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Diff for /imach/src/imach.c between versions 1.246 and 1.266

version 1.246, 2016/09/02 08:49:22	version 1.266, 2017/05/13 07:26:12
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	Revision 1.266 2017/05/13 07:26:12 brouard
	Summary: Version 0.99r13 (improvements and bugs fixed)

	Revision 1.265 2017/04/26 16:22:11 brouard
	Summary: imach 0.99r13 Some bugs fixed

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

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

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

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

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

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

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

	Some cleanings, conformed with updated documentation.

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

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

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

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

	Revision 1.253 2016/12/15 11:59:41 brouard
	Summary: 0.99 in progress

	Revision 1.252 2016/09/15 21:15:37 brouard
	* empty log message *

	Revision 1.251 2016/09/15 15:01:13 brouard
	Summary: not working

	Revision 1.250 2016/09/08 16:07:27 brouard
	Summary: continue

	Revision 1.249 2016/09/07 17:14:18 brouard
	Summary: Starting values from frequencies

	Revision 1.248 2016/09/07 14:10:18 brouard
	* empty log message *

	Revision 1.247 2016/09/02 11:11:21 brouard
	* empty log message *

Revision 1.246 2016/09/02 08:49:22 brouard	Revision 1.246 2016/09/02 08:49:22 brouard
* empty log message *	* empty log message *

Line 113	Line 175
Author: Nicolas Brouard	Author: Nicolas Brouard

Revision 1.210 2015/11/18 17:41:20 brouard	Revision 1.210 2015/11/18 17:41:20 brouard
Summary: Start working on projected prevalences	Summary: Start working on projected prevalences Revision 1.209 2015/11/17 22:12:03 brouard

Revision 1.209 2015/11/17 22:12:03 brouard
Summary: Adding ftolpl parameter	Summary: Adding ftolpl parameter
Author: N Brouard	Author: N Brouard

Line 903 typedef struct {	Line 963 typedef struct {
/* #include <libintl.h> */	/* #include <libintl.h> */
/* #define _(String) gettext (String) */	/* #define _(String) gettext (String) */

#define MAXLINE 1024 /* Was 256. Overflow with 312 with 2 states and 4 covariates. Should be ok */	#define MAXLINE 2048 /* Was 256 and 1024. Overflow with 312 with 2 states and 4 covariates. Should be ok */

#define GNUPLOTPROGRAM "gnuplot"	#define GNUPLOTPROGRAM "gnuplot"
/#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"/	/#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"/
Line 1146 int *TvarsQind;	Line 1206 int *TvarsQind;

#define MAXRESULTLINES 10	#define MAXRESULTLINES 10
int nresult=0;	int nresult=0;
	int parameterline=0; /* # of the parameter (type) line */
int TKresult[MAXRESULTLINES];	int TKresult[MAXRESULTLINES];
int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */	int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */	int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */
Line 2378 void powell(double p[], double **xi, int	Line 2439 void powell(double p[], double **xi, int
flatd++;	flatd++;
}	}
if(flatd >0){	if(flatd >0){
printf("%d flat directions\n",flatd);	printf("%d flat directions: ",flatd);
fprintf(ficlog,"%d flat directions\n",flatd);	fprintf(ficlog,"%d flat directions :",flatd);
for (j=1;j<=n;j++) {	for (j=1;j<=n;j++) {
if(flatdir[j]>0){	if(flatdir[j]>0){
printf("%d ",j);	printf("%d ",j);
Line 2563 Earliest age to start was %d-%d=%d, ncvl	Line 2624 Earliest age to start was %d-%d=%d, ncvl
/* double bprevalim(double bprlim, double *prevacurrent, int nlstate, double x[], double age, double oldm, double savm, double dnewm, double doldm, double dsavm, double ftolpl, int ncvyear, int ij) /	/* double bprevalim(double bprlim, double *prevacurrent, int nlstate, double x[], double age, double oldm, double savm, double dnewm, double doldm, double dsavm, double ftolpl, int ncvyear, int ij) /
double bprevalim(double bprlim, double **prevacurrent, int nlstate, double x[], double age, double ftolpl, int ncvyear, int ij, int nres)	double bprevalim(double bprlim, double **prevacurrent, int nlstate, double x[], double age, double ftolpl, int ncvyear, int ij, int nres)
{	{
/* Computes the prevalence limit in each live state at age x and covariate ij by left multiplying the unit	/* Computes the prevalence limit in each live state at age x and for covariate combination ij (<=2**cptcoveff) by left multiplying the unit
matrix by transitions matrix until convergence is reached with precision ftolpl */	matrix by transitions matrix until convergence is reached with precision ftolpl */
/* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */	/* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */
/* Wx is row vector: population in state 1, population in state 2, population dead */	/* Wx is row vector: population in state 1, population in state 2, population dead */
Line 2584 Earliest age to start was %d-%d=%d, ncvl	Line 2645 Earliest age to start was %d-%d=%d, ncvl
/* If we start from prlim again, prlim tends to a constant matrix */	/* If we start from prlim again, prlim tends to a constant matrix */

int i, ii,j,k;	int i, ii,j,k;
	int first=0;
double min, max, *meandiff, maxmax,sumnew=0.;	double min, max, *meandiff, maxmax,sumnew=0.;
/* double *matprod2(); / /* test */	/* double *matprod2(); / /* test */
double out, cov[NCOVMAX+1], bmij();	double out, cov[NCOVMAX+1], bmij();
Line 2598 Earliest age to start was %d-%d=%d, ncvl	Line 2660 Earliest age to start was %d-%d=%d, ncvl
max=vector(1,nlstate);	max=vector(1,nlstate);
meandiff=vector(1,nlstate);	meandiff=vector(1,nlstate);

dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;	dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
oldm=oldms; savm=savms;	oldm=oldms; savm=savms;

/* Starting with matrix unity */	/* Starting with matrix unity */
for (ii=1;ii<=nlstate+ndeath;ii++)	for (ii=1;ii<=nlstate+ndeath;ii++)
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
oldm[ii][j]=(ii==j ? 1.0 : 0.0);	oldm[ii][j]=(ii==j ? 1.0 : 0.0);
}	}

Line 2623 Earliest age to start was %d-%d=%d, ncvl	Line 2685 Earliest age to start was %d-%d=%d, ncvl
for (k=1; k<=nsd;k++) { /* For single dummy covariates only */	for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
/* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */	/* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];	cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
/* printf("bprevalim Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */	/* printf("bprevalim Dummy agefin=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agefin,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
}	}
/* for (k=1; k<=cptcovn;k++) { */	/* for (k=1; k<=cptcovn;k++) { */
/* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; \/ /	/* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; \/ /
Line 2677 Earliest age to start was %d-%d=%d, ncvl	Line 2739 Earliest age to start was %d-%d=%d, ncvl
/* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, ageminpar, agemaxpar, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind \/ /	/* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, ageminpar, agemaxpar, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind \/ /
/* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind \/ /	/* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind \/ /
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij)); /* Bug Valgrind */	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij)); /* Bug Valgrind */
	/* if((int)age == 70){ */
	/* printf(" Backward prevalim age=%d agefin=%d \n", (int) age, (int) agefin); */
	/* for(i=1; i<=nlstate+ndeath; i++) { */
	/* printf("%d newm= ",i); */
	/* for(j=1;j<=nlstate+ndeath;j++) { */
	/* printf("%f ",newm[i][j]); */
	/* } */
	/* printf("oldm * "); */
	/* for(j=1;j<=nlstate+ndeath;j++) { */
	/* printf("%f ",oldm[i][j]); */
	/* } */
	/* printf(" pmmij "); */
	/* for(j=1;j<=nlstate+ndeath;j++) { */
	/* printf("%f ",pmmij[i][j]); */
	/* } */
	/* printf("\n"); */
	/* } */
	/* } */
savm=oldm;	savm=oldm;
oldm=newm;	oldm=newm;

for(j=1; j<=nlstate; j++){	for(j=1; j<=nlstate; j++){
max[j]=0.;	max[j]=0.;
min[j]=1.;	min[j]=1.;
Line 2709 Earliest age to start was %d-%d=%d, ncvl	Line 2790 Earliest age to start was %d-%d=%d, ncvl
}	}
} /* age loop */	} /* age loop */
/* After some age loop it doesn't converge */	/* After some age loop it doesn't converge */
printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\	if(first){
	first=1;
	printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. Others in log file only...\n\
	Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
	}
	fprintf(ficlog,"Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\
Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);	Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
/* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */	/* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
free_vector(min,1,nlstate);	free_vector(min,1,nlstate);
Line 2724 Oldest age to start was %d-%d=%d, ncvloo	Line 2810 Oldest age to start was %d-%d=%d, ncvloo
double pmij(double ps, double cov, int ncovmodel, double x, int nlstate )	double pmij(double ps, double cov, int ncovmodel, double x, int nlstate )
{	{
/* According to parameters values stored in x and the covariate's values stored in cov,	/* According to parameters values stored in x and the covariate's values stored in cov,
computes the probability to be observed in state j being in state i by appying the	computes the probability to be observed in state j (after stepm years) being in state i by appying the
model to the ncovmodel covariates (including constant and age).	model to the ncovmodel covariates (including constant and age).
lnpijopii=ln(pij/pii)= aij+bijage+cijv1+dijv2+... = sum_nc=1^ncovmodel xij(nc)cov[nc]	lnpijopii=ln(pij/pii)= aij+bijage+cijv1+dijv2+... = sum_nc=1^ncovmodel xij(nc)cov[nc]
and, according on how parameters are entered, the position of the coefficient xij(nc) of the	and, according on how parameters are entered, the position of the coefficient xij(nc) of the
Line 2733 double pmij(double ps, double *cov,	Line 2819 double pmij(double ps, double *cov,
j>=i nc + ((i-1)(nlstate+ndeath-1)+(j-2))ncovmodel	j>=i nc + ((i-1)(nlstate+ndeath-1)+(j-2))ncovmodel
Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,	Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.	sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
Outputs ps[i][j] the probability to be observed in j being in j according to	Outputs ps[i][j] or probability to be observed in j being in i according to
the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]	the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
	Sum on j ps[i][j] should equal to 1.
*/	*/
double s1, lnpijopii;	double s1, lnpijopii;
/double t34;/	/double t34;/
Line 2798 double pmij(double ps, double *cov,	Line 2885 double pmij(double ps, double *cov,
/*	/*
for(i=1; i<= npar; i++) printf("%f ",x[i]);	for(i=1; i<= npar; i++) printf("%f ",x[i]);
goto end;*/	goto end;*/
return ps;	return ps; /* Pointer is unchanged since its call */
}	}

/************* backward transition probabilities *************/	/************* backward transition probabilities *************/
Line 2807 double pmij(double ps, double *cov,	Line 2894 double pmij(double ps, double *cov,
/* double bmij(double ps, double cov, int ncovmodel, double x, int nlstate, double *prevacurrent, double dnewm, double doldm, double dsavm, int ij ) /	/* double bmij(double ps, double cov, int ncovmodel, double x, int nlstate, double *prevacurrent, double dnewm, double doldm, double dsavm, int ij ) /
double bmij(double ps, double cov, int ncovmodel, double x, int nlstate, double ***prevacurrent, int ij )	double bmij(double ps, double cov, int ncovmodel, double x, int nlstate, double ***prevacurrent, int ij )
{	{
/* Computes the backward probability at age agefin and covariate ij	/* Computes the backward probability at age agefin and covariate combination ij. In fact cov is already filled and x too.
* and returns in ps as well as bmij.	* Call to pmij(cov and x), call to cross prevalence, sums and inverses, left multiply, and returns in ps as well as bmij.
*/	*/
int i, ii, j,k;	int i, ii, j,k;

Line 2825 double pmij(double ps, double *cov,	Line 2912 double pmij(double ps, double *cov,

agefin=cov[2];	agefin=cov[2];
/* bmij // age is cov[2], ij is included in cov, but we need for	/* bmij // age is cov[2], ij is included in cov, but we need for
the observed prevalence (with this covariate ij) */	the observed prevalence (with this covariate ij) at beginning of transition */
dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);	/* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
	pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /This is forward probability from agefin to agefin + stepm /
	/* outputs pmmij which is a stochastic matrix */
/* We do have the matrix Px in savm and we need pij */	/* We do have the matrix Px in savm and we need pij */
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
sumnew=0.; /* w1 p11 + w2 p21 only on live states */	sumnew=0.; /* w1 p11 + w2 p21 only on live states N1./N..N11/N1. + N2./N..N21/N2.=(N11+N21)/N..=N.1/N.. */
for (ii=1;ii<=nlstate;ii++){	for (ii=1;ii<=nlstate;ii++){
sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij];	/* sumnew+=dsavm[ii][j]prevacurrent[(int)agefin][ii][ij]; /
	sumnew+=pmmij[ii][j]prevacurrent[(int)agefin][ii][ij]; / Yes prevalence at beginning of transition */
} /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */	} /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
for (ii=1;ii<=nlstate+ndeath;ii++){	if(sumnew >= 1.e-10){
if(sumnew >= 1.e-10){	for (ii=1;ii<=nlstate+ndeath;ii++){
/* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */	/* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
/* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */	/* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
/* }else if(agefin >= agemaxpar+stepm/YEARM){ */	/* }else if(agefin >= agemaxpar+stepm/YEARM){ */
/* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */	/* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
/* }else */	/* }else */
doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);	doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);
}else{	} /End ii /
;	}else{ /* We put the identity matrix */
/* 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); */	for (ii=1;ii<=nlstate+ndeath;ii++){
}	doldm[ii][j]=(ii==j ? 1. : 0.0);
} /End ii /	} /End ii /
} /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */	/* printf("Problem internal bmij A: sum_i w_ip_ij=N.j/N.. <1.e-10 i=%d, j=%d, sumnew=%lf,agefin=%d\n",ii,j,sumnew, (int)agefin); /
/* left Product of this diag matrix by dsavm=Px (newm=dsavmdoldm) /	}
bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */	} /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] or identity*/
	/* left Product of this diag matrix by dsavm=Px (dnewm=dsavmdoldm) /
	/* bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /\* Bug Valgrind \/ /
	bbmij=matprod2(dnewm, pmmij,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */
/* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten\/ /	/* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten\/ /
/* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] \/ /	/* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] \/ /
/* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] \/ /	/* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] \/ /
/* left Product of this matrix by diag matrix of prevalences (savm) */	/* left Product of this matrix by diag matrix of prevalences (savm) */
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
	sumnew=0.;
for (ii=1;ii<=nlstate+ndeath;ii++){	for (ii=1;ii<=nlstate+ndeath;ii++){
	sumnew+=prevacurrent[(int)agefin][ii][ij];
dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);	dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);
}	}
} /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */	/* if(sumnew <0.9){ */
ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */	/* printf("Problem internal bmij B: sum on i wi <0.9: j=%d, sum_i wi=%lf,agefin=%d\n",j,sumnew, (int)agefin); */
	/* } */
	} /* End j, At the end dsavm is diag[(w_i)] */
	/* What if dsavm doesn't sum ii to 1? */
	/* ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /\* Bug Valgrind \/ /
	ps=matprod2(ps, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */
/* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */	/* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
/* end bmij */	/* end bmij */
return ps;	return ps; /pointer is unchanged /
}	}
/************* transition probabilities *************/	/************* transition probabilities *************/

