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version 1.27, 2002/02/28 17:49:07	version 1.50, 2002/06/26 23:25:02
Line 14	Line 14
model. More health states you consider, more time is necessary to reach the	model. More health states you consider, more time is necessary to reach the
Maximum Likelihood of the parameters involved in the model. The	Maximum Likelihood of the parameters involved in the model. The
simplest model is the multinomial logistic model where pij is the	simplest model is the multinomial logistic model where pij is the
probabibility to be observed in state j at the second wave	probability to be observed in state j at the second wave
conditional to be observed in state i at the first wave. Therefore	conditional to be observed in state i at the first wave. Therefore
the model is: log(pij/pii)= aij + bijage+ cijsex + etc , where	the model is: log(pij/pii)= aij + bijage+ cijsex + etc , where
'age' is age and 'sex' is a covariate. If you want to have a more	'age' is age and 'sex' is a covariate. If you want to have a more
Line 56	Line 56
#include <unistd.h>	#include <unistd.h>

#define MAXLINE 256	#define MAXLINE 256
#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"	#define GNUPLOTPROGRAM "gnuplot"
	/#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"/
#define FILENAMELENGTH 80	#define FILENAMELENGTH 80
/#define DEBUG/	/#define DEBUG/
#define windows	#define windows
Line 74	Line 75
#define YEARM 12. /* Number of months per year */	#define YEARM 12. /* Number of months per year */
#define AGESUP 130	#define AGESUP 130
#define AGEBASE 40	#define AGEBASE 40
	#ifdef windows
	#define DIRSEPARATOR '\\'
	#define ODIRSEPARATOR '/'
	#else
	#define DIRSEPARATOR '/'
	#define ODIRSEPARATOR '\\'
	#endif

	char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";
int erreur; /* Error number */	int erreur; /* Error number */
int nvar;	int nvar;
int cptcovn, cptcovage=0, cptcoveff=0,cptcov;	int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
int npar=NPARMAX;	int npar=NPARMAX;
int nlstate=2; /* Number of live states */	int nlstate=2; /* Number of live states */
int ndeath=1; /* Number of dead states */	int ndeath=1; /* Number of dead states */
int ncovmodel, ncov; /* Total number of covariables including constant a121 +b12x ncovmodel=2 */	int ncovmodel, ncovcol; /* Total number of covariables including constant a121 +b12x ncovmodel=2 */
int popbased=0;	int popbased=0;

int wav; / Number of waves for this individuual 0 is possible */	int wav; / Number of waves for this individuual 0 is possible */
Line 95 double jmean; /* Mean space between 2 wa	Line 103 double jmean; /* Mean space between 2 wa
double oldm, newm, *savm; / Working pointers to matrices */	double oldm, newm, *savm; / Working pointers to matrices */
double oldms, newms, *savms; / Fixed working pointers to matrices */	double oldms, newms, *savms; / Fixed working pointers to matrices */
FILE fic,ficpar, ficparo,ficres, ficrespl, ficrespij, ficrest,ficresf,*ficrespop;	FILE fic,ficpar, ficparo,ficres, ficrespl, ficrespij, ficrest,ficresf,*ficrespop;
FILE ficgp,ficresprob,*ficpop;	FILE *ficlog;
	FILE ficgp,ficresprob,ficpop, ficresprobcov, *ficresprobcor;
	FILE *ficresprobmorprev;
	FILE fichtm; / Html File */
FILE *ficreseij;	FILE *ficreseij;
char filerese[FILENAMELENGTH];	char filerese[FILENAMELENGTH];
FILE *ficresvij;	FILE *ficresvij;
char fileresv[FILENAMELENGTH];	char fileresv[FILENAMELENGTH];
FILE *ficresvpl;	FILE *ficresvpl;
char fileresvpl[FILENAMELENGTH];	char fileresvpl[FILENAMELENGTH];
	char title[MAXLINE];
	char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
	char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];

	char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
	char filelog[FILENAMELENGTH]; /* Log file */
	char filerest[FILENAMELENGTH];
	char fileregp[FILENAMELENGTH];
	char popfile[FILENAMELENGTH];

	char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];

#define NR_END 1	#define NR_END 1
#define FREE_ARG char*	#define FREE_ARG char*
Line 135 int imx;	Line 157 int imx;
int stepm;	int stepm;
/* Stepm, step in month: minimum step interpolation*/	/* Stepm, step in month: minimum step interpolation*/

	int estepm;
	/* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/

int m,nb;	int m,nb;
int num, firstpass=0, lastpass=4,cod, ncodemax, Tage;	int num, firstpass=0, lastpass=4,cod, ncodemax, Tage;
double *agev,moisnais, annais, moisdc, andc,mint, *anint;	double *agev,moisnais, annais, moisdc, andc,mint, *anint;
Line 157 static int split( char path, char dirc	Line 182 static int split( char path, char dirc

l1 = strlen( path ); /* length of path */	l1 = strlen( path ); /* length of path */
if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );	if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
#ifdef windows	s= strrchr( path, DIRSEPARATOR ); /* find last / */
s = strrchr( path, '\\' ); /* find last / */
#else
s = strrchr( path, '/' ); /* find last / */
#endif
if ( s == NULL ) { /* no directory, so use current */	if ( s == NULL ) { /* no directory, so use current */
	/*if(strrchr(path, ODIRSEPARATOR )==NULL)
	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( );

Line 228 int nbocc(char *s, char occ)	Line 251 int nbocc(char *s, char occ)

void cutv(char u,char v, char*t, char occ)	void cutv(char u,char v, char*t, char occ)
{	{
	/* cuts string t into u and v where u is ended by char occ excluding it
	and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
	gives u="abcedf" and v="ghi2j" */
int i,lg,j,p=0;	int i,lg,j,p=0;
i=0;	i=0;
for(j=0; j<=strlen(t)-1; j++) {	for(j=0; j<=strlen(t)-1; j++) {
Line 424 double brent(double ax, double bx, doubl	Line 450 double brent(double ax, double bx, doubl
tol2=2.0(tol1=tolfabs(x)+ZEPS);	tol2=2.0(tol1=tolfabs(x)+ZEPS);
/* if (2.0fabs(fp-(fret)) <= ftol(fabs(fp)+fabs(fret)))*/	/* if (2.0fabs(fp-(fret)) <= ftol(fabs(fp)+fabs(fret)))*/
printf(".");fflush(stdout);	printf(".");fflush(stdout);
	fprintf(ficlog,".");fflush(ficlog);
#ifdef DEBUG	#ifdef DEBUG
printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);	printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
	fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
/* if ((fabs(x-xm) <= (tol2-0.5(b-a)))\|\|(2.0fabs(fu-ftemp) <= ftol1.e-2(fabs(fu)+fabs(ftemp)))) { */	/* if ((fabs(x-xm) <= (tol2-0.5(b-a)))\|\|(2.0fabs(fu-ftemp) <= ftol1.e-2(fabs(fu)+fabs(ftemp)))) { */
#endif	#endif
if (fabs(x-xm) <= (tol2-0.5*(b-a))){	if (fabs(x-xm) <= (tol2-0.5*(b-a))){
Line 550 void linmin(double p[], double xi[], int	Line 578 void linmin(double p[], double xi[], int
*fret=brent(ax,xx,bx,f1dim,TOL,&xmin);	*fret=brent(ax,xx,bx,f1dim,TOL,&xmin);
#ifdef DEBUG	#ifdef DEBUG
printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);	printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
	fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
#endif	#endif
for (j=1;j<=n;j++) {	for (j=1;j<=n;j++) {
xi[j] *= xmin;	xi[j] *= xmin;
Line 580 void powell(double p[], double **xi, int	Line 609 void powell(double p[], double **xi, int
ibig=0;	ibig=0;
del=0.0;	del=0.0;
printf("\nPowell iter=%d -2LL=%.12f",iter,*fret);	printf("\nPowell iter=%d -2LL=%.12f",iter,*fret);
	fprintf(ficlog,"\nPowell iter=%d -2LL=%.12f",iter,*fret);
for (i=1;i<=n;i++)	for (i=1;i<=n;i++)
printf(" %d %.12f",i, p[i]);	printf(" %d %.12f",i, p[i]);
	fprintf(ficlog," %d %.12f",i, p[i]);
printf("\n");	printf("\n");
	fprintf(ficlog,"\n");
for (i=1;i<=n;i++) {	for (i=1;i<=n;i++) {
for (j=1;j<=n;j++) xit[j]=xi[j][i];	for (j=1;j<=n;j++) xit[j]=xi[j][i];
fptt=(*fret);	fptt=(*fret);
#ifdef DEBUG	#ifdef DEBUG
printf("fret=%lf \n",*fret);	printf("fret=%lf \n",*fret);
	fprintf(ficlog,"fret=%lf \n",*fret);
#endif	#endif
printf("%d",i);fflush(stdout);	printf("%d",i);fflush(stdout);
	fprintf(ficlog,"%d",i);fflush(ficlog);
linmin(p,xit,n,fret,func);	linmin(p,xit,n,fret,func);
if (fabs(fptt-(*fret)) > del) {	if (fabs(fptt-(*fret)) > del) {
del=fabs(fptt-(*fret));	del=fabs(fptt-(*fret));
Line 597 void powell(double p[], double **xi, int	Line 631 void powell(double p[], double **xi, int
}	}
#ifdef DEBUG	#ifdef DEBUG
printf("%d %.12e",i,(*fret));	printf("%d %.12e",i,(*fret));
	fprintf(ficlog,"%d %.12e",i,(*fret));
for (j=1;j<=n;j++) {	for (j=1;j<=n;j++) {
xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);	xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
printf(" x(%d)=%.12e",j,xit[j]);	printf(" x(%d)=%.12e",j,xit[j]);
	fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
}	}
for(j=1;j<=n;j++)	for(j=1;j<=n;j++) {
printf(" p=%.12e",p[j]);	printf(" p=%.12e",p[j]);
	fprintf(ficlog," p=%.12e",p[j]);
	}
printf("\n");	printf("\n");
	fprintf(ficlog,"\n");
#endif	#endif
}	}
if (2.0fabs(fp-(fret)) <= ftol(fabs(fp)+fabs(fret))) {	if (2.0fabs(fp-(fret)) <= ftol(fabs(fp)+fabs(fret))) {
Line 612 void powell(double p[], double **xi, int	Line 651 void powell(double p[], double **xi, int
k[0]=1;	k[0]=1;
k[1]=-1;	k[1]=-1;
printf("Max: %.12e",(*func)(p));	printf("Max: %.12e",(*func)(p));
for (j=1;j<=n;j++)	fprintf(ficlog,"Max: %.12e",(*func)(p));
	for (j=1;j<=n;j++) {
printf(" %.12e",p[j]);	printf(" %.12e",p[j]);
	fprintf(ficlog," %.12e",p[j]);
	}
printf("\n");	printf("\n");
	fprintf(ficlog,"\n");
for(l=0;l<=1;l++) {	for(l=0;l<=1;l++) {
for (j=1;j<=n;j++) {	for (j=1;j<=n;j++) {
ptt[j]=p[j]+(p[j]-pt[j])*k[l];	ptt[j]=p[j]+(p[j]-pt[j])*k[l];
printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);	printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
	fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
}	}
printf("func(ptt)=%.12e, deriv=%.12e\n",(func)(ptt),(ptt[j]-p[j])/((func)(ptt)-(*func)(p)));	printf("func(ptt)=%.12e, deriv=%.12e\n",(func)(ptt),(ptt[j]-p[j])/((func)(ptt)-(*func)(p)));
	fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(func)(ptt),(ptt[j]-p[j])/((func)(ptt)-(*func)(p)));
}	}
#endif	#endif

Line 648 void powell(double p[], double **xi, int	Line 693 void powell(double p[], double **xi, int
}	}
#ifdef DEBUG	#ifdef DEBUG
printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);	printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
for(j=1;j<=n;j++)	fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
	for(j=1;j<=n;j++){
printf(" %.12e",xit[j]);	printf(" %.12e",xit[j]);
	fprintf(ficlog," %.12e",xit[j]);
	}
printf("\n");	printf("\n");
	fprintf(ficlog,"\n");
#endif	#endif
}	}
}	}
Line 686 double prevalim(double prlim, int nl	Line 735 double prevalim(double prlim, int nl

for (k=1; k<=cptcovn;k++) {	for (k=1; k<=cptcovn;k++) {
cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];	cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
/printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);/	/* printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
}	}
for (k=1; k<=cptcovage;k++)	for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
for (k=1; k<=cptcovprod;k++)	for (k=1; k<=cptcovprod;k++)
cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];	cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];

/printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);/	/printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);/
/printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);/	/printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);/
	/printf("ij=%d cov[3]=%lf \n",ij, cov[3]);/
out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);	out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);

savm=oldm;	savm=oldm;
Line 922 void mlikeli(FILE *ficres,double p[], in	Line 970 void mlikeli(FILE *ficres,double p[], in
for (i=1;i<=npar;i++)	for (i=1;i<=npar;i++)
for (j=1;j<=npar;j++)	for (j=1;j<=npar;j++)
xi[i][j]=(i==j ? 1.0 : 0.0);	xi[i][j]=(i==j ? 1.0 : 0.0);
printf("Powell\n");	printf("Powell\n"); fprintf(ficlog,"Powell\n");
powell(p,xi,npar,ftol,&iter,&fret,func);	powell(p,xi,npar,ftol,&iter,&fret,func);

printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));	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(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 946 void hesscov(double **matcov, double p[]	Line 995 void hesscov(double **matcov, double p[]
hess=matrix(1,npar,1,npar);	hess=matrix(1,npar,1,npar);

printf("\nCalculation of the hessian matrix. Wait...\n");	printf("\nCalculation of the hessian matrix. Wait...\n");
	fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
for (i=1;i<=npar;i++){	for (i=1;i<=npar;i++){
printf("%d",i);fflush(stdout);	printf("%d",i);fflush(stdout);
	fprintf(ficlog,"%d",i);fflush(ficlog);
hess[i][i]=hessii(p,ftolhess,i,delti);	hess[i][i]=hessii(p,ftolhess,i,delti);
/printf(" %f ",p[i]);/	/printf(" %f ",p[i]);/
/printf(" %lf ",hess[i][i]);/	/printf(" %lf ",hess[i][i]);/
Line 957 void hesscov(double **matcov, double p[]	Line 1008 void hesscov(double **matcov, double p[]
for (j=1;j<=npar;j++) {	for (j=1;j<=npar;j++) {
if (j>i) {	if (j>i) {
printf(".%d%d",i,j);fflush(stdout);	printf(".%d%d",i,j);fflush(stdout);
	fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
hess[i][j]=hessij(p,delti,i,j);	hess[i][j]=hessij(p,delti,i,j);
hess[j][i]=hess[i][j];	hess[j][i]=hess[i][j];
/printf(" %lf ",hess[i][j]);/	/printf(" %lf ",hess[i][j]);/
Line 964 void hesscov(double **matcov, double p[]	Line 1016 void hesscov(double **matcov, double p[]
}	}
}	}
printf("\n");	printf("\n");
	fprintf(ficlog,"\n");

printf("\nInverting the hessian to get the covariance matrix. Wait...\n");	printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
	fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");

a=matrix(1,npar,1,npar);	a=matrix(1,npar,1,npar);
y=matrix(1,npar,1,npar);	y=matrix(1,npar,1,npar);
Line 985 void hesscov(double **matcov, double p[]	Line 1039 void hesscov(double **matcov, double p[]
}	}

printf("\n#Hessian matrix#\n");	printf("\n#Hessian matrix#\n");
	fprintf(ficlog,"\n#Hessian matrix#\n");
for (i=1;i<=npar;i++) {	for (i=1;i<=npar;i++) {
for (j=1;j<=npar;j++) {	for (j=1;j<=npar;j++) {
printf("%.3e ",hess[i][j]);	printf("%.3e ",hess[i][j]);
	fprintf(ficlog,"%.3e ",hess[i][j]);
}	}
printf("\n");	printf("\n");
	fprintf(ficlog,"\n");
}	}

/* Recompute Inverse */	/* Recompute Inverse */
Line 1006 void hesscov(double **matcov, double p[]	Line 1063 void hesscov(double **matcov, double p[]
for (i=1;i<=npar;i++){	for (i=1;i<=npar;i++){
y[i][j]=x[i];	y[i][j]=x[i];
printf("%.3e ",y[i][j]);	printf("%.3e ",y[i][j]);
	fprintf(ficlog,"%.3e ",y[i][j]);
}	}
printf("\n");	printf("\n");
	fprintf(ficlog,"\n");
}	}
*/	*/

Line 1049 double hessii( double x[], double delta,	Line 1108 double hessii( double x[], double delta,

#ifdef DEBUG	#ifdef DEBUG
printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);	printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
	fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
#endif	#endif
/if(fabs(k1-2.0fx+k2) <1.e-13){ */	/if(fabs(k1-2.0fx+k2) <1.e-13){ */
if((k1 <khi/nkhi/2.) \|\| (k2 <khi/nkhi/2.)){	if((k1 <khi/nkhi/2.) \|\| (k2 <khi/nkhi/2.)){
Line 1096 double hessij( double x[], double delti[	Line 1156 double hessij( double x[], double delti[
res=(k1-k2-k3+k4)/4.0/delti[thetai]k/delti[thetaj]k/2.; /* Because of L not 2L /	res=(k1-k2-k3+k4)/4.0/delti[thetai]k/delti[thetaj]k/2.; /* Because of L not 2L /
#ifdef DEBUG	#ifdef DEBUG
printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);	printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
	fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
#endif	#endif
}	}
return res;	return res;
Line 1178 void lubksb(double *a, int n, int indx	Line 1239 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 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)
{ /* Some frequencies */	{ /* Some frequencies */

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

pp=vector(1,nlstate);	pp=vector(1,nlstate);
probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);	probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
strcpy(fileresp,"p");	strcpy(fileresp,"p");
strcat(fileresp,fileres);	strcat(fileresp,fileres);
if((ficresp=fopen(fileresp,"w"))==NULL) {	if((ficresp=fopen(fileresp,"w"))==NULL) {
printf("Problem with prevalence resultfile: %s\n", fileresp);	printf("Problem with prevalence resultfile: %s\n", fileresp);
	fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
exit(0);	exit(0);
}	}
freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);	freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
j1=0;	j1=0;

j=cptcoveff;	j=cptcoveff;
if (cptcovn<1) {j=1;ncodemax[1]=1;}	if (cptcovn<1) {j=1;ncodemax[1]=1;}

for(k1=1; k1<=j;k1++){	first=1;
for(i1=1; i1<=ncodemax[k1];i1++){
j1++;
/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
scanf("%d", i);*/
for (i=-1; i<=nlstate+ndeath; i++)
for (jk=-1; jk<=nlstate+ndeath; jk++)
for(m=agemin; m <= agemax+3; m++)
freq[i][jk][m]=0;

dateintsum=0;
k2cpt=0;
for (i=1; i<=imx; i++) {
bool=1;
if (cptcovn>0) {
for (z1=1; z1<=cptcoveff; z1++)
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
bool=0;
}
if (bool==1) {
for(m=firstpass; m<=lastpass; m++){
k2=anint[m][i]+(mint[m][i]/12.);
if ((k2>=dateprev1) && (k2<=dateprev2)) {
if(agev[m][i]==0) agev[m][i]=agemax+1;
if(agev[m][i]==1) agev[m][i]=agemax+2;
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];
if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
dateintsum=dateintsum+k2;
k2cpt++;
}

}	for(k1=1; k1<=j;k1++){
}	for(i1=1; i1<=ncodemax[k1];i1++){
}	j1++;
}	/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
	scanf("%d", i);*/
	for (i=-1; i<=nlstate+ndeath; i++)
	for (jk=-1; jk<=nlstate+ndeath; jk++)
	for(m=agemin; m <= agemax+3; m++)
	freq[i][jk][m]=0;

	dateintsum=0;
	k2cpt=0;
	for (i=1; i<=imx; i++) {
	bool=1;
	if (cptcovn>0) {
	for (z1=1; z1<=cptcoveff; z1++)
	if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
	bool=0;
	}
	if (bool==1) {
	for(m=firstpass; m<=lastpass; m++){
	k2=anint[m][i]+(mint[m][i]/12.);
	if ((k2>=dateprev1) && (k2<=dateprev2)) {
	if(agev[m][i]==0) agev[m][i]=agemax+1;
	if(agev[m][i]==1) agev[m][i]=agemax+2;
	if (m<lastpass) {
	freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
	freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
	}

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

fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);	fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);

if (cptcovn>0) {	if (cptcovn>0) {
fprintf(ficresp, "\n#********** Variable ");	fprintf(ficresp, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
fprintf(ficresp, "**********\n#");	fprintf(ficresp, "**********\n#");
}	}
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);	fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
fprintf(ficresp, "\n");	fprintf(ficresp, "\n");

for(i=(int)agemin; i <= (int)agemax+3; i++){	for(i=(int)agemin; i <= (int)agemax+3; i++){
if(i==(int)agemax+3)	if(i==(int)agemax+3){
printf("Total");	fprintf(ficlog,"Total");
else	}else{
printf("Age %d", i);	if(first==1){
for(jk=1; jk <=nlstate ; jk++){	first=0;
for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)	printf("See log file for details...\n");
pp[jk] += freq[jk][m][i];	}
}	fprintf(ficlog,"Age %d", i);
for(jk=1; jk <=nlstate ; jk++){	}
for(m=-1, pos=0; m <=0 ; m++)	for(jk=1; jk <=nlstate ; jk++){
pos += freq[jk][m][i];	for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
if(pp[jk]>=1.e-10)	pp[jk] += freq[jk][m][i];
printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);	}
else	for(jk=1; jk <=nlstate ; jk++){
printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);	for(m=-1, pos=0; m <=0 ; m++)
}	pos += freq[jk][m][i];
	if(pp[jk]>=1.e-10){
for(jk=1; jk <=nlstate ; jk++){	if(first==1){
for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)	printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
pp[jk] += freq[jk][m][i];	}
}	fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
	}else{
	if(first==1)
	printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
	fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
	}
	}

for(jk=1,pos=0; jk <=nlstate ; jk++)	for(jk=1; jk <=nlstate ; jk++){
pos += pp[jk];	for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
for(jk=1; jk <=nlstate ; jk++){	pp[jk] += freq[jk][m][i];
if(pos>=1.e-5)	}
printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
else	for(jk=1,pos=0; jk <=nlstate ; jk++)
printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);	pos += pp[jk];
if( i <= (int) agemax){	for(jk=1; jk <=nlstate ; jk++){
if(pos>=1.e-5){	if(pos>=1.e-5){
fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);	if(first==1)
probs[i][jk][j1]= pp[jk]/pos;	printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
/printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);/	fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
	}else{
	if(first==1)
	printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
	fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
	}
	if( i <= (int) agemax){
	if(pos>=1.e-5){
	fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
	probs[i][jk][j1]= pp[jk]/pos;
	/printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);/
	}
	else
	fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
	}
}	}
else
fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);	for(jk=-1; jk <=nlstate+ndeath; jk++)
	for(m=-1; m <=nlstate+ndeath; m++)
	if(freq[jk][m][i] !=0 ) {
	if(first==1)
	printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
	fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
	}
	if(i <= (int) agemax)
	fprintf(ficresp,"\n");
	if(first==1)
	printf("Others in log...\n");
	fprintf(ficlog,"\n");
}	}
}	}
for(jk=-1; jk <=nlstate+ndeath; jk++)	}
for(m=-1; m <=nlstate+ndeath; m++)
if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
if(i <= (int) agemax)
fprintf(ficresp,"\n");
printf("\n");
}
}
}
dateintmean=dateintsum/k2cpt;	dateintmean=dateintsum/k2cpt;

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

/* End of Freq */	/* End of Freq */
}	}

/********** Prevalence ******************/	/********** Prevalence ******************/
void prevalence(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 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, double calagedate)
{ /* 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 1324 void prevalence(int agemin, int agemax,	Line 1414 void prevalence(int agemin, int agemax,
j=cptcoveff;	j=cptcoveff;
if (cptcovn<1) {j=1;ncodemax[1]=1;}	if (cptcovn<1) {j=1;ncodemax[1]=1;}

for(k1=1; k1<=j;k1++){	for(k1=1; k1<=j;k1++){
for(i1=1; i1<=ncodemax[k1];i1++){	for(i1=1; i1<=ncodemax[k1];i1++){
j1++;	j1++;

for (i=-1; i<=nlstate+ndeath; i++)	for (i=-1; i<=nlstate+ndeath; i++)
for (jk=-1; jk<=nlstate+ndeath; jk++)	for (jk=-1; jk<=nlstate+ndeath; jk++)
for(m=agemin; m <= agemax+3; m++)	for(m=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++) {
bool=1;	bool=1;
if (cptcovn>0) {	if (cptcovn>0) {
for (z1=1; z1<=cptcoveff; z1++)	for (z1=1; z1<=cptcoveff; z1++)
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)) {
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;
freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];	if (m<lastpass) {
freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];	if (calagedate>0)
	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];
	}
}	}
}	}
}	}
}	}
	for(i=(int)agemin; i <= (int)agemax+3; i++){
for(i=(int)agemin; i <= (int)agemax+3; i++){	for(jk=1; jk <=nlstate ; jk++){
for(jk=1; jk <=nlstate ; jk++){	for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)	pp[jk] += freq[jk][m][i];
pp[jk] += freq[jk][m][i];	}
}	for(jk=1; jk <=nlstate ; jk++){
for(jk=1; jk <=nlstate ; jk++){	for(m=-1, pos=0; m <=0 ; m++)
for(m=-1, pos=0; m <=0 ; m++)
pos += freq[jk][m][i];	pos += freq[jk][m][i];
}	}

