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Diff for /imach/src/imach.c between versions 1.56 and 1.70

version 1.56, 2002/07/24 17:28:25	version 1.70, 2003/02/05 12:40:38
Line 32	Line 32
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 83	Line 83
#define ODIRSEPARATOR '\\'	#define ODIRSEPARATOR '\\'
#endif	#endif

char version[80]="Imach version 0.8k, July 2002, INED-EUROREVES ";	char version[80]="Imach version 0.92, February 2003, INED-EUROREVES ";
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 99 int jmin, jmax; /* min, max spacing betw	Line 99 int jmin, jmax; /* min, max spacing betw
int mle, weightopt;	int mle, weightopt;
int *mw; / mw[mi][i] is number of the mi wave for this individual */	int *mw; / mw[mi][i] is number of the mi wave for this individual */
int *dh; / dh[mi][i] is number of steps between mi,mi+1 for this individual */	int *dh; / dh[mi][i] is number of steps between mi,mi+1 for this individual */
	int *bh; / bh[mi][i] is the bias (+ or -) for this individual if the delay between
	* wave mi and wave mi+1 is not an exact multiple of stepm. */
double jmean; /* Mean space between 2 waves */	double jmean; /* Mean space between 2 waves */
double oldm, newm, *savm; / Working pointers to matrices */	double oldm, newm, *savm; / Working pointers to matrices */
double oldms, newms, *savms; / Fixed working pointers to matrices */	double oldms, newms, *savms; / Fixed working pointers to matrices */
Line 177 double ftolhess; /* Tolerance for comput	Line 179 double ftolhess; /* Tolerance for comput
/************** split ***********************/	/************** split ***********************/
static int split( char path, char dirc, char name, char ext, char *finame )	static int split( char path, char dirc, char name, char ext, char *finame )
{	{
char s; / pointer */	char ss; / pointer */
int l1, l2; /* length counters */	int l1, l2; /* length counters */

l1 = strlen( path ); /* length of path */	l1 = strlen(path ); /* length of path */
if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );	if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
s= strrchr( path, DIRSEPARATOR ); /* find last / */	ss= strrchr( path, DIRSEPARATOR ); /* find last / */
if ( s == 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 */	#if defined(__bsd__) /* get current working directory */
extern char *getwd( );	extern char *getwd( );

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

if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {	if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
#endif	#endif
return( GLOCK_ERROR_GETCWD );	return( GLOCK_ERROR_GETCWD );
}	}
strcpy( name, path ); /* we've got it */	strcpy( name, path ); /* we've got it */
} else { /* strip direcotry from path */	} else { /* strip direcotry from path */
s++; /* after this, the filename */	ss++; /* after this, the filename */
l2 = strlen( s ); /* length of filename */	l2 = strlen( ss ); /* length of filename */
if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );	if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
strcpy( name, s ); /* save file name */	strcpy( name, ss ); /* save file name */
strncpy( dirc, path, l1 - l2 ); /* now the directory */	strncpy( dirc, path, l1 - l2 ); /* now the directory */
dirc[l1-l2] = 0; /* add zero */	dirc[l1-l2] = 0; /* add zero */
}	}
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
s = strrchr( name, '.' ); /* find last / */	ss = strrchr( name, '.' ); /* find last / */
s++;	ss++;
strcpy(ext,s); /* save extension */	strcpy(ext,ss); /* save extension */
l1= strlen( name);	l1= strlen( name);
l2= strlen( s)+1;	l2= strlen(ss)+1;
strncpy( finame, name, l1-l2);	strncpy( finame, name, l1-l2);
finame[l1-l2]= 0;	finame[l1-l2]= 0;
return( 0 ); /* we're done */	return( 0 ); /* we're done */
}	}


Line 277 void nrerror(char error_text[])	Line 279 void nrerror(char error_text[])
{	{
fprintf(stderr,"ERREUR ...\n");	fprintf(stderr,"ERREUR ...\n");
fprintf(stderr,"%s\n",error_text);	fprintf(stderr,"%s\n",error_text);
exit(1);	exit(EXIT_FAILURE);
}	}
/********************* vector *****************/	/********************* vector *****************/
double *vector(int nl, int nh)	double *vector(int nl, int nh)
Line 854 double matprod2(double out, double *	Line 856 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 914 double func( double *x)	Line 918 double func( double *x)
double **out;	double **out;
double sw; /* Sum of weights */	double sw; /* Sum of weights */
double lli; /* Individual log likelihood */	double lli; /* Individual log likelihood */
	int s1, s2;
	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 924 double func( double *x)	Line 930 double func( double *x)
cov[1]=1.;	cov[1]=1.;

for(k=1; k<=nlstate; k++) ll[k]=0.;	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];	if(mle==1){
for(mi=1; mi<= wav[i]-1; mi++){	for (i=1,ipmx=0, sw=0.; i<=imx; i++){
for (ii=1;ii<=nlstate+ndeath;ii++)	for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);	for(mi=1; mi<= wav[i]-1; mi++){
for(d=0; d<dh[mi][i]; d++){	for (ii=1;ii<=nlstate+ndeath;ii++)
newm=savm;	for (j=1;j<=nlstate+ndeath;j++){
cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;	oldm[ii][j]=(ii==j ? 1.0 : 0.0);
for (kk=1; kk<=cptcovage;kk++) {	savm[ii][j]=(ii==j ? 1.0 : 0.0);
cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];	}
}	for(d=0; d<dh[mi][i]; d++){
	newm=savm;
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,	cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));	for (kk=1; kk<=cptcovage;kk++) {
savm=oldm;	cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
oldm=newm;	}
	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]>1.e-8 ?(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]):log((1.+bbh)out[s1][s2]));/
	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]);/
	/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{ /* ml=4 no inter-extrapolation */
	for (i=1,ipmx=0, sw=0.; i<=imx; i++){
	for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
	for(mi=1; mi<= wav[i]-1; mi++){
	for (ii=1;ii<=nlstate+ndeath;ii++)
	for (j=1;j<=nlstate+ndeath;j++){
	oldm[ii][j]=(ii==j ? 1.0 : 0.0);
	savm[ii][j]=(ii==j ? 1.0 : 0.0);
	}
	for(d=0; d<dh[mi][i]; d++){
	newm=savm;
	cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
	for (kk=1; kk<=cptcovage;kk++) {
	cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
	}

