imach/src/imach.c - diff

Return to imach.c CVS log

Up to [Local Repository] / imach / src

Diff for /imach/src/imach.c between versions 1.231 and 1.236

version 1.231, 2016/08/22 07:17:15	version 1.236, 2016/08/25 10:50:18
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	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
	Summary: not working

	Revision 1.232 2016/08/22 14:20:21 brouard
	Summary: not working

Revision 1.231 2016/08/22 07:17:15 brouard	Revision 1.231 2016/08/22 07:17:15 brouard
Summary: not working	Summary: not working

Line 911 int cptcovsnq=0; /**< cptcovsnq number o	Line 926 int cptcovsnq=0; /**< cptcovsnq number o
int cptcovage=0; /*< Number of covariates with age: V3age only =1 */	int cptcovage=0; /*< Number of covariates with age: V3age only =1 */
int cptcovprodnoage=0; /*< Number of covariate products without age /	int cptcovprodnoage=0; /*< Number of covariate products without age /
int cptcoveff=0; /* Total number of covariates to vary for printing results */	int cptcoveff=0; /* Total number of covariates to vary for printing results */
int ncoveff=0; /* Total number of effective covariates 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 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 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 /
int nqtveff=0; /*< ntqveff number of effective time varying quantitative variables /	int nqtveff=0; /*< ntqveff number of effective time varying quantitative variables /
Line 968 char fileresv[FILENAMELENGTH];	Line 988 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 1067 double **cotvar; / Time varying covari	Line 1088 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];
	double Tresult[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) */
	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 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 TvarVind; /< TvarVind[1]=1, TvarVind[2]=2 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 /
	int TvarA; /< TvarA[1]=Tvar[5]=5, TvarA[2]=Tvar[8]=1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 /
	int TvarAind; /< TvarindA[1]=5, TvarAind[2]=8 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 /
int TvarFD; /< TvarFD[1]=V1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 /	int TvarFD; /< TvarFD[1]=V1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 /
int TvarFDind; / TvarFDind[1]=9 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */	int TvarFDind; / TvarFDind[1]=9 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
int TvarFQ; / TvarFQ[1]=V2 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple fixed quantitative variable */	int TvarFQ; / TvarFQ[1]=V2 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple fixed quantitative variable */
Line 1320 int nbocc(char *s, char occ)	Line 1379 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 2211 void powell(double p[], double **xi, int	Line 2270 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 2309 double prevalim(double prlim, int nl	Line 2370 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 2339 double prevalim(double prlim, int nl	Line 2400 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]); */
}	}
/wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; */	for (k=1; k<=cptcovage;k++){
/* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]cov[2]; /	if(Dummy[Tvar[Tage[k]]]){
for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];	cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
for (k=1; k<=cptcovprod;k++) /* Useless */	} else{
/* 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+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++){ /* */
	/* 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]); */
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];	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 2473 Earliest age to start was %d-%d=%d, ncvl	Line 2543 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 2501 Earliest age to start was %d-%d=%d, ncvl	Line 2569 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 2699 double bpmij(double ps, double *cov,	Line 2767 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 2799 double matprod2(double out, double *	Line 2867 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 2835 double *hpxij(double *po, int nhstep	Line 2903 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 3024 double func( double *x)	Line 3110 double func( double *x)
to be observed in j being in i according to the model.	to be observed in j being in i according to the model.
*/	*/
ioffset=2+nagesqr+cptcovage;	ioffset=2+nagesqr+cptcovage;
/* for (k=1; k<=cptcovn;k++){ /\* Simple and product covariates without age* products \/ /	/* Fixed */
for (k=1; k<=ncoveff;k++){ /* Simple and product covariates without age* products */	for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
cov[++ioffset]=covar[Tvar[k]][i];	cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, only V1 is fixed (k=6)*/
}
for(iqv=1; iqv <= nqfveff; iqv++){ /* Quantitatives and Fixed covariates */
cov[++ioffset]=coqvar[Tvar[iqv]][i];
}	}

