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Diff for /imach/src/imach.c between versions 1.233 and 1.237

version 1.233, 2016/08/23 07:40:50	version 1.237, 2016/08/26 09:20:19
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	Revision 1.237 2016/08/26 09:20:19 brouard
	Summary: to valgrind

	Revision 1.236 2016/08/25 10:50:18 brouard
	* empty log message *

	Revision 1.235 2016/08/25 06:59:23 brouard
	* empty log message *

	Revision 1.234 2016/08/23 16:51:20 brouard
	* empty log message *

Revision 1.233 2016/08/23 07:40:50 brouard	Revision 1.233 2016/08/23 07:40:50 brouard
Summary: not working	Summary: not working

Line 920 int cptcoveff=0; /* Total number of cova	Line 932 int cptcoveff=0; /* Total number of cova
int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */	int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */
int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */	int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */
int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */	int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */
	int nsd=0; /*< Total number of single dummy variables (output) /
	int nsq=0; /*< Total number of single quantitative variables (output) /
int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */	int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */
int nqfveff=0; /*< nqfveff Number of Quantitative Fixed Variables Effective /	int nqfveff=0; /*< nqfveff Number of Quantitative Fixed Variables Effective /
int ntveff=0; /*< ntveff number of effective time varying variables /	int ntveff=0; /*< ntveff number of effective time varying variables /
Line 978 char fileresv[FILENAMELENGTH];	Line 991 char fileresv[FILENAMELENGTH];
FILE *ficresvpl;	FILE *ficresvpl;
char fileresvpl[FILENAMELENGTH];	char fileresvpl[FILENAMELENGTH];
char title[MAXLINE];	char title[MAXLINE];
	char model[MAXLINE]; /*< The model line /
char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH];	char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH];
char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];	char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];	char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
Line 1077 double **cotvar; / Time varying covari	Line 1091 double **cotvar; / Time varying covari
double **cotqvar; / Time varying quantitative covariate itqv */	double **cotqvar; / Time varying quantitative covariate itqv */
double idx;	double idx;
int *nbcode, Tvar; /*< model=V2 => Tvar[1]= 2 /	int *nbcode, Tvar; /*< model=V2 => Tvar[1]= 2 /
	/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
	/k 1 2 3 4 5 6 7 8 9 /
	/Tvar[k]= 5 4 3 6 5 2 7 1 1 /
	/* Tndvar[k] 1 2 3 4 5 */
	/TDvar 4 3 6 7 1 / /* For outputs only; combination of dummies fixed or varying */
	/* Tns[k] 1 2 2 4 5 / / Number of single cova */
	/* TvarsD[k] 1 2 3 / / Number of single dummy cova */
	/* TvarsDind 2 3 9 / / position K of single dummy cova */
	/* TvarsQ[k] 1 2 / / Number of single quantitative cova */
	/* TvarsQind 1 6 / / position K of single quantitative cova */
	/* Tprod[i]=k 4 7 */
	/* Tage[i]=k 5 8 */
	/* */
	/* Type */
	/* V 1 2 3 4 5 */
	/* F F V V V */
	/* D Q D D Q */
	/* */
	int *TvarsD;
	int *TvarsDind;
	int *TvarsQ;
	int *TvarsQind;

	#define MAXRESULTLINES 10
	int nresult=0;
	int TKresult[MAXRESULTLINES];
	int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
	int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
	int Tvresult[MAXRESULTLINES][NCOVMAX]; /* For dummy variable , variable # (output) */
	double Tqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
	double Tqinvresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */
	int Tvqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , variable # (output) */

	/* int TDvar; /\< TDvar[1]=4, TDvarF[2]=3, TDvar[3]=6 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 \/ */
int TvarF; /< TvarF[1]=Tvar[6]=2, TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 /	int TvarF; /< TvarF[1]=Tvar[6]=2, TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 /
int TvarFind; /< TvarFind[1]=6, TvarFind[2]=7, Tvarind[3]=9 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 /	int TvarFind; /< TvarFind[1]=6, TvarFind[2]=7, Tvarind[3]=9 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 /
int TvarV; /< TvarV[1]=Tvar[1]=5, TvarV[2]=Tvar[2]=4 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 /	int TvarV; /< TvarV[1]=Tvar[1]=5, TvarV[2]=Tvar[2]=4 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 /
Line 1336 int nbocc(char *s, char occ)	Line 1384 int nbocc(char *s, char occ)
i=0;	i=0;
lg=strlen(s);	lg=strlen(s);
for(i=0; i<= lg; i++) {	for(i=0; i<= lg; i++) {
if (s[i] == occ ) j++;	if (s[i] == occ ) j++;
}	}
return j;	return j;
}	}
Line 2227 void powell(double p[], double **xi, int	Line 2275 void powell(double p[], double **xi, int
if (directest < 0.0) { /* Then we use it for new direction */	if (directest < 0.0) { /* Then we use it for new direction */
#endif	#endif
#ifdef DEBUGLINMIN	#ifdef DEBUGLINMIN
printf("Before linmin in direction P%d-P0\n",n);	printf("Before linmin in direction P%d-P0\n",n);
for (j=1;j<=n;j++) {	for (j=1;j<=n;j++) {
printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);	printf(" Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);	fprintf(ficlog," Before xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
if(j % ncovmodel == 0){	if(j % ncovmodel == 0){
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
}	}
}	}
#endif	#endif
#ifdef LINMINORIGINAL	#ifdef LINMINORIGINAL
linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/	linmin(p,xit,n,fret,func); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
#else	#else
linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/	linmin(p,xit,n,fret,func,&flat); /* computes minimum on the extrapolated direction: changes p and rescales xit.*/
flatdir[i]=flat; /* Function is vanishing in that direction i */	flatdir[i]=flat; /* Function is vanishing in that direction i */
#endif	#endif

#ifdef DEBUGLINMIN	#ifdef DEBUGLINMIN
for (j=1;j<=n;j++) {	for (j=1;j<=n;j++) {
printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);	printf("After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);	fprintf(ficlog,"After xit[%d]= %12.7f p[%d]= %12.7f",j,xit[j],j,p[j]);
if(j % ncovmodel == 0){	if(j % ncovmodel == 0){
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
}	}
}	}
#endif	#endif
for (j=1;j<=n;j++) {	for (j=1;j<=n;j++) {
xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */	xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */	xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
}	}
#ifdef LINMINORIGINAL	#ifdef LINMINORIGINAL
#else	#else
for (j=1, flatd=0;j<=n;j++) {	for (j=1, flatd=0;j<=n;j++) {
if(flatdir[j]>0)	if(flatdir[j]>0)
flatd++;	flatd++;
}	}
if(flatd >0){	if(flatd >0){
printf("%d flat directions\n",flatd);	printf("%d flat directions\n",flatd);
fprintf(ficlog,"%d flat directions\n",flatd);	fprintf(ficlog,"%d flat directions\n",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);
fprintf(ficlog,"%d ",j);	fprintf(ficlog,"%d ",j);
}	}
}	}
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
}	}
#endif	#endif
printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);	printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);	fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);

#ifdef DEBUG	#ifdef DEBUG
printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);	printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);	fprintf(ficlog,"Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
for(j=1;j<=n;j++){	for(j=1;j<=n;j++){
printf(" %lf",xit[j]);	printf(" %lf",xit[j]);
fprintf(ficlog," %lf",xit[j]);	fprintf(ficlog," %lf",xit[j]);
}	}
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
#endif	#endif
} /* end of t or directest negative */	} /* end of t or directest negative */
#ifdef POWELLNOF3INFF1TEST	#ifdef POWELLNOF3INFF1TEST
#else	#else
} /* end if (fptt < fp) */	} /* end if (fptt < fp) */
#endif	#endif
#ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */	#ifdef NODIRECTIONCHANGEDUNTILNITER /* No change in drections until some iterations are done */
} /NODIRECTIONCHANGEDUNTILNITER No change in drections until some iterations are done /	} /NODIRECTIONCHANGEDUNTILNITER No change in drections until some iterations are done /
#else	#else
#endif	#endif
} /* loop iteration */	} /* loop iteration */
}	}

/** Prevalence limit (stable or period prevalence) **************/	/** Prevalence limit (stable or period prevalence) **************/

double prevalim(double prlim, int nlstate, double x[], double age, double oldm, double savm, double ftolpl, int *ncvyear, int ij)	double prevalim(double prlim, int nlstate, double x[], double age, double oldm, double savm, double ftolpl, int *ncvyear, int ij, int nres)
{	{
/* Computes the prevalence limit in each live state at age x and for covariate ij by left multiplying the unit	/* Computes the prevalence limit in each live state at age x and for covariate combination ij
matrix by transitions matrix until convergence is reached with precision ftolpl */	(and selected quantitative values in nres)
	by left multiplying the unit
	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 */
/* or prevalence in state 1, prevalence in state 2, 0 */	/* or prevalence in state 1, prevalence in state 2, 0 */
Line 2325 double prevalim(double prlim, int nl	Line 2375 double prevalim(double prlim, int nl
/* {0.51571254859325999, 0.4842874514067399, */	/* {0.51571254859325999, 0.4842874514067399, */
/* 0.51326036147820708, 0.48673963852179264} */	/* 0.51326036147820708, 0.48673963852179264} */
/* If we start from prlim again, prlim tends to a constant matrix */	/* If we start from prlim again, prlim tends to a constant matrix */

int i, ii,j,k;	int i, ii,j,k;
double min, max, *meandiff, maxmax,sumnew=0.;	double min, max, *meandiff, maxmax,sumnew=0.;
/* double *matprod2(); / /* test */	/* double *matprod2(); / /* test */
Line 2355 double prevalim(double prlim, int nl	Line 2405 double prevalim(double prlim, int nl
cov[2]=agefin;	cov[2]=agefin;
if(nagesqr==1)	if(nagesqr==1)
cov[3]= agefin*agefin;;	cov[3]= agefin*agefin;;
for (k=1; k<=cptcovn;k++) {	for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
/* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */	/* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
/* Here comes the value of the covariate 'ij' */	cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];	/* printf("prevalim 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("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); */	}
	for (k=1; k<=nsq;k++) { /* For single varying covariates only */
	/* Here comes the value of quantitative after renumbering k with single quantitative covariates */
	cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
	/* printf("prevalim Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
	}
	for (k=1; k<=cptcovage;k++){ /* For product with age */
	if(Dummy[Tvar[Tage[k]]]){
	cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
	} else{
	cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
	}
	/* printf("prevalim Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
	}
	for (k=1; k<=cptcovprod;k++){ /* For product without age */
	/* printf("prevalim Prod ij=%d k=%d Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
	if(Dummy[Tvard[k][1]==0]){
	if(Dummy[Tvard[k][2]==0]){
	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
	}else{
	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
	}
	}else{
	if(Dummy[Tvard[k][2]==0]){
	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
	}else{
	cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
	}
	}
}	}
/wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; */
/* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]cov[2]; /
for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
for (k=1; k<=cptcovprod;k++) /* Useless */
/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];

/printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);/	/printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);/
/printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);/	/printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);/
/printf("ij=%d cov[3]=%lf \n",ij, cov[3]);/	/printf("ij=%d cov[3]=%lf \n",ij, cov[3]);/
Line 2489 Earliest age to start was %d-%d=%d, ncvl	Line 2560 Earliest age to start was %d-%d=%d, ncvl
cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];	cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];
/* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); */	/* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); */
}	}
/wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; */
/* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]cov[2]; /
for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];	for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
for (k=1; k<=cptcovprod;k++) /* Useless */	for (k=1; k<=cptcovprod;k++) /* Useless */
/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */	/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
Line 2517 Earliest age to start was %d-%d=%d, ncvl	Line 2586 Earliest age to start was %d-%d=%d, ncvl
}	}
for(j=1; j<=nlstate; j++){	for(j=1; j<=nlstate; j++){
for(i=1;i<=nlstate;i++){	for(i=1;i<=nlstate;i++){
/* bprlim[i][j]= newm[i][j]/(1-sumnew); */	/* bprlim[i][j]= newm[i][j]/(1-sumnew); */
bprlim[i][j]= newm[i][j];	bprlim[i][j]= newm[i][j];
max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */	max[i]=FMAX(max[i],bprlim[i][j]); /* Max in line */
min[i]=FMIN(min[i],bprlim[i][j]);	min[i]=FMIN(min[i],bprlim[i][j]);
}	}
}	}

