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version 1.32, 2002/03/11 14:17:15	version 1.49, 2002/06/20 14:03:39
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 '\\'
	#else
	#define DIRSEPARATOR '/'
	#endif

	char version[80]="Imach version 0.8h, May 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 101 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 ficgp,ficresprob,ficpop, ficresprobcov, *ficresprobcor;
	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 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 153 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 178 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 defined(__bsd__) /* get current working directory */	#if defined(__bsd__) /* get current working directory */
extern char *getwd( );	extern char *getwd( );
Line 686 double prevalim(double prlim, int nl	Line 703 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 1194 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 1212 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 */
}	}

Line 1324 void prevalence(int agemin, float agemax	Line 1343 void prevalence(int agemin, float 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++)
Line 1346 void prevalence(int agemin, float agemax	Line 1365 void prevalence(int agemin, float agemax
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 1497 void tricode(int Tvar, int *nbcode, in	Line 1521 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 1513 void tricode(int Tvar, int *nbcode, in	Line 1538 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 1524 void tricode(int Tvar, int *nbcode, in	Line 1549 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, nstepm, k;	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");

k=1; /* For example stepm=6 months */	if(estepm < stepm){
hstepm=kYEARM; / (a) Every k years of age (in months), for example every k=2 years 24 m */	printf ("Problem %d lower than %d\n",estepm, stepm);
hstepm=stepm; /* or (b) We decided to compute the life expectancy with the smallest unit */	}
	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.	/* 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	nhstepm is the number of hstepm from age to agelim
nstepm is the number of stepm from age to agelin.	nstepm is the number of stepm from age to agelin.
Look at hpijx to understand the reason of that which relies in memory size	Look at hpijx to understand the reason of that which relies in memory size
and note for a fixed period like k years */	and note for a fixed period like estepm months */
/* We decided (b) to get a life expectancy respecting the most precise curvature of the	/* We decided (b) to get a life expectancy respecting the most precise curvature of the
survival function given by stepm (the optimization length). Unfortunately it	survival function given by stepm (the optimization length). Unfortunately it
means that if the survival funtion is printed only each two years of age and if	means that if the survival funtion is printed 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	you sum them up and add 1 year (area under the trapezoids) you won't get the same
results. So we changed our mind and took the option of the best precision.	results. So we changed our mind and took the option of the best precision.
*/	*/
hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */	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 */
nstepm=(int) rint((agelim-age)*YEARM/stepm);	nstepm=(int) rint((agelim-age)*YEARM/stepm);
/* Typically if 20 years nstepm = 2012/6=40 stepm /	/* Typically if 20 years nstepm = 2012/6=40 stepm /
if (stepm >= YEARM) hstepm=1;	/* if (stepm >= YEARM) hstepm=1;*/
nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */	nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
	gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
	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. */	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-1; h++){	for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;	eij[i][j][(int)age] += (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]);*/
	/* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/

}	}

fprintf(ficreseij,"%3.0f",age );	fprintf(ficreseij,"%3.0f",age );
	cptj=0;
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," %9.4f", 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");