} /* end mult */	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]]);	lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
/* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/	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;	} /* end of wave */
} /* end of wave */	} /* end of individual */
} /* end of individual */	} /* End of if */

for(k=1,l=0.; k<=nlstate; k++) l += ll[k];	for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
/* printf("l1=%f l2=%f ",ll[1],ll[2]); */	/* 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 */	l= lipmx/sw; / To get the same order of magnitude as if weight=1 for every body */
Line 974 void mlikeli(FILE *ficres,double p[], in	Line 1133 void mlikeli(FILE *ficres,double p[], in
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));	printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
fprintf(ficlog,"#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 1237 void lubksb(double *a, int n, int indx	Line 1396 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 Tvar, 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 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)
{ /* 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;
Line 1284 void freqsummary(char fileres[], int ag	Line 1443 void freqsummary(char fileres[], int ag
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])	if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
bool=0;	bool=0;
}	}
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)) {
Line 1397 void freqsummary(char fileres[], int ag	Line 1556 void freqsummary(char fileres[], int ag
}	}

/********** 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(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, 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;
double pos, k2;	double pos;
	double y2; /* in fractional years */

pp=vector(1,nlstate);	pp=vector(1,nlstate);

Line 1422 void prevalence(int agemin, float agemax	Line 1586 void prevalence(int agemin, float agemax
for(m=agemin; m <= agemax+3; m++)	for(m=agemin; m <= agemax+3; m++)
freq[i][jk][m]=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 1430 void prevalence(int agemin, float agemax	Line 1594 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]=agemax+1;
if(agev[m][i]==1) agev[m][i]=agemax+2;	if(agev[m][i]==1) agev[m][i]=agemax+2;
if (m<lastpass) {	if (m<lastpass) {
if (calagedate>0)	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]+1-((int)calagedate %12)/12.)] += weight[i];
else
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]][(int)(agemax+3)] += weight[i];
}	}
}	}
}	} /* end selection of waves */
}	}
}	}
for(i=(int)agemin; i <= (int)agemax+3; i++){	for(i=(int)agemin; i <= (int)agemax+3; i++){
Line 1482 void prevalence(int agemin, float agemax	Line 1643 void prevalence(int agemin, float agemax

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

void concatwav(int wav[], int dh, int mw, int *s, double agedc, double **agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)	void concatwav(int wav[], int dh, int bh, int mw, int s, double agedc, double *agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)
{	{
/* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.	/* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
Death is a valid wave (if date is known).	Death is a valid wave (if date is known).
mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i	mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]	dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
and mw[mi+1][i]. dh depends on stepm.	and mw[mi+1][i]. dh depends on stepm.
*/	*/

Line 1545 void concatwav(int wav[], int **dh, int	Line 1706 void concatwav(int wav[], int **dh, int
if (j <= jmin) jmin=j;	if (j <= jmin) jmin=j;
sum=sum+j;	sum=sum+j;
/if (j<0) printf("j=%d num=%d \n",j,i); /	/if (j<0) printf("j=%d num=%d \n",j,i); /
	/* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
}	}
}	}
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;
Line 1558 void concatwav(int wav[], int **dh, int	Line 1721 void concatwav(int wav[], int **dh, int
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){
dh[mi][i]=jk;	if(jl==0){
else	dh[mi][i]=jk;
dh[mi][i]=jk+1;	bh[mi][i]=0;
if(dh[mi][i]==0)	}else{ /* We want a negative bias in order to only have interpolation ie
dh[mi][i]=1; /* At least one step */	* at the price of an extra matrix product in likelihood */
}	dh[mi][i]=jk+1;
}	bh[mi][i]=ju;
	}
	}else{
	if(jl <= -ju){
	dh[mi][i]=jk;
	bh[mi][i]=jl; /* bias is positive if real duration
	* is higher than the multiple of stepm and negative otherwise.
	*/
	}
	else{
	dh[mi][i]=jk+1;
	bh[mi][i]=ju;
	}
	if(dh[mi][i]==0){
	dh[mi][i]=1; /* At least one step */
	bh[mi][i]=ju; /* At least one step */
	printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);
	}
	}
	} /* end if mle */
	} /* end wave */
}	}
jmean=sum/k;	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 1575 void concatwav(int wav[], int **dh, int	Line 1758 void concatwav(int wav[], int **dh, int
/********* Tricode **************************/	/********* Tricode **************************/
void tricode(int Tvar, int *nbcode, int imx)	void tricode(int Tvar, int *nbcode, int imx)
{	{
int Ndum[20],ij=1, k, j, i;
	int Ndum[20],ij=1, k, j, i, maxncov=19;
int cptcode=0;	int cptcode=0;
cptcoveff=0;	cptcoveff=0;

for (k=0; k<19; k++) Ndum[k]=0;	for (k=0; k<maxncov; k++) Ndum[k]=0;
for (k=1; k<=7; k++) ncodemax[k]=0;	for (k=1; k<=7; k++) ncodemax[k]=0;

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

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


	ij=1;
for (i=1; i<=ncodemax[j]; i++) {	for (i=1; i<=ncodemax[j]; i++) {
for (k=0; k<=19; k++) {	for (k=0; k<= maxncov; k++) {
if (Ndum[k] != 0) {	if (Ndum[k] != 0) {
nbcode[Tvar[j]][ij]=k;	nbcode[Tvar[j]][ij]=k;
	/* store the modality in an array. k is a modality. If we have model=V1+V1sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; /

ij++;	ij++;
}	}
Line 1608 void tricode(int Tvar, int *nbcode, in	Line 1795 void tricode(int Tvar, int *nbcode, in
}	}
}	}

for (k=0; k<19; k++) Ndum[k]=0;	for (k=0; k< maxncov; k++) Ndum[k]=0;

