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Diff for /imach/src/imach.c between versions 1.27 and 1.45

version 1.27, 2002/02/28 17:49:07	version 1.45, 2002/05/24 16:34:18
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 82 int cptcovn, cptcovage=0, cptcoveff=0,cp	Line 83 int cptcovn, cptcovage=0, cptcoveff=0,cp
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 135 int imx;	Line 136 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 686 double prevalim(double prlim, int nl	Line 690 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 1178 void lubksb(double *a, int n, int indx	Line 1181 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;
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");
Line 1196 void freqsummary(char fileres[], int ag	Line 1199 void freqsummary(char fileres[], int ag
}	}
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++){	for(k1=1; k1<=j;k1++){
for(i1=1; i1<=ncodemax[k1];i1++){	for(i1=1; i1<=ncodemax[k1];i1++){
j1++;	j1++;
/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);	/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
scanf("%d", i);*/	scanf("%d", i);*/
for (i=-1; i<=nlstate+ndeath; i++)	for (i=-1; i<=nlstate+ndeath; i++)
for (jk=-1; jk<=nlstate+ndeath; jk++)	for (jk=-1; jk<=nlstate+ndeath; jk++)
for(m=agemin; m <= agemax+3; m++)	for(m=agemin; m <= agemax+3; m++)
freq[i][jk][m]=0;	freq[i][jk][m]=0;

dateintsum=0;	dateintsum=0;
k2cpt=0;	k2cpt=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]] += weight[i];	if (m<lastpass) {
freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];	freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {	freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
dateintsum=dateintsum+k2;	}
k2cpt++;
}	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");	printf("Total");
else	else
printf("Age %d", i);	printf("Age %d", 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];
if(pp[jk]>=1.e-10)	if(pp[jk]>=1.e-10)
printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);	printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
else	else
printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);	printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
}	}

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++)	for(jk=1,pos=0; jk <=nlstate ; jk++)
pos += pp[jk];	pos += pp[jk];
for(jk=1; jk <=nlstate ; jk++){	for(jk=1; jk <=nlstate ; jk++){
if(pos>=1.e-5)	if(pos>=1.e-5)
printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);	printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
else	else
printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);	printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
if( i <= (int) agemax){	if( i <= (int) agemax){
if(pos>=1.e-5){	if(pos>=1.e-5){
fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);	fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
probs[i][jk][j1]= pp[jk]/pos;	probs[i][jk][j1]= pp[jk]/pos;
/printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);/	/printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);/
	}
	else
	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 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
	if(i <= (int) agemax)
	fprintf(ficresp,"\n");
	printf("\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 1330 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,pos=0; jk <=nlstate ; jk++) pos += pp[jk];

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

}	}

	}
}	}
}	}


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 1444 void concatwav(int wav[], int **dh, int	Line 1454 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 1462 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 1498 void tricode(int Tvar, int *nbcode, in	Line 1508 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 1514 void tricode(int Tvar, int *nbcode, in	Line 1525 void tricode(int Tvar, int *nbcode, in

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++;
}	}
Line 1525 void tricode(int Tvar, int *nbcode, in	Line 1536 void tricode(int Tvar, int *nbcode, in

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

void evsij(char fileres[], double *eij, double x[], int nlstate, int stepm, int bage, int fage, double oldm, double **savm, int ij)	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);
	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);
}	}
	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 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, int estepm)
{	{
/* 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;	int i, j, nhstepm, hstepm, h, nstepm ;
int k, cptcode;	int k, cptcode;
double *xp;	double *xp;
double gp, gm;	double gp, gm;
double *gradg, *trgradg;	double *gradg, *trgradg;
double ***p3mat;	double ***p3mat;
double age,agelim;	double age,agelim, hf;
int theta;	int theta;

fprintf(ficresvij,"# Covariances of life expectancies\n");	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 1600 void varevsij(char fileres[], double ***	Line 1735 void varevsij(char fileres[], double ***
dnewm=matrix(1,nlstate,1,npar);	dnewm=matrix(1,nlstate,1,npar);
doldm=matrix(1,nlstate,1,nlstate);	doldm=matrix(1,nlstate,1,nlstate);

hstepm=1YEARM; / Every year of age */	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;
	/* 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);
Line 1661 void varevsij(char fileres[], double ***	Line 1810 void varevsij(char fileres[], double ***
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];

