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Diff for /imach/src/imach.c between versions 1.318 and 1.328

version 1.318, 2022/05/24 08:10:59	version 1.328, 2022/07/27 17:40:48
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	Revision 1.328 2022/07/27 17:40:48 brouard
	Summary: valgrind bug fixed by initializing to zero DummyV as well as Tage

	Revision 1.327 2022/07/27 14:47:35 brouard
	Summary: Still a problem for one-step probabilities in case of quantitative variables

	Revision 1.326 2022/07/26 17:33:55 brouard
	Summary: some test with nres=1

	Revision 1.325 2022/07/25 14:27:23 brouard
	Summary: r30

	* imach.c (Module): Error cptcovn instead of nsd in bmij (was
	coredumped, revealed by Feiuno, thank you.

	Revision 1.324 2022/07/23 17:44:26 brouard
	* empty log message *

	Revision 1.323 2022/07/22 12:30:08 brouard
	* imach.c (Module): Output of Wald test in the htm file and not only in the log.

	Revision 1.322 2022/07/22 12:27:48 brouard
	* imach.c (Module): Output of Wald test in the htm file and not only in the log.

	Revision 1.321 2022/07/22 12:04:24 brouard
	Summary: r28

	* imach.c (Module): Output of Wald test in the htm file and not only in the log.

	Revision 1.320 2022/06/02 05:10:11 brouard
	* empty log message *

	Revision 1.319 2022/06/02 04:45:11 brouard
	* imach.c (Module): Adding the Wald tests from the log to the main
	htm for better display of the maximum likelihood estimators.

Revision 1.318 2022/05/24 08:10:59 brouard	Revision 1.318 2022/05/24 08:10:59 brouard
* imach.c (Module): Some attempts to find a bug of wrong estimates	* imach.c (Module): Some attempts to find a bug of wrong estimates
of confidencce intervals with product in the equation modelC	of confidencce intervals with product in the equation modelC
Line 851	Line 887

The same imach parameter file can be used but the option for mle should be -3.	The same imach parameter file can be used but the option for mle should be -3.

Agnès, who wrote this part of the code, tried to keep most of the	Agnès, who wrote this part of the code, tried to keep most of the
former routines in order to include the new code within the former code.	former routines in order to include the new code within the former code.

The output is very simple: only an estimate of the intercept and of	The output is very simple: only an estimate of the intercept and of
Line 1030 Important routines	Line 1066 Important routines
- Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)	- Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.	and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
- printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables	- printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if	o There are 2**cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.	race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.



Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).	Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
Institut national d'études démographiques, Paris.	Institut national d'études démographiques, Paris.
This software have been partly granted by Euro-REVES, a concerted action	This software have been partly granted by Euro-REVES, a concerted action
from the European Union.	from the European Union.
It is copyrighted identically to a GNU software product, ie programme and	It is copyrighted identically to a GNU software product, ie programme and
Line 1100 Important routines	Line 1136 Important routines
#define POWELLNOF3INFF1TEST /* Skip test */	#define POWELLNOF3INFF1TEST /* Skip test */
/* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test \/ /	/* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test \/ /
/* #define MNBRAKORIGINAL /\* Don't use mnbrak fix \/ /	/* #define MNBRAKORIGINAL /\* Don't use mnbrak fix \/ /
	/* #define FLATSUP // Suppresses directions where likelihood is flat */

