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Diff for /imach/src/imach.c between versions 1.254 and 1.265

version 1.254, 2017/03/08 07:13:00	version 1.265, 2017/04/26 16:22:11
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	Revision 1.265 2017/04/26 16:22:11 brouard
	Summary: imach 0.99r13 Some bugs fixed

	Revision 1.264 2017/04/26 06:01:29 brouard
	Summary: Labels in graphs

	Revision 1.263 2017/04/24 15:23:15 brouard
	Summary: to save

	Revision 1.262 2017/04/18 16:48:12 brouard
	* empty log message *

	Revision 1.261 2017/04/05 10:14:09 brouard
	Summary: Bug in E_ as well as in T_ fixed nres-1 vs k1-1

	Revision 1.260 2017/04/04 17:46:59 brouard
	Summary: Gnuplot indexations fixed (humm)

	Revision 1.259 2017/04/04 13:01:16 brouard
	Summary: Some errors to warnings only if date of death is unknown but status is death we could set to pi3

	Revision 1.258 2017/04/03 10:17:47 brouard
	Summary: Version 0.99r12

	Some cleanings, conformed with updated documentation.

	Revision 1.257 2017/03/29 16:53:30 brouard
	Summary: Temp

	Revision 1.256 2017/03/27 05:50:23 brouard
	Summary: Temporary

	Revision 1.255 2017/03/08 16:02:28 brouard
	Summary: IMaCh version 0.99r10 bugs in gnuplot fixed

Revision 1.254 2017/03/08 07:13:00 brouard	Revision 1.254 2017/03/08 07:13:00 brouard
Summary: Fixing data parameter line	Summary: Fixing data parameter line

Line 1168 int *TvarsQind;	Line 1203 int *TvarsQind;

#define MAXRESULTLINES 10	#define MAXRESULTLINES 10
int nresult=0;	int nresult=0;
	int parameterline=0; /* # of the parameter (type) line */
int TKresult[MAXRESULTLINES];	int TKresult[MAXRESULTLINES];
int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */	int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */	int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
Line 2400 void powell(double p[], double **xi, int	Line 2436 void powell(double p[], double **xi, int
flatd++;	flatd++;
}	}
if(flatd >0){	if(flatd >0){
printf("%d flat directions\n",flatd);	printf("%d flat directions: ",flatd);
fprintf(ficlog,"%d flat directions\n",flatd);	fprintf(ficlog,"%d flat directions :",flatd);
for (j=1;j<=n;j++) {	for (j=1;j<=n;j++) {
if(flatdir[j]>0){	if(flatdir[j]>0){
printf("%d ",j);	printf("%d ",j);
Line 2585 Earliest age to start was %d-%d=%d, ncvl	Line 2621 Earliest age to start was %d-%d=%d, ncvl
/* double bprevalim(double bprlim, double *prevacurrent, int nlstate, double x[], double age, double oldm, double savm, double dnewm, double doldm, double dsavm, double ftolpl, int ncvyear, int ij) /	/* double bprevalim(double bprlim, double *prevacurrent, int nlstate, double x[], double age, double oldm, double savm, double dnewm, double doldm, double dsavm, double ftolpl, int ncvyear, int ij) /
double bprevalim(double bprlim, double **prevacurrent, int nlstate, double x[], double age, double ftolpl, int ncvyear, int ij, int nres)	double bprevalim(double bprlim, double **prevacurrent, int nlstate, double x[], double age, double ftolpl, int ncvyear, int ij, int nres)
{	{
/* Computes the prevalence limit in each live state at age x and covariate ij by left multiplying the unit	/* Computes the prevalence limit in each live state at age x and for covariate combination ij (<=2**cptcoveff) by left multiplying the unit
matrix by transitions matrix until convergence is reached with precision ftolpl */	matrix by transitions matrix until convergence is reached with precision ftolpl */
/* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */	/* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
/* Wx is row vector: population in state 1, population in state 2, population dead */	/* Wx is row vector: population in state 1, population in state 2, population dead */
Line 2646 Earliest age to start was %d-%d=%d, ncvl	Line 2682 Earliest age to start was %d-%d=%d, ncvl
for (k=1; k<=nsd;k++) { /* For single dummy covariates only */	for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
/* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */	/* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];	cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
/* printf("bprevalim Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */	/* printf("bprevalim Dummy agefin=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agefin,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
}	}
/* for (k=1; k<=cptcovn;k++) { */	/* for (k=1; k<=cptcovn;k++) { */
/* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; \/ /	/* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; \/ /
Line 4129 void ludcmp(double *a, int n, int indx	Line 4165 void ludcmp(double *a, int n, int indx
big=0.0;	big=0.0;
for (j=1;j<=n;j++)	for (j=1;j<=n;j++)
if ((temp=fabs(a[i][j])) > big) big=temp;	if ((temp=fabs(a[i][j])) > big) big=temp;
if (big == 0.0) nrerror("Singular matrix in routine ludcmp");	if (big == 0.0){
	printf(" Singular Hessian matrix at row %d:\n",i);
	for (j=1;j<=n;j++) {
	printf(" a[%d][%d]=%f,",i,j,a[i][j]);
	fprintf(ficlog," a[%d][%d]=%f,",i,j,a[i][j]);
	}
	fflush(ficlog);
	fclose(ficlog);
	nrerror("Singular matrix in routine ludcmp");
	}
vv[i]=1.0/big;	vv[i]=1.0/big;
}	}
for (j=1;j<=n;j++) {	for (j=1;j<=n;j++) {
Line 4266 void freqsummary(char fileres[], double	Line 4311 void freqsummary(char fileres[], double
int firstpass, int lastpass, int stepm, int weightopt, char model[])	int firstpass, int lastpass, int stepm, int weightopt, char model[])
{ /* Some frequencies as well as proposing some starting values */	{ /* Some frequencies as well as proposing some starting values */

int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0;	int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1;
int iind=0, iage=0;	int iind=0, iage=0;
int mi; /* Effective wave */	int mi; /* Effective wave */
int first;	int first;
Line 4345 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4390 Title=%s <br>Datafile=%s Firstpass=%d La
k2cpt=0;	k2cpt=0;

if(cptcoveff == 0 )	if(cptcoveff == 0 )
nl=1; /* Constant model only */	nl=1; /* Constant and age model only */
else	else
nl=2;	nl=2;

	/* if a constant only model, one pass to compute frequency tables and to write it on ficresp */
	/* Loop on nj=1 or 2 if dummy covariates j!=0
	* Loop on j1(1 to 2**cptcoveff) covariate combination
	* freq[s1][s2][iage] =0.
	* Loop on iind
	* ++freq[s1][s2][iage] weighted
	* end iind
	* if covariate and j!0
	* headers Variable on one line
	* endif cov j!=0
	* header of frequency table by age
	* Loop on age
	* pp[s1]+=freq[s1][s2][iage] weighted
	* pos+=freq[s1][s2][iage] weighted
	* Loop on s1 initial state
	* fprintf(ficresp
	* end s1
	* end age
	* if j!=0 computes starting values
	* end compute starting values
	* end j1
	* end nl
	*/
for (nj = 1; nj <= nl; nj++){ /* nj= 1 constant model, nl number of loops. */	for (nj = 1; nj <= nl; nj++){ /* nj= 1 constant model, nl number of loops. */
if(nj==1)	if(nj==1)
j=0; /* First pass for the constant */	j=0; /* First pass for the constant */
else	else{
j=cptcoveff; /* Other passes for the covariate values */	j=cptcoveff; /* Other passes for the covariate values */
	}
first=1;	first=1;
for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination in order of model, excluding quantitatives, V4=0, V3=0 for example, fixed or varying covariates */	for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on all covariates combination of the model, excluding quantitatives, V4=0, V3=0 for example, fixed or varying covariates */
posproptt=0.;	posproptt=0.;
/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);	/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
scanf("%d", i);*/	scanf("%d", i);*/
for (i=-5; i<=nlstate+ndeath; i++)	for (i=-5; i<=nlstate+ndeath; i++)
for (jk=-5; jk<=nlstate+ndeath; jk++)	for (s2=-5; s2<=nlstate+ndeath; s2++)
for(m=iagemin; m <= iagemax+3; m++)	for(m=iagemin; m <= iagemax+3; m++)
freq[i][jk][m]=0;	freq[i][s2][m]=0;

for (i=1; i<=nlstate; i++) {	for (i=1; i<=nlstate; i++) {
for(m=iagemin; m <= iagemax+3; m++)	for(m=iagemin; m <= iagemax+3; m++)
Line 4379 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4449 Title=%s <br>Datafile=%s Firstpass=%d La
/* dateintsum=0; */	/* dateintsum=0; */
/* k2cpt=0; */	/* k2cpt=0; */