	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;
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 1709 void varprevlim(char fileres[], double *	Line 1859 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 1928 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 fileres[], 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, i1, k1, j1, z1;
int k=0, cptcode;	int k=0, cptcode;
double dnewm,doldm;	double dnewm,doldm;
double *xp;	double *xp;
Line 1795 void varprob(char fileres[], double **ma	Line 1945 void varprob(char fileres[], double **ma
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);
}	}
printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);	printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);

	fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");
	fprintf(ficresprob,"# Age");
	for(i=1; i<=nlstate;i++)
	for(j=1; j<=(nlstate+ndeath);j++)
	fprintf(ficresprob," p%1d-%1d (SE)",i,j);


	fprintf(ficresprob,"\n");


xp=vector(1,npar);	xp=vector(1,npar);
dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);	dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
doldm=matrix(1,(nlstate+ndeath)(nlstate+ndeath),1,(nlstate+ndeath)(nlstate+ndeath));	doldm=matrix(1,(nlstate+ndeath)(nlstate+ndeath),1,(nlstate+ndeath)(nlstate+ndeath));

cov[1]=1;	cov[1]=1;
for (age=bage; age<=fage; age ++){	j=cptcoveff;
cov[2]=age;	if (cptcovn<1) {j=1;ncodemax[1]=1;}
gradg=matrix(1,npar,1,9);	j1=0;
trgradg=matrix(1,9,1,npar);	for(k1=1; k1<=1;k1++){
gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));	for(i1=1; i1<=ncodemax[k1];i1++){
gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));	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#");
	}

for(theta=1; theta <=npar; theta++){	for (age=bage; age<=fage; age ++){
for(i=1; i<=npar; i++)	cov[2]=age;
xp[i] = x[i] + (i==theta ?delti[theta]:0);	for (k=1; k<=cptcovn;k++) {
	cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
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;
gp[k]=pmmij[i][j];
}	}
}	for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
	for (k=1; k<=cptcovprod;k++)
for(i=1; i<=npar; i++)	cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
xp[i] = x[i] - (i==theta ?delti[theta]:0);
	gradg=matrix(1,npar,1,9);
	trgradg=matrix(1,9,1,npar);
	gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));
	gm=vector(1,(nlstate+ndeath)*(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+ndeath); 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);
pmij(pmmij,cov,ncovmodel,xp,nlstate);	k=0;
k=0;	for(i=1; i<=(nlstate+ndeath); i++){
for(i=1; i<=(nlstate+ndeath); i++){	for(j=1; j<=(nlstate+ndeath);j++){
for(j=1; j<=(nlstate+ndeath);j++){	k=k+1;
k=k+1;	gm[k]=pmmij[i][j];
gm[k]=pmmij[i][j];	}
}	}
}

for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)	for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)
gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];	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);
matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);

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

k=0;	for(j=1; j<=(nlstate+ndeath)*(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,1,9,1,npar,1,npar,matcov);
	matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);

	pmij(pmmij,cov,ncovmodel,x,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];
	}
}	}
}

/*printf("\n%d ",(int)age);	/*printf("\n%d ",(int)age);
for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){	for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);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(ficresprob,"\n%d ",(int)age);	fprintf(ficresprob,"\n%d ",(int)age);

for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){
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+ndeath)*(nlstate+ndeath-1);i++)
	fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));

	}
	}
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(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);

}	}
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 optionfile[], \
	char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\
	char version[], 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;	FILE *fichtm;
/char optionfilehtm[FILENAMELENGTH];/	/char optionfilehtm[FILENAMELENGTH];/
Line 1894 void printinghtml(char fileres[], char t	Line 2078 void printinghtml(char fileres[], char t
printf("Problem with %s \n",optionfilehtm), exit(0);	printf("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,"<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>	Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
	\n
Total number of observations=%d <br>	Total number of observations=%d <br>\n
Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>	Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
<hr size=\"2\" color=\"#EC5E5E\">	<hr size=\"2\" color=\"#EC5E5E\">
<li>Outputs files<br><br>\n	<ul><li>Parameter files<br>\n
- Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n	- Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
- Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>	- Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);
- Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>
- Transition probabilities: <a href=\"pij%s\">pij%s</a><br>	fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n
- Copy of the parameter file: <a href=\"o%s\">o%s</a><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
- Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>	- Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
- Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>	- Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
- Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>	- Life expectancies by age and initial health status (estepm=%2d months):
- Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>	<a href=\"e%s\">e%s</a> <br>\n</li>", \
- Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>	jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
<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,"\n<li> Result files (second order: variances)<br>\n
	- Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
	- Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
	- 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, 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," <li>Graphs</li><p>");	fprintf(fichtm," <li>Graphs</li><p>");

