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Diff for /imach/src/imach.c between versions 1.339 and 1.345

version 1.339, 2022/09/09 17:55:22	version 1.345, 2022/09/16 13:40:11
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	Revision 1.345 2022/09/16 13:40:11 brouard
	Summary: Version 0.99r41

	* imach.c (Module): 0.99r41 Was an error when product of timevarying and fixed. Using FixedV[of name] now. Thank you Feinuo

	Revision 1.344 2022/09/14 19:33:30 brouard
	Summary: version 0.99r40

	* imach.c (Module): Fixing names of variables in T_ (thanks to Feinuo)

	Revision 1.343 2022/09/14 14:22:16 brouard
	Summary: version 0.99r39

	* imach.c (Module): Version 0.99r39 with colored dummy covariates
	(fixed or time varying), using new last columns of
	ILK_parameter.txt file.

	Revision 1.342 2022/09/11 19:54:09 brouard
	Summary: 0.99r38

	* imach.c (Module): Adding timevarying products of any kinds,
	should work before shifting cotvar from ncovcol+nqv columns in
	order to have a correspondance between the column of cotvar and
	the id of column.
	(Module): Some cleaning and adding covariates in ILK.txt

	Revision 1.341 2022/09/11 07:58:42 brouard
	Summary: Version 0.99r38

	After adding change in cotvar.

	Revision 1.340 2022/09/11 07:53:11 brouard
	Summary: Version imach 0.99r37

	* imach.c (Module): Adding timevarying products of any kinds,
	should work before shifting cotvar from ncovcol+nqv columns in
	order to have a correspondance between the column of cotvar and
	the id of column.

Revision 1.339 2022/09/09 17:55:22 brouard	Revision 1.339 2022/09/09 17:55:22 brouard
Summary: version 0.99r37	Summary: version 0.99r37

Line 1272 typedef struct {	Line 1311 typedef struct {
#define MAXLINE 2048 /* Was 256 and 1024. 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 GNUPLOTVERSION 5.1
	double gnuplotversion=GNUPLOTVERSION;
/#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"/	/#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"/
#define FILENAMELENGTH 256	#define FILENAMELENGTH 256

Line 1317 char fullversion[]="$Revision$ $Date$";	Line 1358 char fullversion[]="$Revision$ $Date$";
char strstart[80];	char strstart[80];
char optionfilext[10], optionfilefiname[FILENAMELENGTH];	char optionfilext[10], optionfilefiname[FILENAMELENGTH];
int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */	int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
	int debugILK=0; /* debugILK is set by a #d in a comment line */
int nagesqr=0, nforce=0; /* nagesqr=1 if model is including ageage, number of forces /	int nagesqr=0, nforce=0; /* nagesqr=1 if model is including ageage, number of forces /
/* Number of covariates model (1)=V2+V1+ V3age+V2V4 */	/* Number of covariates model (1)=V2+V1+ V3age+V2V4 */
/* Model(2) V1 + V2 + V3 + V8 + V7V8 + V5V6 + V8age + V3age + ageage /	/* Model(2) V1 + V2 + V3 + V8 + V7V8 + V5V6 + V8age + V3age + ageage /
Line 1495 double covar; /< covar[j,i], value	Line 1537 double covar; /< covar[j,i], value
* covar=matrix(0,NCOVMAX,1,n);	* covar=matrix(0,NCOVMAX,1,n);
* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]age; /	* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]age; /
double *coqvar; / Fixed quantitative covariate nqv */	double *coqvar; / Fixed quantitative covariate nqv */
double **cotvar; / Time varying covariate ntv */	double **cotvar; / Time varying covariate start at ncovcol + nqv + (1 to ntv) */
double **cotqvar; / Time varying quantitative covariate itqv */	double **cotqvar; / Time varying quantitative covariate itqv */
double idx;	double idx;
int *nbcode, Tvar; /*< model=V2 => Tvar[1]= 2 /	int *nbcode, Tvar; /*< model=V2 => Tvar[1]= 2 /
Line 1507 int *nbcode, Tvar; /**< model=V2 => Tv	Line 1549 int *nbcode, Tvar; /**< model=V2 => Tv
* cptcovn number of covariates (not including constant and age or age*age) = number of plus sign + 1 = 10+1=11	* cptcovn number of covariates (not including constant and age or age*age) = number of plus sign + 1 = 10+1=11
* For time varying covariate, quanti or dummies	* For time varying covariate, quanti or dummies
* cotqvar[wav][iv(1 to nqtv)][i]= [1][12][i]=(V12) quanti	* cotqvar[wav][iv(1 to nqtv)][i]= [1][12][i]=(V12) quanti
* cotvar[wav][ntv+iv][i]= [3+(1 to nqtv)][i]=(V12) quanti	* cotvar[wav][ncovcol+nqv+ iv(1 to nqtv)][i]= [(1 to nqtv)][i]=(V12) quanti
* cotvar[wav][iv(1 to ntv)][i]= [1][1][i]=(V9) dummies at wav 1	* cotvar[wav][iv(1 to ntv)][i]= [1][1][i]=(V9) dummies at wav 1
* cotvar[wav][iv(1 to ntv)][i]= [1][2][i]=(V10) dummies at wav 1	* cotvar[wav][iv(1 to ntv)][i]= [1][2][i]=(V10) dummies at wav 1
* covar[Vk,i], value of the Vkth fixed covariate dummy or quanti for individual i:	* covar[Vk,i], value of the Vkth fixed covariate dummy or quanti for individual i:
Line 1520 int *nbcode, Tvar; /**< model=V2 => Tv	Line 1562 int *nbcode, Tvar; /**< model=V2 => Tv
# States 1=Coresidence, 2 Living alone, 3 Institution	# States 1=Coresidence, 2 Living alone, 3 Institution
# V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi	# V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi
*/	*/
/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */	/* V5+V4+ V3+V4V3 +V5age+V2 +V1V2+V1age+V1 */
/* k 1 2 3 4 5 6 7 8 9 */	/* kmodel 1 2 3 4 5 6 7 8 9 */
/Typevar[k]= 0 0 0 2 1 0 2 1 0 //0 for simple covariate (dummy, quantitative,/	/Typevar[k]= 0 0 0 2 1 0 2 1 0 //0 for simple covariate (dummy, quantitative,/
/* fixed or varying), 1 for age product, 2 for*/	/* fixed or varying), 1 for age product, 2 for*/
/* product */	/* product */
Line 3880 double func( double *x)	Line 3922 double func( double *x)
int ioffset=0;	int ioffset=0;
int ipos=0,iposold=0,ncovv=0;	int ipos=0,iposold=0,ncovv=0;