Line 3087 double *hpxij(double *po, int nhstep	Line 3187 double *hpxij(double *po, int nhstep
/* double *hbxij(double po, int nhstepm, double age, int hstepm, double x, double *prevacurrent, int nlstate, int stepm, double oldm, double savm, double dnewm, double doldm, double dsavm, int ij ) */	/* double *hbxij(double po, int nhstepm, double age, int hstepm, double x, double *prevacurrent, int nlstate, int stepm, double oldm, double savm, double dnewm, double doldm, double dsavm, int ij ) */
double *hbxij(double po, int nhstepm, double age, int hstepm, double x, double ***prevacurrent, int nlstate, int stepm, int ij )	double *hbxij(double po, int nhstepm, double age, int hstepm, double x, double ***prevacurrent, int nlstate, int stepm, int ij )
{	{
/* Computes the transition matrix starting at age 'age' over	/* For a combination of dummy covariate ij, computes the transition matrix starting at age 'age' over
'nhstepmhstepmstepm' months (i.e. until	'nhstepmhstepmstepm' months (i.e. until
age (in years) age+nhstepmhstepmstepm/12) by multiplying	age (in years) age+nhstepmhstepmstepm/12) by multiplying
nhstepm*hstepm matrices.	nhstepm*hstepm matrices.
Line 3095 double *hbxij(double *po, int nhstep	Line 3195 double *hbxij(double *po, int nhstep
(typically every 2 years instead of every month which is too big	(typically every 2 years instead of every month which is too big
for the memory).	for the memory).
Model is determined by parameters x and covariates have to be	Model is determined by parameters x and covariates have to be
included manually here.	included manually here. Then we use a call to bmij(x and cov)
	The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output
*/	*/

int i, j, d, h, k;	int i, j, d, h, k;
double **out, cov[NCOVMAX+1];	double out, cov[NCOVMAX+1], bmij();
double **newm;	double newm, *newmm;
double agexact;	double agexact;
double agebegin, ageend;	double agebegin, ageend;
double oldm, savm;	double oldm, savm;

oldm=oldms;savm=savms;	newmm=po; /* To be saved */
	oldm=oldms;savm=savms; /* Global pointers */
/* Hstepm could be zero and should return the unit matrix */	/* Hstepm could be zero and should return the unit matrix */
for (i=1;i<=nlstate+ndeath;i++)	for (i=1;i<=nlstate+ndeath;i++)
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
Line 3119 double *hbxij(double *po, int nhstep	Line 3220 double *hbxij(double *po, int nhstep
newm=savm;	newm=savm;
/* Covariates have to be included here again */	/* Covariates have to be included here again */
cov[1]=1.;	cov[1]=1.;
agexact=age-((h-1)hstepm + (d-1))stepm/YEARM; /* age just before transition */	agexact=age-((h-1)hstepm + (d))stepm/YEARM; /* age just before transition, d or d-1? */
/* agexact=age+((h-1)hstepm + (d-1))stepm/YEARM; /\* age just before transition \/ /	/* agexact=age+((h-1)hstepm + (d-1))stepm/YEARM; /\* age just before transition \/ /
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<=cptcovn;k++){
cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];	/* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
/* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */	/* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; \/ /
	cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
	/* printf("hbxij Dummy agexact=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agexact,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */

	}
for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */	for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */
/* cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; /	/* cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; /
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];
Line 3135 double *hbxij(double *po, int nhstep	Line 3240 double *hbxij(double *po, int nhstep
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; /	/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; /


/printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);/	/printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);/
/printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);/	/printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);/
/* Careful transposed matrix */	/* Careful transposed matrix */
/* age is in cov[2] */	/* age is in cov[2], prevacurrent at beginning of transition. */
/* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */	/* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
/* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */	/* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\	out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
Line 3596 double funcone( double *x)	Line 3700 double funcone( double *x)
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 */
	/* for(d=0; d<=0; d++){ /\* Delay between two effective waves Only one matrix to speed up\/ /
/*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]+dstepm/YEARM; / Here d is needed */
cov[2]=agexact;	cov[2]=agexact;
if(nagesqr==1)	if(nagesqr==1)
cov[3]= agexact*agexact;	cov[3]= agexact*agexact;
Line 4100 void ludcmp(double *a, int n, int indx	Line 4205 void ludcmp(double *a, int n, int indx
big=0.0;	big=0.0;
for (j=1;j<=n;j++)	for (j=1;j<=n;j++)
if ((temp=fabs(a[i][j])) > big) big=temp;	if ((temp=fabs(a[i][j])) > big) big=temp;
if (big == 0.0) nrerror("Singular matrix in routine ludcmp");	if (big == 0.0){
	printf(" Singular Hessian matrix at row %d:\n",i);
	for (j=1;j<=n;j++) {
	printf(" a[%d][%d]=%f,",i,j,a[i][j]);
	fprintf(ficlog," a[%d][%d]=%f,",i,j,a[i][j]);
	}
	fflush(ficlog);
	fclose(ficlog);
	nrerror("Singular matrix in routine ludcmp");
	}
vv[i]=1.0/big;	vv[i]=1.0/big;
}	}
for (j=1;j<=n;j++) {	for (j=1;j<=n;j++) {
Line 4166 void pstamp(FILE *fichier)	Line 4280 void pstamp(FILE *fichier)
fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);	fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
}	}

	int linreg(int ifi, int ila, int no, const double x[], const double y[], double a, double* b, double* r, double* sa, double * sb) {

	/* y=a+bx regression */
	double sumx = 0.0; /* sum of x */
	double sumx2 = 0.0; /* sum of x*2 /
	double sumxy = 0.0; /* sum of x * y */
	double sumy = 0.0; /* sum of y */
	double sumy2 = 0.0; /* sum of y*2 /
	double sume2; /* sum of square or residuals */
	double yhat;

	double denom=0;
	int i;
	int ne=*no;

	for ( i=ifi, ne=0;i<=ila;i++) {
	if(!isfinite(x[i]) \|\| !isfinite(y[i])){
	/* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
	continue;
	}
	ne=ne+1;
	sumx += x[i];
	sumx2 += x[i]*x[i];
	sumxy += x[i] * y[i];
	sumy += y[i];
	sumy2 += y[i]*y[i];
	denom = (ne * sumx2 - sumx*sumx);
	/* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
	}

	denom = (ne * sumx2 - sumx*sumx);
	if (denom == 0) {
	// vertical, slope m is infinity
	*b = INFINITY;
	*a = 0;
	if (r) *r = 0;
	return 1;
	}

	b = (ne sumxy - sumx * sumy) / denom;
	a = (sumy sumx2 - sumx * sumxy) / denom;
	if (r!=NULL) {
	r = (sumxy - sumx sumy / ne) / /* compute correlation coeff */
	sqrt((sumx2 - sumxsumx/ne)
	(sumy2 - sumy*sumy/ne));
	}
	*no=ne;
	for ( i=ifi, ne=0;i<=ila;i++) {
	if(!isfinite(x[i]) \|\| !isfinite(y[i])){
	/* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
	continue;
	}
	ne=ne+1;
	yhat = y[i] - a -b* x[i];
	sume2 += yhat * yhat ;

	denom = (ne * sumx2 - sumx*sumx);
	/* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
	}
	sb = sqrt(sume2/(ne-2)/(sumx2 - sumx sumx /ne));
	sa= sb * sqrt(sumx2/ne);

	return 0;
	}

/********** Frequencies ******************/	/********** Frequencies ******************/
void freqsummary(char fileres[], int iagemin, int iagemax, int s, double agev, int nlstate, int imx, \	void freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int s, double agev, int nlstate, int imx, \
int Tvaraff, int invalidvarcomb, int *nbcode, int ncodemax,double mint,double anint, char strstart[], \	int Tvaraff, int invalidvarcomb, int *nbcode, int ncodemax,double mint,double anint, char strstart[], \
int firstpass, int lastpass, int stepm, int weightopt, char model[])	int firstpass, int lastpass, int stepm, int weightopt, char model[])
{ /* Some frequencies */	{ /* Some frequencies as well as proposing some starting values */

int i, m, jk, j1, bool, z1,j, k, iv;	int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1;
int iind=0, iage=0;	int iind=0, iage=0;
int mi; /* Effective wave */	int mi; /* Effective wave */
int first;	int first;
double **freq; / Frequencies */	double **freq; / Frequencies */
	double x, y, a,b,r, sa, sb; /* for regression, y=b+mx and r is the correlation coefficient /
	int no;
double *meanq;	double *meanq;
double **meanqt;	double **meanqt;
double pp, prop, posprop, *pospropt;	double pp, prop, posprop, *pospropt;
Line 4185 void freqsummary(char fileres[], int ia	Line 4366 void freqsummary(char fileres[], int ia
double agebegin, ageend;	double agebegin, ageend;

pp=vector(1,nlstate);	pp=vector(1,nlstate);
prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);	prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */	posprop=vector(1,nlstate); /* Counting the number of transition starting from a live state per age */
pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */	pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
/* prop=matrix(1,nlstate,iagemin,iagemax+3); */	/* prop=matrix(1,nlstate,iagemin,iagemax+3); */
Line 4229 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4410 Title=%s <br>Datafile=%s Firstpass=%d La
}	}
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);	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);	y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
	x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
	freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin-AGEMARGE,iagemax+4+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;

/* 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
Line 4244 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4426 Title=%s <br>Datafile=%s Firstpass=%d La
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
*/	*/
	dateintsum=0;
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 */	k2cpt=0;
posproptt=0.;
/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);	if(cptcoveff == 0 )
scanf("%d", i);*/	nl=1; /* Constant and age model only */
for (i=-5; i<=nlstate+ndeath; i++)	else
for (jk=-5; jk<=nlstate+ndeath; jk++)	nl=2;