/* 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 3045 double func( double *x)	Line 3127 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(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates */	for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
/* cov[ioffset+itv]=cotvar[mw[mi][i]][Tvar[itv]][i]; /\* Not sure, Tvar V4+V3+V5 Tvaraff ? \/ /	cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i];
cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i];	}
}	for (ii=1;ii<=nlstate+ndeath;ii++)
for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */	for (j=1;j<=nlstate+ndeath;j++){
if(cotqvar[mw[mi][i]][iqtv][i] == -1){	oldm[ii][j]=(ii==j ? 1.0 : 0.0);
printf("i=%d, mi=%d, iqtv=%d, cotqvar[mw[mi][i]][iqtv][i]=%f",i,mi,iqtv,cotqvar[mw[mi][i]][iqtv][i]);	savm[ii][j]=(ii==j ? 1.0 : 0.0);
}	}
cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i];	for(d=0; d<dh[mi][i]; d++){
/* cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][iqtv][i]; */	newm=savm;
}	agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
/* ioffset=2+nagesqr+cptcovn+nqv+ntv+nqtv; */	cov[2]=agexact;
for (ii=1;ii<=nlstate+ndeath;ii++)	if(nagesqr==1)
for (j=1;j<=nlstate+ndeath;j++){	cov[3]= agexactagexact; / Should be changed here */
oldm[ii][j]=(ii==j ? 1.0 : 0.0);	for (kk=1; kk<=cptcovage;kk++) {
savm[ii][j]=(ii==j ? 1.0 : 0.0);	cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]agexact; / Tage[kk] gives the data-covariate associated with age */
}	}
for(d=0; d<dh[mi][i]; d++){	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
newm=savm;	1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;	savm=oldm;
cov[2]=agexact;	oldm=newm;
if(nagesqr==1)	} /* end mult */
cov[3]= agexactagexact; / Should be changed here */
for (kk=1; kk<=cptcovage;kk++) {	/lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);/ /* Original formula */
cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]agexact; / Tage[kk] gives the data-covariate associated with age */	/* 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
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,	* (in months) between two waves is not a multiple of stepm, we rounded to
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));	* the nearest (and in case of equal distance, to the lowest) interval but now
savm=oldm;	* we keep into memory the bias bh[mi][i] and also the previous matrix product
oldm=newm;	* (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
} /* end mult */	* probability in order to take into account the bias as a fraction of the way

/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.
* 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
* 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
* (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
* 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 3352 double funcone( double *x)	Line 3425 double funcone( double *x)
ioffset=0;	ioffset=0;
for (i=1,ipmx=0, sw=0.; i<=imx; i++){	for (i=1,ipmx=0, sw=0.; i<=imx; i++){
ioffset=2+nagesqr+cptcovage;	ioffset=2+nagesqr+cptcovage;
	/* Fixed */
/* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */	/* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
for (k=1; k<=ncoveff;k++){ /* Simple and product fixed Dummy covariates without age* products */	/* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products \/ /
cov[++ioffset]=covar[TvarFD[k]][i];/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, only V1 is fixed (k=6)*/	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)*/
for (k=1; k<=nqfveff;k++){ /* Simple and product fixed Quantitative covariates without age* products */	/* cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i]; */
cov[++ioffset]=coqvar[TvarFQ[k]][i];/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, only V2 and V1V2 is fixed (k=6 and 7?)/	/* cov[2+6]=covar[Tvar[6]][i]; */
	/* cov[2+6]=covar[2][i]; V2 */
	/* cov[TvarFind[2]]=covar[Tvar[TvarFind[2]]][i]; */
	/* cov[2+7]=covar[Tvar[7]][i]; */
	/* cov[2+7]=covar[7][i]; V7=V1V2 /
	/* cov[TvarFind[3]]=covar[Tvar[TvarFind[3]]][i]; */
	/* cov[2+9]=covar[Tvar[9]][i]; */
	/* cov[2+9]=covar[1][i]; V1 */
}	}
	/* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products \/ /
	/* cov[++ioffset]=coqvar[TvarFQ[k]][i];/\* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, only V2 and V1V2 is fixed (k=6 and 7?)\/ */
	/* } */
/* for(iqv=1; iqv <= nqfveff; iqv++){ /\* Quantitative fixed covariates \/ /	/* for(iqv=1; iqv <= nqfveff; iqv++){ /\* Quantitative fixed covariates \/ /
/* cov[++ioffset]=coqvar[Tvar[iqv]][i]; /\* Only V2 k=6 and V1V2 7 \/ */	/* cov[++ioffset]=coqvar[Tvar[iqv]][i]; /\* Only V2 k=6 and V1V2 7 \/ */
/* } */	/* } */