#include <math.h>	#include <math.h>
#include <stdio.h>	#include <stdio.h>
Line 1166 typedef struct {	Line 1203 typedef struct {
#define NINTERVMAX 8	#define NINTERVMAX 8
#define NLSTATEMAX 8 /*< Maximum number of live states (for func) /	#define NLSTATEMAX 8 /*< Maximum number of live states (for func) /
#define NDEATHMAX 8 /*< Maximum number of dead states (for func) /	#define NDEATHMAX 8 /*< Maximum number of dead states (for func) /
#define NCOVMAX 30 /*< Maximum number of covariates, including generated covariates V1V2 */	#define NCOVMAX 30 /*< Maximum number of covariates used in the model, including generated covariates V1V2 or V1age /
#define codtabm(h,k) (1 & (h-1) >> (k-1))+1	#define codtabm(h,k) (1 & (h-1) >> (k-1))+1
/#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)/	/#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)/
#define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1	#define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
Line 1194 typedef struct {	Line 1231 typedef struct {
/* $State$ */	/* $State$ */
#include "version.h"	#include "version.h"
char version[]=__IMACH_VERSION__;	char version[]=__IMACH_VERSION__;
char copyright[]="May 2022,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2020, Nihon University 2021-202, INED 2000-2022";	char copyright[]="July 2022,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2020, Nihon University 2021-202, INED 2000-2022";
char fullversion[]="$Revision$ $Date$";	char fullversion[]="$Revision$ $Date$";
char strstart[80];	char strstart[80];
char optionfilext[10], optionfilefiname[FILENAMELENGTH];	char optionfilext[10], optionfilefiname[FILENAMELENGTH];
Line 1376 double **cotvar; / Time varying covari	Line 1413 double **cotvar; / Time varying covari
double **cotqvar; / Time varying quantitative covariate itqv */	double **cotqvar; / Time varying quantitative covariate itqv */
double idx;	double idx;
int *nbcode, Tvar; /*< model=V2 => Tvar[1]= 2 /	int *nbcode, Tvar; /*< model=V2 => Tvar[1]= 2 /
	/* Some documentation */
	/* Design original data
	* V1 V2 V3 V4 V5 V6 V7 V8 Weight ddb ddth d1st s1 V9 V10 V11 V12 s2 V9 V10 V11 V12
	* < ncovcol=6 > nqv=2 (V7 V8) dv dv dv qtv dv dv dvv qtv
	* ntv=3 nqtv=1
	* cptcovn number of covariates (not including constant and age) = # of + plus 1 = 10+1=11
	* For time varying covariate, quanti or dummies
	* 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][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
	* covar[k,i], value of kth fixed covariate dummy or quanti :
	* covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
	* Model V2 + V1 + V3age + V3 + V5V6 + V7V8 + V8age + V8 + V9 + V9*age + V10
	* k= 1 2 3 4 5 6 7 8 9 10 11
	*/
	/* According to the model, more columns can be added to covar by the product of covariates */
/* ncovcol=1(Males=0 Females=1) nqv=1(raedyrs) ntv=2(withoutiadl=0 withiadl=1, witoutadl=0 withoutadl=1) nqtv=1(bmi) nlstate=3 ndeath=1	/* ncovcol=1(Males=0 Females=1) nqv=1(raedyrs) ntv=2(withoutiadl=0 withiadl=1, witoutadl=0 withoutadl=1) nqtv=1(bmi) nlstate=3 ndeath=1
# 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 /	/* k 1 2 3 4 5 6 7 8 9 */
/Tvar[k]= 5 4 3 6 5 2 7 1 1 /	/Typevar[k]= 0 0 0 2 1 0 2 1 0 //0 for simple covariate (dummy, quantitative,/
/* Tndvar[k] 1 2 3 4 5 */	/* fixed or varying), 1 for age product, 2 for*/
/TDvar 4 3 6 7 1 / /* For outputs only; combination of dummies fixed or varying */	/* product */
/* Tns[k] 1 2 2 4 5 / / Number of single cova */	/Dummy[k]= 1 0 0 1 3 1 1 2 0 //Dummy[k] 0=dummy (0 1), 1 quantitative /
/* TvarsD[k] 1 2 3 / / Number of single dummy cova */	/(single or product without age), 2 dummy/
/* TvarsDind 2 3 9 / / position K of single dummy cova */	/* with age product, 3 quant with age product*/
/* TvarsQ[k] 1 2 / / Number of single quantitative cova */	/Tvar[k]= 5 4 3 6 5 2 7 1 1 /
/* TvarsQind 1 6 / / position K of single quantitative cova */	/* nsd 1 2 3 / / Counting single dummies covar fixed or tv */
/* Tprod[i]=k 4 7 */	/TvarsD[nsd] 4 3 1 / /* ID of single dummy cova fixed or timevary*/
/* Tage[i]=k 5 8 */	/TvarsDind[k] 2 3 9 / /* position K of single dummy cova */
/* */	/* nsq 1 2 / / Counting single quantit tv */
	/* TvarsQ[k] 5 2 / / Number of single quantitative cova */
	/* TvarsQind 1 6 / / position K of single quantitative cova */
	/* Tprod[i]=k 1 2 / / Position in model of the ith prod without age */
	/* cptcovage 1 2 / / Counting covage in the model equation /
	/* Tage[cptcovage]=k 5 8 / / Position in the model of ith covage /
	/* Tvard[1][1]@4={4,3,1,2} V4V3 V1V2 / / Position in model of the ith prod without age */
	/* TvarF TvarF[1]=Tvar[6]=2, TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1 ID of fixed covariates or product V2, V1V2, V1 /
	/* TvarFind; TvarFind[1]=6, TvarFind[2]=7, TvarFind[3]=9 // Inverse V2(6) is first fixed (single or prod) */
/* Type */	/* Type */
/* V 1 2 3 4 5 */	/* V 1 2 3 4 5 */
/* F F V V V */	/* F F V V V */
Line 2363 void powell(double p[], double **xi, int	Line 2425 void powell(double p[], double **xi, int
double fp,fptt;	double fp,fptt;
double *xits;	double *xits;
int niterf, itmp;	int niterf, itmp;
#ifdef LINMINORIGINAL
#else

