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Diff for /imach/src/imach.c between versions 1.27 and 1.40

version 1.27, 2002/02/28 17:49:07	version 1.40, 2002/04/19 13:46:19
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 "wgnuplot"
	/#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"/
#define FILENAMELENGTH 80	#define FILENAMELENGTH 80
/#define DEBUG/	/#define DEBUG/
#define windows	#define windows
Line 82 int cptcovn, cptcovage=0, cptcoveff=0,cp	Line 83 int cptcovn, cptcovage=0, cptcoveff=0,cp
int npar=NPARMAX;	int npar=NPARMAX;
int nlstate=2; /* Number of live states */	int nlstate=2; /* Number of live states */
int ndeath=1; /* Number of dead states */	int ndeath=1; /* Number of dead states */
int ncovmodel, ncov; /* Total number of covariables including constant a121 +b12x ncovmodel=2 */	int ncovmodel, ncovcol; /* Total number of covariables including constant a121 +b12x ncovmodel=2 */
int popbased=0;	int popbased=0;

int wav; / Number of waves for this individuual 0 is possible */	int wav; / Number of waves for this individuual 0 is possible */
Line 135 int imx;	Line 136 int imx;
int stepm;	int stepm;
/* Stepm, step in month: minimum step interpolation*/	/* Stepm, step in month: minimum step interpolation*/

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

int m,nb;	int m,nb;
int num, firstpass=0, lastpass=4,cod, ncodemax, Tage;	int num, firstpass=0, lastpass=4,cod, ncodemax, Tage;
double *agev,moisnais, annais, moisdc, andc,mint, *anint;	double *agev,moisnais, annais, moisdc, andc,mint, *anint;
Line 686 double prevalim(double prlim, int nl	Line 690 double prevalim(double prlim, int nl

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

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

savm=oldm;	savm=oldm;
Line 1178 void lubksb(double *a, int n, int indx	Line 1181 void lubksb(double *a, int n, int indx
/********** Frequencies ******************/	/********** Frequencies ******************/
void freqsummary(char fileres[], int agemin, int agemax, int s, double agev, int nlstate, int imx, int Tvar, int nbcode, int ncodemax,double mint,double anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)	void freqsummary(char fileres[], int agemin, int agemax, int s, double agev, int nlstate, int imx, int Tvar, int nbcode, int ncodemax,double mint,double anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
{ /* Some frequencies */	{ /* Some frequencies */

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

pp=vector(1,nlstate);	pp=vector(1,nlstate);
probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);	probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
strcpy(fileresp,"p");	strcpy(fileresp,"p");
Line 1196 void freqsummary(char fileres[], int ag	Line 1199 void freqsummary(char fileres[], int ag
}	}
freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);	freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
j1=0;	j1=0;

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

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

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

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

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

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

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

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

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

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

/********** Prevalence ******************/	/********** Prevalence ******************/
void prevalence(int agemin, int agemax, int s, double agev, int nlstate, int imx, int Tvar, int nbcode, int ncodemax,double mint,double anint, double dateprev1,double dateprev2, double calagedate)	void prevalence(int agemin, float agemax, int s, double agev, int nlstate, int imx, int Tvar, int nbcode, int ncodemax,double mint,double anint, double dateprev1,double dateprev2, double calagedate)
{ /* Some frequencies */	{ /* Some frequencies */

int i, m, jk, k1, i1, j1, bool, z1,z2,j;	int i, m, jk, k1, i1, j1, bool, z1,z2,j;
Line 1332 void prevalence(int agemin, int agemax,	Line 1338 void prevalence(int agemin, int agemax,
for (jk=-1; jk<=nlstate+ndeath; jk++)	for (jk=-1; jk<=nlstate+ndeath; jk++)
for(m=agemin; m <= agemax+3; m++)	for(m=agemin; m <= agemax+3; m++)
freq[i][jk][m]=0;	freq[i][jk][m]=0;

