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Diff for /imach/src/imach.c between versions 1.234 and 1.246

version 1.234, 2016/08/23 16:51:20	version 1.246, 2016/09/02 08:49:22
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	Revision 1.246 2016/09/02 08:49:22 brouard
	* empty log message *

	Revision 1.245 2016/09/02 07:25:01 brouard
	* empty log message *

	Revision 1.244 2016/09/02 07:17:34 brouard
	* empty log message *

	Revision 1.243 2016/09/02 06:45:35 brouard
	* empty log message *

	Revision 1.242 2016/08/30 15:01:20 brouard
	Summary: Fixing a lots

	Revision 1.241 2016/08/29 17:17:25 brouard
	Summary: gnuplot problem in Back projection to fix

	Revision 1.240 2016/08/29 07:53:18 brouard
	Summary: Better

	Revision 1.239 2016/08/26 15:51:03 brouard
	Summary: Improvement in Powell output in order to copy and paste

	Author:

	Revision 1.238 2016/08/26 14:23:35 brouard
	Summary: Starting tests of 0.99

	Revision 1.237 2016/08/26 09:20:19 brouard
	Summary: to valgrind

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

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

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

Line 1020 double dval;	Line 1058 double dval;
#define FTOL 1.0e-10	#define FTOL 1.0e-10

#define NRANSI	#define NRANSI
#define ITMAX 200	#define ITMAX 200
	#define ITPOWMAX 20 /* This is now multiplied by the number of parameters */

#define TOL 2.0e-4	#define TOL 2.0e-4

Line 1105 int *TvarsDind;	Line 1144 int *TvarsDind;
int *TvarsQ;	int *TvarsQ;
int *TvarsQind;	int *TvarsQind;

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

/* int TDvar; /\< TDvar[1]=4, TDvarF[2]=3, TDvar[3]=6 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 \/ */	/* int TDvar; /\< TDvar[1]=4, TDvarF[2]=3, TDvar[3]=6 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 \/ */
int TvarF; /< TvarF[1]=Tvar[6]=2, TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 /	int TvarF; /< TvarF[1]=Tvar[6]=2, TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 /
int TvarFind; /< TvarFind[1]=6, TvarFind[2]=7, Tvarind[3]=9 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 /	int TvarFind; /< TvarFind[1]=6, TvarFind[2]=7, Tvarind[3]=9 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 /
Line 1126 double Tvalsel; /*< Selected modality	Line 1175 double Tvalsel; /*< Selected modality
int Typevar; /< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product /	int Typevar; /< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product /
int Fixed; /* Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */	int Fixed; /* Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
int Dummy; /* Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */	int Dummy; /* Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */
	int DummyV; /* Dummy[v] 0=dummy (0 1), 1 quantitative */
	int FixedV; /* FixedV[v] 0 fixed, 1 varying */
int *Tage;	int *Tage;
int anyvaryingduminmodel=0; /*< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq /	int anyvaryingduminmodel=0; /*< Any varying dummy in Model=1 yes, 0 no, to avoid a loop on waves in freq /
int Tmodelind; /* Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1*/	int Tmodelind; /* Tmodelind[Tvaraff[3]]=9 for V1 position,Tvaraff[1]@9={4, 3, 1, 0, 0, 0, 0, 0, 0}, model=V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1*/
Line 1135 int Ndum; /* Freq of modality (tricode	Line 1186 int Ndum; /* Freq of modality (tricode
/* int *codtab;/ /*< codtab=imatrix(1,100,1,10); /	/* int *codtab;/ /*< codtab=imatrix(1,100,1,10); /
int **Tvard;	int **Tvard;
int Tprod;/< Gives the k position of the k1 product /	int Tprod;/< Gives the k position of the k1 product /
	/* Tprod[k1=1]=3(=V1V4) for V2+V1+V1V4+ageV3 /
int Tposprod; /< Gives the k1 product from the k position /	int Tposprod; /< Gives the k1 product from the k position /
/* Tprod[k1=1]=3(=V1V4) for V2+V1+V1V4+age*V3	/* if V2+V1+V1V4+ageV3+V3V2 TProd[k1=2]=5 (V3V2) */
if V2+V1+V1V4+ageV3+V3V2 TProd[k1=2]=5 (V3V2)	/* Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5(V3V2)]=2 (2nd product without age) /
Tposprod[k]=k1 , Tposprod[3]=1, Tposprod[5]=2
*/
int cptcovprod, Tvaraff, invalidvarcomb;	int cptcovprod, Tvaraff, invalidvarcomb;
double lsurv, lpop, *tpop;	double lsurv, lpop, *tpop;

Line 2038 void powell(double p[], double **xi, int	Line 2088 void powell(double p[], double **xi, int
void linmin(double p[], double xi[], int n, double *fret,	void linmin(double p[], double xi[], int n, double *fret,
double (*func)(double []));	double (*func)(double []));
#else	#else
void linmin(double p[], double xi[], int n, double *fret,	void linmin(double p[], double xi[], int n, double *fret,
double (func)(double []),int flat);	double (func)(double []),int flat);
#endif	#endif
int i,ibig,j;	int i,ibig,j,jk,k;
double del,t,pt,ptt,*xit;	double del,t,pt,ptt,*xit;
double directest;	double directest;
double fp,fptt;	double fp,fptt;
Line 2073 void powell(double p[], double **xi, int	Line 2123 void powell(double p[], double **xi, int
fprintf(ficlog,"\nPowell iter=%d -2LL=%.12f %ld sec. %ld sec.",iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);	fprintf(ficlog,"\nPowell iter=%d -2LL=%.12f %ld sec. %ld sec.",iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
/* fprintf(ficrespow,"%d %.12f %ld",iter,fret,curr_time.tm_sec-start_time.tm_sec); */	/* fprintf(ficrespow,"%d %.12f %ld",iter,fret,curr_time.tm_sec-start_time.tm_sec); */
for (i=1;i<=n;i++) {	for (i=1;i<=n;i++) {
printf(" %d %.12f",i, p[i]);
fprintf(ficlog," %d %.12lf",i, p[i]);
fprintf(ficrespow," %.12lf", p[i]);	fprintf(ficrespow," %.12lf", p[i]);
}	}
	fprintf(ficrespow,"\n");fflush(ficrespow);
	printf("\n#model= 1 + age ");
	fprintf(ficlog,"\n#model= 1 + age ");
	if(nagesqr==1){
	printf(" + age*age ");
	fprintf(ficlog," + age*age ");
	}
	for(j=1;j <=ncovmodel-2;j++){
	if(Typevar[j]==0) {
	printf(" + V%d ",Tvar[j]);
	fprintf(ficlog," + V%d ",Tvar[j]);
	}else if(Typevar[j]==1) {
	printf(" + V%d*age ",Tvar[j]);
	fprintf(ficlog," + V%d*age ",Tvar[j]);
	}else if(Typevar[j]==2) {
	printf(" + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
	fprintf(ficlog," + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
	}
	}
printf("\n");	printf("\n");
	/* printf("12 47.0114589 0.0154322 33.2424412 0.3279905 2.3731903 */
	/* 13 -21.5392400 0.1118147 1.2680506 1.2973408 -1.0663662 */
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
fprintf(ficrespow,"\n");fflush(ficrespow);	for(i=1,jk=1; i <=nlstate; i++){
if(*iter <=3){	for(k=1; k <=(nlstate+ndeath); k++){
	if (k != i) {
	printf("%d%d ",i,k);
	fprintf(ficlog,"%d%d ",i,k);
	for(j=1; j <=ncovmodel; j++){
	printf("%12.7f ",p[jk]);
	fprintf(ficlog,"%12.7f ",p[jk]);
	jk++;
	}
	printf("\n");
	fprintf(ficlog,"\n");
	}
	}
	}
	if(iter <=3 && iter >1){
tml = *localtime(&rcurr_time);	tml = *localtime(&rcurr_time);
strcpy(strcurr,asctime(&tml));	strcpy(strcurr,asctime(&tml));
rforecast_time=rcurr_time;	rforecast_time=rcurr_time;
itmp = strlen(strcurr);	itmp = strlen(strcurr);
if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */	if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */
strcurr[itmp-1]='\0';	strcurr[itmp-1]='\0';
printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);	printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);	fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
for(niterf=10;niterf<=30;niterf+=10){	for(niterf=10;niterf<=30;niterf+=10){
rforecast_time=rcurr_time+(niterf-iter)(rcurr_time-rlast_time);	rforecast_time=rcurr_time+(niterf-iter)(rcurr_time-rlast_time);
forecast_time = *localtime(&rforecast_time);	forecast_time = *localtime(&rforecast_time);
strcpy(strfor,asctime(&forecast_time));	strcpy(strfor,asctime(&forecast_time));
itmp = strlen(strfor);	itmp = strlen(strfor);
if(strfor[itmp-1]=='\n')	if(strfor[itmp-1]=='\n')
strfor[itmp-1]='\0';	strfor[itmp-1]='\0';
printf(" - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);	printf(" - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
fprintf(ficlog," - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);	fprintf(ficlog," - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
}	}
}	}
for (i=1;i<=n;i++) { /* For each direction i */	for (i=1;i<=n;i++) { /* For each direction i */
Line 2151 void powell(double p[], double **xi, int	Line 2234 void powell(double p[], double **xi, int
/* printf("\n"); */	/* printf("\n"); */
/* fprintf(ficlog,"\n"); */	/* fprintf(ficlog,"\n"); */
}	}
if (2.0fabs(fp-(fret)) <= ftol(fabs(fp)+fabs(fret))) { /* Did we reach enough precision? */	/* if (2.0fabs(fp-(fret)) <= ftol(fabs(fp)+fabs(fret))) { /\* Did we reach enough precision? \/ /
	if (2.0fabs(fp-(fret)) <= ftol) { /* Did we reach enough precision? */
/* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */	/* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
/* By adding ageage in a model, the new -2LL should be lower and the difference follows a /	/* By adding ageage in a model, the new -2LL should be lower and the difference follows a /
/* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */	/* a chisquare statistics with 1 degree. To be significant at the 95% level, it should have */
Line 2197 void powell(double p[], double **xi, int	Line 2281 void powell(double p[], double **xi, int
free_vector(pt,1,n);	free_vector(pt,1,n);
return;	return;
} /* enough precision */	} /* enough precision */
if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");	if (iter == ITMAXn) nrerror("powell exceeding maximum iterations.");
for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */	for (j=1;j<=n;j++) { /* Computes the extrapolated point P_0 + 2 (P_n-P_0) */
ptt[j]=2.0*p[j]-pt[j];	ptt[j]=2.0*p[j]-pt[j];
xit[j]=p[j]-pt[j];	xit[j]=p[j]-pt[j];
Line 2333 void powell(double p[], double **xi, int	Line 2417 void powell(double p[], double **xi, int

/** 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 combiation ij by left multiplying the unit	/* Computes the prevalence limit in each live state at age x and for covariate combination ij
	(and selected quantitative values in nres)
	by left multiplying the unit
matrix by transitions matrix until convergence is reached with precision ftolpl */	matrix by transitions matrix until convergence is reached with precision ftolpl */
/* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */	/* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
/* Wx is row vector: population in state 1, population in state 2, population dead */	/* Wx is row vector: population in state 1, population in state 2, population dead */
Line 2387 double prevalim(double prlim, int nl	Line 2473 double prevalim(double prlim, int nl
for (k=1; k<=nsd;k++) { /* For single dummy covariates only */	for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
/* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */	/* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];	cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
printf("prevalim ij=%d k=%d TvarsD[%d]=%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 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)); */
}	}
for (k=1; k<=nsq;k++) { /* For single varying covariates only */	for (k=1; k<=nsq;k++) { /* For single varying covariates only */
/* Here comes the value of quantitative after renumbering k with single quantitative covariates */	/* Here comes the value of quantitative after renumbering k with single quantitative covariates */
/* cov[2+nagesqr+TvarsQind[k]]=qselvar[k]; */	cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
printf("prevalim ij=%d k=%d TvarsQind[%d]=%d \n",ij,k,k,TvarsQind[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 product with age */
/* 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++){
if(Dummy[Tvar[Tage[k]]]){	if(Dummy[Tvar[Tage[k]]]){
cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];	cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
} else{	} else{
;	cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
/* cov[2+nagesqr+Tage[k]]=qselvar[k]; */
}	}
printf("prevalim Age ij=%d k=%d Tage[%d]=%d \n",ij,k,k,Tage[k]);	/* printf("prevalim Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
}	}
for (k=1; k<=cptcovprod;k++){ /* */	for (k=1; k<=cptcovprod;k++){ /* For product without age */
printf("prevalim Prod ij=%d k=%d Tprod[%d]=%d Tvard[%d][1]=%d, Tvard[%d][2]=%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]);	/* 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)];	if(Dummy[Tvard[k][1]==0]){
	if(Dummy[Tvard[k][2]==0]){
	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
	}else{
	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
	}
	}else{
	if(Dummy[Tvard[k][2]==0]){
	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
	}else{
	cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
	}
	}
}	}
/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]);/
Line 2466 Earliest age to start was %d-%d=%d, ncvl	Line 2561 Earliest age to start was %d-%d=%d, ncvl