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

ij=1;	ij=1;
for (i=1; i<=10; i++) {	for (i=1; i<= maxncov; i++) {
if((Ndum[i]!=0) && (i<=ncovcol)){	if((Ndum[i]!=0) && (i<=ncovcol)){
Tvaraff[ij]=i;	Tvaraff[ij]=i; /For printing /
ij++;	ij++;
}	}
}	}

cptcoveff=ij-1;	cptcoveff=ij-1; /Number of simple covariates/
}	}

/********* Health Expectancies **************/	/********* Health Expectancies **************/
Line 1661 void evsij(char fileres[], double ***eij	Line 1849 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 1824 void varevsij(char optionfilefiname[], d	Line 2012 void varevsij(char optionfilefiname[], d
char fileresprobmorprev[FILENAMELENGTH];	char fileresprobmorprev[FILENAMELENGTH];

if(popbased==1){	if(popbased==1){
if(mobilav==1)	if(mobilav!=0)
strcpy(digitp,"-populbased-mobilav-");	strcpy(digitp,"-populbased-mobilav-");
else strcpy(digitp,"-populbased-nomobil-");	else strcpy(digitp,"-populbased-nomobil-");
}	}
Line 1851 void varevsij(char optionfilefiname[], d	Line 2039 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 1873 void varevsij(char optionfilefiname[], d	Line 2061 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 1908 void varevsij(char optionfilefiname[], d	Line 2096 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 1924 void varevsij(char optionfilefiname[], d	Line 2112 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 1946 void varevsij(char optionfilefiname[], d	Line 2134 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 1974 void varevsij(char optionfilefiname[], d	Line 2165 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 2001 void varevsij(char optionfilefiname[], d	Line 2196 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 2016 void varevsij(char optionfilefiname[], d	Line 2212 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 2024 void varevsij(char optionfilefiname[], d	Line 2220 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 2036 void varevsij(char optionfilefiname[], d	Line 2233 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 2072 void varevsij(char optionfilefiname[], d	Line 2272 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.png\"> <br>\n", estepm,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(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.png\";replot;",digitp,digit);
Line 2091 void varevsij(char optionfilefiname[], d	Line 2294 void varevsij(char optionfilefiname[], d
fclose(ficresprobmorprev);	fclose(ficresprobmorprev);
fclose(ficgp);	fclose(ficgp);
fclose(fichtm);	fclose(fichtm);
}	}

/********** 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)
{	{
/* Variance of prevalence limit */	/* Variance of prevalence limit */
/* double prevalim(double prlim, int nlstate, double xp, double age, double oldm, double * savm,double ftolpl);*/	/* double prevalim(double prlim, int nlstate, double xp, double age, double oldm, double savm,double ftolpl);/
double **newm;	double **newm;
double dnewm,doldm;	double dnewm,doldm;
int i, j, nhstepm, hstepm;	int i, j, nhstepm, hstepm;
Line 2237 void varprob(char optionfilefiname[], do	Line 2440 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 2269 void varprob(char optionfilefiname[], do	Line 2473 void varprob(char optionfilefiname[], do

}	}


cov[1]=1;	cov[1]=1;
tj=cptcoveff;	tj=cptcoveff;
if (cptcovn<1) {tj=1;ncodemax[1]=1;}	if (cptcovn<1) {tj=1;ncodemax[1]=1;}
Line 2277 void varprob(char optionfilefiname[], do	Line 2480 void varprob(char optionfilefiname[], do
for(t=1; t<=tj;t++){	for(t=1; t<=tj;t++){
for(i1=1; i1<=ncodemax[t];i1++){	for(i1=1; i1<=ncodemax[t];i1++){
j1++;	j1++;

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 2297 void varprob(char optionfilefiname[], do	Line 2499 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 2350 void varprob(char optionfilefiname[], do	Line 2552 void varprob(char optionfilefiname[], do

matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);	matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
matprod2(doldm,dnewm,1,(nlstate)(nlstate+ndeath),1,npar,1,(nlstate)(nlstate+ndeath),gradg);	matprod2(doldm,dnewm,1,(nlstate)(nlstate+ndeath),1,npar,1,(nlstate)(nlstate+ndeath),gradg);
	free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
	free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
	free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
	free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);

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

k=0;	k=0;
Line 2365 void varprob(char optionfilefiname[], do	Line 2571 void varprob(char optionfilefiname[], do
varpij[i][j][(int)age] = doldm[i][j];	varpij[i][j][(int)age] = doldm[i][j];

/*printf("\n%d ",(int)age);	/*printf("\n%d ",(int)age);
for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){	for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
printf("%e [%e ;%e] ",gm[i],gm[i]-2sqrt(doldm[i][i]),gm[i]+2sqrt(doldm[i][i]));	printf("%e [%e ;%e] ",gm[i],gm[i]-2sqrt(doldm[i][i]),gm[i]+2sqrt(doldm[i][i]));
fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2sqrt(doldm[i][i]),gm[i]+2sqrt(doldm[i][i]));	fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2sqrt(doldm[i][i]),gm[i]+2sqrt(doldm[i][i]));
}*/	}*/

fprintf(ficresprob,"\n%d ",(int)age);	fprintf(ficresprob,"\n%d ",(int)age);
fprintf(ficresprobcov,"\n%d ",(int)age);	fprintf(ficresprobcov,"\n%d ",(int)age);
Line 2396 void varprob(char optionfilefiname[], do	Line 2602 void varprob(char optionfilefiname[], do

/* Confidence intervalle of pij */	/* Confidence intervalle of pij */
/*	/*
fprintf(ficgp,"\nset noparametric;unset label");	fprintf(ficgp,"\nset noparametric;unset label");
fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");	fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");	fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
fprintf(fichtm,"\n<br>Probability with confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);	fprintf(fichtm,"\n<br>Probability with confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);	fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);	fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);	fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
*/	*/

/* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/	/* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
Line 2474 void varprob(char optionfilefiname[], do	Line 2680 void varprob(char optionfilefiname[], do
} /l1 /	} /l1 /
}/* k1 */	}/* k1 */
} /* loop covariates */	} /* loop covariates */
free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
}	}
	free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
	free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
free_vector(xp,1,npar);	free_vector(xp,1,npar);
fclose(ficresprob);	fclose(ficresprob);
fclose(ficresprobcov);	fclose(ficresprobcov);
Line 2616 m=pow(2,cptcoveff);	Line 2818 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 2773 m=pow(2,cptcoveff);	Line 2975 m=pow(2,cptcoveff);
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, cpt, cptcod;	int i, cpt, cptcod;
	int modcovmax =1;
int mobilavrange, mob;	int mobilavrange, mob;
double age;	double age;

	modcovmax=2cptcoveff;/ Max number of modalities. We suppose
	a covariate has 2 modalities */
	if (cptcovn<1) modcovmax=1; /* At least 1 pass */