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

for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];

for(jk=1; jk <=nlstate ; jk++){
if( i <= (int) agemax){
if(pos>=1.e-5){
probs[i][jk][j1]= pp[jk]/pos;
}
}
}

}	}
}
}	for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];

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


free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);	free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
free_vector(pp,1,nlstate);	free_vector(pp,1,nlstate);
Line 1402 void concatwav(int wav[], int **dh, int	Line 1495 void concatwav(int wav[], int **dh, int
int i, mi, m;	int i, mi, m;
/* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;	/* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
double sum=0., jmean=0.;*/	double sum=0., jmean=0.;*/
	int first;
int j, k=0,jk, ju, jl;	int j, k=0,jk, ju, jl;
double sum=0.;	double sum=0.;
	first=0;
jmin=1e+5;	jmin=1e+5;
jmax=-1;	jmax=-1;
jmean=0.;	jmean=0.;
Line 1427 void concatwav(int wav[], int **dh, int	Line 1521 void concatwav(int wav[], int **dh, int
}	}

wav[i]=mi;	wav[i]=mi;
if(mi==0)	if(mi==0){
printf("Warning, no any valid information for:%d line=%d\n",num[i],i);	if(first==0){
	printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
	first=1;
	}
	if(first==1){
	fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
	}
	} /* end mi==0 */
}	}

for(i=1; i<=imx; i++){	for(i=1; i<=imx; i++){
Line 1444 void concatwav(int wav[], int **dh, int	Line 1545 void concatwav(int wav[], int **dh, int
if (j >= jmax) jmax=j;	if (j >= jmax) jmax=j;
if (j <= jmin) jmin=j;	if (j <= jmin) jmin=j;
sum=sum+j;	sum=sum+j;
/* if (j<10) printf("j=%d num=%d ",j,i); */	/if (j<0) printf("j=%d num=%d \n",j,i); /
}	}
}	}
else{	else{
Line 1452 void concatwav(int wav[], int **dh, int	Line 1553 void concatwav(int wav[], int **dh, int
k=k+1;	k=k+1;
if (j >= jmax) jmax=j;	if (j >= jmax) jmax=j;
else if (j <= jmin)jmin=j;	else if (j <= jmin)jmin=j;
/* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */	/* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
sum=sum+j;	sum=sum+j;
}	}
jk= j/stepm;	jk= j/stepm;
Line 1469 void concatwav(int wav[], int **dh, int	Line 1570 void concatwav(int wav[], int **dh, int
}	}
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);
	fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
}	}

/********* Tricode **************************/	/********* Tricode **************************/
void tricode(int Tvar, int *nbcode, int imx)	void tricode(int Tvar, int *nbcode, int imx)
{	{
Line 1498 void tricode(int Tvar, int *nbcode, in	Line 1601 void tricode(int Tvar, int *nbcode, in
for (k=0; k<=19; k++) {	for (k=0; k<=19; k++) {
if (Ndum[k] != 0) {	if (Ndum[k] != 0) {
nbcode[Tvar[j]][ij]=k;	nbcode[Tvar[j]][ij]=k;

ij++;	ij++;
}	}
if (ij > ncodemax[j]) break;	if (ij > ncodemax[j]) break;
Line 1508 void tricode(int Tvar, int *nbcode, in	Line 1612 void tricode(int Tvar, int *nbcode, in
for (k=0; k<19; k++) Ndum[k]=0;	for (k=0; k<19; k++) Ndum[k]=0;

for (i=1; i<=ncovmodel-2; i++) {	for (i=1; i<=ncovmodel-2; i++) {
ij=Tvar[i];	ij=Tvar[i];
Ndum[ij]++;	Ndum[ij]++;
}	}

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

cptcoveff=ij-1;	cptcoveff=ij-1;
}	}

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

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

{	{
/* Health expectancies */	/* Health expectancies */
int i, j, nhstepm, hstepm, h;	int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
double age, agelim,hf;	double age, agelim, hf;
double ***p3mat;	double *p3mat,*varhe;
	double dnewm,doldm;
	double *xp;
	double gp, gm;
	double *gradg, *trgradg;
	int theta;

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

fprintf(ficreseij,"# Health expectancies\n");	fprintf(ficreseij,"# Health expectancies\n");
fprintf(ficreseij,"# Age");	fprintf(ficreseij,"# Age");
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++)	for(j=1; j<=nlstate;j++)
fprintf(ficreseij," %1d-%1d",i,j);	fprintf(ficreseij," %1d-%1d (SE)",i,j);
fprintf(ficreseij,"\n");	fprintf(ficreseij,"\n");

hstepm=1YEARM; / Every j years of age (in month) */	if(estepm < stepm){
hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */	printf ("Problem %d lower than %d\n",estepm, stepm);
	}
	else hstepm=estepm;
	/* We compute the life expectancy from trapezoids spaced every estepm months
	* This is mainly to measure the difference between two models: for example
	* if stepm=24 months pijx are given only every 2 years and by summing them
	* we are calculating an estimate of the Life Expectancy assuming a linear
	* progression inbetween and thus overestimating or underestimating according
	* to the curvature of the survival function. If, for the same date, we
	* estimate the model with stepm=1 month, we can keep estepm to 24 months
	* to compare the new estimate of Life expectancy with the same linear
	* hypothesis. A more precise result, taking into account a more precise
	* curvature will be obtained if estepm is as small as stepm. */

	/* For example we decided to compute the life expectancy with the smallest unit */
	/* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
	nhstepm is the number of hstepm from age to agelim
	nstepm is the number of stepm from age to agelin.
	Look at hpijx to understand the reason of that which relies in memory size
	and note for a fixed period like estepm months */
	/* We decided (b) to get a life expectancy respecting the most precise curvature of the
	survival function given by stepm (the optimization length). Unfortunately it
	means that if the survival funtion is printed only each two years of age and if
	you sum them up and add 1 year (area under the trapezoids) you won't get the same
	results. So we changed our mind and took the option of the best precision.
	*/
	hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */

agelim=AGESUP;	agelim=AGESUP;
for (age=bage; age<=fage; age ++){ /* If stepm=6 months */	for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
/* nhstepm age range expressed in number of stepm */	/* nhstepm age range expressed in number of stepm */
nhstepm=(int) rint((agelim-age)*YEARM/stepm);	nstepm=(int) rint((agelim-age)*YEARM/stepm);
/* Typically if 20 years = 2012/6=40 stepm /	/* Typically if 20 years nstepm = 2012/6=40 stepm /
if (stepm >= YEARM) hstepm=1;	/* if (stepm >= YEARM) hstepm=1;*/
nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */	nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
	gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
	gp=matrix(0,nhstepm,1,nlstate*2);
	gm=matrix(0,nhstepm,1,nlstate*2);

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


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

	/* Computing Variances of health expectancies */

	for(theta=1; theta <=npar; theta++){
	for(i=1; i<=npar; i++){
	xp[i] = x[i] + (i==theta ?delti[theta]:0);
	}
	hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);

	cptj=0;
	for(j=1; j<= nlstate; j++){
	for(i=1; i<=nlstate; i++){
	cptj=cptj+1;
	for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
	gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
	}
	}
	}


	for(i=1; i<=npar; i++)
	xp[i] = x[i] - (i==theta ?delti[theta]:0);
	hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);

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

	/* End theta */

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

	for(h=0; h<=nhstepm-1; h++)
	for(j=1; j<=nlstate*2;j++)
	for(theta=1; theta <=npar; theta++)
	trgradg[h][j][theta]=gradg[h][theta][j];


	for(i=1;i<=nlstate*2;i++)
	for(j=1;j<=nlstate*2;j++)
	varhe[i][j][(int)age] =0.;

	printf("%d\|",(int)age);fflush(stdout);
	fprintf(ficlog,"%d\|",(int)age);fflush(ficlog);
	for(h=0;h<=nhstepm-1;h++){
	for(k=0;k<=nhstepm-1;k++){
	matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
	matprod2(doldm,dnewm,1,nlstate2,1,npar,1,nlstate2,gradg[k]);
	for(i=1;i<=nlstate*2;i++)
	for(j=1;j<=nlstate*2;j++)
	varhe[i][j][(int)age] += doldm[i][j]hfhf;
	}
	}
	/* Computing expectancies */
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++)	for(j=1; j<=nlstate;j++)
for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){	for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
eij[i][j][(int)age] +=p3mat[i][j][h];	eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;

	/* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/

}	}

hf=1;	fprintf(ficreseij,"%3.0f",age );
if (stepm >= YEARM) hf=stepm/YEARM;	cptj=0;
fprintf(ficreseij,"%.0f",age );
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++){	for(j=1; j<=nlstate;j++){
fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);	cptj++;
	fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
}	}
fprintf(ficreseij,"\n");	fprintf(ficreseij,"\n");

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

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

/********** Variance ****************/	/********** Variance ****************/
void varevsij(char fileres[], double *vareij, double matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double oldm, double savm, double **prlim, double ftolpl, int ij)	void varevsij(char optionfilefiname[], double *vareij, double matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double oldm, double savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased)
{	{
/* Variance of health expectancies */	/* Variance of health expectancies */
/* 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, h;	double dnewmp,doldmp;
	int i, j, nhstepm, hstepm, h, nstepm ;
int k, cptcode;	int k, cptcode;
double *xp;	double *xp;
double gp, gm;	double gp, gm; /* for var eij */
double *gradg, *trgradg;	double *gradg, trgradg; /for var eij */
	double gradgp, trgradgp; /* for var p point j */
	double gpp, gmp; /* for var p point j */
	double *varppt; / for var p point j nlstate to nlstate+ndeath */
double ***p3mat;	double ***p3mat;
double age,agelim;	double age,agelim, hf;
int theta;	int theta;
	char digit[4];
	char digitp[16];

fprintf(ficresvij,"# Covariances of life expectancies\n");	char fileresprobmorprev[FILENAMELENGTH];

	if(popbased==1)
	strcpy(digitp,"-populbased-");
	else
	strcpy(digitp,"-stablbased-");

	strcpy(fileresprobmorprev,"prmorprev");
	sprintf(digit,"%-d",ij);
	/printf("DIGIT=%s, ij=%d ijr=%-d\|\n",digit, ij,ij);/
	strcat(fileresprobmorprev,digit); /* Tvar to be done */
	strcat(fileresprobmorprev,digitp); /* Popbased or not */
	strcat(fileresprobmorprev,fileres);
	if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
	printf("Problem with resultfile: %s\n", fileresprobmorprev);
	fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
	}
	printf("Computing total mortality p.j=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,"# Age cov=%-d",ij);
	for(j=nlstate+1; j<=(nlstate+ndeath);j++){
	fprintf(ficresprobmorprev," p.%-d SE",j);
	for(i=1; i<=nlstate;i++)
	fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
	}
	fprintf(ficresprobmorprev,"\n");
	if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
	printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
	fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
	exit(0);
	}
	else{
	fprintf(ficgp,"\n# Routine varevsij");
	}
	if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
	printf("Problem with html file: %s\n", optionfilehtm);
	fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
	exit(0);
	}
	else{
	fprintf(fichtm,"\n<li><h4> Computing step probabilities of dying and weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
	}
	varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);

	fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are the stable prevalence in health states i\n");
fprintf(ficresvij,"# Age");	fprintf(ficresvij,"# Age");
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++)	for(j=1; j<=nlstate;j++)
Line 1599 void varevsij(char fileres[], double ***	Line 1876 void varevsij(char fileres[], double ***
xp=vector(1,npar);	xp=vector(1,npar);
dnewm=matrix(1,nlstate,1,npar);	dnewm=matrix(1,nlstate,1,npar);
doldm=matrix(1,nlstate,1,nlstate);	doldm=matrix(1,nlstate,1,nlstate);
	dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
hstepm=1YEARM; / Every year of age */	doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
	gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
	gpp=vector(nlstate+1,nlstate+ndeath);
	gmp=vector(nlstate+1,nlstate+ndeath);
	trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/

	if(estepm < stepm){
	printf ("Problem %d lower than %d\n",estepm, stepm);
	}
	else hstepm=estepm;
	/* For example we decided to compute the life expectancy with the smallest unit */
	/* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
	nhstepm is the number of hstepm from age to agelim
	nstepm is the number of stepm from age to agelin.
	Look at hpijx to understand the reason of that which relies in memory size
	and note for a fixed period like k years */
	/* We decided (b) to get a life expectancy respecting the most precise curvature of the
	survival function given by stepm (the optimization length). Unfortunately it
	means that if the survival funtion is printed only each two years of age and if
	you sum them up and add 1 year (area under the trapezoids) you won't get the same
	results. So we changed our mind and took the option of the best precision.
	*/
	hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
agelim = AGESUP;	agelim = AGESUP;
for (age=bage; age<=fage; age ++){ /* If stepm=6 months */	for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
nhstepm=(int) rint((agelim-age)YEARM/stepm); / Typically 20 years = 2012/6=40 /	nstepm=(int) rint((agelim-age)YEARM/stepm); / Typically 20 years = 2012/6=40 /
if (stepm >= YEARM) hstepm=1;	nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
gradg=ma3x(0,nhstepm,1,npar,1,nlstate);	gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
gp=matrix(0,nhstepm,1,nlstate);	gp=matrix(0,nhstepm,1,nlstate);
gm=matrix(0,nhstepm,1,nlstate);	gm=matrix(0,nhstepm,1,nlstate);