/* double bprevalim(double bprlim, double *prevacurrent, int nlstate, double x[], double age, double ageminpar, double agemaxpar, double oldm, double savm, double dnewm, double doldm, double dsavm, double ftolpl, int ncvyear, int ij) /	/* double bprevalim(double bprlim, double *prevacurrent, int nlstate, double x[], double age, double ageminpar, double agemaxpar, double oldm, double savm, double dnewm, double doldm, double dsavm, double ftolpl, int ncvyear, int ij) /
/* double bprevalim(double bprlim, double *prevacurrent, int nlstate, double x[], double age, double oldm, double savm, double dnewm, double doldm, double dsavm, double ftolpl, int ncvyear, int ij) /	/* double bprevalim(double bprlim, double *prevacurrent, int nlstate, double x[], double age, double oldm, double savm, double dnewm, double doldm, double dsavm, double ftolpl, int ncvyear, int ij) /
double bprevalim(double bprlim, double **prevacurrent, int nlstate, double x[], double age, double ftolpl, int ncvyear, int ij)	double bprevalim(double bprlim, double **prevacurrent, int nlstate, double x[], double age, double ftolpl, int ncvyear, int ij, int nres)
{	{
/* Computes the prevalence limit in each live state at age x and covariate ij by left multiplying the unit	/* Computes the prevalence limit in each live state at age x and covariate ij by left multiplying the unit
matrix by transitions matrix until convergence is reached with precision ftolpl */	matrix by transitions matrix until convergence is reached with precision ftolpl */
Line 2525 Earliest age to start was %d-%d=%d, ncvl	Line 2620 Earliest age to start was %d-%d=%d, ncvl
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 */
cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];	cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[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("bprevalim Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
	}
	/* for (k=1; k<=cptcovn;k++) { */
	/* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; \/ /
	/* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
	/* /\* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); \/ /
	/* } */
	for (k=1; k<=nsq;k++) { /* For single varying covariates only */
	/* Here comes the value of quantitative after renumbering k with single quantitative covariates */
	cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
	/* printf("prevalim Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
	}
	/* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]cov[2]; /
	/* for (k=1; k<=cptcovprod;k++) /\* Useless \/ /
	/* /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; \/ /
	/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
	for (k=1; k<=cptcovage;k++){ /* For product with age */
	if(Dummy[Tvar[Tage[k]]]){
	cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
	} else{
	cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
	}
	/* printf("prevalim Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
	}
	for (k=1; k<=cptcovprod;k++){ /* For product without age */
	/* printf("prevalim Prod ij=%d k=%d Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
	if(Dummy[Tvard[k][1]==0]){
	if(Dummy[Tvard[k][2]==0]){
	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
	}else{
	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
	}
	}else{
	if(Dummy[Tvard[k][2]==0]){
	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
	}else{
	cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
	}
	}
}	}
/wrong? for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; */
/* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]cov[2]; /
for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]*cov[2];
for (k=1; k<=cptcovprod;k++) /* Useless */
/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];

/printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);/	/printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);/
/printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);/	/printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);/
Line 2715 double pmij(double ps, double *cov,	Line 2842 double pmij(double ps, double *cov,
/* }else */	/* }else */
doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);	doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);
}else{	}else{
printf("ii=%d, i=%d, doldm=%lf dsavm=%lf, probs=%lf, sumnew=%lf,agefin=%d\n",ii,j,doldm[ii][j],dsavm[ii][j],prevacurrent[(int)agefin][ii][ij],sumnew, (int)agefin);	;
	/* printf("ii=%d, i=%d, doldm=%lf dsavm=%lf, probs=%lf, sumnew=%lf,agefin=%d\n",ii,j,doldm[ii][j],dsavm[ii][j],prevacurrent[(int)agefin][ii][ij],sumnew, (int)agefin); */
}	}
} /End ii /	} /End ii /
} /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */	} /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */
Line 2856 double matprod2(double out, double *	Line 2984 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 2892 double *hpxij(double *po, int nhstep	Line 3020 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 3080 double func( double *x)	Line 3226 double func( double *x)
Then computes with function pmij which return a matrix p[i][j] giving the elementary probability	Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
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 ;
/* Fixed */	/* Fixed */
for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */	for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */
cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, only V1 is fixed (k=6)*/	cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, only V1 is fixed (k=6)*/
Line 3099 double func( double *x)	Line 3245 double func( double *x)
*/	*/
for(mi=1; mi<= wav[i]-1; mi++){	for(mi=1; mi<= wav[i]-1; mi++){
for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/	for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i];	/* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
	cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][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++){
Line 3113 double func( double *x)	Line 3260 double func( double *x)
if(nagesqr==1)	if(nagesqr==1)
cov[3]= agexactagexact; / Should be changed here */	cov[3]= agexactagexact; / Should be changed here */
for (kk=1; kk<=cptcovage;kk++) {	for (kk=1; kk<=cptcovage;kk++) {
	if(!FixedV[Tvar[Tage[kk]]])
cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]agexact; / Tage[kk] gives the data-covariate associated with age */	cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]agexact; / Tage[kk] gives the data-covariate associated with age */
	else
	cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
}	}
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));	1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
Line 3395 double funcone( double *x)	Line 3545 double funcone( double *x)
for(k=1; k<=nlstate; k++) ll[k]=0.;	for(k=1; k<=nlstate; k++) ll[k]=0.;
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; */
	ioffset=2+nagesqr;
/* Fixed */	/* 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 \/ /
Line 3422 double funcone( double *x)	Line 3573 double funcone( double *x)
for(mi=1; mi<= wav[i]-1; mi++){ /* Varying with waves */	for(mi=1; mi<= wav[i]-1; mi++){ /* Varying with waves */
/* Wave varying (but not age varying) */	/* Wave varying (but not age varying) */
for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/	for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/
cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i];	/* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */
}	cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
	}
/* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)\/ /	/* 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);
savm[ii][j]=(ii==j ? 1.0 : 0.0);	savm[ii][j]=(ii==j ? 1.0 : 0.0);
}	}

agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */	agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
ageend=agev[mw[mi][i]][i] + (dh[mi][i])stepm/YEARM; / Age at end of effective wave and at the end of transition */	ageend=agev[mw[mi][i]][i] + (dh[mi][i])stepm/YEARM; / Age at end of effective wave and at the end of transition */
for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */	for(d=0; d<dh[mi][i]; d++){ /* Delay between two effective waves */
/*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]	/*dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
and mw[mi+1][i]. dh depends on stepm.*/	and mw[mi+1][i]. dh depends on stepm.*/
newm=savm;	newm=savm;
agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;	agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
cov[2]=agexact;	cov[2]=agexact;
if(nagesqr==1)	if(nagesqr==1)
cov[3]= agexact*agexact;	cov[3]= agexact*agexact;
for (kk=1; kk<=cptcovage;kk++) {	for (kk=1; kk<=cptcovage;kk++) {
cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;	if(!FixedV[Tvar[Tage[kk]]])
}	cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
/* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */	else
/* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */	cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,	}
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));	/* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
/* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */	/* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
/* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
savm=oldm;	1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
oldm=newm;	/* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath, */
	/* 1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate)); */
	savm=oldm;
	oldm=newm;
} /* end mult */	} /* end mult */

s1=s[mw[mi][i]][i];	s1=s[mw[mi][i]][i];
Line 3475 double funcone( double *x)	Line 3630 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,"%09ld %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 */
Line 3855 double hessij( double x[], double **hess	Line 4010 double hessij( double x[], double **hess
kmax=kmax+10;	kmax=kmax+10;
}	}
if(kmax >=10 \|\| firstime ==1){	if(kmax >=10 \|\| firstime ==1){
printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you may increase ftol=%.2e\n",thetai,thetaj, ftol);	printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol);
fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you may increase ftol=%.2e\n",thetai,thetaj, ftol);	fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol);
printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e deltik=%.12e deltjk=%.12e, xi-dek=%.12e xj-dek=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);	printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e deltik=%.12e deltjk=%.12e, xi-dek=%.12e xj-dek=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e deltik=%.12e deltjk=%.12e, xi-dek=%.12e xj-dek=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);	fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e deltik=%.12e deltjk=%.12e, xi-dek=%.12e xj-dek=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
}	}
Line 4044 void freqsummary(char fileres[], int ia	Line 4199 void freqsummary(char fileres[], int ia
fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);	fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
exit(0);	exit(0);
}	}

strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));	strcpy(fileresphtm,subdirfext(optionfilefiname,"PHTM_",".htm"));
if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {	if((ficresphtm=fopen(fileresphtm,"w"))==NULL) {
printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));	printf("Problem with prevalence HTM resultfile '%s' with errno='%s'\n",fileresphtm,strerror(errno));
Line 4054 void freqsummary(char fileres[], int ia	Line 4209 void freqsummary(char fileres[], int ia
}	}
else{	else{
fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \	fprintf(ficresphtm,"<html><head>\n<title>IMaCh PHTM_ %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
<hr size=\"2\" color=\"#EC5E5E\"> \n\	<hr size=\"2\" color=\"#EC5E5E\"> \n \
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\	Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);	fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
}	}
fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition</h4>\n",fileresphtm, fileresphtm);	fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition and dummy covariate value at beginning of transition</h4>\n",fileresphtm, fileresphtm);

strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));	strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {	if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));	printf("Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));	fprintf(ficlog,"Problem with frequency table HTM resultfile '%s' with errno='%s'\n",fileresphtmfr,strerror(errno));
fflush(ficlog);	fflush(ficlog);
exit(70);	exit(70);
}	} else{
else{
fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \	fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
<hr size=\"2\" color=\"#EC5E5E\"> \n\	<hr size=\"2\" color=\"#EC5E5E\"> \n \
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\	Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);	fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
}	}
fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions by age at begin of transition </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);	fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions of the model, by age at begin of transition, and covariate value at the begin of transition (if the covariate is a varying covariate) </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);

freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);	freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+3+AGEMARGE);
j1=0;	j1=0;

/* j=ncoveff; /\* Only fixed dummy covariates \/ /	/* j=ncoveff; /\* Only fixed dummy covariates \/ /
j=cptcoveff; /* Only dummy covariates of the model */	j=cptcoveff; /* Only dummy covariates of the model */
if (cptcovn<1) {j=1;ncodemax[1]=1;}	if (cptcovn<1) {j=1;ncodemax[1]=1;}

first=1;	first=1;

/* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:	/* Detects if a combination j1 is empty: for a multinomial variable like 3 education levels:
reference=low_education V1=0,V2=0	reference=low_education V1=0,V2=0
med_educ V1=1 V2=0,	med_educ V1=1 V2=0,
high_educ V1=0 V2=1	high_educ V1=0 V2=1
Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff	Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff
*/	*/

for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination in order of model, excluding quantitatives V4=0, V3=0 for example, fixed or varying covariates */	for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on covariates combination in order of model, excluding quantitatives V4=0, V3=0 for example, fixed or varying covariates */
posproptt=0.;	posproptt=0.;
/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);	/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
scanf("%d", i);*/	scanf("%d", i);*/
for (i=-5; i<=nlstate+ndeath; i++)	for (i=-5; i<=nlstate+ndeath; i++)
for (jk=-5; jk<=nlstate+ndeath; jk++)	for (jk=-5; jk<=nlstate+ndeath; jk++)
for(m=iagemin; m <= iagemax+3; m++)	for(m=iagemin; m <= iagemax+3; m++)
freq[i][jk][m]=0;	freq[i][jk][m]=0;

for (i=1; i<=nlstate; i++) {	for (i=1; i<=nlstate; i++) {
for(m=iagemin; m <= iagemax+3; m++)	for(m=iagemin; m <= iagemax+3; m++)
prop[i][m]=0;	prop[i][m]=0;
posprop[i]=0;	posprop[i]=0;
pospropt[i]=0;	pospropt[i]=0;
}	}
Line 4112 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4266 Title=%s <br>Datafile=%s Firstpass=%d La
/* meanqt[m][z1]=0.; */	/* meanqt[m][z1]=0.; */
/* } */	/* } */
/* } */	/* } */

dateintsum=0;	dateintsum=0;
k2cpt=0;	k2cpt=0;
/* For that combination of covariate j1, we count and print the frequencies in one pass */	/* For that combination of covariate j1, we count and print the frequencies in one pass */
Line 4191 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4345 Title=%s <br>Datafile=%s Firstpass=%d La
} /* 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
freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */	freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */


/* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/	/* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
pstamp(ficresp);	pstamp(ficresp);
/* if (ncoveff>0) { */	if (cptcoveff>0){
if (cptcoveff>0) {
fprintf(ficresp, "\n#********** Variable ");	fprintf(ficresp, "\n#********** Variable ");
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 ");
	fprintf(ficlog, "\n#********** 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)]);	if(DummyV[z1]){
fprintf(ficresphtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	fprintf(ficresp, "V%d (fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficresphtmfr, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	fprintf(ficresphtm, "V%d (fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
	fprintf(ficresphtmfr, "V%d (fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
	fprintf(ficlog, "V%d (fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
	}else{
	fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
	fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
	fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
	fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
	}
}	}
fprintf(ficresp, "**********\n#");	fprintf(ficresp, "**********\n#");
fprintf(ficresphtm, "**********</h3>\n");	fprintf(ficresphtm, "**********</h3>\n");
fprintf(ficresphtmfr, "**********</h3>\n");	fprintf(ficresphtmfr, "**********</h3>\n");
fprintf(ficlog, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficlog, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficlog, "**********\n");	fprintf(ficlog, "**********\n");
}	}
fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");	fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
for(i=1; i<=nlstate;i++) {	for(i=1; i<=nlstate;i++) {
fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);	fprintf(ficresp, " Age Prev(%d) N(%d) N ",i,i);
fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);	fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
}	}
fprintf(ficresp, "\n");	fprintf(ficresp, "\n");
fprintf(ficresphtm, "\n");	fprintf(ficresphtm, "\n");

/* Header of frequency table by age */	/* Header of frequency table by age */
fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");	fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
fprintf(ficresphtmfr,"<th>Age</th> ");	fprintf(ficresphtmfr,"<th>Age</th> ");
Line 4230 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4390 Title=%s <br>Datafile=%s Firstpass=%d La
}	}
}	}
fprintf(ficresphtmfr, "\n");	fprintf(ficresphtmfr, "\n");

/* For each age */	/* For each age */
for(iage=iagemin; iage <= iagemax+3; iage++){	for(iage=iagemin; iage <= iagemax+3; iage++){
fprintf(ficresphtm,"<tr>");	fprintf(ficresphtm,"<tr>");
if(iage==iagemax+1){	if(iage==iagemax+1){
fprintf(ficlog,"1");	fprintf(ficlog,"1");
fprintf(ficresphtmfr,"<tr><th>0</th> ");	fprintf(ficresphtmfr,"<tr><th>0</th> ");
}else if(iage==iagemax+2){	}else if(iage==iagemax+2){
fprintf(ficlog,"0");	fprintf(ficlog,"0");
fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");	fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
}else if(iage==iagemax+3){	}else if(iage==iagemax+3){
fprintf(ficlog,"Total");	fprintf(ficlog,"Total");
fprintf(ficresphtmfr,"<tr><th>Total</th> ");	fprintf(ficresphtmfr,"<tr><th>Total</th> ");
}else{	}else{
if(first==1){	if(first==1){
first=0;	first=0;
printf("See log file for details...\n");	printf("See log file for details...\n");
}	}
fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);	fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
fprintf(ficlog,"Age %d", iage);	fprintf(ficlog,"Age %d", iage);
}	}
for(jk=1; jk <=nlstate ; jk++){	for(jk=1; jk <=nlstate ; jk++){
for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)	for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
pp[jk] += freq[jk][m][iage];	pp[jk] += freq[jk][m][iage];
}	}
for(jk=1; jk <=nlstate ; jk++){	for(jk=1; jk <=nlstate ; jk++){
for(m=-1, pos=0; m <=0 ; m++)	for(m=-1, pos=0; m <=0 ; m++)
pos += freq[jk][m][iage];	pos += freq[jk][m][iage];
if(pp[jk]>=1.e-10){	if(pp[jk]>=1.e-10){
if(first==1){	if(first==1){
printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);	printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
}	}
fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);	fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
}else{	}else{
if(first==1)	if(first==1)
printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);	printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);	fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
}	}
}	}