flatdir=ivector(1,n);
for (j=1;j<=n;j++) flatdir[j]=0;
#endif

pt=vector(1,n);	pt=vector(1,n);
ptt=vector(1,n);	ptt=vector(1,n);
Line 2378 void powell(double p[], double **xi, int	Line 2434 void powell(double p[], double **xi, int
for (j=1;j<=n;j++) pt[j]=p[j];	for (j=1;j<=n;j++) pt[j]=p[j];
rcurr_time = time(NULL);	rcurr_time = time(NULL);
for (iter=1;;++(iter)) {	for (iter=1;;++(iter)) {
fp=(fret); / From former iteration or initial value */
ibig=0;	ibig=0;
del=0.0;	del=0.0;
rlast_time=rcurr_time;	rlast_time=rcurr_time;
/* (void) gettimeofday(&curr_time,&tzp); */	/* (void) gettimeofday(&curr_time,&tzp); */
rcurr_time = time(NULL);	rcurr_time = time(NULL);
curr_time = *localtime(&rcurr_time);	curr_time = *localtime(&rcurr_time);
printf("\nPowell iter=%d -2LL=%.12f %ld sec. %ld sec.",iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);	printf("\nPowell iter=%d -2LL=%.12f gain=%.12f=%.3g %ld sec. %ld sec.",iter,fret, fp-fret,fp-*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
fprintf(ficlog,"\nPowell iter=%d -2LL=%.12f %ld sec. %ld sec.",iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);	fprintf(ficlog,"\nPowell iter=%d -2LL=%.12f gain=%.12f=%.3g %ld sec. %ld sec.",iter,fret, fp-fret,fp-*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
/* fprintf(ficrespow,"%d %.12f %ld",iter,fret,curr_time.tm_sec-start_time.tm_sec); */	/* fprintf(ficrespow,"%d %.12f %ld",iter,fret,curr_time.tm_sec-start_time.tm_sec); */
	fp=(fret); / From former iteration or initial value */
for (i=1;i<=n;i++) {	for (i=1;i<=n;i++) {
fprintf(ficrespow," %.12lf", p[i]);	fprintf(ficrespow," %.12lf", p[i]);
}	}
Line 2492 void powell(double p[], double **xi, int	Line 2548 void powell(double p[], double **xi, int
/* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */	/* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
/* But p and xit have been updated at the end of linmin, fret corresponds to new p, xit /	/* But p and xit have been updated at the end of linmin, fret corresponds to new p, xit /
/* New value of last point Pn is not computed, P(n-1) */	/* New value of last point Pn is not computed, P(n-1) */
for(j=1;j<=n;j++) {	for(j=1;j<=n;j++) {
if(flatdir[j] >0){	if(flatdir[j] >0){
printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);	printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);	fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
}
/* printf("\n"); */
/* fprintf(ficlog,"\n"); */
}	}
	/* printf("\n"); */
	/* fprintf(ficlog,"\n"); */
	}
/* if (2.0fabs(fp-(fret)) <= ftol(fabs(fp)+fabs(fret))) { /\* Did we reach enough precision? \/ /	/* if (2.0fabs(fp-(fret)) <= ftol(fabs(fp)+fabs(fret))) { /\* Did we reach enough precision? \/ /
if (2.0fabs(fp-(fret)) <= ftol) { /* Did we reach enough precision? */	if (2.0fabs(fp-(fret)) <= ftol) { /* Did we reach enough precision? */
/* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */	/* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
Line 2537 void powell(double p[], double **xi, int	Line 2593 void powell(double p[], double **xi, int
}	}
#endif	#endif