/* For that combination of covariate j1, we count and print the frequencies in one pass */	/* For that combination of covariates j1 (V4=1 V3=0 for example), we count and print the frequencies in one pass */
for (iind=1; iind<=imx; iind++) { /* For each individual iind */	for (iind=1; iind<=imx; iind++) { /* For each individual iind */
bool=1;	bool=1;
if(j !=0){	if(j !=0){
Line 4395 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4465 Title=%s <br>Datafile=%s Firstpass=%d La
/* /\* sumnew+=coqvar[z1][iind]; \/ /	/* /\* sumnew+=coqvar[z1][iind]; \/ /
/* }else */	/* }else */
if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */	if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */
/* Tests if this individual iind responded to combination j1 (V4=1 V3=0) */	/* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */
bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */	bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
/* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",	/* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",
bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),	bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
Line 4406 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4476 Title=%s <br>Datafile=%s Firstpass=%d La
} /* cptcovn > 0 */	} /* cptcovn > 0 */
} /* end any */	} /* end any */
}/* end j==0 */	}/* end j==0 */
if (bool==1){ /* We selected an individual iind satisfying combination j1 or all fixed */	if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */
/* for(m=firstpass; m<=lastpass; m++){ */	/* for(m=firstpass; m<=lastpass; m++){ */
for(mi=1; mi<wav[iind];mi++){ /* For that wave */	for(mi=1; mi<wav[iind];mi++){ /* For that wave */
m=mw[mi][iind];	m=mw[mi][iind];
Line 4468 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4538 Title=%s <br>Datafile=%s Firstpass=%d La


/* 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);*/
pstamp(ficresp);	if(cptcoveff==0 && nj==1) /* no covariate and first pass */
	pstamp(ficresp);
if (cptcoveff>0 && j!=0){	if (cptcoveff>0 && j!=0){
	pstamp(ficresp);
printf( "\n#********** Variable ");	printf( "\n#********** Variable ");
fprintf(ficresp, "\n#********** Variable ");	fprintf(ficresp, "\n#********** Variable ");
fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");	fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
Line 4497 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4569 Title=%s <br>Datafile=%s Firstpass=%d La
fprintf(ficlog, "**********\n");	fprintf(ficlog, "**********\n");
}	}
fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");	fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
	if((cptcoveff==0 && nj==1)\|\| nj==2 ) /* no covariate and first pass */
	fprintf(ficresp, " Age");
	if(nj==2) for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " V%d=%d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
for(i=1; i<=nlstate;i++) {	for(i=1; i<=nlstate;i++) {
fprintf(ficresp, " Age Prev(%d) N(%d) N ",i,i);	if((cptcoveff==0 && nj==1)\|\| nj==2 ) fprintf(ficresp," Prev(%d) N(%d) N ",i,i);
fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);	fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
}	}
fprintf(ficresp, "\n");	if((cptcoveff==0 && nj==1)\|\| nj==2 ) fprintf(ficresp, "\n");
fprintf(ficresphtm, "\n");	fprintf(ficresphtm, "\n");

/* Header of frequency table by age */	/* Header of frequency table by age */
fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");	fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
fprintf(ficresphtmfr,"<th>Age</th> ");	fprintf(ficresphtmfr,"<th>Age</th> ");
for(jk=-1; jk <=nlstate+ndeath; jk++){	for(s2=-1; s2 <=nlstate+ndeath; s2++){
for(m=-1; m <=nlstate+ndeath; m++){	for(m=-1; m <=nlstate+ndeath; m++){
if(jk!=0 && m!=0)	if(s2!=0 && m!=0)
fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);	fprintf(ficresphtmfr,"<th>%d%d</th> ",s2,m);
}	}
}	}
fprintf(ficresphtmfr, "\n");	fprintf(ficresphtmfr, "\n");
Line 4535 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4610 Title=%s <br>Datafile=%s Firstpass=%d La
fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);	fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
fprintf(ficlog,"Age %d", iage);	fprintf(ficlog,"Age %d", iage);
}	}
for(jk=1; jk <=nlstate ; jk++){	for(s1=1; s1 <=nlstate ; s1++){
for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)	for(m=-1, pp[s1]=0; m <=nlstate+ndeath ; m++)
pp[jk] += freq[jk][m][iage];	pp[s1] += freq[s1][m][iage];
}	}
for(jk=1; jk <=nlstate ; jk++){	for(s1=1; s1 <=nlstate ; s1++){
for(m=-1, pos=0; m <=0 ; m++)	for(m=-1, pos=0; m <=0 ; m++)
pos += freq[jk][m][iage];	pos += freq[s1][m][iage];
if(pp[jk]>=1.e-10){	if(pp[s1]>=1.e-10){
if(first==1){	if(first==1){
printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);	printf(" %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
}	}
fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);	fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
}else{	}else{
if(first==1)	if(first==1)
printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);	printf(" %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);	fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
}	}
}	}

for(jk=1; jk <=nlstate ; jk++){	for(s1=1; s1 <=nlstate ; s1++){
/* posprop[jk]=0; */	/* posprop[s1]=0; */
for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */	for(m=0, pp[s1]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
pp[jk] += freq[jk][m][iage];	pp[s1] += freq[s1][m][iage];
} /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */	} /* pp[s1] is the total number of transitions starting from state s1 and any ending status until this age */

for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){	for(s1=1,pos=0, pospropta=0.; s1 <=nlstate ; s1++){
pos += pp[jk]; /* pos is the total number of transitions until this age */	pos += pp[s1]; /* pos is the total number of transitions until this age */
posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state	posprop[s1] += prop[s1][iage]; /* prop is the number of transitions from a live state
from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */	from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state	pospropta += prop[s1][iage]; /* prop is the number of transitions from a live state
from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */	from s1 at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
	}

	/* Writing ficresp */
	if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
	if( iage <= iagemax){
	fprintf(ficresp," %d",iage);
	}
	}else if( nj==2){
	if( iage <= iagemax){
	fprintf(ficresp," %d",iage);
	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
	}
}	}
for(jk=1; jk <=nlstate ; jk++){	for(s1=1; s1 <=nlstate ; s1++){
if(pos>=1.e-5){	if(pos>=1.e-5){
if(first==1)	if(first==1)
printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);	printf(" %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);	fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",s1,pp[s1],s1,100*pp[s1]/pos);
}else{	}else{
if(first==1)	if(first==1)
printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);	printf(" %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);	fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",s1,pp[s1],s1);
}	}
if( iage <= iagemax){	if( iage <= iagemax){
if(pos>=1.e-5){	if(pos>=1.e-5){
fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);	if(cptcoveff==0 && nj==1){ /* no covariate and first pass */
fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);	fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
/probs[iage][jk][j1]= pp[jk]/pos;/	}else if( nj==2){
/printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);/	fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
}	}
else{	fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);	/probs[iage][s1][j1]= pp[s1]/pos;/
fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);	/printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);/
	} else{
	if((cptcoveff==0 && nj==1)\|\| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta);
	fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[s1][iage],pospropta);
}	}
}	}
pospropt[jk] +=posprop[jk];	pospropt[s1] +=posprop[s1];
} /* end loop jk */	} /* end loop s1 */
/* pospropt=0.; */	/* pospropt=0.; */
for(jk=-1; jk <=nlstate+ndeath; jk++){	for(s1=-1; s1 <=nlstate+ndeath; s1++){
for(m=-1; m <=nlstate+ndeath; m++){	for(m=-1; m <=nlstate+ndeath; m++){
if(freq[jk][m][iage] !=0 ) { /* minimizing output */	if(freq[s1][m][iage] !=0 ) { /* minimizing output */
if(first==1){	if(first==1){
printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);	printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]);
}	}
/* printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]); */	/* printf(" %d%d=%.0f",s1,m,freq[s1][m][iage]); */
fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);	fprintf(ficlog," %d%d=%.0f",s1,m,freq[s1][m][iage]);
}	}
if(jk!=0 && m!=0)	if(s1!=0 && m!=0)
fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);	fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[s1][m][iage]);
}	}
} /* end loop jk */	} /* end loop s1 */
posproptt=0.;	posproptt=0.;
for(jk=1; jk <=nlstate; jk++){	for(s1=1; s1 <=nlstate; s1++){
posproptt += pospropt[jk];	posproptt += pospropt[s1];
}	}
fprintf(ficresphtmfr,"</tr>\n ");	fprintf(ficresphtmfr,"</tr>\n ");
if(iage <= iagemax){	fprintf(ficresphtm,"</tr>\n");
fprintf(ficresp,"\n");	if((cptcoveff==0 && nj==1)\|\| nj==2 ) {
fprintf(ficresphtm,"</tr>\n");	if(iage <= iagemax)
	fprintf(ficresp,"\n");
}	}
if(first==1)	if(first==1)
printf("Others in log...\n");	printf("Others in log...\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
} /* end loop age iage */	} /* end loop age iage */