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 */
xp[i] = x[i] + (i==theta ?delti[theta]:0);	xp[i] = x[i] + (i==theta ?delti[theta]:0);
Line 1630 void varevsij(char fileres[], double ***	Line 1929 void varevsij(char fileres[], double ***
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 */
	for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
	for(i=1; i<= nlstate; i++)
	gpp[j] += prlim[i][i]*p3mat[i][j][1];
	}
	/* end force of mortality */

for(i=1; i<=npar; i++) /* Computes gradient */	for(i=1; i<=npar; i++) /* Computes gradient */
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 1647 void varevsij(char fileres[], double ***	Line 1952 void varevsij(char fileres[], double ***
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 */
	for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
	for(i=1; i<= nlstate; i++)
	gmp[j] += prlim[i][i]*p3mat[i][j][1];
	}
	/* end force of mortality */

for(j=1; j<= nlstate; j++)	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 */
	gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
	}

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

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

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

	for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
	for(theta=1; theta <=npar; theta++)
	trgradgp[j][theta]=gradgp[theta][j];

	hf=hstepmstepm/YEARM; / Duration of hstepm expressed in year unit. */
for(i=1;i<=nlstate;i++)	for(i=1;i<=nlstate;i++)
for(j=1;j<=nlstate;j++)	for(j=1;j<=nlstate;j++)
vareij[i][j][(int)age] =0.;	vareij[i][j][(int)age] =0.;

for(h=0;h<=nhstepm;h++){	for(h=0;h<=nhstepm;h++){
for(k=0;k<=nhstepm;k++){	for(k=0;k<=nhstepm;k++){
matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);	matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);	matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
for(i=1;i<=nlstate;i++)	for(i=1;i<=nlstate;i++)
for(j=1;j<=nlstate;j++)	for(j=1;j<=nlstate;j++)
vareij[i][j][(int)age] += doldm[i][j];	vareij[i][j][(int)age] += doldm[i][j]hfhf;
}	}
}	}
h=1;
if (stepm >= YEARM) h=stepm/YEARM;	/* pptj */
	matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
	matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
	for(j=nlstate+1;j<=nlstate+ndeath;j++)
	for(i=nlstate+1;i<=nlstate+ndeath;i++)
	varppt[j][i]=doldmp[j][i];
	/* end ppptj */
	hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);
	prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);

	if (popbased==1) {
	for(i=1; i<=nlstate;i++)
	prlim[i][i]=probs[(int)age][i][ij];
	}

	/* This for computing force of mortality (h=1)as a weighted average */
	for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
	for(i=1; i<= nlstate; i++)
	gmp[j] += prlim[i][i]*p3mat[i][j][1];
	}
	/* end force of mortality */

	fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
	for(j=nlstate+1; j<=(nlstate+ndeath);j++){
	fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
	for(i=1; i<=nlstate;i++){
	fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
	}
	}
	fprintf(ficresprobmorprev,"\n");

fprintf(ficresvij,"%.0f ",age );	fprintf(ficresvij,"%.0f ",age );
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++){	for(j=1; j<=nlstate;j++){
fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);	fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
}	}
fprintf(ficresvij,"\n");	fprintf(ficresvij,"\n");
free_matrix(gp,0,nhstepm,1,nlstate);	free_matrix(gp,0,nhstepm,1,nlstate);
Line 1687 void varevsij(char fileres[], double ***	Line 2038 void varevsij(char fileres[], double ***
free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);	free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
} /* End age */	} /* End age */
	free_vector(gpp,nlstate+1,nlstate+ndeath);
	free_vector(gmp,nlstate+1,nlstate+ndeath);
	free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
	free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
	fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
	/* for(j=nlstate+1; j<= nlstate+ndeath; j++){ // Only the first actually */
	fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
	fprintf(ficgp,"\n plot \"%s\" u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);
	fprintf(ficgp,"\n replot \"%s\" u 1:(($3+1.96$4)%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);
	fprintf(ficgp,"\n replot \"%s\" u 1:(($3-1.96$4)%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);
	fprintf(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 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);

free_vector(xp,1,npar);	free_vector(xp,1,npar);
free_matrix(doldm,1,nlstate,1,npar);	free_matrix(doldm,1,nlstate,1,nlstate);
free_matrix(dnewm,1,nlstate,1,nlstate);	free_matrix(dnewm,1,nlstate,1,npar);
	free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
	free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
	free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
	fclose(ficresprobmorprev);
	fclose(ficgp);
	fclose(fichtm);

}	}

Line 1709 void varprevlim(char fileres[], double *	Line 2079 void varprevlim(char fileres[], double *
double age,agelim;	double age,agelim;
int theta;	int theta;

fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");	fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");
fprintf(ficresvpl,"# Age");	fprintf(ficresvpl,"# Age");
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
fprintf(ficresvpl," %1d-%1d",i,i);	fprintf(ficresvpl," %1d-%1d",i,i);
Line 1778 void varprevlim(char fileres[], double *	Line 2148 void varprevlim(char fileres[], double *
}	}

/********** Variance of one-step probabilities ****************/	/********** Variance of one-step probabilities ****************/
void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)	void varprob(char optionfilefiname[], double *matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int Tvar, int *nbcode, int ncodemax)
{	{
int i, j;	int i, j=0, i1, k1, l1, t, tj;
int k=0, cptcode;	int k2, l2, j1, z1;
	int k=0,l, cptcode;
	int first=1, first1;
	double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;
double dnewm,doldm;	double dnewm,doldm;
double *xp;	double *xp;
double gp, gm;	double gp, gm;
double gradg, trgradg;	double gradg, trgradg;
	double **mu;
double age,agelim, cov[NCOVMAX];	double age,agelim, cov[NCOVMAX];
	double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
int theta;	int theta;
char fileresprob[FILENAMELENGTH];	char fileresprob[FILENAMELENGTH];
	char fileresprobcov[FILENAMELENGTH];
	char fileresprobcor[FILENAMELENGTH];

	double ***varpij;

strcpy(fileresprob,"prob");	strcpy(fileresprob,"prob");
strcat(fileresprob,fileres);	strcat(fileresprob,fileres);
if((ficresprob=fopen(fileresprob,"w"))==NULL) {	if((ficresprob=fopen(fileresprob,"w"))==NULL) {
printf("Problem with resultfile: %s\n", fileresprob);	printf("Problem with resultfile: %s\n", fileresprob);
	fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
}	}
printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);	strcpy(fileresprobcov,"probcov");
	strcat(fileresprobcov,fileres);
	if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
	printf("Problem with resultfile: %s\n", fileresprobcov);
	fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
	}
	strcpy(fileresprobcor,"probcor");
	strcat(fileresprobcor,fileres);
	if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
	printf("Problem with resultfile: %s\n", fileresprobcor);
	fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
	}
	printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
	fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
	printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
	fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
	printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
	fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);

	fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
	fprintf(ficresprob,"# Age");
	fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
	fprintf(ficresprobcov,"# Age");
	fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
	fprintf(ficresprobcov,"# Age");


	for(i=1; i<=nlstate;i++)
	for(j=1; j<=(nlstate+ndeath);j++){
	fprintf(ficresprob," p%1d-%1d (SE)",i,j);
	fprintf(ficresprobcov," p%1d-%1d ",i,j);
	fprintf(ficresprobcor," p%1d-%1d ",i,j);
	}
	fprintf(ficresprob,"\n");
	fprintf(ficresprobcov,"\n");
	fprintf(ficresprobcor,"\n");
xp=vector(1,npar);	xp=vector(1,npar);
dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);	dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
doldm=matrix(1,(nlstate+ndeath)(nlstate+ndeath),1,(nlstate+ndeath)(nlstate+ndeath));	doldm=matrix(1,(nlstate)(nlstate+ndeath),1,(nlstate)(nlstate+ndeath));
	mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
cov[1]=1;	varpij=ma3x(1,nlstate(nlstate+ndeath),1,nlstate(nlstate+ndeath),(int) bage, (int) fage);
for (age=bage; age<=fage; age ++){	first=1;
cov[2]=age;	if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
gradg=matrix(1,npar,1,9);	printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
trgradg=matrix(1,9,1,npar);	fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));	exit(0);
gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));	}
	else{
for(theta=1; theta <=npar; theta++){	fprintf(ficgp,"\n# Routine varprob");
for(i=1; i<=npar; i++)	}
xp[i] = x[i] + (i==theta ?delti[theta]:0);	if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
	printf("Problem with html file: %s\n", optionfilehtm);
pmij(pmmij,cov,ncovmodel,xp,nlstate);	fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
	exit(0);
k=0;	}
for(i=1; i<= (nlstate+ndeath); i++){	else{
for(j=1; j<=(nlstate+ndeath);j++){	fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
k=k+1;	fprintf(fichtm,"\n");
gp[k]=pmmij[i][j];
}
}

for(i=1; i<=npar; i++)	fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
xp[i] = x[i] - (i==theta ?delti[theta]:0);	fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
	fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");

pmij(pmmij,cov,ncovmodel,xp,nlstate);	}
k=0;
for(i=1; i<=(nlstate+ndeath); i++){
for(j=1; j<=(nlstate+ndeath);j++){
k=k+1;
gm[k]=pmmij[i][j];
}
}

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

for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)
for(theta=1; theta <=npar; theta++)
trgradg[j][theta]=gradg[theta][j];

matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);	cov[1]=1;
matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);	tj=cptcoveff;
	if (cptcovn<1) {tj=1;ncodemax[1]=1;}
pmij(pmmij,cov,ncovmodel,x,nlstate);	j1=0;
	for(t=1; t<=tj;t++){
	for(i1=1; i1<=ncodemax[t];i1++){
	j1++;

	if (cptcovn>0) {
	fprintf(ficresprob, "\n#********** Variable ");
	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
	fprintf(ficresprob, "**********\n#");
	fprintf(ficresprobcov, "\n#********** Variable ");
	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
	fprintf(ficresprobcov, "**********\n#");

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


	fprintf(fichtm, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
	for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
	fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");

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

	for (age=bage; age<=fage; age ++){
	cov[2]=age;
	for (k=1; k<=cptcovn;k++) {
	cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
	}
	for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
	for (k=1; k<=cptcovprod;k++)
	cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];

	gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
	trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
	gp=vector(1,(nlstate)*(nlstate+ndeath));
	gm=vector(1,(nlstate)*(nlstate+ndeath));

	for(theta=1; theta <=npar; theta++){
	for(i=1; i<=npar; i++)
	xp[i] = x[i] + (i==theta ?delti[theta]:0);

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

	k=0;
	for(i=1; i<= (nlstate); i++){
	for(j=1; j<=(nlstate+ndeath);j++){
	k=k+1;
	gp[k]=pmmij[i][j];
	}
	}

	for(i=1; i<=npar; i++)
	xp[i] = x[i] - (i==theta ?delti[theta]:0);

	pmij(pmmij,cov,ncovmodel,xp,nlstate);
	k=0;
	for(i=1; i<=(nlstate); i++){
	for(j=1; j<=(nlstate+ndeath);j++){
	k=k+1;
	gm[k]=pmmij[i][j];
	}
	}

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

k=0;	for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
for(i=1; i<=(nlstate+ndeath); i++){	for(theta=1; theta <=npar; theta++)
for(j=1; j<=(nlstate+ndeath);j++){	trgradg[j][theta]=gradg[theta][j];
k=k+1;
gm[k]=pmmij[i][j];	matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);
	matprod2(doldm,dnewm,1,(nlstate)(nlstate+ndeath),1,npar,1,(nlstate)(nlstate+ndeath),gradg);