for(mi=1; mi<= wav[i]-1; mi++){ /* Varying with waves */	for(mi=1; mi<= wav[i]-1; mi++){ /* Varying with waves */
for(itv=1; itv <= ntveff; itv++){ /* Varying dummy covariates (single??)*/	/* Wave varying (but not age varying) */
	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];
	}
	/* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)\/ /
/* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff \/ /	/* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff \/ /
/* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */	/* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */
k=ioffset-2-nagesqr-cptcovage+itv; /* position in simple model */	/* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model \/ /
cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i];	/* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */
/* printf(" i=%d,mi=%d,itv=%d,TmodelInvind[itv]=%d,cotvar[mw[mi][i]][TmodelInvind[itv]][i]=%f\n", i, mi, itv, TmodelInvind[itv],cotvar[mw[mi][i]][TmodelInvind[itv]][i]); */	/* printf(" i=%d,mi=%d,itv=%d,TmodelInvind[itv]=%d,cotvar[mw[mi][i]][TmodelInvind[itv]][i]=%f\n", i, mi, itv, TmodelInvind[itv],cotvar[mw[mi][i]][TmodelInvind[itv]][i]); */
}	/* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates \/ /
for(iqtv=1; iqtv <= nqtveff; iqtv++){ /* Varying quantitatives covariates */	/* iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff \/ /
iv=TmodelInvQind[iqtv]; /* Counting the # varying covariate from 1 to ntveff */	/* /\* printf(" i=%d,mi=%d,iqtv=%d,TmodelInvQind[iqtv]=%d,cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]=%f\n", i, mi, iqtv, TmodelInvQind[iqtv],cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]); \/ /
/* printf(" i=%d,mi=%d,iqtv=%d,TmodelInvQind[iqtv]=%d,cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]=%f\n", i, mi, iqtv, TmodelInvQind[iqtv],cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]); */	/* cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]; */
cov[ioffset+ntveff+iqtv]=cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][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);
Line 3416 double funcone( double *x)	Line 3504 double funcone( double *x)
* is higher than the multiple of stepm and negative otherwise.	* is higher than the multiple of stepm and negative otherwise.
*/	*/
if( s2 > nlstate && (mle <5) ){ /* Jackson */	if( s2 > nlstate && (mle <5) ){ /* Jackson */
lli=log(out[s1][s2] - savm[s1][s2]);	lli=log(out[s1][s2] - savm[s1][s2]);
} else if ( s2==-1 ) { /* alive */	} else if ( s2==-1 ) { /* alive */
for (j=1,survp=0. ; j<=nlstate; j++)	for (j=1,survp=0. ; j<=nlstate; j++)
survp += (1.+bbh)out[s1][j]- bbhsavm[s1][j];	survp += (1.+bbh)out[s1][j]- bbhsavm[s1][j];
lli= log(survp);	lli= log(survp);
}else if (mle==1){	}else if (mle==1){
lli= log((1.+bbh)out[s1][s2]- bbhsavm[s1][s2]); /* linear interpolation */	lli= log((1.+bbh)out[s1][s2]- bbhsavm[s1][s2]); /* linear interpolation */
} else if(mle==2){	} else if(mle==2){
lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)out[s1][s2]- bbhsavm[s1][s2]):log((1.+bbh)out[s1][s2])); / linear interpolation */	lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)out[s1][s2]- bbhsavm[s1][s2]):log((1.+bbh)out[s1][s2])); / linear interpolation */
} else if(mle==3){ /* exponential inter-extrapolation */	} else if(mle==3){ /* exponential inter-extrapolation */
lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]):log((1.+bbh)out[s1][s2])); / exponential inter-extrapolation */	lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]):log((1.+bbh)out[s1][s2])); / exponential inter-extrapolation */
} else if (mle==4){ /* mle=4 no inter-extrapolation */	} else if (mle==4){ /* mle=4 no inter-extrapolation */
lli=log(out[s1][s2]); /* Original formula */	lli=log(out[s1][s2]); /* Original formula */
} else{ /* mle=0 back to 1 */	} else{ /* mle=0 back to 1 */
lli= log((1.+bbh)out[s1][s2]- bbhsavm[s1][s2]); /* linear interpolation */	lli= log((1.+bbh)out[s1][s2]- bbhsavm[s1][s2]); /* linear interpolation */
/lli=log(out[s1][s2]); / /* Original formula */	/lli=log(out[s1][s2]); / /* Original formula */
} /* End of if */	} /* End of if */
ipmx +=1;	ipmx +=1;
sw += weight[i];	sw += weight[i];
ll[s[mw[mi][i]][i]] += 2weight[i]lli;	ll[s[mw[mi][i]][i]] += 2weight[i]lli;
/printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); /	/printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); /
if(globpr){	if(globpr){
fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\	fprintf(ficresilk,"%9ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
%11.6f %11.6f %11.6f ", \	%11.6f %11.6f %11.6f ", \
num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,	num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
2weight[i]lli,out[s1][s2],savm[s1][s2]);	2weight[i]lli,out[s1][s2],savm[s1][s2]);
for(k=1,llt=0.,l=0.; k<=nlstate; k++){	for(k=1,llt=0.,l=0.; k<=nlstate; k++){
llt +=ll[k]*gipmx/gsw;	llt +=ll[k]*gipmx/gsw;
fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);	fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
}	}
fprintf(ficresilk," %10.6f\n", -llt);	fprintf(ficresilk," %10.6f\n", -llt);
}	}
} /* end of wave */	} /* end of wave */
} /* end of individual */	} /* end of individual */
for(k=1,l=0.; k<=nlstate; k++) l += ll[k];	for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
/* printf("l1=%f l2=%f ",ll[1],ll[2]); */	/* printf("l1=%f l2=%f ",ll[1],ll[2]); */
l= lipmx/sw; / To get the same order of magnitude as if weight=1 for every body */	l= lipmx/sw; / To get the same order of magnitude as if weight=1 for every body */
if(globpr==0){ /* First time we count the contributions and weights */	if(globpr==0){ /* First time we count the contributions and weights */
gipmx=ipmx;	gipmx=ipmx;
gsw=sw;	gsw=sw;
}	}
return -l;	return -l;
}	}