	double cotvarv, cotvarvold;
double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];	double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
double **out;	double **out;
double lli; /* Individual log likelihood */	double lli; /* Individual log likelihood */
Line 3911 double func( double *x)	Line 3954 double func( double *x)
*/	*/
ioffset=2+nagesqr ;	ioffset=2+nagesqr ;
/* Fixed */	/* Fixed */
for (kf=1; kf<=ncovf;kf++){ /* For each fixed covariate dummu or quant or prod */	for (kf=1; kf<=ncovf;kf++){ /* For each fixed covariate dummy or quant or prod */
/* # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi */	/* # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi */
/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */	/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
/* TvarF[1]=Tvar[6]=2, TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1 ID of fixed covariates or product V2, V1V2, V1 /	/* TvarF[1]=Tvar[6]=2, TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1 ID of fixed covariates or product V2, V1V2, V1 /
Line 3927 double func( double *x)	Line 3970 double func( double *x)
mw[mi][i] is real wave of the mi th effectve wave */	mw[mi][i] is real wave of the mi th effectve wave */
/* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];	/* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
s2=s[mw[mi+1][i]][i];	s2=s[mw[mi+1][i]][i];
And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]	And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i] because now is moved after nvocol+nqv
But if the variable is not in the model TTvar[iv] is the real variable effective in the model:	But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]	meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
*/	*/
Line 3937 double func( double *x)	Line 3980 double func( double *x)
/* /\* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; but where is the crossproduct? \/ /	/* /\* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; but where is the crossproduct? \/ /
/* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i]; */	/* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i]; */
/* } */	/* } */
for(ncovv=1, ipos=0; ncovv <= ncovvt ; ncovv++){ /* Varying covariates (single and product but no age )*/	for(ncovv=1, iposold=0; ncovv <= ncovvt ; ncovv++){ /* Varying covariates (single and product but no age )*/
itv=TvarVV[ncovv]; /* TvarVV={3, 1, 3} */	itv=TvarVV[ncovv]; /* TvarVV={3, 1, 3} gives the name of each varying covariate */
ipos=TvarVVind[ncovv]; /* TvarVVind={2, 5, 5] */	ipos=TvarVVind[ncovv]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate*/
	if(FixedV[itv]!=0){ /* Not a fixed covariate */
	cotvarv=cotvar[mw[mi][i]][TvarVV[ncovv]][i]; /* cotvar[wav][ncovcol+nqv+iv][i] */
	}else{ /* fixed covariate */
	cotvarv=covar[itv][i]; /* Error: TvarFind gives the name, that is the true column of fixed covariates, but Tvar of the model */
	}
if(ipos!=iposold){ /* Not a product or first of a product */	if(ipos!=iposold){ /* Not a product or first of a product */
/* TvarFind={1,0,0,0} */	cotvarvold=cotvarv;
if(TvarFind[itv]==0){	}else{ /* A second product */
cov[ioffset+ipos]= cotvar[mw[mi][i]][ncovv][i]; /* Should be covar if fixed covar[Tvar[TvarFind[itv]]][i]*/	cotvarv=cotvarv*cotvarvold;
}else{
cov[ioffset+ipos]=covar[Tvar[TvarFind[itv]]][i];
}
}else{
if(TvarFind[itv]==0){
cov[ioffset+ipos]= cotvar[mw[mi][i]][ncovv][i]; / Should be covar if fixed covar[Tvar[TvarFind[itv]]][i]*/
}else{
cov[ioffset+ipos]*=covar[Tvar[TvarFind[itv]]][i];
}
}	}
iposold=ipos;	iposold=ipos;
/* For products */	cov[ioffset+ipos]=cotvarv;
}	}
/* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)\/ /	/* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)\/ /
/* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff \/ /	/* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff \/ /
Line 3988 double func( double *x)	Line 4027 double func( double *x)
if(!FixedV[Tvar[Tage[kk]]])	if(!FixedV[Tvar[Tage[kk]]])
cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]agexact; / Tage[kk] gives the data-covariate associated with age */	cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]agexact; / Tage[kk] gives the data-covariate associated with age */
else	else
cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]][i]*agexact;	cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]][i]agexact; / because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) */
}	}
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));	1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
Line 4084 double func( double *x)	Line 4123 double func( double *x)
}	}
/lli=(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]);/	/lli=(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]);/
/if(lli ==000.0)/	/if(lli ==000.0)/
/printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); /	/* printf("num[i], i=%d, bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
ipmx +=1;	ipmx +=1;
sw += weight[i];	sw += weight[i];
ll[s[mw[mi][i]][i]] += 2weight[i]lli;	ll[s[mw[mi][i]][i]] += 2weight[i]lli;
Line 4101 double func( double *x)	Line 4140 double func( double *x)
cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];	cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];
for(mi=1; mi<= wav[i]-1; mi++){	for(mi=1; mi<= wav[i]-1; mi++){
for(k=1; k <= ncovv ; k++){	for(k=1; k <= ncovv ; k++){
cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];	cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; /* because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) */
}	}
for (ii=1;ii<=nlstate+ndeath;ii++)	for (ii=1;ii<=nlstate+ndeath;ii++)
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
Line 4148 double func( double *x)	Line 4187 double func( double *x)
if(nagesqr==1)	if(nagesqr==1)
cov[3]= agexact*agexact;	cov[3]= agexact*agexact;
for (kk=1; kk<=cptcovage;kk++) {	for (kk=1; kk<=cptcovage;kk++) {
cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;	if(!FixedV[Tvar[Tage[kk]]])
	cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]agexact; / Tage[kk] gives the data-covariate associated with age */
	else
	cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]][i]agexact; / because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) */
}	}
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));	1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
Line 4204 double func( double *x)	Line 4246 double func( double *x)
ipmx +=1;	ipmx +=1;
sw += weight[i];	sw += weight[i];
ll[s[mw[mi][i]][i]] += 2weight[i]lli;	ll[s[mw[mi][i]][i]] += 2weight[i]lli;
/* printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */	/* printf("num[i]=%09ld, i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2])); */
} /* end of wave */	} /* end of wave */
} /* end of individual */	} /* end of individual */
}else{ /* ml=5 no inter-extrapolation no jackson =0.8a */	}else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
Line 4223 double func( double *x)	Line 4265 double func( double *x)
if(nagesqr==1)	if(nagesqr==1)
cov[3]= agexact*agexact;	cov[3]= agexact*agexact;
for (kk=1; kk<=cptcovage;kk++) {	for (kk=1; kk<=cptcovage;kk++) {
cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;	if(!FixedV[Tvar[Tage[kk]]])
	cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]agexact; / Tage[kk] gives the data-covariate associated with age */
	else
	cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]][i]agexact; / because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) */
}	}

out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
Line 4256 double funcone( double *x)	Line 4301 double funcone( double *x)
int ioffset=0;	int ioffset=0;
int ipos=0,iposold=0,ncovv=0;	int ipos=0,iposold=0,ncovv=0;

	double cotvarv, cotvarvold;
double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];	double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
double **out;	double **out;
double lli; /* Individual log likelihood */	double lli; /* Individual log likelihood */
Line 4310 double funcone( double *x)	Line 4356 double funcone( double *x)
mw[mi][i] is real wave of the mi th effectve wave */	mw[mi][i] is real wave of the mi th effectve wave */
/* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];	/* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
s2=s[mw[mi+1][i]][i];	s2=s[mw[mi+1][i]][i];
And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]	And the iv th varying covariate in the DATA is the cotvar[mw[mi+1][i]][ncovcol+nqv+iv][i]
But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
*/	*/
/* This part may be useless now because everythin should be in covar */	/* This part may be useless now because everythin should be in covar */
/* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products \/ /	/* for (k=1; k<=nqfveff;k++){ /\* Simple and product fixed Quantitative covariates without age* products \/ /
Line 4337 double funcone( double *x)	Line 4381 double funcone( double *x)
/* We need the position of the time varying or product in the model */	/* We need the position of the time varying or product in the model */
/* TvarVVind={2,5,5}, for V3 at position 2 and then the product V1V3 is decomposed into V1 and V3 but at same position 5 /	/* TvarVVind={2,5,5}, for V3 at position 2 and then the product V1V3 is decomposed into V1 and V3 but at same position 5 /
/* TvarVV gives the variable name */	/* TvarVV gives the variable name */
for(ncovv=1, ipos=0; ncovv <= ncovvt ; ncovv++){ /* Varying covariates (single and product but no age )*/	/* Other example V1 + V3 + V5 + ageV1 + ageV3 + ageV5 + V1V3 + V3V5 + V1V5
itv=TvarVV[ncovv]; /* TvarVV={3, 1, 3} */	* k= 1 2 3 4 5 6 7 8 9
ipos=TvarVVind[ncovv]; /* TvarVVind={2, 5, 5] */	* varying 1 2 3 4 5
	* ncovv 1 2 3 4 5 6 7 8
	* TvarVV[ncovv] V3 5 1 3 3 5 1 5
	* TvarVVind 2 3 7 7 8 8 9 9
	* TvarFind[k] 1 0 0 0 0 0 0 0 0
	*/
	/* Other model ncovcol=5 nqv=0 ntv=3 nqtv=0 nlstate=3
	/* V2 V3 V4 are fixed V6 V7 are timevarying so V8 and V5 are not in the model and product column will start at 9 Tvar[4]=6
	* FixedV[ncovcol+qv+ntv+nqtv] V5
	* V1 V2 V3 V4 V5 V6 V7 V8
	* 0 0 0 0 0 1 1 1
	* model= V2 + V3 + V4 + V6 + V7 + V6V2 + V7V2 + V6V3 + V7V3 + V6V4 + V7V4
	* kmodel 1 2 3 4 5 6 7 8 9 10 11
	* ncovf 1 2 3
	* ncovvt=14 1 2 3 4 5 6 7 8 9 10 11 12 13 14
	* TvarVV[1]@14 = itv {6, 7, 6, 2, 7, 2, 6, 3, 7, 3, 6, 4, 7, 4}
	* TvarVVind[1]@14= {4, 5, 6, 6, 7, 7, 8, 8, 9, 9, 10, 10, 11, 11}
	* TvarFind[1]@14= {1, 2, 3, 0 <repeats 12 times>}
	* Tvar[1]@20= {2, 3, 4, 6, 7, 9, 10, 11, 12, 13, 14}
	* TvarFind[itv] 0 0 0
	* FixedV[itv] 1 1 1 0 1 0 1 0 1 0 0
	* Tvar[TvarFind[ncovf]]=[1]=2 [2]=3 [4]=4
	* Tvar[TvarFind[itv]] [0]=? ?ncovv 1 à ncovvt]
	* Not a fixed cotvar[mw][itv][i] 6 7 6 2 7, 2, 6, 3, 7, 3, 6, 4, 7, 4}
	* fixed covar[itv] [6] [7] [6][2]
	*/