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

	k=0;
	for(i=1; i<=(nlstate); i++){
	for(j=1; j<=(nlstate+ndeath);j++){
	k=k+1;
	mu[k][(int) age]=pmmij[i][j];
	}
}	}
}	for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
	for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
/*printf("\n%d ",(int)age);	varpij[i][j][(int)age] = doldm[i][j];
for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){


	/*printf("\n%d ",(int)age);
	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(ficresprob,"\n%d ",(int)age);	fprintf(ficresprob,"\n%d ",(int)age);
	fprintf(ficresprobcov,"\n%d ",(int)age);
for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){	fprintf(ficresprobcor,"\n%d ",(int)age);
if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);
if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);	for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
}	fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
	for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
	fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
	fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
	}
	i=0;
	for (k=1; k<=(nlstate);k++){
	for (l=1; l<=(nlstate+ndeath);l++){
	i=i++;
	fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
	fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
	for (j=1; j<=i;j++){
	fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
	fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
	}
	}
	}/* end of loop for state */
	} /* end of loop for age */

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

	/* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
	first1=1;
	for (k1=1; k1<=(nlstate);k1++){
	for (l1=1; l1<=(nlstate+ndeath);l1++){
	if(l1==k1) continue;
	i=(k1-1)*(nlstate+ndeath)+l1;
	for (k2=1; k2<=(nlstate);k2++){
	for (l2=1; l2<=(nlstate+ndeath);l2++){
	if(l2==k2) continue;
	j=(k2-1)*(nlstate+ndeath)+l2;
	if(j<=i) continue;
	for (age=bage; age<=fage; age ++){
	if ((int)age %5==0){
	v1=varpij[i][i][(int)age]/stepmYEARM/stepmYEARM;
	v2=varpij[j][j][(int)age]/stepmYEARM/stepmYEARM;
	cv12=varpij[i][j][(int)age]/stepmYEARM/stepmYEARM;
	mu1=mu[i][(int) age]/stepm*YEARM ;
	mu2=mu[j][(int) age]/stepm*YEARM;
	/* Computing eigen value of matrix of covariance */
	lc1=(v1+v2)+sqrt((v1+v2)(v1+v2) - 4(v1v2-cv12cv12));
	lc2=(v1+v2)-sqrt((v1+v2)(v1+v2) - 4(v1v2-cv12cv12));
	if(first1==1){
	first1=0;
	printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\nOthers in log...\n",v1,v2,cv12,lc1,lc2);
	}
	fprintf(ficlog,"Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);
	/* Eigen vectors */
	v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
	v21=sqrt(1.-v11*v11);
	v12=-v21;
	v22=v11;
	/printf(fignu/
	/* mu1+ v11lc1cost + v12lc2sin(t) */
	/* mu2+ v21lc1cost + v21lc2sin(t) */
	if(first==1){
	first=0;
	fprintf(ficgp,"\nset parametric;set nolabel");
	fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);
	fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
	fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1);
	fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k2,l2,k1,l1);
	fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k2,l2,k1,l1);
	fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);
	fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);
	/* fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)), %11.3e +%.3f(-%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)) t \"%d\"",\
	mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \
	mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);
	*/
	fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)), %11.3e +%.3f(-%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)) not",\
	mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \
	mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));
	}else{
	first=0;
	fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);
	fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);
	/*
	fprintf(ficgp,"\nreplot %11.3e+ %.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)), %11.3e +%.3f(-%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)) t \"%d\"",\
	mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \
	mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);
	*/
	fprintf(ficgp,"\nreplot %11.3e+ %.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)), %11.3e +%.3f(-%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)) not",\
	mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \
	mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));
	}/* if first */
	} /* age mod 5 */
	} /* end loop age */
	fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k2,l2,k1,l1);
	first=1;
	} /l12 /
	} /* k12 */
	} /l1 /
	}/* k1 */
	} /* loop covariates */
	free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));	free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
free_vector(gm,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(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);	free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
	}
	free_vector(xp,1,npar);
	fclose(ficresprob);
	fclose(ficresprobcov);
	fclose(ficresprobcor);
	fclose(ficgp);
	fclose(fichtm);
}	}
free_vector(xp,1,npar);
fclose(ficresprob);

}

/***************** Printing html file *********/	/***************** Printing html file *********/
void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[] ){	void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
	int lastpass, int stepm, int weightopt, char model[],\
	int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
	int popforecast, int estepm ,\
	double jprev1, double mprev1,double anprev1, \
	double jprev2, double mprev2,double anprev2){
int jj1, k1, i1, cpt;	int jj1, k1, i1, cpt;
FILE *fichtm;
/char optionfilehtm[FILENAMELENGTH];/	/char optionfilehtm[FILENAMELENGTH];/
	if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
strcpy(optionfilehtm,optionfile);
strcat(optionfilehtm,".htm");
if((fichtm=fopen(optionfilehtm,"w"))==NULL) {
printf("Problem with %s \n",optionfilehtm), exit(0);	printf("Problem with %s \n",optionfilehtm), exit(0);
	fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
}	}

fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">	fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>	- Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n
	- Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
	- Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
	- Life expectancies by age and initial health status (estepm=%2d months):
	<a href=\"e%s\">e%s</a> <br>\n</li>", \
	jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);

Total number of observations=%d <br>	fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>
<hr size=\"2\" color=\"#EC5E5E\">
<li>Outputs files<br><br>\n
- Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n
- Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>
- Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>
- Transition probabilities: <a href=\"pij%s\">pij%s</a><br>
- Copy of the parameter file: <a href=\"o%s\">o%s</a><br>
- Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>
- Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>
- Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>
- Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>
- Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>
<br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);

fprintf(fichtm," <li>Graphs</li><p>");

m=cptcoveff;	m=cptcoveff;
if (cptcovn < 1) {m=1;ncodemax[1]=1;}	if (cptcovn < 1) {m=1;ncodemax[1]=1;}
Line 1921 fprintf(fichtm," <li>Graphs</li><p>");	Line 2495 fprintf(fichtm," <li>Graphs</li><p>");
jj1=0;	jj1=0;
for(k1=1; k1<=m;k1++){	for(k1=1; k1<=m;k1++){
for(i1=1; i1<=ncodemax[k1];i1++){	for(i1=1; i1<=ncodemax[k1];i1++){
jj1++;	jj1++;
if (cptcovn > 0) {	if (cptcovn > 0) {
fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");	fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
for (cpt=1; cpt<=cptcoveff;cpt++)	for (cpt=1; cpt<=cptcoveff;cpt++)
fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);	fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");	fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
}	}
fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>	/* Pij */
<img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);	fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>
	<img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
	/* Quasi-incidences */
	fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>
	<img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
	/* Stable prevalence in each health state */
for(cpt=1; cpt<nlstate;cpt++){	for(cpt=1; cpt<nlstate;cpt++){
fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>	fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>
<img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);	<img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
}	}
for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
interval) in state (%d): v%s%d%d.gif <br>
<img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
}
for(cpt=1; cpt<=nlstate;cpt++) {	for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>	fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>
<img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);	<img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
}	}
fprintf(fichtm,"\n<br>- Total life expectancy by age and	fprintf(fichtm,"\n<br>- Total life expectancy by age and
health expectancies in states (1) and (2): e%s%d.gif<br>	health expectancies in states (1) and (2): e%s%d.png<br>
<img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);	<img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
fprintf(fichtm,"\n</body>");	} /* end i1 */
}	}/* End k1 */
}	fprintf(fichtm,"</ul>");


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

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

	m=cptcoveff;
	if (cptcovn < 1) {m=1;ncodemax[1]=1;}

	jj1=0;
	for(k1=1; k1<=m;k1++){
	for(i1=1; i1<=ncodemax[k1];i1++){
	jj1++;
	if (cptcovn > 0) {
	fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
	for (cpt=1; cpt<=cptcoveff;cpt++)
	fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
	fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
	}
	for(cpt=1; cpt<=nlstate;cpt++) {
	fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
	interval) in state (%d): v%s%d%d.png <br>
	<img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
	}
	} /* end i1 */
	}/* End k1 */
	fprintf(fichtm,"</ul>");
fclose(fichtm);	fclose(fichtm);
}	}

/***************** Gnuplot file ************/	/***************** Gnuplot file ************/
void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemax, double fage , char pathc[], double p[]){	void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){

int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;	int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
	int ng;
strcpy(optionfilegnuplot,optionfilefiname);	if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
strcat(optionfilegnuplot,".plt");
if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
printf("Problem with file %s",optionfilegnuplot);	printf("Problem with file %s",optionfilegnuplot);
	fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
}	}

#ifdef windows	#ifdef windows
Line 1973 m=pow(2,cptcoveff);	Line 2586 m=pow(2,cptcoveff);
for (k1=1; k1<= m ; k1 ++) {	for (k1=1; k1<= m ; k1 ++) {

#ifdef windows	#ifdef windows
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);	fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
#endif	#endif
#ifdef unix	#ifdef unix
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);	fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);
#endif	#endif

for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
Line 1995 for (i=1; i<= nlstate ; i ++) {	Line 2610 for (i=1; i<= nlstate ; i ++) {
}	}
fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));	fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
#ifdef unix	#ifdef unix
fprintf(ficgp,"\nset ter gif small size 400,300");	fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");
#endif	#endif
fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
}	}
}	}
/2 eme/	/2 eme/

for (k1=1; k1<= m ; k1 ++) {	for (k1=1; k1<= m ; k1 ++) {
fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);	fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
	fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);

for (i=1; i<= nlstate+1 ; i ++) {	for (i=1; i<= nlstate+1 ; i ++) {
k=2*i;	k=2*i;
Line 2028 fprintf(ficgp,"\nset out \"v%s%d%d.gif\"	Line 2643 fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");	if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
else fprintf(ficgp,"\" t\"\" w l 0,");	else fprintf(ficgp,"\" t\"\" w l 0,");
}	}
fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);
}	}

/3eme/	/3eme/

for (k1=1; k1<= m ; k1 ++) {	for (k1=1; k1<= m ; k1 ++) {
for (cpt=1; cpt<= nlstate ; cpt ++) {	for (cpt=1; cpt<= nlstate ; cpt ++) {
k=2+nlstate*(cpt-1);	k=2+nlstate(2cpt-2);
fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);	fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
	fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
	/fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
	for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
	fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
	fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
	for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
	fprintf(ficgp,"\" t \"e%d1\" w l",cpt);

	*/
for (i=1; i< nlstate ; i ++) {	for (i=1; i< nlstate ; i ++) {
fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);	fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);

}	}
fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
}
}	}
	}

/* CV preval stat */	/* CV preval stat */
for (k1=1; k1<= m ; k1 ++) {	for (k1=1; k1<= m ; k1 ++) {
for (cpt=1; cpt<nlstate ; cpt ++) {	for (cpt=1; cpt<nlstate ; cpt ++) {
k=3;	k=3;
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);	fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);

for (i=1; i< nlstate ; i ++)	for (i=1; i< nlstate ; i ++)
fprintf(ficgp,"+$%d",k+i+1);	fprintf(ficgp,"+$%d",k+i+1);
Line 2061 fprintf(ficgp,"\nset out \"v%s%d%d.gif\"	Line 2685 fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
fprintf(ficgp,"+$%d",l+i+1);	fprintf(ficgp,"+$%d",l+i+1);
}	}
fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);	fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);
fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);
}	}
}	}