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

for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){	for(jk=1,pos=0, pospropta=0.; jk <=nlstate ; jk++){
pos += pp[jk]; /* pos is the total number of transitions until this age */	pos += pp[jk]; /* pos is the total number of transitions until this age */
posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state	posprop[jk] += prop[jk][iage]; /* prop is the number of transitions from a live state
from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */	from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state	pospropta += prop[jk][iage]; /* prop is the number of transitions from a live state
from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */	from jk at age iage prop[s[m][iind]][(int)agev[m][iind]] += weight[iind] */
}	}
for(jk=1; jk <=nlstate ; jk++){	for(jk=1; jk <=nlstate ; jk++){
if(pos>=1.e-5){	if(pos>=1.e-5){
if(first==1)	if(first==1)
printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);	printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);	fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
}else{	}else{
if(first==1)	if(first==1)
printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);	printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);	fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
}	}
if( iage <= iagemax){	if( iage <= iagemax){
if(pos>=1.e-5){	if(pos>=1.e-5){
fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);	fprintf(ficresp," %d %.5f %.0f %.0f",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);	fprintf(ficresphtm,"<th>%d</th><td>%.5f</td><td>%.0f</td><td>%.0f</td>",iage,prop[jk][iage]/pospropta, prop[jk][iage],pospropta);
/probs[iage][jk][j1]= pp[jk]/pos;/	/probs[iage][jk][j1]= pp[jk]/pos;/
/printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);/	/printf("\niage=%d jk=%d j1=%d %.5f %.0f %.0f %f",iage,jk,j1,pp[jk]/pos, pp[jk],pos,probs[iage][jk][j1]);/
}	}
else{	else{
fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);	fprintf(ficresp," %d NaNq %.0f %.0f",iage,prop[jk][iage],pospropta);
fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);	fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[jk][iage],pospropta);
}	}
}	}
pospropt[jk] +=posprop[jk];	pospropt[jk] +=posprop[jk];
} /* end loop jk */	} /* end loop jk */
/* pospropt=0.; */	/* pospropt=0.; */
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(freq[jk][m][iage] !=0 ) { /* minimizing output */	if(freq[jk][m][iage] !=0 ) { /* minimizing output */
if(first==1){	if(first==1){
printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);	printf(" %d%d=%.0f",jk,m,freq[jk][m][iage]);
}	}
fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);	fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][iage]);
}	}
if(jk!=0 && m!=0)	if(jk!=0 && m!=0)
fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);	fprintf(ficresphtmfr,"<td>%.0f</td> ",freq[jk][m][iage]);
}	}
} /* end loop jk */	} /* end loop jk */
posproptt=0.;	posproptt=0.;
for(jk=1; jk <=nlstate; jk++){	for(jk=1; jk <=nlstate; jk++){
posproptt += pospropt[jk];	posproptt += pospropt[jk];
}	}
fprintf(ficresphtmfr,"</tr>\n ");	fprintf(ficresphtmfr,"</tr>\n ");
if(iage <= iagemax){	if(iage <= iagemax){
fprintf(ficresp,"\n");	fprintf(ficresp,"\n");
fprintf(ficresphtm,"</tr>\n");	fprintf(ficresphtm,"</tr>\n");
}	}
if(first==1)	if(first==1)
printf("Others in log...\n");	printf("Others in log...\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
} /* end loop age iage */	} /* end loop age iage */
fprintf(ficresphtm,"<tr><th>Tot</th>");	fprintf(ficresphtm,"<tr><th>Tot</th>");
for(jk=1; jk <=nlstate ; jk++){	for(jk=1; jk <=nlstate ; jk++){
if(posproptt < 1.e-5){	if(posproptt < 1.e-5){
fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);	fprintf(ficresphtm,"<td>Nanq</td><td>%.0f</td><td>%.0f</td>",pospropt[jk],posproptt);
}else{	}else{
fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);	fprintf(ficresphtm,"<td>%.5f</td><td>%.0f</td><td>%.0f</td>",pospropt[jk]/posproptt,pospropt[jk],posproptt);
}	}
}	}
fprintf(ficresphtm,"</tr>\n");	fprintf(ficresphtm,"</tr>\n");
Line 4356 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4516 Title=%s <br>Datafile=%s Firstpass=%d La
fprintf(ficresphtmfr,"</table>\n");	fprintf(ficresphtmfr,"</table>\n");
} /* end selected combination of covariate j1 */	} /* end selected combination of covariate j1 */
dateintmean=dateintsum/k2cpt;	dateintmean=dateintsum/k2cpt;

fclose(ficresp);	fclose(ficresp);
fclose(ficresphtm);	fclose(ficresphtm);
fclose(ficresphtmfr);	fclose(ficresphtmfr);
Line 4691 void concatwav(int wav[], int **dh, int	Line 4851 void concatwav(int wav[], int **dh, int

/********* Tricode **************************/	/********* Tricode **************************/
void tricode(int cptcov, int Tvar, int *nbcode, int imx, int Ndum)	void tricode(int cptcov, int Tvar, int *nbcode, int imx, int Ndum)
{	{
/*< Uses cptcovn+2cptcovprod as the number of covariates */	/*< Uses cptcovn+2cptcovprod as the number of covariates */
/* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1	/* Tvar[i]=atoi(stre); find 'n' in Vn and stores in Tvar. If model=V2+V1 Tvar[1]=2 and Tvar[2]=1
* Boring subroutine which should only output nbcode[Tvar[j]][k]	* Boring subroutine which should only output nbcode[Tvar[j]][k]
* Tvar[5] in V2+V1+V3age+V2V4 is 4 (V4) even it is a time varying or quantitative variable	* Tvar[5] in V2+V1+V3age+V2V4 is 4 (V4) even it is a time varying or quantitative variable
* nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);	* nbcode[Tvar[5]][1]= nbcode[4][1]=0, nbcode[4][2]=1 (usually);
*/	*/

int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;	int ij=1, k=0, j=0, i=0, maxncov=NCOVMAX;
int modmaxcovj=0; /* Modality max of covariates j */	int modmaxcovj=0; /* Modality max of covariates j */
int cptcode=0; /* Modality max of covariates j */	int cptcode=0; /* Modality max of covariates j */
int modmincovj=0; /* Modality min of covariates j */	int modmincovj=0; /* Modality min of covariates j */


/* cptcoveff=0; */	/* cptcoveff=0; */
/* cptcov=0; /	/* cptcov=0; /

for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */	for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */

/* Loop on covariates without age and products and no quantitative variable */	/* Loop on covariates without age and products and no quantitative variable */
/* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2age+ V3 + V3V4 keeps V1 + V3 = 2 only \/ /	/* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2age+ V3 + V3V4 keeps V1 + V3 = 2 only \/ /
for (k=1; k<=cptcovt; k++) { /* From model V1 + V2age + V3 + V3V4 keeps V1 + V3 = 2 only */	for (k=1; k<=cptcovt; k++) { /* From model V1 + V2age + V3 + V3V4 keeps V1 + V3 = 2 only */
for (j=-1; (j < maxncov); j++) Ndum[j]=0;	for (j=-1; (j < maxncov); j++) Ndum[j]=0;
if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */	if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
switch(Fixed[k]) {	switch(Fixed[k]) {
case 0: /* Testing on fixed dummy covariate, simple or product of fixed */	case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the modality of this covariate Vj*/	for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the modality of this covariate Vj*/
ij=(int)(covar[Tvar[k]][i]);	ij=(int)(covar[Tvar[k]][i]);
/* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i	/* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
* If product of VnVm, still boolean :	* If product of VnVm, still boolean :
* If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables	* If it was coded 1, 2, 3, 4 should be splitted into 3 boolean variables
* 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */	* 1 => 0 0 0, 2 => 0 0 1, 3 => 0 1 1, 4=1 0 0 */
/* Finds for covariate j, n=Tvar[j] of Vn . ij is the	/* Finds for covariate j, n=Tvar[j] of Vn . ij is the
modality of the nth covariate of individual i. */	modality of the nth covariate of individual i. */
if (ij > modmaxcovj)	if (ij > modmaxcovj)
modmaxcovj=ij;	modmaxcovj=ij;
else if (ij < modmincovj)	else if (ij < modmincovj)
modmincovj=ij;	modmincovj=ij;
if ((ij < -1) && (ij > NCOVMAX)){	if ((ij < -1) && (ij > NCOVMAX)){
printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );	printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
exit(1);	exit(1);
}else	}else
Ndum[ij]++; /counts and stores the occurence of this modality 0, 1, -1/	Ndum[ij]++; /counts and stores the occurence of this modality 0, 1, -1/
/* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */	/* If coded 1, 2, 3 , counts the number of 1 Ndum[1], number of 2, Ndum[2], etc */
/printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);/	/printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);/
/* getting the maximum value of the modality of the covariate	/* getting the maximum value of the modality of the covariate
(should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and	(should be 0 or 1 now) Tvar[j]. If V=sex and male is coded 0 and
female ies 1, then modmaxcovj=1.	female ies 1, then modmaxcovj=1.
*/	*/
} /* end for loop on individuals i */	} /* end for loop on individuals i */
printf(" Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);	printf(" Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
fprintf(ficlog," Minimal and maximal values of %d th covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);	fprintf(ficlog," Minimal and maximal values of %d th (fixed) covariate V%d: min=%d max=%d \n", k, Tvar[k], modmincovj, modmaxcovj);
cptcode=modmaxcovj;	cptcode=modmaxcovj;
/* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */	/* Ndum[0] = frequency of 0 for model-covariate j, Ndum[1] frequency of 1 etc. */
/for (i=0; i<=cptcode; i++) {/	/for (i=0; i<=cptcode; i++) {/
for (j=modmincovj; j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1// For each value j of the modality of model-cov k */	for (j=modmincovj; j<=modmaxcovj; j++) { /* j=-1 ? 0 and 1// For each value j of the modality of model-cov k */
printf("Frequencies of covariates %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);	printf("Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
fprintf(ficlog, "Frequencies of covariates %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);	fprintf(ficlog, "Frequencies of (fixed) covariate %d ie V%d with value %d: %d\n", k, Tvar[k], j, Ndum[j]);
if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */	if( Ndum[j] != 0 ){ /* Counts if nobody answered modality j ie empty modality, we skip it and reorder */
if( j != -1){	if( j != -1){
ncodemax[k]++; /* ncodemax[k]= Number of modalities of the k th	ncodemax[k]++; /* ncodemax[k]= Number of modalities of the k th
covariate for which somebody answered excluding	covariate for which somebody answered excluding
undefined. Usually 2: 0 and 1. */	undefined. Usually 2: 0 and 1. */
}	}
ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th	ncodemaxwundef[k]++; /* ncodemax[j]= Number of modalities of the k th
covariate for which somebody answered including	covariate for which somebody answered including
undefined. Usually 3: -1, 0 and 1. */	undefined. Usually 3: -1, 0 and 1. */
} /* In fact ncodemax[k]=2 (dichotom. variables only) but it could be more for	} /* In fact ncodemax[k]=2 (dichotom. variables only) but it could be more for
* historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */	* historical reasons: 3 if coded 1, 2, 3 and 4 and Ndum[2]=0 */
} /* Ndum[-1] number of undefined modalities */	} /* Ndum[-1] number of undefined modalities */

/* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */	/* j is a covariate, n=Tvar[j] of Vn; Fills nbcode */
/* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */	/* For covariate j, modalities could be 1, 2, 3, 4, 5, 6, 7. */
/* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */	/* If Ndum[1]=0, Ndum[2]=0, Ndum[3]= 635, Ndum[4]=0, Ndum[5]=0, Ndum[6]=27, Ndum[7]=125; */
/* modmincovj=3; modmaxcovj = 7; */	/* modmincovj=3; modmaxcovj = 7; */
/* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */	/* There are only 3 modalities non empty 3, 6, 7 (or 2 if 27 is too few) : ncodemax[j]=3; */
/* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */	/* which will be coded 0, 1, 2 which in binary on 2=3-1 digits are 0=00 1=01, 2=10; */
/* defining two dummy variables: variables V1_1 and V1_2.*/	/* defining two dummy variables: variables V1_1 and V1_2.*/
/* nbcode[Tvar[j]][ij]=k; */	/* nbcode[Tvar[j]][ij]=k; */
/* nbcode[Tvar[j]][1]=0; */	/* nbcode[Tvar[j]][1]=0; */
/* nbcode[Tvar[j]][2]=1; */	/* nbcode[Tvar[j]][2]=1; */
/* nbcode[Tvar[j]][3]=2; */	/* nbcode[Tvar[j]][3]=2; */
/* To be continued (not working yet). */	/* To be continued (not working yet). */
ij=0; /* ij is similar to i but can jump over null modalities */	ij=0; /* ij is similar to i but can jump over null modalities */
for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/	for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
if (Ndum[i] == 0) { /* If nobody responded to this modality k */	if (Ndum[i] == 0) { /* If nobody responded to this modality k */
break;	break;
}	}
ij++;	ij++;
nbcode[Tvar[k]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1*/	nbcode[Tvar[k]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1*/
cptcode = ij; /* New max modality for covar j */	cptcode = ij; /* New max modality for covar j */
} /* end of loop on modality i=-1 to 1 or more */	} /* end of loop on modality i=-1 to 1 or more */
break;	break;
case 1: /* Testing on varying covariate, could be simple and	case 1: /* Testing on varying covariate, could be simple and
* should look at waves or product of fixed *	* should look at waves or product of fixed *
* varying. No time to test -1, assuming 0 and 1 only */	* varying. No time to test -1, assuming 0 and 1 only */
ij=0;	ij=0;
for(i=0; i<=1;i++){	for(i=0; i<=1;i++){
nbcode[Tvar[k]][++ij]=i;	nbcode[Tvar[k]][++ij]=i;
}	}
break;	break;
default:	default:
break;	break;
} /* end switch */	} /* end switch */
} /* end dummy test */	} /* end dummy test */

/* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 \//\ Could be 1 to 4 \//\ cptcode=modmaxcovj \/ /	/* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 \//\ Could be 1 to 4 \//\ cptcode=modmaxcovj \/ /
/* /\recode from 0 \/ */	/* /\recode from 0 \/ */
/* k is a modality. If we have model=V1+V1sex /	/* k is a modality. If we have model=V1+V1sex /
/* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */	/* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
/* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode \/ /	/* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode \/ /
/* } */	/* } */
/* /\* cptcode = ij; \/ /\ New max modality for covar j \/ /	/* /\* cptcode = ij; \/ /\ New max modality for covar j \/ /
/* if (ij > ncodemax[j]) { */	/* if (ij > ncodemax[j]) { */
/* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */	/* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
/* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */	/* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */
/* break; */	/* break; */
/* } */	/* } */
/* } /\* end of loop on modality k \/ /	/* } /\* end of loop on modality k \/ /
} /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/	} /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/

for (k=-1; k< maxncov; k++) Ndum[k]=0;	for (k=-1; k< maxncov; k++) Ndum[k]=0;
/* Look at fixed dummy (single or product) covariates to check empty modalities */	/* Look at fixed dummy (single or product) covariates to check empty modalities */
for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually ageage /	for (i=1; i<=ncovmodel-2-nagesqr; i++) { /* -2, cste and age and eventually ageage /
/* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1V2./	/* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1V2./
ij=Tvar[i]; /* Tvar 5,4,3,6,5,7,1,4 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V4age /	ij=Tvar[i]; /* Tvar 5,4,3,6,5,7,1,4 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V4age /
Ndum[ij]++; /* Count the # of 1, 2 etc: {1,1,1,2,2,1,1} because V1 once, V2 once, two V4 and V5 in above */	Ndum[ij]++; /* Count the # of 1, 2 etc: {1,1,1,2,2,1,1} because V1 once, V2 once, two V4 and V5 in above */
/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, {2, 1, 1, 1, 2, 1, 1, 0, 0} */	/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, {2, 1, 1, 1, 2, 1, 1, 0, 0} */
} /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */	} /* V4+V3+V5, Ndum[1]@5={0, 0, 1, 1, 1} */

ij=0;	ij=0;
/* for (i=0; i<= maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(ageV3), 5(V3V2) 6(V1V4) \/ */	/* for (i=0; i<= maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(ageV3), 5(V3V2) 6(V1V4) \/ */
for (k=1; k<= cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(ageV3), 5(V3V2) 6(V1V4) /	for (k=1; k<= cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(ageV3), 5(V3V2) 6(V1V4) /
/printf("Ndum[%d]=%d\n",i, Ndum[i]);/	/printf("Ndum[%d]=%d\n",i, Ndum[i]);/
/* if((Ndum[i]!=0) && (i<=ncovcol)){ /\* Tvar[i] <= ncovmodel ? \/ /	/* if((Ndum[i]!=0) && (i<=ncovcol)){ /\* Tvar[i] <= ncovmodel ? \/ /
if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){ /* Only Dummy and non empty in the model */	if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){ /* Only Dummy and non empty in the model */
/* If product not in single variable we don't print results */	/* If product not in single variable we don't print results */
/printf("diff Ndum[%d]=%d\n",i, Ndum[i]);/	/printf("diff Ndum[%d]=%d\n",i, Ndum[i]);/
++ij;/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, */	++ij;/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, */
Tvaraff[ij]=Tvar[k]; /* For printing combination // V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, Tvar {5, 4, 3, 6, 5, 2, 7, 1, 1} Tvaraff={4, 3, 1} V4, V3, V1*/	Tvaraff[ij]=Tvar[k]; /* For printing combination // V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, Tvar {5, 4, 3, 6, 5, 2, 7, 1, 1} Tvaraff={4, 3, 1} V4, V3, V1*/
Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */	Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
TmodelInvind[ij]=Tvar[k]- ncovcol-nqv; /* Inverse TmodelInvind[2=V4]=2 second dummy varying cov (V4)4-1-1 {0, 2, 1, } TmodelInvind[3]=1 */	TmodelInvind[ij]=Tvar[k]- ncovcol-nqv; /* Inverse TmodelInvind[2=V4]=2 second dummy varying cov (V4)4-1-1 {0, 2, 1, } TmodelInvind[3]=1 */
if(Fixed[k]!=0)	if(Fixed[k]!=0)
anyvaryingduminmodel=1;	anyvaryingduminmodel=1;
/* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */	/* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv)){ */
/* Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet \/ /	/* Tvaraff[++ij]=-10; /\* Dont'n know how to treat quantitative variables yet \/ /
/* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */	/* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv)){ */
/* Tvaraff[++ij]=i; /\For printing (unclear) \/ */	/* Tvaraff[++ij]=i; /\For printing (unclear) \/ */
/* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */	/* }else if((Ndum[i]!=0) && (i<=ncovcol+nqv+ntv+nqtv)){ */
/* Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet \/ /	/* Tvaraff[++ij]=-20; /\* Dont'n know how to treat quantitative variables yet \/ /
}	}
} /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */	} /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
/* ij--; */	/* ij--; */
/* cptcoveff=ij; /\Number of total covariates\/ */	/* cptcoveff=ij; /\Number of total covariates\/ */
cptcov=ij; /Number of total real effective covariates: effective	cptcov=ij; /Number of total real effective covariates: effective
* because they can be excluded from the model and real	* because they can be excluded from the model and real
* if in the model but excluded because missing values, but how to get k from ij?*/	* if in the model but excluded because missing values, but how to get k from ij?*/
for(j=ij+1; j<= cptcovt; j++){	for(j=ij+1; j<= cptcovt; j++){
Tvaraff[j]=0;	Tvaraff[j]=0;
Tmodelind[j]=0;	Tmodelind[j]=0;
}	}
for(j=ntveff+1; j<= cptcovt; j++){	for(j=ntveff+1; j<= cptcovt; j++){
TmodelInvind[j]=0;	TmodelInvind[j]=0;
}	}
/* To be sorted */	/* To be sorted */
;	;
}	}


/********* 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 4872 void evsij(double ***eij, double x[], in	Line 5032 void evsij(double ***eij, double x[], in
double ***p3mat;	double ***p3mat;
double eip;	double eip;

pstamp(ficreseij);	/* pstamp(ficreseij); */
fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");	fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
fprintf(ficreseij,"# Age");	fprintf(ficreseij,"# Age");
for(i=1; i<=nlstate;i++){	for(i=1; i<=nlstate;i++){
Line 4935 void evsij(double ***eij, double x[], in	Line 5095 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 4970 void evsij(double ***eij, double x[], in	Line 5130 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 5083 void cvevsij(double ***eij, double x[],	Line 5243 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 5125 void cvevsij(double ***eij, double x[],	Line 5285 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 5180 void cvevsij(double ***eij, double x[],	Line 5340 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 5237 void cvevsij(double ***eij, double x[],	Line 5397 void cvevsij(double ***eij, double x[],
fprintf(ficlog,"Computing total mortality p.j=w1p1j+w2p2j+..: result on file '%s' \n",fileresprobmorprev);	fprintf(ficlog,"Computing total mortality p.j=w1p1j+w2p2j+..: result on file '%s' \n",fileresprobmorprev);
pstamp(ficresprobmorprev);	pstamp(ficresprobmorprev);
fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1p1j+w2p2j+... stand dev in()\n",estepm);	fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1p1j+w2p2j+... stand dev in()\n",estepm);
	fprintf(ficresprobmorprev,"# Selected quantitative variables and dummies");
	for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
	fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
	}
	for(j=1;j<=cptcoveff;j++)
	fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,j)]);
	fprintf(ficresprobmorprev,"\n");

fprintf(ficresprobmorprev,"# Age cov=%-d",ij);	fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
for(j=nlstate+1; j<=(nlstate+ndeath);j++){	for(j=nlstate+1; j<=(nlstate+ndeath);j++){
fprintf(ficresprobmorprev," p.%-d SE",j);	fprintf(ficresprobmorprev," p.%-d SE",j);
Line 5306 void cvevsij(double ***eij, double x[],	Line 5474 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, nres);

if (popbased==1) {	if (popbased==1) {
if(mobilav ==0){	if(mobilav ==0){
Line 5318 void cvevsij(double ***eij, double x[],	Line 5486 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 5338 void cvevsij(double ***eij, double x[],	Line 5506 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, nres);

if (popbased==1) {	if (popbased==1) {
if(mobilav ==0){	if(mobilav ==0){
Line 5350 void cvevsij(double ***eij, double x[],	Line 5518 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 5415 void cvevsij(double ***eij, double x[],	Line 5583 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, nres);

if (popbased==1) {	if (popbased==1) {
if(mobilav ==0){	if(mobilav ==0){
Line 5431 void cvevsij(double ***eij, double x[],	Line 5599 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 5494 void cvevsij(double ***eij, double x[],	Line 5662 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 5510 void cvevsij(double ***eij, double x[],	Line 5678 void cvevsij(double ***eij, double x[],

pstamp(ficresvpl);	pstamp(ficresvpl);
fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");	fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
fprintf(ficresvpl,"# Age");	fprintf(ficresvpl,"# Age ");
	if(nresult >=1)
	fprintf(ficresvpl," Result# ");
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
fprintf(ficresvpl," %1d-%1d",i,i);	fprintf(ficresvpl," %1d-%1d",i,i);
fprintf(ficresvpl,"\n");	fprintf(ficresvpl,"\n");
Line 5537 void cvevsij(double ***eij, double x[],	Line 5707 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 5547 void cvevsij(double ***eij, double x[],	Line 5717 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 5596 void cvevsij(double ***eij, double x[],	Line 5766 void cvevsij(double ***eij, double x[],
varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */	varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */

fprintf(ficresvpl,"%.0f ",age );	fprintf(ficresvpl,"%.0f ",age );
	if(nresult >=1)
	fprintf(ficresvpl,"%d ",nres );
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));	fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
fprintf(ficresvpl,"\n");	fprintf(ficresvpl,"\n");
Line 5957 void printinghtml(char fileresu[], char	Line 6129 void printinghtml(char fileresu[], char
int popforecast, int prevfcast, int backcast, int estepm , \	int popforecast, int prevfcast, int backcast, int estepm , \
double jprev1, double mprev1,double anprev1, double dateprev1, \	double jprev1, double mprev1,double anprev1, double dateprev1, \
double jprev2, double mprev2,double anprev2, double dateprev2){	double jprev2, double mprev2,double anprev2, double dateprev2){
int jj1, k1, i1, cpt;	int jj1, k1, i1, cpt, k4, nres;

fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \	fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
<li><a href='#secondorder'>Result files (second order (variance)</a>\n \	<li><a href='#secondorder'>Result files (second order (variance)</a>\n \
</ul>");	</ul>");
	fprintf(fichtm,"<ul><li> model=1+age+%s\n \
	</ul>", model);
fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");	fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",	fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",
jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));	jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
Line 5996 void printinghtml(char fileresu[], char	Line 6170 void printinghtml(char fileresu[], char
if (cptcovn < 1) {m=1;ncodemax[1]=1;}	if (cptcovn < 1) {m=1;ncodemax[1]=1;}

jj1=0;	jj1=0;
for(k1=1; k1<=m;k1++){
	for(nres=1; nres <= nresult; nres++) /* For each resultline */
	for(k1=1; k1<=m;k1++){ /* For each combination of covariate */
	if(TKresult[nres]!= k1)
	continue;

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

/* if(nqfveff+nqtveff 0) / / Test to be done */	/* if(nqfveff+nqtveff 0) / / Test to be done */
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");	fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
Line 6015 void printinghtml(char fileresu[], char	Line 6200 void printinghtml(char fileresu[], char
}	}
}	}
/* aij, bij */	/* aij, bij */
fprintf(fichtm,"<br>- Logit model (yours is: 1+age+%s), for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1.svg\">%s_%d-1.svg</a><br> \	fprintf(fichtm,"<br>- Logit model (yours is: 1+age+%s), for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1-%d.svg\">%s_%d-1-%d.svg</a><br> \
<img src=\"%s_%d-1.svg\">",model,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);	<img src=\"%s_%d-1-%d.svg\">",model,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);
/* Pij */	/* Pij */
fprintf(fichtm,"<br>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2.svg\">%s_%d-2.svg</a><br> \	fprintf(fichtm,"<br>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2-%d.svg\">%s_%d-2-%d.svg</a><br> \
<img src=\"%s_%d-2.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);	<img src=\"%s_%d-2-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);
/* Quasi-incidences */	/* Quasi-incidences */
fprintf(fichtm,"<br>\n- I<sub>ij</sub> or Conditional probabilities to be observed in state j being in state i %d (stepm) months\	fprintf(fichtm,"<br>\n- I<sub>ij</sub> or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \	before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too, \
incidence (rates) are the limit when h tends to zero of the ratio of the probability <sub>h</sub>P<sub>ij</sub> \	incidence (rates) are the limit when h tends to zero of the ratio of the probability <sub>h</sub>P<sub>ij</sub> \
divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3.svg\">%s_%d-3.svg</a><br> \	divided by h: <sub>h</sub>P<sub>ij</sub>/h : <a href=\"%s_%d-3-%d.svg\">%s_%d-3-%d.svg</a><br> \
<img src=\"%s_%d-3.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1,subdirf2(optionfilefiname,"PE_"),jj1);	<img src=\"%s_%d-3-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);
/* Survival functions (period) in state j */	/* Survival functions (period) in state j */
for(cpt=1; cpt<=nlstate;cpt++){	for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"<br>\n- Survival functions in state %d. Or probability to survive in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \	fprintf(fichtm,"<br>\n- Survival functions in state %d. Or probability to survive in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
<img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1,subdirf2(optionfilefiname,"LIJ_"),cpt,jj1);	<img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
}	}
/* State specific survival functions (period) */	/* State specific survival functions (period) */
for(cpt=1; cpt<=nlstate;cpt++){	for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\	fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\
Or probability to survive in various states (1 to %d) being in state %d at different ages. \	Or probability to survive in various states (1 to %d) being in state %d at different ages. \
<a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> <img src=\"%s_%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1,subdirf2(optionfilefiname,"LIJT_"),cpt,jj1);	<a href=\"%s_%d-%d-%d.svg\">%s_%d%d-%d.svg</a><br> <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
}	}
/* Period (stable) prevalence in each health state */	/* Period (stable) prevalence in each health state */
for(cpt=1; cpt<=nlstate;cpt++){	for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a><br> \	fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
<img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1,subdirf2(optionfilefiname,"P_"),cpt,jj1);	<img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
}	}
if(backcast==1){	if(backcast==1){
/* Period (stable) back prevalence in each health state */	/* Period (stable) back prevalence in each health state */
for(cpt=1; cpt<=nlstate;cpt++){	for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"<br>\n- Convergence to period (stable) back prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a><br> \	fprintf(fichtm,"<br>\n- Convergence to period (stable) back prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
<img src=\"%s_%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1,subdirf2(optionfilefiname,"PB_"),cpt,jj1);	<img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
}	}
}	}
if(prevfcast==1){	if(prevfcast==1){
/* Projection of prevalence up to period (stable) prevalence in each health state */	/* Projection of prevalence up to period (stable) prevalence in each health state */
for(cpt=1; cpt<=nlstate;cpt++){	for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s%d_%d.svg\">%s%d_%d.svg</a><br> \	fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
<img src=\"%s_%d-%d.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1,subdirf2(optionfilefiname,"PROJ_"),cpt,jj1);	<img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
}	}
}	}

for(cpt=1; cpt<=nlstate;cpt++) {	for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d%d.svg\">%s_%d%d.svg</a> <br> \	fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a> <br> \
<img src=\"%s_%d%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1,subdirf2(optionfilefiname,"EXP_"),cpt,jj1);	<img src=\"%s_%d-%d-%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
}	}
/* } /\* end i1 \/ /	/* } /\* end i1 \/ /
}/* End k1 */	}/* End k1 */
Line 6117 See page 'Matrix of variance-covariance	Line 6302 See page 'Matrix of variance-covariance
if (cptcovn < 1) {m=1;ncodemax[1]=1;}	if (cptcovn < 1) {m=1;ncodemax[1]=1;}

jj1=0;	jj1=0;