Line 4060 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4148 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 4142 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4230 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 4166 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4254 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 4803 void concatwav(int wav[], int **dh, int	Line 4891 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 4876 void evsij(double ***eij, double x[], in	Line 4964 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 4911 void evsij(double ***eij, double x[], in	Line 4999 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 5024 void cvevsij(double ***eij, double x[],	Line 5112 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 5066 void cvevsij(double ***eij, double x[],	Line 5154 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 5121 void cvevsij(double ***eij, double x[],	Line 5209 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 5247 void cvevsij(double ***eij, double x[],	Line 5335 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 5259 void cvevsij(double ***eij, double x[],	Line 5347 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 5279 void cvevsij(double ***eij, double x[],	Line 5367 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 5291 void cvevsij(double ***eij, double x[],	Line 5379 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 5356 void cvevsij(double ***eij, double x[],	Line 5444 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 5372 void cvevsij(double ***eij, double x[],	Line 5460 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 5435 void cvevsij(double ***eij, double x[],	Line 5523 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 5478 void cvevsij(double ***eij, double x[],	Line 5566 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 5488 void cvevsij(double ***eij, double x[],	Line 5576 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 6094 void printinggnuplot(char fileresu[], ch	Line 6182 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,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 6143 void printinggnuplot(char fileresu[], ch	Line 6232 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 6153 void printinggnuplot(char fileresu[], ch	Line 6247 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 6214 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 6314 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 6226 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 6330 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 6263 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 6371 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 and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
Line 6279 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 6390 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 6309 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 6423 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 (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
	for(nres=1; nres <= nresult; nres++) /* For each resultline */
	if(TKresult[nres]!= k)
	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);
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* 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 6321 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 6437 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 6351 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6470 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 6363 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6485 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 6839 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6964 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 6878 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 7003 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 6906 void prevforecast(char fileres[], double	Line 7031 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 6938 void prevforecast(char fileres[], double	Line 7063 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 6947 void prevforecast(char fileres[], double	Line 7075 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 6961 void prevforecast(char fileres[], double	Line 7093 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 7591 int readdata(char datafile[], int firsto	Line 7723 int readdata(char datafile[], int firsto
/* Loops on waves */	/* Loops on waves */
for (j=maxwav;j>=1;j--){	for (j=maxwav;j>=1;j--){
for (iv=nqtv;iv>=1;iv--){ /* Loop on time varying quantitative variables */	for (iv=nqtv;iv>=1;iv--){ /* Loop on time varying quantitative variables */
cutv(stra, strb, line, ' ');	cutv(stra, strb, line, ' ');
if(strb[0]=='.') { /* Missing value */	if(strb[0]=='.') { /* Missing value */
lval=-1;	lval=-1;
cotqvar[j][iv][i]=-1; /* 0.0/0.0 */	cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
if(isalpha(strb[1])) { /* .m or .d Really Missing value */	cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value. Exiting.\n", strb, linei,i,line,iv, nqtv, j);	if(isalpha(strb[1])) { /* .m or .d Really Missing value */
fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value. Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog);	printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value. Exiting.\n", strb, linei,i,line,iv, nqtv, j);
return 1;	fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value. Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog);
}	return 1;
}else{	}
errno=0;	}else{
/* what_kind_of_number(strb); */	errno=0;
dval=strtod(strb,&endptr);	/* what_kind_of_number(strb); */
/* if( strb[0]=='\0' \|\| (endptr != '\0')){ /	dval=strtod(strb,&endptr);
/* if(strb != endptr && endptr == '\0') /	/* if( strb[0]=='\0' \|\| (endptr != '\0')){ /
/* dval=dlval; */	/* if(strb != endptr && endptr == '\0') /
/* if (errno == ERANGE && (lval == LONG_MAX \|\| lval == LONG_MIN)) */	/* dval=dlval; */
if( strb[0]=='\0' \|\| (*endptr != '\0')){	/* if (errno == ERANGE && (lval == LONG_MAX \|\| lval == LONG_MIN)) */
printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, nqtv, j,maxwav);	if( strb[0]=='\0' \|\| (*endptr != '\0')){
fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line, iv, nqtv, j,maxwav);fflush(ficlog);	printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, nqtv, j,maxwav);
return 1;	fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line, iv, nqtv, j,maxwav);fflush(ficlog);
}	return 1;
cotqvar[j][iv][i]=dval;	}
}	cotqvar[j][iv][i]=dval;
strcpy(line,stra);	cotvar[j][ntv+iv][i]=dval;
	}
	strcpy(line,stra);
}/* end loop ntqv */	}/* end loop ntqv */