Line 2070 fprintf(ficgp,"\nset out \"v%s%d%d.gif\"	Line 2693 fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
for(k=1; k <=(nlstate+ndeath); k++){	for(k=1; k <=(nlstate+ndeath); k++){
if (k != i) {	if (k != i) {
for(j=1; j <=ncovmodel; j++){	for(j=1; j <=ncovmodel; j++){

fprintf(ficgp,"p%d=%f ",jk,p[jk]);	fprintf(ficgp,"p%d=%f ",jk,p[jk]);
jk++;	jk++;
fprintf(ficgp,"\n");	fprintf(ficgp,"\n");
}	}
}	}
}	}
}

for(jk=1; jk <=m; jk++) {
fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot [%.f:%.f] ",agemin,agemax);
i=1;
for(k2=1; k2<=nlstate; k2++) {
k3=i;
for(k=1; k<=(nlstate+ndeath); k++) {
if (k != k2){
fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
ij=1;
for(j=3; j <=ncovmodel; j++) {
if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
fprintf(ficgp,"+p%d%dx",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
ij++;
}
else
fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
}
fprintf(ficgp,")/(1");

for(k1=1; k1 <=nlstate; k1++){
fprintf(ficgp,"+exp(p%d+p%dx",k3+(k1-1)ncovmodel,k3+(k1-1)*ncovmodel+1);
ij=1;
for(j=3; j <=ncovmodel; j++){
if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
fprintf(ficgp,"+p%d%dx",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
ij++;
}
else
fprintf(ficgp,"+p%d%d",k3+(k1-1)ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
}
fprintf(ficgp,")");
}
fprintf(ficgp,") t \"p%d%d\" ", k2,k);
if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
i=i+ncovmodel;
}
}
}	}
fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);
}	for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
	for(jk=1; jk <=m; jk++) {
fclose(ficgp);	fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
	if (ng==2)
	fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
	else
	fprintf(ficgp,"\nset title \"Probability\"\n");
	fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
	i=1;
	for(k2=1; k2<=nlstate; k2++) {
	k3=i;
	for(k=1; k<=(nlstate+ndeath); k++) {
	if (k != k2){
	if(ng==2)
	fprintf(ficgp," %fexp(p%d+p%dx",YEARM/stepm,i,i+1);
	else
	fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
	ij=1;
	for(j=3; j <=ncovmodel; j++) {
	if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
	fprintf(ficgp,"+p%d%dx",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
	ij++;
	}
	else
	fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
	}
	fprintf(ficgp,")/(1");

	for(k1=1; k1 <=nlstate; k1++){
	fprintf(ficgp,"+exp(p%d+p%dx",k3+(k1-1)ncovmodel,k3+(k1-1)*ncovmodel+1);
	ij=1;
	for(j=3; j <=ncovmodel; j++){
	if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
	fprintf(ficgp,"+p%d%dx",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
	ij++;
	}
	else
	fprintf(ficgp,"+p%d%d",k3+(k1-1)ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
	}
	fprintf(ficgp,")");
	}
	fprintf(ficgp,") t \"p%d%d\" ", k2,k);
	if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
	i=i+ncovmodel;
	}
	} /* end k */
	} /* end k2 */
	} /* end jk */
	} /* end ng */
	fclose(ficgp);
} /* end gnuplot */	} /* end gnuplot */


/************* Moving average ************/	/************* Moving average ************/
void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){	void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){

int i, cpt, cptcod;	int i, cpt, cptcod;
for (agedeb=agemin; agedeb<=fage; agedeb++)	for (agedeb=ageminpar; agedeb<=fage; agedeb++)
for (i=1; i<=nlstate;i++)	for (i=1; i<=nlstate;i++)
for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)	for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)
mobaverage[(int)agedeb][i][cptcod]=0.;	mobaverage[(int)agedeb][i][cptcod]=0.;

for (agedeb=agemin+4; agedeb<=fage; agedeb++){	for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){
for (i=1; i<=nlstate;i++){	for (i=1; i<=nlstate;i++){
for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){	for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
for (cpt=0;cpt<=4;cpt++){	for (cpt=0;cpt<=4;cpt++){
Line 2148 void movingaverage(double agedeb, double	Line 2778 void movingaverage(double agedeb, double


/************ Forecasting ****************/	/************ Forecasting ****************/
prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double agemin, 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 agedeb, double fage, int popforecast, char popfile[], double anproj2,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;
Line 2159 prevforecast(char fileres[], double anpr	Line 2789 prevforecast(char fileres[], double anpr

agelim=AGESUP;	agelim=AGESUP;
calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;	calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;

prevalence(agemin, 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, calagedate);


strcpy(fileresf,"f");	strcpy(fileresf,"f");
strcat(fileresf,fileres);	strcat(fileresf,fileres);
if((ficresf=fopen(fileresf,"w"))==NULL) {	if((ficresf=fopen(fileresf,"w"))==NULL) {
printf("Problem with forecast resultfile: %s\n", fileresf);	printf("Problem with forecast resultfile: %s\n", fileresf);
	fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
}	}
printf("Computing forecasting: result on file '%s' \n", fileresf);	printf("Computing forecasting: result on file '%s' \n", fileresf);
	fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);

if (cptcoveff==0) ncodemax[cptcoveff]=1;	if (cptcoveff==0) ncodemax[cptcoveff]=1;

if (mobilav==1) {	if (mobilav==1) {
mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);	mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
movingaverage(agedeb, fage, agemin, mobaverage);	movingaverage(agedeb, fage, ageminpar, mobaverage);
}	}

stepsize=(int) (stepm+YEARM-1)/YEARM;	stepsize=(int) (stepm+YEARM-1)/YEARM;
Line 2210 calagedate=(anproj1+mproj1/12.+jproj1/36	Line 2842 calagedate=(anproj1+mproj1/12.+jproj1/36
for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {	for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {
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+cpt);

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

Line 2221 calagedate=(anproj1+mproj1/12.+jproj1/36	Line 2853 calagedate=(anproj1+mproj1/12.+jproj1/36

for (h=0; h<=nhstepm; h++){	for (h=0; h<=nhstepm; h++){
if (h==(int) (calagedate+YEARM*cpt)) {	if (h==(int) (calagedate+YEARM*cpt)) {
fprintf(ficresf,"\n %.f ",agedeb+hhstepm/YEARMstepm);	fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+hhstepm/YEARMstepm);
}	}
for(j=1; j<=nlstate+ndeath;j++) {	for(j=1; j<=nlstate+ndeath;j++) {
kk1=0.;kk2=0;	kk1=0.;kk2=0;
Line 2250 calagedate=(anproj1+mproj1/12.+jproj1/36	Line 2882 calagedate=(anproj1+mproj1/12.+jproj1/36
fclose(ficresf);	fclose(ficresf);
}	}
/************ Forecasting ****************/	/************ Forecasting ****************/
populforecast(char fileres[], double anproj1,double mproj1,double jproj1,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,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;
Line 2259 populforecast(char fileres[], double anp	Line 2891 populforecast(char fileres[], double anp
double *p3mat,tabpop,**tabpopprev;	double *p3mat,tabpop,**tabpopprev;
char filerespop[FILENAMELENGTH];	char filerespop[FILENAMELENGTH];

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=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;	calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;

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


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


strcpy(filerespop,"pop");	strcpy(filerespop,"pop");
strcat(filerespop,fileres);	strcat(filerespop,fileres);
if((ficrespop=fopen(filerespop,"w"))==NULL) {	if((ficrespop=fopen(filerespop,"w"))==NULL) {
printf("Problem with forecast resultfile: %s\n", filerespop);	printf("Problem with forecast resultfile: %s\n", filerespop);
	fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
}	}
printf("Computing forecasting: result on file '%s' \n", filerespop);	printf("Computing forecasting: result on file '%s' \n", filerespop);
	fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);

if (cptcoveff==0) ncodemax[cptcoveff]=1;	if (cptcoveff==0) ncodemax[cptcoveff]=1;

if (mobilav==1) {	if (mobilav==1) {
mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);	mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
movingaverage(agedeb, fage, agemin, mobaverage);	movingaverage(agedeb, fage, ageminpar, mobaverage);
}	}

stepsize=(int) (stepm+YEARM-1)/YEARM;	stepsize=(int) (stepm+YEARM-1)/YEARM;
Line 2292 calagedate=(anproj1+mproj1/12.+jproj1/36	Line 2926 calagedate=(anproj1+mproj1/12.+jproj1/36
if (popforecast==1) {	if (popforecast==1) {
if((ficpop=fopen(popfile,"r"))==NULL) {	if((ficpop=fopen(popfile,"r"))==NULL) {
printf("Problem with population file : %s\n",popfile);exit(0);	printf("Problem with population file : %s\n",popfile);exit(0);
	fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
}	}
popage=ivector(0,AGESUP);	popage=ivector(0,AGESUP);
popeffectif=vector(0,AGESUP);	popeffectif=vector(0,AGESUP);
Line 2312 calagedate=(anproj1+mproj1/12.+jproj1/36	Line 2947 calagedate=(anproj1+mproj1/12.+jproj1/36
fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
}	}
fprintf(ficrespop,"******\n");	fprintf(ficrespop,"******\n");
fprintf(ficrespop,"# StartingAge FinalAge");	fprintf(ficrespop,"# Age");
for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);	for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
if (popforecast==1) fprintf(ficrespop," [Population]");	if (popforecast==1) fprintf(ficrespop," [Population]");

for (cpt=0; cpt<=0;cpt++) {	for (cpt=0; cpt<=0;cpt++) {
fprintf(ficrespop,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);	fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);

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

Line 2329 calagedate=(anproj1+mproj1/12.+jproj1/36	Line 2964 calagedate=(anproj1+mproj1/12.+jproj1/36

for (h=0; h<=nhstepm; h++){	for (h=0; h<=nhstepm; h++){
if (h==(int) (calagedate+YEARM*cpt)) {	if (h==(int) (calagedate+YEARM*cpt)) {
fprintf(ficrespop,"\n %.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++) {
kk1=0.;kk2=0;	kk1=0.;kk2=0;
Line 2349 calagedate=(anproj1+mproj1/12.+jproj1/36	Line 2984 calagedate=(anproj1+mproj1/12.+jproj1/36
for(i=1; i<=nlstate;i++){	for(i=1; i<=nlstate;i++){
kk1=0.;	kk1=0.;
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+(calagedate+12cpt)hstepm/YEARMstepm-1)];
}	}

if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++) fprintf(ficrespop," %.3f",tabpopprev[(int)(agedeb+1)][j][cptcod]);	if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)
	fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
}	}
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
}	}
Line 2362 if (h==(int)(calagedate+12*cpt)) for(j=1	Line 2998 if (h==(int)(calagedate+12*cpt)) for(j=1

/******/	/******/

for (cpt=1; cpt<=4;cpt++) {	for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
fprintf(ficrespop,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);	fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){	for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){
nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);	nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);
nhstepm = nhstepm/hstepm;	nhstepm = nhstepm/hstepm;

Line 2373 if (h==(int)(calagedate+12*cpt)) for(j=1	Line 3009 if (h==(int)(calagedate+12*cpt)) for(j=1
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) (calagedate+YEARM*cpt)) {
fprintf(ficresf,"\n %.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++) {
kk1=0.;kk2=0;	kk1=0.;kk2=0;
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," %.3f", kk1);	if (h==(int)(calagedate+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 2410 int main(int argc, char *argv[])	Line 3046 int main(int argc, char *argv[])

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 agemin=1.e20, agemax=-1.e20;	double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;

double fret;	double fret;
double **xi,tmp,delta;	double **xi,tmp,delta;
Line 2419 int main(int argc, char *argv[])	Line 3055 int main(int argc, char *argv[])
double ***p3mat;	double ***p3mat;
int *indx;	int *indx;
char line[MAXLINE], linepar[MAXLINE];	char line[MAXLINE], linepar[MAXLINE];
char title[MAXLINE];	char path[80],pathc[80],pathcd[80],pathtot[80],model[80];
char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];

char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];

char filerest[FILENAMELENGTH];
char fileregp[FILENAMELENGTH];
char popfile[FILENAMELENGTH];
char path[80],pathc[80],pathcd[80],pathtot[80],model[20];
int firstobs=1, lastobs=10;	int firstobs=1, lastobs=10;
int sdeb, sfin; /* Status at beginning and end */	int sdeb, sfin; /* Status at beginning and end */
int c, h , cpt,l;	int c, h , cpt,l;
Line 2437 int main(int argc, char *argv[])	Line 3064 int main(int argc, char *argv[])
int jnais,jdc,jint4,jint1,jint2,jint3,outcome,adl,*tab;	int jnais,jdc,jint4,jint1,jint2,jint3,outcome,adl,*tab;
int mobilav=0,popforecast=0;	int mobilav=0,popforecast=0;
int hstepm, nhstepm;	int hstepm, nhstepm;
double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;	double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;

double bage, fage, age, agelim, agebase;	double bage, fage, age, agelim, agebase;
double ftolpl=FTOL;	double ftolpl=FTOL;
Line 2455 int main(int argc, char *argv[])	Line 3082 int main(int argc, char *argv[])
double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;	double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;


char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";
char *alph[]={"a","a","b","c","d","e"}, str[4];	char *alph[]={"a","a","b","c","d","e"}, str[4];


Line 2468 int main(int argc, char *argv[])	Line 3094 int main(int argc, char *argv[])
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);

printf("\n%s",version);	printf("\n%s",version);
if(argc <=1){	if(argc <=1){
Line 2490 int main(int argc, char *argv[])	Line 3116 int main(int argc, char *argv[])