Line 2715 double bpmij(double ps, double *cov,	Line 2784 double bpmij(double ps, double *cov,
/double t34;/	/double t34;/
int i,j, nc, ii, jj;	int i,j, nc, ii, jj;

for(i=1; i<= nlstate; i++){	for(i=1; i<= nlstate; i++){
for(j=1; j<i;j++){	for(j=1; j<i;j++){
for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){	for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
/lnpijopii += param[i][j][nc]cov[nc];*/	/lnpijopii += param[i][j][nc]cov[nc];*/
lnpijopii += x[nc+((i-1)(nlstate+ndeath-1)+j-1)ncovmodel]*cov[nc];	lnpijopii += x[nc+((i-1)(nlstate+ndeath-1)+j-1)ncovmodel]*cov[nc];
/* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */	/* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
}	}
ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */	ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
/* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */	/* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
}	}
for(j=i+1; j<=nlstate+ndeath;j++){	for(j=i+1; j<=nlstate+ndeath;j++){
for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){	for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
/lnpijopii += x[(i-1)nlstatencovmodel+(j-2)ncovmodel+nc+(i-1)(ndeath-1)ncovmodel]cov[nc];/	/lnpijopii += x[(i-1)nlstatencovmodel+(j-2)ncovmodel+nc+(i-1)(ndeath-1)ncovmodel]cov[nc];/
lnpijopii += x[nc + ((i-1)(nlstate+ndeath-1)+(j-2))ncovmodel]*cov[nc];	lnpijopii += x[nc + ((i-1)(nlstate+ndeath-1)+(j-2))ncovmodel]*cov[nc];
/* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */	/* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
}	}
ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */	ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
}	}
}	}

for(i=1; i<= nlstate; i++){	for(i=1; i<= nlstate; i++){
s1=0;	s1=0;
for(j=1; j<i; j++){	for(j=1; j<i; j++){
s1+=exp(ps[i][j]); /* In fact sums pij/pii */	s1+=exp(ps[i][j]); /* In fact sums pij/pii */
/printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); /	/printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); /
}	}
for(j=i+1; j<=nlstate+ndeath; j++){	for(j=i+1; j<=nlstate+ndeath; j++){
s1+=exp(ps[i][j]); /* In fact sums pij/pii */	s1+=exp(ps[i][j]); /* In fact sums pij/pii */
/printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); /	/printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); /
}	}
/* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */	/* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
ps[i][i]=1./(s1+1.);	ps[i][i]=1./(s1+1.);
/* Computing other pijs */	/* Computing other pijs */
for(j=1; j<i; j++)	for(j=1; j<i; j++)
ps[i][j]= exp(ps[i][j])*ps[i][i];	ps[i][j]= exp(ps[i][j])*ps[i][i];
for(j=i+1; j<=nlstate+ndeath; j++)	for(j=i+1; j<=nlstate+ndeath; j++)
ps[i][j]= exp(ps[i][j])*ps[i][i];	ps[i][j]= exp(ps[i][j])*ps[i][i];
/* ps[i][nlstate+1]=1.-s1- ps[i][i];/ / Sum should be 1 */	/* ps[i][nlstate+1]=1.-s1- ps[i][i];/ / Sum should be 1 */
} /* end i */	} /* end i */

for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){	for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
for(jj=1; jj<= nlstate+ndeath; jj++){	for(jj=1; jj<= nlstate+ndeath; jj++){
ps[ii][jj]=0;	ps[ii][jj]=0;
ps[ii][ii]=1;	ps[ii][ii]=1;
}	}
}	}
/* Added for backcast / / Transposed matrix too */	/* Added for backcast / / Transposed matrix too */
for(jj=1; jj<= nlstate+ndeath; jj++){	for(jj=1; jj<= nlstate+ndeath; jj++){
s1=0.;	s1=0.;
for(ii=1; ii<= nlstate+ndeath; ii++){	for(ii=1; ii<= nlstate+ndeath; ii++){
s1+=ps[ii][jj];	s1+=ps[ii][jj];
}	}
for(ii=1; ii<= nlstate; ii++){	for(ii=1; ii<= nlstate; ii++){
ps[ii][jj]=ps[ii][jj]/s1;	ps[ii][jj]=ps[ii][jj]/s1;
}	}
}	}
/* Transposition */	/* Transposition */
for(jj=1; jj<= nlstate+ndeath; jj++){	for(jj=1; jj<= nlstate+ndeath; jj++){
for(ii=jj; ii<= nlstate+ndeath; ii++){	for(ii=jj; ii<= nlstate+ndeath; ii++){
s1=ps[ii][jj];	s1=ps[ii][jj];
ps[ii][jj]=ps[jj][ii];	ps[ii][jj]=ps[jj][ii];
ps[jj][ii]=s1;	ps[jj][ii]=s1;
}	}
}	}
/* for(ii=1; ii<= nlstate+ndeath; ii++){ */	/* for(ii=1; ii<= nlstate+ndeath; ii++){ */
/* for(jj=1; jj<= nlstate+ndeath; jj++){ */	/* for(jj=1; jj<= nlstate+ndeath; jj++){ */
/* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */	/* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
/* } */	/* } */
/* printf("\n "); */	/* printf("\n "); */
/* } */	/* } */
/* printf("\n ");printf("%lf ",cov[2]);*/	/* printf("\n ");printf("%lf ",cov[2]);*/
/*	/*
for(i=1; i<= npar; i++) printf("%f ",x[i]);	for(i=1; i<= npar; i++) printf("%f ",x[i]);
goto end;*/	goto end;*/
return ps;	return ps;
}	}


Line 2815 double matprod2(double out, double *	Line 2884 double matprod2(double out, double *

/*********** Higher Matrix Product *************/	/*********** Higher Matrix Product *************/

double *hpxij(double po, int nhstepm, double age, int hstepm, double x, int nlstate, int stepm, double oldm, double savm, int ij )	double *hpxij(double po, int nhstepm, double age, int hstepm, double x, int nlstate, int stepm, double oldm, double savm, int ij, int nres )
{	{
/* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over	/* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over
'nhstepmhstepmstepm' months (i.e. until	'nhstepmhstepmstepm' months (i.e. until
Line 2851 double *hpxij(double *po, int nhstep	Line 2920 double *hpxij(double *po, int nhstep
cov[2]=agexact;	cov[2]=agexact;
if(nagesqr==1)	if(nagesqr==1)
cov[3]= agexact*agexact;	cov[3]= agexact*agexact;
for (k=1; k<=cptcovn;k++)	for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];	/* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
/* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */	cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */	/* printf("hpxij 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)); */
/* cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; /	}
cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];	for (k=1; k<=nsq;k++) { /* For single varying covariates only */
/* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]cov[2]; /	/* Here comes the value of quantitative after renumbering k with single quantitative covariates */
for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */	cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];	/* printf("hPxij Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; /	}
	for (k=1; k<=cptcovage;k++){
	if(Dummy[Tvar[Tage[k]]]){
	cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
	} else{
	cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
	}
	/* printf("hPxij Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
	}
	for (k=1; k<=cptcovprod;k++){ /* */
	/* printf("hPxij Prod ij=%d k=%d Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
	}
	/* for (k=1; k<=cptcovn;k++) */
	/* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
	/* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 \/ /
	/* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]cov[2]; /
	/* for (k=1; k<=cptcovprod;k++) /\* Useless because included in cptcovn \/ /
	/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]nbcode[Tvard[k][2]][codtabm(ij,k)]; /


/printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);/	/printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);/
Line 3041 double func( double *x)	Line 3128 double func( double *x)
*/	*/
ioffset=2+nagesqr+cptcovage;	ioffset=2+nagesqr+cptcovage;
/* Fixed */	/* Fixed */
for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */	for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, only V1 is fixed (k=6)*/	cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, only V1 is fixed (k=6)*/
}	}
/* In model V2+V1V4+ageV3+V3V2 Tvar[1] is V2, Tvar[2=V1V4]	/* In model V2+V1V4+ageV3+V3V2 Tvar[1] is V2, Tvar[2=V1V4]
is 6, Tvar[3=ageV3] should not be computed because of age Tvar[4=V3V2]	is 6, Tvar[3=ageV3] should not be computed because of age Tvar[4=V3V2]
has been calculated etc */	has been calculated etc */
Line 3057 double func( double *x)	Line 3144 double func( double *x)
meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]	meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
*/	*/
for(mi=1; mi<= wav[i]-1; mi++){	for(mi=1; mi<= wav[i]-1; mi++){
for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/	for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i];	cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i];
}	}
for (ii=1;ii<=nlstate+ndeath;ii++)	for (ii=1;ii<=nlstate+ndeath;ii++)
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
oldm[ii][j]=(ii==j ? 1.0 : 0.0);	oldm[ii][j]=(ii==j ? 1.0 : 0.0);
savm[ii][j]=(ii==j ? 1.0 : 0.0);	savm[ii][j]=(ii==j ? 1.0 : 0.0);
}	}
for(d=0; d<dh[mi][i]; d++){	for(d=0; d<dh[mi][i]; d++){
newm=savm;	newm=savm;
agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;	agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
cov[2]=agexact;	cov[2]=agexact;
if(nagesqr==1)	if(nagesqr==1)
cov[3]= agexactagexact; / Should be changed here */	cov[3]= agexactagexact; / Should be changed here */
for (kk=1; kk<=cptcovage;kk++) {	for (kk=1; kk<=cptcovage;kk++) {
cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]agexact; / Tage[kk] gives the data-covariate associated with age */	cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]agexact; / Tage[kk] gives the data-covariate associated with age */
}	}
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));	1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
savm=oldm;	savm=oldm;
oldm=newm;	oldm=newm;
} /* end mult */	} /* end mult */

/lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);/ /* Original formula */	/lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);/ /* Original formula */
/* But now since version 0.9 we anticipate for bias at large stepm.	/* But now since version 0.9 we anticipate for bias at large stepm.
* If stepm is larger than one month (smallest stepm) and if the exact delay	* If stepm is larger than one month (smallest stepm) and if the exact delay
* (in months) between two waves is not a multiple of stepm, we rounded to	* (in months) between two waves is not a multiple of stepm, we rounded to
* the nearest (and in case of equal distance, to the lowest) interval but now	* the nearest (and in case of equal distance, to the lowest) interval but now
* we keep into memory the bias bh[mi][i] and also the previous matrix product	* we keep into memory the bias bh[mi][i] and also the previous matrix product
* (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the	* (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
* probability in order to take into account the bias as a fraction of the way	* probability in order to take into account the bias as a fraction of the way
* from savm to out if bh is negative or even beyond if bh is positive. bh varies	* from savm to out if bh is negative or even beyond if bh is positive. bh varies
* -stepm/2 to stepm/2 .	* -stepm/2 to stepm/2 .
* For stepm=1 the results are the same as for previous versions of Imach.	* For stepm=1 the results are the same as for previous versions of Imach.
* For stepm > 1 the results are less biased than in previous versions.	* For stepm > 1 the results are less biased than in previous versions.
*/	*/
s1=s[mw[mi][i]][i];	s1=s[mw[mi][i]][i];
s2=s[mw[mi+1][i]][i];	s2=s[mw[mi+1][i]][i];
bbh=(double)bh[mi][i]/(double)stepm;	bbh=(double)bh[mi][i]/(double)stepm;
/* bias bh is positive if real duration	/* bias bh is positive if real duration
* is higher than the multiple of stepm and negative otherwise.	* is higher than the multiple of stepm and negative otherwise.
*/	*/
/* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]):log((1.+bbh)out[s1][s2]));/	/* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]):log((1.+bbh)out[s1][s2]));/
if( s2 > nlstate){	if( s2 > nlstate){
/* i.e. if s2 is a death state and if the date of death is known	/* i.e. if s2 is a death state and if the date of death is known
then the contribution to the likelihood is the probability to	then the contribution to the likelihood is the probability to
die between last step unit time and current step unit time,	die between last step unit time and current step unit time,
which is also equal to probability to die before dh	which is also equal to probability to die before dh
minus probability to die before dh-stepm .	minus probability to die before dh-stepm .
In version up to 0.92 likelihood was computed	In version up to 0.92 likelihood was computed
as if date of death was unknown. Death was treated as any other	as if date of death was unknown. Death was treated as any other
health state: the date of the interview describes the actual state	health state: the date of the interview describes the actual state
and not the date of a change in health state. The former idea was	and not the date of a change in health state. The former idea was
to consider that at each interview the state was recorded	to consider that at each interview the state was recorded
(healthy, disable or death) and IMaCh was corrected; but when we	(healthy, disable or death) and IMaCh was corrected; but when we
introduced the exact date of death then we should have modified	introduced the exact date of death then we should have modified
the contribution of an exact death to the likelihood. This new	the contribution of an exact death to the likelihood. This new
contribution is smaller and very dependent of the step unit	contribution is smaller and very dependent of the step unit
stepm. It is no more the probability to die between last interview	stepm. It is no more the probability to die between last interview
and month of death but the probability to survive from last	and month of death but the probability to survive from last
interview up to one month before death multiplied by the	interview up to one month before death multiplied by the
probability to die within a month. Thanks to Chris	probability to die within a month. Thanks to Chris
Jackson for correcting this bug. Former versions increased	Jackson for correcting this bug. Former versions increased
mortality artificially. The bad side is that we add another loop	mortality artificially. The bad side is that we add another loop
which slows down the processing. The difference can be up to 10%	which slows down the processing. The difference can be up to 10%
lower mortality.	lower mortality.
*/	*/
/* If, at the beginning of the maximization mostly, the	/* If, at the beginning of the maximization mostly, the
cumulative probability or probability to be dead is	cumulative probability or probability to be dead is
constant (ie = 1) over time d, the difference is equal to	constant (ie = 1) over time d, the difference is equal to
0. out[s1][3] = savm[s1][3]: probability, being at state	0. out[s1][3] = savm[s1][3]: probability, being at state
s1 at precedent wave, to be dead a month before current	s1 at precedent wave, to be dead a month before current
wave is equal to probability, being at state s1 at	wave is equal to probability, being at state s1 at
precedent wave, to be dead at mont of the current	precedent wave, to be dead at mont of the current
wave. Then the observed probability (that this person died)	wave. Then the observed probability (that this person died)
is null according to current estimated parameter. In fact,	is null according to current estimated parameter. In fact,
it should be very low but not zero otherwise the log go to	it should be very low but not zero otherwise the log go to
infinity.	infinity.
*/	*/
/* #ifdef INFINITYORIGINAL */	/* #ifdef INFINITYORIGINAL */
/* lli=log(out[s1][s2] - savm[s1][s2]); */	/* lli=log(out[s1][s2] - savm[s1][s2]); */
/* #else */	/* #else */
Line 4017 void freqsummary(char fileres[], int ia	Line 4104 void freqsummary(char fileres[], int ia
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\	Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);	fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
}	}
fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition</h4>\n",fileresphtm, fileresphtm);	fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition and dummy covariate value at beginning of transition</h4>\n",fileresphtm, fileresphtm);

strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));	strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {	if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
Line 4078 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4165 Title=%s <br>Datafile=%s Firstpass=%d La
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(anyvaryingduminmodel==0){ /* If All fixed covariates */	if(anyvaryingduminmodel==0){ /* If All fixed covariates */
if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */	if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
/* for (z1=1; z1<= nqfveff; z1++) { */	/* for (z1=1; z1<= nqfveff; z1++) { */
/* meanq[z1]+=coqvar[Tvar[z1]][iind]; /\* Computes mean of quantitative with selected filter \/ /	/* meanq[z1]+=coqvar[Tvar[z1]][iind]; /\* Computes mean of quantitative with selected filter \/ /
/* } */	/* } */
for (z1=1; z1<=cptcoveff; z1++) {	for (z1=1; z1<=cptcoveff; z1++) {
/* if(Tvaraff[z1] ==-20){ */	/* if(Tvaraff[z1] ==-20){ */
/* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; \/ /	/* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; \/ /
/* }else if(Tvaraff[z1] ==-10){ */	/* }else if(Tvaraff[z1] ==-10){ */
/* /\* sumnew+=coqvar[z1][iind]; \/ /	/* /\* sumnew+=coqvar[z1][iind]; \/ /
/* }else */	/* }else */
if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){	if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){
/* Tests if this individual iind responded to j1 (V4=1 V3=0) */	/* Tests if this individual iind responded to j1 (V4=1 V3=0) */
bool=0;	bool=0;
/* 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),
j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/	j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
/* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/	/* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
} /* Onlyf fixed */	} /* Onlyf fixed */
} /* end z1 */	} /* end z1 */
} /* cptcovn > 0 */	} /* cptcovn > 0 */
} /* end any */	} /* end any */
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 or all fixed */
/* 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];
if(anyvaryingduminmodel==1){ /* Some are varying covariates */	if(anyvaryingduminmodel==1){ /* Some are varying covariates */
for (z1=1; z1<=cptcoveff; z1++) {	for (z1=1; z1<=cptcoveff; z1++) {
if( Fixed[Tmodelind[z1]]==1){	if( Fixed[Tmodelind[z1]]==1){
iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;	iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */	if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */
bool=0;	bool=0;
}else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */	}else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {	if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
bool=0;	bool=0;
}	}
}	}
}	}
}/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */	}/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */
/* bool =0 we keep that guy which corresponds to the combination of dummy values */	/* bool =0 we keep that guy which corresponds to the combination of dummy values */
if(bool==1){	if(bool==1){
/* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]	/* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
and mw[mi+1][iind]. dh depends on stepm. */	and mw[mi+1][iind]. dh depends on stepm. */
agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/	agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
ageend=agev[m][iind]+(dh[m][iind])stepm/YEARM; / Age at end of wave and transition */	ageend=agev[m][iind]+(dh[m][iind])stepm/YEARM; / Age at end of wave and transition */
if(m >=firstpass && m <=lastpass){	if(m >=firstpass && m <=lastpass){
k2=anint[m][iind]+(mint[m][iind]/12.);	k2=anint[m][iind]+(mint[m][iind]/12.);
/if ((k2>=dateprev1) && (k2<=dateprev2)) {/	/if ((k2>=dateprev1) && (k2<=dateprev2)) {/
if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */	if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */	if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */	if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */
prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */	prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
if (m<lastpass) {	if (m<lastpass) {
/* if(s[m][iind]==4 && s[m+1][iind]==4) */	/* if(s[m][iind]==4 && s[m+1][iind]==4) */
/* printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind]); */	/* printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind]); */
if(s[m][iind]==-1)	if(s[m][iind]==-1)
printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));	printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));
freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */	freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
/* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */	/* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 // At age of beginning of transition, where status is known */	freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 // At age of beginning of transition, where status is known */
}	}
} /* end if between passes */	} /* end if between passes */
if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {	if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {
dateintsum=dateintsum+k2;	dateintsum=dateintsum+k2;
k2cpt++;	k2cpt++;
/* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */	/* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
}	}
} /* end bool 2 */	} /* end bool 2 */
} /* end m */	} /* end m */
} /* end bool */	} /* end bool */
} /* end iind = 1 to imx */	} /* end iind = 1 to imx */
/* prop[s][age] is feeded for any initial and valid live state as well as	/* prop[s][age] is feeded for any initial and valid live state as well as
Line 4160 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4247 Title=%s <br>Datafile=%s Firstpass=%d La
fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");	fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");	fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
for (z1=1; z1<=cptcoveff; z1++){	for (z1=1; z1<=cptcoveff; z1++){
fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
}	}
fprintf(ficresp, "**********\n#");	fprintf(ficresp, "**********\n#");
fprintf(ficresphtm, "**********</h3>\n");	fprintf(ficresphtm, "**********</h3>\n");
Line 4184 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4271 Title=%s <br>Datafile=%s Firstpass=%d La
fprintf(ficresphtmfr,"<th>Age</th> ");	fprintf(ficresphtmfr,"<th>Age</th> ");
for(jk=-1; jk <=nlstate+ndeath; jk++){	for(jk=-1; jk <=nlstate+ndeath; jk++){
for(m=-1; m <=nlstate+ndeath; m++){	for(m=-1; m <=nlstate+ndeath; m++){
if(jk!=0 && m!=0)	if(jk!=0 && m!=0)
fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);	fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
}	}
}	}
fprintf(ficresphtmfr, "\n");	fprintf(ficresphtmfr, "\n");
Line 4821 void concatwav(int wav[], int **dh, int	Line 4908 void concatwav(int wav[], int **dh, int

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

void evsij(double *eij, double x[], int nlstate, int stepm, int bage, int fage, double oldm, double **savm, int cij, int estepm,char strstart[] )	void evsij(double *eij, double x[], int nlstate, int stepm, int bage, int fage, double oldm, double **savm, int cij, int estepm,char strstart[], int nres )

{	{
/* Health expectancies, no variances */	/* Health expectancies, no variances */
Line 4894 void evsij(double ***eij, double x[], in	Line 4981 void evsij(double ***eij, double x[], in
/* Computed by stepm unit matrices, product of hstepma matrices, stored	/* Computed by stepm unit matrices, product of hstepma matrices, stored
in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */	in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */

hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);	hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);

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

Line 4929 void evsij(double ***eij, double x[], in	Line 5016 void evsij(double ***eij, double x[], in

}	}

void cvevsij(double *eij, double x[], int nlstate, int stepm, int bage, int fage, double oldm, double savm, int cij, int estepm,double delti[],double matcov,char strstart[] )	void cvevsij(double *eij, double x[], int nlstate, int stepm, int bage, int fage, double oldm, double savm, int cij, int estepm,double delti[],double matcov,char strstart[], int nres )

{	{
/* Covariances of health expectancies eij and of total life expectancies according	/* Covariances of health expectancies eij and of total life expectancies according
Line 5042 void cvevsij(double ***eij, double x[],	Line 5129 void cvevsij(double ***eij, double x[],
xp[i] = x[i] + (i==theta ?delti[theta]:0);	xp[i] = x[i] + (i==theta ?delti[theta]:0);
xm[i] = x[i] - (i==theta ?delti[theta]:0);	xm[i] = x[i] - (i==theta ?delti[theta]:0);
}	}
hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);	hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij, nres);
hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);	hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij, nres);

for(j=1; j<= nlstate; j++){	for(j=1; j<= nlstate; j++){
for(i=1; i<=nlstate; i++){	for(i=1; i<=nlstate; i++){
Line 5084 void cvevsij(double ***eij, double x[],	Line 5171 void cvevsij(double ***eij, double x[],
}	}

/* Computing expectancies */	/* Computing expectancies */
hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);	hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++)	for(j=1; j<=nlstate;j++)
for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){	for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
Line 5139 void cvevsij(double ***eij, double x[],	Line 5226 void cvevsij(double ***eij, double x[],
}	}

/********** Variance ****************/	/********** Variance ****************/
void varevsij(char optionfilefiname[], double *vareij, double matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double oldm, double savm, double *prlim, double ftolpl, int ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])	void varevsij(char optionfilefiname[], double *vareij, double matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double oldm, double savm, double *prlim, double ftolpl, int ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[], int nres)
{	{
/* Variance of health expectancies */	/* Variance of health expectancies */
/* double prevalim(double prlim, int nlstate, double xp, double age, double oldm, double * savm,double ftolpl);*/	/* double prevalim(double prlim, int nlstate, double xp, double age, double oldm, double * savm,double ftolpl);*/
Line 5265 void cvevsij(double ***eij, double x[],	Line 5352 void cvevsij(double ***eij, double x[],
xp[i] = x[i] + (i==theta ?delti[theta]:0);	xp[i] = x[i] + (i==theta ?delti[theta]:0);
}	}

prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);	prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nresult);

if (popbased==1) {	if (popbased==1) {
if(mobilav ==0){	if(mobilav ==0){
Line 5277 void cvevsij(double ***eij, double x[],	Line 5364 void cvevsij(double ***eij, double x[],
}	}
}	}

hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij); /* Returns p3mat[i][j][h] for h=1 to nhstepm */	hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres); /* Returns p3mat[i][j][h] for h=1 to nhstepm */
for(j=1; j<= nlstate; j++){	for(j=1; j<= nlstate; j++){
for(h=0; h<=nhstepm; h++){	for(h=0; h<=nhstepm; h++){
for(i=1, gp[h][j]=0.;i<=nlstate;i++)	for(i=1, gp[h][j]=0.;i<=nlstate;i++)
Line 5297 void cvevsij(double ***eij, double x[],	Line 5384 void cvevsij(double ***eij, double x[],
for(i=1; i<=npar; i++) /* Computes gradient x - delta */	for(i=1; i<=npar; i++) /* Computes gradient x - delta */
xp[i] = x[i] - (i==theta ?delti[theta]:0);	xp[i] = x[i] - (i==theta ?delti[theta]:0);

prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij);	prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nresult);

if (popbased==1) {	if (popbased==1) {
if(mobilav ==0){	if(mobilav ==0){
Line 5309 void cvevsij(double ***eij, double x[],	Line 5396 void cvevsij(double ***eij, double x[],
}	}
}	}

hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);	hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres);

for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */	for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
for(h=0; h<=nhstepm; h++){	for(h=0; h<=nhstepm; h++){
Line 5374 void cvevsij(double ***eij, double x[],	Line 5461 void cvevsij(double ***eij, double x[],
/* end ppptj */	/* end ppptj */
/* x centered again */	/* x centered again */

prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij);	prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ncvyearp,ij, nresult);

if (popbased==1) {	if (popbased==1) {
if(mobilav ==0){	if(mobilav ==0){
Line 5390 void cvevsij(double ***eij, double x[],	Line 5477 void cvevsij(double ***eij, double x[],
computed over hstepm (estepm) matrices product = hstepm*stepm months)	computed over hstepm (estepm) matrices product = hstepm*stepm months)
as a weighted average of prlim.	as a weighted average of prlim.
*/	*/
hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);	hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij, nres);
for(j=nlstate+1;j<=nlstate+ndeath;j++){	for(j=nlstate+1;j<=nlstate+ndeath;j++){
for(i=1,gmp[j]=0.;i<= nlstate; i++)	for(i=1,gmp[j]=0.;i<= nlstate; i++)
gmp[j] += prlim[i][i]*p3mat[i][j][1];	gmp[j] += prlim[i][i]*p3mat[i][j][1];
Line 5453 void cvevsij(double ***eij, double x[],	Line 5540 void cvevsij(double ***eij, double x[],
} /* end varevsij */	} /* end varevsij */

/********** Variance of prevlim ****************/	/********** Variance of prevlim ****************/
void varprevlim(char fileres[], double varpl, double matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double oldm, double savm, double *prlim, double ftolpl, int ncvyearp, int ij, char strstart[])	void varprevlim(char fileres[], double varpl, double matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double oldm, double savm, double *prlim, double ftolpl, int ncvyearp, int ij, char strstart[], int nres)
{	{
/* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/	/* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
/* double prevalim(double prlim, int nlstate, double xp, double age, double oldm, double savm,double ftolpl);/	/* double prevalim(double prlim, int nlstate, double xp, double age, double oldm, double savm,double ftolpl);/
Line 5496 void cvevsij(double ***eij, double x[],	Line 5583 void cvevsij(double ***eij, double x[],
xp[i] = x[i] + (i==theta ?delti[theta]:0);	xp[i] = x[i] + (i==theta ?delti[theta]:0);
}	}
if((int)age==79 \|\|(int)age== 80 \|\|(int)age== 81 )	if((int)age==79 \|\|(int)age== 80 \|\|(int)age== 81 )
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);	prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
else	else
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);	prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
for(i=1;i<=nlstate;i++){	for(i=1;i<=nlstate;i++){
gp[i] = prlim[i][i];	gp[i] = prlim[i][i];
mgp[theta][i] = prlim[i][i];	mgp[theta][i] = prlim[i][i];
Line 5506 void cvevsij(double ***eij, double x[],	Line 5593 void cvevsij(double ***eij, double x[],
for(i=1; i<=npar; i++) /* Computes gradient */	for(i=1; i<=npar; i++) /* Computes gradient */
xp[i] = x[i] - (i==theta ?delti[theta]:0);	xp[i] = x[i] - (i==theta ?delti[theta]:0);
if((int)age==79 \|\|(int)age== 80 \|\|(int)age== 81 )	if((int)age==79 \|\|(int)age== 80 \|\|(int)age== 81 )
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);	prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
else	else
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij);	prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
for(i=1;i<=nlstate;i++){	for(i=1;i<=nlstate;i++){
gm[i] = prlim[i][i];	gm[i] = prlim[i][i];
mgm[theta][i] = prlim[i][i];	mgm[theta][i] = prlim[i][i];
Line 5916 void printinghtml(char fileresu[], char	Line 6003 void printinghtml(char fileresu[], char
int popforecast, int prevfcast, int backcast, int estepm , \	int popforecast, int prevfcast, 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;	int jj1, k1, i1, cpt, k4, nres;

fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \	fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
<li><a href='#secondorder'>Result files (second order (variance)</a>\n \	<li><a href='#secondorder'>Result files (second order (variance)</a>\n \
</ul>");	</ul>");
	fprintf(fichtm,"<ul><li> model=1+age+%s\n \
	</ul>", model);
fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");	fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",	fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",
jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));	jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
Line 5955 void printinghtml(char fileresu[], char	Line 6044 void printinghtml(char fileresu[], char
if (cptcovn < 1) {m=1;ncodemax[1]=1;}	if (cptcovn < 1) {m=1;ncodemax[1]=1;}

jj1=0;	jj1=0;

	for(nres=1; nres <= nresult; nres++) /* For each resultline */
for(k1=1; k1<=m;k1++){	for(k1=1; k1<=m;k1++){
	if(TKresult[nres]!= k1)
	continue;