if(mobilav==1\|\|mobilav ==3 \|\|mobilav==5 \|\|mobilav== 7){	if(mobilav==1\|\|mobilav ==3 \|\|mobilav==5 \|\|mobilav== 7){
if(mobilav==1) mobilavrange=5; /* default */	if(mobilav==1) mobilavrange=5; /* default */
else mobilavrange=mobilav;	else mobilavrange=mobilav;
for (age=bage; age<=fage; age++)	for (age=bage; age<=fage; age++)
for (i=1; i<=nlstate;i++)	for (i=1; i<=nlstate;i++)
for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)	for (cptcod=1;cptcod<=modcovmax;cptcod++)
mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];	mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
/* We keep the original values on the extreme ages bage, fage and for	/* We keep the original values on the extreme ages bage, fage and for
fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2	fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
Line 2789 int movingaverage(double ***probs, doubl	Line 2997 int movingaverage(double ***probs, doubl
for (mob=3;mob <=mobilavrange;mob=mob+2){	for (mob=3;mob <=mobilavrange;mob=mob+2){
for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){	for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
for (i=1; i<=nlstate;i++){	for (i=1; i<=nlstate;i++){
for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){	for (cptcod=1;cptcod<=modcovmax;cptcod++){
mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];	mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
for (cpt=1;cpt<=(mob-1)/2;cpt++){	for (cpt=1;cpt<=(mob-1)/2;cpt++){
mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];	mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
Line 2806 int movingaverage(double ***probs, doubl	Line 3014 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;
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(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 2844 calagedate=(anproj1+mproj1/12.+jproj1/36	Line 3054 calagedate=(anproj1+mproj1/12.+jproj1/36
stepsize=(int) (stepm+YEARM-1)/YEARM;	stepsize=(int) (stepm+YEARM-1)/YEARM;
if (stepm<=12) stepsize=1;	if (stepm<=12) stepsize=1;

agelim=AGESUP;

hstepm=1;	hstepm=1;
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 2857 calagedate=(anproj1+mproj1/12.+jproj1/36	Line 3066 calagedate=(anproj1+mproj1/12.+jproj1/36
if(jprojmean==0) jprojmean=1;	if(jprojmean==0) jprojmean=1;
if(mprojmean==0) jprojmean=1;	if(mprojmean==0) jprojmean=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");
	for(cptcov=1, k=0;cptcov<=cptcoveff;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++) {
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; 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 (h==(int) (YEARM*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+1][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+1)][i][cptcod];
}	}
	if (h==(int)(YEARM*yearp))
	fprintf(ficresf," %.3f", p3mat[i][j][h]);
}	}
if (h==(int)(calagedate+12*cpt)){	if (h==(int)(YEARM*yearp)){
fprintf(ficresf," %.3f", kk1);	fprintf(ficresf," %.3f", ppij);

}	}
}	}
}	}
Line 2913 calagedate=(anproj1+mproj1/12.+jproj1/36	Line 3127 calagedate=(anproj1+mproj1/12.+jproj1/36

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, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;	double calagedatem, agelim, kk1, kk2;
double popeffectif,popcount;	double popeffectif,popcount;
double *p3mat,tabpop,**tabpopprev;	double *p3mat,tabpop,**tabpopprev;
double ***mobaverage;	double ***mobaverage;
Line 2927 populforecast(char fileres[], double anp	Line 3142 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(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);


strcpy(filerespop,"pop");	strcpy(filerespop,"pop");
Line 2975 populforecast(char fileres[], double anp	Line 3190 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 2990 populforecast(char fileres[], double anp	Line 3205 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 2999 populforecast(char fileres[], double anp	Line 3214 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 3011 populforecast(char fileres[], double anp	Line 3226 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 3022 populforecast(char fileres[], double anp	Line 3237 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 3036 populforecast(char fileres[], double anp	Line 3251 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 3044 populforecast(char fileres[], double anp	Line 3259 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 3052 populforecast(char fileres[], double anp	Line 3267 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 3079 populforecast(char fileres[], double anp	Line 3294 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 i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;	int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
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 3098 int main(int argc, char *argv[])	Line 3313 int main(int argc, char *argv[])
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,adl,*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, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;

double bage, fage, age, agelim, agebase;	double bage, fage, age, agelim, agebase;
double ftolpl=FTOL;	double ftolpl=FTOL;
Line 3117 int main(int argc, char *argv[])	Line 3333 int main(int argc, char *argv[])
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,mproj1,anproj1,jproj2,mproj2,anproj2;


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

Line 3128 int main(int argc, char *argv[])	Line 3343 int main(int argc, char *argv[])
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];

/* long total_usecs;	/* long total_usecs;
struct timeval start_time, end_time;	struct timeval start_time, end_time;

gettimeofday(&start_time, (struct timezone)0); / /* at first time */	gettimeofday(&start_time, (struct timezone)0); / /* at first time */
getcwd(pathcd, size);	getcwd(pathcd, size);

printf("\n%s",version);	printf("\n%s",version);
Line 3147 int main(int argc, char *argv[])	Line 3362 int main(int argc, char *argv[])
/* 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, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
chdir(path);	chdir(path);
replace(pathc,path);	replace(pathc,path);

/-------- arguments in the command line --------/	/-------- arguments in the command line --------/

/* Log file */	/* Log file */
strcat(filelog, optionfilefiname);	strcat(filelog, optionfilefiname);
Line 3199 int main(int argc, char *argv[])	Line 3414 int main(int argc, char *argv[])
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);
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);
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);
puts(line);	puts(line);
Line 3209 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3424 while((c=getc(ficpar))=='#' && c!= EOF){


covar=matrix(0,NCOVMAX,1,n);	covar=matrix(0,NCOVMAX,1,n);
cptcovn=0;	cptcovn=0; /Number of covariates, i.e. number of '+' in model statement/
if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;	if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;

ncovmodel=2+cptcovn;	ncovmodel=2+cptcovn; /Number of variables = cptcovn + intercept + age /
nvar=ncovmodel-1; /* Suppressing age as a basic covariate */	nvar=ncovmodel-1; /* Suppressing age as a basic covariate */

/* Read guess parameters */	/* Read guess parameters */
Line 3226 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3441 while((c=getc(ficpar))=='#' && c!= EOF){
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++){	for(j=1; j <=nlstate+ndeath-1; j++){
fscanf(ficpar,"%1d%1d",&i1,&j1);	fscanf(ficpar,"%1d%1d",&i1,&j1);
fprintf(ficparo,"%1d%1d",i1,j1);	fprintf(ficparo,"%1d%1d",i1,j1);
Line 3250 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3465 while((c=getc(ficpar))=='#' && c!= EOF){
fprintf(ficparo,"\n");	fprintf(ficparo,"\n");
}	}

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

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

Line 3323 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3538 while((c=getc(ficpar))=='#' && c!= EOF){
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");