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

	/* Log file */
	strcat(filelog, optionfilefiname);
	strcat(filelog,".log"); /* */
	if((ficlog=fopen(filelog,"w"))==NULL) {
	printf("Problem with logfile %s\n",filelog);
	goto end;
	}
	fprintf(ficlog,"Log filename:%s\n",filelog);
	fprintf(ficlog,"\n%s",version);
	fprintf(ficlog,"\nEnter the parameter file name: ");
	fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
	fflush(ficlog);

	/* */
strcpy(fileres,"r");	strcpy(fileres,"r");
strcat(fileres, optionfilefiname);	strcat(fileres, optionfilefiname);
strcat(fileres,".txt"); /* Other files have txt extension */	strcat(fileres,".txt"); /* Other files have txt extension */
Line 2498 int main(int argc, char *argv[])	Line 3138 int main(int argc, char *argv[])

if((ficpar=fopen(optionfile,"r"))==NULL) {	if((ficpar=fopen(optionfile,"r"))==NULL) {
printf("Problem with optionfile %s\n",optionfile);	printf("Problem with optionfile %s\n",optionfile);
	fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
goto end;	goto end;
}	}

strcpy(filereso,"o");	strcpy(filereso,"o");
strcat(filereso,fileres);	strcat(filereso,fileres);
if((ficparo=fopen(filereso,"w"))==NULL) {	if((ficparo=fopen(filereso,"w"))==NULL) {
printf("Problem with Output resultfile: %s\n", filereso);goto end;	printf("Problem with Output resultfile: %s\n", filereso);
	fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
	goto end;
}	}

/* Reads comments: lines beginning with '#' */	/* Reads comments: lines beginning with '#' */
Line 2516 int main(int argc, char *argv[])	Line 3159 int main(int argc, char *argv[])
}	}
ungetc(c,ficpar);	ungetc(c,ficpar);

fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &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 ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, 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 ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,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);
Line 2550 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3193 while((c=getc(ficpar))=='#' && c!= EOF){
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);
printf("%1d%1d",i,j);	if(mle==1)
	printf("%1d%1d",i,j);
	fprintf(ficlog,"%1d%1d",i,j);
for(k=1; k<=ncovmodel;k++){	for(k=1; k<=ncovmodel;k++){
fscanf(ficpar," %lf",&param[i][j][k]);	fscanf(ficpar," %lf",&param[i][j][k]);
printf(" %lf",param[i][j][k]);	if(mle==1){
	printf(" %lf",param[i][j][k]);
	fprintf(ficlog," %lf",param[i][j][k]);
	}
	else
	fprintf(ficlog," %lf",param[i][j][k]);
fprintf(ficparo," %lf",param[i][j][k]);	fprintf(ficparo," %lf",param[i][j][k]);
}	}
fscanf(ficpar,"\n");	fscanf(ficpar,"\n");
printf("\n");	if(mle==1)
	printf("\n");
	fprintf(ficlog,"\n");
fprintf(ficparo,"\n");	fprintf(ficparo,"\n");
}	}

Line 2605 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3257 while((c=getc(ficpar))=='#' && c!= EOF){
matcov=matrix(1,npar,1,npar);	matcov=matrix(1,npar,1,npar);
for(i=1; i <=npar; i++){	for(i=1; i <=npar; i++){
fscanf(ficpar,"%s",&str);	fscanf(ficpar,"%s",&str);
printf("%s",str);	if(mle==1)
	printf("%s",str);
	fprintf(ficlog,"%s",str);
fprintf(ficparo,"%s",str);	fprintf(ficparo,"%s",str);
for(j=1; j <=i; j++){	for(j=1; j <=i; j++){
fscanf(ficpar," %le",&matcov[i][j]);	fscanf(ficpar," %le",&matcov[i][j]);
printf(" %.5le",matcov[i][j]);	if(mle==1){
	printf(" %.5le",matcov[i][j]);
	fprintf(ficlog," %.5le",matcov[i][j]);
	}
	else
	fprintf(ficlog," %.5le",matcov[i][j]);
fprintf(ficparo," %.5le",matcov[i][j]);	fprintf(ficparo," %.5le",matcov[i][j]);
}	}
fscanf(ficpar,"\n");	fscanf(ficpar,"\n");
printf("\n");	if(mle==1)
	printf("\n");
	fprintf(ficlog,"\n");
fprintf(ficparo,"\n");	fprintf(ficparo,"\n");
}	}
for(i=1; i <=npar; i++)	for(i=1; i <=npar; i++)
for(j=i+1;j<=npar;j++)	for(j=i+1;j<=npar;j++)
matcov[i][j]=matcov[j][i];	matcov[i][j]=matcov[j][i];

printf("\n");	if(mle==1)
	printf("\n");
	fprintf(ficlog,"\n");


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

	/-------- 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;
}	}

n= lastobs;	n= lastobs;
Line 2670 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3340 while((c=getc(ficpar))=='#' && c!= EOF){
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=ncov;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);
Line 2689 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3359 while((c=getc(ficpar))=='#' && c!= EOF){
if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;	if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;	if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;	if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
}	}*/
	/* for (i=1; i<=imx; i++){
for (i=1; i<=imx; i++)	if (s[4][i]==9) s[4][i]=-1;
if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i]));*/	printf("%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]));}*/


/* Calculation of the number of parameter from char model*/	/* Calculation of the number of parameter from char model*/
Tvar=ivector(1,15);	Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
Tprod=ivector(1,15);	Tprod=ivector(1,15);
Tvaraff=ivector(1,15);	Tvaraff=ivector(1,15);
Tvard=imatrix(1,15,1,2);	Tvard=imatrix(1,15,1,2);
Line 2708 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3379 while((c=getc(ficpar))=='#' && c!= EOF){
cptcovn=j+1;	cptcovn=j+1;
cptcovprod=j1;	cptcovprod=j1;


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

for(i=(j+1); i>=1;i--){	for(i=(j+1); i>=1;i--){
cutv(stra,strb,modelsav,'+');	cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */
if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);	if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze 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,'*')) {	if (strchr(strb,'')) { / Model includes a product */
cutv(strd,strc,strb,'*');	cutv(strd,strc,strb,''); / strdstrc VmVn (if not age)/
if (strcmp(strc,"age")==0) {	if (strcmp(strc,"age")==0) { /* Vnage /
cptcovprod--;	cptcovprod--;
cutv(strb,stre,strd,'V');	cutv(strb,stre,strd,'V');
Tvar[i]=atoi(stre);	Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
cptcovage++;	cptcovage++;
Tage[cptcovage]=i;	Tage[cptcovage]=i;
/printf("stre=%s ", stre);/	/printf("stre=%s ", stre);/
}	}
else if (strcmp(strd,"age")==0) {	else if (strcmp(strd,"age")==0) { /* or ageVn /
cptcovprod--;	cptcovprod--;
cutv(strb,stre,strc,'V');	cutv(strb,stre,strc,'V');
Tvar[i]=atoi(stre);	Tvar[i]=atoi(stre);
cptcovage++;	cptcovage++;
Tage[cptcovage]=i;	Tage[cptcovage]=i;
}	}
else {	else { /* Age is not in the model */
cutv(strb,stre,strc,'V');	cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
Tvar[i]=ncov+k1;	Tvar[i]=ncovcol+k1;
cutv(strb,strc,strd,'V');	cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
Tprod[k1]=i;	Tprod[k1]=i;
Tvard[k1][1]=atoi(strc);	Tvard[k1][1]=atoi(strc); /* m*/
Tvard[k1][2]=atoi(stre);	Tvard[k1][2]=atoi(stre); /* n */
Tvar[cptcovn+k2]=Tvard[k1][1];	Tvar[cptcovn+k2]=Tvard[k1][1];
Tvar[cptcovn+k2+1]=Tvard[k1][2];	Tvar[cptcovn+k2+1]=Tvard[k1][2];
for (k=1; k<=lastobs;k++)	for (k=1; k<=lastobs;k++)
covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];	covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
k1++;	k1++;
k2=k2+2;	k2=k2+2;
}	}
}	}
else {	else { /* no more sum */
/printf("d=%s c=%s b=%s\n", strd,strc,strb);/	/printf("d=%s c=%s b=%s\n", strd,strc,strb);/
/* scanf("%d",i);*/	/* scanf("%d",i);*/
cutv(strd,strc,strb,'V');	cutv(strd,strc,strb,'V');
Line 2761 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3432 while((c=getc(ficpar))=='#' && c!= EOF){
strcpy(modelsav,stra);	strcpy(modelsav,stra);
/*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);	/*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
scanf("%d",i);*/	scanf("%d",i);*/
}	} /* end of loop + */
}	} /* end model */

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

Line 2776 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3448 while((c=getc(ficpar))=='#' && c!= EOF){
/-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;
	}
	}

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];
else {	/if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;/
	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);
agev[m][i]=-1;	agev[m][i]=-1;
}	}
}	}
Line 2826 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3503 while((c=getc(ficpar))=='#' && c!= EOF){
for (i=1; i<=imx; i++) {	for (i=1; i<=imx; i++) {
for(m=1; (m<= maxwav); m++){	for(m=1; (m<= maxwav); m++){
if (s[m][i] > (nlstate+ndeath)) {	if (s[m][i] > (nlstate+ndeath)) {
printf("Error: Wrong value in nlstate or ndeath\n");	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;	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);

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);
Line 2866 printf("Total number of individuals= %d,	Line 3545 printf("Total number of individuals= %d,
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;	if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
	/* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
}	}
}	}
}	}
}	}
	/* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
	codtab[1][2]=1;codtab[2][2]=2; */
/*for(i=1; i <=m ;i++){	/* for(i=1; i <=m ;i++){
for(k=1; k <=cptcovn; k++){	for(k=1; k <=cptcovn; k++){
printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);	printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
}	}
printf("\n");	printf("\n");
}	}
scanf("%d",i);*/	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'. */
Line 2901 printf("Total number of individuals= %d,	Line 3581 printf("Total number of individuals= %d,
}	}

/--------- results files --------------/	/--------- results files --------------/
fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,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\n");	fprintf(ficres,"# Parameters nlstatenlstatencov a121 + b12 age + ...\n");
printf("# Parameters\n");	printf("# 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(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(ficres,"%f ",p[jk]);	fprintf(ficres,"%f ",p[jk]);
jk++;	jk++;
}	}
printf("\n");	printf("\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\n");	fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
printf("# Scales\n");	printf("# Scales (for hessian or gradient estimation)\n");
for(i=1,jk=1; i <=nlstate; i++){	fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
for(j=1; j <=nlstate+ndeath; j++){	for(i=1,jk=1; i <=nlstate; i++){
if (j!=i) {	for(j=1; j <=nlstate+ndeath; j++){
fprintf(ficres,"%1d%1d",i,j);	if (j!=i) {
printf("%1d%1d",i,j);	fprintf(ficres,"%1d%1d",i,j);
for(k=1; k<=ncovmodel;k++){	printf("%1d%1d",i,j);
printf(" %.5e",delti[jk]);	fprintf(ficlog,"%1d%1d",i,j);
fprintf(ficres," %.5e",delti[jk]);	for(k=1; k<=ncovmodel;k++){
jk++;	printf(" %.5e",delti[jk]);
}	fprintf(ficlog," %.5e",delti[jk]);
printf("\n");	fprintf(ficres," %.5e",delti[jk]);
fprintf(ficres,"\n");	jk++;
}	}
}	printf("\n");
	fprintf(ficlog,"\n");
	fprintf(ficres,"\n");
	}
}	}
	}
k=1;
fprintf(ficres,"# Covariance\n");	k=1;
printf("# Covariance\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");
for(i=1;i<=npar;i++){	if(mle==1)
/* if (k>nlstate) k=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");
i1=(i-1)/(ncovmodel*nlstate)+1;	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(ficres,"%s%d%d",alph[k],i1,tab[i]);	for(i=1;i<=npar;i++){
printf("%s%d%d",alph[k],i1,tab[i]);*/	/* if (k>nlstate) k=1;
fprintf(ficres,"%3d",i);	i1=(i-1)/(ncovmodel*nlstate)+1;
printf("%3d",i);	fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
for(j=1; j<=i;j++){	printf("%s%d%d",alph[k],i1,tab[i]);*/
fprintf(ficres," %.5e",matcov[i][j]);	fprintf(ficres,"%3d",i);
printf(" %.5e",matcov[i][j]);	if(mle==1)
}	printf("%3d",i);
fprintf(ficres,"\n");	fprintf(ficlog,"%3d",i);
printf("\n");	for(j=1; j<=i;j++){
k++;	fprintf(ficres," %.5e",matcov[i][j]);
}	if(mle==1)
	printf(" %.5e",matcov[i][j]);
while((c=getc(ficpar))=='#' && c!= EOF){	fprintf(ficlog," %.5e",matcov[i][j]);
ungetc(c,ficpar);	}
fgets(line, MAXLINE, ficpar);	fprintf(ficres,"\n");
puts(line);	if(mle==1)
fputs(line,ficparo);	printf("\n");
}	fprintf(ficlog,"\n");
ungetc(c,ficpar);	k++;
	}