/* for(i1=1; i1<=ncodemax[k1];i1++){ */	/* for(i1=1; i1<=ncodemax[k1];i1++){ */
jj1++;	jj1++;
if (cptcovn > 0) {	if (cptcovn > 0) {
fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");	fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
for (cpt=1; cpt<=cptcoveff;cpt++){	for (cpt=1; cpt<=cptcoveff;cpt++){
fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);	fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout);	printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
	/* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]); */
	/* printf(" V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);fflush(stdout); */
}	}
	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
	fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);fflush(stdout);
	}

/* if(nqfveff+nqtveff 0) / / Test to be done */	/* if(nqfveff+nqtveff 0) / / Test to be done */
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");	fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
Line 6076 See page 'Matrix of variance-covariance	Line 6176 See page 'Matrix of variance-covariance
if (cptcovn < 1) {m=1;ncodemax[1]=1;}	if (cptcovn < 1) {m=1;ncodemax[1]=1;}

jj1=0;	jj1=0;

	for(nres=1; nres <= nresult; nres++) /* For each resultline */
for(k1=1; k1<=m;k1++){	for(k1=1; k1<=m;k1++){
	if(TKresult[nres]!= k1)
	continue;
/* for(i1=1; i1<=ncodemax[k1];i1++){ */	/* for(i1=1; i1<=ncodemax[k1];i1++){ */
jj1++;	jj1++;
if (cptcovn > 0) {	if (cptcovn > 0) {
fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");	fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
for (cpt=1; cpt<=cptcoveff;cpt++) /*< cptcoveff number of variables /	for (cpt=1; cpt<=cptcoveff;cpt++) /*< cptcoveff number of variables /
fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,cpt)]);	fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);
	/* fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtabm(jj1,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," ************\n<hr size=\"2\" color=\"#EC5E5E\">");	fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");

if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
Line 6112 void printinggnuplot(char fileresu[], ch	Line 6221 void printinggnuplot(char fileresu[], ch

char dirfileres[132],optfileres[132];	char dirfileres[132],optfileres[132];
char gplotcondition[132];	char gplotcondition[132];
int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=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;
int vpopbased;	int vpopbased;
int ioffset; /* variable offset for columns */	int ioffset; /* variable offset for columns */
	int nres=0; /* Index of resultline */

/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */	/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
/* printf("Problem with file %s",optionfilegnuplot); */	/* printf("Problem with file %s",optionfilegnuplot); */
Line 6161 void printinggnuplot(char fileresu[], ch	Line 6271 void printinggnuplot(char fileresu[], ch
strcpy(optfileres,"vpl");	strcpy(optfileres,"vpl");
/* 1eme*/	/* 1eme*/
for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */	for (cpt=1; cpt<= nlstate ; cpt ++) { /* For each live state */
for (k1=1; k1<= m && selected(k1) ; k1 ++) { /* For each valid combination of covariate */	for (k1=1; k1<= m ; k1 ++) /* For each valid combination of covariate */
/* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files ");	/* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
	if(TKresult[nres]!= k1)
	continue;
	/* We are interested in selected combination by the resultline */
	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);
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 6171 void printinggnuplot(char fileresu[], ch	Line 6286 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 is the value of the covariate lv, 0 or 1 */	vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
/* 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);
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
}	}
	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
	printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	}
	printf("\n#\n");
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);
continue;	continue;
}	}

fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);	fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);
fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);	fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);
fprintf(ficgp,"set xlabel \"Age\" \n\	fprintf(ficgp,"set xlabel \"Age\" \n\
set ylabel \"Probability\" \n \	set ylabel \"Probability\" \n \
set ter svg size 640, 480\n \	set ter svg size 640, 480\n \
plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);	plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);

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)");
Line 6232 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 6353 plot [%.f:%.f] \"%s\" every :::%d::%d u
fprintf(ficgp,"\nset out \n");	fprintf(ficgp,"\nset out \n");
} /* k1 */	} /* k1 */
} /* cpt */	} /* cpt */
/2 eme/
for (k1=1; k1<= m ; k1 ++) {


	/2 eme/
	for (k1=1; k1<= m ; k1 ++)
	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
	if(TKresult[nres]!= k1)
	continue;
fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");	fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
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 6244 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 6369 plot [%.f:%.f] \"%s\" every :::%d::%d u
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);
}	}
	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
	printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	}
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 6281 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 6410 plot [%.f:%.f] \"%s\" every :::%d::%d u
} /* state */	} /* state */
} /* vpopbased */	} /* vpopbased */
fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */	fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
} /* k1 */	} /* k1 end 2 eme*/


/3eme/	/3eme/
for (k1=1; k1<= m ; k1 ++) {	for (k1=1; k1<= m ; k1 ++)
	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
	if(TKresult[nres]!= k)
	continue;

for (cpt=1; cpt<= nlstate ; cpt ++) {	for (cpt=1; cpt<= nlstate ; cpt ++) {
fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: cov=%d state=%d",k1, cpt);	fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: combination=%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 dummy combination 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 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
Line 6297 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 6429 plot [%.f:%.f] \"%s\" every :::%d::%d u
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);
}	}
	/* for(k=1; k <= ncovds; k++){ */
	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,"\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 6327 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 6463 plot [%.f:%.f] \"%s\" every :::%d::%d u

/* 4eme */	/* 4eme */
/* Survival functions (period) from state i in state j by initial state i */	/* Survival functions (period) from state i in state j by initial state i */
for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */	for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
	if(TKresult[nres]!= k1)
	continue;

for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
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);
Line 6339 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 6478 plot [%.f:%.f] \"%s\" every :::%d::%d u
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);
}	}
	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,"\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 6369 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6511 plot [%.f:%.f] ", ageminpar, agemaxpar)

/* 5eme */	/* 5eme */
/* Survival functions (period) from state i in state j by final state j */	/* Survival functions (period) from state i in state j by final state j */
for (k1=1; k1<= m ; k1 ++) { /* For each covariate if any */	for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
	if(TKresult[nres]!= k1)
	continue;
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */

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);
Line 6381 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6526 plot [%.f:%.f] ", ageminpar, agemaxpar)
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);
}	}
	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,"\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 6419 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6567 plot [%.f:%.f] ", ageminpar, agemaxpar)

/* 6eme */	/* 6eme */
/* CV preval stable (period) for each covariate */	/* CV preval stable (period) for each covariate */
for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2*k), if any covariate is present /	for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
	if(TKresult[nres]!= k1)
	continue;
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */

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);
Line 6431 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6582 plot [%.f:%.f] ", ageminpar, agemaxpar)
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);
}	}
	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,"\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 6462 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6616 plot [%.f:%.f] ", ageminpar, agemaxpar)
/* 7eme */	/* 7eme */
if(backcast == 1){	if(backcast == 1){
/* CV back preval stable (period) for each covariate */	/* CV back preval stable (period) for each covariate */
for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2*k), if any covariate is present /	for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
	if(TKresult[nres]!= k1)
	continue;
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);	fprintf(ficgp,"\n#\n#\n#CV Back 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 */
Line 6473 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6630 plot [%.f:%.f] ", ageminpar, agemaxpar)
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);
}	}
	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,"\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 6509 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6669 plot [%.f:%.f] ", ageminpar, agemaxpar)
if(prevfcast==1){	if(prevfcast==1){
/* Projection from cross-sectional to stable (period) for each covariate */	/* Projection from cross-sectional to stable (period) for each covariate */

for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2*k), if any covariate is present /	for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
	if(TKresult[nres]!= k1)
	continue;
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
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 */
Line 6520 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6683 plot [%.f:%.f] ", ageminpar, agemaxpar)
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);
}	}
	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,"\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 6631 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6797 plot [%.f:%.f] ", ageminpar, agemaxpar)
fprintf(ficgp,"# +exp(a14+b14age+c14ageage+d14V1+e14V1*age)+...)\n");	fprintf(ficgp,"# +exp(a14+b14age+c14ageage+d14V1+e14V1*age)+...)\n");
fprintf(ficgp,"#\n");	fprintf(ficgp,"#\n");
for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/	for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
	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,"# ng=%d\n",ng);	fprintf(ficgp,"# ng=%d\n",ng);
fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);	fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
for(jk=1; jk <=m; jk++) {	for(jk=1; jk <=m; jk++) /* For each combination of covariate */
fprintf(ficgp,"# jk=%d\n",jk);	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
	if(TKresult[nres]!= jk)
	continue;
	fprintf(ficgp,"# Combination of dummy jk=%d and ",jk);
	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,"\n#\n");
fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);	fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);
fprintf(ficgp,"\nset ter svg size 640, 480 ");	fprintf(ficgp,"\nset ter svg size 640, 480 ");
if (ng==1){	if (ng==1){
Line 6675 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6850 plot [%.f:%.f] ", ageminpar, agemaxpar)
break;	break;
}	}
ij=1;/* To be checked else nbcode[0][0] wrong */	ij=1;/* To be checked else nbcode[0][0] wrong */
for(j=3; j <=ncovmodel-nagesqr; j++) {	ijp=1; /* product no age */
	/* for(j=3; j <=ncovmodel-nagesqr; j++) { */
	for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
/* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */	/* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
if(ij <=cptcovage) { /* Bug valgrind */	if(j==Tage[ij]) { /* Product by age */
if((j-2)==Tage[ij]) { /* Bug valgrind */	if(ij <=cptcovage) { /* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, 2 V5 and V1 */
fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);	if(Dummy[j]==0){
/* 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+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
	}else{ /* quantitative */
	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])]); */
	}
ij++;	ij++;
}	}
}	}else if(j==Tprod[ijp]) { /* */
else	/* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
fprintf(ficgp,"+p%d%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); / Valgrind bug nbcode */	if(ijp <=cptcovprod) { /* Product */
}	if(Dummy[Tvard[ijp][1]]==0){/* Vn is dummy */
	if(Dummy[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,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
	}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,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
	}
	}else{ /* VnVm Vn is quanti /
	if(Dummy[Tvard[ijp][2]]==0){
	fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
	}else{ /* Both quanti */
	fprintf(ficgp,"+p%d%f%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
	}
	}
	}
	} else{ /* simple covariate */
	/* fprintf(ficgp,"+p%d%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(jk,j)]); /\ Valgrind bug nbcode \/ /
	if(Dummy[j]==0){
	fprintf(ficgp,"+p%d%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); / */
	}else{ /* quantitative */
	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])]); */
	}
	} /* end simple */
	} /* end j */
}else{	}else{
i=i-ncovmodel;	i=i-ncovmodel;
if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */	if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
Line 6704 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6910 plot [%.f:%.f] ", ageminpar, agemaxpar)

ij=1;	ij=1;
for(j=3; j <=ncovmodel-nagesqr; j++){	for(j=3; j <=ncovmodel-nagesqr; j++){
if(ij <=cptcovage) { /* Bug valgrind */	if((j-2)==Tage[ij]) { /* Bug valgrind */
if((j-2)==Tage[ij]) { /* 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+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,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+(k1-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); /
ij++;	ij++;
Line 6857 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 7063 plot [%.f:%.f] ", ageminpar, agemaxpar)
} /* end bad */	} /* end bad */

for (age=bage; age<=fage; age++){	for (age=bage; age<=fage; age++){
printf("%d %d ", cptcod, (int)age);	/* printf("%d %d ", cptcod, (int)age); */
sumnewp[cptcod]=0.;	sumnewp[cptcod]=0.;
sumnewm[cptcod]=0.;	sumnewm[cptcod]=0.;
for (i=1; i<=nlstate;i++){	for (i=1; i<=nlstate;i++){
Line 6896 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 7102 plot [%.f:%.f] ", ageminpar, agemaxpar)


/************ Forecasting ****************/	/************ Forecasting ****************/
void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){	void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
/* proj1, year, month, day of starting projection	/* proj1, year, month, day of starting projection
agemin, agemax range of age	agemin, agemax range of age
dateprev1 dateprev2 range of dates during which prevalence is computed	dateprev1 dateprev2 range of dates during which prevalence is computed
anproj2 year of en of projection (same day and month as proj1).	anproj2 year of en of projection (same day and month as proj1).
*/	*/
int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;	int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
double agec; /* generic age */	double agec; /* generic age */
double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;	double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
double popeffectif,popcount;	double popeffectif,popcount;
Line 6924 void prevforecast(char fileres[], double	Line 7130 void prevforecast(char fileres[], double
printf("Problem with forecast resultfile: %s\n", fileresf);	printf("Problem with forecast resultfile: %s\n", fileresf);
fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);	fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
}	}
printf("Computing forecasting: result on file '%s', please wait... \n", fileresf);	printf("\nComputing forecasting: result on file '%s', please wait... \n", fileresf);
fprintf(ficlog,"Computing forecasting: result on file '%s', please wait... \n", fileresf);	fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);

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

Line 6956 void prevforecast(char fileres[], double	Line 7162 void prevforecast(char fileres[], double
fprintf(ficresf,"#**** Routine prevforecast \n");	fprintf(ficresf,"#**** Routine prevforecast \n");