for (i=1; i<=imx; i++) {	for (i=1; i<=imx; i++) {
bool=1;	bool=1;
if (cptcovn>0) {	if (cptcovn>0) {
for (z1=1; z1<=cptcoveff; z1++)	for (z1=1; z1<=cptcoveff; z1++)
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])	if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])
bool=0;	bool=0;
}	}
if (bool==1) {	if (bool==1) {
for(m=firstpass; m<=lastpass; m++){	for(m=firstpass; m<=lastpass; m++){
k2=anint[m][i]+(mint[m][i]/12.);	k2=anint[m][i]+(mint[m][i]/12.);
if ((k2>=dateprev1) && (k2<=dateprev2)) {	if ((k2>=dateprev1) && (k2<=dateprev2)) {
if(agev[m][i]==0) agev[m][i]=agemax+1;	if(agev[m][i]==0) agev[m][i]=agemax+1;
if(agev[m][i]==1) agev[m][i]=agemax+2;	if(agev[m][i]==1) agev[m][i]=agemax+2;
freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];	if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];	/* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += 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++)
Line 1444 void concatwav(int wav[], int **dh, int	Line 1449 void concatwav(int wav[], int **dh, int
if (j >= jmax) jmax=j;	if (j >= jmax) jmax=j;
if (j <= jmin) jmin=j;	if (j <= jmin) jmin=j;
sum=sum+j;	sum=sum+j;
/* if (j<10) printf("j=%d num=%d ",j,i); */	/if (j<0) printf("j=%d num=%d \n",j,i); /
}	}
}	}
else{	else{
Line 1452 void concatwav(int wav[], int **dh, int	Line 1457 void concatwav(int wav[], int **dh, int
k=k+1;	k=k+1;
if (j >= jmax) jmax=j;	if (j >= jmax) jmax=j;
else if (j <= jmin)jmin=j;	else if (j <= jmin)jmin=j;
/* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */	/* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
sum=sum+j;	sum=sum+j;
}	}
jk= j/stepm;	jk= j/stepm;
Line 1498 void tricode(int Tvar, int *nbcode, in	Line 1503 void tricode(int Tvar, int *nbcode, in
for (k=0; k<=19; k++) {	for (k=0; k<=19; k++) {
if (Ndum[k] != 0) {	if (Ndum[k] != 0) {
nbcode[Tvar[j]][ij]=k;	nbcode[Tvar[j]][ij]=k;

ij++;	ij++;
}	}
if (ij > ncodemax[j]) break;	if (ij > ncodemax[j]) break;
Line 1514 void tricode(int Tvar, int *nbcode, in	Line 1520 void tricode(int Tvar, int *nbcode, in

ij=1;	ij=1;
for (i=1; i<=10; i++) {	for (i=1; i<=10; i++) {
if((Ndum[i]!=0) && (i<=ncov)){	if((Ndum[i]!=0) && (i<=ncovcol)){
Tvaraff[ij]=i;	Tvaraff[ij]=i;
ij++;	ij++;
}	}
Line 1525 void tricode(int Tvar, int *nbcode, in	Line 1531 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)
{	{
/* Health expectancies */	/* Health expectancies */
int i, j, nhstepm, hstepm, h;	int i, j, nhstepm, hstepm, h, nstepm;
double age, agelim,hf;	double age, agelim, hf;
double ***p3mat;	double ***p3mat;

fprintf(ficreseij,"# Health expectancies\n");	fprintf(ficreseij,"# Health expectancies\n");
Line 1539 void evsij(char fileres[], double ***eij	Line 1545 void evsij(char fileres[], double ***eij
fprintf(ficreseij," %1d-%1d",i,j);	fprintf(ficreseij," %1d-%1d",i,j);
fprintf(ficreseij,"\n");	fprintf(ficreseij,"\n");

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

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

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

	/for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++) printf("%f %.5f\n", age12+h, p3mat[1][1][h]);*/

	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++)
for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){	for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
eij[i][j][(int)age] +=p3mat[i][j][h];	eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
	/* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
}	}
	fprintf(ficreseij,"%3.0f",age );
hf=1;
if (stepm >= YEARM) hf=stepm/YEARM;
fprintf(ficreseij,"%.0f",age );
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++){	for(j=1; j<=nlstate;j++){
fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);	fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);
}	}
fprintf(ficreseij,"\n");	fprintf(ficreseij,"\n");
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
Line 1574 void evsij(char fileres[], double ***eij	Line 1606 void evsij(char fileres[], double ***eij
}	}

/********** 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,"# Covariances of life expectancies\n");
Line 1600 void varevsij(char fileres[], double ***	Line 1632 void varevsij(char fileres[], double ***
dnewm=matrix(1,nlstate,1,npar);	dnewm=matrix(1,nlstate,1,npar);
doldm=matrix(1,nlstate,1,nlstate);	doldm=matrix(1,nlstate,1,nlstate);

hstepm=1YEARM; / Every year of age */	if(estepm < stepm){
hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */	printf ("Problem %d lower than %d\n",estepm, stepm);
	}
	else hstepm=estepm;
	/* For example we decided to compute the life expectancy with the smallest unit */
	/* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
	nhstepm is the number of hstepm from age to agelim
	nstepm is the number of stepm from age to agelin.
	Look at hpijx to understand the reason of that which relies in memory size
	and note for a fixed period like k years */
	/* We decided (b) to get a life expectancy respecting the most precise curvature of the
	survival function given by stepm (the optimization length). Unfortunately it
	means that if the survival funtion is printed only each two years of age and if
	you sum them up and add 1 year (area under the trapezoids) you won't get the same
	results. So we changed our mind and took the option of the best precision.
	*/
	hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
agelim = AGESUP;	agelim = AGESUP;
for (age=bage; age<=fage; age ++){ /* If stepm=6 months */	for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
nhstepm=(int) rint((agelim-age)YEARM/stepm); / Typically 20 years = 2012/6=40 /	nstepm=(int) rint((agelim-age)YEARM/stepm); / Typically 20 years = 2012/6=40 /
if (stepm >= YEARM) hstepm=1;	nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
gradg=ma3x(0,nhstepm,1,npar,1,nlstate);	gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
gp=matrix(0,nhstepm,1,nlstate);	gp=matrix(0,nhstepm,1,nlstate);
Line 1661 void varevsij(char fileres[], double ***	Line 1707 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 1778 void varprevlim(char fileres[], double *	Line 1825 void varprevlim(char fileres[], double *
}	}

