresf,"#**** Routine prevforecast \n");

	/* if (h==(int)(YEARMyearp)){ /
	for(cptcov=1, k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){	for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
k=k+1;	k=k+1;
fprintf(ficresf,"\n#******");	fprintf(ficresf,"\n#******");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcoveff;j++) {
fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
}	}
fprintf(ficresf,"******\n");	fprintf(ficresf,"******\n");
fprintf(ficresf,"# StartingAge FinalAge");	fprintf(ficresf,"# Covariate valuofcovar yearproj age");
for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);	for(j=1; j<=nlstate+ndeath;j++){
	for(i=1; i<=nlstate;i++)
	fprintf(ficresf," p%d%d",i,j);
for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {	fprintf(ficresf," p.%d",j);
	}
	for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
fprintf(ficresf,"\n");	fprintf(ficresf,"\n");
fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);	fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);

for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){	for (agec=fage; agec>=(ageminpar-1); agec--){
nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);	nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
nhstepm = nhstepm/hstepm;	nhstepm = nhstepm/hstepm;

p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
oldm=oldms;savm=savms;	oldm=oldms;savm=savms;
hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);	hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);

for (h=0; h<=nhstepm; h++){	for (h=0; h<=nhstepm; h++){
if (h==(int) (calagedate+YEARM*cpt)) {	if (hhstepm/YEARMstepm ==yearp) {
fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+hhstepm/YEARMstepm);	fprintf(ficresf,"\n");
	for(j=1;j<=cptcoveff;j++)
	fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
	fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+hhstepm/YEARMstepm);
}	}
for(j=1; j<=nlstate+ndeath;j++) {	for(j=1; j<=nlstate+ndeath;j++) {
kk1=0.;kk2=0;	ppij=0.;
for(i=1; i<=nlstate;i++) {	for(i=1; i<=nlstate;i++) {
if (mobilav==1)	if (mobilav==1)
kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];	ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
else {	else {
kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];	ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
}	}
	if (hhstepm/YEARMstepm== yearp) {
}	fprintf(ficresf," %.3f", p3mat[i][j][h]);
if (h==(int)(calagedate+12*cpt)){	}
fprintf(ficresf," %.3f", kk1);	} /* end i */
	if (hhstepm/YEARMstepm==yearp) {
	fprintf(ficresf," %.3f", ppij);
}	}
}	}/* end j */
}	} /* end h */
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
}	} /* end agec */
}	} /* end yearp */
}	} /* end cptcod */
}	} /* end cptcov */

if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);	if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);

fclose(ficresf);	fclose(ficresf);
}	}
/************ Forecasting ****************/
	/************ Forecasting *not tested NB***********/
populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){	populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){

int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;	int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
int *popage;	int *popage;
double calagedate, agelim, kk1, kk2;	double calagedatem, agelim, kk1, kk2;
double popeffectif,popcount;	double popeffectif,popcount;
double *p3mat,tabpop,**tabpopprev;	double *p3mat,tabpop,**tabpopprev;
double ***mobaverage;	double ***mobaverage;
Line 3000 populforecast(char fileres[], double anp	Line 3465 populforecast(char fileres[], double anp
tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);	tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);	tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
agelim=AGESUP;	agelim=AGESUP;
calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;	calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;

prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);	prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);


strcpy(filerespop,"pop");	strcpy(filerespop,"pop");
Line 3048 populforecast(char fileres[], double anp	Line 3513 populforecast(char fileres[], double anp
for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];	for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
}	}

for(cptcov=1;cptcov<=i2;cptcov++){	for(cptcov=1,k=0;cptcov<=i2;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){	for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
k=k+1;	k=k+1;
fprintf(ficrespop,"\n#******");	fprintf(ficrespop,"\n#******");
Line 3063 populforecast(char fileres[], double anp	Line 3528 populforecast(char fileres[], double anp
for (cpt=0; cpt<=0;cpt++) {	for (cpt=0; cpt<=0;cpt++) {
fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);	fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);

for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){	for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);	nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
nhstepm = nhstepm/hstepm;	nhstepm = nhstepm/hstepm;