fprintf(ficresphtm,"<tr><th>Tot</th>");	fprintf(ficresphtm,"<tr><th>Tot</th>");
for(jk=1; jk <=nlstate ; jk++){	for(s1=1; s1 <=nlstate ; s1++){
if(posproptt < 1.e-5){	if(posproptt < 1.e-5){
fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);	fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[s1],posproptt);
}else{	}else{
fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);	fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[s1]/posproptt,pospropt[s1],posproptt);
}	}
}	}
fprintf(ficresphtm,"</tr>\n");	fprintf(ficresphtm,"</tr>\n");
Line 4632 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4724 Title=%s <br>Datafile=%s Firstpass=%d La
if(posproptt < 1.e-5){	if(posproptt < 1.e-5){
fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);	fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);	fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
fprintf(ficres,"\n This combination (%d) is not valid and no result will be produced\n\n",j1);	fprintf(ficlog,"# This combination (%d) is not valid and no result will be produced\n",j1);
	printf("# This combination (%d) is not valid and no result will be produced\n",j1);
invalidvarcomb[j1]=1;	invalidvarcomb[j1]=1;
}else{	}else{
fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);	fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
Line 4642 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4735 Title=%s <br>Datafile=%s Firstpass=%d La
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
if(j!=0){	if(j!=0){
printf("#Freqsummary: Starting values for combination j1=%d:\n", j1);	printf("#Freqsummary: Starting values for combination j1=%d:\n", j1);
for(i=1,jk=1; i <=nlstate; i++){	for(i=1,s1=1; i <=nlstate; i++){
for(k=1; k <=(nlstate+ndeath); k++){	for(k=1; k <=(nlstate+ndeath); k++){
if (k != i) {	if (k != i) {
for(jj=1; jj <=ncovmodel; jj++){ /* For counting jk */	for(jj=1; jj <=ncovmodel; jj++){ /* For counting s1 */
if(jj==1){ /* Constant case (in fact cste + age) */	if(jj==1){ /* Constant case (in fact cste + age) */
if(j1==1){ /* All dummy covariates to zero */	if(j1==1){ /* All dummy covariates to zero */
freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */	freq[i][k][iagemax+4]=freq[i][k][iagemax+3]; /* Stores case 0 0 0 */
freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */	freq[i][i][iagemax+4]=freq[i][i][iagemax+3]; /* Stores case 0 0 0 */
printf("%d%d ",i,k);	printf("%d%d ",i,k);
fprintf(ficlog,"%d%d ",i,k);	fprintf(ficlog,"%d%d ",i,k);
printf("%12.7f ln(%.0f/%.0f)= %f, OR=%f sd=%f \n",p[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]),freq[i][k][iagemax+3]/freq[i][i][iagemax+3], sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]));	printf("%12.7f ln(%.0f/%.0f)= %f, OR=%f sd=%f \n",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]),freq[i][k][iagemax+3]/freq[i][i][iagemax+3], sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]));
fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f \n",p[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));	fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f \n",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
pstart[jk]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);	pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
}	}
}else if((j1==1) && (jj==2 \|\| nagesqr==1)){ /* age or ageage parameter without covariate V4age (to be done later) */	}else if((j1==1) && (jj==2 \|\| nagesqr==1)){ /* age or ageage parameter without covariate V4age (to be done later) */
for(iage=iagemin; iage <= iagemax+3; iage++){	for(iage=iagemin; iage <= iagemax+3; iage++){
x[iage]= (double)iage;	x[iage]= (double)iage;
y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);	y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);
/* printf("i=%d, k=%d, jk=%d, j1=%d, jj=%d, y[%d]=%f\n",i,k,jk,j1,jj, iage, y[iage]); */	/* printf("i=%d, k=%d, s1=%d, j1=%d, jj=%d, y[%d]=%f\n",i,k,s1,j1,jj, iage, y[iage]); */
}	}
linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+bx with standard errors /	linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+bx with standard errors /
pstart[jk]=b;	pstart[s1]=b;
pstart[jk-1]=a;	pstart[s1-1]=a;
}else if( j1!=1 && (j1==2 \|\| (log(j1-1.)/log(2.)-(int)(log(j1-1.)/log(2.))) <0.010) && ( TvarsDind[(int)(log(j1-1.)/log(2.))+1]+2+nagesqr == jj) && Dummy[jj-2-nagesqr]==0){ /* We want only if the position, jj, in model corresponds to unique covariate equal to 1 in j1 combination */	}else if( j1!=1 && (j1==2 \|\| (log(j1-1.)/log(2.)-(int)(log(j1-1.)/log(2.))) <0.010) && ( TvarsDind[(int)(log(j1-1.)/log(2.))+1]+2+nagesqr == jj) && Dummy[jj-2-nagesqr]==0){ /* We want only if the position, jj, in model corresponds to unique covariate equal to 1 in j1 combination */
printf("j1=%d, jj=%d, (int)(log(j1-1.)/log(2.))+1=%d, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(int)(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);	printf("j1=%d, jj=%d, (int)(log(j1-1.)/log(2.))+1=%d, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(int)(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);
printf("j1=%d, jj=%d, (log(j1-1.)/log(2.))+1=%f, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);	printf("j1=%d, jj=%d, (log(j1-1.)/log(2.))+1=%f, TvarsDind[(int)(log(j1-1.)/log(2.))+1]=%d\n",j1, jj,(log(j1-1.)/log(2.))+1,TvarsDind[(int)(log(j1-1.)/log(2.))+1]);
pstart[jk]= log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]));	pstart[s1]= log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]));
printf("%d%d ",i,k);	printf("%d%d ",i,k);
fprintf(ficlog,"%d%d ",i,k);	fprintf(ficlog,"%d%d ",i,k);
printf("jk=%d,i=%d,k=%d,p[%d]=%12.7f ln((%.0f/%.0f)/(%.0f/%.0f))= %f, OR=%f sd=%f \n",jk,i,k,jk,p[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3],freq[i][k][iagemax+4],freq[i][i][iagemax+4], log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4])),(freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]), sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]+1/freq[i][k][iagemax+4]+1/freq[i][i][iagemax+4]));	printf("s1=%d,i=%d,k=%d,p[%d]=%12.7f ln((%.0f/%.0f)/(%.0f/%.0f))= %f, OR=%f sd=%f \n",s1,i,k,s1,p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3],freq[i][k][iagemax+4],freq[i][i][iagemax+4], log((freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4])),(freq[i][k][iagemax+3]/freq[i][i][iagemax+3])/(freq[i][k][iagemax+4]/freq[i][i][iagemax+4]), sqrt(1/freq[i][k][iagemax+3]+1/freq[i][i][iagemax+3]+1/freq[i][k][iagemax+4]+1/freq[i][i][iagemax+4]));
}else{ /* Other cases, like quantitative fixed or varying covariates */	}else{ /* Other cases, like quantitative fixed or varying covariates */
;	;
}	}
/* printf("%12.7f )", param[i][jj][k]); */	/* printf("%12.7f )", param[i][jj][k]); */
/* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */	/* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
jk++;	s1++;
} /* end jj */	} /* end jj */
} /* end k!= i */	} /* end k!= i */
} /* end k */	} /* end k */
} /* end i, jk */	} /* end i, s1 */
} /* end j !=0 */	} /* end j !=0 */
} /* end selected combination of covariate j1 */	} /* end selected combination of covariate j1 */
if(j==0){ /* We can estimate starting values from the occurences in each case */	if(j==0){ /* We can estimate starting values from the occurences in each case */
printf("#Freqsummary: Starting values for the constants:\n");	printf("#Freqsummary: Starting values for the constants:\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
for(i=1,jk=1; i <=nlstate; i++){	for(i=1,s1=1; i <=nlstate; i++){
for(k=1; k <=(nlstate+ndeath); k++){	for(k=1; k <=(nlstate+ndeath); k++){
if (k != i) {	if (k != i) {
printf("%d%d ",i,k);	printf("%d%d ",i,k);
fprintf(ficlog,"%d%d ",i,k);	fprintf(ficlog,"%d%d ",i,k);
for(jj=1; jj <=ncovmodel; jj++){	for(jj=1; jj <=ncovmodel; jj++){
pstart[jk]=p[jk]; /* Setting pstart to p values by default */	pstart[s1]=p[s1]; /* Setting pstart to p values by default */
if(jj==1){ /* Age has to be done */	if(jj==1){ /* Age has to be done */
pstart[jk]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);	pstart[s1]= log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]);
printf("%12.7f ln(%.0f/%.0f)= %12.7f ",p[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));	printf("%12.7f ln(%.0f/%.0f)= %12.7f ",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f ",p[jk],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));	fprintf(ficlog,"%12.7f ln(%.0f/%.0f)= %12.7f ",p[s1],freq[i][k][iagemax+3],freq[i][i][iagemax+3], log(freq[i][k][iagemax+3]/freq[i][i][iagemax+3]));
}	}
/* printf("%12.7f )", param[i][jj][k]); */	/* printf("%12.7f )", param[i][jj][k]); */
/* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */	/* fprintf(ficlog,"%12.7f )", param[i][jj][k]); */
jk++;	s1++;
}	}
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
Line 4710 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4803 Title=%s <br>Datafile=%s Firstpass=%d La
}	}
printf("#Freqsummary\n");	printf("#Freqsummary\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
for(jk=-1; jk <=nlstate+ndeath; jk++){	for(s1=-1; s1 <=nlstate+ndeath; s1++){
for(m=-1; m <=nlstate+ndeath; m++){	for(s2=-1; s2 <=nlstate+ndeath; s2++){
/* param[i]\|j][k]= freq[jk][m][iagemax+3] */	/* param[i]\|j][k]= freq[s1][s2][iagemax+3] */
printf(" %d%d=%.0f",jk,m,freq[jk][m][iagemax+3]);	printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iagemax+3]);	fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]);
/* if(freq[jk][m][iage] !=0 ) { /\* minimizing output \/ /	/* if(freq[s1][s2][iage] !=0 ) { /\* minimizing output \/ /
/* printf(" %d%d=%.0f",jk,m,freq[jk][m][iagemax+3]); */	/* printf(" %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
/* fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iagemax+3]); */	/* fprintf(ficlog," %d%d=%.0f",s1,s2,freq[s1][s2][iagemax+3]); */
/* } */	/* } */
}	}
} /* end loop jk */	} /* end loop s1 */

printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
Line 4914 void concatwav(int wav[], int **dh, int	Line 5007 void concatwav(int wav[], int **dh, int
#else	#else
if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){	if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
if(firsthree == 0){	if(firsthree == 0){
printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);	printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p%d%d .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);
firsthree=1;	firsthree=1;
}	}
fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);	fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p%d%d .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);
mw[++mi][i]=m;	mw[++mi][i]=m;
mli=m;	mli=m;
}	}
Line 4944 void concatwav(int wav[], int **dh, int	Line 5037 void concatwav(int wav[], int **dh, int
/* if(mi==0) never been interviewed correctly before death */	/* if(mi==0) never been interviewed correctly before death */
/* Only death is a correct wave */	/* Only death is a correct wave */
mw[mi][i]=m;	mw[mi][i]=m;
}	} /* else not in a death state */
#ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE	#ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
else if ((int) andc[i] != 9999) { /* Status is negative. A death occured after lastpass, we can't take it into account because of potential bias */	else if ((int) andc[i] != 9999) { /* Date of death is known */
/* m++; */
/* mi++; */
/* s[m][i]=nlstate+1; /\* We are setting the status to the last of non live state \/ /
/* mw[mi][i]=m; */
if ((int)anint[m][i]!= 9999) { /* date of last interview is known */	if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */	if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */
nbwarn++;	nbwarn++;
Line 4963 void concatwav(int wav[], int **dh, int	Line 5052 void concatwav(int wav[], int **dh, int
}else{ /* Death occured afer last wave potential bias */	}else{ /* Death occured afer last wave potential bias */
nberr++;	nberr++;
if(firstwo==0){	if(firstwo==0){
printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );	printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
firstwo=1;	firstwo=1;
}	}
fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );	fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\n\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
}	}
}else{ /* end date of interview is known */	}else{ /* if date of interview is unknown */
/* death is known but not confirmed by death status at any wave */	/* death is known but not confirmed by death status at any wave */
if(firstfour==0){	if(firstfour==0){
printf("Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );	printf("Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
Line 4999 void concatwav(int wav[], int **dh, int	Line 5088 void concatwav(int wav[], int **dh, int
if (stepm <=0)	if (stepm <=0)
dh[mi][i]=1;	dh[mi][i]=1;
else{	else{
if (s[mw[mi+1][i]][i] > nlstate) { /* A death */	if (s[mw[mi+1][i]][i] > nlstate) { /* A death, but what if date is unknown? */
if (agedc[i] < 2*AGESUP) {	if (agedc[i] < 2*AGESUP) {
j= rint(agedc[i]12-agev[mw[mi][i]][i]12);	j= rint(agedc[i]12-agev[mw[mi][i]][i]12);
if(j==0) j=1; /* Survives at least one month after exam */	if(j==0) j=1; /* Survives at least one month after exam */
Line 6361 To be simple, these graphs help to under	Line 6450 To be simple, these graphs help to under
void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \	void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
int lastpass, int stepm, int weightopt, char model[],\	int lastpass, int stepm, int weightopt, char model[],\
int imx,int jmin, int jmax, double jmeanint,char rfileres[],\	int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
int popforecast, int prevfcast, int backcast, int estepm , \	int popforecast, int mobilav, int prevfcast, int mobilavproj, int backcast, int estepm , \
double jprev1, double mprev1,double anprev1, double dateprev1, \	double jprev1, double mprev1,double anprev1, double dateprev1, \
double jprev2, double mprev2,double anprev2, double dateprev2){	double jprev2, double mprev2,double anprev2, double dateprev2){
int jj1, k1, i1, cpt, k4, nres;	int jj1, k1, i1, cpt, k4, nres;
Line 6399 void printinghtml(char fileresu[], char	Line 6488 void printinghtml(char fileresu[], char
<a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));	<a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
}	}

fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");

m=pow(2,cptcoveff);	m=pow(2,cptcoveff);
if (cptcovn < 1) {m=1;ncodemax[1]=1;}	if (cptcovn < 1) {m=1;ncodemax[1]=1;}

	fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");

	jj1=0;

	fprintf(fichtm," \n<ul>");
	for(nres=1; nres <= nresult; nres++) /* For each resultline */
	for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
	if(m != 1 && TKresult[nres]!= k1)
	continue;
	jj1++;
	if (cptcovn > 0) {
	fprintf(fichtm,"\n<li><a size=\"1\" color=\"#EC5E5E\" href=\"#rescov");
	for (cpt=1; cpt<=cptcoveff;cpt++){
	fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
	}
	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
	fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
	}
	fprintf(fichtm,"\">");

	/* if(nqfveff+nqtveff 0) / / Test to be done */
	fprintf(fichtm,"************ Results for covariates");
	for (cpt=1; cpt<=cptcoveff;cpt++){
	fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
	}
	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
	fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	}
	if(invalidvarcomb[k1]){
	fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1);
	continue;
	}
	fprintf(fichtm,"</a></li>");
	} /* cptcovn >0 */
	}
	fprintf(fichtm," \n</ul>");

jj1=0;	jj1=0;

for(nres=1; nres <= nresult; nres++) /* For each resultline */	for(nres=1; nres <= nresult; nres++) /* For each resultline */
Line 6414 void printinghtml(char fileresu[], char	Line 6539 void printinghtml(char fileresu[], char
/* for(i1=1; i1<=ncodemax[k1];i1++){ */	/* for(i1=1; i1<=ncodemax[k1];i1++){ */
jj1++;	jj1++;
if (cptcovn > 0) {	if (cptcovn > 0) {
	fprintf(fichtm,"\n<p><a name=\"rescov");
	for (cpt=1; cpt<=cptcoveff;cpt++){
	fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
	}
	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
	fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
	}
	fprintf(fichtm,"\"</a>");