	for(ncovv=1, iposold=0; ncovv <= ncovvt ; ncovv++){ /* Varying covariates (single and product but no age) including individual from products */
	itv=TvarVV[ncovv]; /* TvarVV={3, 1, 3} gives the name of each varying covariate, exploding product */
	ipos=TvarVVind[ncovv]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate*/
	/* if(TvarFind[itv]==0){ /\* Not a fixed covariate? Could be a fixed covariate of a product with a higher than ncovcol+nqv, itv \/ /
	if(FixedV[itv]!=0){ /* Not a fixed covariate? Could be a fixed covariate of a product with a higher than ncovcol+nqv, itv */
	cotvarv=cotvar[mw[mi][i]][TvarVV[ncovv]][i]; /* because cotvar starts now at first ncovcol+nqv+ntv+nqtv (1 to nqtv) */
	}else{ /* fixed covariate */
	/* cotvarv=covar[Tvar[TvarFind[itv]]][i]; /\* Error: TvarFind gives the name, that is the true column of fixed covariates, but Tvar of the model \/ /
	cotvarv=covar[itv][i]; /* Error: TvarFind gives the name, that is the true column of fixed covariates, but Tvar of the model */
	}
if(ipos!=iposold){ /* Not a product or first of a product */	if(ipos!=iposold){ /* Not a product or first of a product */
/* TvarFind={1,0,0,0} */	cotvarvold=cotvarv;
if(TvarFind[itv]==0){	}else{ /* A second product */
cov[ioffset+ipos]= cotvar[mw[mi][i]][ncovv][i]; /* Should be covar if fixed covar[Tvar[TvarFind[itv]]][i]*/	cotvarv=cotvarv*cotvarvold;
}else{
cov[ioffset+ipos]=covar[Tvar[TvarFind[itv]]][i];
}
}else{
if(TvarFind[itv]==0){
cov[ioffset+ipos]= cotvar[mw[mi][i]][ncovv][i]; / Should be covar if fixed covar[Tvar[TvarFind[itv]]][i]*/
}else{
cov[ioffset+ipos]*=covar[Tvar[TvarFind[itv]]][i];
}
}	}
iposold=ipos;	iposold=ipos;
	cov[ioffset+ipos]=cotvarv;
/* For products */	/* For products */
}	}
/* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates single \/ /	/* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates single \/ /
Line 4397 double funcone( double *x)	Line 4469 double funcone( double *x)
if(!FixedV[Tvar[Tage[kk]]])	if(!FixedV[Tvar[Tage[kk]]])
cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;	cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;
else	else
cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]][i]*agexact;	cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]][i]agexact; / because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) */
}	}
/* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */	/* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
/* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */	/* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
Line 4452 double funcone( double *x)	Line 4524 double funcone( double *x)
ipmx +=1;	ipmx +=1;
sw += weight[i];	sw += weight[i];
ll[s[mw[mi][i]][i]] += 2weight[i]lli;	ll[s[mw[mi][i]][i]] += 2weight[i]lli;
/* printf("Funcone i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2])); */	/* Printing covariates values for each contribution for checking */
	/* printf("num[i]=%09ld, i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2])); */
if(globpr){	if(globpr){
fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\	fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
%11.6f %11.6f %11.6f ", \	%11.6f %11.6f %11.6f ", \
num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,	num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
2weight[i]lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2]));	2weight[i]lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2]));
/* printf("%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\ */	/* printf("%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\ */
/* %11.6f %11.6f %11.6f ", \ */	/* %11.6f %11.6f %11.6f ", \ */
/* num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]gipmx/gsw, /	/* num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]gipmx/gsw, /
/* 2weight[i]lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2])); */	/* 2weight[i]lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2])); */
for(k=1,llt=0.,l=0.; k<=nlstate; k++){	for(k=1,llt=0.,l=0.; k<=nlstate; k++){
llt +=ll[k]*gipmx/gsw;	llt +=ll[k]*gipmx/gsw;
fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);	fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
/* printf(" %10.6f",-ll[k]gipmx/gsw); /	/* printf(" %10.6f",-ll[k]gipmx/gsw); /
}	}
fprintf(ficresilk," %10.6f\n", -llt);	fprintf(ficresilk," %10.6f ", -llt);
/* printf(" %10.6f\n", -llt); */	/* printf(" %10.6f\n", -llt); */
}	/* if(debugILK){ /\* debugILK is set by a #d in a comment line \/ /
	/* fprintf(ficresilk,"%09ld ", num[i]); / / not necessary */
	for (kf=1; kf<=ncovf;kf++){ /* Simple and product fixed covariates without age* products // Missing values are set to -1 but should be dropped */
	fprintf(ficresilk," %g",covar[Tvar[TvarFind[kf]]][i]);
	}
	for(ncovv=1, iposold=0; ncovv <= ncovvt ; ncovv++){ /* Varying covariates (single and product but no age) including individual from products */
	ipos=TvarVVind[ncovv]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate*/
	if(ipos!=iposold){ /* Not a product or first of a product */
	fprintf(ficresilk," %g",cov[ioffset+ipos]);
	/* printf(" %g",cov[ioffset+ipos]); */
	}else{
	fprintf(ficresilk,"*");
	/* printf(""); /
	}
	iposold=ipos;
	}
	for (kk=1; kk<=cptcovage;kk++) {
	if(!FixedV[Tvar[Tage[kk]]]){
	fprintf(ficresilk," %g*age",covar[Tvar[Tage[kk]]][i]);
	/* printf(" %gage",covar[Tvar[Tage[kk]]][i]); /
	}else{
	fprintf(ficresilk," %gage",cotvar[mw[mi][i]][Tvar[Tage[kk]]][i]);/ because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) */
	/* printf(" %gage",cotvar[mw[mi][i]][Tvar[Tage[kk]]][i]);/\ because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) \/ /
	}
	}
	/* printf("\n"); */
	/* } /\* End debugILK \/ /
	fprintf(ficresilk,"\n");
	} /* End if globpr */
} /* end of wave */	} /* end of wave */
} /* end of individual */	} /* end of individual */
for(k=1,l=0.; k<=nlstate; k++) l += ll[k];	for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
Line 4479 double funcone( double *x)	Line 4580 double funcone( double *x)
gipmx=ipmx;	gipmx=ipmx;
gsw=sw;	gsw=sw;
}	}
return -l;	return -l;
}	}


Line 4490 void likelione(FILE *ficres,double p[],	Line 4591 void likelione(FILE *ficres,double p[],
the selection of individuals/waves and	the selection of individuals/waves and
to check the exact contribution to the likelihood.	to check the exact contribution to the likelihood.
Plotting could be done.	Plotting could be done.
*/	*/
int k;	void pstamp(FILE *ficres);
	int k, kf, kk, kvar, ncovv, iposold, ipos;

if(globpri !=0){ / Just counts and sums, no printings */	if(globpri !=0){ / Just counts and sums, no printings */
strcpy(fileresilk,"ILK_");	strcpy(fileresilk,"ILK_");
Line 4500 void likelione(FILE *ficres,double p[],	Line 4602 void likelione(FILE *ficres,double p[],
printf("Problem with resultfile: %s\n", fileresilk);	printf("Problem with resultfile: %s\n", fileresilk);
fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);	fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
}	}
	pstamp(ficresilk);fprintf(ficresilk,"# model=1+age+%s\n",model);
fprintf(ficresilk, "#individual(line's_record) count ageb ageend s1 s2 wave# effective_wave# number_of_matrices_product pij weight weight/gpw -2ln(pij)weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2llweightXnumber_of_contribs/sum_of_weights) and_total\n");	fprintf(ficresilk, "#individual(line's_record) count ageb ageend s1 s2 wave# effective_wave# number_of_matrices_product pij weight weight/gpw -2ln(pij)weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2llweightXnumber_of_contribs/sum_of_weights) and_total\n");
fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");	fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
/* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2weight[i]lli,out[s1][s2],savm[s1][s2]); */	/* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2weight[i]lli,out[s1][s2],savm[s1][s2]); */
for(k=1; k<=nlstate; k++)	for(k=1; k<=nlstate; k++)
fprintf(ficresilk," -2gipw/gswweight*ll[%d]++",k);	fprintf(ficresilk," -2gipw/gswweight*ll[%d]++",k);
fprintf(ficresilk," -2gipw/gswweight*ll(total)\n");	fprintf(ficresilk," -2gipw/gswweight*ll(total) ");
}
	/* if(debugILK){ /\* debugILK is set by a #d in a comment line \/ /
	for(kf=1;kf <= ncovf; kf++){
	fprintf(ficresilk,"V%d",Tvar[TvarFind[kf]]);
	/* printf("V%d",Tvar[TvarFind[kf]]); */
	}
	for(ncovv=1, iposold=0; ncovv <= ncovvt ; ncovv++){
	ipos=TvarVVind[ncovv]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate */
	if(ipos!=iposold){ /* Not a product or first of a product */
	/* printf(" %d",ipos); */
	fprintf(ficresilk," V%d",TvarVV[ncovv]);
	}else{
	/* printf(""); /
	fprintf(ficresilk,"*");
	}
	iposold=ipos;
	}
	for (kk=1; kk<=cptcovage;kk++) {
	if(!FixedV[Tvar[Tage[kk]]]){
	/* printf(" %dage(Fixed)",Tvar[Tage[kk]]); /
	fprintf(ficresilk," %d*age(Fixed)",Tvar[Tage[kk]]);
	}else{
	fprintf(ficresilk," %dage(Varying)",Tvar[Tage[kk]]);/ because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) */
	/* printf(" %dage(Varying)",Tvar[Tage[kk]]);/\ because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) \/ /
	}
	}
	/* } /\* End if debugILK \/ /
	/* printf("\n"); */
	fprintf(ficresilk,"\n");
	} /* End glogpri */

fretone=(func)(p);	fretone=(func)(p);
if(*globpri !=0){	if(*globpri !=0){
Line 4518 void likelione(FILE *ficres,double p[],	Line 4650 void likelione(FILE *ficres,double p[],
fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));	fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
fprintf(fichtm,"\n<br>Equation of the model: <b>model=1+age+%s</b><br>\n",model);	fprintf(fichtm,"\n<br>Equation of the model: <b>model=1+age+%s</b><br>\n",model);

for (k=1; k<= nlstate ; k++) {
fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Dot's sizes are related to corresponding weight: <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
<img src=\"%s-p%dj.png\">",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
}
fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \	fprintf(fichtm,"<br>- The function drawn is -2Log(L) in Log scale: by state of origin <a href=\"%s-ori.png\">%s-ori.png</a><br> \
<img src=\"%s-ori.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));	<img src=\"%s-ori.png\">\n",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));
fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \	fprintf(fichtm,"<br>- and by state of destination <a href=\"%s-dest.png\">%s-dest.png</a><br> \
<img src=\"%s-dest.png\">",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));	<img src=\"%s-dest.png\">\n",subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"),subdirf2(optionfilefiname,"ILK_"));

	for (k=1; k<= nlstate ; k++) {
	fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Dot's sizes are related to corresponding weight: <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br>\n \
	<img src=\"%s-p%dj.png\">\n",k,k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k);
	for(kf=1; kf <= ncovf; kf++){ /* For each simple dummy covariate of the model */
	/* kvar=Tvar[TvarFind[kf]]; / / variable */
	fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j with colored covariate V%d. Same dot size of all points but with a different color for transitions with dummy variable V%d=1 at beginning of transition (keeping former color for V%d=0): <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
	<img src=\"%s-p%dj-%d.png\">",k,k,Tvar[TvarFind[kf]],Tvar[TvarFind[kf]],Tvar[TvarFind[kf]],subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,Tvar[TvarFind[kf]]);
	}
	for(ncovv=1, iposold=0; ncovv <= ncovvt ; ncovv++){ /* Loop on the time varying extended covariates (with extension of VnVm /
	ipos=TvarVVind[ncovv]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate */
	kvar=TvarVV[ncovv]; /* TvarVV={3, 1, 3} gives the name of each varying covariate */
	/* printf("DebugILK fichtm ncovv=%d, kvar=TvarVV[ncovv]=V%d, ipos=TvarVVind[ncovv]=%d, Dummy[ipos]=%d, Typevar[ipos]=%d\n", ncovv,kvar,ipos,Dummy[ipos],Typevar[ipos]); */
	if(ipos!=iposold){ /* Not a product or first of a product */
	/* fprintf(ficresilk," V%d",TvarVV[ncovv]); */
	/* printf(" DebugILK fichtm ipos=%d != iposold=%d\n", ipos, iposold); */
	if(Dummy[ipos]==0 && Typevar[ipos]==0){ /* Only if dummy time varying: Dummy(0, 1=quant singor prod without age,2 dummyage, 3quantage) Typevar (0 single, 1=age,2=Vnvm) */
	fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j with colored time varying dummy covariate V%d. Same dot size of all points but with a different color for transitions with dummy variable V%d=1 at beginning of transition (keeping former color for V%d=0): <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
	<img src=\"%s-p%dj-%d.png\">",k,k,kvar,kvar,kvar,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,kvar);
	} /* End only for dummies time varying (single?) */
	}else{ /* Useless product */
	/* printf(""); /
	/* fprintf(ficresilk,""); /
	}
	iposold=ipos;
	} /* For each time varying covariate */
	} /* End loop on states */