/********** Variance of one-step probabilities ****************/	/********** Variance of one-step probabilities ****************/
void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)	void varprob(char fileres[], double *matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int Tvar, int *nbcode, int ncodemax)
{	{
int i, j;	int i, j, i1, k1, j1, z1;
int k=0, cptcode;	int k=0, cptcode;
double dnewm,doldm;	double dnewm,doldm;
double *xp;	double *xp;
Line 1803 void varprob(char fileres[], double **ma	Line 1850 void varprob(char fileres[], double **ma
doldm=matrix(1,(nlstate+ndeath)(nlstate+ndeath),1,(nlstate+ndeath)(nlstate+ndeath));	doldm=matrix(1,(nlstate+ndeath)(nlstate+ndeath),1,(nlstate+ndeath)(nlstate+ndeath));

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

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

for(theta=1; theta <=npar; theta++){	for (age=bage; age<=fage; age ++){
for(i=1; i<=npar; i++)	cov[2]=age;
xp[i] = x[i] + (i==theta ?delti[theta]:0);	for (k=1; k<=cptcovn;k++) {
	cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
pmij(pmmij,cov,ncovmodel,xp,nlstate);

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

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

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

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

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

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

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

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

matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);
matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);

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

k=0;	for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)
for(i=1; i<=(nlstate+ndeath); i++){	for(theta=1; theta <=npar; theta++)
for(j=1; j<=(nlstate+ndeath);j++){	trgradg[j][theta]=gradg[theta][j];
k=k+1;
gm[k]=pmmij[i][j];	matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);
	matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);

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

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

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


printf("%e [%e ;%e] ",gm[i],gm[i]-2sqrt(doldm[i][i]),gm[i]+2sqrt(doldm[i][i]));	printf("%e [%e ;%e] ",gm[i],gm[i]-2sqrt(doldm[i][i]),gm[i]+2sqrt(doldm[i][i]));
}*/	}*/

fprintf(ficresprob,"\n%d ",(int)age);	fprintf(ficresprob,"\n%d ",(int)age);

for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){
if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);
if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);
}

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

	}
	}
free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));	free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));	free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);	free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);	free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
}	}
free_vector(xp,1,npar);	free_vector(xp,1,npar);
fclose(ficresprob);	fclose(ficresprob);

}	}

/***************** Printing html file *********/	/***************** Printing html file *********/
void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[] ){	void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
	int lastpass, int stepm, int weightopt, char model[],\
	int imx,int jmin, int jmax, double jmeanint,char optionfile[], \
	char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\
	char version[], int popforecast, int estepm ){
int jj1, k1, i1, cpt;	int jj1, k1, i1, cpt;
FILE *fichtm;	FILE *fichtm;
/char optionfilehtm[FILENAMELENGTH];/	/char optionfilehtm[FILENAMELENGTH];/
Line 1894 void printinghtml(char fileres[], char t	Line 1963 void printinghtml(char fileres[], char t
printf("Problem with %s \n",optionfilehtm), exit(0);	printf("Problem with %s \n",optionfilehtm), exit(0);
}	}

fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">	fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>	Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n
	\n
Total number of observations=%d <br>	Total number of observations=%d <br>\n
Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>	Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n
<hr size=\"2\" color=\"#EC5E5E\">	<hr size=\"2\" color=\"#EC5E5E\">
<li>Outputs files<br><br>\n	<ul><li>Outputs files<br>\n
- Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n	- Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n
- Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>	- Gnuplot file name: <a href=\"%s\">%s</a><br>\n
- Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>	- Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n
- Transition probabilities: <a href=\"pij%s\">pij%s</a><br>	- Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n
- Copy of the parameter file: <a href=\"o%s\">o%s</a><br>	- Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n
- Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>	- Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
- Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>
- Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>	fprintf(fichtm,"\n
- Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>	- Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n
- Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>	- Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n
<br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);	- Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n
	- Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);

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

m=cptcoveff;	m=cptcoveff;
Line 1953 fclose(fichtm);	Line 2029 fclose(fichtm);
}	}