/* if (h==(int)(YEARMyearp)){ /	/* if (h==(int)(YEARMyearp)){ /
for(k=1;k<=i1;k++){	for(nres=1; nres <= nresult; nres++) /* For each resultline */
	for(k=1; k<=i1;k++){
	if(TKresult[nres]!= k)
	continue;
if(invalidvarcomb[k]){	if(invalidvarcomb[k]){
printf("\nCombination (%d) projection ignored because no cases \n",k);	printf("\nCombination (%d) projection ignored because no cases \n",k);
continue;	continue;
Line 6965 void prevforecast(char fileres[], double	Line 7174 void prevforecast(char fileres[], double
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcoveff;j++) {
fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
}	}
	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
	printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	}
fprintf(ficresf," yearproj age");	fprintf(ficresf," yearproj age");
for(j=1; j<=nlstate+ndeath;j++){	for(j=1; j<=nlstate+ndeath;j++){
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
Line 6979 void prevforecast(char fileres[], double	Line 7192 void prevforecast(char fileres[], double
nhstepm = nhstepm/hstepm;	nhstepm = nhstepm/hstepm;
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
oldm=oldms;savm=savms;	oldm=oldms;savm=savms;
hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);	hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);

for (h=0; h<=nhstepm; h++){	for (h=0; h<=nhstepm; h++){
if (hhstepm/YEARMstepm ==yearp) {	if (hhstepm/YEARMstepm ==yearp) {
Line 7847 int readdata(char datafile[], int firsto	Line 8060 int readdata(char datafile[], int firsto
return (1);	return (1);
}	}

void removespace(char *stri){/, char stro[]) {*/	void removefirstspace(char *stri){/, char stro[]) {*/
char p1 = stri, p2 = stri;	char p1 = stri, p2 = stri;
do	while (*p2 == ' ')
while (*p2 == ' ')	p2++;
p2++;	/* while ((p1++ = p2++) !=0) */
while (p1++ == p2++);	/* ; */
*stri=p1;	/* do */
	/* while (p2 == ' ') /
	/* p2++; */
	/* while (p1++ == p2++); */
	*stri=p2;
}	}

int decoderesult ( char resultline[])	int decoderesult ( char resultline[], int nres)
/< This routine decode one result line and returns the combination # of dummy covariates only /	/< This routine decode one result line and returns the combination # of dummy covariates only /
{	{
int j=0, k=0;	int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;
char resultsav[MAXLINE];	char resultsav[MAXLINE];
	int resultmodel[MAXLINE];
	int modelresult[MAXLINE];
char stra[80], strb[80], strc[80], strd[80],stre[80];	char stra[80], strb[80], strc[80], strd[80],stre[80];

removespace(&resultline);	removefirstspace(&resultline);
printf("decoderesult:%s\n",resultline);	printf("decoderesult:%s\n",resultline);

if (strstr(resultline,"v") !=0){	if (strstr(resultline,"v") !=0){
Line 7875 int decoderesult ( char resultline[])	Line 8094 int decoderesult ( char resultline[])
if (strlen(resultsav) >1){	if (strlen(resultsav) >1){
j=nbocc(resultsav,'='); /*< j=Number of covariate values'=' /	j=nbocc(resultsav,'='); /*< j=Number of covariate values'=' /
}	}
	if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
for(k=1; k<=j;k++){ /* Loop on total covariates of the model */	printf("ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' '	fprintf(ficlog,"ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */	}
cutl(strc,strd,strb,'='); /* strb:V4=1 strc=1 strd=V4 */	for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */
	if(nbocc(resultsav,'=') >1){
	cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' '
	resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */
	cutl(strc,strd,strb,'='); /* strb:V4=1 strc=1 strd=V4 */
	}else
	cutl(strc,strd,resultsav,'=');
Tvalsel[k]=atof(strc); /* 1 */	Tvalsel[k]=atof(strc); /* 1 */

cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;	cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
Tvarsel[k]=atoi(strc);	Tvarsel[k]=atoi(strc);
/* Typevarsel[k]=1; /\* 1 for age product \/ /	/* Typevarsel[k]=1; /\* 1 for age product \/ /
Line 7889 int decoderesult ( char resultline[])	Line 8114 int decoderesult ( char resultline[])
if (nbocc(stra,'=') >0)	if (nbocc(stra,'=') >0)
strcpy(resultsav,stra); /* and analyzes it */	strcpy(resultsav,stra); /* and analyzes it */
}	}
	/* Checking for missing or useless values in comparison of current model needs */
	for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
	if(Typevar[k1]==0){ /* Single covariate in model */
	match=0;
	for(k2=1; k2 <=j;k2++){/* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
	if(Tvar[k1]==Tvarsel[k2]) {/* Tvar[1]=5 == Tvarsel[2]=5 */
	modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2 modelresult[3]=3 modelresult[6]=4 modelresult[9]=5 */
	match=1;
	break;
	}
	}
	if(match == 0){
	printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
	}
	}
	}
	/* Checking for missing or useless values in comparison of current model needs */
	for(k2=1; k2 <=j;k2++){ /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
	match=0;
	for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
	if(Typevar[k1]==0){ /* Single */
	if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4 */
	resultmodel[k1]=k2; /* resultmodel[2]=1 resultmodel[1]=2 resultmodel[3]=3 resultmodel[6]=4 resultmodel[9]=5 */
	++match;
	}
	}
	}
	if(match == 0){
	printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);
	}else if(match > 1){
	printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
	}
	}

	/* We need to deduce which combination number is chosen and save quantitative values */
	/* model line V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
	/* result line V4=1 V5=25.1 V3=0 V2=8 V1=1 */
	/* should give a combination of dummy V4=1, V3=0, V1=1 => V42(0) + V32*(1) + V12*(2) = 5 + (1offset) = 6/
	/* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
	/* should give a combination of dummy V4=1, V3=1, V1=0 => V42(0) + V32*(1) + V12*(2) = 3 + (1offset) = 4/
	/* 1 0 0 0 */
	/* 2 1 0 0 */
	/* 3 0 1 0 */
	/* 4 1 1 0 / / V4=1, V3=1, V1=0 */
	/* 5 0 0 1 */
	/* 6 1 0 1 / / V4=1, V3=0, V1=1 */
	/* 7 0 1 1 */
	/* 8 1 1 1 */
	/* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */
	/* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */
	/* V5age V5 known which value for nres? /
	/* Tqinvresult[2]=8 Tqinvresult[1]=25.1 */
	for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* model line */
	if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */
	k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */
	k2=(int)Tvarsel[k3]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
	k+=Tvalsel[k3]pow(2,k4); / Tvalsel[1]=1 */
	Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1) Tresult[nres][2]=0(V3=0) */
	Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
	Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
	printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);
	k4++;;
	} else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */
	k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */
	k2q=(int)Tvarsel[k3q]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
	Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
	Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
	Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
	printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
	k4q++;;
	}
	}

	TKresult[nres]=++k; /* Combination for the nresult and the model */
return (0);	return (0);
}	}
int selected( int kvar){ /* Selected combination of covariates */
if(Tvarsel[kvar])
return (0);
else
return(1);
}
int decodemodel( char model[], int lastobs)	int decodemodel( char model[], int lastobs)
/**< This routine decodes the model and returns:	/**< This routine decodes the model and returns:
* Model V1+V2+V3+V8+V7V8+V5V6+V8age+V3age+age*age	* Model V1+V2+V3+V8+V7V8+V5V6+V8age+V3age+age*age
Line 7936 int decodemodel( char model[], int lasto	Line 8230 int decodemodel( char model[], int lasto
if ((strpt=strstr(model,"age*age")) !=0){	if ((strpt=strstr(model,"age*age")) !=0){
printf(" strpt=%s, model=%s\n",strpt, model);	printf(" strpt=%s, model=%s\n",strpt, model);
if(strpt != model){	if(strpt != model){
printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \	printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
'model=1+age+ageage+V1.' or 'model=1+age+ageage+V1+V1*age.', please swap as well as \n \	'model=1+age+ageage+V1.' or 'model=1+age+ageage+V1+V1*age.', please swap as well as \n \
corresponding column of parameters.\n",model);	corresponding column of parameters.\n",model);
fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \	fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \
'model=1+age+ageage+V1.' or 'model=1+age+ageage+V1+V1*age.', please swap as well as \n \	'model=1+age+ageage+V1.' or 'model=1+age+ageage+V1+V1*age.', please swap as well as \n \
corresponding column of parameters.\n",model); fflush(ficlog);	corresponding column of parameters.\n",model); fflush(ficlog);
return 1;	return 1;
}	}
nagesqr=1;	nagesqr=1;
if (strstr(model,"+age*age") !=0)	if (strstr(model,"+age*age") !=0)
substrchaine(modelsav, model, "+age*age");	substrchaine(modelsav, model, "+age*age");
else if (strstr(model,"age*age+") !=0)	else if (strstr(model,"age*age+") !=0)
substrchaine(modelsav, model, "age*age+");	substrchaine(modelsav, model, "age*age+");
else	else
substrchaine(modelsav, model, "age*age");	substrchaine(modelsav, model, "age*age");
}else	}else
nagesqr=0;	nagesqr=0;
if (strlen(modelsav) >1){	if (strlen(modelsav) >1){
Line 8020 int decodemodel( char model[], int lasto	Line 8314 int decodemodel( char model[], int lasto
}	}
cptcovage=0;	cptcovage=0;
for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */	for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */
cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'	cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'
modelsav==V2+V1+V4+V3age strb=V3age stra=V2+V1+V4 */	modelsav==V2+V1+V4+V3age strb=V3age stra=V2+V1+V4 */
if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */	if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
/* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/	/* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
/scanf("%d",i);/	/scanf("%d",i);/
if (strchr(strb,'')) { /< Model includes a product V2+V1+V4+V3age strb=V3age /	if (strchr(strb,'')) { /< Model includes a product V2+V1+V4+V3age strb=V3age /
cutl(strc,strd,strb,''); /< strdstrc VmVn: strb=V3age(input) strc=age strd=V3 ; V3V2 strc=V2, strd=V3 /	cutl(strc,strd,strb,''); /< strdstrc VmVn: strb=V3age(input) strc=age strd=V3 ; V3V2 strc=V2, strd=V3 /
if (strcmp(strc,"age")==0) { /*< Model includes age: Vnage */	if (strcmp(strc,"age")==0) { /*< Model includes age: Vnage */
/* covar is not filled and then is empty */	/* covar is not filled and then is empty */
cptcovprod--;	cptcovprod--;
cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */	cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
Tvar[k]=atoi(stre); /* V2+V1+V4+V3age Tvar[4]=3 ; V1+V2age Tvar[2]=2; V1+V1age Tvar[2]=1 /	Tvar[k]=atoi(stre); /* V2+V1+V4+V3age Tvar[4]=3 ; V1+V2age Tvar[2]=2; V1+V1age Tvar[2]=1 /
Typevar[k]=1; /* 1 for age product */	Typevar[k]=1; /* 1 for age product */
cptcovage++; /* Sums the number of covariates which include age as a product */	cptcovage++; /* Sums the number of covariates which include age as a product */
Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1age Tvar[2]=1, Tage[1]=2 /	Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1age Tvar[2]=1, Tage[1]=2 /
/printf("stre=%s ", stre);/	/printf("stre=%s ", stre);/
} else if (strcmp(strd,"age")==0) { /* or ageVn /	} else if (strcmp(strd,"age")==0) { /* or ageVn /
cptcovprod--;	cptcovprod--;
cutl(stre,strb,strc,'V');	cutl(stre,strb,strc,'V');
Tvar[k]=atoi(stre);	Tvar[k]=atoi(stre);
Typevar[k]=1; /* 1 for age product */	Typevar[k]=1; /* 1 for age product */
cptcovage++;	cptcovage++;
Tage[cptcovage]=k;	Tage[cptcovage]=k;
} else { /* Age is not in the model product V2+V1+V1V4+V3age+V3V2 strb=V3V2*/	} else { /* Age is not in the model product V2+V1+V1V4+V3age+V3V2 strb=V3V2*/
/* loops on k1=1 (V3V2) and k1=2 V4V3 */	/* loops on k1=1 (V3V2) and k1=2 V4V3 */
cptcovn++;	cptcovn++;
cptcovprodnoage++;k1++;	cptcovprodnoage++;k1++;
cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3V2 stre=3 strc=/	cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3V2 stre=3 strc=/
Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but	Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
because this model-covariate is a construction we invent a new column	because this model-covariate is a construction we invent a new column
which is after existing variables ncovcol+nqv+ntv+nqtv + k1	which is after existing variables ncovcol+nqv+ntv+nqtv + k1
If already ncovcol=4 and model=V2+V1+V1V4+ageV3+V3*V2	If already ncovcol=4 and model=V2+V1+V1V4+ageV3+V3*V2
Tvar[3=V1V4]=4+1 Tvar[5=V3V2]=4 + 2= 6, etc */	Tvar[3=V1V4]=4+1 Tvar[5=V3V2]=4 + 2= 6, etc */
Typevar[k]=2; /* 2 for double fixed dummy covariates */	Typevar[k]=2; /* 2 for double fixed dummy covariates */
cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */	cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
Tprod[k1]=k; /* Tprod[1]=3(=V1V4) for V2+V1+V1V4+ageV3+V3V2 */	Tprod[k1]=k; /* Tprod[1]=3(=V1V4) for V2+V1+V1V4+ageV3+V3V2 */
Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */	Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */
Tvard[k1][1] =atoi(strc); /* m 1 for V1*/	Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
Tvard[k1][2] =atoi(stre); /* n 4 for V4*/	Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in VnVm at the end of Tvar /	k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in VnVm at the end of Tvar /
/* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) \/ /	/* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) \/ /
/* Tvar[cptcovt+k2+1]=Tvard[k1][2]; /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) \/ /	/* Tvar[cptcovt+k2+1]=Tvard[k1][2]; /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) \/ /
/ncovcol=4 and model=V2+V1+V1V4+ageV3+V3V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */	/ncovcol=4 and model=V2+V1+V1V4+ageV3+V3V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
/* 1 2 3 4 5 \| Tvar[5+1)=1, Tvar[7]=2 */	/* 1 2 3 4 5 \| Tvar[5+1)=1, Tvar[7]=2 */
for (i=1; i<=lastobs;i++){	for (i=1; i<=lastobs;i++){
/* Computes the new covariate which is a product of	/* Computes the new covariate which is a product of
covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */	covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];	covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
}	}
} /* End age is not in the model */	} /* End age is not in the model */
} /* End if model includes a product */	} /* End if model includes a product */
else { /* no more sum */	else { /* no more sum */
/printf("d=%s c=%s b=%s\n", strd,strc,strb);/	/printf("d=%s c=%s b=%s\n", strd,strc,strb);/
/* scanf("%d",i);*/	/* scanf("%d",i);*/
cutl(strd,strc,strb,'V');	cutl(strd,strc,strb,'V');
ks++; /*< Number of simple covariates dummy or quantitative, fixe or varying /	ks++; /*< Number of simple covariates dummy or quantitative, fixe or varying /
cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */	cptcovn++; /** V4+V3+V5: V4 and V3 timevarying dummy covariates, V5 timevarying quantitative */
Tvar[k]=atoi(strd);	Tvar[k]=atoi(strd);
Typevar[k]=0; /* 0 for simple covariates */	Typevar[k]=0; /* 0 for simple covariates */
}	}
strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */	strcpy(modelsav,stra); /* modelsav=V2+V1+V4 stra=V2+V1+V4 */
/*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);	/*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
scanf("%d",i);*/	scanf("%d",i);*/
} /* end of loop + on total covariates */	} /* end of loop + on total covariates */
Line 8120 Typevar: 0 for simple covariate (dummy,	Line 8414 Typevar: 0 for simple covariate (dummy,
Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\	Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);	Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);