Line 3072 populforecast(char fileres[], double anp	Line 3537 populforecast(char fileres[], double anp
hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);	hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);

for (h=0; h<=nhstepm; h++){	for (h=0; h<=nhstepm; h++){
if (h==(int) (calagedate+YEARM*cpt)) {	if (h==(int) (calagedatem+YEARM*cpt)) {
fprintf(ficrespop,"\n %3.f ",agedeb+hhstepm/YEARMstepm);	fprintf(ficrespop,"\n %3.f ",agedeb+hhstepm/YEARMstepm);
}	}
for(j=1; j<=nlstate+ndeath;j++) {	for(j=1; j<=nlstate+ndeath;j++) {
Line 3084 populforecast(char fileres[], double anp	Line 3549 populforecast(char fileres[], double anp
kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];	kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
}	}
}	}
if (h==(int)(calagedate+12*cpt)){	if (h==(int)(calagedatem+12*cpt)){
tabpop[(int)(agedeb)][j][cptcod]=kk1;	tabpop[(int)(agedeb)][j][cptcod]=kk1;
/*fprintf(ficrespop," %.3f", kk1);	/*fprintf(ficrespop," %.3f", kk1);
if (popforecast==1) fprintf(ficrespop," [%.f]", kk1popeffectif[(int)agedeb+1]);/	if (popforecast==1) fprintf(ficrespop," [%.f]", kk1popeffectif[(int)agedeb+1]);/
Line 3095 populforecast(char fileres[], double anp	Line 3560 populforecast(char fileres[], double anp
for(j=1; j<=nlstate;j++){	for(j=1; j<=nlstate;j++){
kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];	kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
}	}
tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1popeffectif[(int)(agedeb+(calagedate+12cpt)hstepm/YEARMstepm-1)];	tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1popeffectif[(int)(agedeb+(calagedatem+12cpt)hstepm/YEARMstepm-1)];
}	}

if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)	if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++)
fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);	fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
}	}
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
Line 3109 populforecast(char fileres[], double anp	Line 3574 populforecast(char fileres[], double anp

for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {	for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);	fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){	for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){
nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);	nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
nhstepm = nhstepm/hstepm;	nhstepm = nhstepm/hstepm;

Line 3117 populforecast(char fileres[], double anp	Line 3582 populforecast(char fileres[], double anp
oldm=oldms;savm=savms;	oldm=oldms;savm=savms;
hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);	hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
for (h=0; h<=nhstepm; h++){	for (h=0; h<=nhstepm; h++){
if (h==(int) (calagedate+YEARM*cpt)) {	if (h==(int) (calagedatem+YEARM*cpt)) {
fprintf(ficresf,"\n %3.f ",agedeb+hhstepm/YEARMstepm);	fprintf(ficresf,"\n %3.f ",agedeb+hhstepm/YEARMstepm);
}	}
for(j=1; j<=nlstate+ndeath;j++) {	for(j=1; j<=nlstate+ndeath;j++) {
Line 3125 populforecast(char fileres[], double anp	Line 3590 populforecast(char fileres[], double anp
for(i=1; i<=nlstate;i++) {	for(i=1; i<=nlstate;i++) {
kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];	kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
}	}
if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);	if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);
}	}
}	}
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
Line 3144 populforecast(char fileres[], double anp	Line 3609 populforecast(char fileres[], double anp
free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);	free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);	free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
fclose(ficrespop);	fclose(ficrespop);
}	} /* End of popforecast */

	int fileappend(FILE fichier, char optionfile)
	{
	if((fichier=fopen(optionfile,"a"))==NULL) {
	printf("Problem with file: %s\n", optionfile);
	fprintf(ficlog,"Problem with file: %s\n", optionfile);
	return (1);
	}

	}
/***********************************************/	/***********************************************/
/************** Main Program ***************/	/************** Main Program ***************/
/***********************************************/	/***********************************************/
Line 3153 populforecast(char fileres[], double anp	Line 3627 populforecast(char fileres[], double anp
int main(int argc, char *argv[])	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,cptcode, cptcod;	int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
	int jj;
	int numlinepar=0; /* Current linenumber of parameter file */
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 3165 int main(int argc, char *argv[])	Line 3641 int main(int argc, char *argv[])
double ***mobaverage;	double ***mobaverage;
int *indx;	int *indx;
char line[MAXLINE], linepar[MAXLINE];	char line[MAXLINE], linepar[MAXLINE];
char path[80],pathc[80],pathcd[80],pathtot[80],model[80];	char path[132],pathc[132],pathcd[132],pathtot[132],model[132];
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;
int ju,jl, mi;	int ju,jl, mi;
int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;	int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
int jnais,jdc,jint4,jint1,jint2,jint3,*outcome,tab;	int jnais,jdc,jint4,jint1,jint2,jint3,*outcome,tab;
	int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
int mobilav=0,popforecast=0;	int mobilav=0,popforecast=0;
int hstepm, nhstepm;	int hstepm, nhstepm;
double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;	double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
	double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;