/-------- Rewriting paramater file ----------/	/-------- Rewriting paramater file ----------/
strcpy(rfileres,"r"); /* "Rparameterfile */	strcpy(rfileres,"r"); /* "Rparameterfile */
strcat(rfileres,optionfilefiname); /* Parameter file first name*/	strcat(rfileres,optionfilefiname); /* Parameter file first name*/
strcat(rfileres,"."); /* */	strcat(rfileres,"."); /* */
strcat(rfileres,optionfilext); /* Other files have txt extension */	strcat(rfileres,optionfilext); /* Other files have txt extension */
if((ficres =fopen(rfileres,"w"))==NULL) {	if((ficres =fopen(rfileres,"w"))==NULL) {
printf("Problem writing new parameter file: %s\n", fileres);goto end;	printf("Problem writing new parameter file: %s\n", fileres);goto end;
fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;	fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
}	}
fprintf(ficres,"#%s\n",version);	fprintf(ficres,"#%s\n",version);

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

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=ivector(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);
andc=vector(1,n);	andc=vector(1,n);
agedc=vector(1,n);	agedc=vector(1,n);
cod=ivector(1,n);	cod=ivector(1,n);
weight=vector(1,n);	weight=vector(1,n);
for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */	for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
mint=matrix(1,maxwav,1,n);	mint=matrix(1,maxwav,1,n);
anint=matrix(1,maxwav,1,n);	anint=matrix(1,maxwav,1,n);
s=imatrix(1,maxwav+1,1,n);	s=imatrix(1,maxwav+1,1,n);
adl=imatrix(1,maxwav+1,1,n);	tab=ivector(1,NCOVMAX);
tab=ivector(1,NCOVMAX);	ncodemax=ivector(1,8);
ncodemax=ivector(1,8);
	i=1;
i=1;	while (fgets(line, MAXLINE, fic) != NULL) {
while (fgets(line, MAXLINE, fic) != NULL) {	if ((i >= firstobs) && (i <=lastobs)) {
if ((i >= firstobs) && (i <=lastobs)) {

for (j=maxwav;j>=1;j--){	for (j=maxwav;j>=1;j--){
cutv(stra, strb,line,' '); s[j][i]=atoi(strb);	cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
strcpy(line,stra);	strcpy(line,stra);
cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);	cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);	cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
}	}

cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);	cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);	cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);

cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);	cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);	cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);

cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);	cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
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);	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("%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;}*/

i=i+1;	i=i+1;
}	}
}	}
/* printf("ii=%d", ij);	/* printf("ii=%d", ij);
scanf("%d",i);*/	scanf("%d",i);*/
imx=i-1; /* Number of individuals */	imx=i-1; /* Number of individuals */

/* for (i=1; i<=imx; i++){	/* for (i=1; i<=imx; i++){
Line 3409 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3623 while((c=getc(ficpar))=='#' && c!= EOF){
Tvard=imatrix(1,15,1,2);	Tvard=imatrix(1,15,1,2);
Tage=ivector(1,15);	Tage=ivector(1,15);

if (strlen(model) >1){	if (strlen(model) >1){ /* If there is at least 1 covariate */
j=0, j1=0, k1=1, k2=1;	j=0, j1=0, k1=1, k2=1;
j=nbocc(model,'+');	j=nbocc(model,'+'); /* j=Number of '+' */
j1=nbocc(model,'*');	j1=nbocc(model,''); / j1=Number of '' /
cptcovn=j+1;	cptcovn=j+1;
cptcovprod=j1;	cptcovprod=j1; /Number of products /

strcpy(modelsav,model);	strcpy(modelsav,model);
if ((strcmp(model,"age")==0) \|\| (strcmp(model,"age*age")==0)){	if ((strcmp(model,"age")==0) \|\| (strcmp(model,"age*age")==0)){
Line 3423 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3637 while((c=getc(ficpar))=='#' && c!= EOF){
goto end;	goto end;
}	}

	/* This loop fills the array Tvar from the string 'model'.*/

for(i=(j+1); i>=1;i--){	for(i=(j+1); i>=1;i--){
cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */	cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */	if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
/* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/	/* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
/scanf("%d",i);/	/scanf("%d",i);/
if (strchr(strb,'')) { / Model includes a product */	if (strchr(strb,'')) { / Model includes a product */
Line 3472 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3688 while((c=getc(ficpar))=='#' && c!= EOF){
} /* end of loop + */	} /* end of loop + */
} /* end model */	} /* end model */

	/*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
	If model=V1+V1age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0/

/* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);	/* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
printf("cptcovprod=%d ", cptcovprod);	printf("cptcovprod=%d ", cptcovprod);
fprintf(ficlog,"cptcovprod=%d ", cptcovprod);	fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
scanf("%d ",i);*/
fclose(fic);	scanf("%d ",i);
	fclose(fic);*/

/* if(mle==1){*/	/* if(mle==1){*/
if (weightopt != 1) { /* Maximisation without weights*/	if (weightopt != 1) { /* Maximisation without weights*/
for(i=1;i<=n;i++) weight[i]=1.0;	for(i=1;i<=n;i++) weight[i]=1.0;
}	}
/-calculation of age at interview from date of interview and age at death -/	/-calculation of age at interview from date of interview and age at death -/
agev=matrix(1,maxwav,1,imx);	agev=matrix(1,maxwav,1,imx);

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 ((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(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
}
}	}
	}

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=1; (m<= maxwav); 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(moisdc[i]!=99 && 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 (andc[i]!=9999){
printf("Warning negative age at death: %d line:%d\n",num[i],i);	printf("Warning negative age at death: %d 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: %d 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
agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);	years but with the precision of a
if(mint[m][i]==99 \|\| anint[m][i]==9999)	month */
agev[m][i]=1;	agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
else if(agev[m][i] <agemin){	if(mint[m][i]==99 \|\| anint[m][i]==9999)
agemin=agev[m][i];
/printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);/
}
else if(agev[m][i] >agemax){
agemax=agev[m][i];
/* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
}
/agev[m][i]=anint[m][i]-annais[i];/
/* agev[m][i] = age[i]+2m;/
}
else { /* =9 */
agev[m][i]=1;	agev[m][i]=1;
s[m][i]=-1;	else if(agev[m][i] <agemin){
	agemin=agev[m][i];
	/printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);/
	}
	else if(agev[m][i] >agemax){
	agemax=agev[m][i];
	/* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
}	}
	/agev[m][i]=anint[m][i]-annais[i];/
	/* agev[m][i] = age[i]+2m;/
}	}
else /= 0 Unknown /	else { /* =9 */
agev[m][i]=1;	agev[m][i]=1;
	s[m][i]=-1;
	}
}	}
	else /= 0 Unknown /
	agev[m][i]=1;
}	}
for (i=1; i<=imx; i++) {
for(m=1; (m<= maxwav); m++){	}
if (s[m][i] > (nlstate+ndeath)) {	for (i=1; i<=imx; i++) {
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);	for(m=1; (m<= maxwav); m++){
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);	if (s[m][i] > (nlstate+ndeath)) {
goto end;	printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
}	fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);
	goto end;
}	}
}	}
	}