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

	for (i=1; i<=nlstate; i++) {
for(m=iagemin; m <= iagemax+3; m++)	for(m=iagemin; m <= iagemax+3; m++)
freq[i][jk][m]=0;	prop[i][m]=0;
	posprop[i]=0;
for (i=1; i<=nlstate; i++) {	pospropt[i]=0;
for(m=iagemin; m <= iagemax+3; m++)	}
prop[i][m]=0;	/* for (z1=1; z1<= nqfveff; z1++) { */
posprop[i]=0;	/* meanq[z1]+=0.; */
pospropt[i]=0;	/* for(m=1;m<=lastpass;m++){ */
}	/* meanqt[m][z1]=0.; */
/* for (z1=1; z1<= nqfveff; z1++) { */	/* } */
/* meanq[z1]+=0.; */	/* } */
/* for(m=1;m<=lastpass;m++){ */
/* meanqt[m][z1]=0.; */	/* dateintsum=0; */
/* } */	/* k2cpt=0; */
/* } */
	/* For that combination of covariates j1 (V4=1 V3=0 for example), we count and print the frequencies in one pass */
dateintsum=0;	for (iind=1; iind<=imx; iind++) { /* For each individual iind */
k2cpt=0;	bool=1;
/* For that combination of covariate j1, we count and print the frequencies in one pass */	if(j !=0){
for (iind=1; iind<=imx; iind++) { /* For each individual iind */	if(anyvaryingduminmodel==0){ /* If All fixed covariates */
bool=1;	if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
if(anyvaryingduminmodel==0){ /* If All fixed covariates */	/* for (z1=1; z1<= nqfveff; z1++) { */
if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */	/* meanq[z1]+=coqvar[Tvar[z1]][iind]; /\* Computes mean of quantitative with selected filter \/ /
/* for (z1=1; z1<= nqfveff; z1++) { */	/* } */
/* meanq[z1]+=coqvar[Tvar[z1]][iind]; /\* Computes mean of quantitative with selected filter \/ /	for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
/* } */	/* if(Tvaraff[z1] ==-20){ */
for (z1=1; z1<=cptcoveff; z1++) {	/* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; \/ /
/* if(Tvaraff[z1] ==-20){ */	/* }else if(Tvaraff[z1] ==-10){ */
/* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; \/ /	/* /\* sumnew+=coqvar[z1][iind]; \/ /
/* }else if(Tvaraff[z1] ==-10){ */	/* }else */
/* /\* sumnew+=coqvar[z1][iind]; \/ /	if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */
/* }else */	/* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */
if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){	bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
/* Tests if this individual iind responded to j1 (V4=1 V3=0) */	/* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",
bool=0;	bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),
/* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",	j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),	/* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/	} /* Onlyf fixed */
/* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/	} /* end z1 */
} /* Onlyf fixed */	} /* cptcovn > 0 */
} /* end z1 */	} /* end any */
} /* cptcovn > 0 */	}/* end j==0 */
} /* end any */	if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */
if (bool==1){ /* We selected an individual iind satisfying combination j1 or all fixed */	/* for(m=firstpass; m<=lastpass; m++){ */
/* for(m=firstpass; m<=lastpass; m++){ */	for(mi=1; mi<wav[iind];mi++){ /* For that wave */
for(mi=1; mi<wav[iind];mi++){ /* For that wave */	m=mw[mi][iind];
m=mw[mi][iind];	if(j!=0){
if(anyvaryingduminmodel==1){ /* Some are varying covariates */	if(anyvaryingduminmodel==1){ /* Some are varying covariates */
for (z1=1; z1<=cptcoveff; z1++) {	for (z1=1; z1<=cptcoveff; z1++) {
if( Fixed[Tmodelind[z1]]==1){	if( Fixed[Tmodelind[z1]]==1){
iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;	iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */	if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality. If covariate's
bool=0;	value is -1, we don't select. It differs from the
}else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */	constant and age model which counts them. */
if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {	bool=0; /* not selected */
bool=0;	}else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
	if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {
	bool=0;
	}
	}
}	}
	}/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */
	} /* end j==0 */
	/* bool =0 we keep that guy which corresponds to the combination of dummy values */
	if(bool==1){
	/* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
	and mw[mi+1][iind]. dh depends on stepm. */
	agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
	ageend=agev[m][iind]+(dh[m][iind])stepm/YEARM; / Age at end of wave and transition */
	if(m >=firstpass && m <=lastpass){
	k2=anint[m][iind]+(mint[m][iind]/12.);
	/if ((k2>=dateprev1) && (k2<=dateprev2)) {/
	if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */
	if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */
	if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */
	prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
	if (m<lastpass) {
	/* if(s[m][iind]==4 && s[m+1][iind]==4) */
	/* printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind]); */
	if(s[m][iind]==-1)
	printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));
	freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
	/* if((int)agev[m][iind] == 55) */
	/* printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
	/* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
	freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 // At age of beginning of transition, where status is known */
	}
	} /* end if between passes */
	if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99) && (j==0)) {
	dateintsum=dateintsum+k2; /* on all covariates ?*/
	k2cpt++;
	/* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */
}	}
}	}else{
}/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */	bool=1;
/* bool =0 we keep that guy which corresponds to the combination of dummy values */	}/* end bool 2 */
if(bool==1){	} /* end m */
/* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]	} /* end bool */
and mw[mi+1][iind]. dh depends on stepm. */	} /* end iind = 1 to imx */
agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/	/* prop[s][age] is feeded for any initial and valid live state as well as
ageend=agev[m][iind]+(dh[m][iind])stepm/YEARM; / Age at end of wave and transition */	freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */
if(m >=firstpass && m <=lastpass){
k2=anint[m][iind]+(mint[m][iind]/12.);
/if ((k2>=dateprev1) && (k2<=dateprev2)) {/	/* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
if(agev[m][iind]==0) agev[m][iind]=iagemax+1; /* All ages equal to 0 are in iagemax+1 */	if(cptcoveff==0 && nj==1) /* no covariate and first pass */
if(agev[m][iind]==1) agev[m][iind]=iagemax+2; /* All ages equal to 1 are in iagemax+2 */	pstamp(ficresp);
if (s[m][iind]>0 && s[m][iind]<=nlstate) /* If status at wave m is known and a live state */	if (cptcoveff>0 && j!=0){
prop[s[m][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */	pstamp(ficresp);
if (m<lastpass) {	printf( "\n#********** Variable ");
/* if(s[m][iind]==4 && s[m+1][iind]==4) */	fprintf(ficresp, "\n#********** Variable ");
/* printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind]); */	fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
if(s[m][iind]==-1)	fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));	fprintf(ficlog, "\n#********** Variable ");
freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */	for (z1=1; z1<=cptcoveff; z1++){
/* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */	if(!FixedV[Tvaraff[z1]]){
freq[s[m][iind]][s[m+1][iind]][iagemax+3] += weight[iind]; /* Total is in iagemax+3 // At age of beginning of transition, where status is known */	printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
}	fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
} /* end if between passes */	fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
if ((agev[m][iind]>1) && (agev[m][iind]< (iagemax+3)) && (anint[m][iind]!=9999) && (mint[m][iind]!=99)) {	fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
dateintsum=dateintsum+k2;	fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
k2cpt++;	}else{
/* printf("iind=%ld dateintmean = %lf dateintsum=%lf k2cpt=%lf k2=%lf\n",iind, dateintsum/k2cpt, dateintsum,k2cpt, k2); */	printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
}	fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
} /* end bool 2 */	fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
} /* end m */	fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
} /* end bool */	fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
} /* end iind = 1 to imx */	}
/* 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 */	printf( "**********\n#");
	fprintf(ficresp, "**********\n#");
	fprintf(ficresphtm, "**********</h3>\n");
/* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/	fprintf(ficresphtmfr, "**********</h3>\n");
pstamp(ficresp);	fprintf(ficlog, "**********\n");
if (cptcoveff>0){	}
fprintf(ficresp, "\n#********** Variable ");	fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");	if((cptcoveff==0 && nj==1)\|\| nj==2 ) /* no covariate and first pass */
fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");	fprintf(ficresp, " Age");
fprintf(ficlog, "\n#********** Variable ");	if(nj==2) for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " V%d=%d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
for (z1=1; z1<=cptcoveff; z1++){	for(i=1; i<=nlstate;i++) {
if(DummyV[z1]){	if((cptcoveff==0 && nj==1)\|\| nj==2 ) fprintf(ficresp," Prev(%d) N(%d) N ",i,i);
fprintf(ficresp, "V%d (fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
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)]);	if((cptcoveff==0 && nj==1)\|\| nj==2 ) fprintf(ficresp, "\n");
fprintf(ficlog, "V%d (fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	fprintf(ficresphtm, "\n");

	/* Header of frequency table by age */
	fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
	fprintf(ficresphtmfr,"<th>Age</th> ");
	for(s2=-1; s2 <=nlstate+ndeath; s2++){
	for(m=-1; m <=nlstate+ndeath; m++){
	if(s2!=0 && m!=0)
	fprintf(ficresphtmfr,"<th>%d%d</th> ",s2,m);
	}
	}
	fprintf(ficresphtmfr, "\n");

	/* For each age */
	for(iage=iagemin; iage <= iagemax+3; iage++){
	fprintf(ficresphtm,"<tr>");
	if(iage==iagemax+1){
	fprintf(ficlog,"1");
	fprintf(ficresphtmfr,"<tr><th>0</th> ");
	}else if(iage==iagemax+2){
	fprintf(ficlog,"0");
	fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
	}else if(iage==iagemax+3){
	fprintf(ficlog,"Total");
	fprintf(ficresphtmfr,"<tr><th>Total</th> ");
}else{	}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(ficresphtm, "**********</h3>\n");
fprintf(ficresphtmfr, "**********</h3>\n");
fprintf(ficlog, "**********\n");
}
fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
for(i=1; i<=nlstate;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(ficresp, "\n");
fprintf(ficresphtm, "\n");

/* Header of frequency table by age */
fprintf(ficresphtmfr,"<table style=\"text-align:center; border: 1px solid\">");
fprintf(ficresphtmfr,"<th>Age</th> ");
for(jk=-1; jk <=nlstate+ndeath; jk++){
for(m=-1; m <=nlstate+ndeath; m++){
if(jk!=0 && m!=0)
fprintf(ficresphtmfr,"<th>%d%d</th> ",jk,m);
}
}
fprintf(ficresphtmfr, "\n");

/* For each age */
for(iage=iagemin; iage <= iagemax+3; iage++){
fprintf(ficresphtm,"<tr>");
if(iage==iagemax+1){
fprintf(ficlog,"1");
fprintf(ficresphtmfr,"<tr><th>0</th> ");
}else if(iage==iagemax+2){
fprintf(ficlog,"0");
fprintf(ficresphtmfr,"<tr><th>Unknown</th> ");
}else if(iage==iagemax+3){
fprintf(ficlog,"Total");
fprintf(ficresphtmfr,"<tr><th>Total</th> ");
}else{
if(first==1){
first=0;
printf("See log file for details...\n");
}
fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
fprintf(ficlog,"Age %d", iage);
}
for(jk=1; jk <=nlstate ; jk++){
for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
pp[jk] += freq[jk][m][iage];
}
for(jk=1; jk <=nlstate ; jk++){
for(m=-1, pos=0; m <=0 ; m++)
pos += freq[jk][m][iage];
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]);	first=0;
	printf("See log file for details...\n");
	}
	fprintf(ficresphtmfr,"<tr><th>%d</th> ",iage);
	fprintf(ficlog,"Age %d", iage);
	}
	for(s1=1; s1 <=nlstate ; s1++){
	for(m=-1, pp[s1]=0; m <=nlstate+ndeath ; m++)
	pp[s1] += freq[s1][m][iage];
	}
	for(s1=1; s1 <=nlstate ; s1++){
	for(m=-1, pos=0; m <=0 ; m++)
	pos += freq[s1][m][iage];
	if(pp[s1]>=1.e-10){
	if(first==1){
	printf(" %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
	}
	fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",s1,pp[s1],s1,100*pos/pp[s1]);
	}else{
	if(first==1)
	printf(" %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
	fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",s1,pp[s1],s1);
}	}
fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
}else{
if(first==1)
printf(" %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(s1=1; s1 <=nlstate ; s1++){
/* posprop[jk]=0; */	/* posprop[s1]=0; */
for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */	for(m=0, pp[s1]=0; m <=nlstate+ndeath; m++)/* Summing on all ages */
pp[jk] += freq[jk][m][iage];	pp[s1] += freq[s1][m][iage];
} /* pp[jk] is the total number of transitions starting from state jk and any ending status until this age */	} /* pp[s1] is the total number of transitions starting from state s1 and any ending status until this age */

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

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

	printf("\n");
	fprintf(ficlog,"\n");
	} /* end j=0 */
	} /* end j */

	if(mle == -2){ /* We want to use these values as starting values */
	for(i=1, jk=1; i <=nlstate; i++){
	for(j=1; j <=nlstate+ndeath; j++){
	if(j!=i){
	/ca[0]= k+'a'-1;ca[1]='\0';/
	printf("%1d%1d",i,j);
	fprintf(ficparo,"%1d%1d",i,j);
	for(k=1; k<=ncovmodel;k++){
	/* printf(" %lf",param[i][j][k]); */
	/* fprintf(ficparo," %lf",param[i][j][k]); */
	p[jk]=pstart[jk];
	printf(" %f ",pstart[jk]);
	fprintf(ficparo," %f ",pstart[jk]);
	jk++;
	}
	printf("\n");
	fprintf(ficparo,"\n");
	}
}	}
}	}
fprintf(ficresphtm,"</tr>\n");	} /* end mle=-2 */
fprintf(ficresphtm,"</table>\n");
fprintf(ficresphtmfr,"</table>\n");
if(posproptt < 1.e-5){
fprintf(ficresphtm,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
fprintf(ficresphtmfr,"\n <p><b> This combination (%d) is not valid and no result will be produced</b></p>",j1);
fprintf(ficres,"\n This combination (%d) is not valid and no result will be produced\n\n",j1);
invalidvarcomb[j1]=1;
}else{
fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);
invalidvarcomb[j1]=0;
}
fprintf(ficresphtmfr,"</table>\n");
} /* end selected combination of covariate j1 */
dateintmean=dateintsum/k2cpt;	dateintmean=dateintsum/k2cpt;

fclose(ficresp);	fclose(ficresp);
Line 4522 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4888 Title=%s <br>Datafile=%s Firstpass=%d La
fclose(ficresphtmfr);	fclose(ficresphtmfr);
free_vector(meanq,1,nqfveff);	free_vector(meanq,1,nqfveff);
free_matrix(meanqt,1,lastpass,1,nqtveff);	free_matrix(meanqt,1,lastpass,1,nqtveff);
free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+3+AGEMARGE);	free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
	free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
	free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
free_vector(pospropt,1,nlstate);	free_vector(pospropt,1,nlstate);
free_vector(posprop,1,nlstate);	free_vector(posprop,1,nlstate);
free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+3+AGEMARGE);	free_matrix(prop,1,nlstate,iagemin-AGEMARGE, iagemax+4+AGEMARGE);
free_vector(pp,1,nlstate);	free_vector(pp,1,nlstate);
/* End of freqsummary */	/* End of freqsummary */
}	}
Line 4552 void prevalence(double ***probs, double	Line 4920 void prevalence(double ***probs, double
iagemin= (int) agemin;	iagemin= (int) agemin;
iagemax= (int) agemax;	iagemax= (int) agemax;
/pp=vector(1,nlstate);/	/pp=vector(1,nlstate);/
prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+3+AGEMARGE);	prop=matrix(1,nlstate,iagemin-AGEMARGE,iagemax+4+AGEMARGE);
/* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/	/* freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
j1=0;	j1=0;