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

fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");	fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");

if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
Line 6133 See page 'Matrix of variance-covariance	Line 6327 See page 'Matrix of variance-covariance
}	}
for(cpt=1; cpt<=nlstate;cpt++) {	for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \	fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \
prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d.svg\"> %s_%d-%d.svg</a>\n <br>\	prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d-%d.svg\"> %s_%d-%d-%d.svg</a>\n <br>\
<img src=\"%s_%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1,subdirf2(optionfilefiname,"V_"),cpt,jj1);	<img src=\"%s_%d-%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
}	}
fprintf(fichtm,"\n<br>- Total life expectancy by age and \	fprintf(fichtm,"\n<br>- Total life expectancy by age and \
health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \	health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
true period expectancies (those weighted with period prevalences are also\	true period expectancies (those weighted with period prevalences are also\
drawn in addition to the population based expectancies computed using\	drawn in addition to the population based expectancies computed using\
observed and cahotic prevalences: <a href=\"%s_%d.svg\">%s_%d.svg</a>\n<br>\	observed and cahotic prevalences: <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>\n<br>\
<img src=\"%s_%d.svg\">",subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1,subdirf2(optionfilefiname,"E_"),jj1);	<img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
/* } /\* end i1 \/ /	/* } /\* end i1 \/ /
}/* End k1 */	}/* End k1 */
	}/* End nres */
fprintf(fichtm,"</ul>");	fprintf(fichtm,"</ul>");
fflush(fichtm);	fflush(fichtm);
}	}
Line 6153 void printinggnuplot(char fileresu[], ch	Line 6348 void printinggnuplot(char fileresu[], ch

char dirfileres[132],optfileres[132];	char dirfileres[132],optfileres[132];
char gplotcondition[132];	char gplotcondition[132];
int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;	int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,k4=0,ij=0, ijp=0, l=0;
int lv=0, vlv=0, kl=0;	int lv=0, vlv=0, kl=0;
int ng=0;	int ng=0;
int vpopbased;	int vpopbased;
int ioffset; /* variable offset for columns */	int ioffset; /* variable offset for columns */
	int nres=0; /* Index of resultline */

/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */	/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
/* printf("Problem with file %s",optionfilegnuplot); */	/* printf("Problem with file %s",optionfilegnuplot); */
Line 6201 void printinggnuplot(char fileresu[], ch	Line 6397 void printinggnuplot(char fileresu[], ch
strcpy(dirfileres,optionfilefiname);	strcpy(dirfileres,optionfilefiname);
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 */
for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */	if(TKresult[nres]!= k1)
lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */	continue;
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* We are interested in selected combination by the resultline */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt);
vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */	for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
/* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */	lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	/* 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 */
fprintf(ficgp,"\n#\n");	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
if(invalidvarcomb[k1]){	vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	/* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
continue;	/* printf(" V%d=%d ",Tvaraff[k],vlv); */
}	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
	}
fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1);	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficgp,"\n#set out \"V_%s_%d-%d.svg\" \n",optionfilefiname,cpt,k1);	/* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
fprintf(ficgp,"set xlabel \"Age\" \n\	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
set ylabel \"Probability\" \n \	}
set ter svg size 640, 480\n \	/* printf("\n#\n"); */
plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"%%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1);	fprintf(ficgp,"\n#\n");
	if(invalidvarcomb[k1]){
for (i=1; i<= nlstate ; i ++) {	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
if (i==cpt) fprintf(ficgp," %%lf (%%lf)");	continue;
else fprintf(ficgp," %%lf (%%lf)");	}
}
fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
for (i=1; i<= nlstate ; i ++) {	fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
if (i==cpt) fprintf(ficgp," %%lf (%%lf)");	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres);
else fprintf(ficgp," %%lf (%%lf)");
}	for (i=1; i<= nlstate ; i ++) {
fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"%%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1);	if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
for (i=1; i<= nlstate ; i ++) {	else fprintf(ficgp," %%lf (%%lf)");
if (i==cpt) fprintf(ficgp," %%lf (%%lf)");	}
else fprintf(ficgp," %%lf (%%lf)");	fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres);
}	for (i=1; i<= nlstate ; i ++) {
fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));	if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */	else fprintf(ficgp," %%lf (%%lf)");
/* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */	}
fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1 */	fprintf(ficgp,"\" t\"95%% CI\" w l lt 1,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres);
if(cptcoveff ==0){	for (i=1; i<= nlstate ; i ++) {
fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line ", 2+(cpt-1), cpt );	if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
}else{	else fprintf(ficgp," %%lf (%%lf)");
kl=0;	}
for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */	fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence\" w l lt 2",subdirf2(fileresu,"P_"),k1-1,k1-1,2+4*(cpt-1));
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */	if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	if(cptcoveff ==0){
vlv= nbcode[Tvaraff[k]][lv];	fprintf(ficgp,"$%d)) t 'Backward prevalence in state %d' with line lt 3", 2+(cpt-1), cpt );
kl++;	}else{
/* kl=6+(cpt-1)(nlstate+1)+1+(i-1); /\ 6+(1-1)(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 \/ */	kl=0;
/6+(cpt-1)(nlstate+1)+1+(i-1)+(nlstate+1)nlstate; 6+(1-1)(2+1)+1+(1-1) +(2+1)2=13 /	for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
/6+1+(i-1)+(nlstate+1)nlstate; 6+1+(1-1) +(2+1)2=13 /	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
/* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
if(k==cptcoveff){	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
4+(cpt-1), cpt ); /* 4 or 6 ?*/	vlv= nbcode[Tvaraff[k]][lv];
}else{
fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
kl++;	kl++;
}	/* kl=6+(cpt-1)(nlstate+1)+1+(i-1); /\ 6+(1-1)(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 \/ */
} /* end covariate */	/6+(cpt-1)(nlstate+1)+1+(i-1)+(nlstate+1)nlstate; 6+(1-1)(2+1)+1+(1-1) +(2+1)2=13 /
} /* end if no covariate */	/6+1+(i-1)+(nlstate+1)nlstate; 6+1+(1-1) +(2+1)2=13 /
} /* end if backcast */	/* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
fprintf(ficgp,"\nset out \n");	if(k==cptcoveff){
	fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
	2+cptcoveff2+(cpt-1), cpt ); / 4 or 6 ?*/
	}else{
	fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);
	kl++;
	}
	} /* end covariate */
	} /* end if no covariate */
	} /* end if backcast */
	fprintf(ficgp,"\nset out \n");
	} /* nres */
} /* k1 */	} /* k1 */
} /* cpt */	} /* cpt */
/2 eme/
for (k1=1; k1<= m ; k1 ++) {

fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	/2 eme/
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	for (k1=1; k1<= m ; k1 ++){
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	if(TKresult[nres]!= k1)
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	continue;
vlv= nbcode[Tvaraff[k]][lv];	fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
}
fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
continue;
}

fprintf(ficgp,"\nset out \"%s_%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1);
for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
if(vpopbased==0)
fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
else
fprintf(ficgp,"\nreplot ");
for (i=1; i<= nlstate+1 ; i ++) {
k=2*i;
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);
for (j=1; j<= nlstate+1 ; j ++) {
if (j==i) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%lf (%%lf)");
}
if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
for (j=1; j<= nlstate+1 ; j ++) {
if (j==i) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%lf (%%lf)");
}
fprintf(ficgp,"\" t\"\" w l lt 0,");
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
for (j=1; j<= nlstate+1 ; j ++) {
if (j==i) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%lf (%%lf)");
}
if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
} /* state */
} /* vpopbased */
fprintf(ficgp,"\nset out;set out \"%s_%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1); /* Buggy gnuplot */
} /* k1 */


/3eme/
for (k1=1; k1<= m ; k1 ++) {

for (cpt=1; cpt<= nlstate ; cpt ++) {
fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: cov=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
/* 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 6338 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 6494 plot [%.f:%.f] \"%s\" every :::%d::%d u
vlv= nbcode[Tvaraff[k]][lv];	vlv= nbcode[Tvaraff[k]][lv];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
}	}
	/* for(k=1; k <= ncovds; k++){ */
	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
	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);
continue;	continue;
}	}

/* k=2+nlstate(2cpt-2); */	fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);
k=2+(nlstate+1)*(cpt-1);	for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
fprintf(ficgp,"\nset out \"%s_%d%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1);	if(vpopbased==0)
fprintf(ficgp,"set ter svg size 640, 480\n\	fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
	else
	fprintf(ficgp,"\nreplot ");
	for (i=1; i<= nlstate+1 ; i ++) {
	k=2*i;
	fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);
	for (j=1; j<= nlstate+1 ; j ++) {
	if (j==i) fprintf(ficgp," %%lf (%%lf)");
	else fprintf(ficgp," %%lf (%%lf)");
	}
	if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
	else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
	fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
	for (j=1; j<= nlstate+1 ; j ++) {
	if (j==i) fprintf(ficgp," %%lf (%%lf)");
	else fprintf(ficgp," %%lf (%%lf)");
	}
	fprintf(ficgp,"\" t\"\" w l lt 0,");
	fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);
	for (j=1; j<= nlstate+1 ; j ++) {
	if (j==i) fprintf(ficgp," %%lf (%%lf)");
	else fprintf(ficgp," %%lf (%%lf)");
	}
	if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l lt 0");
	else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
	} /* state */
	} /* vpopbased */
	fprintf(ficgp,"\nset out;set out \"%s_%d-%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1,nres); /* Buggy gnuplot */
	} /* end nres */
	} /* k1 end 2 eme*/


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

	for (cpt=1; cpt<= nlstate ; 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 */
	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(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
	vlv= nbcode[Tvaraff[k]][lv];
	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
	}
	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");
	if(invalidvarcomb[k1]){
	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
	continue;
	}

	/* k=2+nlstate(2cpt-2); */
	k=2+(nlstate+1)*(cpt-1);
	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
	fprintf(ficgp,"set ter svg size 640, 480\n\
plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);	plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);
/fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);	/fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");	for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
fprintf(ficgp,"\" t \"e%d1\" w l",cpt);	fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);	fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");	for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
fprintf(ficgp,"\" t \"e%d1\" w l",cpt);	fprintf(ficgp,"\" t \"e%d1\" w l",cpt);

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

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

/* 4eme */	/* 4eme */
/* Survival functions (period) from state i in state j by initial state i */	/* Survival functions (period) from state i in state j by initial state i */
for (k1=1; k1<= m ; k1 ++) { /* For each multivariate if any */	for (k1=1; k1<=m; k1++){ /* For each covariate and each value */
	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */	if(TKresult[nres]!= k1)
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 */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
}
fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
continue;	continue;
}	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
	fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1);	for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
set ter svg size 640, 480\n \	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
unset log y\n \	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
plot [%.f:%.f] ", ageminpar, agemaxpar);	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
k=3;	vlv= nbcode[Tvaraff[k]][lv];
for (i=1; i<= nlstate ; i ++){	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
if(i==1){
fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
}else{
fprintf(ficgp,", '' ");
}	}
l=(nlstate+ndeath)*(i-1)+1;	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
for (j=2; j<= nlstate+ndeath ; j ++)	}
fprintf(ficgp,"+$%d",k+l+j-1);	fprintf(ficgp,"\n#\n");
fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);	if(invalidvarcomb[k1]){
} /* nlstate */	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
fprintf(ficgp,"\nset out\n");	continue;
} /* end cpt state*/	}
} /* end covariate */
	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
	set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
	k=3;
	for (i=1; i<= nlstate ; i ++){
	if(i==1){
	fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
	}else{
	fprintf(ficgp,", '' ");
	}
	l=(nlstate+ndeath)*(i-1)+1;
	fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l);
	for (j=2; j<= nlstate+ndeath ; j ++)
	fprintf(ficgp,"+$%d",k+l+j-1);
	fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
	} /* nlstate */
	fprintf(ficgp,"\nset out\n");
	} /* end cpt state*/
	} /* end nres */
	} /* end covariate k1 */

/* 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 (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
	if(TKresult[nres]!= k1)
fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
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(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
}
fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
continue;	continue;
}	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);
	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 */
	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
	vlv= nbcode[Tvaraff[k]][lv];
	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
	}
	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");
	if(invalidvarcomb[k1]){
	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
	continue;
	}

fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
set ter svg size 640, 480\n \	set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
unset log y\n \	k=3;
plot [%.f:%.f] ", ageminpar, agemaxpar);	for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
k=3;	if(j==1)
for (j=1; j<= nlstate ; j ++){ /* Lived in state j */	fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));
if(j==1)	else
fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJ_"));	fprintf(ficgp,", '' ");
else	l=(nlstate+ndeath)*(cpt-1) +j;
fprintf(ficgp,", '' ");	fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);
l=(nlstate+ndeath)*(cpt-1) +j;	/* for (i=2; i<= nlstate+ndeath ; i ++) */
fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):($%d",k1,k+l);	/* fprintf(ficgp,"+$%d",k+l+i-1); */
/* for (i=2; i<= nlstate+ndeath ; i ++) */	fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);
/* fprintf(ficgp,"+$%d",k+l+i-1); */	} /* nlstate */
fprintf(ficgp,") t \"l(%d,%d)\" w l",cpt,j);	fprintf(ficgp,", '' ");
} /* nlstate */	fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);
fprintf(ficgp,", '' ");	for (j=1; j<= nlstate ; j ++){ /* Lived in state j */
fprintf(ficgp," u (($1==%d && (floor($2)%%5 == 0)) ? ($3):1/0):(",k1);	l=(nlstate+ndeath)*(cpt-1) +j;
for (j=1; j<= nlstate ; j ++){ /* Lived in state j */	if(j < nlstate)
l=(nlstate+ndeath)*(cpt-1) +j;	fprintf(ficgp,"$%d +",k+l);
if(j < nlstate)	else
fprintf(ficgp,"$%d +",k+l);	fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
else	}
fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);	fprintf(ficgp,"\nset out\n");
}	} /* end cpt state*/
fprintf(ficgp,"\nset out\n");	} /* end covariate */
} /* end cpt state*/	} /* end nres */
} /* end covariate */