for (iv=ntv;iv>=1;iv--){ /* Loop on time varying dummies */	for (iv=ntv;iv>=1;iv--){ /* Loop on time varying dummies */
cutv(stra, strb, line, ' ');	cutv(stra, strb, line, ' ');
if(strb[0]=='.') { /* Missing value */	if(strb[0]=='.') { /* Missing value */
lval=-1;	lval=-1;
}else{	}else{
errno=0;	errno=0;
lval=strtol(strb,&endptr,10);	lval=strtol(strb,&endptr,10);
/* if (errno == ERANGE && (lval == LONG_MAX \|\| lval == LONG_MIN))*/	/* if (errno == ERANGE && (lval == LONG_MAX \|\| lval == LONG_MIN))*/
if( strb[0]=='\0' \|\| (*endptr != '\0')){	if( strb[0]=='\0' \|\| (*endptr != '\0')){
printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th dummy covariate out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, ntv, j,maxwav);	printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th dummy covariate out of %d measured at wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, ntv, j,maxwav);
fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d dummy covariate out of %d measured wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, ntv,j,maxwav);fflush(ficlog);	fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d dummy covariate out of %d measured wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,iv, ntv,j,maxwav);fflush(ficlog);
return 1;	return 1;
}	}
}	}
if(lval <-1 \|\| lval >1){	if(lval <-1 \|\| lval >1){
printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \	printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \	Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \	for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
For example, for multinomial values like 1, 2 and 3,\n \	For example, for multinomial values like 1, 2 and 3,\n \
build V1=0 V2=0 for the reference value (1),\n \	build V1=0 V2=0 for the reference value (1),\n \
V1=1 V2=0 for (2) \n \	V1=1 V2=0 for (2) \n \
and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \	and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
output of IMaCh is often meaningless.\n \	output of IMaCh is often meaningless.\n \
Exiting.\n",lval,linei, i,line,j);	Exiting.\n",lval,linei, i,line,j);
fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \	fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \	Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \	for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
For example, for multinomial values like 1, 2 and 3,\n \	For example, for multinomial values like 1, 2 and 3,\n \
build V1=0 V2=0 for the reference value (1),\n \	build V1=0 V2=0 for the reference value (1),\n \
V1=1 V2=0 for (2) \n \	V1=1 V2=0 for (2) \n \
and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \	and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
output of IMaCh is often meaningless.\n \	output of IMaCh is often meaningless.\n \
Exiting.\n",lval,linei, i,line,j);fflush(ficlog);	Exiting.\n",lval,linei, i,line,j);fflush(ficlog);
return 1;	return 1;
}	}
cotvar[j][iv][i]=(double)(lval);	cotvar[j][iv][i]=(double)(lval);
strcpy(line,stra);	strcpy(line,stra);
}/* end loop ntv */	}/* end loop ntv */