m=cptcoveff;	m=cptcoveff;
Line 1921 fprintf(fichtm," <li>Graphs</li><p>");	Line 2117 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++) {	for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident	fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident
interval) in state (%d): v%s%d%d.gif <br>	interval) in state (%d): v%s%d%d.png <br>
<img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);	<img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
}	}
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>");	fprintf(fichtm,"\n</body>");
}	}
}	}
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[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], 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);	strcpy(optionfilegnuplot,optionfilefiname);
strcat(optionfilegnuplot,".plt");	strcat(optionfilegnuplot,".gp.txt");
if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {	if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
printf("Problem with file %s",optionfilegnuplot);	printf("Problem with file %s",optionfilegnuplot);
}	}
Line 1973 m=pow(2,cptcoveff);	Line 2174 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 2198 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 2231 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 2273 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 2077 fprintf(ficgp,"\nset out \"v%s%d%d.gif\"	Line 2288 fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
}	}
}	}
}	}
}	}

for(jk=1; jk <=m; jk++) {	for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot [%.f:%.f] ",agemin,agemax);	for(jk=1; jk <=m; jk++) {
i=1;	fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);
for(k2=1; k2<=nlstate; k2++) {	if (ng==2)
k3=i;	fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
for(k=1; k<=(nlstate+ndeath); k++) {	else
if (k != k2){	fprintf(ficgp,"\nset title \"Probability\"\n");
fprintf(ficgp," exp(p%d+p%d*x",i,i+1);	fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
ij=1;	i=1;
for(j=3; j <=ncovmodel; j++) {	for(k2=1; k2<=nlstate; k2++) {
if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {	k3=i;
fprintf(ficgp,"+p%d%dx",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);	for(k=1; k<=(nlstate+ndeath); k++) {
ij++;	if (k != k2){
}	if(ng==2)
else	fprintf(ficgp," %fexp(p%d+p%dx",stepm/YEARM,i,i+1);
fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);	else
}	fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
fprintf(ficgp,")/(1");	ij=1;
	for(j=3; j <=ncovmodel; j++) {
for(k1=1; k1 <=nlstate; k1++){	if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
fprintf(ficgp,"+exp(p%d+p%dx",k3+(k1-1)ncovmodel,k3+(k1-1)*ncovmodel+1);	fprintf(ficgp,"+p%d%dx",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
ij=1;	ij++;
for(j=3; j <=ncovmodel; j++){	}
if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {	else
fprintf(ficgp,"+p%d%dx",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);	fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
ij++;	}
}	fprintf(ficgp,")/(1");
else
fprintf(ficgp,"+p%d%d",k3+(k1-1)ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);	for(k1=1; k1 <=nlstate; k1++){
}	fprintf(ficgp,"+exp(p%d+p%dx",k3+(k1-1)ncovmodel,k3+(k1-1)*ncovmodel+1);
fprintf(ficgp,")");	ij=1;
}	for(j=3; j <=ncovmodel; j++){
fprintf(ficgp,") t \"p%d%d\" ", k2,k);	if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");	fprintf(ficgp,"+p%d%dx",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
i=i+ncovmodel;	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);	fclose(ficgp);
}

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 2367 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 2378 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);
Line 2174 calagedate=(anproj1+mproj1/12.+jproj1/36	Line 2393 calagedate=(anproj1+mproj1/12.+jproj1/36

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 2429 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 2440 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 2469 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 2478 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) {
Line 2278 calagedate=(anproj1+mproj1/12.+jproj1/36	Line 2497 calagedate=(anproj1+mproj1/12.+jproj1/36

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 2312 calagedate=(anproj1+mproj1/12.+jproj1/36	Line 2531 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 2548 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 2568 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 2582 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 2593 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 2630 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 2423 int main(int argc, char *argv[])	Line 2643 int main(int argc, char *argv[])
char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];	char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];	char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];

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

char filerest[FILENAMELENGTH];	char filerest[FILENAMELENGTH];
char fileregp[FILENAMELENGTH];	char fileregp[FILENAMELENGTH];
Line 2437 int main(int argc, char *argv[])	Line 2657 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 2675 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 version[80]="Imach version 0.8f, May 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 2688 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 2516 int main(int argc, char *argv[])	Line 2736 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\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d 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 2623 while((c=getc(ficpar))=='#' && c!= EOF){	Line 2843 while((c=getc(ficpar))=='#' && c!= EOF){
printf("\n");	printf("\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(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;
}	}
Line 2670 while((c=getc(ficpar))=='#' && c!= EOF){	Line 2895 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 2914 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);
Tprod=ivector(1,15);	Tprod=ivector(1,15);
Line 2708 while((c=getc(ficpar))=='#' && c!= EOF){	Line 2934 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);
Line 2739 while((c=getc(ficpar))=='#' && c!= EOF){	Line 2964 while((c=getc(ficpar))=='#' && c!= EOF){
}	}
else {	else {
cutv(strb,stre,strc,'V');	cutv(strb,stre,strc,'V');
Tvar[i]=ncov+k1;	Tvar[i]=ncovcol+k1;
cutv(strb,strc,strd,'V');	cutv(strb,strc,strd,'V');
Tprod[k1]=i;	Tprod[k1]=i;
Tvard[k1][1]=atoi(strc);	Tvard[k1][1]=atoi(strc);
Line 2747 while((c=getc(ficpar))=='#' && c!= EOF){	Line 2972 while((c=getc(ficpar))=='#' && c!= EOF){
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;
}	}
Line 2764 while((c=getc(ficpar))=='#' && c!= EOF){	Line 2989 while((c=getc(ficpar))=='#' && c!= EOF){
}	}
}	}