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 ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);	fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
Line 6435 void printinghtml(char fileresu[], char	Line 6569 void printinghtml(char fileresu[], char
}	}
}	}
/* aij, bij */	/* aij, bij */
fprintf(fichtm,"<br>- Logit model (yours is: 1+age+%s), for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1-%d.svg\">%s_%d-1-%d.svg</a><br> \	fprintf(fichtm,"<br>- Logit model (yours is: logit(pij)=log(pij/pii)= aij+ bij age+%s) as a function of age: <a href=\"%s_%d-1-%d.svg\">%s_%d-1-%d.svg</a><br> \
<img src=\"%s_%d-1-%d.svg\">",model,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);	<img src=\"%s_%d-1-%d.svg\">",model,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);
/* Pij */	/* Pij */
fprintf(fichtm,"<br>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2-%d.svg\">%s_%d-2-%d.svg</a><br> \	fprintf(fichtm,"<br>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2-%d.svg\">%s_%d-2-%d.svg</a><br> \
Line 6459 divided by h: <sub>h</sub>P<sub>ij</sub>	Line 6593 divided by h: <sub>h</sub>P<sub>ij</sub>
}	}
/* Period (stable) prevalence in each health state */	/* Period (stable) prevalence in each health state */
for(cpt=1; cpt<=nlstate;cpt++){	for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \	fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability for a person being in state (1 to %d) at different ages, to be in state %d some years after. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
<img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);	<img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
}	}
if(backcast==1){	if(backcast==1){
/* Period (stable) back prevalence in each health state */	/* Period (stable) back prevalence in each health state */
for(cpt=1; cpt<=nlstate;cpt++){	for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"<br>\n- Convergence to period (stable) back prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \	fprintf(fichtm,"<br>\n- Convergence to mixed (stable) back prevalence in state %d. Or probability for a person to be in state %d at a younger age, knowing that she/he was in state (1 to %d) at different older ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
<img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);	<img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
}	}
}	}
if(prevfcast==1){	if(prevfcast==1){
/* Projection of prevalence up to period (stable) prevalence in each health state */	/* Projection of prevalence up to period (stable) prevalence in each health state */
for(cpt=1; cpt<=nlstate;cpt++){	for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \	fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
<img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);	<img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
}	}
}	}

Line 6561 See page 'Matrix of variance-covariance	Line 6695 See page 'Matrix of variance-covariance
}	}
}	}
for(cpt=1; cpt<=nlstate;cpt++) {	for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \	fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \
prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d-%d.svg\"> %s_%d-%d-%d.svg</a>\n <br>\	prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d-%d.svg\"> %s_%d-%d-%d.svg</a>\n <br>\
<img src=\"%s_%d-%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);	<img src=\"%s_%d-%d-%d.svg\">",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
}	}
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). If popbased=1 the smooth (due to the model) \	health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
Line 6582 true period expectancies (those weighted	Line 6716 true period expectancies (those weighted
void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){	void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){

char dirfileres[132],optfileres[132];	char dirfileres[132],optfileres[132];
char gplotcondition[132];	char gplotcondition[132], gplotlabel[132];
int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,k4=0,ij=0, ijp=0, l=0;	int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,k4=0,ij=0, ijp=0, l=0;
int lv=0, vlv=0, kl=0;	int lv=0, vlv=0, kl=0;
int ng=0;	int ng=0;
Line 6641 void printinggnuplot(char fileresu[], ch	Line 6775 void printinggnuplot(char fileresu[], ch
/* We are interested in selected combination by the resultline */	/* We are interested in selected combination by the resultline */
/* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */	/* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt);	fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt);
	strcpy(gplotlabel,"(");
for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */	for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */	lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
Line 6650 void printinggnuplot(char fileresu[], ch	Line 6785 void printinggnuplot(char fileresu[], ch
/* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */	/* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
/* printf(" V%d=%d ",Tvaraff[k],vlv); */	/* printf(" V%d=%d ",Tvaraff[k],vlv); */
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
/* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */	/* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	}
	strcpy(gplotlabel+strlen(gplotlabel),")");
/* printf("\n#\n"); */	/* printf("\n#\n"); */
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
	/k1=k1-1;/ /* To be checked */
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
continue;	continue;
}	}

fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);	fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres);	fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
	/* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */
	/* k1-1 error should be nres-1*/
for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," %%lf (%%lf)");	if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%lf (%%lf)");	else fprintf(ficgp," %%lf (%%lf)");
}	}
fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres);	fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," %%lf (%%lf)");	if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%lf (%%lf)");	else fprintf(ficgp," %%lf (%%lf)");
}	}
fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres);	fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," %%lf (%%lf)");	if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%lf (%%lf)");	else fprintf(ficgp," %%lf (%%lf)");
}	}
fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));	/* fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4(cpt-1)); /

	fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" u 1:((",subdirf2(fileresu,"P_"));
	if(cptcoveff ==0){
	fprintf(ficgp,"$%d)) t 'Observed prevalence in state %d' with line lt 3", 2+(cpt-1), cpt );
	}else{
	kl=0;
	for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
	vlv= nbcode[Tvaraff[k]][lv];
	kl++;
	/* kl=6+(cpt-1)(nlstate+1)+1+(i-1); /\ 6+(1-1)(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 \/ */
	/6+(cpt-1)(nlstate+1)+1+(i-1)+(nlstate+1)nlstate; 6+(1-1)(2+1)+1+(1-1) +(2+1)2=13 /
	/6+1+(i-1)+(nlstate+1)nlstate; 6+1+(1-1) +(2+1)2=13 /
	/* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
	if(k==cptcoveff){
	fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Observed prevalence in state %d' w l lt 2",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
	2+cptcoveff2+3(cpt-1), cpt ); /* 4 or 6 ?*/
	}else{
	fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
	kl++;
	}
	} /* end covariate */
	} /* end if no covariate */

if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */	if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
/* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */	/* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */	fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
Line 6709 void printinggnuplot(char fileresu[], ch	Line 6877 void printinggnuplot(char fileresu[], ch
} /* end covariate */	} /* end covariate */
} /* end if no covariate */	} /* end if no covariate */
} /* end if backcast */	} /* end if backcast */
fprintf(ficgp,"\nset out \n");	fprintf(ficgp,"\nset out ;unset label;\n");
} /* nres */	} /* nres */
} /* k1 */	} /* k1 */
} /* cpt */	} /* cpt */
Line 6721 void printinggnuplot(char fileresu[], ch	Line 6889 void printinggnuplot(char fileresu[], ch
if(m != 1 && TKresult[nres]!= k1)	if(m != 1 && TKresult[nres]!= k1)
continue;	continue;
fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");	fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
	strcpy(gplotlabel,"(");
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
Line 6728 void printinggnuplot(char fileresu[], ch	Line 6897 void printinggnuplot(char fileresu[], ch
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];	vlv= nbcode[Tvaraff[k]][lv];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
/* for(k=1; k <= ncovds; k++){ */	/* for(k=1; k <= ncovds; k++){ */
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}
	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
Line 6742 void printinggnuplot(char fileresu[], ch	Line 6914 void printinggnuplot(char fileresu[], ch

fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);	fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);
for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/	for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
if(vpopbased==0)	fprintf(ficgp,"\nset label \"popbased %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",vpopbased,gplotlabel);
	if(vpopbased==0){
fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);	fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
else	}else
fprintf(ficgp,"\nreplot ");	fprintf(ficgp,"\nreplot ");
for (i=1; i<= nlstate+1 ; i ++) {	for (i=1; i<= nlstate+1 ; i ++) {
k=2*i;	k=2*i;
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);	fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1, vpopbased);
for (j=1; j<= nlstate+1 ; j ++) {	for (j=1; j<= nlstate+1 ; j ++) {
if (j==i) fprintf(ficgp," %%lf (%%lf)");	if (j==i) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%lf (%%lf)");	else fprintf(ficgp," %%lf (%%lf)");
}	}
if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);	if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);	else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);	fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
for (j=1; j<= nlstate+1 ; j ++) {	for (j=1; j<= nlstate+1 ; j ++) {
if (j==i) fprintf(ficgp," %%lf (%%lf)");	if (j==i) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%lf (%%lf)");	else fprintf(ficgp," %%lf (%%lf)");
}	}
fprintf(ficgp,"\" t\"\" w l lt 0,");	fprintf(ficgp,"\" t\"\" w l lt 0,");
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);	fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
for (j=1; j<= nlstate+1 ; j ++) {	for (j=1; j<= nlstate+1 ; j ++) {
if (j==i) fprintf(ficgp," %%lf (%%lf)");	if (j==i) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%lf (%%lf)");	else fprintf(ficgp," %%lf (%%lf)");
Line 6770 void printinggnuplot(char fileresu[], ch	Line 6943 void printinggnuplot(char fileresu[], ch
else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");	else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
} /* state */	} /* state */
} /* vpopbased */	} /* vpopbased */
fprintf(ficgp,"\nset out;set out \"%s_%d-%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1,nres); /* Buggy gnuplot */	fprintf(ficgp,"\nset out;set out \"%s_%d-%d.svg\"; replot; set out; unset label;\n",subdirf2(optionfilefiname,"E_"),k1,nres); /* Buggy gnuplot */
} /* end nres */	} /* end nres */
} /* k1 end 2 eme*/	} /* k1 end 2 eme*/