#ifdef LINMINORIGINAL
#else
free_ivector(flatdir,1,n);
#endif
free_vector(xit,1,n);	free_vector(xit,1,n);
free_vector(xits,1,n);	free_vector(xits,1,n);
free_vector(ptt,1,n);	free_vector(ptt,1,n);
Line 2654 void powell(double p[], double **xi, int	Line 2706 void powell(double p[], double **xi, int
}	}
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
	#ifdef FLATSUP
	free_vector(xit,1,n);
	free_vector(xits,1,n);
	free_vector(ptt,1,n);
	free_vector(pt,1,n);
	return;
	#endif
}	}
#endif	#endif
printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);	printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
Line 2738 void powell(double p[], double **xi, int	Line 2797 void powell(double p[], double **xi, int
newm=savm;	newm=savm;
/* Covariates have to be included here again */	/* Covariates have to be included here again */
cov[2]=agefin;	cov[2]=agefin;
if(nagesqr==1)	if(nagesqr==1){
cov[3]= agefin*agefin;;	cov[3]= agefin*agefin;
	}
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)];
	/* cov[++k1]=nbcode[TvarsD[k]][codtabm(ij,k)]; */
/* printf("prevalim Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */	/* printf("prevalim Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
}	}
for (k=1; k<=nsq;k++) { /* For single varying covariates only */	for (k=1; k<=nsq;k++) { /* For single varying covariates only */
/* Here comes the value of quantitative after renumbering k with single quantitative covariates */	/* Here comes the value of quantitative after renumbering k with single quantitative covariates */
cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];	cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
	/* cov[++k1]=Tqresult[nres][k]; */
/* printf("prevalim Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */	/* printf("prevalim Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
}	}
for (k=1; k<=cptcovage;k++){ /* For product with age */	for (k=1; k<=cptcovage;k++){ /* For product with age */
if(Dummy[Tvar[Tage[k]]]){	if(Dummy[Tage[k]]==2){ /* dummy with age */
cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];	cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
} else{	/* cov[++k1]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]cov[2]; /
cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];	} else if(Dummy[Tage[k]]==3){ /* quantitative with age */
	cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
	/* cov[++k1]=Tqresult[nres][k]; */
}	}
/* printf("prevalim Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */	/* printf("prevalim Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
}	}
Line 2763 void powell(double p[], double **xi, int	Line 2827 void powell(double p[], double **xi, int
if(Dummy[Tvard[k][1]==0]){	if(Dummy[Tvard[k][1]==0]){
if(Dummy[Tvard[k][2]==0]){	if(Dummy[Tvard[k][2]==0]){
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
	/* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
}else{	}else{
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
	/* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k]; */
}	}
}else{	}else{
if(Dummy[Tvard[k][2]==0]){	if(Dummy[Tvard[k][2]==0]){
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
	/* cov[++k1]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]]; */
}else{	}else{
cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];	cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
	/* cov[++k1]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]]; */
}	}
}	}
}	}
Line 2779 void powell(double p[], double **xi, int	Line 2847 void powell(double p[], double **xi, int
/printf("ij=%d cov[3]=%lf \n",ij, cov[3]);/	/printf("ij=%d cov[3]=%lf \n",ij, cov[3]);/
/* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */	/* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
/* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind \/ /	/* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind \/ /
/* age and covariate values of ij are in 'cov' */	/* age and covariate values of ij are in 'cov' */
out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */	out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */

savm=oldm;	savm=oldm;
Line 2902 void powell(double p[], double **xi, int	Line 2970 void powell(double p[], double **xi, int
/* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */	/* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
/* Covariates have to be included here again */	/* Covariates have to be included here again */
cov[2]=agefin;	cov[2]=agefin;
if(nagesqr==1)	if(nagesqr==1){
cov[3]= agefin*agefin;;	cov[3]= agefin*agefin;;
	}
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)];
Line 2924 void powell(double p[], double **xi, int	Line 2993 void powell(double p[], double **xi, int
/* /\* 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])]; \/ /
/* 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)]; */
for (k=1; k<=cptcovage;k++){ /* For product with age */	for (k=1; k<=cptcovage;k++){ /* For product with age */
if(Dummy[Tvar[Tage[k]]]){	/* if(Dummy[Tvar[Tage[k]]]== 2){ /\* dummy with age \/ ERROR ???/
	if(Dummy[Tage[k]]== 2){ /* dummy with age */
cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];	cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
} else{	} else if(Dummy[Tage[k]]== 3){ /* quantitative with age */
cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];	cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
}	}
/* printf("prevalim Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */	/* printf("prevalim Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
}	}
Line 3083 double pmij(double ps, double *cov,	Line 3153 double pmij(double ps, double *cov,
ps[i][i]=1./(s1+1.);	ps[i][i]=1./(s1+1.);
/* Computing other pijs */	/* Computing other pijs */
for(j=1; j<i; j++)	for(j=1; j<i; j++)
ps[i][j]= exp(ps[i][j])*ps[i][i];	ps[i][j]= exp(ps[i][j])ps[i][i];/ Bug valgrind */
for(j=i+1; j<=nlstate+ndeath; j++)	for(j=i+1; j<=nlstate+ndeath; j++)
ps[i][j]= exp(ps[i][j])*ps[i][i];	ps[i][j]= exp(ps[i][j])*ps[i][i];
/* ps[i][nlstate+1]=1.-s1- ps[i][i];/ / Sum should be 1 */	/* ps[i][nlstate+1]=1.-s1- ps[i][i];/ / Sum should be 1 */
Line 3141 double pmij(double ps, double *cov,	Line 3211 double pmij(double ps, double *cov,
/* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */	/* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */

/* P_x */	/* P_x */
pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /This is forward probability from agefin to agefin + stepm /	pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /This is forward probability from agefin to agefin + stepm //* Bug valgrind */
/* outputs pmmij which is a stochastic matrix in row */	/* outputs pmmij which is a stochastic matrix in row */

/* Diag(w_x) */	/* Diag(w_x) */
Line 3353 double *hpxij(double *po, int nhstep	Line 3423 double *hpxij(double *po, int nhstep
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-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<=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 */
	/* codtabm(ij,k) (1 & (ij-1) >> (k-1))+1 */
	/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
	/* k 1 2 3 4 5 6 7 8 9 */
	/Tvar[k]= 5 4 3 6 5 2 7 1 1 /
	/* nsd 1 2 3 / / Counting single dummies covar fixed or tv */
	/TvarsD[nsd] 4 3 1 / /* ID of single dummy cova fixed or timevary*/
	/TvarsDind[k] 2 3 9 / /* position K of single dummy cova */
cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];	cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
/* printf("hpxij Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */	/* printf("hpxij Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
}	}
for (k=1; k<=nsq;k++) { /* For single varying covariates only */	for (k=1; k<=nsq;k++) { /* For single varying covariates only */
/* Here comes the value of quantitative after renumbering k with single quantitative covariates */	/* Here comes the value of quantitative after renumbering k with single quantitative covariates */
cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];	cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
/* printf("hPxij Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */	/* printf("hPxij Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
}	}
for (k=1; k<=cptcovage;k++){	for (k=1; k<=cptcovage;k++){ /* For product with age V1+V1age +V4 +ageV3 */
if(Dummy[Tvar[Tage[k]]]){	/* 1+2 Tage[1]=2 TVar[2]=1 Dummy[2]=2, Tage[2]=4 TVar[4]=3 Dummy[4]=3 quant*/
	/* */
	if(Dummy[Tage[k]]== 2){ /* dummy with age */
	/* if(Dummy[Tvar[Tage[k]]]== 2){ /\* dummy with age \/ /
cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];	cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
} else{	} else if(Dummy[Tage[k]]== 3){ /* quantitative with age */
cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];	cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
}	}
/* printf("hPxij Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */	/* printf("hPxij Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
}	}
for (k=1; k<=cptcovprod;k++){ /* */	for (k=1; k<=cptcovprod;k++){ /* For product without age */
/* printf("hPxij Prod ij=%d k=%d Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */	/* printf("hPxij Prod ij=%d k=%d Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];	/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
	if(Dummy[Tvard[k][1]==0]){
	if(Dummy[Tvard[k][2]==0]){
	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
	}else{
	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
	}
	}else{
	if(Dummy[Tvard[k][2]==0]){
	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
	}else{
	cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
	}
	}
}	}
/* 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)]; */
Line 3387 double *hpxij(double *po, int nhstep	Line 3481 double *hpxij(double *po, int nhstep