	/* if(debugILK){ */
	/* for(kf=1; kf <= ncovf; kf++){ /\* For each simple dummy covariate of the model \/ /
	/* /\* kvar=Tvar[TvarFind[kf]]; \/ /\ variable \/ /
	/* for (k=1; k<= nlstate ; k++) { */
	/* fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j with colored covariate V%. Same dot size of all points but with a different color for transitions with dummy variable V%d=1 at beginning of transition (keeping former color for V%d=0): <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \ */
	/* <img src=\"%s-p%dj-%d.png\">",k,k,Tvar[TvarFind[kf]],Tvar[TvarFind[kf]],Tvar[TvarFind[kf]],subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,Tvar[TvarFind[kf]]); */
	/* } */
	/* } */
	/* for(ncovv=1, iposold=0; ncovv <= ncovvt ; ncovv++){ /\* Loop on the time varying extended covariates (with extension of VnVm \/ */
	/* ipos=TvarVVind[ncovv]; /\* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate \/ /
	/* kvar=TvarVV[ncovv]; /\* TvarVV={3, 1, 3} gives the name of each varying covariate \/ /
	/* /\* printf("DebugILK fichtm ncovv=%d, kvar=TvarVV[ncovv]=V%d, ipos=TvarVVind[ncovv]=%d, Dummy[ipos]=%d, Typevar[ipos]=%d\n", ncovv,kvar,ipos,Dummy[ipos],Typevar[ipos]); \/ /
	/* if(ipos!=iposold){ /\* Not a product or first of a product \/ /
	/* /\* fprintf(ficresilk," V%d",TvarVV[ncovv]); \/ /
	/* /\* printf(" DebugILK fichtm ipos=%d != iposold=%d\n", ipos, iposold); \/ /
	/* if(Dummy[ipos]==0 && Typevar[ipos]==0){ /\* Only if dummy time varying: Dummy(0, 1=quant singor prod without age,2 dummyage, 3quantage) Typevar (0 single, 1=age,2=Vnvm) \/ /
	/* for (k=1; k<= nlstate ; k++) { */
	/* fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Same dot size of all points but with a different color for transitions with dummy variable V%d=1 at beginning of transition (keeping former color for V%d=0): <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \ */
	/* <img src=\"%s-p%dj-%d.png\">",k,k,kvar,kvar,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,subdirf2(optionfilefiname,"ILK_"),k,kvar); */
	/* } /\* End state \/ /
	/* } /\* End only for dummies time varying (single?) \/ /
	/* }else{ /\* Useless product \/ /
	/* /\* printf(""); \/ */
	/* /\* fprintf(ficresilk,""); \/ */
	/* } */
	/* iposold=ipos; */
	/* } /\* For each time varying covariate \/ /
	/* }/\* End debugILK \/ /
fflush(fichtm);	fflush(fichtm);
}	}/* End globpri */
return;	return;
}	}

Line 5249 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5433 Title=%s <br>Datafile=%s Firstpass=%d La
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; /\* Good \/ /
	iv= Tvar[Tmodelind[z1]]; /* Good // because cotvar starts now at first at ncovcol+nqv+ntv */
if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) /* iv=1 to ntv, right modality. If covariate's	if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) /* iv=1 to ntv, right modality. If covariate's
value is -1, we don't select. It differs from the	value is -1, we don't select. It differs from the
constant and age model which counts them. */	constant and age model which counts them. */
Line 5330 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5515 Title=%s <br>Datafile=%s Firstpass=%d La
fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");	fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");	fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
fprintf(ficlog, "\n#********** Variable ");	fprintf(ficlog, "\n#********** Variable ");
for (z1=1; z1<=cptcovs; z1++){	for (z1=1; z1<=cptcoveff; z1++){
if(!FixedV[Tvaraff[z1]]){	if(!FixedV[Tvaraff[z1]]){
printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);	printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);	fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
Line 5786 void prevalence(double ***probs, double	Line 5971 void prevalence(double ***probs, double
/* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */	/* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
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]];/* because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) */
if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) /* iv=1 to ntv, right modality */	if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) /* iv=1 to ntv, right modality */
bool=0;	bool=0;
}else if( Fixed[Tmodelind[z1]]== 0) /* fixed */	}else if( Fixed[Tmodelind[z1]]== 0) /* fixed */
Line 6095 void concatwav(int wav[], int **dh, int	Line 6280 void concatwav(int wav[], int **dh, int
/* Loop on covariates without age and products and no quantitative variable */	/* Loop on covariates without age and products and no quantitative variable */
for (k=1; k<=cptcovt; k++) { /* cptcovt: total number of covariates of the model (2) nbocc(+)+1 = 8 excepting constant and age and ageage /	for (k=1; k<=cptcovt; k++) { /* cptcovt: total number of covariates of the model (2) nbocc(+)+1 = 8 excepting constant and age and ageage /
for (j=-1; (j < maxncov); j++) Ndum[j]=0;	for (j=-1; (j < maxncov); j++) Ndum[j]=0;
printf("Testing k=%d, cptcovt=%d\n",k, cptcovt);	/* printf("Testing k=%d, cptcovt=%d\n",k, cptcovt); */
if(Dummy[k]==0 && Typevar[k] !=1 && Typevar[k] != 2){ /* Dummy covariate and not age product nor fixed product */	if(Dummy[k]==0 && Typevar[k] !=1 && Typevar[k] != 2){ /* Dummy covariate and not age product nor fixed product */
switch(Fixed[k]) {	switch(Fixed[k]) {
case 0: /* Testing on fixed dummy covariate, simple or product of fixed */	case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
Line 6193 void concatwav(int wav[], int **dh, int	Line 6378 void concatwav(int wav[], int **dh, int
break;	break;
} /* end switch */	} /* end switch */
} /* end dummy test */	} /* end dummy test */
if(Dummy[k]==1 && Typevar[k] !=1){ /* Quantitative covariate and not age product */	if(Dummy[k]==1 && Typevar[k] !=1 && Fixed ==0){ /* Fixed Quantitative covariate and not age product */
for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the modality of this covariate Vj*/	for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the modality of this covariate Vj*/
if(Tvar[k]<=0 \|\| Tvar[k]>=NCOVMAX){	if(Tvar[k]<=0 \|\| Tvar[k]>=NCOVMAX){
printf("Error k=%d \n",k);	printf("Error k=%d \n",k);
Line 6659 void concatwav(int wav[], int **dh, int	Line 6844 void concatwav(int wav[], int **dh, int
/* fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */	/* fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
/* } */	/* } */
for (j=1; j<= cptcovs; j++){ /* For each selected (single) quantitative value / / To be done*/	for (j=1; j<= cptcovs; j++){ /* For each selected (single) quantitative value / / To be done*/
	/* fprintf(ficresprobmorprev," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]); */
fprintf(ficresprobmorprev," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);	fprintf(ficresprobmorprev," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
}	}
/* for(j=1;j<=cptcoveff;j++) */	/* for(j=1;j<=cptcoveff;j++) */
Line 7293 To be simple, these graphs help to under	Line 7479 To be simple, these graphs help to under

for(nres=1;nres <=nresult; nres++){ /* For each resultline */	for(nres=1;nres <=nresult; nres++){ /* For each resultline */
for(j1=1; j1<=tj;j1++){ /* For any combination of dummy covariates, fixed and varying */	for(j1=1; j1<=tj;j1++){ /* For any combination of dummy covariates, fixed and varying */
printf("Varprob TKresult[nres]=%d j1=%d, nres=%d, cptcovn=%d, cptcoveff=%d tj=%d cptcovs=%d\n", TKresult[nres], j1, nres, cptcovn, cptcoveff, tj, cptcovs);	/* printf("Varprob TKresult[nres]=%d j1=%d, nres=%d, cptcovn=%d, cptcoveff=%d tj=%d cptcovs=%d\n", TKresult[nres], j1, nres, cptcovn, cptcoveff, tj, cptcovs); */
if(tj != 1 && TKresult[nres]!= j1)	if(tj != 1 && TKresult[nres]!= j1)
continue;	continue;

Line 7309 To be simple, these graphs help to under	Line 7495 To be simple, these graphs help to under