for(k=1, ncovf=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */	for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */
if (Tvar[k] <=ncovcol && (Typevar[k]==0 \|\| Typevar[k]==2)){ /* Simple or product fixed dummy (<=ncovcol) covariates */	if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
	Fixed[k]= 0;
	Dummy[k]= 0;
	ncoveff++;
	ncovf++;
	nsd++;
	modell[k].maintype= FTYPE;
	TvarsD[nsd]=Tvar[k];
	TvarsDind[nsd]=k;
	TvarF[ncovf]=Tvar[k];
	TvarFind[ncovf]=k;
	TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
	TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
	}else if( Tvar[k] <=ncovcol && Typevar[k]==2){ /* Product of fixed dummy (<=ncovcol) covariates */
Fixed[k]= 0;	Fixed[k]= 0;
Dummy[k]= 0;	Dummy[k]= 0;
ncoveff++;	ncoveff++;
ncovf++;	ncovf++;
modell[k].maintype= FTYPE;	modell[k].maintype= FTYPE;
TvarF[ncovf]=Tvar[k];	TvarF[ncovf]=Tvar[k];
TvarFind[ncovf]=k;	TvarFind[ncovf]=k;
TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */	TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */	TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
}else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){ /* Remind that product VnVm are added in k/ /* Only simple fixed quantitative variable */	}else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){ /* Remind that product VnVm are added in k/ /* Only simple fixed quantitative variable */
Fixed[k]= 0;	Fixed[k]= 0;
Dummy[k]= 1;	Dummy[k]= 1;
nqfveff++;	nqfveff++;
modell[k].maintype= FTYPE;	modell[k].maintype= FTYPE;
modell[k].subtype= FQ;	modell[k].subtype= FQ;
	nsq++;
	TvarsQ[nsq]=Tvar[k];
	TvarsQind[nsq]=k;
ncovf++;	ncovf++;
TvarF[ncovf]=Tvar[k];	TvarF[ncovf]=Tvar[k];
TvarFind[ncovf]=k;	TvarFind[ncovf]=k;
TvarFQ[nqfveff]=Tvar[k]-ncovcol; /* TvarFQ[1]=V2-1=1st in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple fixed quantitative variable */	TvarFQ[nqfveff]=Tvar[k]-ncovcol; /* TvarFQ[1]=V2-1=1st in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple fixed quantitative variable */
TvarFQind[nqfveff]=k; /* TvarFQind[1]=6 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple fixed quantitative variable */	TvarFQind[nqfveff]=k; /* TvarFQind[1]=6 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple fixed quantitative variable */
}else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){	}else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying variables */
Fixed[k]= 1;	Fixed[k]= 1;
Dummy[k]= 0;	Dummy[k]= 0;
ntveff++; /* Only simple time varying dummy variable */	ntveff++; /* Only simple time varying dummy variable */
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VD;	modell[k].subtype= VD;
ncovv++; /* Only simple time varying variables */	nsd++;
TvarV[ncovv]=Tvar[k];	TvarsD[nsd]=Tvar[k];
TvarVind[ncovv]=k;	TvarsDind[nsd]=k;
	ncovv++; /* Only simple time varying variables */
	TvarV[ncovv]=Tvar[k];
	TvarVind[ncovv]=k;
TvarVD[ntveff]=Tvar[k]; /* TvarVD[1]=V4 TvarVD[2]=V3 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple time varying dummy variable */	TvarVD[ntveff]=Tvar[k]; /* TvarVD[1]=V4 TvarVD[2]=V3 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple time varying dummy variable */
TvarVDind[ntveff]=k; /* TvarVDind[1]=2 TvarVDind[2]=3 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple time varying dummy variable */	TvarVDind[ntveff]=k; /* TvarVDind[1]=2 TvarVDind[2]=3 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple time varying dummy variable */
printf("Quasi Tmodelind[%d]=%d,Tvar[Tmodelind[%d]]=V%d, ncovcol=%d, nqv=%d,Tvar[k]- ncovcol-nqv=%d\n",ntveff,k,ntveff,Tvar[k], ncovcol, nqv,Tvar[k]- ncovcol-nqv);	printf("Quasi Tmodelind[%d]=%d,Tvar[Tmodelind[%d]]=V%d, ncovcol=%d, nqv=%d,Tvar[k]- ncovcol-nqv=%d\n",ntveff,k,ntveff,Tvar[k], ncovcol, nqv,Tvar[k]- ncovcol-nqv);
printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);	printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
}else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/	}else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/
Fixed[k]= 1;	Fixed[k]= 1;
Dummy[k]= 1;	Dummy[k]= 1;
nqtveff++;	nqtveff++;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VQ;	modell[k].subtype= VQ;
ncovv++; /* Only simple time varying variables */	ncovv++; /* Only simple time varying variables */
TvarV[ncovv]=Tvar[k];	nsq++;
TvarVind[ncovv]=k;	TvarsQ[nsq]=Tvar[k];
	TvarsQind[nsq]=k;
	TvarV[ncovv]=Tvar[k];
	TvarVind[ncovv]=k;
TvarVQ[nqtveff]=Tvar[k]; /* TvarVQ[1]=V5 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple time varying quantitative variable */	TvarVQ[nqtveff]=Tvar[k]; /* TvarVQ[1]=V5 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple time varying quantitative variable */
TvarVQind[nqtveff]=k; /* TvarVQind[1]=1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple time varying quantitative variable */	TvarVQind[nqtveff]=k; /* TvarVQind[1]=1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple time varying quantitative variable */
TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */	TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
/* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable \/ /	/* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable \/ /
printf("Quasi TmodelQind[%d]=%d,Tvar[TmodelQind[%d]]=V%d, ncovcol=%d, nqv=%d, ntv=%d,Tvar[k]- ncovcol-nqv-ntv=%d\n",nqtveff,k,nqtveff,Tvar[k], ncovcol, nqv, ntv, Tvar[k]- ncovcol-nqv-ntv);	printf("Quasi TmodelQind[%d]=%d,Tvar[TmodelQind[%d]]=V%d, ncovcol=%d, nqv=%d, ntv=%d,Tvar[k]- ncovcol-nqv-ntv=%d\n",nqtveff,k,nqtveff,Tvar[k], ncovcol, nqv, ntv, Tvar[k]- ncovcol-nqv-ntv);
printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);	printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);
}else if (Typevar[k] == 1) { /* product with age */	}else if (Typevar[k] == 1) { /* product with age */
ncova++;	ncova++;
TvarA[ncova]=Tvar[k];	TvarA[ncova]=Tvar[k];
TvarAind[ncova]=k;	TvarAind[ncova]=k;
if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */	if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
Fixed[k]= 2;	Fixed[k]= 2;
Dummy[k]= 2;	Dummy[k]= 2;
modell[k].maintype= ATYPE;	modell[k].maintype= ATYPE;
modell[k].subtype= APFD;	modell[k].subtype= APFD;
/* ncoveff++; */	/* ncoveff++; */
}else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product VnVm are added in k/	}else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product VnVm are added in k/
Fixed[k]= 2;	Fixed[k]= 2;
Dummy[k]= 3;	Dummy[k]= 3;
modell[k].maintype= ATYPE;	modell[k].maintype= ATYPE;
modell[k].subtype= APFQ; /* Product age * fixed quantitative */	modell[k].subtype= APFQ; /* Product age * fixed quantitative */
/* nqfveff++; /\* Only simple fixed quantitative variable \/ /	/* nqfveff++; /\* Only simple fixed quantitative variable \/ /
}else if( Tvar[k] <=ncovcol+nqv+ntv ){	}else if( Tvar[k] <=ncovcol+nqv+ntv ){
Fixed[k]= 3;	Fixed[k]= 3;
Dummy[k]= 2;	Dummy[k]= 2;
modell[k].maintype= ATYPE;	modell[k].maintype= ATYPE;
modell[k].subtype= APVD; /* Product age * varying dummy */	modell[k].subtype= APVD; /* Product age * varying dummy */
/* ntveff++; /\* Only simple time varying dummy variable \/ /	/* ntveff++; /\* Only simple time varying dummy variable \/ /
}else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){	}else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
Fixed[k]= 3;	Fixed[k]= 3;
Dummy[k]= 3;	Dummy[k]= 3;
modell[k].maintype= ATYPE;	modell[k].maintype= ATYPE;
modell[k].subtype= APVQ; /* Product age * varying quantitative */	modell[k].subtype= APVQ; /* Product age * varying quantitative */
/* nqtveff++;/\* Only simple time varying quantitative variable \/ /	/* nqtveff++;/\* Only simple time varying quantitative variable \/ /
}	}
}else if (Typevar[k] == 2) { /* product without age */	}else if (Typevar[k] == 2) { /* product without age */
k1=Tposprod[k];	k1=Tposprod[k];
if(Tvard[k1][1] <=ncovcol){	if(Tvard[k1][1] <=ncovcol){
if(Tvard[k1][2] <=ncovcol){	if(Tvard[k1][2] <=ncovcol){
Fixed[k]= 1;	Fixed[k]= 1;
Dummy[k]= 0;	Dummy[k]= 0;
modell[k].maintype= FTYPE;	modell[k].maintype= FTYPE;
modell[k].subtype= FPDD; /* Product fixed dummy * fixed dummy */	modell[k].subtype= FPDD; /* Product fixed dummy * fixed dummy */
ncovf++; /* Fixed variables without age */	ncovf++; /* Fixed variables without age */
TvarF[ncovf]=Tvar[k];	TvarF[ncovf]=Tvar[k];
TvarFind[ncovf]=k;	TvarFind[ncovf]=k;
}else if(Tvard[k1][2] <=ncovcol+nqv){	}else if(Tvard[k1][2] <=ncovcol+nqv){
Fixed[k]= 0; /* or 2 ?*/	Fixed[k]= 0; /* or 2 ?*/
Dummy[k]= 1;	Dummy[k]= 1;
modell[k].maintype= FTYPE;	modell[k].maintype= FTYPE;
modell[k].subtype= FPDQ; /* Product fixed dummy * fixed quantitative */	modell[k].subtype= FPDQ; /* Product fixed dummy * fixed quantitative */
ncovf++; /* Varying variables without age */	ncovf++; /* Varying variables without age */
TvarF[ncovf]=Tvar[k];	TvarF[ncovf]=Tvar[k];
TvarFind[ncovf]=k;	TvarFind[ncovf]=k;
}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
Fixed[k]= 1;	Fixed[k]= 1;
Dummy[k]= 0;	Dummy[k]= 0;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPDD; /* Product fixed dummy * varying dummy */	modell[k].subtype= VPDD; /* Product fixed dummy * varying dummy */
ncovv++; /* Varying variables without age */	ncovv++; /* Varying variables without age */
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k;	TvarVind[ncovv]=k;
}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
Fixed[k]= 1;	Fixed[k]= 1;
Dummy[k]= 1;	Dummy[k]= 1;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPDQ; /* Product fixed dummy * varying quantitative */	modell[k].subtype= VPDQ; /* Product fixed dummy * varying quantitative */
ncovv++; /* Varying variables without age */	ncovv++; /* Varying variables without age */
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k;	TvarVind[ncovv]=k;
}	}
}else if(Tvard[k1][1] <=ncovcol+nqv){	}else if(Tvard[k1][1] <=ncovcol+nqv){
if(Tvard[k1][2] <=ncovcol){	if(Tvard[k1][2] <=ncovcol){
Fixed[k]= 0; /* or 2 ?*/	Fixed[k]= 0; /* or 2 ?*/
Dummy[k]= 1;	Dummy[k]= 1;
modell[k].maintype= FTYPE;	modell[k].maintype= FTYPE;
modell[k].subtype= FPDQ; /* Product fixed quantitative * fixed dummy */	modell[k].subtype= FPDQ; /* Product fixed quantitative * fixed dummy */
ncovf++; /* Fixed variables without age */	ncovf++; /* Fixed variables without age */
TvarF[ncovf]=Tvar[k];	TvarF[ncovf]=Tvar[k];
TvarFind[ncovf]=k;	TvarFind[ncovf]=k;
}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
Fixed[k]= 1;	Fixed[k]= 1;
Dummy[k]= 1;	Dummy[k]= 1;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPDQ; /* Product fixed quantitative * varying dummy */	modell[k].subtype= VPDQ; /* Product fixed quantitative * varying dummy */
ncovv++; /* Varying variables without age */	ncovv++; /* Varying variables without age */
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k;	TvarVind[ncovv]=k;
}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
Fixed[k]= 1;	Fixed[k]= 1;
Dummy[k]= 1;	Dummy[k]= 1;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPQQ; /* Product fixed quantitative * varying quantitative */	modell[k].subtype= VPQQ; /* Product fixed quantitative * varying quantitative */
ncovv++; /* Varying variables without age */	ncovv++; /* Varying variables without age */
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k;	TvarVind[ncovv]=k;
ncovv++; /* Varying variables without age */	ncovv++; /* Varying variables without age */
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k;	TvarVind[ncovv]=k;
}	}
}else if(Tvard[k1][1] <=ncovcol+nqv+ntv){	}else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
if(Tvard[k1][2] <=ncovcol){	if(Tvard[k1][2] <=ncovcol){
Fixed[k]= 1;	Fixed[k]= 1;
Dummy[k]= 1;	Dummy[k]= 1;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPDD; /* Product time varying dummy * fixed dummy */	modell[k].subtype= VPDD; /* Product time varying dummy * fixed dummy */
ncovv++; /* Varying variables without age */	ncovv++; /* Varying variables without age */
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k;	TvarVind[ncovv]=k;
}else if(Tvard[k1][2] <=ncovcol+nqv){	}else if(Tvard[k1][2] <=ncovcol+nqv){
Fixed[k]= 1;	Fixed[k]= 1;
Dummy[k]= 1;	Dummy[k]= 1;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPDQ; /* Product time varying dummy * fixed quantitative */	modell[k].subtype= VPDQ; /* Product time varying dummy * fixed quantitative */
ncovv++; /* Varying variables without age */	ncovv++; /* Varying variables without age */
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k;	TvarVind[ncovv]=k;
}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
Fixed[k]= 1;	Fixed[k]= 1;
Dummy[k]= 0;	Dummy[k]= 0;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPDD; /* Product time varying dummy * time varying dummy */	modell[k].subtype= VPDD; /* Product time varying dummy * time varying dummy */
ncovv++; /* Varying variables without age */	ncovv++; /* Varying variables without age */
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k;	TvarVind[ncovv]=k;
}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
Fixed[k]= 1;	Fixed[k]= 1;
Dummy[k]= 1;	Dummy[k]= 1;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPDQ; /* Product time varying dummy * time varying quantitative */	modell[k].subtype= VPDQ; /* Product time varying dummy * time varying quantitative */
ncovv++; /* Varying variables without age */	ncovv++; /* Varying variables without age */
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k;	TvarVind[ncovv]=k;
}	}
}else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){	}else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
if(Tvard[k1][2] <=ncovcol){	if(Tvard[k1][2] <=ncovcol){
Fixed[k]= 1;	Fixed[k]= 1;
Dummy[k]= 1;	Dummy[k]= 1;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPDQ; /* Product time varying quantitative * fixed dummy */	modell[k].subtype= VPDQ; /* Product time varying quantitative * fixed dummy */
ncovv++; /* Varying variables without age */	ncovv++; /* Varying variables without age */
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k;	TvarVind[ncovv]=k;
}else if(Tvard[k1][2] <=ncovcol+nqv){	}else if(Tvard[k1][2] <=ncovcol+nqv){
Fixed[k]= 1;	Fixed[k]= 1;
Dummy[k]= 1;	Dummy[k]= 1;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPQQ; /* Product time varying quantitative * fixed quantitative */	modell[k].subtype= VPQQ; /* Product time varying quantitative * fixed quantitative */
ncovv++; /* Varying variables without age */	ncovv++; /* Varying variables without age */
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k;	TvarVind[ncovv]=k;
}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
Fixed[k]= 1;	Fixed[k]= 1;
Dummy[k]= 1;	Dummy[k]= 1;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPDQ; /* Product time varying quantitative * time varying dummy */	modell[k].subtype= VPDQ; /* Product time varying quantitative * time varying dummy */
ncovv++; /* Varying variables without age */	ncovv++; /* Varying variables without age */
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k;	TvarVind[ncovv]=k;
}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
Fixed[k]= 1;	Fixed[k]= 1;
Dummy[k]= 1;	Dummy[k]= 1;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPQQ; /* Product time varying quantitative * time varying quantitative */	modell[k].subtype= VPQQ; /* Product time varying quantitative * time varying quantitative */
ncovv++; /* Varying variables without age */	ncovv++; /* Varying variables without age */
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k;	TvarVind[ncovv]=k;
}	}
}else{	}else{
printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);	printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);	fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
} /* end k1 */	} /* end k1 */
}else{	}else{
printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);	printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
Line 8348 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 8664 Dummy[k] 0=dummy (0 1), 1 quantitative (
for(k1=1; k1<= cptcovt;k1++){	for(k1=1; k1<= cptcovt;k1++){
for(k2=1; k2 <k1;k2++){	for(k2=1; k2 <k1;k2++){
if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){	if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){
if((Typevar[k1] == 0 \|\| Typevar[k1] == 1)){ /* Simple or age product */	if((Typevar[k1] == 0 \|\| Typevar[k1] == 1)){ /* Simple or age product */
if(Tvar[k1]==Tvar[k2]){	if(Tvar[k1]==Tvar[k2]){
printf("Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);	printf("Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);
fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);	fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);
return(1);	return(1);
}	}
}else if (Typevar[k1] ==2){	}else if (Typevar[k1] ==2){
k3=Tposprod[k1];	k3=Tposprod[k1];
k4=Tposprod[k2];	k4=Tposprod[k2];
if( ((Tvard[k3][1]== Tvard[k4][1])&&(Tvard[k3][2]== Tvard[k4][2])) \|\| ((Tvard[k3][1]== Tvard[k4][2])&&(Tvard[k3][2]== Tvard[k4][1])) ){	if( ((Tvard[k3][1]== Tvard[k4][1])&&(Tvard[k3][2]== Tvard[k4][2])) \|\| ((Tvard[k3][1]== Tvard[k4][2])&&(Tvard[k3][2]== Tvard[k4][1])) ){
printf("Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);	printf("Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);
fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);	fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);
return(1);	return(1);
}	}
}	}
}	}
}	}
}	}
printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);	printf("ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);	fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
printf("ncovf=%d, ncovv=%d, ncova=%d\n",ncovf,ncovv,ncova);	printf("ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);
fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d\n",ncovf,ncovv,ncova);	fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd, nsq);
return (0); /* with covar[new additional covariate if product] and Tage if age */	return (0); /* with covar[new additional covariate if product] and Tage if age */
/endread:/	/endread:/
printf("Exiting decodemodel: ");	printf("Exiting decodemodel: ");
Line 8684 void syscompilerinfo(int logged)	Line 9000 void syscompilerinfo(int logged)