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);

free_vector(severity,1,maxwav);	free_vector(severity,1,maxwav);
free_imatrix(outcome,1,maxwav+1,1,n);	free_imatrix(outcome,1,maxwav+1,1,n);
free_vector(moisnais,1,n);	free_vector(moisnais,1,n);
free_vector(annais,1,n);	free_vector(annais,1,n);
/* free_matrix(mint,1,maxwav,1,n);	/* free_matrix(mint,1,maxwav,1,n);
free_matrix(anint,1,maxwav,1,n);*/	free_matrix(anint,1,maxwav,1,n);*/
free_vector(moisdc,1,n);	free_vector(moisdc,1,n);
free_vector(andc,1,n);	free_vector(andc,1,n);


wav=ivector(1,imx);	wav=ivector(1,imx);
dh=imatrix(1,lastpass-firstpass+1,1,imx);	dh=imatrix(1,lastpass-firstpass+1,1,imx);
mw=imatrix(1,lastpass-firstpass+1,1,imx);	bh=imatrix(1,lastpass-firstpass+1,1,imx);
	mw=imatrix(1,lastpass-firstpass+1,1,imx);

/* Concatenates waves */	/* Concatenates waves */
concatwav(wav, dh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);	concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);

	/* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */

Tcode=ivector(1,100);	Tcode=ivector(1,100);
nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);	nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
ncodemax[1]=1;	ncodemax[1]=1;
if (cptcovn > 0) tricode(Tvar,nbcode,imx);	if (cptcovn > 0) tricode(Tvar,nbcode,imx);

codtab=imatrix(1,100,1,10);	codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of
h=0;	the estimations*/
m=pow(2,cptcoveff);	h=0;
	m=pow(2,cptcoveff);

for(k=1;k<=cptcoveff; k++){	for(k=1;k<=cptcoveff; k++){
for(i=1; i <=(m/pow(2,k));i++){	for(i=1; i <=(m/pow(2,k));i++){
for(j=1; j <= ncodemax[k]; j++){	for(j=1; j <= ncodemax[k]; j++){
for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){	for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
h++;	h++;
if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;	if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
/* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/	/* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
}	}
}
}
}
/* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
codtab[1][2]=1;codtab[2][2]=2; */
/* for(i=1; i <=m ;i++){
for(k=1; k <=cptcovn; k++){
printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
}
printf("\n");
}	}
scanf("%d",i);*/	}
	}
	/* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
	codtab[1][2]=1;codtab[2][2]=2; */
	/* for(i=1; i <=m ;i++){
	for(k=1; k <=cptcovn; k++){
	printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
	}
	printf("\n");
	}
	scanf("%d",i);*/

/* 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'. */



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 */
savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */	savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */	oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */

/* For Powell, parameters are in a vector p[] starting at p[1]
so we point p on param[1][1] so that p[1] maps on param[1][1][1] */	/* For Powell, parameters are in a vector p[] starting at p[1]
p=param[1][1]; /* (((param +1)+1)+0) /	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) /

if(mle==1){	if(mle>=1){ /* Could be 1 or 2 */
mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);	mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
}	}

/--------- results files --------------/	/--------- results files --------------/
fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);	fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);


jk=1;	jk=1;
fprintf(ficres,"# Parameters nlstatenlstatencov a121 + b12 age + ...\n");	fprintf(ficres,"# Parameters nlstatenlstatencov a121 + b12 age + ...\n");
printf("# Parameters nlstatenlstatencov a121 + b12 age + ...\n");	printf("# Parameters nlstatenlstatencov a121 + b12 age + ...\n");
fprintf(ficlog,"# Parameters nlstatenlstatencov a121 + b12 age + ...\n");	fprintf(ficlog,"# Parameters nlstatenlstatencov a121 + b12 age + ...\n");
for(i=1,jk=1; i <=nlstate; i++){	for(i=1,jk=1; i <=nlstate; i++){
for(k=1; k <=(nlstate+ndeath); k++){	for(k=1; k <=(nlstate+ndeath); k++){
if (k != i)	if (k != i)
{	{
printf("%d%d ",i,k);	printf("%d%d ",i,k);
fprintf(ficlog,"%d%d ",i,k);	fprintf(ficlog,"%d%d ",i,k);
fprintf(ficres,"%1d%1d ",i,k);	fprintf(ficres,"%1d%1d ",i,k);
for(j=1; j <=ncovmodel; j++){	for(j=1; j <=ncovmodel; j++){
printf("%f ",p[jk]);	printf("%f ",p[jk]);
fprintf(ficlog,"%f ",p[jk]);	fprintf(ficlog,"%f ",p[jk]);
fprintf(ficres,"%f ",p[jk]);	fprintf(ficres,"%f ",p[jk]);
jk++;	jk++;
}	}
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
fprintf(ficres,"\n");	fprintf(ficres,"\n");
}	}
}	}
}	}
if(mle==1){	if(mle==1){
/* 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);
}	}
fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");	fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
printf("# Scales (for hessian or gradient estimation)\n");	printf("# Scales (for hessian or gradient estimation)\n");
fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");	fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
for(i=1,jk=1; i <=nlstate; i++){	for(i=1,jk=1; i <=nlstate; i++){
for(j=1; j <=nlstate+ndeath; j++){	for(j=1; j <=nlstate+ndeath; j++){
if (j!=i) {	if (j!=i) {
fprintf(ficres,"%1d%1d",i,j);	fprintf(ficres,"%1d%1d",i,j);
printf("%1d%1d",i,j);	printf("%1d%1d",i,j);
fprintf(ficlog,"%1d%1d",i,j);	fprintf(ficlog,"%1d%1d",i,j);
for(k=1; k<=ncovmodel;k++){	for(k=1; k<=ncovmodel;k++){
printf(" %.5e",delti[jk]);	printf(" %.5e",delti[jk]);
fprintf(ficlog," %.5e",delti[jk]);	fprintf(ficlog," %.5e",delti[jk]);
fprintf(ficres," %.5e",delti[jk]);	fprintf(ficres," %.5e",delti[jk]);
jk++;	jk++;
}	}
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
fprintf(ficres,"\n");	fprintf(ficres,"\n");
}	}
}	}
}	}