double bage, fage, age, agelim, agebase;	double bage, fage, age, agelim, agebase;
double ftolpl=FTOL;	double ftolpl=FTOL;
Line 3189 int main(int argc, char *argv[])	Line 3667 int main(int argc, char *argv[])
double *varpl; / Variances of prevalence limits by age */	double *varpl; / Variances of prevalence limits by age */
double *epj, vepp;	double *epj, vepp;
double kk1, kk2;	double kk1, kk2;
double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;	double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;

char *alph[]={"a","a","b","c","d","e"}, str[4];	char *alph[]={"a","a","b","c","d","e"}, str[4];


char z[1]="c", occ;	char z[1]="c", occ;
#include <sys/time.h>
#include <time.h>
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 strt, strtend;
	char *stratrunc;
	int lstra;

	long total_usecs;
	struct timeval start_time, end_time, curr_time;
	struct timezone tzp;
	extern int gettimeofday();
	struct tm tmg, tm, gmtime(), localtime();
	long time_value;
	extern long time();

/* long total_usecs;	/* gettimeofday(&start_time, (struct timezone)0); / /* at first time */
struct timeval start_time, end_time;	(void) gettimeofday(&start_time,&tzp);
	tm = *localtime(&start_time.tv_sec);
gettimeofday(&start_time, (struct timezone)0); / /* at first time */	tmg = *gmtime(&start_time.tv_sec);
	strt=asctime(&tm);

	/* printf("Localtime (at start)=%s",strt); */
	/* tp.tv_sec = tp.tv_sec +86400; */
	/* tm = localtime(&start_time.tv_sec); /
	/* tmg.tm_year=tmg.tm_year +dsigndyear; /
	/* tmg.tm_mon=tmg.tm_mon +dsigndmonth; /
	/* tmg.tm_hour=tmg.tm_hour + 1; */
	/* tp.tv_sec = mktime(&tmg); */
	/* strt=asctime(&tmg); */
	/* printf("Time(after) =%s",strt); */
	/* (void) time (&time_value);
	* printf("time=%d,t-=%d\n",time_value,time_value-86400);
	* tm = *localtime(&time_value);
	* strt=asctime(&tm);
	* printf("tim_value=%d,asctime=%s\n",time_value,strt);
	*/

getcwd(pathcd, size);	getcwd(pathcd, size);

printf("\n%s",version);	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);	scanf("%s",pathtot);
Line 3213 int main(int argc, char *argv[])	Line 3719 int main(int argc, char *argv[])
else{	else{
strcpy(pathtot,argv[1]);	strcpy(pathtot,argv[1]);
}	}
/if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");/	/if(getcwd(pathcd, 132)!= NULL)printf ("Error pathcd\n");/
/*cygwin_split_path(pathtot,path,optionfile);	/*cygwin_split_path(pathtot,path,optionfile);
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(pathtot,path,optionfile,optionfilext,optionfilefiname);	split(pathtot,path,optionfile,optionfilext,optionfilefiname);
printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);	printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
chdir(path);	chdir(path);
replace(pathc,path);	replace(pathc,path);

Line 3233 int main(int argc, char *argv[])	Line 3739 int main(int argc, char *argv[])
goto end;	goto end;
}	}
fprintf(ficlog,"Log filename:%s\n",filelog);	fprintf(ficlog,"Log filename:%s\n",filelog);
fprintf(ficlog,"\n%s",version);	fprintf(ficlog,"\n%s\n%s",version,fullversion);
fprintf(ficlog,"\nEnter the parameter file name: ");	fprintf(ficlog,"\nEnter the parameter file name: ");
fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);	fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);

	printf("Localtime (at start)=%s",strt);
	fprintf(ficlog,"Localtime (at start)=%s",strt);
fflush(ficlog);	fflush(ficlog);

/* */	/* */
Line 3248 int main(int argc, char *argv[])	Line 3757 int main(int argc, char *argv[])
if((ficpar=fopen(optionfile,"r"))==NULL) {	if((ficpar=fopen(optionfile,"r"))==NULL) {
printf("Problem with optionfile %s\n",optionfile);	printf("Problem with optionfile %s\n",optionfile);
fprintf(ficlog,"Problem with optionfile %s\n",optionfile);	fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
	fflush(ficlog);
goto end;	goto end;
}	}

Line 3256 int main(int argc, char *argv[])	Line 3766 int main(int argc, char *argv[])
if((ficparo=fopen(filereso,"w"))==NULL) {	if((ficparo=fopen(filereso,"w"))==NULL) {
printf("Problem with Output resultfile: %s\n", filereso);	printf("Problem with Output resultfile: %s\n", filereso);
fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);	fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
	fflush(ficlog);
goto end;	goto end;
}	}