/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]);/
/* right multiplication of oldm by the current matrix */	/* right multiplication of oldm by the current matrix */
out=matprod2(newm,oldm,1,nlstate+ndeath,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));	pmij(pmmij,cov,ncovmodel,x,nlstate));
/* if((int)age == 70){ */	/* if((int)age == 70){ */
Line 3462 double *hbxij(double *po, int nhstep	Line 3556 double *hbxij(double *po, int nhstep
cov[2]=agexact;	cov[2]=agexact;
if(nagesqr==1)	if(nagesqr==1)
cov[3]= agexact*agexact;	cov[3]= agexact*agexact;
for (k=1; k<=cptcovn;k++){	for (k=1; k<=nsd;k++){ /* For single dummy covariates only // cptcovn error */
/* 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)];	cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];/* Bug valgrind */
/* 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)); */	/* 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<=nsq;k++) { /* For single varying covariates only */	for (k=1; k<=nsq;k++) { /* For single varying covariates only */
Line 3473 double *hbxij(double *po, int nhstep	Line 3567 double *hbxij(double *po, int nhstep
cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];	cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
/* printf("hPxij Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */	/* printf("hPxij Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
}	}
for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 */	for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 // For product with age */
if(Dummy[Tvar[Tage[k]]]){	/* if(Dummy[Tvar[Tage[k]]]== 2){ /\* dummy with age error!!!\/ /
	if(Dummy[Tage[k]]== 2){ /* dummy with age */
cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];	cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
} else{	} else if(Dummy[Tage[k]]== 3){ /* quantitative with age */
cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];	cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
}	}
/* printf("hBxij Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */	/* printf("hBxij Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
}	}
for (k=1; k<=cptcovprod;k++){ /* Useless because included in cptcovn */	for (k=1; k<=cptcovprod;k++){ /* Useless because included in cptcovn */
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
	if(Dummy[Tvard[k][1]==0]){
	if(Dummy[Tvard[k][2]==0]){
	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
	}else{
	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
	}
	}else{
	if(Dummy[Tvard[k][2]==0]){
	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
	}else{
	cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
	}
	}
}	}
/printf("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]);/
Line 3492 double *hbxij(double *po, int nhstep	Line 3600 double *hbxij(double *po, int nhstep
/* 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),\
1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);	1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);/* Bug valgrind */
/* if((int)age == 70){ */	/* if((int)age == 70){ */
/* printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */	/* printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
/* for(i=1; i<=nlstate+ndeath; i++) { */	/* for(i=1; i<=nlstate+ndeath; i++) { */
Line 3578 double func( double *x)	Line 3686 double func( double *x)
*/	*/
ioffset=2+nagesqr ;	ioffset=2+nagesqr ;
/* Fixed */	/* Fixed */
for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */	for (k=1; k<=ncovf;k++){ /* For each fixed covariate dummu or quant or prod */
cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, only V1 is fixed (k=6)*/	/* # 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 */
	/* TvarF[1]=Tvar[6]=2, TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1 ID of fixed covariates or product V2, V1V2, V1 /
	/* TvarFind; TvarFind[1]=6, TvarFind[2]=7, TvarFind[3]=9 // Inverse V2(6) is first fixed (single or prod) */
	cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, only V1 is fixed (TvarFind[1]=6)*/
	/* V1V2 (7) TvarFind[2]=7, TvarFind[3]=9 /
}	}
/* In model V2+V1V4+ageV3+V3V2 Tvar[1] is V2, Tvar[2=V1V4]	/* In model V2+V1V4+ageV3+V3V2 Tvar[1] is V2, Tvar[2=V1V4]
is 6, Tvar[3=ageV3] should not be computed because of age Tvar[4=V3V2]	is 5, Tvar[3=ageV3] should not be computed because of age Tvar[4=V3V2]=6
has been calculated etc */	has been calculated etc */
/* For an individual i, wav[i] gives the number of effective waves */	/* For an individual i, wav[i] gives the number of effective waves */
/* We compute the contribution to Likelihood of each effective transition	/* We compute the contribution to Likelihood of each effective transition
Line 3594 double func( double *x)	Line 3707 double func( double *x)
meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]	meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
*/	*/
for(mi=1; mi<= wav[i]-1; mi++){	for(mi=1; mi<= wav[i]-1; mi++){
for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/	for(k=1; k <= ncovv ; k++){ /* Varying covariates in the model (single and product but no age )"V5+V4+V3+V4V3+V5age+V1age+V1" +TvarVind 1,2,3,4(V4V3) Tvar[1]@7{5, 4, 3, 6, 5, 1, 1 ; 6 because the created covar is after V5 and is 6, minus 1+1, 3,2,1,4 positions in cotvar*/
/* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */	/* 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 (ii=1;ii<=nlstate+ndeath;ii++)	for (ii=1;ii<=nlstate+ndeath;ii++)
Line 3721 double func( double *x)	Line 3834 double func( double *x)
} /* end of individual */	} /* end of individual */
} else if(mle==2){	} else if(mle==2){
for (i=1,ipmx=0, sw=0.; i<=imx; i++){	for (i=1,ipmx=0, sw=0.; i<=imx; i++){
for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];	ioffset=2+nagesqr ;
	for (k=1; k<=ncovf;k++)
	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++){
	cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
	}
for (ii=1;ii<=nlstate+ndeath;ii++)	for (ii=1;ii<=nlstate+ndeath;ii++)
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
oldm[ii][j]=(ii==j ? 1.0 : 0.0);	oldm[ii][j]=(ii==j ? 1.0 : 0.0);
Line 4079 void likelione(FILE *ficres,double p[],	Line 4197 void likelione(FILE *ficres,double p[],