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

int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;	int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;

strcpy(optionfilegnuplot,optionfilefiname);	strcpy(optionfilegnuplot,optionfilefiname);
strcat(optionfilegnuplot,".plt");	strcat(optionfilegnuplot,".gp.txt");
if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {	if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
printf("Problem with file %s",optionfilegnuplot);	printf("Problem with file %s",optionfilegnuplot);
}	}
Line 1973 m=pow(2,cptcoveff);	Line 2049 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,"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",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,"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 2003 fprintf(ficgp,"\nset out \"v%s%d%d.gif\"	Line 2079 fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
/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,"set ylabel \"Years\" \nset ter gif small size 400,300\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 2036 fprintf(ficgp,"\nset out \"v%s%d%d.gif\"	Line 2112 fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
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*(cpt-1);
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,"set ter gif small size 400,300\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);
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+i,cpt,i+1);
}	}
Line 2048 fprintf(ficgp,"\nset out \"v%s%d%d.gif\"	Line 2124 fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
for (k1=1; k1<= m ; k1 ++) {	for (k1=1; k1<= m ; k1 ++) {
for (cpt=1; cpt<nlstate ; cpt ++) {	for (cpt=1; cpt<nlstate ; cpt ++) {
k=3;	k=3;
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);	fprintf(ficgp,"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",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 2080 fprintf(ficgp,"\nset out \"v%s%d%d.gif\"	Line 2156 fprintf(ficgp,"\nset out \"v%s%d%d.gif\"
}	}

for(jk=1; jk <=m; jk++) {	for(jk=1; jk <=m; jk++) {
fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot [%.f:%.f] ",agemin,agemax);	fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot [%.f:%.f] ",ageminpar,agemaxpar);
i=1;	i=1;
for(k2=1; k2<=nlstate; k2++) {	for(k2=1; k2<=nlstate; k2++) {
k3=i;	k3=i;
Line 2125 ij=1;	Line 2201 ij=1;


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

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

for (agedeb=agemin+4; agedeb<=fage; agedeb++){	for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){
for (i=1; i<=nlstate;i++){	for (i=1; i<=nlstate;i++){
for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){	for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
for (cpt=0;cpt<=4;cpt++){	for (cpt=0;cpt<=4;cpt++){
Line 2148 void movingaverage(double agedeb, double	Line 2224 void movingaverage(double agedeb, double


/************ Forecasting ****************/	/************ Forecasting ****************/
prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){	prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){

int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;	int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
int *popage;	int *popage;
Line 2159 prevforecast(char fileres[], double anpr	Line 2235 prevforecast(char fileres[], double anpr

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

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

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


strcpy(fileresf,"f");	strcpy(fileresf,"f");
strcat(fileresf,fileres);	strcat(fileresf,fileres);
Line 2174 calagedate=(anproj1+mproj1/12.+jproj1/36	Line 2250 calagedate=(anproj1+mproj1/12.+jproj1/36

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

stepsize=(int) (stepm+YEARM-1)/YEARM;	stepsize=(int) (stepm+YEARM-1)/YEARM;
Line 2210 calagedate=(anproj1+mproj1/12.+jproj1/36	Line 2286 calagedate=(anproj1+mproj1/12.+jproj1/36
for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {	for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {
fprintf(ficresf,"\n");	fprintf(ficresf,"\n");
fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);	fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);

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

Line 2221 calagedate=(anproj1+mproj1/12.+jproj1/36	Line 2297 calagedate=(anproj1+mproj1/12.+jproj1/36

for (h=0; h<=nhstepm; h++){	for (h=0; h<=nhstepm; h++){
if (h==(int) (calagedate+YEARM*cpt)) {	if (h==(int) (calagedate+YEARM*cpt)) {
fprintf(ficresf,"\n %.f ",agedeb+hhstepm/YEARMstepm);	fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+hhstepm/YEARMstepm);
}	}
for(j=1; j<=nlstate+ndeath;j++) {	for(j=1; j<=nlstate+ndeath;j++) {
kk1=0.;kk2=0;	kk1=0.;kk2=0;
Line 2250 calagedate=(anproj1+mproj1/12.+jproj1/36	Line 2326 calagedate=(anproj1+mproj1/12.+jproj1/36
fclose(ficresf);	fclose(ficresf);
}	}
/************ Forecasting ****************/	/************ Forecasting ****************/
populforecast(char fileres[], double anproj1,double mproj1,double jproj1,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){	populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){

int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;	int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
int *popage;	int *popage;
Line 2259 populforecast(char fileres[], double anp	Line 2335 populforecast(char fileres[], double anp
double *p3mat,tabpop,**tabpopprev;	double *p3mat,tabpop,**tabpopprev;
char filerespop[FILENAMELENGTH];	char filerespop[FILENAMELENGTH];

tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);	tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);	tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
agelim=AGESUP;	agelim=AGESUP;
calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;	calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;

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


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


strcpy(filerespop,"pop");	strcpy(filerespop,"pop");
strcat(filerespop,fileres);	strcat(filerespop,fileres);
if((ficrespop=fopen(filerespop,"w"))==NULL) {	if((ficrespop=fopen(filerespop,"w"))==NULL) {
Line 2278 calagedate=(anproj1+mproj1/12.+jproj1/36	Line 2354 calagedate=(anproj1+mproj1/12.+jproj1/36