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

fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);	fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
Line 6472 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6705 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);
continue;	continue;
}	}

fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
set ter svg size 640, 480\n \	set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
unset log y\n \
plot [%.f:%.f] ", ageminpar, agemaxpar);
k=3; /* Offset */	k=3; /* Offset */
for (i=1; i<= nlstate ; i ++){	for (i=1; i<= nlstate ; i ++){
if(i==1)	if(i==1)
Line 6503 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6737 plot [%.f:%.f] ", ageminpar, agemaxpar)
/* 7eme */	/* 7eme */
if(backcast == 1){	if(backcast == 1){
/* CV back preval stable (period) for each covariate */	/* CV back preval stable (period) for each covariate */
for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2*k), if any covariate is present /	for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
	if(TKresult[nres]!= k1)
	continue;
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);	fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
Line 6514 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6751 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);
continue;	continue;
}	}

fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
set ter svg size 640, 480\n \	set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
unset log y\n \
plot [%.f:%.f] ", ageminpar, agemaxpar);
k=3; /* Offset */	k=3; /* Offset */
for (i=1; i<= nlstate ; i ++){	for (i=1; i<= nlstate ; i ++){
if(i==1)	if(i==1)
Line 6550 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6788 plot [%.f:%.f] ", ageminpar, agemaxpar)
if(prevfcast==1){	if(prevfcast==1){
/* Projection from cross-sectional to stable (period) for each covariate */	/* Projection from cross-sectional to stable (period) for each covariate */

for (k1=1; k1<= m ; k1 ++) { /* For each covariate combination (1 to m=2*k), if any covariate is present /	for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
	if(TKresult[nres]!= k1)
	continue;
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);	fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */	for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
Line 6561 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6802 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 6568 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6812 plot [%.f:%.f] ", ageminpar, agemaxpar)
}	}

fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");	fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
set ter svg size 640, 480\n \	set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
unset log y\n \
plot [%.f:%.f] ", ageminpar, agemaxpar);
for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */	for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
/# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3/	/# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3/
/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 /	/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 /
Line 6639 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6881 plot [%.f:%.f] ", ageminpar, agemaxpar)
} /* End if prevfcast */	} /* End if prevfcast */


/* proba elementaires */	/* 9eme writing MLE parameters */
fprintf(ficgp,"\n##############\n#MLE estimated parameters\n#############\n");	fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");
for(i=1,jk=1; i <=nlstate; i++){	for(i=1,jk=1; i <=nlstate; i++){
fprintf(ficgp,"# initial state %d\n",i);	fprintf(ficgp,"# initial state %d\n",i);
for(k=1; k <=(nlstate+ndeath); k++){	for(k=1; k <=(nlstate+ndeath); k++){
Line 6657 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6899 plot [%.f:%.f] ", ageminpar, agemaxpar)
fprintf(ficgp,"##############\n#\n");	fprintf(ficgp,"##############\n#\n");

/goto avoid;/	/goto avoid;/
fprintf(ficgp,"\n##############\n#Graphics of probabilities or incidences\n#############\n");	/* 10eme Graphics of probabilities or incidences using written MLE parameters */
	fprintf(ficgp,"\n##############\n#10eme Graphics of probabilities or incidences\n#############\n");
fprintf(ficgp,"# logi(p12/p11)=a12+b12age+c12ageage+d12V1+e12V1*age\n");	fprintf(ficgp,"# logi(p12/p11)=a12+b12age+c12ageage+d12V1+e12V1*age\n");
fprintf(ficgp,"# logi(p12/p11)=p1 +p2age +p3ageage+ p4V1+ p5V1age\n");	fprintf(ficgp,"# logi(p12/p11)=p1 +p2age +p3ageage+ p4V1+ p5V1age\n");
fprintf(ficgp,"# logi(p13/p11)=a13+b13age+c13ageage+d13V1+e13V1*age\n");	fprintf(ficgp,"# logi(p13/p11)=a13+b13age+c13ageage+d13V1+e13V1*age\n");
Line 6672 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6915 plot [%.f:%.f] ", ageminpar, agemaxpar)
fprintf(ficgp,"# +exp(a14+b14age+c14ageage+d14V1+e14V1*age)+...)\n");	fprintf(ficgp,"# +exp(a14+b14age+c14ageage+d14V1+e14V1*age)+...)\n");
fprintf(ficgp,"#\n");	fprintf(ficgp,"#\n");
for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/	for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
fprintf(ficgp,"# ng=%d\n",ng);	fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);	fprintf(ficgp,"#model=%s \n",model);
for(jk=1; jk <=m; jk++) {	fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
fprintf(ficgp,"# jk=%d\n",jk);	fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng);	for(jk=1; jk <=m; jk++) /* For each combination of covariate */
	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
	if(TKresult[nres]!= jk)
	continue;
	fprintf(ficgp,"# Combination of dummy jk=%d and ",jk);
	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	}
	fprintf(ficgp,"\n#\n");
	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng,nres);
fprintf(ficgp,"\nset ter svg size 640, 480 ");	fprintf(ficgp,"\nset ter svg size 640, 480 ");
if (ng==1){	if (ng==1){
fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12x) could be nice /	fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12x) could be nice /
Line 6716 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 6968 plot [%.f:%.f] ", ageminpar, agemaxpar)
break;	break;
}	}
ij=1;/* To be checked else nbcode[0][0] wrong */	ij=1;/* To be checked else nbcode[0][0] wrong */
for(j=3; j <=ncovmodel-nagesqr; j++) {	ijp=1; /* product no age */
	/* for(j=3; j <=ncovmodel-nagesqr; j++) { */
	for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
/* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */	/* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
if(ij <=cptcovage) { /* Bug valgrind */	if(j==Tage[ij]) { /* Product by age */
if((j-2)==Tage[ij]) { /* Bug valgrind */	if(ij <=cptcovage) { /* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, 2 V5 and V1 */
fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);	if(DummyV[j]==0){
/* fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */	fprintf(ficgp,"+p%d%dx",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
	}else{ /* quantitative */
	fprintf(ficgp,"+p%d%fx",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
	/* fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
	}
ij++;	ij++;
}	}
}	}else if(j==Tprod[ijp]) { /* */
else	/* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
fprintf(ficgp,"+p%d%d",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,j-2)]); / Valgrind bug nbcode */	if(ijp <=cptcovprod) { /* Product */
}	if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
	if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
	/* fprintf(ficgp,"+p%d%d%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(jk,j)],nbcode[Tvard[ijp][2]][codtabm(jk,j)]); */
	fprintf(ficgp,"+p%d%d%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
	}else{ /* Vn is dummy and Vm is quanti */
	/* fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(jk,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
	fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
	}
	}else{ /* VnVm Vn is quanti /
	if(DummyV[Tvard[ijp][2]]==0){
	fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
	}else{ /* Both quanti */
	fprintf(ficgp,"+p%d%f%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
	}
	}
	ijp++;
	}
	} else{ /* simple covariate */
	/* fprintf(ficgp,"+p%d%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(jk,j)]); /\ Valgrind bug nbcode \/ /
	if(Dummy[j]==0){
	fprintf(ficgp,"+p%d%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); / */
	}else{ /* quantitative */
	fprintf(ficgp,"+p%d%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); / */
	/* fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */
	}
	} /* end simple */
	} /* end j */
}else{	}else{
i=i-ncovmodel;	i=i-ncovmodel;
if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */	if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */
Line 6745 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 7029 plot [%.f:%.f] ", ageminpar, agemaxpar)

ij=1;	ij=1;
for(j=3; j <=ncovmodel-nagesqr; j++){	for(j=3; j <=ncovmodel-nagesqr; j++){
if(ij <=cptcovage) { /* Bug valgrind */	if((j-2)==Tage[ij]) { /* Bug valgrind */
if((j-2)==Tage[ij]) { /* Bug valgrind */	if(ij <=cptcovage) { /* Bug valgrind */
fprintf(ficgp,"+p%d%dx",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);	fprintf(ficgp,"+p%d%dx",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);
/* fprintf(ficgp,"+p%d%dx",k3+(k1-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); /	/* fprintf(ficgp,"+p%d%dx",k3+(k1-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); /
ij++;	ij++;
Line 6898 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 7182 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 6937 plot [%.f:%.f] ", ageminpar, agemaxpar)	Line 7221 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 6965 void prevforecast(char fileres[], double	Line 7249 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 6997 void prevforecast(char fileres[], double	Line 7281 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 7006 void prevforecast(char fileres[], double	Line 7293 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 */
	fprintf(ficresf," 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 7020 void prevforecast(char fileres[], double	Line 7310 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 7613 int readdata(char datafile[], int firsto	Line 7903 int readdata(char datafile[], int firsto
/-------- data file ----------/	/-------- data file ----------/
FILE *fic;	FILE *fic;
char dummy[]=" ";	char dummy[]=" ";
int i=0, j=0, n=0, iv=0;	int i=0, j=0, n=0, iv=0, v;
int lstra;	int lstra;
int linei, month, year,iout;	int linei, month, year,iout;
char line[MAXLINE], linetmp[MAXLINE];	char line[MAXLINE], linetmp[MAXLINE];
char stra[MAXLINE], strb[MAXLINE];	char stra[MAXLINE], strb[MAXLINE];
char *stratrunc;	char *stratrunc;

	DummyV=ivector(1,NCOVMAX); /* 1 to 3 */
	FixedV=ivector(1,NCOVMAX); /* 1 to 3 */

	for(v=1; v <=ncovcol;v++){
	DummyV[v]=0;
	FixedV[v]=0;
	}
	for(v=ncovcol+1; v <=ncovcol+nqv;v++){
	DummyV[v]=1;
	FixedV[v]=0;
	}
	for(v=ncovcol+nqv+1; v <=ncovcol+nqv+ntv;v++){
	DummyV[v]=0;
	FixedV[v]=1;
	}
	for(v=ncovcol+nqv+ntv+1; v <=ncovcol+nqv+ntv+nqtv;v++){
	DummyV[v]=1;
	FixedV[v]=1;
	}
	for(v=1; v <=ncovcol+nqv+ntv+nqtv;v++){
	printf("Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
	fprintf(ficlog,"Covariate type in the data: V%d, DummyV(V%d)=%d, FixedV(V%d)=%d\n",v,v,DummyV[v],v,FixedV[v]);
	}

if((fic=fopen(datafile,"r"))==NULL) {	if((fic=fopen(datafile,"r"))==NULL) {
printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);	printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
Line 7650 int readdata(char datafile[], int firsto	Line 7962 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 */
cotvar[j][ntv+iv][i]=-1; /* For performance reasons */	cotvar[j][ntv+iv][i]=-1; /* For performance reasons */
if(isalpha(strb[1])) { /* .m or .d Really Missing value */	if(isalpha(strb[1])) { /* .m or .d Really Missing value */
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);	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);
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);	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;	return 1;
}	}
}else{	}else{
errno=0;	errno=0;
/* what_kind_of_number(strb); */	/* what_kind_of_number(strb); */
dval=strtod(strb,&endptr);	dval=strtod(strb,&endptr);
/* if( strb[0]=='\0' \|\| (endptr != '\0')){ /	/* if( strb[0]=='\0' \|\| (endptr != '\0')){ /
/* if(strb != endptr && endptr == '\0') /	/* if(strb != endptr && endptr == '\0') /
/* dval=dlval; */	/* dval=dlval; */
/* 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 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);	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);
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);	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;	return 1;
}	}
cotqvar[j][iv][i]=dval;	cotqvar[j][iv][i]=dval;
cotvar[j][ntv+iv][i]=dval;	cotvar[j][ntv+iv][i]=dval;
}	}
strcpy(line,stra);	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 7890 int readdata(char datafile[], int firsto	Line 8202 int readdata(char datafile[], int firsto

void removefirstspace(char *stri){/, char stro[]) {*/	void removefirstspace(char *stri){/, char stro[]) {*/
char p1 = stri, p2 = stri;	char p1 = stri, p2 = stri;
if (*p2 == ' ')	while (*p2 == ' ')
p2++;	p2++;
/* while ((p1++ = p2++) !=0) */	/* while ((p1++ = p2++) !=0) */
/* ; */	/* ; */
Line 7901 void removefirstspace(char *stri){/, c	Line 8213 void removefirstspace(char *stri){/, c
*stri=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, k1=0, k2=0, match=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 resultmodel[MAXLINE];
int modelresult[MAXLINE];	int modelresult[MAXLINE];
Line 7942 int decoderesult ( char resultline[])	Line 8254 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 if no missing or useless values in comparison of current model needs */	/* Checking for missing or useless values in comparison of current model needs */
for(k1=1; k1<= cptcovt ;k1++){ /* model line */	for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
if(Typevar[k1]==0){	if(Typevar[k1]==0){ /* Single covariate in model */
match=0;	match=0;
for(k2=1; k2 <=j;k2++){	for(k2=1; k2 <=j;k2++){/* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
if(Tvar[k1]==Tvarsel[k2]) {	if(Tvar[k1]==Tvarsel[k2]) {/* Tvar[1]=5 == Tvarsel[2]=5 */
modelresult[k2]=k1;	modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2 modelresult[3]=3 modelresult[6]=4 modelresult[9]=5 */
match=1;	match=1;
break;	break;
}	}
Line 7958 int decoderesult ( char resultline[])	Line 8270 int decoderesult ( char resultline[])
}	}
}	}
}	}
	/* Checking for missing or useless values in comparison of current model needs */
for(k2=1; k2 <=j;k2++){ /* result line */	for(k2=1; k2 <=j;k2++){ /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
match=0;	match=0;
for(k1=1; k1<= cptcovt ;k1++){ /* model line */	for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
if(Typevar[k1]==0){	if(Typevar[k1]==0){ /* Single */
if(Tvar[k1]==Tvarsel[k2]) {	if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4 */
resultmodel[k1]=k2;	resultmodel[k1]=k2; /* resultmodel[2]=1 resultmodel[1]=2 resultmodel[3]=3 resultmodel[6]=4 resultmodel[9]=5 */
++match;	++match;
}	}
}	}
Line 7975 int decoderesult ( char resultline[])	Line 8287 int decoderesult ( char resultline[])
printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);	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 */	/* We need to deduce which combination number is chosen and save quantitative values */
	/* model line V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
	/* result line V4=1 V5=25.1 V3=0 V2=8 V1=1 */
	/* should give a combination of dummy V4=1, V3=0, V1=1 => V42(0) + V32*(1) + V12*(2) = 5 + (1offset) = 6/
	/* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
	/* should give a combination of dummy V4=1, V3=1, V1=0 => V42(0) + V32*(1) + V12*(2) = 3 + (1offset) = 4/
	/* 1 0 0 0 */
	/* 2 1 0 0 */
	/* 3 0 1 0 */
	/* 4 1 1 0 / / V4=1, V3=1, V1=0 */
	/* 5 0 0 1 */
	/* 6 1 0 1 / / V4=1, V3=0, V1=1 */
	/* 7 0 1 1 */
	/* 8 1 1 1 */
	/* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */
	/* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */
	/* V5age V5 known which value for nres? /
	/* Tqinvresult[2]=8 Tqinvresult[1]=25.1 */
	for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* model line */
	if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */
	k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */
	k2=(int)Tvarsel[k3]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
	k+=Tvalsel[k3]pow(2,k4); / Tvalsel[1]=1 */
	Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1) Tresult[nres][2]=0(V3=0) */
	Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
	Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
	printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);
	k4++;;
	} else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */
	k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */
	k2q=(int)Tvarsel[k3q]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */
	Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
	Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
	Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
	printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
	k4q++;;
	}
	}