/*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);
scanf("%d ",i);*/	scanf("%d ",i);*/
fclose(fic);	fclose(fic);
Line 2776 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3001 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);
agev[m][i]=-1;	agev[m][i]=-1;
Line 2866 printf("Total number of individuals= %d,	Line 3095 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 3131 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");
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)
Line 2928 printf("Total number of individuals= %d,	Line 3158 printf("Total number of individuals= %d,
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++){	for(i=1,jk=1; i <=nlstate; i++){
for(j=1; j <=nlstate+ndeath; j++){	for(j=1; j <=nlstate+ndeath; j++){
if (j!=i) {	if (j!=i) {
Line 2947 printf("Total number of individuals= %d,	Line 3177 printf("Total number of individuals= %d,
}	}

k=1;	k=1;
fprintf(ficres,"# 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");
printf("# Covariance\n");	printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
for(i=1;i<=npar;i++){	for(i=1;i<=npar;i++){
/* if (k>nlstate) k=1;	/* if (k>nlstate) k=1;
i1=(i-1)/(ncovmodel*nlstate)+1;	i1=(i-1)/(ncovmodel*nlstate)+1;
Line 2972 printf("Total number of individuals= %d,	Line 3202 printf("Total number of individuals= %d,
fputs(line,ficparo);	fputs(line,ficparo);
}	}
ungetc(c,ficpar);	ungetc(c,ficpar);
	estepm=0;
fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);	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) {	if (fage <= 2) {
bage = agemin;	bage = ageminpar;
fage = agemax;	fage = agemaxpar;
}	}

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

while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);	ungetc(c,ficpar);
Line 3009 printf("Total number of individuals= %d,	Line 3239 printf("Total number of individuals= %d,
dateprev2=anprev2+mprev2/12.+jprev2/365.;	dateprev2=anprev2+mprev2/12.+jprev2/365.;

fscanf(ficpar,"pop_based=%d\n",&popbased);	fscanf(ficpar,"pop_based=%d\n",&popbased);
fprintf(ficparo,"pop_based=%d\n",popbased);	fprintf(ficparo,"pop_based=%d\n",popbased);
fprintf(ficres,"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);
Line 3019 printf("Total number of individuals= %d,	Line 3249 printf("Total number of individuals= %d,
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,"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,"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,"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);


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

	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(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);	printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);

/------------ free_vector -------------/	/------------ free_vector -------------/
chdir(path);	chdir(path);
Line 3039 fprintf(ficres,"popforecast=%d popfile=%	Line 3283 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 --------/	/--------- index.htm --------/

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


/--------------- Prevalence limit --------------/	/--------------- Prevalence limit --------------/
Line 3077 fprintf(ficres,"popforecast=%d popfile=%	Line 3309 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 3138 fprintf(ficres,"popforecast=%d popfile=%	Line 3370 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 %.0f %.0f",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(fileres, 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);
}	}


Line 3192 populforecast(fileres, anproj1,mproj1,jp	Line 3422 populforecast(fileres, anproj1,mproj1,jp
printf("Problem with variance resultfile: %s\n", fileresv);exit(0);	printf("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);
	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++){
Line 3204 populforecast(fileres, anproj1,mproj1,jp	Line 3436 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(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);



Line 3225 populforecast(fileres, anproj1,mproj1,jp	Line 3458 populforecast(fileres, anproj1,mproj1,jp
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 3466 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 3305 populforecast(fileres, anproj1,mproj1,jp	Line 3540 populforecast(fileres, anproj1,mproj1,jp
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)	if(erreur >0)
printf("End of Imach with error %d\n",erreur);	printf("End of Imach with error or warning %d\n",erreur);
else printf("End of Imach\n");	else printf("End of Imach\n");
/* gettimeofday(&end_time, (struct timezone)0);/ /* after time */	/* gettimeofday(&end_time, (struct timezone)0);/ /* after time */

Line 3329 populforecast(fileres, anproj1,mproj1,jp	Line 3564 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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	Added in v.1.45