Line 4562 void prevalence(double ***probs, double	Line 4930 void prevalence(double ***probs, double
first=1;	first=1;
for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */	for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
for (i=1; i<=nlstate; i++)	for (i=1; i<=nlstate; i++)
for(iage=iagemin-AGEMARGE; iage <= iagemax+3+AGEMARGE; iage++)	for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
prop[i][iage]=0.0;	prop[i][iage]=0.0;
printf("Prevalence combination of varying and fixed dummies %d\n",j1);	printf("Prevalence combination of varying and fixed dummies %d\n",j1);
/* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */	/* fprintf(ficlog," V%d=%d ",Tvaraff[j1],nbcode[Tvaraff[j1]][codtabm(k,j1)]); */
Line 4593 void prevalence(double ***probs, double	Line 4961 void prevalence(double ***probs, double
if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */	if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
if(agev[m][i]==0) agev[m][i]=iagemax+1;	if(agev[m][i]==0) agev[m][i]=iagemax+1;
if(agev[m][i]==1) agev[m][i]=iagemax+2;	if(agev[m][i]==1) agev[m][i]=iagemax+2;
if((int)agev[m][i] <iagemin-AGEMARGE \|\| (int)agev[m][i] >iagemax+3+AGEMARGE){	if((int)agev[m][i] <iagemin-AGEMARGE \|\| (int)agev[m][i] >iagemax+4+AGEMARGE){
printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m);	printf("Error on individual # %d agev[m][i]=%f <%d-%d or > %d+3+%d m=%d; either change agemin or agemax or fix data\n",i, agev[m][i],iagemin,AGEMARGE, iagemax,AGEMARGE,m);
exit(1);	exit(1);
}	}
Line 4619 void prevalence(double ***probs, double	Line 4987 void prevalence(double ***probs, double
} else{	} else{
if(first==1){	if(first==1){
first=0;	first=0;
printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,j1,probs[i][jk][j1]);	printf("Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);
	fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);
	}else{
	fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);
}	}
}	}
}	}
Line 4630 void prevalence(double ***probs, double	Line 5001 void prevalence(double ***probs, double

/* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/	/* free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
/free_vector(pp,1,nlstate);/	/free_vector(pp,1,nlstate);/
free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+3+AGEMARGE);	free_matrix(prop,1,nlstate, iagemin-AGEMARGE,iagemax+4+AGEMARGE);
} /* End of prevalence */	} /* End of prevalence */

/*********** Waves Concatenation *************/	/*********** Waves Concatenation *************/
Line 4679 void concatwav(int wav[], int **dh, int	Line 5050 void concatwav(int wav[], int **dh, int
#else	#else
if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){	if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){
if(firsthree == 0){	if(firsthree == 0){
printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);	printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p%d%d .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);
firsthree=1;	firsthree=1;
}	}
fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as pi. .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m);	fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p%d%d .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);
mw[++mi][i]=m;	mw[++mi][i]=m;
mli=m;	mli=m;
}	}
Line 4709 void concatwav(int wav[], int **dh, int	Line 5080 void concatwav(int wav[], int **dh, int
/* if(mi==0) never been interviewed correctly before death */	/* if(mi==0) never been interviewed correctly before death */
/* Only death is a correct wave */	/* Only death is a correct wave */
mw[mi][i]=m;	mw[mi][i]=m;
}	} /* else not in a death state */
#ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE	#ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
else if ((int) andc[i] != 9999) { /* Status is negative. A death occured after lastpass, we can't take it into account because of potential bias */	else if ((int) andc[i] != 9999) { /* Date of death is known */
/* m++; */
/* mi++; */
/* s[m][i]=nlstate+1; /\* We are setting the status to the last of non live state \/ /
/* mw[mi][i]=m; */
if ((int)anint[m][i]!= 9999) { /* date of last interview is known */	if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */	if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */
nbwarn++;	nbwarn++;
Line 4728 void concatwav(int wav[], int **dh, int	Line 5095 void concatwav(int wav[], int **dh, int
}else{ /* Death occured afer last wave potential bias */	}else{ /* Death occured afer last wave potential bias */
nberr++;	nberr++;
if(firstwo==0){	if(firstwo==0){
printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );	printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
firstwo=1;	firstwo=1;
}	}
fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );	fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\n\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
}	}
}else{ /* end date of interview is known */	}else{ /* if date of interview is unknown */
/* death is known but not confirmed by death status at any wave */	/* death is known but not confirmed by death status at any wave */
if(firstfour==0){	if(firstfour==0){
printf("Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );	printf("Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );
Line 4764 void concatwav(int wav[], int **dh, int	Line 5131 void concatwav(int wav[], int **dh, int
if (stepm <=0)	if (stepm <=0)
dh[mi][i]=1;	dh[mi][i]=1;
else{	else{
if (s[mw[mi+1][i]][i] > nlstate) { /* A death */	if (s[mw[mi+1][i]][i] > nlstate) { /* A death, but what if date is unknown? */
if (agedc[i] < 2*AGESUP) {	if (agedc[i] < 2*AGESUP) {
j= rint(agedc[i]12-agev[mw[mi][i]][i]12);	j= rint(agedc[i]12-agev[mw[mi][i]][i]12);
if(j==0) j=1; /* Survives at least one month after exam */	if(j==0) j=1; /* Survives at least one month after exam */
Line 5861 void varprob(char optionfilefiname[], do	Line 6228 void varprob(char optionfilefiname[], do
fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");	fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
fprintf(fichtm,"\n");	fprintf(fichtm,"\n");

fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back.</li>\n",optionfilehtmcov);	fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back. %s</li>\n",optionfilehtmcov,optionfilehtmcov);
fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);	fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \	fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
and drawn. It helps understanding how is the covariance between two incidences.\	and drawn. It helps understanding how is the covariance between two incidences.\
Line 6078 To be simple, these graphs help to under	Line 6445 To be simple, these graphs help to under
fprintf(ficgp,"\nset parametric;unset label");	fprintf(ficgp,"\nset parametric;unset label");
fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);	fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
fprintf(ficgp,"\nset ter svg size 640, 480");	fprintf(ficgp,"\nset ter svg size 640, 480");
fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\	fprintf(fichtmcov,"\n<p><br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
:<a href=\"%s_%d%1d%1d-%1d%1d.svg\"> \	:<a href=\"%s_%d%1d%1d-%1d%1d.svg\"> \
%s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\	%s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \	subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \
Line 6089 To be simple, these graphs help to under	Line 6456 To be simple, these graphs help to under
fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);	fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);	fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)), %11.3e +%.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)) not", \	fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)), %11.3e +%.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)) not", \
mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \	mu1,std,v11,sqrt(lc1),v12,sqrt(fabs(lc2)), \
mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));	mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(lc2))); /* For gnuplot only */
}else{	}else{
first=0;	first=0;
fprintf(fichtmcov," %d (%.3f),",(int) age, c12);	fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);	fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);	fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
fprintf(ficgp,"\nreplot %11.3e+ %.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)), %11.3e +%.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)) not", \	fprintf(ficgp,"\nreplot %11.3e+ %.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)), %11.3e +%.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)) not", \
mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \	mu1,std,v11,sqrt(lc1),v12,sqrt(fabs(lc2)), \
mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));	mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(lc2)));
}/* if first */	}/* if first */
} /* age mod 5 */	} /* age mod 5 */
} /* end loop age */	} /* end loop age */
Line 6126 To be simple, these graphs help to under	Line 6493 To be simple, these graphs help to under
void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \	void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
int lastpass, int stepm, int weightopt, char model[],\	int lastpass, int stepm, int weightopt, char model[],\
int imx,int jmin, int jmax, double jmeanint,char rfileres[],\	int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
int popforecast, int prevfcast, int backcast, int estepm , \	int popforecast, int mobilav, int prevfcast, int mobilavproj, int backcast, int estepm , \
double jprev1, double mprev1,double anprev1, double dateprev1, \	double jprev1, double mprev1,double anprev1, double dateprev1, \
double jprev2, double mprev2,double anprev2, double dateprev2){	double jprev2, double mprev2,double anprev2, double dateprev2){
int jj1, k1, i1, cpt, k4, nres;	int jj1, k1, i1, cpt, k4, nres;
Line 6164 void printinghtml(char fileresu[], char	Line 6531 void printinghtml(char fileresu[], char
<a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));	<a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileresu,"F_"),subdirf2(fileresu,"F_"));
}	}

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

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

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

	jj1=0;

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

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

jj1=0;	jj1=0;

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

fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");	fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
for (cpt=1; cpt<=cptcoveff;cpt++){	for (cpt=1; cpt<=cptcoveff;cpt++){
fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);	fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
Line 6200 void printinghtml(char fileresu[], char	Line 6612 void printinghtml(char fileresu[], char
}	}
}	}
/* aij, bij */	/* aij, bij */
fprintf(fichtm,"<br>- Logit model (yours is: 1+age+%s), for example: logit(pij)=log(pij/pii)= aij+ bij age + V1 age + etc. as a function of age: <a href=\"%s_%d-1-%d.svg\">%s_%d-1-%d.svg</a><br> \	fprintf(fichtm,"<br>- Logit model (yours is: logit(pij)=log(pij/pii)= aij+ bij age+%s) as a function of age: <a href=\"%s_%d-1-%d.svg\">%s_%d-1-%d.svg</a><br> \
<img src=\"%s_%d-1-%d.svg\">",model,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);	<img src=\"%s_%d-1-%d.svg\">",model,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);
/* Pij */	/* Pij */
fprintf(fichtm,"<br>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2-%d.svg\">%s_%d-2-%d.svg</a><br> \	fprintf(fichtm,"<br>\n- P<sub>ij</sub> or conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s_%d-2-%d.svg\">%s_%d-2-%d.svg</a><br> \
Line 6224 divided by h: <sub>h</sub>P<sub>ij</sub>	Line 6636 divided by h: <sub>h</sub>P<sub>ij</sub>
}	}
/* Period (stable) prevalence in each health state */	/* Period (stable) prevalence in each health state */
for(cpt=1; cpt<=nlstate;cpt++){	for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \	fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability for a person being in state (1 to %d) at different ages, to be in state %d some years after. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
<img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);	<img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
}	}
if(backcast==1){	if(backcast==1){
/* Period (stable) back prevalence in each health state */	/* Period (stable) back prevalence in each health state */
for(cpt=1; cpt<=nlstate;cpt++){	for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"<br>\n- Convergence to period (stable) back prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \	fprintf(fichtm,"<br>\n- Convergence to mixed (stable) back prevalence in state %d. Or probability for a person to be in state %d at a younger age, knowing that she/he was in state (1 to %d) at different older ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
<img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);	<img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
}	}
}	}
if(prevfcast==1){	if(prevfcast==1){
/* Projection of prevalence up to period (stable) prevalence in each health state */	/* Projection of prevalence up to period (stable) prevalence in each health state */
for(cpt=1; cpt<=nlstate;cpt++){	for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \	fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d) up to period (stable) prevalence in state %d. Or probability to be in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
<img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);	<img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
}	}
}	}

Line 6305 See page 'Matrix of variance-covariance	Line 6717 See page 'Matrix of variance-covariance

for(nres=1; nres <= nresult; nres++){ /* For each resultline */	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)	if(m != 1 && TKresult[nres]!= k1)
continue;	continue;
/* for(i1=1; i1<=ncodemax[k1];i1++){ */	/* for(i1=1; i1<=ncodemax[k1];i1++){ */
jj1++;	jj1++;
Line 6326 See page 'Matrix of variance-covariance	Line 6738 See page 'Matrix of variance-covariance
}	}
}	}
for(cpt=1; cpt<=nlstate;cpt++) {	for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"\n<br>- Observed (cross-sectional) and period (incidence based) \	fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \
prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d-%d.svg\"> %s_%d-%d-%d.svg</a>\n <br>\	prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d-%d.svg\"> %s_%d-%d-%d.svg</a>\n <br>\
<img src=\"%s_%d-%d-%d.svg\">",cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);	<img src=\"%s_%d-%d-%d.svg\">",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
}	}
fprintf(fichtm,"\n<br>- Total life expectancy by age and \	fprintf(fichtm,"\n<br>- Total life expectancy by age and \
health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \	health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
Line 6344 true period expectancies (those weighted	Line 6756 true period expectancies (those weighted
}	}

/***************** Gnuplot file ************/	/***************** Gnuplot file ************/
void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){	void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[], int offyear){

char dirfileres[132],optfileres[132];	char dirfileres[132],optfileres[132];
char gplotcondition[132];	char gplotcondition[132], gplotlabel[132];
int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,k4=0,ij=0, ijp=0, l=0;	int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,k4=0,ij=0, ijp=0, l=0;
int lv=0, vlv=0, kl=0;	int lv=0, vlv=0, kl=0;
int ng=0;	int ng=0;
int vpopbased;	int vpopbased;
int ioffset; /* variable offset for columns */	int ioffset; /* variable offset for columns */
int nres=0; /* Index of resultline */	int nres=0; /* Index of resultline */
	int istart=1; /* For starting graphs in projections */