/* Including quantitative variables of the resultline to be done */	/* Including quantitative variables of the resultline to be done */
for (z1=1; z1<=cptcovs; z1++){ /* Loop on each variable of this resultline */	for (z1=1; z1<=cptcovs; z1++){ /* Loop on each variable of this resultline */
printf("Varprob modelresult[%d][%d]=%d model=1+age+%s \n",nres, z1, modelresult[nres][z1], model);	/* printf("Varprob modelresult[%d][%d]=%d model=1+age+%s \n",nres, z1, modelresult[nres][z1], model); */
fprintf(ficlog,"Varprob modelresult[%d][%d]=%d model=1+age+%s \n",nres, z1, modelresult[nres][z1], model);	fprintf(ficlog,"Varprob modelresult[%d][%d]=%d model=1+age+%s \n",nres, z1, modelresult[nres][z1], model);
/* fprintf(ficlog,"Varprob modelresult[%d][%d]=%d model=1+age+%s resultline[%d]=%s \n",nres, z1, modelresult[nres][z1], model, nres, resultline[nres]); */	/* fprintf(ficlog,"Varprob modelresult[%d][%d]=%d model=1+age+%s resultline[%d]=%s \n",nres, z1, modelresult[nres][z1], model, nres, resultline[nres]); */
if(Dummy[modelresult[nres][z1]]==0){/* Dummy variable of the variable in position modelresult in the model corresponding to z1 in resultline */	if(Dummy[modelresult[nres][z1]]==0){/* Dummy variable of the variable in position modelresult in the model corresponding to z1 in resultline */
Line 7968 void printinggnuplot(char fileresu[], ch	Line 8154 void printinggnuplot(char fileresu[], ch

char dirfileres[132],optfileres[132];	char dirfileres[132],optfileres[132];
char gplotcondition[132], gplotlabel[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,kf=0,kvar=0,kk=0,ipos=0,iposold=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;
Line 7994 void printinggnuplot(char fileresu[], ch	Line 8180 void printinggnuplot(char fileresu[], ch
fprintf(ficgp,"yoff=(%d > 2? 0:1);\n",nlstate);	fprintf(ficgp,"yoff=(%d > 2? 0:1);\n",nlstate);
fprintf(ficgp,"\n#Peripheral arrows\nset for [i=1:%d] for [j=1:%d] arrow i10+j from cos(pi((1-(%d/2)2./%d)/2+(i-1)2./%d))-(i!=j?(i-j)/abs(i-j)delta:0), yoff +sin(pi((1-(%d/2)2./%d)/2+(i-1)2./%d)) + (i!=j?(i-j)/abs(i-j)delta:0) rto -0.95(cos(pi((1-(%d/2)2./%d)/2+(i-1)2./%d))+(i!=j?(i-j)/abs(i-j)delta:0) - cos(pi((1-(%d/2)2./%d)/2+(j-1)2./%d)) + (i!=j?(i-j)/abs(i-j)delta2:0)), -0.95(sin(pi((1-(%d/2)2./%d)/2+(i-1)2./%d)) + (i!=j?(i-j)/abs(i-j)delta:0) - sin(pi((1-(%d/2)2./%d)/2+(j-1)2./%d))+( i!=j?(i-j)/abs(i-j)*delta2:0)) ls (i < j? 1:2)\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);	fprintf(ficgp,"\n#Peripheral arrows\nset for [i=1:%d] for [j=1:%d] arrow i10+j from cos(pi((1-(%d/2)2./%d)/2+(i-1)2./%d))-(i!=j?(i-j)/abs(i-j)delta:0), yoff +sin(pi((1-(%d/2)2./%d)/2+(i-1)2./%d)) + (i!=j?(i-j)/abs(i-j)delta:0) rto -0.95(cos(pi((1-(%d/2)2./%d)/2+(i-1)2./%d))+(i!=j?(i-j)/abs(i-j)delta:0) - cos(pi((1-(%d/2)2./%d)/2+(j-1)2./%d)) + (i!=j?(i-j)/abs(i-j)delta2:0)), -0.95(sin(pi((1-(%d/2)2./%d)/2+(i-1)2./%d)) + (i!=j?(i-j)/abs(i-j)delta:0) - sin(pi((1-(%d/2)2./%d)/2+(j-1)2./%d))+( i!=j?(i-j)/abs(i-j)*delta2:0)) ls (i < j? 1:2)\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);

fprintf(ficgp,"\n#Centripete arrows (turning in other direction (1-i) instead of (i-1)) \nset for [i=1:%d] arrow (%d+1)10+i from cos(pi((1-(%d/2)2./%d)/2+(1-i)2./%d))-(i!=j?(i-j)/abs(i-j)delta:0), yoff +sin(pi((1-(%d/2)2./%d)/2+(1-i)2./%d)) + (i!=j?(i-j)/abs(i-j)delta:0) rto -0.80(cos(pi((1-(%d/2)2./%d)/2+(1-i)2./%d))+(i!=j?(i-j)/abs(i-j)delta:0) ), -0.80(sin(pi((1-(%d/2)2./%d)/2+(1-i)2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) + yoff ) ls 4\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);	fprintf(ficgp,"\n#Centripete arrows (turning in other direction (1-i) instead of (i-1)) \nset for [i=1:%d] for [j=1:%d] arrow (%d+1)10+i from cos(pi((1-(%d/2)2./%d)/2+(1-i)2./%d))-(i!=j?(i-j)/abs(i-j)delta:0), yoff +sin(pi((1-(%d/2)2./%d)/2+(1-i)2./%d)) + (i!=j?(i-j)/abs(i-j)delta:0) rto -0.80(cos(pi((1-(%d/2)2./%d)/2+(1-i)2./%d))+(i!=j?(i-j)/abs(i-j)delta:0) ), -0.80(sin(pi((1-(%d/2)2./%d)/2+(1-i)2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) + yoff ) ls 4\n",nlstate, nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
fprintf(ficgp,"\n#show arrow\nunset label\n");	fprintf(ficgp,"\n#show arrow\nunset label\n");
fprintf(ficgp,"\n#States labels, starting from 2 (2-i) instead of (1-i), was (i-1)\nset for [i=1:%d] label i sprintf(\"State %%d\",i) center at cos(pi((1-(%d/2)2./%d)/2+(2-i)2./%d)), yoff+sin(pi((1-(%d/2)2./%d)/2+(2-i)2./%d)) font \"helvetica, 16\" tc rgbcolor \"blue\"\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);	fprintf(ficgp,"\n#States labels, starting from 2 (2-i) instead of (1-i), was (i-1)\nset for [i=1:%d] label i sprintf(\"State %%d\",i) center at cos(pi((1-(%d/2)2./%d)/2+(2-i)2./%d)), yoff+sin(pi((1-(%d/2)2./%d)/2+(2-i)2./%d)) font \"helvetica, 16\" tc rgbcolor \"blue\"\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
fprintf(ficgp,"\nset label %d+1 sprintf(\"State %%d\",%d+1) center at 0.,0. font \"helvetica, 16\" tc rgbcolor \"red\"\n",nlstate,nlstate);	fprintf(ficgp,"\nset label %d+1 sprintf(\"State %%d\",%d+1) center at 0.,0. font \"helvetica, 16\" tc rgbcolor \"red\"\n",nlstate,nlstate);
Line 8031 void printinggnuplot(char fileresu[], ch	Line 8217 void printinggnuplot(char fileresu[], ch
fprintf(ficgp,"\nset out;unset log\n");	fprintf(ficgp,"\nset out;unset log\n");
/* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */	/* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */

	/* Plot the probability implied in the likelihood by covariate value */
	fprintf(ficgp,"\nset ter pngcairo size 640, 480");
	/* if(debugILK==1){ */
	for(kf=1; kf <= ncovf; kf++){ /* For each simple dummy covariate of the model */
	kvar=Tvar[TvarFind[kf]]; /* variable */
	k=18+Tvar[TvarFind[kf]];/offset because there are 18 columns in the ILK_ file /
	for (i=1; i<= nlstate ; i ++) {
	fprintf(ficgp,"\nset out \"%s-p%dj-%d.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i,kvar);
	fprintf(ficgp,"unset log;\n# For each simple dummy covariate of the model \n plot \"%s\"",subdirf(fileresilk));
	fprintf(ficgp," u 2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? 7 : 9):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt variable ps 0.4 lc variable \\\n",i,1,k,k,i,1,kvar);
	for (j=2; j<= nlstate+ndeath ; j ++) {
	fprintf(ficgp,",\\\n \"\" u 2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? 7 : 9):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt variable ps 0.4 lc variable ",i,j,k,k,i,j,kvar);
	}
	fprintf(ficgp,";\nset out; unset ylabel;\n");
	}
	} /* End of each covariate dummy */
	for(ncovv=1, iposold=0, kk=0; ncovv <= ncovvt ; ncovv++){
	/* Other example V1 + V3 + V5 + ageV1 + ageV3 + ageV5 + V1V3 + V3V5 + V1V5
	* kmodel = 1 2 3 4 5 6 7 8 9
	* varying 1 2 3 4 5
	* ncovv 1 2 3 4 5 6 7 8
	* TvarVV[ncovv] V3 5 1 3 3 5 1 5
	* TvarVVind[ncovv]=kmodel 2 3 7 7 8 8 9 9
	* TvarFind[kmodel] 1 0 0 0 0 0 0 0 0
	* kdata ncovcol=[V1 V2] nqv=0 ntv=[V3 V4] nqtv=V5
	* Dummy[kmodel] 0 0 1 2 2 3 1 1 1
	*/
	ipos=TvarVVind[ncovv]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate */
	kvar=TvarVV[ncovv]; /* TvarVV={3, 1, 3} gives the name of each varying covariate */
	/* printf("DebugILK ficgp ncovv=%d, kvar=TvarVV[ncovv]=%d, ipos=TvarVVind[ncovv]=%d, Dummy[ipos]=%d, Typevar[ipos]=%d\n", ncovv,kvar,ipos,Dummy[ipos],Typevar[ipos]); */
	if(ipos!=iposold){ /* Not a product or first of a product */
	/* printf(" %d",ipos); */
	/* fprintf(ficresilk," V%d",TvarVV[ncovv]); */
	/* printf(" DebugILK ficgp suite ipos=%d != iposold=%d\n", ipos, iposold); */
	kk++; /* Position of the ncovv column in ILK_ */
	k=18+ncovf+kk; /offset because there are 18 columns in the ILK_ file plus ncovf fixed covariate /
	if(Dummy[ipos]==0 && Typevar[ipos]==0){ /* Only if dummy time varying: Dummy(0, 1=quant singor prod without age,2 dummyage, 3quantage) Typevar (0 single, 1=age,2=Vnvm) */
	for (i=1; i<= nlstate ; i ++) {
	fprintf(ficgp,"\nset out \"%s-p%dj-%d.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i,kvar);
	fprintf(ficgp,"unset log;\n# For each simple dummy covariate of the model \n plot \"%s\"",subdirf(fileresilk));