	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 1609 void varevsij(char fileres[], double ***	Line 1744 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 1670 void varevsij(char fileres[], double ***	Line 1819 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 1718 void varprevlim(char fileres[], double *	Line 1868 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 1787 void varprevlim(char fileres[], double *	Line 1937 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;
	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);
}	}
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);
	}
	strcpy(fileresprobcor,"probcor");
	strcat(fileresprobcor,fileres);
	if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
	printf("Problem with resultfile: %s\n", fileresprobcor);
	}
	printf("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);
	printf("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);	exit(0);
gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));	}
gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));	else{
	fprintf(ficgp,"\n# Routine varprob");
for(theta=1; theta <=npar; theta++){	}
for(i=1; i<=npar; i++)	if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
xp[i] = x[i] + (i==theta ?delti[theta]:0);	printf("Problem with html file: %s\n", optionfilehtm);
	exit(0);
pmij(pmmij,cov,ncovmodel,xp,nlstate);	}
	else{
k=0;	fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
for(i=1; i<= (nlstate+ndeath); i++){	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");
for(j=1; j<=(nlstate+ndeath);j++){	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");
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;	cov[1]=1;
for(i=1; i<=(nlstate+ndeath); i++){	tj=cptcoveff;
for(j=1; j<=(nlstate+ndeath);j++){	if (cptcovn<1) {tj=1;ncodemax[1]=1;}
k=k+1;	j1=0;
gm[k]=pmmij[i][j];	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+ndeath)*(nlstate+ndeath); i++)	for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)
gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];	gradg[theta][i]=(gp[i]-gm[i])/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)*(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(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 */
	/* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
	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));
	printf("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);
	}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);
	}/* 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[],char rfileres[] ){	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(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.71c </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
Total number of observations=%d <br>	- Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>	- Life expectancies by age and initial health status (estepm=%2d months):
<hr size=\"2\" color=\"#EC5E5E\">	<a href=\"e%s\">e%s</a> <br>\n</li>", \
<li>Outputs files<br><br>\n	jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
- 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>	fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
- Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>	- Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
- Transition probabilities: <a href=\"pij%s\">pij%s</a><br>	- Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
- Copy of the parameter file: <a href=\"o%s\">o%s</a><br>	- Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n
- Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>	- Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n
- Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>	- 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: <a href=\"t%s\">t%s</a> <br>	- Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
- Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>	- 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);
- Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>
- Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>	if(popforecast==1) fprintf(fichtm,"\n
<br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);	- 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
fprintf(fichtm," <li>Graphs</li><p>");	<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><b>Graphs</b></li><p>");

m=cptcoveff;	m=cptcoveff;
if (cptcovn < 1) {m=1;ncodemax[1]=1;}	if (cptcovn < 1) {m=1;ncodemax[1]=1;}
Line 1931 fprintf(fichtm," <li>Graphs</li><p>");	Line 2260 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>");
}
}	}
	}
fclose(fichtm);	fclose(fichtm);
}	}

/***************** Gnuplot file ************/	/***************** Gnuplot file ************/
void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, 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);
}	}

Line 1983 m=pow(2,cptcoveff);	Line 2314 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 2005 for (i=1; i<= nlstate ; i ++) {	Line 2338 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 2038 fprintf(ficgp,"\nset out \"v%s%d%d.gif\"	Line 2371 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,agemaxpar,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 2071 fprintf(ficgp,"\nset out \"v%s%d%d.gif\"	Line 2413 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 2087 fprintf(ficgp,"\nset out \"v%s%d%d.gif\"	Line 2428 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,agemaxpar);	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",YEARM/stepm,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 2158 void movingaverage(double agedeb, double	Line 2507 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 2170 prevforecast(char fileres[], double anpr	Line 2519 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");
Line 2184 calagedate=(anproj1+mproj1/12.+jproj1/36	Line 2533 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 2221 calagedate=(anproj1+mproj1/12.+jproj1/36	Line 2570 calagedate=(anproj1+mproj1/12.+jproj1/36
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 2231 calagedate=(anproj1+mproj1/12.+jproj1/36	Line 2580 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 2260 calagedate=(anproj1+mproj1/12.+jproj1/36	Line 2609 calagedate=(anproj1+mproj1/12.+jproj1/36
fclose(ficresf);	fclose(ficresf);
}	}
/************ Forecasting ****************/	/************ Forecasting ****************/
populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){	populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){

int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;	int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
int *popage;	int *popage;
Line 2274 populforecast(char fileres[], double anp	Line 2623 populforecast(char fileres[], double anp
agelim=AGESUP;	agelim=AGESUP;
calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;	calagedate=(anpyram+mpyram/12.+jpyram/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(filerespop,"pop");	strcpy(filerespop,"pop");
Line 2288 populforecast(char fileres[], double anp	Line 2637 populforecast(char fileres[], double anp