/* 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 6401 void printinggnuplot(char fileresu[], ch	Line 6814 void printinggnuplot(char fileresu[], ch
for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */	for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
/* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */	/* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
if(TKresult[nres]!= k1)	if(m != 1 && TKresult[nres]!= k1)
continue;	continue;
/* We are interested in selected combination by the resultline */	/* We are interested in selected combination by the resultline */
/* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */	/* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt);	fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt);
	strcpy(gplotlabel,"(");
for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */	for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */	lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
Line 6415 void printinggnuplot(char fileresu[], ch	Line 6829 void printinggnuplot(char fileresu[], ch
/* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */	/* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */
/* printf(" V%d=%d ",Tvaraff[k],vlv); */	/* printf(" V%d=%d ",Tvaraff[k],vlv); */
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
/* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */	/* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	}
	strcpy(gplotlabel+strlen(gplotlabel),")");
/* printf("\n#\n"); */	/* printf("\n#\n"); */
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
	/k1=k1-1;/ /* To be checked */
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
continue;	continue;
}	}

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

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

if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */	if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
/* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */	/* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */	fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
Line 6474 void printinggnuplot(char fileresu[], ch	Line 6921 void printinggnuplot(char fileresu[], ch
} /* end covariate */	} /* end covariate */
} /* end if no covariate */	} /* end if no covariate */
} /* end if backcast */	} /* end if backcast */
fprintf(ficgp,"\nset out \n");	fprintf(ficgp,"\nset out ;unset label;\n");
} /* nres */	} /* nres */
} /* k1 */	} /* k1 */
} /* cpt */	} /* cpt */
Line 6483 void printinggnuplot(char fileresu[], ch	Line 6930 void printinggnuplot(char fileresu[], ch
/2 eme/	/2 eme/
for (k1=1; k1<= m ; k1 ++){	for (k1=1; k1<= m ; k1 ++){
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
if(TKresult[nres]!= k1)	if(m != 1 && TKresult[nres]!= k1)
continue;	continue;
fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");	fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
	strcpy(gplotlabel,"(");
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
Line 6493 void printinggnuplot(char fileresu[], ch	Line 6941 void printinggnuplot(char fileresu[], ch
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];	vlv= nbcode[Tvaraff[k]][lv];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
/* for(k=1; k <= ncovds; k++){ */	/* for(k=1; k <= ncovds; k++){ */
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}
	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
Line 6507 void printinggnuplot(char fileresu[], ch	Line 6958 void printinggnuplot(char fileresu[], ch

fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);	fprintf(ficgp,"\nset out \"%s_%d-%d.svg\" \n",subdirf2(optionfilefiname,"E_"),k1,nres);
for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/	for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
if(vpopbased==0)	fprintf(ficgp,"\nset label \"popbased %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",vpopbased,gplotlabel);
	if(vpopbased==0){
fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);	fprintf(ficgp,"set ylabel \"Years\" \nset ter svg size 640, 480\nplot [%.f:%.f] ",ageminpar,fage);
else	}else
fprintf(ficgp,"\nreplot ");	fprintf(ficgp,"\nreplot ");
for (i=1; i<= nlstate+1 ; i ++) {	for (i=1; i<= nlstate+1 ; i ++) {
k=2*i;	k=2*i;
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1, vpopbased);	fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ?$4 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1, vpopbased);
for (j=1; j<= nlstate+1 ; j ++) {	for (j=1; j<= nlstate+1 ; j ++) {
if (j==i) fprintf(ficgp," %%lf (%%lf)");	if (j==i) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%lf (%%lf)");	else fprintf(ficgp," %%lf (%%lf)");
}	}
if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);	if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l lt %d, \\\n",i);
else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);	else fprintf(ficgp,"\" t\"LE in state (%d)\" w l lt %d, \\\n",i-1,i+1);
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);	fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4-$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
for (j=1; j<= nlstate+1 ; j ++) {	for (j=1; j<= nlstate+1 ; j ++) {
if (j==i) fprintf(ficgp," %%lf (%%lf)");	if (j==i) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%lf (%%lf)");	else fprintf(ficgp," %%lf (%%lf)");
}	}
fprintf(ficgp,"\" t\"\" w l lt 0,");	fprintf(ficgp,"\" t\"\" w l lt 0,");
fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),k1-1,k1-1,vpopbased);	fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2==%d && $4!=0 ? $4+$5*2 : 1/0) \"%%lf %%lf %%lf",subdirf2(fileresu,"T_"),nres-1,nres-1,vpopbased);
for (j=1; j<= nlstate+1 ; j ++) {	for (j=1; j<= nlstate+1 ; j ++) {
if (j==i) fprintf(ficgp," %%lf (%%lf)");	if (j==i) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%lf (%%lf)");	else fprintf(ficgp," %%lf (%%lf)");
Line 6535 void printinggnuplot(char fileresu[], ch	Line 6987 void printinggnuplot(char fileresu[], ch
else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");	else fprintf(ficgp,"\" t\"\" w l lt 0,\\\n");
} /* state */	} /* state */
} /* vpopbased */	} /* vpopbased */
fprintf(ficgp,"\nset out;set out \"%s_%d-%d.svg\"; replot; set out; \n",subdirf2(optionfilefiname,"E_"),k1,nres); /* Buggy gnuplot */	fprintf(ficgp,"\nset out;set out \"%s_%d-%d.svg\"; replot; set out; unset label;\n",subdirf2(optionfilefiname,"E_"),k1,nres); /* Buggy gnuplot */
} /* end nres */	} /* end nres */
} /* k1 end 2 eme*/	} /* k1 end 2 eme*/

Line 6543 void printinggnuplot(char fileresu[], ch	Line 6995 void printinggnuplot(char fileresu[], ch
/3eme/	/3eme/
for (k1=1; k1<= m ; k1 ++){	for (k1=1; k1<= m ; k1 ++){
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
if(TKresult[nres]!= k1)	if(m != 1 && TKresult[nres]!= k1)
continue;	continue;

for (cpt=1; cpt<= nlstate ; cpt ++) {	for (cpt=1; cpt<= nlstate ; cpt ++) {
fprintf(ficgp,"\n# 3d: Life expectancy with EXP_ files: combination=%d state=%d",k1, cpt);	fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files: combination=%d state=%d",k1, cpt);
	strcpy(gplotlabel,"(");
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
Line 6555 void printinggnuplot(char fileresu[], ch	Line 7008 void printinggnuplot(char fileresu[], ch
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];	vlv= nbcode[Tvaraff[k]][lv];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}
	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
Line 6568 void printinggnuplot(char fileresu[], ch	Line 7024 void printinggnuplot(char fileresu[], ch
/* k=2+nlstate(2cpt-2); */	/* k=2+nlstate(2cpt-2); */
k=2+(nlstate+1)*(cpt-1);	k=2+(nlstate+1)*(cpt-1);
fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
	fprintf(ficgp,"set label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);
fprintf(ficgp,"set ter svg size 640, 480\n\	fprintf(ficgp,"set ter svg size 640, 480\n\
plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),k1-1,k1-1,k,cpt);	plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileresu,"E_"),nres-1,nres-1,k,cpt);
/fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);	/fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");	for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
fprintf(ficgp,"\" t \"e%d1\" w l",cpt);	fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
Line 6579 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 7036 plot [%.f:%.f] \"%s\" every :::%d::%d u

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

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

Line 6592 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 7050 plot [%.f:%.f] \"%s\" every :::%d::%d u
/* 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 covariate and each value */	for (k1=1; k1<=m; k1++){ /* For each covariate and each value */
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
if(TKresult[nres]!= k1)	if(m != 1 && TKresult[nres]!= k1)
continue;	continue;
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
	strcpy(gplotlabel,"(");
fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);	fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
Line 6603 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 7062 plot [%.f:%.f] \"%s\" every :::%d::%d u
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];	vlv= nbcode[Tvaraff[k]][lv];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}
	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
Line 6614 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 7076 plot [%.f:%.f] \"%s\" every :::%d::%d u
}	}

fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
	fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);	set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
k=3;	k=3;
Line 6629 set ter svg size 640, 480\nunset log y\n	Line 7092 set ter svg size 640, 480\nunset log y\n
fprintf(ficgp,"+$%d",k+l+j-1);	fprintf(ficgp,"+$%d",k+l+j-1);
fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);	fprintf(ficgp,")) t \"l(%d,%d)\" w l",i,cpt);
} /* nlstate */	} /* nlstate */
fprintf(ficgp,"\nset out\n");	fprintf(ficgp,"\nset out; unset label;\n");
} /* end cpt state*/	} /* end cpt state*/
} /* end nres */	} /* end nres */
} /* end covariate k1 */	} /* end covariate k1 */
Line 6638 set ter svg size 640, 480\nunset log y\n	Line 7101 set ter svg size 640, 480\nunset log y\n
/* 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 combination if any */	for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
if(TKresult[nres]!= k1)	if(m != 1 && TKresult[nres]!= k1)
continue;	continue;
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
	strcpy(gplotlabel,"(");
fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);	fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
Line 6649 set ter svg size 640, 480\nunset log y\n	Line 7113 set ter svg size 640, 480\nunset log y\n
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];	vlv= nbcode[Tvaraff[k]][lv];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}
	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
Line 6660 set ter svg size 640, 480\nunset log y\n	Line 7127 set ter svg size 640, 480\nunset log y\n
}	}

fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
	fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability to be alive\" \n\
set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);	set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
k=3;	k=3;
Line 6683 set ter svg size 640, 480\nunset log y\n	Line 7151 set ter svg size 640, 480\nunset log y\n
else	else
fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);	fprintf(ficgp,"$%d) t\"l(%d,.)\" w l",k+l,cpt);
}	}
fprintf(ficgp,"\nset out\n");	fprintf(ficgp,"\nset out; unset label;\n");
} /* end cpt state*/	} /* end cpt state*/
} /* end covariate */	} /* end covariate */
} /* end nres */	} /* end nres */
Line 6692 set ter svg size 640, 480\nunset log y\n	Line 7160 set ter svg size 640, 480\nunset log y\n
/* CV preval stable (period) for each covariate */	/* CV preval stable (period) for each covariate */
for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */	for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
if(TKresult[nres]!= k1)	if(m != 1 && TKresult[nres]!= k1)
continue;	continue;
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
	strcpy(gplotlabel,"(");
fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);	fprintf(ficgp,"\n#\n#\n#CV preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
Line 6704 set ter svg size 640, 480\nunset log y\n	Line 7172 set ter svg size 640, 480\nunset log y\n
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];	vlv= nbcode[Tvaraff[k]][lv];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}
	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
Line 6715 set ter svg size 640, 480\nunset log y\n	Line 7186 set ter svg size 640, 480\nunset log y\n
}	}

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

Line 6739 set ter svg size 640, 480\nunset log y\n	Line 7211 set ter svg size 640, 480\nunset log y\n
/* 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 if any */	for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
if(TKresult[nres]!= k1)	if(m != 1 && TKresult[nres]!= k1)
continue;	continue;
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life ending state */
fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);	strcpy(gplotlabel,"(");
	fprintf(ficgp,"\n#\n#\n#CV Back preval stable (period): 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
Line 6750 set ter svg size 640, 480\nunset log y\n	Line 7223 set ter svg size 640, 480\nunset log y\n
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];	vlv= nbcode[Tvaraff[k]][lv];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}
	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
Line 6761 set ter svg size 640, 480\nunset log y\n	Line 7237 set ter svg size 640, 480\nunset log y\n
}	}

fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
	fprintf(ficgp,"set label \"Ending alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);	set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
k=3; /* Offset */	k=3; /* Offset */
for (i=1; i<= nlstate ; i ++){	for (i=1; i<= nlstate ; i ++){ /* State of origin */
if(i==1)	if(i==1)
fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));	fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
else	else
fprintf(ficgp,", '' ");	fprintf(ficgp,", '' ");
/* l=(nlstate+ndeath)(i-1)+1; /	/* l=(nlstate+ndeath)(i-1)+1; /
l=(nlstate+ndeath)*(cpt-1)+1;	l=(nlstate+ndeath)(cpt-1)+1; / fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2(nlstate+ndeath) /
/* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier \/ /	/* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier \/ /
/* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier \/ /	/* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier \/ /
fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+(cpt-1)+i-1); /* a vérifier */	fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */
/* for (j=2; j<= nlstate ; j ++) */	/* for (j=2; j<= nlstate ; j ++) */
/* fprintf(ficgp,"+$%d",k+l+j-1); */	/* fprintf(ficgp,"+$%d",k+l+j-1); */
/* /\* fprintf(ficgp,"+$%d",k+l+j-1); \/ /	/* /\* fprintf(ficgp,"+$%d",k+l+j-1); \/ /
fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);	fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);
} /* nlstate */	} /* nlstate */
fprintf(ficgp,"\nset out\n");	fprintf(ficgp,"\nset out; unset label;\n");
} /* end cpt state*/	} /* end cpt state*/
} /* end covariate */	} /* end covariate */
} /* End if backcast */	} /* End if backcast */
Line 6790 set ter svg size 640, 480\nunset log y\n	Line 7267 set ter svg size 640, 480\nunset log y\n

for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */	for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
if(TKresult[nres]!= k1)	if(m != 1 && TKresult[nres]!= k1)
continue;	continue;
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
	strcpy(gplotlabel,"(");
fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);	fprintf(ficgp,"\n#\n#\n#Projection of prevalence to stable (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */	for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
Line 6801 set ter svg size 640, 480\nunset log y\n	Line 7279 set ter svg size 640, 480\nunset log y\n
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];	vlv= nbcode[Tvaraff[k]][lv];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}
	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
Line 6813 set ter svg size 640, 480\nunset log y\n	Line 7294 set ter svg size 640, 480\nunset log y\n

fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");	fprintf(ficgp,"# hpijx=probability over h years, hp.jx is weighted by observed prev\n ");
fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
	fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);	set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
	/* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 \/ /
	istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
	/istart=1;/ /* Could be one if by state, but nlstate+1 is w.i projection only */
	for (i=istart; 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 /
/# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3/	/# 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 /
if(i==1){	if(i==istart){
fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));	fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
}else{	}else{
fprintf(ficgp,",\\\n '' ");	fprintf(ficgp,",\\\n '' ");
Line 6832 set ter svg size 640, 480\nunset log y\n	Line 7318 set ter svg size 640, 480\nunset log y\n
/# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4/	/# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4/
/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 /	/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 /
fprintf(ficgp," u %d:(", ioffset);	fprintf(ficgp," u %d:(", ioffset);
if(i==nlstate+1)	if(i==nlstate+1){
fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ", \	fprintf(ficgp," $%d/(1.-$%d)):5 t 'pw.%d' with line lc variable ", \
ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)nlstate,cpt );	ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)nlstate,cpt );
else	fprintf(ficgp,",\\\n '' ");
	fprintf(ficgp," u %d:(",ioffset);
	fprintf(ficgp," (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", \
	offyear, \
	ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)nlstate,cpt );
	}else
fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \	fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)nlstate,i,cpt );	ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)nlstate,i,cpt );
}else{ /* more than 2 covariates */	}else{ /* more than 2 covariates */
Line 6867 set ter svg size 640, 480\nunset log y\n	Line 7358 set ter svg size 640, 480\nunset log y\n
/6+1+(i-1)+(nlstate+1)nlstate; 6+1+(1-1) +(2+1)2=13 /	/6+1+(i-1)+(nlstate+1)nlstate; 6+1+(1-1) +(2+1)2=13 /
/* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/	/* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
if(i==nlstate+1){	if(i==nlstate+1){
fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \	fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0):5 t 'p.%d' with line lc variable", gplotcondition, \
	ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)nlstate,cpt );
	fprintf(ficgp,",\\\n '' ");
	fprintf(ficgp," u %d:(",ioffset);
	fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", gplotcondition, \
	offyear, \
ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)nlstate,cpt );	ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)nlstate,cpt );
	/* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
}else{	}else{
fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \	fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)nlstate,i,cpt );	ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)nlstate,i,cpt );
}	}
} /* end if covariate */	} /* end if covariate */
} /* nlstate */	} /* nlstate */
fprintf(ficgp,"\nset out\n");	fprintf(ficgp,"\nset out; unset label;\n");
} /* end cpt state*/	} /* end cpt state*/
} /* end covariate */	} /* end covariate */
} /* End if prevfcast */	} /* End if prevfcast */
Line 6918 set ter svg size 640, 480\nunset log y\n	Line 7415 set ter svg size 640, 480\nunset log y\n
fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");	fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
fprintf(ficgp,"#model=%s \n",model);	fprintf(ficgp,"#model=%s \n",model);
fprintf(ficgp,"# Type of graphic ng=%d\n",ng);	fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
fprintf(ficgp,"# jk=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */	fprintf(ficgp,"# k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
for(jk=1; jk <=m; jk++) /* For each combination of covariate */	for(k1=1; k1 <=m; k1++) /* For each combination of covariate */
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
if(TKresult[nres]!= jk)	if(m != 1 && TKresult[nres]!= k1)
continue;	continue;
fprintf(ficgp,"# Combination of dummy jk=%d and ",jk);	fprintf(ficgp,"\n\n# Combination of dummy k1=%d which is ",k1);
	strcpy(gplotlabel,"(");
	sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);
	for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */
	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
	vlv= nbcode[Tvaraff[k]][lv];
	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}
	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),jk,ng,nres);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);
	fprintf(ficgp,"\nset label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);
fprintf(ficgp,"\nset ter svg size 640, 480 ");	fprintf(ficgp,"\nset ter svg size 640, 480 ");
if (ng==1){	if (ng==1){
fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12x) could be nice /	fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12x) could be nice /
Line 6978 set ter svg size 640, 480\nunset log y\n	Line 7489 set ter svg size 640, 480\nunset log y\n
fprintf(ficgp,"+p%d%dx",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;	fprintf(ficgp,"+p%d%dx",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
}else{ /* quantitative */	}else{ /* quantitative */
fprintf(ficgp,"+p%d%fx",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */	fprintf(ficgp,"+p%d%fx",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
/* fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */	/* fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
}	}
ij++;	ij++;
}	}
Line 6987 set ter svg size 640, 480\nunset log y\n	Line 7498 set ter svg size 640, 480\nunset log y\n
if(ijp <=cptcovprod) { /* Product */	if(ijp <=cptcovprod) { /* Product */
if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */	if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */	if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
/* fprintf(ficgp,"+p%d%d%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(jk,j)],nbcode[Tvard[ijp][2]][codtabm(jk,j)]); */	/* fprintf(ficgp,"+p%d%d%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */
fprintf(ficgp,"+p%d%d%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);	fprintf(ficgp,"+p%d%d%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
}else{ /* Vn is dummy and Vm is quanti */	}else{ /* Vn is dummy and Vm is quanti */
/* fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(jk,j)],Tqinvresult[nres][Tvard[ijp][2]]); */	/* fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);	fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
}	}
}else{ /* VnVm Vn is quanti /	}else{ /* VnVm Vn is quanti /
Line 7003 set ter svg size 640, 480\nunset log y\n	Line 7514 set ter svg size 640, 480\nunset log y\n
ijp++;	ijp++;
}	}
} else{ /* simple covariate */	} else{ /* simple covariate */
/* fprintf(ficgp,"+p%d%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(jk,j)]); /\ Valgrind bug nbcode \/ /	/* fprintf(ficgp,"+p%d%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\ Valgrind bug nbcode \/ /
if(Dummy[j]==0){	if(Dummy[j]==0){
fprintf(ficgp,"+p%d%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); / */	fprintf(ficgp,"+p%d%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); / */
}else{ /* quantitative */	}else{ /* quantitative */
fprintf(ficgp,"+p%d%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); / */	fprintf(ficgp,"+p%d%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); / */
/* fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); */	/* fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
}	}
} /* end simple */	} /* end simple */
} /* end j */	} /* end j */
Line 7021 set ter svg size 640, 480\nunset log y\n	Line 7532 set ter svg size 640, 480\nunset log y\n
if(ng != 1){	if(ng != 1){
fprintf(ficgp,")/(1");	fprintf(ficgp,")/(1");

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

ij=1;	ij=1;
for(j=3; j <=ncovmodel-nagesqr; j++){	for(j=3; j <=ncovmodel-nagesqr; j++){
if((j-2)==Tage[ij]) { /* Bug valgrind */	if((j-2)==Tage[ij]) { /* Bug valgrind */
if(ij <=cptcovage) { /* Bug valgrind */	if(ij <=cptcovage) { /* Bug valgrind */
fprintf(ficgp,"+p%d%dx",k3+(k1-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);	fprintf(ficgp,"+p%d%dx",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);
/* fprintf(ficgp,"+p%d%dx",k3+(k1-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,Tvar[j-2])]); /	/* fprintf(ficgp,"+p%d%dx",k3+(cpt-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); /
ij++;	ij++;
}	}
}	}
else	else
fprintf(ficgp,"+p%d%d",k3+(k1-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(jk,j-2)]);/* Valgrind bug nbcode */	fprintf(ficgp,"+p%d%d",k3+(cpt-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);/* Valgrind bug nbcode */
}	}
fprintf(ficgp,")");	fprintf(ficgp,")");
}	}
Line 7057 set ter svg size 640, 480\nunset log y\n	Line 7568 set ter svg size 640, 480\nunset log y\n
i=i+ncovmodel;	i=i+ncovmodel;
} /* end k */	} /* end k */
} /* end k2 */	} /* end k2 */
fprintf(ficgp,"\n set out\n");	fprintf(ficgp,"\n set out; unset label;\n");
} /* end jk */	} /* end k1 */
} /* end ng */	} /* end ng */
/* avoid: */	/* avoid: */
fflush(ficgp);	fflush(ficgp);
Line 7074 set ter svg size 640, 480\nunset log y\n	Line 7585 set ter svg size 640, 480\nunset log y\n
int mobilavrange, mob;	int mobilavrange, mob;
int iage=0;	int iage=0;

double sum=0.;	double sum=0., sumr=0.;
double age;	double age;
double sumnewp, sumnewm;	double sumnewp, sumnewm, *sumnewmr;
double agemingood, agemaxgood; /* Currently identical for all covariates */	double agemingood, agemaxgood;
	double agemingoodr, agemaxgoodr;


/* modcovmax=2cptcoveff;/\ Max number of modalities. We suppose */	/* modcovmax=2cptcoveff;/\ Max number of modalities. We suppose */
Line 7085 set ter svg size 640, 480\nunset log y\n	Line 7597 set ter svg size 640, 480\nunset log y\n

sumnewp = vector(1,ncovcombmax);	sumnewp = vector(1,ncovcombmax);
sumnewm = vector(1,ncovcombmax);	sumnewm = vector(1,ncovcombmax);
	sumnewmr = vector(1,ncovcombmax);
agemingood = vector(1,ncovcombmax);	agemingood = vector(1,ncovcombmax);
	agemingoodr = vector(1,ncovcombmax);
agemaxgood = vector(1,ncovcombmax);	agemaxgood = vector(1,ncovcombmax);
	agemaxgoodr = vector(1,ncovcombmax);

for (cptcod=1;cptcod<=ncovcombmax;cptcod++){	for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
sumnewm[cptcod]=0.;	sumnewm[cptcod]=0.; sumnewmr[cptcod]=0.;
sumnewp[cptcod]=0.;	sumnewp[cptcod]=0.;
agemingood[cptcod]=0;	agemingood[cptcod]=0, agemingoodr[cptcod]=0;
agemaxgood[cptcod]=0;	agemaxgood[cptcod]=0, agemaxgoodr[cptcod]=0;
}	}
if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */	if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */

if(mobilav==1\|\|mobilav ==3 \|\|mobilav==5 \|\|mobilav== 7){	if(mobilav==-1 \|\| mobilav==1\|\|mobilav ==3 \|\|mobilav==5 \|\|mobilav== 7){
if(mobilav==1) mobilavrange=5; /* default */	if(mobilav==1 \|\| mobilav==-1) mobilavrange=5; /* default */
else mobilavrange=mobilav;	else mobilavrange=mobilav;
for (age=bage; age<=fage; age++)	for (age=bage; age<=fage; age++)
for (i=1; i<=nlstate;i++)	for (i=1; i<=nlstate;i++)
Line 7109 set ter svg size 640, 480\nunset log y\n	Line 7624 set ter svg size 640, 480\nunset log y\n
*/	*/
for (mob=3;mob <=mobilavrange;mob=mob+2){	for (mob=3;mob <=mobilavrange;mob=mob+2){
for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){	for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
for (i=1; i<=nlstate;i++){	for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
for (cptcod=1;cptcod<=ncovcombmax;cptcod++){	sumnewm[cptcod]=0.;
	for (i=1; i<=nlstate;i++){
mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];	mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
for (cpt=1;cpt<=(mob-1)/2;cpt++){	for (cpt=1;cpt<=(mob-1)/2;cpt++){
mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];	mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];	mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
}	}
mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;	mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
}	sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
}	} /* end i */
	if(sumnewm[cptcod] >1.e-3) mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/sumnewm[cptcod]; /* Rescaling to sum one */
	} /* end cptcod */
}/* end age */	}/* end age */
}/* end mob */	}/* end mob */
}else	}else{
	printf("Error internal in movingaverage, mobilav=%d.\n",mobilav);
return -1;	return -1;
for (cptcod=1;cptcod<=ncovcombmax;cptcod++){	}

	for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ /* for each combination */
/* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */	/* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
if(invalidvarcomb[cptcod]){	if(invalidvarcomb[cptcod]){
printf("\nCombination (%d) ignored because no cases \n",cptcod);	printf("\nCombination (%d) ignored because no cases \n",cptcod);
continue;	continue;
}	}