k=1;	fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");	if(mle==1)
if(mle==1)	printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");	fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");	for(i=1,k=1;i<=npar;i++){
for(i=1;i<=npar;i++){	/* if (k>nlstate) k=1;
/* if (k>nlstate) k=1;	i1=(i-1)/(ncovmodel*nlstate)+1;
i1=(i-1)/(ncovmodel*nlstate)+1;	fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);	printf("%s%d%d",alph[k],i1,tab[i]);
printf("%s%d%d",alph[k],i1,tab[i]);*/	*/
fprintf(ficres,"%3d",i);	fprintf(ficres,"%3d",i);
if(mle==1)	if(mle==1)
printf("%3d",i);	printf("%3d",i);
fprintf(ficlog,"%3d",i);	fprintf(ficlog,"%3d",i);
for(j=1; j<=i;j++){	for(j=1; j<=i;j++){
fprintf(ficres," %.5e",matcov[i][j]);	fprintf(ficres," %.5e",matcov[i][j]);
if(mle==1)	if(mle==1)
printf(" %.5e",matcov[i][j]);	printf(" %.5e",matcov[i][j]);
fprintf(ficlog," %.5e",matcov[i][j]);	fprintf(ficlog," %.5e",matcov[i][j]);
}	}
fprintf(ficres,"\n");	fprintf(ficres,"\n");
if(mle==1)	if(mle==1)
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
k++;	k++;
}	}

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);
puts(line);	puts(line);
fputs(line,ficparo);	fputs(line,ficparo);
}	}
ungetc(c,ficpar);	ungetc(c,ficpar);
estepm=0;
fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);	estepm=0;
if (estepm==0 \|\| estepm < stepm) estepm=stepm;	fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
if (fage <= 2) {	if (estepm==0 \|\| estepm < stepm) estepm=stepm;
bage = ageminpar;	if (fage <= 2) {
fage = agemaxpar;	bage = ageminpar;
}	fage = agemaxpar;
	}

fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");	fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);	fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);	fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);

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);
puts(line);	puts(line);
fputs(line,ficparo);	fputs(line,ficparo);
}	}
ungetc(c,ficpar);	ungetc(c,ficpar);

fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);	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);
fgets(line, MAXLINE, ficpar);	fgets(line, MAXLINE, ficpar);
puts(line);	puts(line);
fputs(line,ficparo);	fputs(line,ficparo);
}	}
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 3753 printf("Total number of individuals= %d,	Line 3980 printf("Total number of individuals= %d,
}	}
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 mobilaverage=%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 mobilaverage=%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 mobilaverage=%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);
fgets(line, MAXLINE, ficpar);	fgets(line, MAXLINE, ficpar);
puts(line);	puts(line);
Line 3770 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3999 while((c=getc(ficpar))=='#' && c!= EOF){
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,Tvar,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);	/------------ gnuplot -------------/
strcat(optionfilegnuplot,".gp");	strcpy(optionfilegnuplot,optionfilefiname);
if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {	strcat(optionfilegnuplot,".gp");
printf("Problem with file %s",optionfilegnuplot);	if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
}	printf("Problem with file %s",optionfilegnuplot);
else{	}
fprintf(ficgp,"\n# %s\n", version);	else{
fprintf(ficgp,"# %s\n", optionfilegnuplot);	fprintf(ficgp,"\n# %s\n", version);
fprintf(ficgp,"set missing 'NaNq'\n");	fprintf(ficgp,"# %s\n", optionfilegnuplot);
}	fprintf(ficgp,"set missing 'NaNq'\n");
fclose(ficgp);	}
printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);	fclose(ficgp);
/--------- index.htm --------/	printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
	/--------- index.htm --------/

strcpy(optionfilehtm,optionfile);	strcpy(optionfilehtm,optionfile);
strcat(optionfilehtm,".htm");	strcat(optionfilehtm,".htm");
Line 3804 Interval (in months) between two waves:	Line 4034 Interval (in months) between two waves:
- 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);	- 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);	fclose(fichtm);

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

free_ivector(wav,1,imx);	free_ivector(wav,1,imx);
free_imatrix(dh,1,lastpass-firstpass+1,1,imx);	free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
free_imatrix(mw,1,lastpass-firstpass+1,1,imx);	free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
free_ivector(num,1,n);	free_imatrix(mw,1,lastpass-firstpass+1,1,imx);
free_vector(agedc,1,n);	free_ivector(num,1,n);
/free_matrix(covar,1,NCOVMAX,1,n);/	free_vector(agedc,1,n);
fclose(ficparo);	/free_matrix(covar,0,NCOVMAX,1,n);/
fclose(ficres);	/free_matrix(covar,1,NCOVMAX,1,n);/
	fclose(ficparo);
	fclose(ficres);


/--------------- Prevalence limit (stable prevalence) --------------/	/--------------- Prevalence limit (stable prevalence) --------------/
Line 3835 Interval (in months) between two waves:	Line 4067 Interval (in months) between two waves:
fprintf(ficrespl,"\n");	fprintf(ficrespl,"\n");

prlim=matrix(1,nlstate,1,nlstate);	prlim=matrix(1,nlstate,1,nlstate);
pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
k=0;
agebase=ageminpar;	agebase=ageminpar;
agelim=agemaxpar;	agelim=agemaxpar;
ftolpl=1.e-10;	ftolpl=1.e-10;
i1=cptcoveff;	i1=cptcoveff;
if (cptcovn < 1){i1=1;}	if (cptcovn < 1){i1=1;}

for(cptcov=1;cptcov<=i1;cptcov++){	for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){	for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
k=k+1;	k=k+1;
/printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);/	/printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);/
fprintf(ficrespl,"\n#******");	fprintf(ficrespl,"\n#******");
printf("\n#******");	printf("\n#******");
fprintf(ficlog,"\n#******");	fprintf(ficlog,"\n#******");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcoveff;j++) {
fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
}	}
fprintf(ficrespl,"******\n");	fprintf(ficrespl,"******\n");
printf("******\n");	printf("******\n");
fprintf(ficlog,"******\n");	fprintf(ficlog,"******\n");