	if(gnuplotversion >=5.2){ /* Former gnuplot versions do not have variable pointsize!! */
	/* printf("DebugILK gnuplotversion=%g >=5.2\n",gnuplotversion); */
	fprintf(ficgp," u 2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? 7 : 9):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt variable ps 0.4 lc variable \\\n",i,1,k,k,i,1,kvar);
	for (j=2; j<= nlstate+ndeath ; j ++) {
	fprintf(ficgp,",\\\n \"\" u 2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? 7 : 9):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt variable ps 0.4 lc variable ",i,j,k,k,i,j,kvar);
	}
	}else{
	/* printf("DebugILK gnuplotversion=%g <5.2\n",gnuplotversion); */
	fprintf(ficgp," u 2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt 7 ps 0.4 lc variable \\\n",i,1,k,i,1,kvar);
	for (j=2; j<= nlstate+ndeath ; j ++) {
	fprintf(ficgp,",\\\n \"\" u 2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt 7 ps 0.4 lc variable ",i,j,k,i,j,kvar);
	}
	}
	fprintf(ficgp,";\nset out; unset ylabel;\n");
	}
	}/* End if dummy varying */
	}else{ /Product /
	/* printf(""); /
	/* fprintf(ficresilk,""); /
	}
	iposold=ipos;
	} /* For each time varying covariate */
	/* } /\* debugILK==1 \/ /
	/* unset log; plot "rrtest1_sorted_4/ILK_rrtest1_sorted_4.txt" u 2:($4 == 1 && $5==2 ? $9 : 1/0):5 t "p12" with points lc variable */
	/* fprintf(ficgp,"\nset log y;plot \"%s\" u 2:(-$11):3 t \"All sample, all transitions\" with dots lc variable",subdirf(fileresilk)); */
	/* fprintf(ficgp,"\nreplot \"%s\" u 2:($3 <= 3 ? -$11 : 1/0):3 t \"First 3 individuals\" with line lc variable", subdirf(fileresilk)); */
	fprintf(ficgp,"\nset out;unset log\n");
	/* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */



strcpy(dirfileres,optionfilefiname);	strcpy(dirfileres,optionfilefiname);
strcpy(optfileres,"vpl");	strcpy(optfileres,"vpl");
/* 1eme*/	/* 1eme*/
Line 10317 int readdata(char datafile[], int firsto	Line 10575 int readdata(char datafile[], int firsto
if(strb[0]=='.') { /* Missing value */	if(strb[0]=='.') { /* Missing value */
lval=-1;	lval=-1;
cotqvar[j][iv][i]=-1; /* 0.0/0.0 */	cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
cotvar[j][ntv+iv][i]=-1; /* For performance reasons */	cotvar[j][ncovcol+nqv+ntv+iv][i]=-1; /* For performance reasons */
if(isalpha(strb[1])) { /* .m or .d Really Missing value */	if(isalpha(strb[1])) { /* .m or .d Really Missing value */
printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value. Exiting.\n", strb, linei,i,line,iv, nqtv, j);	printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value. Exiting.\n", strb, linei,i,line,iv, nqtv, j);
fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value. Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog);	fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value. Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog);
Line 10337 int readdata(char datafile[], int firsto	Line 10595 int readdata(char datafile[], int firsto
return 1;	return 1;
}	}
cotqvar[j][iv][i]=dval;	cotqvar[j][iv][i]=dval;
cotvar[j][ntv+iv][i]=dval;	cotvar[j][ncovcol+nqv+ntv+iv][i]=dval; /* because cotvar starts now at first ntv */
}	}
strcpy(line,stra);	strcpy(line,stra);
}/* end loop ntqv */	}/* end loop ntqv */
Line 10377 int readdata(char datafile[], int firsto	Line 10635 int readdata(char datafile[], int firsto
Exiting.\n",lval,linei, i,line,iv,j);fflush(ficlog);	Exiting.\n",lval,linei, i,line,iv,j);fflush(ficlog);
return 1;	return 1;
}	}
cotvar[j][iv][i]=(double)(lval);	cotvar[j][ncovcol+nqv+iv][i]=(double)(lval);
strcpy(line,stra);	strcpy(line,stra);
}/* end loop ntv */	}/* end loop ntv */

Line 10590 int decoderesult( char resultline[], int	Line 10848 int decoderesult( char resultline[], int
printf("decoderesult:%s\n",resultline);	printf("decoderesult:%s\n",resultline);