/* Statuses at wave */	/* Statuses at wave */
cutv(stra, strb, line, ' ');	cutv(stra, strb, line, ' ');
if(strb[0]=='.') { /* Missing value */	if(strb[0]=='.') { /* Missing value */
lval=-1;	lval=-1;
}else{	}else{
errno=0;	errno=0;
lval=strtol(strb,&endptr,10);	lval=strtol(strb,&endptr,10);
/* if (errno == ERANGE && (lval == LONG_MAX \|\| lval == LONG_MIN))*/	/* if (errno == ERANGE && (lval == LONG_MAX \|\| lval == LONG_MIN))*/
if( strb[0]=='\0' \|\| (*endptr != '\0')){	if( strb[0]=='\0' \|\| (*endptr != '\0')){
printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);	printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);
fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);	fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
return 1;	return 1;
}	}
}	}

s[j][i]=lval;	s[j][i]=lval;
Line 7827 int readdata(char datafile[], int firsto	Line 7961 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){
printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);	printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
Line 7855 int decoderesult ( char resultline[])	Line 7995 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 7869 int decoderesult ( char resultline[])	Line 8015 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[2]=5 == Tvarsel[1]=4 */
	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]=5 == 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 */
	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] = 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];
	Tvresult[nres][k4+1]=(int)Tvarsel[k3];
	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];
	Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q];
	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 7916 int decodemodel( char model[], int lasto	Line 8125 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 8029 int decodemodel( char model[], int lasto	Line 8238 int decodemodel( char model[], int lasto
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 */
Line 8100 Typevar: 0 for simple covariate (dummy,	Line 8309 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, 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;	Fixed[k]= 0;
Dummy[k]= 0;	Dummy[k]= 0;
ncoveff++;	ncoveff++;
modell[k].maintype= FTYPE;	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;
	Dummy[k]= 0;
	ncoveff++;
	ncovf++;
	modell[k].maintype= FTYPE;
	TvarF[ncovf]=Tvar[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++;
	TvarF[ncovf]=Tvar[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;
	nsd++;
	TvarsD[nsd]=Tvar[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 */
	nsq++;
	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++;
	TvarA[ncova]=Tvar[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 */
}else if(Tvard[k1][2] <=ncovcol+nqv){	ncovf++; /* Fixed variables without age */
Fixed[k]= 0; /* or 2 ?*/	TvarF[ncovf]=Tvar[k];
Dummy[k]= 1;	TvarFind[ncovf]=k;
modell[k].maintype= FTYPE;	}else if(Tvard[k1][2] <=ncovcol+nqv){
modell[k].subtype= FPDQ; /* Product fixed dummy * fixed quantitative */	Fixed[k]= 0; /* or 2 ?*/
}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){	Dummy[k]= 1;
Fixed[k]= 1;	modell[k].maintype= FTYPE;
Dummy[k]= 0;	modell[k].subtype= FPDQ; /* Product fixed dummy * fixed quantitative */
modell[k].maintype= VTYPE;	ncovf++; /* Varying variables without age */
modell[k].subtype= VPDD; /* Product fixed dummy * varying dummy */	TvarF[ncovf]=Tvar[k];
}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){	TvarFind[ncovf]=k;
Fixed[k]= 1;	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
Dummy[k]= 1;	Fixed[k]= 1;
modell[k].maintype= VTYPE;	Dummy[k]= 0;
modell[k].subtype= VPDQ; /* Product fixed dummy * varying quantitative */	modell[k].maintype= VTYPE;
}	modell[k].subtype= VPDD; /* Product fixed dummy * varying dummy */
	ncovv++; /* Varying variables without age */
	TvarV[ncovv]=Tvar[k];
	TvarVind[ncovv]=k;
	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
	Fixed[k]= 1;
	Dummy[k]= 1;
	modell[k].maintype= VTYPE;
	modell[k].subtype= VPDQ; /* Product fixed dummy * varying quantitative */
	ncovv++; /* Varying variables without age */
	TvarV[ncovv]=Tvar[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 */
}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){	ncovf++; /* Fixed variables without age */
Fixed[k]= 1;	TvarF[ncovf]=Tvar[k];
Dummy[k]= 1;	TvarFind[ncovf]=k;
modell[k].maintype= VTYPE;	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
modell[k].subtype= VPDQ; /* Product fixed quantitative * varying dummy */	Fixed[k]= 1;
}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){	Dummy[k]= 1;
Fixed[k]= 1;	modell[k].maintype= VTYPE;
Dummy[k]= 1;	modell[k].subtype= VPDQ; /* Product fixed quantitative * varying dummy */
modell[k].maintype= VTYPE;	ncovv++; /* Varying variables without age */
modell[k].subtype= VPQQ; /* Product fixed quantitative * varying quantitative */	TvarV[ncovv]=Tvar[k];
}	TvarVind[ncovv]=k;
	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