	TKresult[nres]=++k; /* Combination for the nresult and the model */
return (0);	return (0);
}	}
int selected( int kvar){ /* Selected combination of covariates */
if(Tvarsel[kvar])
return (0);
else
return(1);
}
int decodemodel( char model[], int lastobs)	int decodemodel( char model[], int lastobs)
/**< This routine decodes the model and returns:	/**< This routine decodes the model and returns:
* Model V1+V2+V3+V8+V7V8+V5V6+V8age+V3age+age*age	* Model V1+V2+V3+V8+V7V8+V5V6+V8age+V3age+age*age
Line 8002 int decodemodel( char model[], int lasto	Line 8347 int decodemodel( char model[], int lasto
* - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7V8 and V5V6 .	* - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7V8 and V5V6 .
*/	*/
{	{
int i, j, k, ks;	int i, j, k, ks, v;
int j1, k1, k2, k3, k4;	int j1, k1, k2, k3, k4;
char modelsav[80];	char modelsav[80];
char stra[80], strb[80], strc[80], strd[80],stre[80];	char stra[80], strb[80], strc[80], strd[80],stre[80];
Line 8208 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 8553 Dummy[k] 0=dummy (0 1), 1 quantitative (
Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\	Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
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;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}
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 */	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 ){ /* Simple fixed dummy (<=ncovcol) covariates */	if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
Fixed[k]= 0;	Fixed[k]= 0;
Line 8233 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 8578 Dummy[k] 0=dummy (0 1), 1 quantitative (
TvarFind[ncovf]=k;	TvarFind[ncovf]=k;
TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */	TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */	TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
}else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){ /* Remind that product VnVm are added in k/ /* Only simple fixed quantitative variable */	}else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){/* Remind that product VnVm are added in k Only simple fixed quantitative variable /
Fixed[k]= 0;	Fixed[k]= 0;
Dummy[k]= 1;	Dummy[k]= 1;
nqfveff++;	nqfveff++;
Line 8247 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 8592 Dummy[k] 0=dummy (0 1), 1 quantitative (
TvarFind[ncovf]=k;	TvarFind[ncovf]=k;
TvarFQ[nqfveff]=Tvar[k]-ncovcol; /* TvarFQ[1]=V2-1=1st in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple fixed quantitative variable */	TvarFQ[nqfveff]=Tvar[k]-ncovcol; /* TvarFQ[1]=V2-1=1st in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple fixed quantitative variable */
TvarFQind[nqfveff]=k; /* TvarFQind[1]=6 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple fixed quantitative variable */	TvarFQind[nqfveff]=k; /* TvarFQind[1]=6 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple fixed quantitative variable */
}else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying variables */	}else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying dummy 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 */
Line 8258 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 8603 Dummy[k] 0=dummy (0 1), 1 quantitative (
TvarsDind[nsd]=k;	TvarsDind[nsd]=k;
ncovv++; /* Only simple time varying variables */	ncovv++; /* Only simple time varying variables */
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k;	TvarVind[ncovv]=k; /* TvarVind[2]=2 TvarVind[3]=3 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Any time varying singele */
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);
Line 8274 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 8619 Dummy[k] 0=dummy (0 1), 1 quantitative (
TvarsQ[nsq]=Tvar[k];	TvarsQ[nsq]=Tvar[k];
TvarsQind[nsq]=k;	TvarsQind[nsq]=k;
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k;	TvarVind[ncovv]=k; /* TvarVind[1]=1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Any time varying singele */
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 */
Line 8286 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 8631 Dummy[k] 0=dummy (0 1), 1 quantitative (
TvarA[ncova]=Tvar[k];	TvarA[ncova]=Tvar[k];
TvarAind[ncova]=k;	TvarAind[ncova]=k;
if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */	if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
Fixed[k]= 2;	Fixed[k]= 2;
Dummy[k]= 2;	Dummy[k]= 2;
modell[k].maintype= ATYPE;	modell[k].maintype= ATYPE;
modell[k].subtype= APFD;	modell[k].subtype= APFD;
/* ncoveff++; */	/* ncoveff++; */
}else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product VnVm are added in k/	}else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product VnVm are added in k/
Fixed[k]= 2;	Fixed[k]= 2;
Dummy[k]= 3;	Dummy[k]= 3;
modell[k].maintype= ATYPE;	modell[k].maintype= ATYPE;
modell[k].subtype= APFQ; /* Product age * fixed quantitative */	modell[k].subtype= APFQ; /* Product age * fixed quantitative */
/* nqfveff++; /\* Only simple fixed quantitative variable \/ /	/* nqfveff++; /\* Only simple fixed quantitative variable \/ /
}else if( Tvar[k] <=ncovcol+nqv+ntv ){	}else if( Tvar[k] <=ncovcol+nqv+ntv ){
Fixed[k]= 3;	Fixed[k]= 3;
Dummy[k]= 2;	Dummy[k]= 2;
modell[k].maintype= ATYPE;	modell[k].maintype= ATYPE;
modell[k].subtype= APVD; /* Product age * varying dummy */	modell[k].subtype= APVD; /* Product age * varying dummy */
/* ntveff++; /\* Only simple time varying dummy variable \/ /	/* ntveff++; /\* Only simple time varying dummy variable \/ /
}else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){	}else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
Fixed[k]= 3;	Fixed[k]= 3;
Dummy[k]= 3;	Dummy[k]= 3;
modell[k].maintype= ATYPE;	modell[k].maintype= ATYPE;
modell[k].subtype= APVQ; /* Product age * varying quantitative */	modell[k].subtype= APVQ; /* Product age * varying quantitative */
/* nqtveff++;/\* Only simple time varying quantitative variable \/ /	/* nqtveff++;/\* Only simple time varying quantitative variable \/ /
}	}
}else if (Typevar[k] == 2) { /* product without age */	}else if (Typevar[k] == 2) { /* product without age */
k1=Tposprod[k];	k1=Tposprod[k];
if(Tvard[k1][1] <=ncovcol){	if(Tvard[k1][1] <=ncovcol){
if(Tvard[k1][2] <=ncovcol){	if(Tvard[k1][2] <=ncovcol){
Fixed[k]= 1;	Fixed[k]= 1;
Dummy[k]= 0;	Dummy[k]= 0;
modell[k].maintype= FTYPE;	modell[k].maintype= FTYPE;
modell[k].subtype= FPDD; /* Product fixed dummy * fixed dummy */	modell[k].subtype= FPDD; /* Product fixed dummy * fixed dummy */
ncovf++; /* Fixed variables without age */	ncovf++; /* Fixed variables without age */
TvarF[ncovf]=Tvar[k];	TvarF[ncovf]=Tvar[k];
TvarFind[ncovf]=k;	TvarFind[ncovf]=k;
}else if(Tvard[k1][2] <=ncovcol+nqv){	}else if(Tvard[k1][2] <=ncovcol+nqv){
Fixed[k]= 0; /* or 2 ?*/	Fixed[k]= 0; /* or 2 ?*/
Dummy[k]= 1;	Dummy[k]= 1;
modell[k].maintype= FTYPE;	modell[k].maintype= FTYPE;
modell[k].subtype= FPDQ; /* Product fixed dummy * fixed quantitative */	modell[k].subtype= FPDQ; /* Product fixed dummy * fixed quantitative */
ncovf++; /* Varying variables without age */	ncovf++; /* Varying variables without age */
TvarF[ncovf]=Tvar[k];	TvarF[ncovf]=Tvar[k];
TvarFind[ncovf]=k;	TvarFind[ncovf]=k;
}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
Fixed[k]= 1;	Fixed[k]= 1;
Dummy[k]= 0;	Dummy[k]= 0;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPDD; /* Product fixed dummy * varying dummy */	modell[k].subtype= VPDD; /* Product fixed dummy * varying dummy */
ncovv++; /* Varying variables without age */	ncovv++; /* Varying variables without age */
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k;	TvarVind[ncovv]=k;
}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
Fixed[k]= 1;	Fixed[k]= 1;
Dummy[k]= 1;	Dummy[k]= 1;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPDQ; /* Product fixed dummy * varying quantitative */	modell[k].subtype= VPDQ; /* Product fixed dummy * varying quantitative */
ncovv++; /* Varying variables without age */	ncovv++; /* Varying variables without age */
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k;	TvarVind[ncovv]=k;
}	}
}else if(Tvard[k1][1] <=ncovcol+nqv){	}else if(Tvard[k1][1] <=ncovcol+nqv){
if(Tvard[k1][2] <=ncovcol){	if(Tvard[k1][2] <=ncovcol){
Fixed[k]= 0; /* or 2 ?*/	Fixed[k]= 0; /* or 2 ?*/
Dummy[k]= 1;	Dummy[k]= 1;
modell[k].maintype= FTYPE;	modell[k].maintype= FTYPE;
modell[k].subtype= FPDQ; /* Product fixed quantitative * fixed dummy */	modell[k].subtype= FPDQ; /* Product fixed quantitative * fixed dummy */
ncovf++; /* Fixed variables without age */	ncovf++; /* Fixed variables without age */
TvarF[ncovf]=Tvar[k];	TvarF[ncovf]=Tvar[k];
TvarFind[ncovf]=k;	TvarFind[ncovf]=k;
}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
Fixed[k]= 1;	Fixed[k]= 1;
Dummy[k]= 1;	Dummy[k]= 1;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPDQ; /* Product fixed quantitative * varying dummy */	modell[k].subtype= VPDQ; /* Product fixed quantitative * varying dummy */
ncovv++; /* Varying variables without age */	ncovv++; /* Varying variables without age */
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k;	TvarVind[ncovv]=k;
}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
Fixed[k]= 1;	Fixed[k]= 1;
Dummy[k]= 1;	Dummy[k]= 1;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPQQ; /* Product fixed quantitative * varying quantitative */	modell[k].subtype= VPQQ; /* Product fixed quantitative * varying quantitative */
ncovv++; /* Varying variables without age */	ncovv++; /* Varying variables without age */
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k;	TvarVind[ncovv]=k;
ncovv++; /* Varying variables without age */	ncovv++; /* Varying variables without age */
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k;	TvarVind[ncovv]=k;
}	}
}else if(Tvard[k1][1] <=ncovcol+nqv+ntv){	}else if(Tvard[k1][1] <=ncovcol+nqv+ntv){
if(Tvard[k1][2] <=ncovcol){	if(Tvard[k1][2] <=ncovcol){
Fixed[k]= 1;	Fixed[k]= 1;
Dummy[k]= 1;	Dummy[k]= 1;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPDD; /* Product time varying dummy * fixed dummy */	modell[k].subtype= VPDD; /* Product time varying dummy * fixed dummy */
ncovv++; /* Varying variables without age */	ncovv++; /* Varying variables without age */
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k;	TvarVind[ncovv]=k;
}else if(Tvard[k1][2] <=ncovcol+nqv){	}else if(Tvard[k1][2] <=ncovcol+nqv){
Fixed[k]= 1;	Fixed[k]= 1;
Dummy[k]= 1;	Dummy[k]= 1;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPDQ; /* Product time varying dummy * fixed quantitative */	modell[k].subtype= VPDQ; /* Product time varying dummy * fixed quantitative */
ncovv++; /* Varying variables without age */	ncovv++; /* Varying variables without age */
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k;	TvarVind[ncovv]=k;
}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
Fixed[k]= 1;	Fixed[k]= 1;
Dummy[k]= 0;	Dummy[k]= 0;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPDD; /* Product time varying dummy * time varying dummy */	modell[k].subtype= VPDD; /* Product time varying dummy * time varying dummy */
ncovv++; /* Varying variables without age */	ncovv++; /* Varying variables without age */
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k;	TvarVind[ncovv]=k;
}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
Fixed[k]= 1;	Fixed[k]= 1;
Dummy[k]= 1;	Dummy[k]= 1;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPDQ; /* Product time varying dummy * time varying quantitative */	modell[k].subtype= VPDQ; /* Product time varying dummy * time varying quantitative */
ncovv++; /* Varying variables without age */	ncovv++; /* Varying variables without age */
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k;	TvarVind[ncovv]=k;
}	}
}else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){	}else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){
if(Tvard[k1][2] <=ncovcol){	if(Tvard[k1][2] <=ncovcol){
Fixed[k]= 1;	Fixed[k]= 1;
Dummy[k]= 1;	Dummy[k]= 1;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPDQ; /* Product time varying quantitative * fixed dummy */	modell[k].subtype= VPDQ; /* Product time varying quantitative * fixed dummy */
ncovv++; /* Varying variables without age */	ncovv++; /* Varying variables without age */
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k;	TvarVind[ncovv]=k;
}else if(Tvard[k1][2] <=ncovcol+nqv){	}else if(Tvard[k1][2] <=ncovcol+nqv){
Fixed[k]= 1;	Fixed[k]= 1;
Dummy[k]= 1;	Dummy[k]= 1;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPQQ; /* Product time varying quantitative * fixed quantitative */	modell[k].subtype= VPQQ; /* Product time varying quantitative * fixed quantitative */
ncovv++; /* Varying variables without age */	ncovv++; /* Varying variables without age */
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k;	TvarVind[ncovv]=k;
}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
Fixed[k]= 1;	Fixed[k]= 1;
Dummy[k]= 1;	Dummy[k]= 1;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPDQ; /* Product time varying quantitative * time varying dummy */	modell[k].subtype= VPDQ; /* Product time varying quantitative * time varying dummy */
ncovv++; /* Varying variables without age */	ncovv++; /* Varying variables without age */
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k;	TvarVind[ncovv]=k;
}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
Fixed[k]= 1;	Fixed[k]= 1;
Dummy[k]= 1;	Dummy[k]= 1;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPQQ; /* Product time varying quantitative * time varying quantitative */	modell[k].subtype= VPQQ; /* Product time varying quantitative * time varying quantitative */
ncovv++; /* Varying variables without age */	ncovv++; /* Varying variables without age */
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k;	TvarVind[ncovv]=k;
}	}
}else{	}else{
printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);	printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);	fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
} /* end k1 */	} /end k1/
}else{	}else{
printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);	printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
fprintf(ficlog,"Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);	fprintf(ficlog,"Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
Line 8795 void syscompilerinfo(int logged)	Line 9140 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 8823 int prevalence_limit(double p, double	Line 9168 int prevalence_limit(double p, double
i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */	i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
if (cptcovn < 1){i1=1;}	if (cptcovn < 1){i1=1;}