/* Reads comments: lines beginning with '#' */	/* Reads comments: lines beginning with '#' */
	numlinepar=0;
while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);	ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);	fgets(line, MAXLINE, ficpar);
	numlinepar++;
puts(line);	puts(line);
fputs(line,ficparo);	fputs(line,ficparo);
	fputs(line,ficlog);
}	}
ungetc(c,ficpar);	ungetc(c,ficpar);

fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);	fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
	numlinepar++;
printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);	printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);	fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
	fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
	fflush(ficlog);
while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);	ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);	fgets(line, MAXLINE, ficpar);
	numlinepar++;
puts(line);	puts(line);
fputs(line,ficparo);	fputs(line,ficparo);
	fputs(line,ficlog);
}	}
ungetc(c,ficpar);	ungetc(c,ficpar);


covar=matrix(0,NCOVMAX,1,n);	covar=matrix(0,NCOVMAX,1,n);
cptcovn=0; /Number of covariates, i.e. number of '+' in model statement/	cptcovn=0; /Number of covariates, i.e. number of '+' in model statement/
Line 3292 int main(int argc, char *argv[])	Line 3811 int main(int argc, char *argv[])
while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);	ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);	fgets(line, MAXLINE, ficpar);
	numlinepar++;
puts(line);	puts(line);
fputs(line,ficparo);	fputs(line,ficparo);
	fputs(line,ficlog);
}	}
ungetc(c,ficpar);	ungetc(c,ficpar);

param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);	param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
for(i=1; i <=nlstate; i++)	for(i=1; i <=nlstate; i++){
for(j=1; j <=nlstate+ndeath-1; j++){	j=0;
	for(jj=1; jj <=nlstate+ndeath; jj++){
	if(jj==i) continue;
	j++;
fscanf(ficpar,"%1d%1d",&i1,&j1);	fscanf(ficpar,"%1d%1d",&i1,&j1);
	if ((i1 != i) && (j1 != j)){
	printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
	exit(1);
	}
fprintf(ficparo,"%1d%1d",i1,j1);	fprintf(ficparo,"%1d%1d",i1,j1);
if(mle==1)	if(mle==1)
printf("%1d%1d",i,j);	printf("%1d%1d",i,j);
Line 3316 int main(int argc, char *argv[])	Line 3844 int main(int argc, char *argv[])
fprintf(ficparo," %lf",param[i][j][k]);	fprintf(ficparo," %lf",param[i][j][k]);
}	}
fscanf(ficpar,"\n");	fscanf(ficpar,"\n");
	numlinepar++;
if(mle==1)	if(mle==1)
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
fprintf(ficparo,"\n");	fprintf(ficparo,"\n");
}	}
	}
	fflush(ficlog);

npar= (nlstate+ndeath-1)nlstatencovmodel; /* Number of parameters*/	npar= (nlstate+ndeath-1)nlstatencovmodel; /* Number of parameters*/

p=param[1][1];	p=param[1][1];
Line 3330 int main(int argc, char *argv[])	Line 3861 int main(int argc, char *argv[])
while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);	ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);	fgets(line, MAXLINE, ficpar);
	numlinepar++;
puts(line);	puts(line);
fputs(line,ficparo);	fputs(line,ficparo);
	fputs(line,ficlog);
}	}
ungetc(c,ficpar);	ungetc(c,ficpar);

delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);	delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */	/* delti=vector(1,npar); // Scale of each paramater (output from hesscov) */
for(i=1; i <=nlstate; i++){	for(i=1; i <=nlstate; i++){
for(j=1; j <=nlstate+ndeath-1; j++){	for(j=1; j <=nlstate+ndeath-1; j++){
fscanf(ficpar,"%1d%1d",&i1,&j1);	fscanf(ficpar,"%1d%1d",&i1,&j1);
	if ((i1-i)*(j1-j)!=0){
	printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
	exit(1);
	}
printf("%1d%1d",i,j);	printf("%1d%1d",i,j);
fprintf(ficparo,"%1d%1d",i1,j1);	fprintf(ficparo,"%1d%1d",i1,j1);
	fprintf(ficlog,"%1d%1d",i1,j1);
for(k=1; k<=ncovmodel;k++){	for(k=1; k<=ncovmodel;k++){
fscanf(ficpar,"%le",&delti3[i][j][k]);	fscanf(ficpar,"%le",&delti3[i][j][k]);
printf(" %le",delti3[i][j][k]);	printf(" %le",delti3[i][j][k]);
fprintf(ficparo," %le",delti3[i][j][k]);	fprintf(ficparo," %le",delti3[i][j][k]);
	fprintf(ficlog," %le",delti3[i][j][k]);
}	}
fscanf(ficpar,"\n");	fscanf(ficpar,"\n");
	numlinepar++;
printf("\n");	printf("\n");
fprintf(ficparo,"\n");	fprintf(ficparo,"\n");
	fprintf(ficlog,"\n");
}	}
}	}
	fflush(ficlog);

delti=delti3[1][1];	delti=delti3[1][1];