	Fixed[k]= 1;
	Dummy[k]= 1;
	modell[k].maintype= VTYPE;
	modell[k].subtype= VPQQ; /* Product fixed quantitative * varying quantitative */
	ncovv++; /* Varying variables without age */
	TvarV[ncovv]=Tvar[k];
	TvarVind[ncovv]=k;
	ncovv++; /* Varying variables without age */
	TvarV[ncovv]=Tvar[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 */
}else if(Tvard[k1][2] <=ncovcol+nqv){	ncovv++; /* Varying variables without age */
Fixed[k]= 1;	TvarV[ncovv]=Tvar[k];
Dummy[k]= 1;	TvarVind[ncovv]=k;
modell[k].maintype= VTYPE;	}else if(Tvard[k1][2] <=ncovcol+nqv){
modell[k].subtype= VPDQ; /* Product time varying dummy * fixed quantitative */	Fixed[k]= 1;
}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){	Dummy[k]= 1;
Fixed[k]= 1;	modell[k].maintype= VTYPE;
Dummy[k]= 0;	modell[k].subtype= VPDQ; /* Product time varying dummy * fixed quantitative */
modell[k].maintype= VTYPE;	ncovv++; /* Varying variables without age */
modell[k].subtype= VPDD; /* Product time varying dummy * time varying dummy */	TvarV[ncovv]=Tvar[k];
}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){	TvarVind[ncovv]=k;
Fixed[k]= 1;	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
Dummy[k]= 1;	Fixed[k]= 1;
modell[k].maintype= VTYPE;	Dummy[k]= 0;
modell[k].subtype= VPDQ; /* Product time varying dummy * time varying quantitative */	modell[k].maintype= VTYPE;
}	modell[k].subtype= VPDD; /* Product time varying dummy * time varying dummy */
	ncovv++; /* Varying variables without age */
	TvarV[ncovv]=Tvar[k];
	TvarVind[ncovv]=k;
	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
	Fixed[k]= 1;
	Dummy[k]= 1;
	modell[k].maintype= VTYPE;
	modell[k].subtype= VPDQ; /* Product time varying dummy * time varying quantitative */
	ncovv++; /* Varying variables without age */
	TvarV[ncovv]=Tvar[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 */
}else if(Tvard[k1][2] <=ncovcol+nqv){	ncovv++; /* Varying variables without age */
Fixed[k]= 1;	TvarV[ncovv]=Tvar[k];
Dummy[k]= 1;	TvarVind[ncovv]=k;
modell[k].maintype= VTYPE;	}else if(Tvard[k1][2] <=ncovcol+nqv){
modell[k].subtype= VPQQ; /* Product time varying quantitative * fixed quantitative */	Fixed[k]= 1;
}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){	Dummy[k]= 1;
Fixed[k]= 1;	modell[k].maintype= VTYPE;
Dummy[k]= 1;	modell[k].subtype= VPQQ; /* Product time varying quantitative * fixed quantitative */
modell[k].maintype= VTYPE;	ncovv++; /* Varying variables without age */
modell[k].subtype= VPDQ; /* Product time varying quantitative * time varying dummy */	TvarV[ncovv]=Tvar[k];
}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){	TvarVind[ncovv]=k;
Fixed[k]= 1;	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
Dummy[k]= 1;	Fixed[k]= 1;
modell[k].maintype= VTYPE;	Dummy[k]= 1;
modell[k].subtype= VPQQ; /* Product time varying quantitative * time varying quantitative */	modell[k].maintype= VTYPE;
}	modell[k].subtype= VPDQ; /* Product time varying quantitative * time varying dummy */
	ncovv++; /* Varying variables without age */
	TvarV[ncovv]=Tvar[k];
	TvarVind[ncovv]=k;
	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
	Fixed[k]= 1;
	Dummy[k]= 1;
	modell[k].maintype= VTYPE;
	modell[k].subtype= VPQQ; /* Product time varying quantitative * time varying quantitative */
	ncovv++; /* Varying variables without age */
	TvarV[ncovv]=Tvar[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 8265 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 8559 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, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);
	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 8599 void syscompilerinfo(int logged)	Line 8895 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 8624 int prevalence_limit(double p, double	Line 8920 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 8642 int prevalence_limit(double p, double	Line 8942 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 8661 int prevalence_limit(double p, double	Line 8965 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 8683 int back_prevalence_limit(double *p, dou	Line 8987 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 8714 int back_prevalence_limit(double *p, dou	Line 9018 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 8724 int back_prevalence_limit(double *p, dou	Line 9031 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 8782 int hPijx(double *p, int bage, int fage)	Line 9094 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 8809 int hPijx(double *p, int bage, int fage)	Line 9121 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 8823 int hPijx(double *p, int bage, int fage)	Line 9142 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 8949 int main(int argc, char *argv[])	Line 9268 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 8967 int main(int argc, char *argv[])	Line 9287 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 9281 int main(int argc, char *argv[])	Line 9601 int main(int argc, char *argv[])