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

stepsize=(int) (stepm+YEARM-1)/YEARM;	stepsize=(int) (stepm+YEARM-1)/YEARM;
Line 2312 calagedate=(anproj1+mproj1/12.+jproj1/36	Line 2388 calagedate=(anproj1+mproj1/12.+jproj1/36
fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
}	}
fprintf(ficrespop,"******\n");	fprintf(ficrespop,"******\n");
fprintf(ficrespop,"# StartingAge FinalAge");	fprintf(ficrespop,"# Age");
for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);	for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
if (popforecast==1) fprintf(ficrespop," [Population]");	if (popforecast==1) fprintf(ficrespop," [Population]");

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

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

Line 2329 calagedate=(anproj1+mproj1/12.+jproj1/36	Line 2405 calagedate=(anproj1+mproj1/12.+jproj1/36

for (h=0; h<=nhstepm; h++){	for (h=0; h<=nhstepm; h++){
if (h==(int) (calagedate+YEARM*cpt)) {	if (h==(int) (calagedate+YEARM*cpt)) {
fprintf(ficrespop,"\n %.f ",agedeb+hhstepm/YEARMstepm);	fprintf(ficrespop,"\n %3.f ",agedeb+hhstepm/YEARMstepm);
}	}
for(j=1; j<=nlstate+ndeath;j++) {	for(j=1; j<=nlstate+ndeath;j++) {
kk1=0.;kk2=0;	kk1=0.;kk2=0;
Line 2349 calagedate=(anproj1+mproj1/12.+jproj1/36	Line 2425 calagedate=(anproj1+mproj1/12.+jproj1/36
for(i=1; i<=nlstate;i++){	for(i=1; i<=nlstate;i++){
kk1=0.;	kk1=0.;
for(j=1; j<=nlstate;j++){	for(j=1; j<=nlstate;j++){
kk1= kk1+Tabpop[(int)(agedeb)][j][cptcod];	kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];
}	}
tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1popeffectif[(int)(agedeb+(calagedate+12cpt)hstepm/YEARMstepm-1)];	tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1popeffectif[(int)(agedeb+(calagedate+12cpt)hstepm/YEARMstepm-1)];
}	}

if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++) fprintf(ficrespop," %.3f",tabpopprev[(int)(agedeb+1)][j][cptcod]);	if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)
	fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
}	}
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
}	}
Line 2362 if (h==(int)(calagedate+12*cpt)) for(j=1	Line 2439 if (h==(int)(calagedate+12*cpt)) for(j=1

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

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

Line 2373 if (h==(int)(calagedate+12*cpt)) for(j=1	Line 2450 if (h==(int)(calagedate+12*cpt)) for(j=1
hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);	hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);
for (h=0; h<=nhstepm; h++){	for (h=0; h<=nhstepm; h++){
if (h==(int) (calagedate+YEARM*cpt)) {	if (h==(int) (calagedate+YEARM*cpt)) {
fprintf(ficresf,"\n %.f ",agedeb+hhstepm/YEARMstepm);	fprintf(ficresf,"\n %3.f ",agedeb+hhstepm/YEARMstepm);
}	}
for(j=1; j<=nlstate+ndeath;j++) {	for(j=1; j<=nlstate+ndeath;j++) {
kk1=0.;kk2=0;	kk1=0.;kk2=0;
for(i=1; i<=nlstate;i++) {	for(i=1; i<=nlstate;i++) {
kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];	kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];
}	}
if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %.3f", kk1);	if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);
}	}
}	}
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
Line 2410 int main(int argc, char *argv[])	Line 2487 int main(int argc, char *argv[])

int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;	int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;
double agedeb, agefin,hf;	double agedeb, agefin,hf;
double agemin=1.e20, agemax=-1.e20;	double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;

double fret;	double fret;
double **xi,tmp,delta;	double **xi,tmp,delta;
Line 2423 int main(int argc, char *argv[])	Line 2500 int main(int argc, char *argv[])
char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];	char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];	char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];

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

char filerest[FILENAMELENGTH];	char filerest[FILENAMELENGTH];
char fileregp[FILENAMELENGTH];	char fileregp[FILENAMELENGTH];
Line 2437 int main(int argc, char *argv[])	Line 2514 int main(int argc, char *argv[])
int jnais,jdc,jint4,jint1,jint2,jint3,outcome,adl,*tab;	int jnais,jdc,jint4,jint1,jint2,jint3,outcome,adl,*tab;
int mobilav=0,popforecast=0;	int mobilav=0,popforecast=0;
int hstepm, nhstepm;	int hstepm, nhstepm;
double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;	double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;

double bage, fage, age, agelim, agebase;	double bage, fage, age, agelim, agebase;
double ftolpl=FTOL;	double ftolpl=FTOL;
Line 2455 int main(int argc, char *argv[])	Line 2532 int main(int argc, char *argv[])
double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;	double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;


char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";	char version[80]="Imach version 0.8b, 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 2468 int main(int argc, char *argv[])	Line 2545 int main(int argc, char *argv[])
struct timeval start_time, end_time;	struct timeval start_time, end_time;