int prevalence_limit(double p, double prlim, double ageminpar, double agemaxpar, double ftolpl, int ncvyearp){	int prevalence_limit(double p, double prlim, double ageminpar, double agemaxpar, double ftolpl, int ncvyearp){
/--------------- Prevalence limit (period or stable prevalence) --------------/	/--------------- Prevalence limit (period or stable prevalence) --------------/
int i, j, k, i1 ;	int i, j, k, i1, k4=0, nres=0 ;
/* double ftolpl = 1.e-10; */	/* double ftolpl = 1.e-10; */
double age, agebase, agelim;	double age, agebase, agelim;
double tot;	double tot;
Line 8709 int prevalence_limit(double p, double	Line 9025 int prevalence_limit(double p, double
agelim=agemaxpar;	agelim=agemaxpar;

/* i1=pow(2,ncoveff); */	/* i1=pow(2,ncoveff); */
i1=pow(2,cptcoveff); /* Number of dummy covariates */	i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
if (cptcovn < 1){i1=1;}	if (cptcovn < 1){i1=1;}

	for(nres=1; nres <= nresult; nres++) /* For each resultline */
for(k=1; k<=i1;k++){	for(k=1; k<=i1;k++){
	if(TKresult[nres]!= k)
	continue;

/* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */	/* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
/* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */	/* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
//for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){	//for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
Line 8727 int prevalence_limit(double p, double	Line 9047 int prevalence_limit(double p, double
printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
}	}
	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
	printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	}
fprintf(ficrespl,"******\n");	fprintf(ficrespl,"******\n");
printf("******\n");	printf("******\n");
fprintf(ficlog,"******\n");	fprintf(ficlog,"******\n");
Line 8746 int prevalence_limit(double p, double	Line 9070 int prevalence_limit(double p, double

for (age=agebase; age<=agelim; age++){	for (age=agebase; age<=agelim; age++){
/* for (age=agebase; age<=agebase; age++){ */	/* for (age=agebase; age<=agebase; age++){ */
prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k);	prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
fprintf(ficrespl,"%.0f ",age );	fprintf(ficrespl,"%.0f ",age );
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
Line 8768 int back_prevalence_limit(double *p, dou	Line 9092 int back_prevalence_limit(double *p, dou
/* Computes the back prevalence limit for any combination of covariate values	/* Computes the back prevalence limit for any combination of covariate values
* at any age between ageminpar and agemaxpar	* at any age between ageminpar and agemaxpar
*/	*/
int i, j, k, i1 ;	int i, j, k, i1, nres=0 ;
/* double ftolpl = 1.e-10; */	/* double ftolpl = 1.e-10; */
double age, agebase, agelim;	double age, agebase, agelim;
double tot;	double tot;
Line 8799 int back_prevalence_limit(double *p, dou	Line 9123 int back_prevalence_limit(double *p, dou
i1=pow(2,cptcoveff);	i1=pow(2,cptcoveff);
if (cptcovn < 1){i1=1;}	if (cptcovn < 1){i1=1;}

for(k=1; k<=i1;k++){	for(nres=1; nres <= nresult; nres++) /* For each resultline */
	for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
	if(TKresult[nres]!= k)
	continue;
//printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));	//printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
fprintf(ficresplb,"#******");	fprintf(ficresplb,"#******");
printf("#******");	printf("#******");
Line 8809 int back_prevalence_limit(double *p, dou	Line 9136 int back_prevalence_limit(double *p, dou
printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
}	}
	for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
	printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
	fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
	fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
	}
fprintf(ficresplb,"******\n");	fprintf(ficresplb,"******\n");
printf("******\n");	printf("******\n");
fprintf(ficlog,"******\n");	fprintf(ficlog,"******\n");
Line 8867 int hPijx(double *p, int bage, int fage)	Line 9199 int hPijx(double *p, int bage, int fage)
int agelim;	int agelim;
int hstepm;	int hstepm;
int nhstepm;	int nhstepm;
int h, i, i1, j, k;	int h, i, i1, j, k, k4, nres=0;

double agedeb;	double agedeb;
double ***p3mat;	double ***p3mat;
Line 8894 int hPijx(double *p, int bage, int fage)	Line 9226 int hPijx(double *p, int bage, int fage)
/* 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++){\/ */
/* k=k+1; */	/* k=k+1; */
for (k=1; k <= (int) pow(2,cptcoveff); k++){	for(nres=1; nres <= nresult; nres++) /* For each resultline */
	for(k=1; k<=i1;k++){
	if(TKresult[nres]!= k)
	continue;
fprintf(ficrespij,"\n#****** ");	fprintf(ficrespij,"\n#****** ");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
	printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	}
fprintf(ficrespij,"******\n");	fprintf(ficrespij,"******\n");

for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */	for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
Line 8908 int hPijx(double *p, int bage, int fage)	Line 9247 int hPijx(double *p, int bage, int fage)

p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
oldm=oldms;savm=savms;	oldm=oldms;savm=savms;
hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);	hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");	fprintf(ficrespij,"# Cov Agex agex+h hpijx 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++)
Line 9034 int main(int argc, char *argv[])	Line 9373 int main(int argc, char *argv[])
int itimes;	int itimes;
int NDIM=2;	int NDIM=2;
int vpopbased=0;	int vpopbased=0;
	int nres=0;

char ca[32], cb[32];	char ca[32], cb[32];
/* FILE fichtm; //* Html File */	/* FILE fichtm; //* Html File */
Line 9052 int main(int argc, char *argv[])	Line 9392 int main(int argc, char *argv[])
char line[MAXLINE];	char line[MAXLINE];
char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];	char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];

char model[MAXLINE], modeltemp[MAXLINE];	char modeltemp[MAXLINE];
char resultline[MAXLINE];	char resultline[MAXLINE];

char pathr[MAXLINE], pathimach[MAXLINE];	char pathr[MAXLINE], pathimach[MAXLINE];
Line 9419 int main(int argc, char *argv[])	Line 9759 int main(int argc, char *argv[])

param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);	param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
for(i=1; i <=nlstate; i++){	for(i=1; i <=nlstate; i++){
j=0;	j=0;
for(jj=1; jj <=nlstate+ndeath; jj++){	for(jj=1; jj <=nlstate+ndeath; jj++){
if(jj==i) continue;	if(jj==i) continue;
j++;	j++;
fscanf(ficpar,"%1d%1d",&i1,&j1);	fscanf(ficpar,"%1d%1d",&i1,&j1);
if ((i1 != i) \|\| (j1 != jj)){	if ((i1 != i) \|\| (j1 != jj)){
printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \	printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
It might be a problem of design; if ncovcol and the model are correct\n \	It might be a problem of design; if ncovcol and the model are correct\n \
run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);	run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
exit(1);	exit(1);
}	}
fprintf(ficparo,"%1d%1d",i1,j1);	fprintf(ficparo,"%1d%1d",i1,j1);
if(mle==1)	if(mle==1)
printf("%1d%1d",i,jj);	printf("%1d%1d",i,jj);
fprintf(ficlog,"%1d%1d",i,jj);	fprintf(ficlog,"%1d%1d",i,jj);
for(k=1; k<=ncovmodel;k++){	for(k=1; k<=ncovmodel;k++){
fscanf(ficpar," %lf",&param[i][j][k]);	fscanf(ficpar," %lf",&param[i][j][k]);
if(mle==1){	if(mle==1){
printf(" %lf",param[i][j][k]);	printf(" %lf",param[i][j][k]);
fprintf(ficlog," %lf",param[i][j][k]);	fprintf(ficlog," %lf",param[i][j][k]);
}	}
else	else
fprintf(ficlog," %lf",param[i][j][k]);	fprintf(ficlog," %lf",param[i][j][k]);
fprintf(ficparo," %lf",param[i][j][k]);	fprintf(ficparo," %lf",param[i][j][k]);
}	}
fscanf(ficpar,"\n");	fscanf(ficpar,"\n");
numlinepar++;	numlinepar++;
if(mle==1)	if(mle==1)
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
fprintf(ficparo,"\n");	fprintf(ficparo,"\n");
}	}
}	}
fflush(ficlog);	fflush(ficlog);