strcpy(resultsav,resultline);	strcpy(resultsav,resultline);
printf("Decoderesult resultsav=\"%s\" resultline=\"%s\"\n", resultsav, resultline);	/* printf("Decoderesult resultsav=\"%s\" resultline=\"%s\"\n", resultsav, resultline); */
if (strlen(resultsav) >1){	if (strlen(resultsav) >1){
j=nbocc(resultsav,'='); /*< j=Number of covariate values'=' in this resultline /	j=nbocc(resultsav,'='); /*< j=Number of covariate values'=' in this resultline /
}	}
Line 10650 int decoderesult( char resultline[], int	Line 10908 int decoderesult( char resultline[], int
if(Tvar[k1]==Tvarsel[k2]) {/* Tvar is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5 */	if(Tvar[k1]==Tvarsel[k2]) {/* Tvar is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5 */
modelresult[nres][k2]=k1;/* we found a Vn=1 corrresponding to Vnage in the model modelresult[2]=1 modelresult[1]=2 modelresult[3]=3 modelresult[6]=4 modelresult[9]=5 /	modelresult[nres][k2]=k1;/* we found a Vn=1 corrresponding to Vnage in the model modelresult[2]=1 modelresult[1]=2 modelresult[3]=3 modelresult[6]=4 modelresult[9]=5 /
resultmodel[nres][k1]=k2; /* Added here */	resultmodel[nres][k1]=k2; /* Added here */
printf("Decoderesult first modelresult[k2=%d]=%d (k1) V%d*AGE\n",k2,k1,Tvar[k1]);	/* printf("Decoderesult first modelresult[k2=%d]=%d (k1) V%dAGE\n",k2,k1,Tvar[k1]); /
match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */	match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
break;	break;
}	}
Line 10663 int decoderesult( char resultline[], int	Line 10921 int decoderesult( char resultline[], int
}else if(Typevar[k1]==2){ /* Product No age We want to get the position in the resultline of the product in the model line*/	}else if(Typevar[k1]==2){ /* Product No age We want to get the position in the resultline of the product in the model line*/
/* resultmodel[nres][of such a Vn * Vm product k1] is not unique, so can't exist, we feed Tvard[k1][1] and [2] */	/* resultmodel[nres][of such a Vn * Vm product k1] is not unique, so can't exist, we feed Tvard[k1][1] and [2] */
match=0;	match=0;
printf("Decoderesult very first Product Tvardk[k1=%d][1]=%d Tvardk[k1=%d][2]=%d V%d * V%d\n",k1,Tvardk[k1][1],k1,Tvardk[k1][2],Tvardk[k1][1],Tvardk[k1][2]);	/* printf("Decoderesult very first Product Tvardk[k1=%d][1]=%d Tvardk[k1=%d][2]=%d V%d * V%d\n",k1,Tvardk[k1][1],k1,Tvardk[k1][2],Tvardk[k1][1],Tvardk[k1][2]); */
for(k2=1; k2 <=j;k2++){/* Loop on resultline. In result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */	for(k2=1; k2 <=j;k2++){/* Loop on resultline. In result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
if(Tvardk[k1][1]==Tvarsel[k2]) {/* Tvardk is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5 */	if(Tvardk[k1][1]==Tvarsel[k2]) {/* Tvardk is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5 */
/* modelresult[k2]=k1; */	/* modelresult[k2]=k1; */
printf("Decoderesult first Product modelresult[k2=%d]=%d (k1) V%d * \n",k2,k1,Tvarsel[k2]);	/* printf("Decoderesult first Product modelresult[k2=%d]=%d (k1) V%d * \n",k2,k1,Tvarsel[k2]); */
match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */	match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
}	}
}	}
Line 10680 int decoderesult( char resultline[], int	Line 10938 int decoderesult( char resultline[], int
for(k2=1; k2 <=j;k2++){/* Loop on resultline. In result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */	for(k2=1; k2 <=j;k2++){/* Loop on resultline. In result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
if(Tvardk[k1][2]==Tvarsel[k2]) {/* Tvardk is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5 */	if(Tvardk[k1][2]==Tvarsel[k2]) {/* Tvardk is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5 */
/* modelresult[k2]=k1;*/	/* modelresult[k2]=k1;*/
printf("Decoderesult second Product modelresult[k2=%d]=%d (k1) * V%d \n ",k2,k1,Tvarsel[k2]);	/* printf("Decoderesult second Product modelresult[k2=%d]=%d (k1) * V%d \n ",k2,k1,Tvarsel[k2]); */
match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */	match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
break;	break;
}	}
Line 10740 int decoderesult( char resultline[], int	Line 10998 int decoderesult( char resultline[], int
/* k counting number of combination of single dummies in the equation model */	/* k counting number of combination of single dummies in the equation model */
/* k4 counting single dummies in the equation model */	/* k4 counting single dummies in the equation model */
/* k4q counting single quantitatives in the equation model */	/* k4q counting single quantitatives in the equation model */
if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Dummy and Single, k1 is sorting according to MODEL, but k3 to resultline */	if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Dummy and Single, fixed or timevarying, k1 is sorting according to MODEL, but k3 to resultline */
/* k4+1= (not always if quant in model) position in the resultline V(Tvarsel)=Tvalsel=Tresult[nres][pos](value); V(Tvresult[nres][pos] (variable): V(variable)=value) */	/* k4+1= (not always if quant in model) position in the resultline V(Tvarsel)=Tvalsel=Tresult[nres][pos](value); V(Tvresult[nres][pos] (variable): V(variable)=value) */
/* modelresult[k3]=k1: k3th position in the result line corresponds to the k1 position in the model line (doesn't work with products)*/	/* modelresult[k3]=k1: k3th position in the result line corresponds to the k1 position in the model line (doesn't work with products)*/
/* Value in the (current nres) resultline of the variable at the k1th position in the model equation resultmodel[nres][k1]= k3 */	/* Value in the (current nres) resultline of the variable at the k1th position in the model equation resultmodel[nres][k1]= k3 */
Line 10764 int decoderesult( char resultline[], int	Line 11022 int decoderesult( char resultline[], int
Tvresult[nres][k3]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */	Tvresult[nres][k3]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */	Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
precov[nres][k1]=Tvalsel[k3]; /* Value from resultline of the variable at the k1 position in the model */	precov[nres][k1]=Tvalsel[k3]; /* Value from resultline of the variable at the k1 position in the model */
printf("Decoderesult Dummy k=%d, k1=%d precov[nres=%d][k1=%d]=%.f V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k1, nres, k1,precov[nres][k1], k2, k3, (int)Tvalsel[k3], k4);	/* printf("Decoderesult Dummy k=%d, k1=%d precov[nres=%d][k1=%d]=%.f V(k2=V%d)= Tvalsel[%d]=%d, 2*(%d)\n",k, k1, nres, k1,precov[nres][k1], k2, k3, (int)Tvalsel[k3], k4); /
k4++;;	k4++;;
}else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Quantitative and single */	}else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Quantitative and single */
/* Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline */	/* Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline */
Line 10782 int decoderesult( char resultline[], int	Line 11040 int decoderesult( char resultline[], int
Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */	Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */	TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
precov[nres][k1]=Tvalsel[k3q];	precov[nres][k1]=Tvalsel[k3q];
printf("Decoderesult Quantitative nres=%d,precov[nres=%d][k1=%d]=%.f V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, nres, k1,precov[nres][k1], k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);	/* printf("Decoderesult Quantitative nres=%d,precov[nres=%d][k1=%d]=%.f V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, nres, k1,precov[nres][k1], k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]); */
k4q++;;	k4q++;;
}else if( Dummy[k1]==2 ){ /* For dummy with age product */	}else if( Dummy[k1]==2 ){ /* For dummy with age product */
/* Tvar[k1]; / / Age variable */	/* Tvar[k1]; / / Age variable */
Line 10792 int decoderesult( char resultline[], int	Line 11050 int decoderesult( char resultline[], int
k2=(int)Tvarsel[k3]; /* nres=1 k1=2=>k3=1 Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 (V4); k1=3=>k3=2 Tvarsel[2]=3 (V3)*/	k2=(int)Tvarsel[k3]; /* nres=1 k1=2=>k3=1 Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 (V4); k1=3=>k3=2 Tvarsel[2]=3 (V3)*/
TinvDoQresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* TinvDoQresult[nres][4]=1 */	TinvDoQresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* TinvDoQresult[nres][4]=1 */
precov[nres][k1]=Tvalsel[k3];	precov[nres][k1]=Tvalsel[k3];
printf("Decoderesult Dummy with age k=%d, k1=%d precov[nres=%d][k1=%d]=%.f Tvar[%d]=V%d k2=Tvarsel[%d]=%d Tvalsel[%d]=%d\n",k, k1, nres, k1,precov[nres][k1], k1, Tvar[k1], k3,(int)Tvarsel[k3], k3, (int)Tvalsel[k3]);	/* printf("Decoderesult Dummy with age k=%d, k1=%d precov[nres=%d][k1=%d]=%.f Tvar[%d]=V%d k2=Tvarsel[%d]=%d Tvalsel[%d]=%d\n",k, k1, nres, k1,precov[nres][k1], k1, Tvar[k1], k3,(int)Tvarsel[k3], k3, (int)Tvalsel[k3]); */
}else if( Dummy[k1]==3 ){ /* For quant with age product */	}else if( Dummy[k1]==3 ){ /* For quant with age product */
k3q= resultmodel[nres][k1]; /* resultmodel[1(V5)] = 25.1=k3q */	k3q= resultmodel[nres][k1]; /* resultmodel[1(V5)] = 25.1=k3q */
k2q=(int)Tvarsel[k3q]; /* Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */	k2q=(int)Tvarsel[k3q]; /* Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */
TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* TinvDoQresult[nres][5]=25.1 */	TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* TinvDoQresult[nres][5]=25.1 */
precov[nres][k1]=Tvalsel[k3q];	precov[nres][k1]=Tvalsel[k3q];
printf("Decoderesult Quantitative with age nres=%d, k1=%d, precov[nres=%d][k1=%d]=%f Tvar[%d]=V%d V(k2q=%d)= Tvarsel[%d]=%d, Tvalsel[%d]=%f\n",nres, k1, nres, k1,precov[nres][k1], k1, Tvar[k1], k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);	/* printf("Decoderesult Quantitative with age nres=%d, k1=%d, precov[nres=%d][k1=%d]=%f Tvar[%d]=V%d V(k2q=%d)= Tvarsel[%d]=%d, Tvalsel[%d]=%f\n",nres, k1, nres, k1,precov[nres][k1], k1, Tvar[k1], k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]); */
}else if(Typevar[k1]==2 ){ /* For product quant or dummy (not with age) */	}else if(Typevar[k1]==2 ){ /* For product quant or dummy (not with age) */
precov[nres][k1]=TinvDoQresult[nres][Tvardk[k1][1]] * TinvDoQresult[nres][Tvardk[k1][2]];	precov[nres][k1]=TinvDoQresult[nres][Tvardk[k1][1]] * TinvDoQresult[nres][Tvardk[k1][2]];
printf("Decoderesult Quantitative or Dummy (not with age) nres=%d k1=%d precov[nres=%d][k1=%d]=%.f V%d(=%.f) * V%d(=%.f) \n",nres, k1, nres, k1,precov[nres][k1], Tvardk[k1][1], TinvDoQresult[nres][Tvardk[k1][1]], Tvardk[k1][2], TinvDoQresult[nres][Tvardk[k1][2]]);	/* printf("Decoderesult Quantitative or Dummy (not with age) nres=%d k1=%d precov[nres=%d][k1=%d]=%.f V%d(=%.f) * V%d(=%.f) \n",nres, k1, nres, k1,precov[nres][k1], Tvardk[k1][1], TinvDoQresult[nres][Tvardk[k1][1]], Tvardk[k1][2], TinvDoQresult[nres][Tvardk[k1][2]]); */
}else{	}else{
printf("Error Decoderesult probably a product Dummy[%d]==%d && Typevar[%d]==%d\n", k1, Dummy[k1], k1, Typevar[k1]);	printf("Error Decoderesult probably a product Dummy[%d]==%d && Typevar[%d]==%d\n", k1, Dummy[k1], k1, Typevar[k1]);
fprintf(ficlog,"Error Decoderesult probably a product Dummy[%d]==%d && Typevar[%d]==%d\n", k1, Dummy[k1], k1, Typevar[k1]);	fprintf(ficlog,"Error Decoderesult probably a product Dummy[%d]==%d && Typevar[%d]==%d\n", k1, Dummy[k1], k1, Typevar[k1]);
Line 10890 int decodemodel( char model[], int lasto	Line 11148 int decodemodel( char model[], int lasto
* Model V2 + V1 + V3age + V3 + V5V6 + V7V8 + V8age + V8	* Model V2 + V1 + V3age + V3 + V5V6 + V7V8 + V8age + V8
* k= 1 2 3 4 5 6 7 8	* k= 1 2 3 4 5 6 7 8
* cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8	* cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
* covar[k,i], value of kth covariate if not including age for individual i:	* covar[k,i], are for fixed covariates, value of kth covariate if not including age for individual i:
* covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)	* covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
* Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[2]=1 Tvar[4]=3 Tvar[8]=8	* Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
* if multiplied by age: V3age Tvar[3=V3age]=3 (V3) Tvar[7]=8 and	* if multiplied by age: V3age Tvar[3=V3age]=3 (V3) Tvar[7]=8 and
* Tage[++cptcovage]=k	* Tage[++cptcovage]=k
* if products, new covar are created after ncovcol with k1	* if products, new covar are created after ncovcol + nqv (quanti fixed) with k1
* Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11	* Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
* Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product	* Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
* Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8	* Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
* Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];	* Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
* Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted	* Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
* V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11	* V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
* < ncovcol=8 >	* < ncovcol=8 8 fixed covariate. Additional starts at 9 (V5V6) and 10(V7V8) >
* Model V2 + V1 + V3age + V3 + V5V6 + V7V8 + V8age + V8 d1 d1 d2 d2	* Model V2 + V1 + V3age + V3 + V5V6 + V7V8 + V8age + V8 d1 d1 d2 d2
* k= 1 2 3 4 5 6 7 8 9 10 11 12	* k= 1 2 3 4 5 6 7 8 9 10 11 12
* Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8	* Tvard[k]= 2 1 3 3 10 11 8 8 5 6 7 8
* p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}	* p Tvar[1]@12={2, 1, 3, 3, 9, 10, 8, 8}
* p Tprod[1]@2={ 6, 5}	* p Tprod[1]@2={ 6, 5}
*p Tvard[1][1]@4= {7, 8, 5, 6}	*p Tvard[1][1]@4= {7, 8, 5, 6}
* covar[k][i]= V2 V1 ? V3 V5V6? V7V8? ? V8	* covar[k][i]= V2 V1 ? V3 V5V6? V7V8? ? V8
Line 11050 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 11308 Dummy[k] 0=dummy (0 1), 1 quantitative (
Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\	Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\	Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);	Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
for(k=-1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}	for(k=-1;k<=NCOVMAX; k++){ Fixed[k]=0; Dummy[k]=0;}
for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0, ncovvt=0;k<=cptcovt; k++){ /* or cptocvt */	for(k=1;k<=NCOVMAX; k++){TvarFind[k]=0; TvarVind[k]=0;}
	for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0, ncovvt=0;k<=cptcovt; k++){ /* or cptocvt loop on k from model */
if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */	if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
Fixed[k]= 0;	Fixed[k]= 0;
Dummy[k]= 0;	Dummy[k]= 0;
Line 11139 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 11398 Dummy[k] 0=dummy (0 1), 1 quantitative (
TvarVQind[nqtveff]=k; /* TvarVQind[1]=1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple time varying quantitative variable */	TvarVQind[nqtveff]=k; /* TvarVQind[1]=1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple time varying quantitative variable */
TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */	TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
/* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable \/ /	/* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable \/ /
printf("Quasi TmodelQind[%d]=%d,Tvar[TmodelQind[%d]]=V%d, ncovcol=%d, nqv=%d, ntv=%d,Tvar[k]- ncovcol-nqv-ntv=%d\n",nqtveff,k,nqtveff,Tvar[k], ncovcol, nqv, ntv, Tvar[k]- ncovcol-nqv-ntv);	/* printf("Quasi TmodelQind[%d]=%d,Tvar[TmodelQind[%d]]=V%d, ncovcol=%d, nqv=%d, ntv=%d,Tvar[k]- ncovcol-nqv-ntv=%d\n",nqtveff,k,nqtveff,Tvar[k], ncovcol, nqv, ntv, Tvar[k]- ncovcol-nqv-ntv); */
printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);	/* printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv); */
}else if (Typevar[k] == 1) { /* product with age */	}else if (Typevar[k] == 1) { /* product with age */
ncova++;	ncova++;
TvarA[ncova]=Tvar[k];	TvarA[ncova]=Tvar[k];
Line 11322 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 11581 Dummy[k] 0=dummy (0 1), 1 quantitative (
printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);	printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
fprintf(ficlog,"Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);	fprintf(ficlog,"Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
}	}
printf("Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);	/* printf("Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]); */
printf(" modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype);	/* printf(" modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype); */
fprintf(ficlog,"Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);	fprintf(ficlog,"Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);
}	}
/* Searching for doublons in the model */	/* Searching for doublons in the model */
Line 12477 int main(int argc, char *argv[])	Line 12736 int main(int argc, char *argv[])
numlinepar++;	numlinepar++;
if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */	if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
z[0]=line[1];	z[0]=line[1];
	}else if(line[1]=='d'){ /* For debugging individual values of covariates in ficresilk */
	debugILK=1;printf("DebugILK\n");
}	}
/* printf("***line [1] = %c \n",line[1]); /	/* printf("***line [1] = %c \n",line[1]); /
fputs(line, stdout);	fputs(line, stdout);
Line 12490 int main(int argc, char *argv[])	Line 12751 int main(int argc, char *argv[])
covar=matrix(0,NCOVMAX,firstobs,lastobs); /*< used in readdata /	covar=matrix(0,NCOVMAX,firstobs,lastobs); /*< used in readdata /
if(nqv>=1)coqvar=matrix(1,nqv,firstobs,lastobs); /*< Fixed quantitative covariate /	if(nqv>=1)coqvar=matrix(1,nqv,firstobs,lastobs); /*< Fixed quantitative covariate /
if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,firstobs,lastobs); /*< Time varying quantitative covariate /	if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,firstobs,lastobs); /*< Time varying quantitative covariate /
if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,firstobs,lastobs); /*< Time varying covariate (dummy and quantitative)/	/* if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,firstobs,lastobs); /\*< Time varying covariate (dummy and quantitative)\/ */
	if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,ncovcol+nqv+1,ncovcol+nqv+ntv+nqtv,firstobs,lastobs); /*< Might be better /
cptcovn=0; /Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn/	cptcovn=0; /Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn/
/* v1+v2+v3+v2v4+v5age makes cptcovn = 5	/* v1+v2+v3+v2v4+v5age makes cptcovn = 5
v1+v2age+v2v3 makes cptcovn = 3	v1+v2age+v2v3 makes cptcovn = 3
Line 13774 Please run with mle=-1 to get a correct	Line 14036 Please run with mle=-1 to get a correct
case 13:	case 13:
num_filled=sscanf(line,"result:%[^\n]\n",resultlineori);	num_filled=sscanf(line,"result:%[^\n]\n",resultlineori);
nresult++; /* Sum of resultlines */	nresult++; /* Sum of resultlines */
printf("Result %d: result:%s\n",nresult, resultlineori);	/* printf("Result %d: result:%s\n",nresult, resultlineori); */
/* removefirstspace(&resultlineori); */	/* removefirstspace(&resultlineori); */