	/* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); / / Hasn't to to freed here otherwise delti is no more allocated */

/* Reads comments: lines beginning with '#' */	/* Reads comments: lines beginning with '#' */
while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);	ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);	fgets(line, MAXLINE, ficpar);
	numlinepar++;
puts(line);	puts(line);
fputs(line,ficparo);	fputs(line,ficparo);
	fputs(line,ficlog);
}	}
ungetc(c,ficpar);	ungetc(c,ficpar);

Line 3374 int main(int argc, char *argv[])	Line 3922 int main(int argc, char *argv[])
fscanf(ficpar," %le",&matcov[i][j]);	fscanf(ficpar," %le",&matcov[i][j]);
if(mle==1){	if(mle==1){
printf(" %.5le",matcov[i][j]);	printf(" %.5le",matcov[i][j]);
fprintf(ficlog," %.5le",matcov[i][j]);
}	}
else	fprintf(ficlog," %.5le",matcov[i][j]);
fprintf(ficlog," %.5le",matcov[i][j]);
fprintf(ficparo," %.5le",matcov[i][j]);	fprintf(ficparo," %.5le",matcov[i][j]);
}	}
fscanf(ficpar,"\n");	fscanf(ficpar,"\n");
	numlinepar++;
if(mle==1)	if(mle==1)
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
Line 3394 int main(int argc, char *argv[])	Line 3941 int main(int argc, char *argv[])
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");

	fflush(ficlog);

/-------- Rewriting paramater file ----------/	/-------- Rewriting paramater file ----------/
strcpy(rfileres,"r"); /* "Rparameterfile */	strcpy(rfileres,"r"); /* "Rparameterfile */
Line 3415 int main(int argc, char *argv[])	Line 3963 int main(int argc, char *argv[])
n= lastobs;	n= lastobs;
severity = vector(1,maxwav);	severity = vector(1,maxwav);
outcome=imatrix(1,maxwav+1,1,n);	outcome=imatrix(1,maxwav+1,1,n);
num=ivector(1,n);	num=lvector(1,n);
moisnais=vector(1,n);	moisnais=vector(1,n);
annais=vector(1,n);	annais=vector(1,n);
moisdc=vector(1,n);	moisdc=vector(1,n);
Line 3451 int main(int argc, char *argv[])	Line 3999 int main(int argc, char *argv[])
for (j=ncovcol;j>=1;j--){	for (j=ncovcol;j>=1;j--){
cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);	cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
}	}
num[i]=atol(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)){	/*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
printf("%d %.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;}*/	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;	i=i+1;
}	}
Line 3470 int main(int argc, char *argv[])	Line 4024 int main(int argc, char *argv[])
}*/	}*/
/* for (i=1; i<=imx; i++){	/* for (i=1; i<=imx; i++){
if (s[4][i]==9) s[4][i]=-1;	if (s[4][i]==9) s[4][i]=-1;
printf("%d %.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]));}*/	printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i]));}*/

	for (i=1; i<=imx; i++)

	/*if ((s[3][i]==3) \|\| (s[4][i]==3)) weight[i]=0.08;
	else weight[i]=1;*/

/* Calculation of the number of parameter from char model*/	/* Calculation of the number of parameter 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(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
Tprod=ivector(1,15);	Tprod=ivector(1,15);
Line 3564 int main(int argc, char *argv[])	Line 4122 int main(int argc, char *argv[])

for (i=1; i<=imx; i++) {	for (i=1; i<=imx; i++) {
for(m=2; (m<= maxwav); m++) {	for(m=2; (m<= maxwav); m++) {
if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){	if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
anint[m][i]=9999;	anint[m][i]=9999;
s[m][i]=-1;	s[m][i]=-1;
}	}
if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;	if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
	printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
	fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
	s[m][i]=-1;
	}
	if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
	printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);
	fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);
	s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
	}
}	}
}	}