covar=matrix(0,NCOVMAX,1,n); /*< used in readdata /	covar=matrix(0,NCOVMAX,1,n); /*< used in readdata /
coqvar=matrix(1,nqv,1,n); /*< Fixed quantitative covariate /	coqvar=matrix(1,nqv,1,n); /*< Fixed quantitative covariate /
cotvar=ma3x(1,maxwav,1,ntv,1,n); /*< Time varying covariate /	cotvar=ma3x(1,maxwav,1,ntv+nqtv,1,n); /*< Time varying covariate (dummy and quantitative)/
cotqvar=ma3x(1,maxwav,1,nqtv,1,n); /*< Time varying quantitative covariate /	cotqvar=ma3x(1,maxwav,1,nqtv,1,n); /*< Time varying quantitative covariate /
cptcovn=0; /Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn/	cptcovn=0; /Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn/
/* v1+v2+v3+v2v4+v5age makes cptcovn = 5	/* v1+v2+v3+v2v4+v5age makes cptcovn = 5
Line 9334 int main(int argc, char *argv[])	Line 9654 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 9385 run imach with mle=-1 to get a correct t	Line 9705 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 9497 Please run with mle=-1 to get a correct	Line 9817 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 9518 Please run with mle=-1 to get a correct	Line 9838 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); /* */
	TvarFind=ivector(1,NCOVMAX); /* */
	TvarV=ivector(1,NCOVMAX); /* */
	TvarVind=ivector(1,NCOVMAX); /* */
	TvarA=ivector(1,NCOVMAX); /* */
	TvarAind=ivector(1,NCOVMAX); /* */
TvarFD=ivector(1,NCOVMAX); /* */	TvarFD=ivector(1,NCOVMAX); /* */
TvarFDind=ivector(1,NCOVMAX); /* */	TvarFDind=ivector(1,NCOVMAX); /* */
TvarFQ=ivector(1,NCOVMAX); /* */	TvarFQ=ivector(1,NCOVMAX); /* */
Line 9536 Please run with mle=-1 to get a correct	Line 9866 Please run with mle=-1 to get a correct
TvarVQind=ivector(1,NCOVMAX); /* */	TvarVQind=ivector(1,NCOVMAX); /* */

Tvalsel=vector(1,NCOVMAX); /* */	Tvalsel=vector(1,NCOVMAX); /* */
	Tvarsel=ivector(1,NCOVMAX); /* */
Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */	Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */	Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */	Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
Line 10341 Please run with mle=-1 to get a correct	Line 10672 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 10358 Please run with mle=-1 to get a correct	Line 10690 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 10446 Please run with mle=-1 to get a correct	Line 10784 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 10454 Please run with mle=-1 to get a correct	Line 10793 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 10509 Please run with mle=-1 to get a correct	Line 10849 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 10569 Please run with mle=-1 to get a correct	Line 10922 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 10588 Please run with mle=-1 to get a correct	Line 10952 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 10617 Please run with mle=-1 to get a correct	Line 10988 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 10631 Please run with mle=-1 to get a correct	Line 11002 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 10668 Please run with mle=-1 to get a correct	Line 11039 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 10691 Please run with mle=-1 to get a correct	Line 11062 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 10700 Please run with mle=-1 to get a correct	Line 11077 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 10741 Please run with mle=-1 to get a correct	Line 11123 Please run with mle=-1 to get a correct
free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);	free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);	free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);	free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);
free_ma3x(cotvar,1,maxwav,1,ntv,1,n);	free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n);
free_matrix(coqvar,1,maxwav,1,n);	free_matrix(coqvar,1,maxwav,1,n);
free_matrix(covar,0,NCOVMAX,1,n);	free_matrix(covar,0,NCOVMAX,1,n);
free_matrix(matcov,1,npar,1,npar);	free_matrix(matcov,1,npar,1,npar);
Line 10757 Please run with mle=-1 to get a correct	Line 11139 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(TvarFind,1,NCOVMAX);
	free_ivector(TvarV,1,NCOVMAX);
	free_ivector(TvarVind,1,NCOVMAX);
	free_ivector(TvarA,1,NCOVMAX);
	free_ivector(TvarAind,1,NCOVMAX);
free_ivector(TvarFQ,1,NCOVMAX);	free_ivector(TvarFQ,1,NCOVMAX);
free_ivector(TvarFQind,1,NCOVMAX);	free_ivector(TvarFQind,1,NCOVMAX);
free_ivector(TvarVD,1,NCOVMAX);	free_ivector(TvarVD,1,NCOVMAX);

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

Removed from v.1.231
changed lines
	Added in v.1.236