if(strstr(resultlineori,"v") !=0){	if(strstr(resultlineori,"v") !=0){
Line 13783 Please run with mle=-1 to get a correct	Line 14045 Please run with mle=-1 to get a correct
return 1;	return 1;
}	}
trimbb(resultline, resultlineori); /* Suppressing double blank in the resultline */	trimbb(resultline, resultlineori); /* Suppressing double blank in the resultline */
printf("Decoderesult resultline=\"%s\" resultlineori=\"%s\"\n", resultline, resultlineori);	/* printf("Decoderesult resultline=\"%s\" resultlineori=\"%s\"\n", resultline, resultlineori); */
if(nresult > MAXRESULTLINESPONE-1){	if(nresult > MAXRESULTLINESPONE-1){
printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINESPONE-1,nresult,rfileres);	printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINESPONE-1,nresult,rfileres);
fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINESPONE-1,nresult,rfileres);	fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINESPONE-1,nresult,rfileres);
Line 14120 Please run with mle=-1 to get a correct	Line 14382 Please run with mle=-1 to get a correct
/* Tvresult[nres][j] Name of the variable at position j in this resultline */	/* Tvresult[nres][j] Name of the variable at position j in this resultline */
/* Tresult[nres][j] Value of this variable at position j could be a float if quantitative */	/* Tresult[nres][j] Value of this variable at position j could be a float if quantitative */
/* We give up with the combinations!! */	/* We give up with the combinations!! */
printf("\n j=%d In computing T_ Dummy[modelresult[%d][%d]]=%d, modelresult[%d][%d]=%d cptcovs=%d, cptcoveff=%d Fixed[modelresult[nres][j]]=%d\n", j, nres, j, Dummy[modelresult[nres][j]],nres,j,modelresult[nres][j],cptcovs, cptcoveff,Fixed[modelresult[nres][j]]); /* end if dummy or quanti */	/* if(debugILK) */
	/* printf("\n j=%d In computing T_ Dummy[modelresult[%d][%d]]=%d, modelresult[%d][%d]=%d cptcovs=%d, cptcoveff=%d Fixed[modelresult[nres][j]]=%d\n", j, nres, j, Dummy[modelresult[nres][j]],nres,j,modelresult[nres][j],cptcovs, cptcoveff,Fixed[modelresult[nres][j]]); /\* end if dummy or quanti \/ /

if(Dummy[modelresult[nres][j]]==0){/* Dummy variable of the variable in position modelresult in the model corresponding to j in resultline */	if(Dummy[modelresult[nres][j]]==0){/* Dummy variable of the variable in position modelresult in the model corresponding to j in resultline */
printf("V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][j]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline */	/* printf("V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][j]); /\* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline \/ / /* TinvDoQresult[nres][Name of the variable] */
fprintf(ficlog,"V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][j]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline */	printf("V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]); /* Output of each value for the combination TKresult[nres], ordered by the covariate values in the resultline */
fprintf(ficrest,"V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][j]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline */	fprintf(ficlog,"V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline */
	fprintf(ficrest,"V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline */
if(Fixed[modelresult[nres][j]]==0){ /* Fixed */	if(Fixed[modelresult[nres][j]]==0){ /* Fixed */
printf("fixed ");fprintf(ficlog,"fixed ");fprintf(ficrest,"fixed ");	printf("fixed ");fprintf(ficlog,"fixed ");fprintf(ficrest,"fixed ");
}else{	}else{
Line 14294 Please run with mle=-1 to get a correct	Line 14558 Please run with mle=-1 to get a correct
free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);	free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);	free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);	free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,firstobs,lastobs);	/* if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,firstobs,lastobs); */
	if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,ncovcol+nqv+1,ncovcol+nqv+ntv+nqtv,firstobs,lastobs);
if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,firstobs,lastobs);	if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,firstobs,lastobs);
if(nqv>=1)free_matrix(coqvar,1,nqv,firstobs,lastobs);	if(nqv>=1)free_matrix(coqvar,1,nqv,firstobs,lastobs);
free_matrix(covar,0,NCOVMAX,firstobs,lastobs);	free_matrix(covar,0,NCOVMAX,firstobs,lastobs);

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Removed from v.1.339
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	Added in v.1.345