agemingood[cptcod]=fage-(mob-1)/2;	for (age=fage-(mob-1)/2; age>=bage+(mob-1)/2; age--){ /looking for the youngest and oldest good age /
for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */
sumnewm[cptcod]=0.;	sumnewm[cptcod]=0.;
	sumnewmr[cptcod]=0.;
for (i=1; i<=nlstate;i++){	for (i=1; i<=nlstate;i++){
sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];	sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
	sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
	}
	if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
	agemingoodr[cptcod]=age;
}	}
if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */	if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
agemingood[cptcod]=age;	agemingood[cptcod]=age;
}else{ /* bad */	}
for (i=1; i<=nlstate;i++){	} /* age */
mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];	for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ /looking for the youngest and oldest good age /
} /* i */
} /* end bad */
}/* age */
sum=0.;
for (i=1; i<=nlstate;i++){
sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];
}
if(fabs(sum - 1.) > 1.e-3) { /* bad */
printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any descending age!\n",cptcod);
/* for (i=1; i<=nlstate;i++){ */
/* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
/* } /\* i \/ /
} /* end bad */
/* else{ /\* We found some ages summing to one, we will smooth the oldest \/ /
/* From youngest, finding the oldest wrong */
agemaxgood[cptcod]=bage+(mob-1)/2;
for (age=bage+(mob-1)/2; age<=fage; age++){
sumnewm[cptcod]=0.;	sumnewm[cptcod]=0.;
	sumnewmr[cptcod]=0.;
for (i=1; i<=nlstate;i++){	for (i=1; i<=nlstate;i++){
sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];	sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
	sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
	}
	if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
	agemaxgoodr[cptcod]=age;
}	}
if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */	if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
agemaxgood[cptcod]=age;	agemaxgood[cptcod]=age;
}else{ /* bad */	}
for (i=1; i<=nlstate;i++){	} /* age */
mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];	/* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */
} /* i */	/* but they will change */
	for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */
	sumnewm[cptcod]=0.;
	sumnewmr[cptcod]=0.;
	for (i=1; i<=nlstate;i++){
	sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
	sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
	}
	if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
	if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
	agemaxgoodr[cptcod]=age; /* age min */
	for (i=1; i<=nlstate;i++)
	mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
	}else{ /* bad we change the value with the values of good ages */
	for (i=1; i<=nlstate;i++){
	mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgoodr[cptcod]][i][cptcod];
	} /* i */
	} /* end bad */
	}else{
	if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
	agemaxgood[cptcod]=age;
	}else{ /* bad we change the value with the values of good ages */
	for (i=1; i<=nlstate;i++){
	mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
	} /* i */
	} /* end bad */
	}/* end else */
	sum=0.;sumr=0.;
	for (i=1; i<=nlstate;i++){
	sum+=mobaverage[(int)age][i][cptcod];
	sumr+=probs[(int)age][i][cptcod];
	}
	if(fabs(sum - 1.) > 1.e-3) { /* bad */
	printf("Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, bage);
	} /* end bad */
	/* else{ /\* We found some ages summing to one, we will smooth the oldest \/ /
	if(fabs(sumr - 1.) > 1.e-3) { /* bad */
	printf("Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, bage);
} /* end bad */	} /* end bad */
}/* age */	}/* age */
sum=0.;
for (i=1; i<=nlstate;i++){	for (age=bage+(mob-1)/2; age<=fage; age++){/* From youngest, finding the oldest wrong */
sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];	sumnewm[cptcod]=0.;
}	sumnewmr[cptcod]=0.;
if(fabs(sum - 1.) > 1.e-3) { /* bad */	for (i=1; i<=nlstate;i++){
printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any ascending age!\n",cptcod);	sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
/* for (i=1; i<=nlstate;i++){ */	sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
/* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */	}
/* } /\* i \/ /	if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
} /* end bad */	if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good */
	agemingoodr[cptcod]=age;
	for (i=1; i<=nlstate;i++)
	mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
	}else{ /* bad we change the value with the values of good ages */
	for (i=1; i<=nlstate;i++){
	mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingoodr[cptcod]][i][cptcod];
	} /* i */
	} /* end bad */
	}else{
	if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
	agemingood[cptcod]=age;
	}else{ /* bad */
	for (i=1; i<=nlstate;i++){
	mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
	} /* i */
	} /* end bad */
	}/* end else */
	sum=0.;sumr=0.;
	for (i=1; i<=nlstate;i++){
	sum+=mobaverage[(int)age][i][cptcod];
	sumr+=mobaverage[(int)age][i][cptcod];
	}
	if(fabs(sum - 1.) > 1.e-3) { /* bad */
	printf("Moving average B1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you decrease fage=%d?\n",cptcod, sum, (int) age, fage);
	} /* end bad */
	/* else{ /\* We found some ages summing to one, we will smooth the oldest \/ /
	if(fabs(sumr - 1.) > 1.e-3) { /* bad */
	printf("Moving average B2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase fage=%d\n",cptcod,sumr, (int)age, fage);
	} /* end bad */
	}/* age */


for (age=bage; age<=fage; age++){	for (age=bage; age<=fage; age++){
/* printf("%d %d ", cptcod, (int)age); */	/* printf("%d %d ", cptcod, (int)age); */
Line 7194 set ter svg size 640, 480\nunset log y\n	Line 7775 set ter svg size 640, 480\nunset log y\n
}	}
/* printf("\n"); */	/* printf("\n"); */
/* } */	/* } */

/* brutal averaging */	/* brutal averaging */
for (i=1; i<=nlstate;i++){	/* for (i=1; i<=nlstate;i++){ */
for (age=1; age<=bage; age++){	/* for (age=1; age<=bage; age++){ */
mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];	/* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
/* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */	/* /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); \/ /
}	/* } */
for (age=fage; age<=AGESUP; age++){	/* for (age=fage; age<=AGESUP; age++){ */
mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];	/* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod]; */
/* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */	/* /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); \/ /
}	/* } */
} /* end i status */	/* } /\* end i status \/ /
for (i=nlstate+1; i<=nlstate+ndeath;i++){	/* for (i=nlstate+1; i<=nlstate+ndeath;i++){ */
for (age=1; age<=AGESUP; age++){	/* for (age=1; age<=AGESUP; age++){ */
/printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);/	/* /\printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);\/ */
mobaverage[(int)age][i][cptcod]=0.;	/* mobaverage[(int)age][i][cptcod]=0.; */
}	/* } */
}	/* } */
}/* end cptcod */	}/* end cptcod */
free_vector(sumnewm,1, ncovcombmax);	free_vector(agemaxgoodr,1, ncovcombmax);
free_vector(sumnewp,1, ncovcombmax);
free_vector(agemaxgood,1, ncovcombmax);	free_vector(agemaxgood,1, ncovcombmax);
free_vector(agemingood,1, ncovcombmax);	free_vector(agemingood,1, ncovcombmax);
	free_vector(agemingoodr,1, ncovcombmax);
	free_vector(sumnewmr,1, ncovcombmax);
	free_vector(sumnewm,1, ncovcombmax);
	free_vector(sumnewp,1, ncovcombmax);
return 0;	return 0;
}/* End movingaverage */	}/* End movingaverage */

Line 7283 set ter svg size 640, 480\nunset log y\n	Line 7868 set ter svg size 640, 480\nunset log y\n
/* if (h==(int)(YEARMyearp)){ /	/* if (h==(int)(YEARMyearp)){ /
for(nres=1; nres <= nresult; nres++) /* For each resultline */	for(nres=1; nres <= nresult; nres++) /* For each resultline */
for(k=1; k<=i1;k++){	for(k=1; k<=i1;k++){
if(TKresult[nres]!= k)	if(i1 != 1 && TKresult[nres]!= k)
continue;	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);
Line 7322 set ter svg size 640, 480\nunset log y\n	Line 7907 set ter svg size 640, 480\nunset log y\n
for(j=1; j<=nlstate+ndeath;j++) {	for(j=1; j<=nlstate+ndeath;j++) {
ppij=0.;	ppij=0.;
for(i=1; i<=nlstate;i++) {	for(i=1; i<=nlstate;i++) {
if (mobilav==1)	/* if (mobilav>=1) */
ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][k];	ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][k];
else {	/* else { / / even if mobilav==-1 we use mobaverage */
ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];	/* ppij=ppij+p3mat[i][j][h]probs[(int)(agec)][i][k]; /
}	/* } */
if (hhstepm/YEARMstepm== yearp) {	if (hhstepm/YEARMstepm== yearp) {
fprintf(ficresf," %.3f", p3mat[i][j][h]);	fprintf(ficresf," %.3f", p3mat[i][j][h]);
}	}
Line 7338 set ter svg size 640, 480\nunset log y\n	Line 7923 set ter svg size 640, 480\nunset log y\n
} /* end h */	} /* end h */
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
} /* end agec */	} /* end agec */
	/* diffyear=(int) anproj1+yearp-ageminpar-1; */
	/printf("Prevforecast %d+%d-%d=diffyear=%d\n",(int) anproj1, (int)yearp,(int)ageminpar,(int) anproj1-(int)ageminpar);/
} /* end yearp */	} /* end yearp */
} /* end k */	} /* end k */

Line 8234 int decoderesult ( char resultline[], in	Line 8821 int decoderesult ( char resultline[], in
if (strlen(resultsav) >1){	if (strlen(resultsav) >1){
j=nbocc(resultsav,'='); /*< j=Number of covariate values'=' /	j=nbocc(resultsav,'='); /*< j=Number of covariate values'=' /
}	}
	if(j == 0){ /* Resultline but no = */
	TKresult[nres]=0; /* Combination for the nresult and the model */
	return (0);
	}

if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */	if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
printf("ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);	printf("ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
fprintf(ficlog,"ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);	fprintf(ficlog,"ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
Line 8833 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 9425 Dummy[k] 0=dummy (0 1), 1 quantitative (
}	}

int calandcheckages(int imx, int maxwav, double agemin, double agemax, int nberr, int nbwarn )	int calandcheckages(int imx, int maxwav, double agemin, double agemax, int nberr, int nbwarn )
{	{/* Check ages at death */
int i, m;	int i, m;
int firstone=0;	int firstone=0;

Line 8848 int calandcheckages(int imx, int maxwav,	Line 9440 int calandcheckages(int imx, int maxwav,
nberr = nberr + 1;	nberr = nberr + 1;
if(firstone == 0){	if(firstone == 0){
firstone=1;	firstone=1;
printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\nOther similar cases in log file\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);	printf("Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we do not believe in a death, skipped.\nOther similar cases in log file\n", *nberr,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m);
}	}
fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results can be biased (%d) because status is a death state %d at wave %d. Wave dropped.\n",(int)moisdc[i],(int)andc[i],num[i],i, *nberr,s[m][i],m);	fprintf(ficlog,"Warning (#%d)! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown but status is a death state %d at wave %d. If you don't know the vital status, please enter -2. If he/she is still alive but don't know the state, please code with '-1 or '.'. Here, we do not believe in a death, skipped.\n", *nberr,(int)moisdc[i],(int)andc[i],num[i],i,s[m][i],m);
s[m][i]=-1;	s[m][i]=-1; /* Droping the death status */
}	}
if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){	if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
(*nberr)++;	(*nberr)++;
printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);	printf("Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\nOther similar cases in log file\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m);
fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);	fprintf(ficlog,"Error (#%d)! Month of death of individual %ld on line %d was unknown (%2d) (year of death is %4d) and status is a death state %d at wave %d. Please impute an arbitrary (or not) month and rerun. Currently this transition to death will be skipped (status is set to -2).\n", *nberr, num[i],i,(int)moisdc[i],(int)andc[i],s[m][i],m);
s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */	s[m][i]=-2; /* We prefer to skip it (and to skip it in version 0.8a1 too */
}	}
}	}
}	}
Line 9170 int prevalence_limit(double p, double	Line 9762 int prevalence_limit(double p, double

for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */	for(k=1; k<=i1;k++){ /* For each combination k of dummy covariates in the model */
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
if(TKresult[nres]!= k)	if(i1 != 1 && TKresult[nres]!= k)
continue;	continue;

/* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */	/* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
Line 9267 int back_prevalence_limit(double *p, dou	Line 9859 int back_prevalence_limit(double *p, dou

for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */	for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
if(TKresult[nres]!= k)	if(i1 != 1 && TKresult[nres]!= k)
continue;	continue;
//printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));	//printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));
fprintf(ficresplb,"#******");	fprintf(ficresplb,"#******");
Line 9314 int back_prevalence_limit(double *p, dou	Line 9906 int back_prevalence_limit(double *p, dou
}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,nres);	bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);
	/* printf("TOTOT\n"); */
	/* exit(1); */
}	}
fprintf(ficresplb,"%.0f ",age );	fprintf(ficresplb,"%.0f ",age );
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
Line 9326 int back_prevalence_limit(double *p, dou	Line 9920 int back_prevalence_limit(double *p, dou
fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);	fprintf(ficresplb," %.3f %d\n", tot, *ncvyearp);
} /* Age */	} /* Age */
/* was end of cptcod */	/* was end of cptcod */
	/fprintf(ficresplb,"\n");/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */
} /* end of any combination */	} /* end of any combination */
} /* end of nres */	} /* end of nres */
/* hBijx(p, bage, fage); */	/* hBijx(p, bage, fage); */
Line 9370 int hPijx(double *p, int bage, int fage)	Line 9965 int hPijx(double *p, int bage, int fage)
/* k=k+1; */	/* k=k+1; */
for(nres=1; nres <= nresult; nres++) /* For each resultline */	for(nres=1; nres <= nresult; nres++) /* For each resultline */
for(k=1; k<=i1;k++){	for(k=1; k<=i1;k++){
if(TKresult[nres]!= k)	if(i1 != 1 && TKresult[nres]!= k)
continue;	continue;
fprintf(ficrespij,"\n#****** ");	fprintf(ficrespij,"\n#****** ");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
Line 9442 int hPijx(double *p, int bage, int fage)	Line 10037 int hPijx(double *p, int bage, int fage)

/* hstepm=1; aff par mois*/	/* hstepm=1; aff par mois*/
pstamp(ficrespijb);	pstamp(ficrespijb);
fprintf(ficrespijb,"#****** h Pij x Back Probability to be in state i at age x-h being in j at x ");	fprintf(ficrespijb,"#****** h Bij x Back probability to be in state i at age x-h being in j at x: B1j+B2j+...=1 ");
i1= pow(2,cptcoveff);	i1= pow(2,cptcoveff);
/* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */	/* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
/* /\for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){\/ */	/* /\for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){\/ */
/* k=k+1; */	/* k=k+1; */
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */	for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
if(TKresult[nres]!= k)	if(i1 != 1 && TKresult[nres]!= k)
continue;	continue;
fprintf(ficrespijb,"\n#****** ");	fprintf(ficrespijb,"\n#****** ");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
Line 9458 int hPijx(double *p, int bage, int fage)	Line 10053 int hPijx(double *p, int bage, int fage)
fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
}	}
fprintf(ficrespijb,"******\n");	fprintf(ficrespijb,"******\n");
if(invalidvarcomb[k]){	if(invalidvarcomb[k]){ /* Is it necessary here? */
fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);	fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
continue;	continue;
}	}
Line 9471 int hPijx(double *p, int bage, int fage)	Line 10066 int hPijx(double *p, int bage, int fage)