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

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

	while((c=getc(ficpar))=='#' && c!= EOF){
	ungetc(c,ficpar);
	fgets(line, MAXLINE, ficpar);
	puts(line);
	fputs(line,ficparo);
	}
	ungetc(c,ficpar);

fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);	fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);
	fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
if (fage <= 2) {	fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
bage = agemin;
fage = agemax;	while((c=getc(ficpar))=='#' && c!= EOF){
}	ungetc(c,ficpar);
	fgets(line, MAXLINE, ficpar);
fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");	puts(line);
fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);	fputs(line,ficparo);
fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);	}
	ungetc(c,ficpar);

while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);	dateprev1=anprev1+mprev1/12.+jprev1/365.;
fgets(line, MAXLINE, ficpar);	dateprev2=anprev2+mprev2/12.+jprev2/365.;
puts(line);
fputs(line,ficparo);	fscanf(ficpar,"pop_based=%d\n",&popbased);
}	fprintf(ficparo,"pop_based=%d\n",popbased);
ungetc(c,ficpar);	fprintf(ficres,"pop_based=%d\n",popbased);

fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);
fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);

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);
Line 3003 printf("Total number of individuals= %d,	Line 3715 printf("Total number of individuals= %d,
fputs(line,ficparo);	fputs(line,ficparo);
}	}
ungetc(c,ficpar);	ungetc(c,ficpar);


dateprev1=anprev1+mprev1/12.+jprev1/365.;	fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);
dateprev2=anprev2+mprev2/12.+jprev2/365.;	fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);
	fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);

fscanf(ficpar,"pop_based=%d\n",&popbased);
fprintf(ficparo,"pop_based=%d\n",popbased);
fprintf(ficres,"pop_based=%d\n",popbased);

while((c=getc(ficpar))=='#' && c!= EOF){	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,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);
fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);	fscanf(ficpar,"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 starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);	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);

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,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);

/------------ gnuplot -------------/	/------------ gnuplot -------------/
printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemax,fage, pathc,p);	strcpy(optionfilegnuplot,optionfilefiname);
	strcat(optionfilegnuplot,".gp");
	if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
	printf("Problem with file %s",optionfilegnuplot);
	}
	fclose(ficgp);
	printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
	/--------- index.htm --------/

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

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

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

/------------ free_vector -------------/	/------------ free_vector -------------/
chdir(path);	chdir(path);
Line 3039 fprintf(ficres,"popforecast=%d popfile=%	Line 3776 fprintf(ficres,"popforecast=%d popfile=%
/free_matrix(covar,1,NCOVMAX,1,n);/	/free_matrix(covar,1,NCOVMAX,1,n);/
fclose(ficparo);	fclose(ficparo);
fclose(ficres);	fclose(ficres);

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

fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);
printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);
fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);
/--------- index.htm --------/

printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm);


/--------------- Prevalence limit --------------/	/--------------- Prevalence limit --------------/

strcpy(filerespl,"pl");	strcpy(filerespl,"pl");
strcat(filerespl,fileres);	strcat(filerespl,fileres);
if((ficrespl=fopen(filerespl,"w"))==NULL) {	if((ficrespl=fopen(filerespl,"w"))==NULL) {
printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;	printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;
	fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;
}	}
printf("Computing prevalence limit: result on file '%s' \n", filerespl);	printf("Computing prevalence limit: result on file '%s' \n", filerespl);
	fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);
fprintf(ficrespl,"#Prevalence limit\n");	fprintf(ficrespl,"#Prevalence limit\n");
fprintf(ficrespl,"#Age ");	fprintf(ficrespl,"#Age ");
for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);	for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
Line 3077 fprintf(ficres,"popforecast=%d popfile=%	Line 3800 fprintf(ficres,"popforecast=%d popfile=%
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 */
k=0;	k=0;
agebase=agemin;	agebase=ageminpar;
agelim=agemax;	agelim=agemaxpar;
ftolpl=1.e-10;	ftolpl=1.e-10;
i1=cptcoveff;	i1=cptcoveff;
if (cptcovn < 1){i1=1;}	if (cptcovn < 1){i1=1;}
Line 3088 fprintf(ficres,"popforecast=%d popfile=%	Line 3811 fprintf(ficres,"popforecast=%d popfile=%
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#******");
for(j=1;j<=cptcoveff;j++)	printf("\n#******");
	fprintf(ficlog,"\n#******");
	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]]);
	fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
	}
fprintf(ficrespl,"******\n");	fprintf(ficrespl,"******\n");
	printf("******\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);
Line 3108 fprintf(ficres,"popforecast=%d popfile=%	Line 3838 fprintf(ficres,"popforecast=%d popfile=%
strcpy(filerespij,"pij"); strcat(filerespij,fileres);	strcpy(filerespij,"pij"); strcat(filerespij,fileres);
if((ficrespij=fopen(filerespij,"w"))==NULL) {	if((ficrespij=fopen(filerespij,"w"))==NULL) {
printf("Problem with Pij resultfile: %s\n", filerespij);goto end;	printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
	fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
}	}
printf("Computing pij: result on file '%s' \n", filerespij);	printf("Computing pij: result on file '%s' \n", filerespij);
	fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);

stepsize=(int) (stepm+YEARM-1)/YEARM;	stepsize=(int) (stepm+YEARM-1)/YEARM;
/if (stepm<=24) stepsize=2;/	/if (stepm<=24) stepsize=2;/
Line 3117 fprintf(ficres,"popforecast=%d popfile=%	Line 3849 fprintf(ficres,"popforecast=%d popfile=%
agelim=AGESUP;	agelim=AGESUP;
hstepm=stepsizeYEARM; / Every year of age */	hstepm=stepsizeYEARM; / Every year of age */
hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */	hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */

	/* hstepm=1; aff par mois*/

k=0;	k=0;
for(cptcov=1;cptcov<=i1;cptcov++){	for(cptcov=1;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){	for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
Line 3130 fprintf(ficres,"popforecast=%d popfile=%	Line 3864 fprintf(ficres,"popforecast=%d popfile=%
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/

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);
Line 3138 fprintf(ficres,"popforecast=%d popfile=%	Line 3875 fprintf(ficres,"popforecast=%d popfile=%
for(j=1; j<=nlstate+ndeath;j++)	for(j=1; j<=nlstate+ndeath;j++)
fprintf(ficrespij," %1d-%1d",i,j);	fprintf(ficrespij," %1d-%1d",i,j);
fprintf(ficrespij,"\n");	fprintf(ficrespij,"\n");
for (h=0; h<=nhstepm; h++){	for (h=0; h<=nhstepm; h++){
fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ hhstepm/YEARMstepm );	fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ hhstepm/YEARMstepm );
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate+ndeath;j++)	for(j=1; j<=nlstate+ndeath;j++)
fprintf(ficrespij," %.5f", p3mat[i][j][h]);	fprintf(ficrespij," %.5f", p3mat[i][j][h]);
fprintf(ficrespij,"\n");	fprintf(ficrespij,"\n");
}	}
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
fprintf(ficrespij,"\n");	fprintf(ficrespij,"\n");
}	}
}	}
}	}

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

fclose(ficrespij);	fclose(ficrespij);


/---------- Forecasting ------------------/	/---------- Forecasting ------------------/
if(stepm == 1) {	if((stepm == 1) && (strcmp(model,".")==0)){
prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);	prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
populforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);	if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
free_matrix(mint,1,maxwav,1,n);	}
free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);
free_vector(weight,1,n);}
else{	else{
erreur=108;	erreur=108;
printf("Error %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);	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 3175 populforecast(fileres, anproj1,mproj1,jp	Line 3911 populforecast(fileres, anproj1,mproj1,jp
strcat(filerest,fileres);	strcat(filerest,fileres);
if((ficrest=fopen(filerest,"w"))==NULL) {	if((ficrest=fopen(filerest,"w"))==NULL) {
printf("Problem with total LE resultfile: %s\n", filerest);goto end;	printf("Problem with total LE resultfile: %s\n", filerest);goto end;
	fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
}	}
printf("Computing Total LEs with variances: file '%s' \n", filerest);	printf("Computing Total LEs with variances: file '%s' \n", filerest);
	fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);


strcpy(filerese,"e");	strcpy(filerese,"e");
strcat(filerese,fileres);	strcat(filerese,fileres);
if((ficreseij=fopen(filerese,"w"))==NULL) {	if((ficreseij=fopen(filerese,"w"))==NULL) {
printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);	printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
	fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
}	}
printf("Computing Health Expectancies: result on file '%s' \n", filerese);	printf("Computing Health Expectancies: result on file '%s' \n", filerese);
	fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);

strcpy(fileresv,"v");	strcpy(fileresv,"v");
strcat(fileresv,fileres);	strcat(fileresv,fileres);
if((ficresvij=fopen(fileresv,"w"))==NULL) {	if((ficresvij=fopen(fileresv,"w"))==NULL) {
printf("Problem with variance resultfile: %s\n", fileresv);exit(0);	printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
	fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
}	}
printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);	printf("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);

k=0;	k=0;
for(cptcov=1;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#****** ");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
Line 3204 populforecast(fileres, anproj1,mproj1,jp	Line 3948 populforecast(fileres, anproj1,mproj1,jp

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

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

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

vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);	vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
oldm=oldms;savm=savms;	oldm=oldms;savm=savms;
varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);	varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0);
	if(popbased==1){
	varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);
	}


fprintf(ficrest,"#Total LEs with variances: e.. (std) ");	fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);	for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
fprintf(ficrest,"\n");	fprintf(ficrest,"\n");

hf=1;
if (stepm >= YEARM) hf=stepm/YEARM;
epj=vector(1,nlstate+1);	epj=vector(1,nlstate+1);
for(age=bage; age <=fage ;age++){	for(age=bage; age <=fage ;age++){
prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);	prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
Line 3235 populforecast(fileres, anproj1,mproj1,jp	Line 3980 populforecast(fileres, anproj1,mproj1,jp
prlim[i][i]=probs[(int)age][i][k];	prlim[i][i]=probs[(int)age][i][k];
}	}

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

for(i=1, vepp=0.;i <=nlstate;i++)	for(i=1, vepp=0.;i <=nlstate;i++)
for(j=1;j <=nlstate;j++)	for(j=1;j <=nlstate;j++)
vepp += vareij[i][j][(int)age];	vepp += vareij[i][j][(int)age];
fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));	fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
for(j=1;j <=nlstate;j++){	for(j=1;j <=nlstate;j++){
fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));	fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
}	}
fprintf(ficrest,"\n");	fprintf(ficrest,"\n");
}	}
}	}
}	}
	free_matrix(mint,1,maxwav,1,n);
	free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);
	free_vector(weight,1,n);
fclose(ficreseij);	fclose(ficreseij);
fclose(ficresvij);	fclose(ficresvij);
fclose(ficrest);	fclose(ficrest);
Line 3304 populforecast(fileres, anproj1,mproj1,jp	Line 4053 populforecast(fileres, anproj1,mproj1,jp
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(erreur >0)	fprintf(fichtm,"\n</body>");
printf("End of Imach with error %d\n",erreur);	fclose(fichtm);
else printf("End of Imach\n");	fclose(ficgp);


	if(erreur >0){
	printf("End of Imach with error or warning %d\n",erreur);
	fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
	}else{
	printf("End of Imach\n");
	fprintf(ficlog,"End of Imach\n");
	}
	printf("See log file on %s\n",filelog);
	fclose(ficlog);
/* gettimeofday(&end_time, (struct timezone)0);/ /* after time */	/* gettimeofday(&end_time, (struct timezone)0);/ /* after time */

/* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/	/* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/
Line 3329 populforecast(fileres, anproj1,mproj1,jp	Line 4089 populforecast(fileres, anproj1,mproj1,jp

#ifdef windows	#ifdef windows
while (z[0] != 'q') {	while (z[0] != 'q') {
chdir(path);	/* chdir(path); */
printf("\nType e to edit output files, c to start again, and q for exiting: ");	printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
scanf("%s",z);	scanf("%s",z);
if (z[0] == 'c') system("./imach");	if (z[0] == 'c') system("./imach");
else if (z[0] == 'e') {	else if (z[0] == 'e') system(optionfilehtm);
chdir(path);	else if (z[0] == 'g') system(plotcmd);
system(optionfilehtm);
}
else if (z[0] == 'q') exit(0);	else if (z[0] == 'q') exit(0);
}	}
#endif	#endif

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Removed from v.1.27
changed lines
	Added in v.1.50