Line 6782 void printinggnuplot(char fileresu[], ch	Line 6955 void printinggnuplot(char fileresu[], ch
continue;	continue;

for (cpt=1; cpt<= nlstate ; cpt ++) {	for (cpt=1; cpt<= nlstate ; cpt ++) {
fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: combination=%d state=%d",k1, cpt);	fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files: combination=%d state=%d",k1, cpt);
	strcpy(gplotlabel,"(");
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
Line 6790 void printinggnuplot(char fileresu[], ch	Line 6964 void printinggnuplot(char fileresu[], ch
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];	vlv= nbcode[Tvaraff[k]][lv];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}
	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
Line 6803 void printinggnuplot(char fileresu[], ch	Line 6980 void printinggnuplot(char fileresu[], ch
/* k=2+nlstate(2cpt-2); */	/* k=2+nlstate(2cpt-2); */
k=2+(nlstate+1)*(cpt-1);	k=2+(nlstate+1)*(cpt-1);
fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
	fprintf(ficgp,"set label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);
fprintf(ficgp,"set ter svg size 640, 480\n\	fprintf(ficgp,"set ter svg size 640, 480\n\
plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);	plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),nres-1,nres-1,k,cpt);
/fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);	/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) ");	for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
fprintf(ficgp,"\" t \"e%d1\" w l",cpt);	fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
Line 6814 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 6992 plot [%.f:%.f] \"%s\" every :::%d::%d u

*/	*/
for (i=1; i< nlstate ; i ++) {	for (i=1; i< nlstate ; i ++) {
fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+i,cpt,i+1);	fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileresu,"E_"),nres-1,nres-1,k+i,cpt,i+1);
/* fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2i,cpt,i+1);/	/* fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2i,cpt,i+1);/

}	}
fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),k1-1,k1-1,k+nlstate,cpt);	fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileresu,"E_"),nres-1,nres-1,k+nlstate,cpt);
}	}
	fprintf(ficgp,"\nunset label;\n");
} /* end nres */	} /* end nres */
} /* end kl 3eme */	} /* end kl 3eme */

Line 6830 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 7009 plot [%.f:%.f] \"%s\" every :::%d::%d u
if(m != 1 && TKresult[nres]!= k1)	if(m != 1 && TKresult[nres]!= k1)
continue;	continue;
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
	strcpy(gplotlabel,"(");
fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);	fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
Line 6838 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 7018 plot [%.f:%.f] \"%s\" every :::%d::%d u
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];	vlv= nbcode[Tvaraff[k]][lv];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}
	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
Line 6849 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 7032 plot [%.f:%.f] \"%s\" every :::%d::%d u
}	}

fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
	fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);	set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
k=3;	k=3;
Line 6864 set ter svg size 640, 480\nunset log y\n	Line 7048 set ter svg size 640, 480\nunset log y\n
fprintf(ficgp,"+$%d",k+l+j-1);	fprintf(ficgp,"+$%d",k+l+j-1);
fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);	fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
} /* nlstate */	} /* nlstate */
fprintf(ficgp,"\nset out\n");	fprintf(ficgp,"\nset out; unset label;\n");
} /* end cpt state*/	} /* end cpt state*/
} /* end nres */	} /* end nres */
} /* end covariate k1 */	} /* end covariate k1 */
Line 6876 set ter svg size 640, 480\nunset log y\n	Line 7060 set ter svg size 640, 480\nunset log y\n
if(m != 1 && TKresult[nres]!= k1)	if(m != 1 && TKresult[nres]!= k1)
continue;	continue;
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
	strcpy(gplotlabel,"(");
fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);	fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
Line 6884 set ter svg size 640, 480\nunset log y\n	Line 7069 set ter svg size 640, 480\nunset log y\n
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];	vlv= nbcode[Tvaraff[k]][lv];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}
	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
Line 6895 set ter svg size 640, 480\nunset log y\n	Line 7083 set ter svg size 640, 480\nunset log y\n
}	}

fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
	fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);	set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
k=3;	k=3;
Line 6918 set ter svg size 640, 480\nunset log y\n	Line 7107 set ter svg size 640, 480\nunset log y\n
else	else
fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);	fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
}	}
fprintf(ficgp,"\nset out\n");	fprintf(ficgp,"\nset out; unset label;\n");
} /* end cpt state*/	} /* end cpt state*/
} /* end covariate */	} /* end covariate */
} /* end nres */	} /* end nres */
Line 6929 set ter svg size 640, 480\nunset log y\n	Line 7118 set ter svg size 640, 480\nunset log y\n
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
if(m != 1 && TKresult[nres]!= k1)	if(m != 1 && TKresult[nres]!= k1)
continue;	continue;
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
	strcpy(gplotlabel,"(");
fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);	fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
Line 6939 set ter svg size 640, 480\nunset log y\n	Line 7128 set ter svg size 640, 480\nunset log y\n
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];	vlv= nbcode[Tvaraff[k]][lv];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}
	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
Line 6950 set ter svg size 640, 480\nunset log y\n	Line 7142 set ter svg size 640, 480\nunset log y\n
}	}

fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1,nres);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
	fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);	set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
k=3; /* Offset */	k=3; /* Offset */
for (i=1; i<= nlstate ; i ++){	for (i=1; i<= nlstate ; i ++){ /* State of origin */
if(i==1)	if(i==1)
fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));	fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
else	else
fprintf(ficgp,", '' ");	fprintf(ficgp,", '' ");
l=(nlstate+ndeath)*(i-1)+1;	l=(nlstate+ndeath)(i-1)+1; / 1, 1+ nlstate+ndeath, 1+2(nlstate+ndeath) /
fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);	fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
for (j=2; j<= nlstate ; j ++)	for (j=2; j<= nlstate ; j ++)
fprintf(ficgp,"+$%d",k+l+j-1);	fprintf(ficgp,"+$%d",k+l+j-1);
fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);	fprintf(ficgp,")) t \"prev(%d,%d)\" w l",i,cpt);
} /* nlstate */	} /* nlstate */
fprintf(ficgp,"\nset out\n");	fprintf(ficgp,"\nset out; unset label;\n");
} /* end cpt state*/	} /* end cpt state*/
} /* end covariate */	} /* end covariate */

Line 6976 set ter svg size 640, 480\nunset log y\n	Line 7169 set ter svg size 640, 480\nunset log y\n
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
if(m != 1 && TKresult[nres]!= k1)	if(m != 1 && TKresult[nres]!= k1)
continue;	continue;
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life ending state */
fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);	strcpy(gplotlabel,"(");
	fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
Line 6985 set ter svg size 640, 480\nunset log y\n	Line 7179 set ter svg size 640, 480\nunset log y\n
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];	vlv= nbcode[Tvaraff[k]][lv];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}
	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
Line 6996 set ter svg size 640, 480\nunset log y\n	Line 7193 set ter svg size 640, 480\nunset log y\n
}	}

fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
	fprintf(ficgp,"set label \"Ending alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);	set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
k=3; /* Offset */	k=3; /* Offset */
for (i=1; i<= nlstate ; i ++){	for (i=1; i<= nlstate ; i ++){ /* State of origin */
if(i==1)	if(i==1)
fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));	fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
else	else
fprintf(ficgp,", '' ");	fprintf(ficgp,", '' ");
/* l=(nlstate+ndeath)(i-1)+1; /	/* l=(nlstate+ndeath)(i-1)+1; /
l=(nlstate+ndeath)*(cpt-1)+1;	l=(nlstate+ndeath)(cpt-1)+1; / fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2(nlstate+ndeath) /
/* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier \/ /	/* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier \/ /
/* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier \/ /	/* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier \/ /
fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */	fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */
/* for (j=2; j<= nlstate ; j ++) */	/* for (j=2; j<= nlstate ; j ++) */
/* fprintf(ficgp,"+$%d",k+l+j-1); */	/* fprintf(ficgp,"+$%d",k+l+j-1); */
/* /\* fprintf(ficgp,"+$%d",k+l+j-1); \/ /	/* /\* fprintf(ficgp,"+$%d",k+l+j-1); \/ /
fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);	fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
} /* nlstate */	} /* nlstate */
fprintf(ficgp,"\nset out\n");	fprintf(ficgp,"\nset out; unset label;\n");
} /* end cpt state*/	} /* end cpt state*/
} /* end covariate */	} /* end covariate */
} /* End if backcast */	} /* End if backcast */
Line 7028 set ter svg size 640, 480\nunset log y\n	Line 7226 set ter svg size 640, 480\nunset log y\n
if(m != 1 && TKresult[nres]!= k1)	if(m != 1 && TKresult[nres]!= k1)
continue;	continue;
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
	strcpy(gplotlabel,"(");
fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);	fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */	for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
Line 7036 set ter svg size 640, 480\nunset log y\n	Line 7235 set ter svg size 640, 480\nunset log y\n
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];	vlv= nbcode[Tvaraff[k]][lv];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}
	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
Line 7048 set ter svg size 640, 480\nunset log y\n	Line 7250 set ter svg size 640, 480\nunset log y\n

fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");	fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
	fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);	set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */	for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
Line 7110 set ter svg size 640, 480\nunset log y\n	Line 7313 set ter svg size 640, 480\nunset log y\n
}	}
} /* end if covariate */	} /* end if covariate */
} /* nlstate */	} /* nlstate */
fprintf(ficgp,"\nset out\n");	fprintf(ficgp,"\nset out; unset label;\n");
} /* end cpt state*/	} /* end cpt state*/
} /* end covariate */	} /* end covariate */
} /* End if prevfcast */	} /* End if prevfcast */
Line 7153 set ter svg size 640, 480\nunset log y\n	Line 7356 set ter svg size 640, 480\nunset log y\n
fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");	fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
fprintf(ficgp,"#model=%s \n",model);	fprintf(ficgp,"#model=%s \n",model);
fprintf(ficgp,"# Type of graphic ng=%d\n",ng);	fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */	fprintf(ficgp,"# k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
for(jk=1; jk <=m; jk++) /* For each combination of covariate */	for(k1=1; k1 <=m; k1++) /* For each combination of covariate */
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
if(m != 1 && TKresult[nres]!= jk)	if(m != 1 && TKresult[nres]!= k1)
continue;	continue;
fprintf(ficgp,"# Combination of dummy jk=%d and ",jk);	fprintf(ficgp,"\n\n# Combination of dummy k1=%d which is ",k1);
	strcpy(gplotlabel,"(");
	sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);
	for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
	vlv= nbcode[Tvaraff[k]][lv];
	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}
	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng,nres);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);
	fprintf(ficgp,"\nset label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);
fprintf(ficgp,"\nset ter svg size 640, 480 ");	fprintf(ficgp,"\nset ter svg size 640, 480 ");
if (ng==1){	if (ng==1){
fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12x) could be nice /	fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12x) could be nice /
Line 7213 set ter svg size 640, 480\nunset log y\n	Line 7430 set ter svg size 640, 480\nunset log y\n
fprintf(ficgp,"+p%d%dx",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;	fprintf(ficgp,"+p%d%dx",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
}else{ /* quantitative */	}else{ /* quantitative */
fprintf(ficgp,"+p%d%fx",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */	fprintf(ficgp,"+p%d%fx",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
/* fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */	/* fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
}	}
ij++;	ij++;
}	}
Line 7222 set ter svg size 640, 480\nunset log y\n	Line 7439 set ter svg size 640, 480\nunset log y\n
if(ijp <=cptcovprod) { /* Product */	if(ijp <=cptcovprod) { /* Product */
if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */	if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */	if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
/* fprintf(ficgp,"+p%d%d%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(jk,j)],nbcode[Tvard[ijp][2]][codtabm(jk,j)]); */	/* fprintf(ficgp,"+p%d%d%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */
fprintf(ficgp,"+p%d%d%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);	fprintf(ficgp,"+p%d%d%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
}else{ /* Vn is dummy and Vm is quanti */	}else{ /* Vn is dummy and Vm is quanti */
/* fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(jk,j)],Tqinvresult[nres][Tvard[ijp][2]]); */	/* fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);	fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
}	}
}else{ /* VnVm Vn is quanti /	}else{ /* VnVm Vn is quanti /
Line 7238 set ter svg size 640, 480\nunset log y\n	Line 7455 set ter svg size 640, 480\nunset log y\n
ijp++;	ijp++;
}	}
} else{ /* simple covariate */	} else{ /* simple covariate */
/* fprintf(ficgp,"+p%d%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(jk,j)]); /\ Valgrind bug nbcode \/ /	/* fprintf(ficgp,"+p%d%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\ Valgrind bug nbcode \/ /
if(Dummy[j]==0){	if(Dummy[j]==0){
fprintf(ficgp,"+p%d%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); / */	fprintf(ficgp,"+p%d%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); / */
}else{ /* quantitative */	}else{ /* quantitative */
fprintf(ficgp,"+p%d%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); / */	fprintf(ficgp,"+p%d%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); / */
/* fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */	/* fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
}	}
} /* end simple */	} /* end simple */
} /* end j */	} /* end j */
Line 7256 set ter svg size 640, 480\nunset log y\n	Line 7473 set ter svg size 640, 480\nunset log y\n
if(ng != 1){	if(ng != 1){
fprintf(ficgp,")/(1");	fprintf(ficgp,")/(1");

for(k1=1; k1 <=nlstate; k1++){	for(cpt=1; cpt <=nlstate; cpt++){
if(nagesqr==0)	if(nagesqr==0)
fprintf(ficgp,"+exp(p%d+p%dx",k3+(k1-1)ncovmodel,k3+(k1-1)*ncovmodel+1);	fprintf(ficgp,"+exp(p%d+p%dx",k3+(cpt-1)ncovmodel,k3+(cpt-1)*ncovmodel+1);
else /* nagesqr =1 */	else /* nagesqr =1 */
fprintf(ficgp,"+exp(p%d+p%dx+p%dxx",k3+(k1-1)ncovmodel,k3+(k1-1)ncovmodel+1,k3+(k1-1)ncovmodel+1+nagesqr);	fprintf(ficgp,"+exp(p%d+p%dx+p%dxx",k3+(cpt-1)ncovmodel,k3+(cpt-1)ncovmodel+1,k3+(cpt-1)ncovmodel+1+nagesqr);

ij=1;	ij=1;
for(j=3; j <=ncovmodel-nagesqr; j++){	for(j=3; j <=ncovmodel-nagesqr; j++){
if((j-2)==Tage[ij]) { /* Bug valgrind */	if((j-2)==Tage[ij]) { /* Bug valgrind */
if(ij <=cptcovage) { /* Bug valgrind */	if(ij <=cptcovage) { /* Bug valgrind */
fprintf(ficgp,"+p%d%dx",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);	fprintf(ficgp,"+p%d%dx",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);
/* fprintf(ficgp,"+p%d%dx",k3+(k1-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); /	/* fprintf(ficgp,"+p%d%dx",k3+(cpt-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); /
ij++;	ij++;
}	}
}	}
else	else
fprintf(ficgp,"+p%d%d",k3+(k1-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);/* Valgrind bug nbcode */	fprintf(ficgp,"+p%d%d",k3+(cpt-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);/* Valgrind bug nbcode */
}	}
fprintf(ficgp,")");	fprintf(ficgp,")");
}	}
Line 7292 set ter svg size 640, 480\nunset log y\n	Line 7509 set ter svg size 640, 480\nunset log y\n
i=i+ncovmodel;	i=i+ncovmodel;
} /* end k */	} /* end k */
} /* end k2 */	} /* end k2 */
fprintf(ficgp,"\n set out\n");	fprintf(ficgp,"\n set out; unset label;\n");
} /* end jk */	} /* end k1 */
} /* end ng */	} /* end ng */
/* avoid: */	/* avoid: */
fflush(ficgp);	fflush(ficgp);
Line 9088 int calandcheckages(int imx, int maxwav,	Line 9305 int calandcheckages(int imx, int maxwav,
nberr = nberr + 1;	nberr = nberr + 1;
if(firstone == 0){	if(firstone == 0){
firstone=1;	firstone=1;
printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\nOther similar cases in log file\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);	printf("Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we do not believe in a death, skipped.\nOther similar cases in log file\n", *nberr,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m);
}	}
fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);	fprintf(ficlog,"Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we do not believe in a death, skipped.\n", *nberr,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m);
s[m][i]=-1;	s[m][i]=-1; /* Droping the death status */
}	}
if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){	if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
(*nberr)++;	(*nberr)++;
printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);	printf("Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\nOther similar cases in log file\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m);
fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);	fprintf(ficlog,"Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m);
s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */	s[m][i]=-2; /* We prefer to skip it (and to skip it in version 0.8a1 too */
}	}
}	}
}	}
Line 9566 int back_prevalence_limit(double *p, dou	Line 9783 int back_prevalence_limit(double *p, dou
fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);	fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
} /* Age */	} /* Age */
/* was end of cptcod */	/* was end of cptcod */
	/fprintf(ficresplb,"\n");/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */
} /* end of any combination */	} /* end of any combination */
} /* end of nres */	} /* end of nres */
/* hBijx(p, bage, fage); */	/* hBijx(p, bage, fage); */
Line 9682 int hPijx(double *p, int bage, int fage)	Line 9900 int hPijx(double *p, int bage, int fage)