/* nhstepm=nhstepmYEARM; aff par mois/	/* nhstepm=nhstepmYEARM; aff par mois/

p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
	/* and memory limitations if stepm is small */

/* oldm=oldms;savm=savms; */	/* oldm=oldms;savm=savms; */
/* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */	/* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);	hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);
/* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */	/* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
fprintf(ficrespijb,"# Cov Agex agex-h hpijx with i,j=");	fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate+ndeath;j++)	for(j=1; j<=nlstate+ndeath;j++)
fprintf(ficrespijb," %1d-%1d",i,j);	fprintf(ficrespijb," %1d-%1d",i,j);
Line 9522 int main(int argc, char *argv[])	Line 10119 int main(int argc, char *argv[])
int NDIM=2;	int NDIM=2;
int vpopbased=0;	int vpopbased=0;
int nres=0;	int nres=0;
	int endishere=0;

char ca[32], cb[32];	char ca[32], cb[32];
/* FILE fichtm; //* Html File */	/* FILE fichtm; //* Html File */
Line 9566 int main(int argc, char *argv[])	Line 10164 int main(int argc, char *argv[])
double **prlim;	double **prlim;
double **bprlim;	double **bprlim;
double **param; / Matrix of parameters */	double **param; / Matrix of parameters */
double *p;	double **paramstart; / Matrix of starting parameter values */
	double p, pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */
double *matcov; / Matrix of covariance */	double *matcov; / Matrix of covariance */
double *hess; / Hessian matrix */	double *hess; / Hessian matrix */
double **delti3; / Scale */	double **delti3; / Scale */
Line 9802 int main(int argc, char *argv[])	Line 10401 int main(int argc, char *argv[])
break;	break;
}	}
if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){	if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
if (num_filled == 0)	if (num_filled == 0){
model[0]='\0';	printf("ERROR %d: Model should be at minimum 'model=1+age.' WITHOUT space:'%s'\n",num_filled, line);
else if (num_filled != 1){	fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' WITHOUT space:'%s'\n",num_filled, line);
	model[0]='\0';
	goto end;
	} else if (num_filled != 1){
printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);	printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);	fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
model[0]='\0';	model[0]='\0';
Line 9877 int main(int argc, char *argv[])	Line 10479 int main(int argc, char *argv[])
delti=delti3[1][1];	delti=delti3[1][1];
/delti=vector(1,npar); //* Scale of each paramater (output from hesscov)*/	/delti=vector(1,npar); //* Scale of each paramater (output from hesscov)*/
if(mle==-1){ /* Print a wizard for help writing covariance matrix */	if(mle==-1){ /* Print a wizard for help writing covariance matrix */
	/* We could also provide initial parameters values giving by simple logistic regression
	* only one way, that is without matrix product. We will have nlstate maximizations */
	/* for(i=1;i<nlstate;i++){ */
	/* /\reducing xi for 1 to npar to 1 to ncovmodel; \/ */
	/* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
	/* } */
prwizard(ncovmodel, nlstate, ndeath, model, ficparo);	prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);	printf(" You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);	fprintf(ficlog," You chose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
Line 9906 int main(int argc, char *argv[])	Line 10514 int main(int argc, char *argv[])
ungetc(c,ficpar);	ungetc(c,ficpar);

param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);	param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
	paramstart= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
for(i=1; i <=nlstate; i++){	for(i=1; i <=nlstate; i++){
j=0;	j=0;
for(jj=1; jj <=nlstate+ndeath; jj++){	for(jj=1; jj <=nlstate+ndeath; jj++){
Line 9942 run imach with mle=-1 to get a correct t	Line 10551 run imach with mle=-1 to get a correct t
}	}
fflush(ficlog);	fflush(ficlog);

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

/* Reads comments: lines beginning with '#' */	/* Reads comments: lines beginning with '#' */
while((c=getc(ficpar))=='#' && c!= EOF){	while((c=getc(ficpar))=='#' && c!= EOF){
Line 10208 Please run with mle=-1 to get a correct	Line 10818 Please run with mle=-1 to get a correct
*/	*/

concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);	concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
/* */	/* Concatenates waves */

free_vector(moisdc,1,n);	free_vector(moisdc,1,n);
free_vector(andc,1,n);	free_vector(andc,1,n);
Line 10389 Title=%s <br>Datafile=%s Firstpass=%d La	Line 10999 Title=%s <br>Datafile=%s Firstpass=%d La
/* Calculates basic frequencies. Computes observed prevalence at single age	/* Calculates basic frequencies. Computes observed prevalence at single age
and for any valid combination of covariates	and for any valid combination of covariates
and prints on file fileres'p'. */	and prints on file fileres'p'. */
freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \	freqsummary(fileres, p, pstart, agemin, agemax, s, agev, nlstate, imx, Tvaraff, invalidvarcomb, nbcode, ncodemax,mint,anint,strstart, \
firstpass, lastpass, stepm, weightopt, model);	firstpass, lastpass, stepm, weightopt, model);

fprintf(fichtm,"\n");	fprintf(fichtm,"\n");
Line 10411 Interval (in months) between two waves:	Line 11021 Interval (in months) between two waves:
/* For mortality only */	/* For mortality only */
if (mle==-3){	if (mle==-3){
ximort=matrix(1,NDIM,1,NDIM);	ximort=matrix(1,NDIM,1,NDIM);
for(i=1;i<=NDIM;i++)	for(i=1;i<=NDIM;i++)
for(j=1;j<=NDIM;j++)	for(j=1;j<=NDIM;j++)
ximort[i][j]=0.;	ximort[i][j]=0.;
/* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */	/* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
cens=ivector(1,n);	cens=ivector(1,n);
ageexmed=vector(1,n);	ageexmed=vector(1,n);
Line 10649 Please run with mle=-1 to get a correct	Line 11259 Please run with mle=-1 to get a correct
printf("\n");	printf("\n");
if(mle>=1){ /* Could be 1 or 2, Real Maximization */	if(mle>=1){ /* Could be 1 or 2, Real Maximization */
/* mlikeli uses func not funcone */	/* mlikeli uses func not funcone */
	/* for(i=1;i<nlstate;i++){ */
	/* /\reducing xi for 1 to npar to 1 to ncovmodel; \/ */
	/* mlikeli(ficres,p, ncovmodel, ncovmodel, nlstate, ftol, funcnoprod); */
	/* } */
mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);	mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
}	}
if(mle==0) {/* No optimization, will print the likelihoods for the datafile */	if(mle==0) {/* No optimization, will print the likelihoods for the datafile */
Line 10864 Please run with mle=-1 to get a correct	Line 11478 Please run with mle=-1 to get a correct
fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);	fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d, ftolpl=%e\n",ageminpar,agemaxpar,bage,fage, estepm, ftolpl);

/* Other stuffs, more or less useful */	/* Other stuffs, more or less useful */
while((c=getc(ficpar))=='#' && c!= EOF){	while(fgets(line, MAXLINE, ficpar)) {
ungetc(c,ficpar);	/* If line starts with a # it is a comment */
fgets(line, MAXLINE, ficpar);	if (line[0] == '#') {
fputs(line,stdout);	numlinepar++;
fputs(line,ficparo);	fputs(line,stdout);
}	fputs(line,ficparo);
ungetc(c,ficpar);	fputs(line,ficlog);
	continue;
fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);	}else
fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);	break;
fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);

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


dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;

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

while((c=getc(ficpar))=='#' && c!= EOF){
ungetc(c,ficpar);
fgets(line, MAXLINE, ficpar);
fputs(line,stdout);
fputs(line,ficres);
fputs(line,ficparo);
}	}
ungetc(c,ficpar);
	if((num_filled=sscanf(line,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav)) !=EOF){
fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);	if (num_filled != 7) {
printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);	printf("Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);	fprintf(ficlog,"Error: Not 7 (data)parameters in line but %d, for example:begin-prev-date=1/1/1990 end-prev-date=1/6/2004 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);	goto end;
/* day and month of proj2 are not used but only year anproj2.*/	}
	printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
while((c=getc(ficpar))=='#' && c!= EOF){	fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
ungetc(c,ficpar);	fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
fgets(line, MAXLINE, ficpar);	fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
fputs(line,stdout);
fputs(line,ficparo);
fputs(line,ficres);
}	}
ungetc(c,ficpar);

fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);
fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
/* day and month of proj2 are not used but only year anproj2.*/

/* Results */
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 10935 Please run with mle=-1 to get a correct	Line 11510 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){
if (num_filled == 0){	dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
resultline[0]='\0';	dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
break;
} else if (num_filled != 1){	if((num_filled=sscanf(line,"pop_based=%d\n",&popbased)) !=EOF){
printf("ERROR %d: result line should be at minimum 'result=' %s\n",num_filled, line);	if (num_filled != 1) {
}	printf("Error: Not 1 (data)parameters in line but %d, for example:pop_based=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
nresult++; /* Sum of resultlines */	fprintf(ficlog,"Error: Not 1 (data)parameters in line but %d, for example: pop_based=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
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;	goto end;
}	}
decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */	printf("pop_based=%d\n",popbased);
fprintf(ficparo,"result: %s\n",resultline);	fprintf(ficlog,"pop_based=%d\n",popbased);
fprintf(ficres,"result: %s\n",resultline);	fprintf(ficparo,"pop_based=%d\n",popbased);
fprintf(ficlog,"result: %s\n",resultline);	fprintf(ficres,"pop_based=%d\n",popbased);
while(fgets(line, MAXLINE, ficpar)) {	}

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

/* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */	/* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint); */
/* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */	/* ,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2); */
Line 10991 Please run with mle=-1 to get a correct	Line 11631 Please run with mle=-1 to get a correct
This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\	This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);	Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
}else{	}else{
printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p);	printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)ageminpar);
}	}
printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \	printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
model,imx,jmin,jmax,jmean,rfileres,popforecast,prevfcast,backcast, estepm, \	model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,backcast, estepm, \
jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);	jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);

/------------ free_vector -------------/	/------------ free_vector -------------/
Line 11047 Please run with mle=-1 to get a correct	Line 11687 Please run with mle=-1 to get a correct
mobaverage=mobaverages;	mobaverage=mobaverages;
if (mobilav!=0) {	if (mobilav!=0) {
printf("Movingaveraging observed prevalence\n");	printf("Movingaveraging observed prevalence\n");
	fprintf(ficlog,"Movingaveraging observed prevalence\n");
if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){	if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilav)!=0){
fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);	fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
printf(" Error in movingaverage mobilav=%d\n",mobilav);	printf(" Error in movingaverage mobilav=%d\n",mobilav);
}	}
}	}
/* /\* Prevalence for each covariates in probs[age][status][cov] \/ /	/* else if(mobilavproj==-1){ /\* Forcing raw observed prevalences \/ /
/* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */	/* for(i=1;i<=AGESUP;i++) */
	/* for(j=1;j<=nlstate;j++) */
	/* for(k=1;k<=ncovcombmax;k++) */
	/* mobaverages[i][j][k]=probs[i][j][k]; */
	/* /\* /\\* 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); \/ /
	/* } */
else if (mobilavproj !=0) {	else if (mobilavproj !=0) {
printf("Movingaveraging projected observed prevalence\n");	printf("Movingaveraging projected observed prevalence\n");
	fprintf(ficlog,"Movingaveraging projected observed prevalence\n");
if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){	if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);	fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);	printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
Line 11118 Please run with mle=-1 to get a correct	Line 11766 Please run with mle=-1 to get a correct

for(nres=1; nres <= nresult; nres++) /* For each resultline */	for(nres=1; nres <= nresult; nres++) /* For each resultline */
for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */	for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
if(TKresult[nres]!= k)	if(i1 != 1 && TKresult[nres]!= k)
continue;	continue;
fprintf(ficreseij,"\n#****** ");	fprintf(ficreseij,"\n#****** ");
printf("\n#****** ");	printf("\n#****** ");
Line 11191 Please run with mle=-1 to get a correct	Line 11839 Please run with mle=-1 to get a correct

for(nres=1; nres <= nresult; nres++) /* For each resultline */	for(nres=1; nres <= nresult; nres++) /* For each resultline */
for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */	for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
if(TKresult[nres]!= k)	if(i1 != 1 && TKresult[nres]!= k)
continue;	continue;
printf("\n#****** Result for:");	printf("\n#****** Result for:");
fprintf(ficrest,"\n#****** Result for:");	fprintf(ficrest,"\n#****** Result for:");
Line 11332 Please run with mle=-1 to get a correct	Line 11980 Please run with mle=-1 to get a correct

for(nres=1; nres <= nresult; nres++) /* For each resultline */	for(nres=1; nres <= nresult; nres++) /* For each resultline */
for(k=1; k<=i1;k++){	for(k=1; k<=i1;k++){
if(TKresult[nres]!= k)	if(i1 != 1 && TKresult[nres]!= k)
continue;	continue;
fprintf(ficresvpl,"\n#****** ");	fprintf(ficresvpl,"\n#****** ");
printf("\n#****** ");	printf("\n#****** ");

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

Removed from v.1.246
changed lines
	Added in v.1.266