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 2329 populforecast(char fileres[], double anp	Line 2678 populforecast(char fileres[], double anp
for (cpt=0; cpt<=0;cpt++) {	for (cpt=0; cpt<=0;cpt++) {
fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);	fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);

for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(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 2375 populforecast(char fileres[], double anp	Line 2724 populforecast(char fileres[], double anp

for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {	for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {
fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);	fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);
for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(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 2421 int main(int argc, char *argv[])	Line 2770 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, agemaxpar=-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 2430 int main(int argc, char *argv[])	Line 2779 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 optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];

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

char filerest[FILENAMELENGTH];
char fileregp[FILENAMELENGTH];
char popfile[FILENAMELENGTH];
char path[80],pathc[80],pathcd[80],pathtot[80],model[20];	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 */
Line 2448 int main(int argc, char *argv[])	Line 2788 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,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;	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 2466 int main(int argc, char *argv[])	Line 2806 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 0.71c, March 2002, INED-EUROREVES ";
char *alph[]={"a","a","b","c","d","e"}, str[4];	char *alph[]={"a","a","b","c","d","e"}, str[4];


Line 2479 int main(int argc, char *argv[])	Line 2818 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 2527 int main(int argc, char *argv[])	Line 2866 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 2686 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3025 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 2705 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3044 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 2724 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3064 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 2755 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3094 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 2763 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3102 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 2780 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3119 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 2792 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3131 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 2882 printf("Total number of individuals= %d,	Line 3225 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 2917 printf("Total number of individuals= %d,	Line 3261 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= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, weightopt,model);	fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);


jk=1;	jk=1;
fprintf(ficres,"# Parameters\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 2944 printf("Total number of individuals= %d,	Line 3288 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 2963 printf("Total number of individuals= %d,	Line 3307 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 2988 printf("Total number of individuals= %d,	Line 3332 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,&agemaxpar, &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 = agemaxpar;	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,agemaxpar,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,agemaxpar,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 3056 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3400 while((c=getc(ficpar))=='#' && c!= EOF){
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,agemaxpar,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
	- Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,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 3070 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3440 while((c=getc(ficpar))=='#' && c!= EOF){
fclose(ficparo);	fclose(ficparo);
fclose(ficres);	fclose(ficres);

/--------- index.htm --------/

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


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

strcpy(filerespl,"pl");	strcpy(filerespl,"pl");
Line 3095 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3461 while((c=getc(ficpar))=='#' && c!= EOF){
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=agemaxpar;	agelim=agemaxpar;
ftolpl=1.e-10;	ftolpl=1.e-10;
i1=cptcoveff;	i1=cptcoveff;
Line 3135 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3501 while((c=getc(ficpar))=='#' && c!= EOF){
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 3148 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3516 while((c=getc(ficpar))=='#' && c!= EOF){
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 3156 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3527 while((c=getc(ficpar))=='#' && c!= EOF){
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);

Line 3178 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3549 while((c=getc(ficpar))=='#' && c!= EOF){
if((stepm == 1) && (strcmp(model,".")==0)){	if((stepm == 1) && (strcmp(model,".")==0)){
prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);	prevforecast(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);	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("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);	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 3210 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3579 while((c=getc(ficpar))=='#' && c!= EOF){
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 3222 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3593 while((c=getc(ficpar))=='#' && c!= EOF){

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 3243 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3615 while((c=getc(ficpar))=='#' && c!= EOF){
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 3253 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3623 while((c=getc(ficpar))=='#' && c!= EOF){
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 3322 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3696 while((c=getc(ficpar))=='#' && c!= EOF){
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);

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


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 3347 while((c=getc(ficpar))=='#' && c!= EOF){	Line 3726 while((c=getc(ficpar))=='#' && c!= EOF){

#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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