for (i=1; i<=imx; i++) {	for (i=1; i<=imx; i++) {
agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);	agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
for(m=1; (m<= maxwav); m++){	for(m=firstpass; (m<= lastpass); m++){
if(s[m][i] >0){	if(s[m][i] >0){
if (s[m][i] >= nlstate+1) {	if (s[m][i] >= nlstate+1) {
if(agedc[i]>0)	if(agedc[i]>0)
if(moisdc[i]!=99 && andc[i]!=9999)	if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
agev[m][i]=agedc[i];	agev[m][i]=agedc[i];
/if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;/	/if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;/
else {	else {
if (andc[i]!=9999){	if ((int)andc[i]!=9999){
printf("Warning negative age at death: %d line:%d\n",num[i],i);	printf("Warning negative age at death: %ld line:%d\n",num[i],i);
fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);	fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
agev[m][i]=-1;	agev[m][i]=-1;
}	}
}	}
}	}
else if(s[m][i] !=9){ /* Should no more exist */	else if(s[m][i] !=9){ /* Standard case, age in fractional
	years but with the precision of a
	month */
agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);	agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
if(mint[m][i]==99 \|\| anint[m][i]==9999)	if((int)mint[m][i]==99 \|\| (int)anint[m][i]==9999)
agev[m][i]=1;	agev[m][i]=1;
else if(agev[m][i] <agemin){	else if(agev[m][i] <agemin){
agemin=agev[m][i];	agemin=agev[m][i];
Line 3615 int main(int argc, char *argv[])	Line 4184 int main(int argc, char *argv[])

}	}
for (i=1; i<=imx; i++) {	for (i=1; i<=imx; i++) {
for(m=1; (m<= maxwav); m++){	for(m=firstpass; (m<=lastpass); m++){
if (s[m][i] > (nlstate+ndeath)) {	if (s[m][i] > (nlstate+ndeath)) {
printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);	printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);	fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
Line 3624 int main(int argc, char *argv[])	Line 4193 int main(int argc, char *argv[])
}	}
}	}

	/*for (i=1; i<=imx; i++){
	for (m=firstpass; (m<lastpass); m++){
	printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
	}

	}*/

printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);	printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);	fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);

Line 3678 int main(int argc, char *argv[])	Line 4254 int main(int argc, char *argv[])
}	}
scanf("%d",i);*/	scanf("%d",i);*/

	/------------ gnuplot -------------/
	strcpy(optionfilegnuplot,optionfilefiname);
	strcat(optionfilegnuplot,".gp");
	if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
	printf("Problem with file %s",optionfilegnuplot);
	}
	else{
	fprintf(ficgp,"\n# %s\n", version);
	fprintf(ficgp,"# %s\n", optionfilegnuplot);
	fprintf(ficgp,"set missing 'NaNq'\n");
	}
	fclose(ficgp);
	/--------- index.htm --------/

	strcpy(optionfilehtm,optionfile);
	strcat(optionfilehtm,".htm");
	if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
	printf("Problem with %s \n",optionfilehtm), exit(0);
	}

	fprintf(fichtm,"<body> <font size=\"2\">%s <br> %s</font> \
	<hr size=\"2\" color=\"#EC5E5E\"> \n\
	Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
	\n\
	<hr size=\"2\" color=\"#EC5E5E\">\
	<ul><li><h4>Parameter files</h4>\n\
	- Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
	- Log file of the run: <a href=\"%s\">%s</a><br>\n\
	- Gnuplot file name: <a href=\"%s\">%s</a>\n\
	- Date and time at start: %s</ul>\n",\
	version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt,\
	model,fileres,fileres,\
	filelog,filelog,optionfilegnuplot,optionfilegnuplot,strt);
	fclose(fichtm);

/* Calculates basic frequencies. Computes observed prevalence at single age	/* Calculates basic frequencies. Computes observed prevalence at single age
and prints on file fileres'p'. */	and prints on file fileres'p'. */
	freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);

	if(fileappend(fichtm, optionfilehtm)){
	fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
	Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
	Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
	imx,agemin,agemax,jmin,jmax,jmean);
	fclose(fichtm);
	}
pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */	pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */	oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */	newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
Line 3692 int main(int argc, char *argv[])	Line 4311 int main(int argc, char *argv[])
so we point p on param[1][1] so that p[1] maps on param[1][1][1] */	so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
p=param[1][1]; /* (((param +1)+1)+0) /	p=param[1][1]; /* (((param +1)+1)+0) /

	globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
	likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
	printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
	for (k=1; k<=npar;k++)
	printf(" %d %8.5f",k,p[k]);
	printf("\n");
	globpr=1; /* to print the contributions */
	likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
	printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
	for (k=1; k<=npar;k++)
	printf(" %d %8.5f",k,p[k]);
	printf("\n");
if(mle>=1){ /* Could be 1 or 2 */	if(mle>=1){ /* Could be 1 or 2 */
mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);	mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
}	}
Line 3723 int main(int argc, char *argv[])	Line 4354 int main(int argc, char *argv[])
}	}
}	}
}	}
if(mle==1){	if(mle!=0){
/* Computing hessian and covariance matrix */	/* Computing hessian and covariance matrix */
ftolhess=ftol; /* Usually correct */	ftolhess=ftol; /* Usually correct */
hesscov(matcov, p, npar, delti, ftolhess, func);	hesscov(matcov, p, npar, delti, ftolhess, func);
Line 3808 int main(int argc, char *argv[])	Line 4439 int main(int argc, char *argv[])
fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);	fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);	fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);	fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
	printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
	fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);