/* Reads scales values */	/* Reads scales values */
p=param[1][1];	p=param[1][1];

Line 9470 run imach with mle=-1 to get a correct t	Line 9810 run imach with mle=-1 to get a correct t

for(i=1; i <=nlstate; i++){	for(i=1; i <=nlstate; i++){
for(j=1; j <=nlstate+ndeath-1; j++){	for(j=1; j <=nlstate+ndeath-1; j++){
fscanf(ficpar,"%1d%1d",&i1,&j1);	fscanf(ficpar,"%1d%1d",&i1,&j1);
if ( (i1-i) * (j1-j) != 0){	if ( (i1-i) * (j1-j) != 0){
printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);	printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
exit(1);	exit(1);
}	}
printf("%1d%1d",i,j);	printf("%1d%1d",i,j);
fprintf(ficparo,"%1d%1d",i1,j1);	fprintf(ficparo,"%1d%1d",i1,j1);
fprintf(ficlog,"%1d%1d",i1,j1);	fprintf(ficlog,"%1d%1d",i1,j1);
for(k=1; k<=ncovmodel;k++){	for(k=1; k<=ncovmodel;k++){
fscanf(ficpar,"%le",&delti3[i][j][k]);	fscanf(ficpar,"%le",&delti3[i][j][k]);
printf(" %le",delti3[i][j][k]);	printf(" %le",delti3[i][j][k]);
fprintf(ficparo," %le",delti3[i][j][k]);	fprintf(ficparo," %le",delti3[i][j][k]);
fprintf(ficlog," %le",delti3[i][j][k]);	fprintf(ficlog," %le",delti3[i][j][k]);
}	}
fscanf(ficpar,"\n");	fscanf(ficpar,"\n");
numlinepar++;	numlinepar++;
printf("\n");	printf("\n");
fprintf(ficparo,"\n");	fprintf(ficparo,"\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
}	}
}	}
fflush(ficlog);	fflush(ficlog);

/* Reads covariance matrix */	/* Reads covariance matrix */
delti=delti3[1][1];	delti=delti3[1][1];

Line 9582 Please run with mle=-1 to get a correct	Line 9922 Please run with mle=-1 to get a correct
agedc=vector(1,n);	agedc=vector(1,n);
cod=ivector(1,n);	cod=ivector(1,n);
for(i=1;i<=n;i++){	for(i=1;i<=n;i++){
num[i]=0;	num[i]=0;
moisnais[i]=0;	moisnais[i]=0;
annais[i]=0;	annais[i]=0;
moisdc[i]=0;	moisdc[i]=0;
andc[i]=0;	andc[i]=0;
agedc[i]=0;	agedc[i]=0;
cod[i]=0;	cod[i]=0;
weight[i]=1.0; /* Equal weights, 1 by default */	weight[i]=1.0; /* Equal weights, 1 by default */
}	}
mint=matrix(1,maxwav,1,n);	mint=matrix(1,maxwav,1,n);
anint=matrix(1,maxwav,1,n);	anint=matrix(1,maxwav,1,n);
s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */	s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */
Line 9603 Please run with mle=-1 to get a correct	Line 9943 Please run with mle=-1 to get a correct
goto end;	goto end;

/* Calculation of the number of parameters from char model */	/* Calculation of the number of parameters from char model */
/* modelsav=V2+V1+V4+ageV3 strb=ageV3 stra=V2+V1+V4	/* modelsav=V2+V1+V4+ageV3 strb=ageV3 stra=V2+V1+V4
k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4	k=4 (age*V3) Tvar[k=4]= 3 (from V3) Tag[cptcovage=1]=4
k=3 V4 Tvar[k=3]= 4 (from V4)	k=3 V4 Tvar[k=3]= 4 (from V4)
k=2 V1 Tvar[k=2]= 1 (from V1)	k=2 V1 Tvar[k=2]= 1 (from V1)
k=1 Tvar[1]=2 (from V2)	k=1 Tvar[1]=2 (from V2)
*/	*/

Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */	Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
	TvarsDind=ivector(1,NCOVMAX); /* */
	TvarsD=ivector(1,NCOVMAX); /* */
	TvarsQind=ivector(1,NCOVMAX); /* */
	TvarsQ=ivector(1,NCOVMAX); /* */
TvarF=ivector(1,NCOVMAX); /* */	TvarF=ivector(1,NCOVMAX); /* */
TvarFind=ivector(1,NCOVMAX); /* */	TvarFind=ivector(1,NCOVMAX); /* */
TvarV=ivector(1,NCOVMAX); /* */	TvarV=ivector(1,NCOVMAX); /* */
Line 10433 Please run with mle=-1 to get a correct	Line 10777 Please run with mle=-1 to get a correct
/* day and month of proj2 are not used but only year anproj2.*/	/* day and month of proj2 are not used but only year anproj2.*/

/* Results */	/* Results */
	nresult=0;
while(fgets(line, MAXLINE, ficpar)) {	while(fgets(line, MAXLINE, ficpar)) {
/* If line starts with a # it is a comment */	/* If line starts with a # it is a comment */
if (line[0] == '#') {	if (line[0] == '#') {
Line 10450 Please run with mle=-1 to get a correct	Line 10795 Please run with mle=-1 to get a correct
else if (num_filled != 1){	else if (num_filled != 1){
printf("ERROR %d: result line should be at minimum 'result=' %s\n",num_filled, line);	printf("ERROR %d: result line should be at minimum 'result=' %s\n",num_filled, line);
}	}
printf("Result %d: result line should be at minimum 'line=' %s, result=%s\n",num_filled, line, resultline);	nresult++; /* Sum of resultlines */
decoderesult(resultline);	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 */
while(fgets(line, MAXLINE, ficpar)) {	while(fgets(line, MAXLINE, ficpar)) {
/* If line starts with a # it is a comment */	/* If line starts with a # it is a comment */
if (line[0] == '#') {	if (line[0] == '#') {
Line 10538 Please run with mle=-1 to get a correct	Line 10889 Please run with mle=-1 to get a correct
mobaverages[i][j][k]=0.;	mobaverages[i][j][k]=0.;
mobaverage=mobaverages;	mobaverage=mobaverages;
if (mobilav!=0) {	if (mobilav!=0) {
	printf("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 10546 Please run with mle=-1 to get a correct	Line 10898 Please run with mle=-1 to get a correct
/* /\* Prevalence for each covariates in probs[age][status][cov] \/ /	/* /\* Prevalence for each covariates in probs[age][status][cov] \/ /
/* 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");
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);
Line 10601 Please run with mle=-1 to get a correct	Line 10954 Please run with mle=-1 to get a correct
printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);	printf("Computing Health Expectancies: result on file '%s' ...", filerese);fflush(stdout);
fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);	fprintf(ficlog,"Computing Health Expectancies: result on file '%s' ...", filerese);fflush(ficlog);

for (k=1; k <= (int) pow(2,cptcoveff); k++){ /* For any combination of dummy covariates, fixed and varying */	i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
	if (cptcovn < 1){i1=1;}

	for(nres=1; nres <= nresult; nres++) /* For each resultline */
	for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
	if(TKresult[nres]!= k)
	continue;
fprintf(ficreseij,"\n#****** ");	fprintf(ficreseij,"\n#****** ");
	printf("\n#****** ");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcoveff;j++) {
fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
	printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
	}
	for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
	printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
	fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
}	}
fprintf(ficreseij,"******\n");	fprintf(ficreseij,"******\n");
	printf("******\n");

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

free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);	free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
}	}
Line 10661 Please run with mle=-1 to get a correct	Line 11027 Please run with mle=-1 to get a correct
/*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++){*/

for (k=1; k <= (int) pow(2,cptcoveff); k++){	i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
printf("\n#****** ");	if (cptcovn < 1){i1=1;}
fprintf(ficrest,"\n#****** ");
fprintf(ficlog,"\n#****** ");	for(nres=1; nres <= nresult; nres++) /* For each resultline */
	for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
	if(TKresult[nres]!= k)
	continue;
	printf("\n#****** Selected:");
	fprintf(ficrest,"\n#****** Selected:");
	fprintf(ficlog,"\n#****** Selected:");
for(j=1;j<=cptcoveff;j++){	for(j=1;j<=cptcoveff;j++){
printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
}	}
	for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
	printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
	fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
	fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
	}
fprintf(ficrest,"******\n");	fprintf(ficrest,"******\n");
fprintf(ficlog,"******\n");	fprintf(ficlog,"******\n");
printf("******\n");	printf("******\n");
Line 10680 Please run with mle=-1 to get a correct	Line 11057 Please run with mle=-1 to get a correct
fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
}	}
	for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
	fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
	fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
	}
fprintf(ficresstdeij,"******\n");	fprintf(ficresstdeij,"******\n");
fprintf(ficrescveij,"******\n");	fprintf(ficrescveij,"******\n");

fprintf(ficresvij,"\n#****** ");	fprintf(ficresvij,"\n#****** ");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
	for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
	fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
	}
fprintf(ficresvij,"******\n");	fprintf(ficresvij,"******\n");

eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);	eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
oldm=oldms;savm=savms;	oldm=oldms;savm=savms;
printf(" cvevsij combination#=%d, ",k);	printf(" cvevsij ");
fprintf(ficlog, " cvevsij combination#=%d, ",k);	fprintf(ficlog, " cvevsij ");
cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);	cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart, nres);
printf(" end cvevsij \n ");	printf(" end cvevsij \n ");
fprintf(ficlog, " end cvevsij \n ");	fprintf(ficlog, " end cvevsij \n ");

Line 10709 Please run with mle=-1 to get a correct	Line 11093 Please run with mle=-1 to get a correct
cptcod= 0; /* To be deleted */	cptcod= 0; /* To be deleted */
printf("varevsij vpopbased=%d \n",vpopbased);	printf("varevsij vpopbased=%d \n",vpopbased);
fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);	fprintf(ficlog, "varevsij vpopbased=%d \n",vpopbased);
varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */	varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart, nres); /* cptcod not initialized Intel */
fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are ");	fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are ");
if(vpopbased==1)	if(vpopbased==1)
fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);	fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
Line 10723 Please run with mle=-1 to get a correct	Line 11107 Please run with mle=-1 to get a correct
printf("Computing age specific period (stable) prevalences in each health state \n");	printf("Computing age specific period (stable) prevalences in each health state \n");
fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");	fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");
for(age=bage; age <=fage ;age++){	for(age=bage; age <=fage ;age++){
prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k); /ZZ Is it the correct prevalim /	prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /ZZ Is it the correct prevalim /
if (vpopbased==1) {	if (vpopbased==1) {
if(mobilav ==0){	if(mobilav ==0){
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
Line 10760 Please run with mle=-1 to get a correct	Line 11144 Please run with mle=-1 to get a correct
free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);	free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);	free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
free_vector(epj,1,nlstate+1);	free_vector(epj,1,nlstate+1);
printf("done \n");fflush(stdout);	printf("done selection\n");fflush(stdout);
fprintf(ficlog,"done\n");fflush(ficlog);	fprintf(ficlog,"done selection\n");fflush(ficlog);

/}/	/}/
} /* End k */	} /* End k selection */

printf("done State-specific expectancies\n");fflush(stdout);	printf("done State-specific expectancies\n");fflush(stdout);
fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);	fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);
Line 10783 Please run with mle=-1 to get a correct	Line 11167 Please run with mle=-1 to get a correct
/*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++){*/

for (k=1; k <= (int) pow(2,cptcoveff); k++){	i1=pow(2,cptcoveff);
	if (cptcovn < 1){i1=1;}

	for(nres=1; nres <= nresult; nres++) /* For each resultline */
	for(k=1; k<=i1;k++){
	if(TKresult[nres]!= k)
	continue;
fprintf(ficresvpl,"\n#****** ");	fprintf(ficresvpl,"\n#****** ");
printf("\n#****** ");	printf("\n#****** ");
fprintf(ficlog,"\n#****** ");	fprintf(ficlog,"\n#****** ");
Line 10792 Please run with mle=-1 to get a correct	Line 11182 Please run with mle=-1 to get a correct
fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
}	}
	for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
	printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
	fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
	fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
	}
fprintf(ficresvpl,"******\n");	fprintf(ficresvpl,"******\n");
printf("******\n");	printf("******\n");
fprintf(ficlog,"******\n");	fprintf(ficlog,"******\n");

varpl=matrix(1,nlstate,(int) bage, (int) fage);	varpl=matrix(1,nlstate,(int) bage, (int) fage);
oldm=oldms;savm=savms;	oldm=oldms;savm=savms;
varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart);	varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart, nres);
free_matrix(varpl,1,nlstate,(int) bage, (int)fage);	free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
/}/	/}/
}	}
Line 10849 Please run with mle=-1 to get a correct	Line 11244 Please run with mle=-1 to get a correct
free_ivector(Fixed,-1,NCOVMAX);	free_ivector(Fixed,-1,NCOVMAX);
free_ivector(Typevar,-1,NCOVMAX);	free_ivector(Typevar,-1,NCOVMAX);
free_ivector(Tvar,1,NCOVMAX);	free_ivector(Tvar,1,NCOVMAX);
	free_ivector(TvarsQ,1,NCOVMAX);
	free_ivector(TvarsQind,1,NCOVMAX);
	free_ivector(TvarsD,1,NCOVMAX);
	free_ivector(TvarsDind,1,NCOVMAX);
free_ivector(TvarFD,1,NCOVMAX);	free_ivector(TvarFD,1,NCOVMAX);
free_ivector(TvarFDind,1,NCOVMAX);	free_ivector(TvarFDind,1,NCOVMAX);
free_ivector(TvarF,1,NCOVMAX);	free_ivector(TvarF,1,NCOVMAX);

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

Removed from v.1.233
changed lines
	Added in v.1.237