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

printf("\n%s",version);	printf("\n%s",version);
if(argc <=1){	if(argc <=1){
Line 2516 int main(int argc, char *argv[])	Line 2593 int main(int argc, char *argv[])
}	}
ungetc(c,ficpar);	ungetc(c,ficpar);

fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);	fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);	printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);	fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);	ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);	fgets(line, MAXLINE, ficpar);
Line 2623 while((c=getc(ficpar))=='#' && c!= EOF){	Line 2700 while((c=getc(ficpar))=='#' && c!= EOF){
printf("\n");	printf("\n");


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

	/-------- data file ----------/
if((fic=fopen(datafile,"r"))==NULL) {	if((fic=fopen(datafile,"r"))==NULL) {
printf("Problem with datafile: %s\n", datafile);goto end;	printf("Problem with datafile: %s\n", datafile);goto end;
}	}
Line 2670 while((c=getc(ficpar))=='#' && c!= EOF){	Line 2752 while((c=getc(ficpar))=='#' && c!= EOF){
cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);	cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);

cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);	cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
for (j=ncov;j>=1;j--){	for (j=ncovcol;j>=1;j--){
cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);	cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
}	}
num[i]=atol(stra);	num[i]=atol(stra);
Line 2689 while((c=getc(ficpar))=='#' && c!= EOF){	Line 2771 while((c=getc(ficpar))=='#' && c!= EOF){
if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;	if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;	if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;	if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
}	}*/
	/* for (i=1; i<=imx; i++){
for (i=1; i<=imx; i++)	if (s[4][i]==9) s[4][i]=-1;
if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i]));*/	printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i]));}*/


/* Calculation of the number of parameter from char model*/	/* Calculation of the number of parameter from char model*/
Tvar=ivector(1,15);	Tvar=ivector(1,15);
Tprod=ivector(1,15);	Tprod=ivector(1,15);
Line 2708 while((c=getc(ficpar))=='#' && c!= EOF){	Line 2791 while((c=getc(ficpar))=='#' && c!= EOF){
cptcovn=j+1;	cptcovn=j+1;
cptcovprod=j1;	cptcovprod=j1;


strcpy(modelsav,model);	strcpy(modelsav,model);
if ((strcmp(model,"age")==0) \|\| (strcmp(model,"age*age")==0)){	if ((strcmp(model,"age")==0) \|\| (strcmp(model,"age*age")==0)){
printf("Error. Non available option model=%s ",model);	printf("Error. Non available option model=%s ",model);
Line 2739 while((c=getc(ficpar))=='#' && c!= EOF){	Line 2821 while((c=getc(ficpar))=='#' && c!= EOF){
}	}
else {	else {
cutv(strb,stre,strc,'V');	cutv(strb,stre,strc,'V');
Tvar[i]=ncov+k1;	Tvar[i]=ncovcol+k1;
cutv(strb,strc,strd,'V');	cutv(strb,strc,strd,'V');
Tprod[k1]=i;	Tprod[k1]=i;
Tvard[k1][1]=atoi(strc);	Tvard[k1][1]=atoi(strc);
Line 2747 while((c=getc(ficpar))=='#' && c!= EOF){	Line 2829 while((c=getc(ficpar))=='#' && c!= EOF){
Tvar[cptcovn+k2]=Tvard[k1][1];	Tvar[cptcovn+k2]=Tvard[k1][1];
Tvar[cptcovn+k2+1]=Tvard[k1][2];	Tvar[cptcovn+k2+1]=Tvard[k1][2];
for (k=1; k<=lastobs;k++)	for (k=1; k<=lastobs;k++)
covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];	covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
k1++;	k1++;
k2=k2+2;	k2=k2+2;
}	}
Line 2764 while((c=getc(ficpar))=='#' && c!= EOF){	Line 2846 while((c=getc(ficpar))=='#' && c!= EOF){
}	}
}	}

/*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);	/* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
printf("cptcovprod=%d ", cptcovprod);	printf("cptcovprod=%d ", cptcovprod);
scanf("%d ",i);*/	scanf("%d ",i);*/
fclose(fic);	fclose(fic);
Line 2776 while((c=getc(ficpar))=='#' && c!= EOF){	Line 2858 while((c=getc(ficpar))=='#' && c!= EOF){
/-calculation of age at interview from date of interview and age at death -/	/-calculation of age at interview from date of interview and age at death -/
agev=matrix(1,maxwav,1,imx);	agev=matrix(1,maxwav,1,imx);

for (i=1; i<=imx; i++)	for (i=1; i<=imx; i++) {
for(m=2; (m<= maxwav); m++)	for(m=2; (m<= maxwav); m++) {
if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){	if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
anint[m][i]=9999;	anint[m][i]=9999;
s[m][i]=-1;	s[m][i]=-1;
}	}
	if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
	}
	}