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(i=1; i<=nlstate;i++)	for(j=1;j<=cptcoveff;j++)
	fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
	for(i=1; i<=nlstate;i++)
fprintf(ficrespl," %.5f", prlim[i][i]);	fprintf(ficrespl," %.5f", prlim[i][i]);
fprintf(ficrespl,"\n");	fprintf(ficrespl,"\n");
}
}	}
}	}
	}
fclose(ficrespl);	fclose(ficrespl);

/------------- h Pij x at various ages ------------/	/------------- h Pij x at various ages ------------/
Line 3893 Interval (in months) between two waves:	Line 4122 Interval (in months) between two waves:

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

k=0;	fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
for(cptcov=1;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;
fprintf(ficrespij,"\n#****** ");	fprintf(ficrespij,"\n#****** ");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
fprintf(ficrespij,"******\n");	fprintf(ficrespij,"******\n");

for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */	for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
nhstepm=(int) rint((agelim-agedeb)YEARM/stepm); / Typically 20 years = 2012/6=40 /	nhstepm=(int) rint((agelim-agedeb)YEARM/stepm); / Typically 20 years = 2012/6=40 /
nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */	nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */

/* nhstepm=nhstepmYEARM; aff par mois/	/* nhstepm=nhstepmYEARM; aff par mois/

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(j=1; j<=nlstate+ndeath;j++)
	fprintf(ficrespij," %1d-%1d",i,j);
	fprintf(ficrespij,"\n");
	for (h=0; h<=nhstepm; h++){
	fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ 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," %1d-%1d",i,j);	fprintf(ficrespij," %.5f", p3mat[i][j][h]);
fprintf(ficrespij,"\n");
for (h=0; h<=nhstepm; h++){
fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ hhstepm/YEARMstepm );
for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate+ndeath;j++)
fprintf(ficrespij," %.5f", p3mat[i][j][h]);
fprintf(ficrespij,"\n");
}
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
fprintf(ficrespij,"\n");	fprintf(ficrespij,"\n");
}	}
	free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
	fprintf(ficrespij,"\n");
	}
}	}
}	}

Line 3935 Interval (in months) between two waves:	Line 4164 Interval (in months) between two waves:


/---------- 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{	if (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 3975 Interval (in months) between two waves:	Line 4207 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;
prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);	prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, 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);
if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){	if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
Line 3985 Interval (in months) between two waves:	Line 4218 Interval (in months) between two waves:
}	}
}	}

k=0;	for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcov=1;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){	for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
k=k+1;	k=k+1;
fprintf(ficrest,"\n#****** ");	fprintf(ficrest,"\n#****** ");
Line 4013 Interval (in months) between two waves:	Line 4245 Interval (in months) between two waves:
varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);	varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
if(popbased==1){	if(popbased==1){
varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);	varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
}	}


fprintf(ficrest,"#Total LEs with variances: e.. (std) ");	fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
Line 4051 Interval (in months) between two waves:	Line 4283 Interval (in months) between two waves:
}	}
fprintf(ficrest,"\n");	fprintf(ficrest,"\n");
}	}
	free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
	free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
	free_vector(epj,1,nlstate+1);
}	}
}	}
free_matrix(mint,1,maxwav,1,n);	free_vector(weight,1,n);
free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);	free_imatrix(Tvard,1,15,1,2);
free_vector(weight,1,n);	free_imatrix(s,1,maxwav+1,1,n);
	free_matrix(anint,1,maxwav,1,n);
	free_matrix(mint,1,maxwav,1,n);
	free_ivector(cod,1,n);
	free_ivector(tab,1,NCOVMAX);
fclose(ficreseij);	fclose(ficreseij);
fclose(ficresvij);	fclose(ficresvij);
fclose(ficrest);	fclose(ficrest);
fclose(ficpar);	fclose(ficpar);
free_vector(epj,1,nlstate+1);

/------- Variance of stable prevalence------/	/------- Variance of stable prevalence------/

Line 4072 free_matrix(mint,1,maxwav,1,n);	Line 4310 free_matrix(mint,1,maxwav,1,n);
}	}
printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);	printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);

k=0;	for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcov=1;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){	for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
k=k+1;	k=k+1;
fprintf(ficresvpl,"\n#****** ");	fprintf(ficresvpl,"\n#****** ");
Line 4083 free_matrix(mint,1,maxwav,1,n);	Line 4320 free_matrix(mint,1,maxwav,1,n);

varpl=matrix(1,nlstate,(int) bage, (int) fage);	varpl=matrix(1,nlstate,(int) bage, (int) fage);
oldm=oldms;savm=savms;	oldm=oldms;savm=savms;
varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);	varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
	free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
}	}
}	}

fclose(ficresvpl);	fclose(ficresvpl);

/---------- End : free ----------------/	/---------- End : free ----------------/
free_matrix(varpl,1,nlstate,(int) bage, (int)fage);

free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);


free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);	free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);	free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);	free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);	free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);

	free_matrix(covar,0,NCOVMAX,1,n);
free_matrix(matcov,1,npar,1,npar);	free_matrix(matcov,1,npar,1,npar);
free_vector(delti,1,npar);	free_vector(delti,1,npar);
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_ivector(ncodemax,1,8);
	free_ivector(Tvar,1,15);
	free_ivector(Tprod,1,15);
	free_ivector(Tvaraff,1,15);
	free_ivector(Tage,1,15);
	free_ivector(Tcode,1,100);

fprintf(fichtm,"\n</body>");	fprintf(fichtm,"\n</body>");
fclose(fichtm);	fclose(fichtm);
Line 4127 free_matrix(mint,1,maxwav,1,n);	Line 4366 free_matrix(mint,1,maxwav,1,n);
/printf("Total time was %d uSec.\n", total_usecs);/	/printf("Total time was %d uSec.\n", total_usecs);/
/------ End -----------/	/------ End -----------/

	end:
end:
#ifdef windows	#ifdef windows
/* chdir(pathcd);*/	/* chdir(pathcd);*/
#endif	#endif
Line 4136 free_matrix(mint,1,maxwav,1,n);	Line 4374 free_matrix(mint,1,maxwav,1,n);
/system("../gp37mgw/wgnuplot graph.plt");/	/system("../gp37mgw/wgnuplot graph.plt");/
/system("cd ../gp37mgw");/	/system("cd ../gp37mgw");/
/* system("..\\gp37mgw\\wgnuplot graph.plt");*/	/* system("..\\gp37mgw\\wgnuplot graph.plt");*/
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: %s\n",plotcmd);fflush(stdout);
system(plotcmd);	system(plotcmd);

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

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Removed from v.1.56
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	Added in v.1.70