for(k=1; k<=i1;k++){	for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */
/* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
/* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */	if(TKresult[nres]!= k)
//for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){	continue;
/* k=k+1; */
/* to clean */
//printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
fprintf(ficrespl,"#******");
printf("#******");
fprintf(ficlog,"#******");
for(j=1;j<=cptcoveff ;j++) {/* all covariates */
fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
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(ficrespl,"******\n");
printf("******\n");
fprintf(ficlog,"******\n");
if(invalidvarcomb[k]){
printf("\nCombination (%d) ignored because no case \n",k);
fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
continue;
}

fprintf(ficrespl,"#Age ");	/* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
for(j=1;j<=cptcoveff;j++) {	/* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	//for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
}	/* k=k+1; */
for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);	/* to clean */
fprintf(ficrespl,"Total Years_to_converge\n");	//printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
	fprintf(ficrespl,"#******");
	printf("#******");
	fprintf(ficlog,"#******");
	for(j=1;j<=cptcoveff ;j++) {/* all covariates */
	fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/
	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)]);
	}
	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
	printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	}
	fprintf(ficrespl,"******\n");
	printf("******\n");
	fprintf(ficlog,"******\n");
	if(invalidvarcomb[k]){
	printf("\nCombination (%d) ignored because no case \n",k);
	fprintf(ficrespl,"#Combination (%d) ignored because no case \n",k);
	fprintf(ficlog,"\nCombination (%d) ignored because no case \n",k);
	continue;
	}

	fprintf(ficrespl,"#Age ");
	for(j=1;j<=cptcoveff;j++) {
	fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
	}
	for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
	fprintf(ficrespl,"Total Years_to_converge\n");

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)]);
tot=0.;	tot=0.;
for(i=1; i<=nlstate;i++){	for(i=1; i<=nlstate;i++){
tot += prlim[i][i];	tot += prlim[i][i];
fprintf(ficrespl," %.5f", prlim[i][i]);	fprintf(ficrespl," %.5f", prlim[i][i]);
}	}
fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);	fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
} /* Age */	} /* Age */
/* was end of cptcod */	/* was end of cptcod */
} /* cptcov */	} /* cptcov */
	} /* nres */
return 0;	return 0;
}	}

Line 8879 int back_prevalence_limit(double *p, dou	Line 9234 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 8910 int back_prevalence_limit(double *p, dou	Line 9265 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 */
//printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));	for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
fprintf(ficresplb,"#******");	if(TKresult[nres]!= k)
printf("#******");	continue;
fprintf(ficlog,"#******");	//printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
for(j=1;j<=cptcoveff ;j++) {/* all covariates */	fprintf(ficresplb,"#******");
fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	printf("#******");
printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficlog,"#******");
fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	for(j=1;j<=cptcoveff ;j++) {/* all covariates */
}	fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficresplb,"******\n");	printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
printf("******\n");	fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficlog,"******\n");	}
if(invalidvarcomb[k]){	for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
printf("\nCombination (%d) ignored because no cases \n",k);	printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);	fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);	fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
continue;	}
}	fprintf(ficresplb,"******\n");
	printf("******\n");
	fprintf(ficlog,"******\n");
	if(invalidvarcomb[k]){
	printf("\nCombination (%d) ignored because no cases \n",k);
	fprintf(ficresplb,"#Combination (%d) ignored because no cases \n",k);
	fprintf(ficlog,"\nCombination (%d) ignored because no cases \n",k);
	continue;
	}

fprintf(ficresplb,"#Age ");	fprintf(ficresplb,"#Age ");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcoveff;j++) {
fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
}	}
for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);	for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);
fprintf(ficresplb,"Total Years_to_converge\n");	fprintf(ficresplb,"Total Years_to_converge\n");


for (age=agebase; age<=agelim; age++){	for (age=agebase; age<=agelim; age++){
/* for (age=agebase; age<=agebase; age++){ */	/* for (age=agebase; age<=agebase; age++){ */
if(mobilavproj > 0){	if(mobilavproj > 0){
/* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */	/* bprevalim(bprlim, mobaverage, nlstate, p, age, ageminpar, agemaxpar, oldm, savm, doldm, dsavm, ftolpl, ncvyearp, k); */
/* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */	/* bprevalim(bprlim, mobaverage, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k);	bprevalim(bprlim, mobaverage, nlstate, p, age, ftolpl, ncvyearp, k, nres);
}else if (mobilavproj == 0){	}else if (mobilavproj == 0){
printf("There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);	printf("There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
fprintf(ficlog,"There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);	fprintf(ficlog,"There is no chance to get back prevalence limit if data aren't non zero and summing to 1, please try a non null mobil_average(=%d) parameter or mobil_average=-1 if you want to try at your own risk.\n",mobilavproj);
exit(1);	exit(1);
}else{	}else{
/* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */	/* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k);	bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);
}	}
fprintf(ficresplb,"%.0f ",age );	fprintf(ficresplb,"%.0f ",age );
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
tot=0.;	tot=0.;
for(i=1; i<=nlstate;i++){	for(i=1; i<=nlstate;i++){
tot += bprlim[i][i];	tot += bprlim[i][i];
fprintf(ficresplb," %.5f", bprlim[i][i]);	fprintf(ficresplb," %.5f", bprlim[i][i]);
}	}
fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);	fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
} /* Age */	} /* Age */
/* was end of cptcod */	/* was end of cptcod */
} /* cptcov */	} /* end of any combination */
	} /* end of nres */
/* hBijx(p, bage, fage); */	/* hBijx(p, bage, fage); */
/* fclose(ficrespijb); */	/* fclose(ficrespijb); */

Line 8978 int hPijx(double *p, int bage, int fage)	Line 9341 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 9005 int hPijx(double *p, int bage, int fage)	Line 9368 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 9019 int hPijx(double *p, int bage, int fage)	Line 9389 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 9049 int hPijx(double *p, int bage, int fage)	Line 9419 int hPijx(double *p, int bage, int fage)
int ageminl;	int ageminl;
int hstepm;	int hstepm;
int nhstepm;	int nhstepm;
int h, i, i1, j, k;	int h, i, i1, j, k, nres;

double agedeb;	double agedeb;
double ***p3mat;	double ***p3mat;
Line 9077 int hPijx(double *p, int bage, int fage)	Line 9447 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 */
fprintf(ficrespijb,"\n#****** ");	for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
for(j=1;j<=cptcoveff;j++)	if(TKresult[nres]!= k)
fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	continue;
fprintf(ficrespijb,"******\n");	fprintf(ficrespijb,"\n#****** ");
if(invalidvarcomb[k]){	for(j=1;j<=cptcoveff;j++)
fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);	fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
continue;	for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
}	fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
	}
/* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months \/ /	fprintf(ficrespijb,"******\n");
for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */	if(invalidvarcomb[k]){
/* nhstepm=(int) rint((agelim-agedeb)YEARM/stepm); /\ Typically 20 years = 2012/6=40 \/ */	fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
nhstepm=(int) rint((agedeb-ageminl)YEARM/stepm); / Typically 20 years = 2012/6=40 /	continue;
nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */	}

/* nhstepm=nhstepmYEARM; aff par mois/	/* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months \/ /
	for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	/* nhstepm=(int) rint((agelim-agedeb)YEARM/stepm); /\ Typically 20 years = 2012/6=40 \/ */
/* oldm=oldms;savm=savms; */	nhstepm=(int) rint((agedeb-ageminl)YEARM/stepm); / Typically 20 years = 2012/6=40 /
/* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */	nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 */
hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);
/* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */	/* nhstepm=nhstepmYEARM; aff par mois/
fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");
for(i=1; i<=nlstate;i++)	p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
for(j=1; j<=nlstate+ndeath;j++)	/* oldm=oldms;savm=savms; */
fprintf(ficrespijb," %1d-%1d",i,j);	/* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
fprintf(ficrespijb,"\n");	hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);
for (h=0; h<=nhstepm; h++){	/* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
/agedebphstep = agedeb + hhstepm/YEARMstepm;/	fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");
fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - hhstepm/YEARMstepm );
/* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + hhstepm/YEARMstepm ); */
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate+ndeath;j++)	for(j=1; j<=nlstate+ndeath;j++)
fprintf(ficrespijb," %.5f", p3mat[i][j][h]);	fprintf(ficrespijb," %1d-%1d",i,j);
fprintf(ficrespijb,"\n");	fprintf(ficrespijb,"\n");
}	for (h=0; h<=nhstepm; h++){
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	/agedebphstep = agedeb + hhstepm/YEARMstepm;/
fprintf(ficrespijb,"\n");	fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - hhstepm/YEARMstepm );
}	/* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + hhstepm/YEARMstepm ); */
/}/	for(i=1; i<=nlstate;i++)
}	for(j=1; j<=nlstate+ndeath;j++)
	fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
	fprintf(ficrespijb,"\n");
	}
	free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
	fprintf(ficrespijb,"\n");
	} /* end age deb */
	} /* end combination */
	} /* end nres */
return 0;	return 0;
} /* hBijx */	} /* hBijx */

Line 9145 int main(int argc, char *argv[])	Line 9521 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 10522 Please run with mle=-1 to get a correct	Line 10899 Please run with mle=-1 to get a correct
ungetc(c,ficpar);	ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);	fgets(line, MAXLINE, ficpar);
fputs(line,stdout);	fputs(line,stdout);
	fputs(line,ficres);
fputs(line,ficparo);	fputs(line,ficparo);
}	}
ungetc(c,ficpar);	ungetc(c,ficpar);
Line 10538 Please run with mle=-1 to get a correct	Line 10916 Please run with mle=-1 to get a correct
fgets(line, MAXLINE, ficpar);	fgets(line, MAXLINE, ficpar);
fputs(line,stdout);	fputs(line,stdout);
fputs(line,ficparo);	fputs(line,ficparo);
	fputs(line,ficres);
}	}
ungetc(c,ficpar);	ungetc(c,ficpar);

Line 10548 Please run with mle=-1 to get a correct	Line 10927 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 10555 Please run with mle=-1 to get a correct	Line 10935 Please run with mle=-1 to get a correct
fputs(line,stdout);	fputs(line,stdout);
fputs(line,ficparo);	fputs(line,ficparo);
fputs(line,ficlog);	fputs(line,ficlog);
	fputs(line,ficres);
continue;	continue;
}else	}else
break;	break;
}	}
	if (!feof(ficpar))
while((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){	while((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){
if (num_filled == 0)	if (num_filled == 0){
resultline[0]='\0';	resultline[0]='\0';
else if (num_filled != 1){	break;
	} 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 */
	fprintf(ficparo,"result: %s\n",resultline);
	fprintf(ficres,"result: %s\n",resultline);
	fprintf(ficlog,"result: %s\n",resultline);
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] == '#') {
numlinepar++;	numlinepar++;
fputs(line,stdout);	fputs(line,stdout);
fputs(line,ficparo);	fputs(line,ficparo);
	fputs(line,ficres);
fputs(line,ficlog);	fputs(line,ficlog);
continue;	continue;
}else	}else
Line 10582 Please run with mle=-1 to get a correct	Line 10975 Please run with mle=-1 to get a correct
break;	break;
else{ /* Processess output results for this combination of covariate values */	else{ /* Processess output results for this combination of covariate values */
}	}
}	} /* end while */



Line 10653 Please run with mle=-1 to get a correct	Line 11046 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 10661 Please run with mle=-1 to get a correct	Line 11055 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 10715 Please run with mle=-1 to get a correct	Line 11110 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);

	pstamp(ficreseij);

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 10776 Please run with mle=-1 to get a correct	Line 11186 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#****** Result for:");
	fprintf(ficrest,"\n#****** Result for:");
	fprintf(ficlog,"\n#****** Result for:");
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 10795 Please run with mle=-1 to get a correct	Line 11216 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#****** ");
	/* pstamp(ficresvij); */
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 10824 Please run with mle=-1 to get a correct	Line 11253 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 10838 Please run with mle=-1 to get a correct	Line 11267 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 10875 Please run with mle=-1 to get a correct	Line 11304 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 10898 Please run with mle=-1 to get a correct	Line 11327 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 10907 Please run with mle=-1 to get a correct	Line 11342 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 10962 Please run with mle=-1 to get a correct	Line 11402 Please run with mle=-1 to get a correct
free_ivector(ncodemaxwundef,1,NCOVMAX);	free_ivector(ncodemaxwundef,1,NCOVMAX);
free_ivector(Dummy,-1,NCOVMAX);	free_ivector(Dummy,-1,NCOVMAX);
free_ivector(Fixed,-1,NCOVMAX);	free_ivector(Fixed,-1,NCOVMAX);
	free_ivector(DummyV,1,NCOVMAX);
	free_ivector(FixedV,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(TvarsQ,1,NCOVMAX);

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

Removed from v.1.234
changed lines
	Added in v.1.246