for (i=1; i<=imx; i++) {	for (i=1; i<=imx; i++) {
agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);	agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
for(m=1; (m<= maxwav); m++){	for(m=1; (m<= maxwav); m++){
if(s[m][i] >0){	if(s[m][i] >0){
if (s[m][i] == nlstate+1) {	if (s[m][i] >= nlstate+1) {
if(agedc[i]>0)	if(agedc[i]>0)
if(moisdc[i]!=99 && andc[i]!=9999)	if(moisdc[i]!=99 && andc[i]!=9999)
agev[m][i]=agedc[i];	agev[m][i]=agedc[i];
else {	/if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;/
	else {
if (andc[i]!=9999){	if (andc[i]!=9999){
printf("Warning negative age at death: %d line:%d\n",num[i],i);	printf("Warning negative age at death: %d line:%d\n",num[i],i);
agev[m][i]=-1;	agev[m][i]=-1;
Line 2866 printf("Total number of individuals= %d,	Line 2952 printf("Total number of individuals= %d,
for(j=1; j <= ncodemax[k]; j++){	for(j=1; j <= ncodemax[k]; j++){
for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){	for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
h++;	h++;
if (h>m) h=1;codtab[h][k]=j;	if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
	/* printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
}	}
}	}
}	}
}	}
	/* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);
	codtab[1][2]=1;codtab[2][2]=2; */
/*for(i=1; i <=m ;i++){	/* for(i=1; i <=m ;i++){
for(k=1; k <=cptcovn; k++){	for(k=1; k <=cptcovn; k++){
printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);	printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
}	}
printf("\n");	printf("\n");
}	}
scanf("%d",i);*/	scanf("%d",i);*/

/* Calculates basic frequencies. Computes observed prevalence at single age	/* Calculates basic frequencies. Computes observed prevalence at single age
and prints on file fileres'p'. */	and prints on file fileres'p'. */
Line 2901 printf("Total number of individuals= %d,	Line 2988 printf("Total number of individuals= %d,
}	}

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


jk=1;	jk=1;
fprintf(ficres,"# Parameters\n");	fprintf(ficres,"# Parameters nlstatenlstatencov a121 + b12 age + ...\n");
printf("# Parameters\n");	printf("# Parameters nlstatenlstatencov a121 + b12 age + ...\n");
for(i=1,jk=1; i <=nlstate; i++){	for(i=1,jk=1; i <=nlstate; i++){
for(k=1; k <=(nlstate+ndeath); k++){	for(k=1; k <=(nlstate+ndeath); k++){
if (k != i)	if (k != i)
Line 2928 printf("Total number of individuals= %d,	Line 3015 printf("Total number of individuals= %d,
ftolhess=ftol; /* Usually correct */	ftolhess=ftol; /* Usually correct */
hesscov(matcov, p, npar, delti, ftolhess, func);	hesscov(matcov, p, npar, delti, ftolhess, func);
}	}
fprintf(ficres,"# Scales\n");	fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
printf("# Scales\n");	printf("# Scales (for hessian or gradient estimation)\n");
for(i=1,jk=1; i <=nlstate; i++){	for(i=1,jk=1; i <=nlstate; i++){
for(j=1; j <=nlstate+ndeath; j++){	for(j=1; j <=nlstate+ndeath; j++){
if (j!=i) {	if (j!=i) {
Line 2947 printf("Total number of individuals= %d,	Line 3034 printf("Total number of individuals= %d,
}	}

k=1;	k=1;
fprintf(ficres,"# Covariance\n");	fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
printf("# Covariance\n");	printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
for(i=1;i<=npar;i++){	for(i=1;i<=npar;i++){
/* if (k>nlstate) k=1;	/* if (k>nlstate) k=1;
i1=(i-1)/(ncovmodel*nlstate)+1;	i1=(i-1)/(ncovmodel*nlstate)+1;
Line 2972 printf("Total number of individuals= %d,	Line 3059 printf("Total number of individuals= %d,
fputs(line,ficparo);	fputs(line,ficparo);
}	}
ungetc(c,ficpar);	ungetc(c,ficpar);
	estepm=0;
fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);	fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
	if (estepm==0 \|\| estepm < stepm) estepm=stepm;
if (fage <= 2) {	if (fage <= 2) {
bage = agemin;	bage = ageminpar;
fage = agemax;	fage = agemaxpar;
}	}

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

while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);	ungetc(c,ficpar);
Line 3009 printf("Total number of individuals= %d,	Line 3096 printf("Total number of individuals= %d,
dateprev2=anprev2+mprev2/12.+jprev2/365.;	dateprev2=anprev2+mprev2/12.+jprev2/365.;

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

while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);	ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);	fgets(line, MAXLINE, ficpar);
Line 3019 printf("Total number of individuals= %d,	Line 3106 printf("Total number of individuals= %d,
fputs(line,ficparo);	fputs(line,ficparo);
}	}
ungetc(c,ficpar);	ungetc(c,ficpar);
fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);
fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);	fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);
fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);	fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);
	fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);


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

	fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
	fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
	fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);