while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);	ungetc(c,ficpar);
Line 3818 int main(int argc, char *argv[])	Line 4451 int main(int argc, char *argv[])
ungetc(c,ficpar);	ungetc(c,ficpar);


dateprev1=anprev1+mprev1/12.+jprev1/365.;	dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
dateprev2=anprev2+mprev2/12.+jprev2/365.;	dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;

fscanf(ficpar,"pop_based=%d\n",&popbased);	fscanf(ficpar,"pop_based=%d\n",&popbased);
fprintf(ficparo,"pop_based=%d\n",popbased);	fprintf(ficparo,"pop_based=%d\n",popbased);
Line 3833 int main(int argc, char *argv[])	Line 4466 int main(int argc, char *argv[])
}	}
ungetc(c,ficpar);	ungetc(c,ficpar);

fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);	fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);	fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);	printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
	fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
	fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
	/* day and month of proj2 are not used but only year anproj2.*/

while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);	ungetc(c,ficpar);
Line 3850 int main(int argc, char *argv[])	Line 4485 int main(int argc, char *argv[])
fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);	fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);	fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);

freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);	/* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
	/,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);/

/------------ gnuplot -------------/
strcpy(optionfilegnuplot,optionfilefiname);
strcat(optionfilegnuplot,".gp");
if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
printf("Problem with file %s",optionfilegnuplot);
}
else{
fprintf(ficgp,"\n# %s\n", version);
fprintf(ficgp,"# %s\n", optionfilegnuplot);
fprintf(ficgp,"set missing 'NaNq'\n");
}
fclose(ficgp);
printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);	printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
/--------- index.htm --------/

strcpy(optionfilehtm,optionfile);	printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
strcat(optionfilehtm,".htm");	model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
if((fichtm=fopen(optionfilehtm,"w"))==NULL) {	jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
printf("Problem with %s \n",optionfilehtm), exit(0);
}

fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
\n
Total number of observations=%d <br>\n
Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
<hr size=\"2\" color=\"#EC5E5E\">
<ul><li><h4>Parameter files</h4>\n
- Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
- Log file of the run: <a href=\"%s\">%s</a><br>\n
- Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);
fclose(fichtm);

printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);

/------------ free_vector -------------/	/------------ free_vector -------------/
chdir(path);	chdir(path);
Line 3894 Interval (in months) between two waves:	Line 4501 Interval (in months) between two waves:
free_imatrix(dh,1,lastpass-firstpass+1,1,imx);	free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
free_imatrix(bh,1,lastpass-firstpass+1,1,imx);	free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
free_imatrix(mw,1,lastpass-firstpass+1,1,imx);	free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
free_ivector(num,1,n);	free_lvector(num,1,n);
free_vector(agedc,1,n);	free_vector(agedc,1,n);
free_matrix(covar,0,NCOVMAX,1,n);	/free_matrix(covar,0,NCOVMAX,1,n);/
/free_matrix(covar,1,NCOVMAX,1,n);/	/free_matrix(covar,1,NCOVMAX,1,n);/
fclose(ficparo);	fclose(ficparo);
fclose(ficres);	fclose(ficres);
Line 3943 Interval (in months) between two waves:	Line 4550 Interval (in months) between two waves:

for (age=agebase; age<=agelim; age++){	for (age=agebase; age<=agelim; age++){
prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);	prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
fprintf(ficrespl,"%.0f",age );	fprintf(ficrespl,"%.0f ",age );
	for(j=1;j<=cptcoveff;j++)
	fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
fprintf(ficrespl," %.5f", prlim[i][i]);	fprintf(ficrespl," %.5f", prlim[i][i]);
fprintf(ficrespl,"\n");	fprintf(ficrespl,"\n");
Line 3971 Interval (in months) between two waves:	Line 4580 Interval (in months) between two waves:

/* hstepm=1; aff par mois*/	/* hstepm=1; aff par mois*/

	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++){
k=k+1;	k=k+1;
Line 3988 Interval (in months) between two waves:	Line 4598 Interval (in months) between two waves:
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
oldm=oldms;savm=savms;	oldm=oldms;savm=savms;
hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);	hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
fprintf(ficrespij,"# Age");	fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
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++)
fprintf(ficrespij," %1d-%1d",i,j);	fprintf(ficrespij," %1d-%1d",i,j);
fprintf(ficrespij,"\n");	fprintf(ficrespij,"\n");
for (h=0; h<=nhstepm; h++){	for (h=0; h<=nhstepm; h++){
fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ hhstepm/YEARMstepm );	fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ hhstepm/YEARMstepm );
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++)
fprintf(ficrespij," %.5f", p3mat[i][j][h]);	fprintf(ficrespij," %.5f", p3mat[i][j][h]);
Line 4006 Interval (in months) between two waves:	Line 4616 Interval (in months) between two waves:
}	}
}	}

varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);	varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);

fclose(ficrespij);	fclose(ficrespij);

	probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);

/---------- Forecasting ------------------/	/---------- Forecasting ------------------/
if((stepm == 1) && (strcmp(model,".")==0)){	/if((stepm == 1) && (strcmp(model,".")==0)){/
prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);	if(prevfcast==1){
if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);	/* if(stepm ==1){*/
}	prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
else{	/* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
erreur=108;	/* } */
printf("Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);	/* else{ */
fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);	/* erreur=108; */
	/* printf("Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
	/* fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
	/* } */
}	}


Line 4053 Interval (in months) between two waves:	Line 4667 Interval (in months) between two waves:
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);

calagedate=-1;	/* 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);
prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);	/* 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) {	if (mobilav!=0) {
mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);	mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
Line 4179 Interval (in months) between two waves:	Line 4795 Interval (in months) between two waves:
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(matcov,1,npar,1,npar);	free_matrix(matcov,1,npar,1,npar);
free_vector(delti,1,npar);	/free_vector(delti,1,npar);/
	free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
free_matrix(agev,1,maxwav,1,imx);	free_matrix(agev,1,maxwav,1,imx);
free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);	free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);	if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
	free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);

free_ivector(ncodemax,1,8);	free_ivector(ncodemax,1,8);
free_ivector(Tvar,1,15);	free_ivector(Tvar,1,15);
free_ivector(Tprod,1,15);	free_ivector(Tprod,1,15);
Line 4192 Interval (in months) between two waves:	Line 4812 Interval (in months) between two waves:
free_ivector(Tage,1,15);	free_ivector(Tage,1,15);
free_ivector(Tcode,1,100);	free_ivector(Tcode,1,100);

fprintf(fichtm,"\n</body>");	/* fclose(fichtm);*/
fclose(fichtm);	/* fclose(ficgp);/ / ALready done */
fclose(ficgp);


if(erreur >0){	if(erreur >0){
Line 4207 Interval (in months) between two waves:	Line 4826 Interval (in months) between two waves:
printf("See log file on %s\n",filelog);	printf("See log file on %s\n",filelog);
fclose(ficlog);	fclose(ficlog);
/* gettimeofday(&end_time, (struct timezone)0);/ /* after time */	/* gettimeofday(&end_time, (struct timezone)0);/ /* after time */
	(void) gettimeofday(&end_time,&tzp);
/* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/	tm = *localtime(&end_time.tv_sec);
/printf("Total time was %d uSec.\n", total_usecs);/	tmg = *gmtime(&end_time.tv_sec);
	strtend=asctime(&tm);
	printf("Localtime at start %s and at end=%s",strt, strtend);
	fprintf(ficlog,"Localtime at start %s and at end=%s",strt, strtend);
	/* printf("Total time used %d Sec\n", asc_time(end_time.tv_sec -start_time.tv_sec);*/

	printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
	fprintf(ficlog,"Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
	/* printf("Total time was %d uSec.\n", total_usecs);*/
	if(fileappend(fichtm,optionfilehtm)){
	fprintf(fichtm,"<br>Localtime at start %s and at end=%s<br>",strt, strtend);
	fclose(fichtm);
	}
/------ End -----------/	/------ End -----------/

end:	end:
Line 4223 Interval (in months) between two waves:	Line 4854 Interval (in months) between two waves:
strcpy(plotcmd,GNUPLOTPROGRAM);	strcpy(plotcmd,GNUPLOTPROGRAM);
strcat(plotcmd," ");	strcat(plotcmd," ");
strcat(plotcmd,optionfilegnuplot);	strcat(plotcmd,optionfilegnuplot);
printf("Starting: %s\n",plotcmd);fflush(stdout);	printf("Starting graphs with: %s",plotcmd);fflush(stdout);
system(plotcmd);	system(plotcmd);
	printf(" Wait...");

/#ifdef windows/	/#ifdef windows/
while (z[0] != 'q') {	while (z[0] != 'q') {

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	Added in v.1.86