/* hstepm=1; aff par mois*/	/* hstepm=1; aff par mois*/
pstamp(ficrespijb);	pstamp(ficrespijb);
fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");	fprintf(ficrespijb,"#****** h Bij x Back probability to be in state i at age x-h being in j at x: B1j+B2j+...=1 ");
i1= pow(2,cptcoveff);	i1= pow(2,cptcoveff);
/* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */	/* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
/* /\for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){\/ */	/* /\for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){\/ */
Line 9698 int hPijx(double *p, int bage, int fage)	Line 9916 int hPijx(double *p, int bage, int fage)
fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
}	}
fprintf(ficrespijb,"******\n");	fprintf(ficrespijb,"******\n");
if(invalidvarcomb[k]){	if(invalidvarcomb[k]){ /* Is it necessary here? */
fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);	fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
continue;	continue;
}	}
Line 9716 int hPijx(double *p, int bage, int fage)	Line 9934 int hPijx(double *p, int bage, int fage)
/* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */	/* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);	hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);
/* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */	/* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");	fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
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(ficrespijb," %1d-%1d",i,j);	fprintf(ficrespijb," %1d-%1d",i,j);
Line 9762 int main(int argc, char *argv[])	Line 9980 int main(int argc, char *argv[])
int NDIM=2;	int NDIM=2;
int vpopbased=0;	int vpopbased=0;
int nres=0;	int nres=0;
	int endishere=0;

char ca[32], cb[32];	char ca[32], cb[32];
/* FILE fichtm; //* Html File */	/* FILE fichtm; //* Html File */
Line 10043 int main(int argc, char *argv[])	Line 10262 int main(int argc, char *argv[])
break;	break;
}	}
if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){	if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
if (num_filled == 0)	if (num_filled == 0){
model[0]='\0';	printf("ERROR %d: Model should be at minimum 'model=1+age.' WITHOUT space:'%s'\n",num_filled, line);
else if (num_filled != 1){	fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' WITHOUT space:'%s'\n",num_filled, line);
	model[0]='\0';
	goto end;
	} else if (num_filled != 1){
printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);	printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);	fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
model[0]='\0';	model[0]='\0';
Line 11136 Please run with mle=-1 to get a correct	Line 11358 Please run with mle=-1 to get a correct
fprintf(ficlog,"Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);	fprintf(ficlog,"Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
goto end;	goto end;
}	}
/* fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav); */
printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);	printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);	fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);	fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);	fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
}	}

Line 11172 Please run with mle=-1 to get a correct	Line 11392 Please run with mle=-1 to get a correct
fprintf(ficres,"pop_based=%d\n",popbased);	fprintf(ficres,"pop_based=%d\n",popbased);
}	}

while(fgets(line, MAXLINE, ficpar)) {
/* If line starts with a # it is a comment */
if (line[0] == '#') {
numlinepar++;
fputs(line,stdout);
fputs(line,ficparo);
fputs(line,ficlog);
continue;
}else
break;
}
/* while((c=getc(ficpar))=='#' && c!= EOF){ */
/* ungetc(c,ficpar); */
/* fgets(line, MAXLINE, ficpar); */
/* fputs(line,stdout); */
/* fputs(line,ficres); */
/* fputs(line,ficparo); */
/* } */
/* ungetc(c,ficpar); */

/* fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj); */
if((num_filled=sscanf(line,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj)) !=EOF){
if (num_filled != 8) {
printf("Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
goto end;
}
fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
/* day and month of proj2 are not used but only year anproj2.*/
}
while(fgets(line, MAXLINE, ficpar)) {
/* If line starts with a # it is a comment */
if (line[0] == '#') {
numlinepar++;
fputs(line,stdout);
fputs(line,ficparo);
fputs(line,ficlog);
continue;
}else
break;
}
/* while((c=getc(ficpar))=='#' && c!= EOF){ */
/* ungetc(c,ficpar); */
/* fgets(line, MAXLINE, ficpar); */
/* fputs(line,stdout); */
/* fputs(line,ficparo); */
/* fputs(line,ficres); */
/* } */
/* ungetc(c,ficpar); */

fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);
if((num_filled=sscanf(line,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj)) !=EOF){
if (num_filled != 8) {
printf("Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 finloal-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 finloal-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
goto end;
}
printf("backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
/* day and month of proj2 are not used but only year anproj2.*/
}
/* Results */	/* Results */
nresult=0;	nresult=0;
while(fgets(line, MAXLINE, ficpar)) {	do{
/* If line starts with a # it is a comment */	if(!fgets(line, MAXLINE, ficpar)){
if (line[0] == '#') {	endishere=1;
	parameterline=14;
	}else if (line[0] == '#') {
	/* If line starts with a # it is a comment */
numlinepar++;	numlinepar++;
fputs(line,stdout);	fputs(line,stdout);
fputs(line,ficparo);	fputs(line,ficparo);
fputs(line,ficlog);	fputs(line,ficlog);
fputs(line,ficres);
continue;	continue;
}else	}else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))
break;	parameterline=11;
}	else if(sscanf(line,"backcast=%[^\n]\n",modeltemp))
if (!feof(ficpar))	parameterline=12;
while((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){	else if(sscanf(line,"result:%[^\n]\n",modeltemp))
if (num_filled == 0){	parameterline=13;
resultline[0]='\0';	else{
printf("Warning %d: no result line should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);	parameterline=14;
break;
} else if (num_filled != 1){
printf("ERROR %d: result line should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
}
nresult++; /* Sum of resultlines */
printf("Result %d: result=%s\n",nresult, resultline);
if(nresult > MAXRESULTLINES){
printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
goto end;
}
decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
fprintf(ficparo,"result: %s\n",resultline);
fprintf(ficres,"result: %s\n",resultline);
fprintf(ficlog,"result: %s\n",resultline);
while(fgets(line, MAXLINE, ficpar)) {
/* If line starts with a # it is a comment */
if (line[0] == '#') {
numlinepar++;
fputs(line,stdout);
fputs(line,ficparo);
fputs(line,ficres);
fputs(line,ficlog);
continue;
}else
break;
}	}
if (feof(ficpar))	switch (parameterline){
	case 11:
	if((num_filled=sscanf(line,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj)) !=EOF){
	if (num_filled != 8) {
	printf("Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
	fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
	goto end;
	}
	fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
	printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
	fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
	fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
	/* day and month of proj2 are not used but only year anproj2.*/
	}
break;	break;
else{ /* Processess output results for this combination of covariate values */	case 12:
}	/fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);/
} /* end while */	if((num_filled=sscanf(line,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj)) !=EOF){
	if (num_filled != 8) {
	printf("Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
	fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
	goto end;
	}
	printf("backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
	fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
	fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
	fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
	/* day and month of proj2 are not used but only year anproj2.*/
	}
	break;
	case 13:
	if((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
	if (num_filled == 0){
	resultline[0]='\0';
	printf("Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);
	fprintf(ficlog,"Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);
	break;
	} else if (num_filled != 1){
	printf("ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
	fprintf(ficlog,"ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);
	}
	nresult++; /* Sum of resultlines */
	printf("Result %d: result=%s\n",nresult, resultline);
	if(nresult > MAXRESULTLINES){
	printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
	fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);
	goto end;
	}
	decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
	fprintf(ficparo,"result: %s\n",resultline);
	fprintf(ficres,"result: %s\n",resultline);
	fprintf(ficlog,"result: %s\n",resultline);
	break;
	case 14:
	if(ncovmodel >2 && nresult==0 ){
	printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
	goto end;
	}
	break;
	default:
	nresult=1;
	decoderesult(".",nresult ); /* No covariate */
	}
	} /* End switch parameterline */
	}while(endishere==0); /* End do */

/* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */	/* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
/* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */	/* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
Line 11307 Please run with mle=-1 to get a correct	Line 11495 Please run with mle=-1 to get a correct
printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p);	printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p);
}	}
printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \	printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \	model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,backcast, estepm, \
jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);	jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);

/------------ free_vector -------------/	/------------ free_vector -------------/
Line 11360 Please run with mle=-1 to get a correct	Line 11548 Please run with mle=-1 to get a correct
mobaverage=mobaverages;	mobaverage=mobaverages;
if (mobilav!=0) {	if (mobilav!=0) {
printf("Movingaveraging observed prevalence\n");	printf("Movingaveraging observed prevalence\n");
	fprintf(ficlog,"Movingaveraging observed prevalence\n");
if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){	if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);	fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
printf(" Error in movingaverage mobilav=%d\n",mobilav);	printf(" Error in movingaverage mobilav=%d\n",mobilav);
Line 11369 Please run with mle=-1 to get a correct	Line 11558 Please run with mle=-1 to get a correct
/* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */	/* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
else if (mobilavproj !=0) {	else if (mobilavproj !=0) {
printf("Movingaveraging projected observed prevalence\n");	printf("Movingaveraging projected observed prevalence\n");
	fprintf(ficlog,"Movingaveraging projected observed prevalence\n");
if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){	if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);	fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);	printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);

FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>

Removed from v.1.254
changed lines
	Added in v.1.265