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

/------------ gnuplot -------------/	/------------ gnuplot -------------/
printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemax,fage, pathc,p);	printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);

/------------ free_vector -------------/	/------------ free_vector -------------/
chdir(path);	chdir(path);
Line 3039 fprintf(ficres,"popforecast=%d popfile=%	Line 3140 fprintf(ficres,"popforecast=%d popfile=%
/free_matrix(covar,1,NCOVMAX,1,n);/	/free_matrix(covar,1,NCOVMAX,1,n);/
fclose(ficparo);	fclose(ficparo);
fclose(ficres);	fclose(ficres);

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

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

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


/--------------- Prevalence limit --------------/	/--------------- Prevalence limit --------------/
Line 3077 fprintf(ficres,"popforecast=%d popfile=%	Line 3166 fprintf(ficres,"popforecast=%d popfile=%
savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */	savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */	oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
k=0;	k=0;
agebase=agemin;	agebase=ageminpar;
agelim=agemax;	agelim=agemaxpar;
ftolpl=1.e-10;	ftolpl=1.e-10;
i1=cptcoveff;	i1=cptcoveff;
if (cptcovn < 1){i1=1;}	if (cptcovn < 1){i1=1;}
Line 3138 fprintf(ficres,"popforecast=%d popfile=%	Line 3227 fprintf(ficres,"popforecast=%d popfile=%
for(j=1; j<=nlstate+ndeath;j++)	for(j=1; j<=nlstate+ndeath;j++)
fprintf(ficrespij," %1d-%1d",i,j);	fprintf(ficrespij," %1d-%1d",i,j);
fprintf(ficrespij,"\n");	fprintf(ficrespij,"\n");
for (h=0; h<=nhstepm; h++){	for (h=0; h<=nhstepm; h++){
fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ hhstepm/YEARMstepm );	fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ hhstepm/YEARMstepm );
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate+ndeath;j++)	for(j=1; j<=nlstate+ndeath;j++)
fprintf(ficrespij," %.5f", p3mat[i][j][h]);	fprintf(ficrespij," %.5f", p3mat[i][j][h]);
fprintf(ficrespij,"\n");	fprintf(ficrespij,"\n");
}	}
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
fprintf(ficrespij,"\n");	fprintf(ficrespij,"\n");
}	}
}	}
}	}

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

fclose(ficrespij);	fclose(ficrespij);


/---------- Forecasting ------------------/	/---------- Forecasting ------------------/
if(stepm == 1) {	if((stepm == 1) && (strcmp(model,".")==0)){
prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);	prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
populforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);	if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);
free_matrix(mint,1,maxwav,1,n);	free_matrix(mint,1,maxwav,1,n);
free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);	free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);
free_vector(weight,1,n);}	free_vector(weight,1,n);}
else{	else{
erreur=108;	erreur=108;
printf("Error %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);	printf("Warning %d!! You can only forecast the prevalences if the optimization\n has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);
}	}


Line 3204 populforecast(fileres, anproj1,mproj1,jp	Line 3293 populforecast(fileres, anproj1,mproj1,jp

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

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

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



Line 3225 populforecast(fileres, anproj1,mproj1,jp	Line 3314 populforecast(fileres, anproj1,mproj1,jp
for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);	for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
fprintf(ficrest,"\n");	fprintf(ficrest,"\n");

hf=1;
if (stepm >= YEARM) hf=stepm/YEARM;
epj=vector(1,nlstate+1);	epj=vector(1,nlstate+1);
for(age=bage; age <=fage ;age++){	for(age=bage; age <=fage ;age++){
prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);	prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
Line 3235 populforecast(fileres, anproj1,mproj1,jp	Line 3322 populforecast(fileres, anproj1,mproj1,jp
prlim[i][i]=probs[(int)age][i][k];	prlim[i][i]=probs[(int)age][i][k];
}	}

fprintf(ficrest," %.0f",age);	fprintf(ficrest," %4.0f",age);
for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){	for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
for(i=1, epj[j]=0.;i <=nlstate;i++) {	for(i=1, epj[j]=0.;i <=nlstate;i++) {
epj[j] += prlim[i][i]hfeij[i][j][(int)age];	epj[j] += prlim[i][i]*eij[i][j][(int)age];
}	}
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");
}	}
Line 3305 populforecast(fileres, anproj1,mproj1,jp	Line 3392 populforecast(fileres, anproj1,mproj1,jp
free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);	free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);

if(erreur >0)	if(erreur >0)
printf("End of Imach with error %d\n",erreur);	printf("End of Imach with error or warning %d\n",erreur);
else printf("End of Imach\n");	else printf("End of Imach\n");
/* gettimeofday(&end_time, (struct timezone)0);/ /* after time */	/* gettimeofday(&end_time, (struct timezone)0);/ /* after time */

Line 3329 populforecast(fileres, anproj1,mproj1,jp	Line 3416 populforecast(fileres, anproj1,mproj1,jp

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

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