void mlikeli(FILE ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (func)(double []))	void mlikeli(FILE ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (func)(double []))
{	{
int i,j, iter=0;	int i,j,k, jk, jkk=0, iter=0;
double **xi;	double **xi;
double fret;	double fret;
double fretone; /* Only one call to likelihood */	double fretone; /* Only one call to likelihood */
Line 4113 void mlikeli(FILE *ficres,double p[], in	Line 4231 void mlikeli(FILE *ficres,double p[], in
if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);	if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
fprintf(ficrespow,"\n");	fprintf(ficrespow,"\n");
#ifdef POWELL	#ifdef POWELL
	#ifdef LINMINORIGINAL
	#else /* LINMINORIGINAL */

	flatdir=ivector(1,npar);
	for (j=1;j<=npar;j++) flatdir[j]=0;
	#endif /LINMINORIGINAL /

	#ifdef FLATSUP
	powell(p,xi,npar,ftol,&iter,&fret,flatdir,func);
	/* reorganizing p by suppressing flat directions */
	for(i=1, jk=1; i <=nlstate; i++){
	for(k=1; k <=(nlstate+ndeath); k++){
	if (k != i) {
	printf("%d%d flatdir[%d]=%d",i,k,jk, flatdir[jk]);
	if(flatdir[jk]==1){
	printf(" To be skipped %d%d flatdir[%d]=%d ",i,k,jk, flatdir[jk]);
	}
	for(j=1; j <=ncovmodel; j++){
	printf("%12.7f ",p[jk]);
	jk++;
	}
	printf("\n");
	}
	}
	}
	/* skipping */
	/* for(i=1, jk=1, jkk=1;(flatdir[jk]==0)&& (i <=nlstate); i++){ */
	for(i=1, jk=1, jkk=1;i <=nlstate; i++){
	for(k=1; k <=(nlstate+ndeath); k++){
	if (k != i) {
	printf("%d%d flatdir[%d]=%d",i,k,jk, flatdir[jk]);
	if(flatdir[jk]==1){
	printf(" To be skipped %d%d flatdir[%d]=%d jk=%d p[%d] ",i,k,jk, flatdir[jk],jk, jk);
	for(j=1; j <=ncovmodel; jk++,j++){
	printf(" p[%d]=%12.7f",jk, p[jk]);
	/q[jjk]=p[jk];/
	}
	}else{
	printf(" To be kept %d%d flatdir[%d]=%d jk=%d q[%d]=p[%d] ",i,k,jk, flatdir[jk],jk, jkk, jk);
	for(j=1; j <=ncovmodel; jk++,jkk++,j++){
	printf(" p[%d]=%12.7f=q[%d]",jk, p[jk],jkk);
	/q[jjk]=p[jk];/
	}
	}
	printf("\n");
	}
	fflush(stdout);
	}
	}
	powell(p,xi,npar,ftol,&iter,&fret,flatdir,func);
	#else /* FLATSUP */
powell(p,xi,npar,ftol,&iter,&fret,func);	powell(p,xi,npar,ftol,&iter,&fret,func);
#endif	#endif /* FLATSUP */

	#ifdef LINMINORIGINAL
	#else
	free_ivector(flatdir,1,npar);
	#endif /* LINMINORIGINAL*/
	#endif /* POWELL */

#ifdef NLOPT	#ifdef NLOPT
#ifdef NEWUOA	#ifdef NEWUOA
Line 4142 void mlikeli(FILE *ficres,double p[], in	Line 4317 void mlikeli(FILE *ficres,double p[], in
}	}
nlopt_destroy(opt);	nlopt_destroy(opt);
#endif	#endif
	#ifdef FLATSUP
	/* npared = npar -flatd/ncovmodel; */
	/* xired= matrix(1,npared,1,npared); */
	/* paramred= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */
	/* powell(pred,xired,npared,ftol,&iter,&fret,flatdir,func); */
	/* free_matrix(xire,1,npared,1,npared); */
	#else /* FLATSUP */
	#endif /* FLATSUP */
free_matrix(xi,1,npar,1,npar);	free_matrix(xi,1,npar,1,npar);
fclose(ficrespow);	fclose(ficrespow);
printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));	printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
Line 4593 void freqsummary(char fileres[], double	Line 4776 void freqsummary(char fileres[], double
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\	Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);	fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
}	}
fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition and dummy covariate value at beginning of transition</h4>\n",fileresphtm, fileresphtm);	fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies (weight=%d) and prevalence by age at begin of transition and dummy covariate value at beginning of transition</h4>\n",fileresphtm, fileresphtm, weightopt);

strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));	strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {	if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
Line 4603 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4786 Title=%s <br>Datafile=%s Firstpass=%d La
exit(70);	exit(70);
} else{	} else{
fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \	fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
<hr size=\"2\" color=\"#EC5E5E\"> \n \	,<hr size=\"2\" color=\"#EC5E5E\"> \n \
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\	Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);	fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
}	}
fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions 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>(weight=%d) 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,weightopt);

y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);	y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);	x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
Line 4785 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4968 Title=%s <br>Datafile=%s Firstpass=%d La
/* } */	/* } */
} /* end bool */	} /* end bool */
} /* end iind = 1 to imx */	} /* end iind = 1 to imx */
/* prop[s][age] is feeded for any initial and valid live state as well as	/* prop[s][age] is fed for any initial and valid live state as well as
freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */	freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */


Line 5980 void concatwav(int wav[], int **dh, int	Line 6163 void concatwav(int wav[], int **dh, int
varhe[ij][ji][(int)age] += doldm[ij][ji]hfhf;	varhe[ij][ji][(int)age] += doldm[ij][ji]hfhf;
}	}
}	}
	/* if((int)age ==50){ */
	/* printf(" age=%d cij=%d nres=%d varhe[%d][%d]=%f ",(int)age, cij, nres, 1,2,varhe[1][2]); */
	/* } */
/* Computing expectancies */	/* Computing expectancies */
hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);	hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
Line 6643 void varprob(char optionfilefiname[], do	Line 6828 void varprob(char optionfilefiname[], do
int k2, l2, j1, z1;	int k2, l2, j1, z1;
int k=0, l;	int k=0, l;
int first=1, first1, first2;	int first=1, first1, first2;
	int nres=0; /* New */
double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;	double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
double dnewm,doldm;	double dnewm,doldm;
double *xp;	double *xp;
Line 6731 To be simple, these graphs help to under	Line 6917 To be simple, these graphs help to under
if (cptcovn<1) {tj=1;ncodemax[1]=1;}	if (cptcovn<1) {tj=1;ncodemax[1]=1;}
j1=0;	j1=0;
for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates or only once*/	for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates or only once*/
	for(nres=1;nres <=1; nres++){ /* For each resultline */
	/* for(nres=1;nres <=nresult; nres++){ /\* For each resultline \/ /
if (cptcovn>0) {	if (cptcovn>0) {
fprintf(ficresprob, "\n#********** Variable ");	fprintf(ficresprob, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
Line 6745 To be simple, these graphs help to under	Line 6933 To be simple, these graphs help to under


fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");	fprintf(fichtmcov, "\n<hr size=\"2\" color=\"#EC5E5E\">********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	/* for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]); */
	for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtmcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");	fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");

fprintf(ficresprobcor, "\n#********** Variable ");	fprintf(ficresprobcor, "\n#********** Variable ");
Line 6765 To be simple, these graphs help to under	Line 6954 To be simple, these graphs help to under
cov[2]=age;	cov[2]=age;
if(nagesqr==1)	if(nagesqr==1)
cov[3]= age*age;	cov[3]= age*age;
for (k=1; k<=cptcovn;k++) {	/* for (k=1; k<=cptcovn;k++) { */
cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];	/* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)]; */
	for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
	/* Here comes the value of the covariate 'j1' after renumbering k with single dummy covariates */
	cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(j1,k)];
/cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];//* j1 1 2 3 4	/cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];//* j1 1 2 3 4
* 1 1 1 1 1	* 1 1 1 1 1
* 2 2 1 1 1	* 2 2 1 1 1
Line 6774 To be simple, these graphs help to under	Line 6966 To be simple, these graphs help to under
*/	*/
/* nbcode[1][1]=0 nbcode[1][2]=1;*/	/* nbcode[1][1]=0 nbcode[1][2]=1;*/
}	}
/* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; /	/* V2+V1+V4+V3age Tvar[4]=3 ; V1+V2age Tvar[2]=2; V1+V1age Tvar[2]=1, Tage[1]=2 /
for (k=1; k<=cptcovage;k++) cov[2+Tage[k]+nagesqr]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];	/* ) p nbcode[Tvar[Tage[k]]][(1 & (ij-1) >> (k-1))+1] */
for (k=1; k<=cptcovprod;k++)	/for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; */
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];	for (k=1; k<=cptcovage;k++){ /* For product with age */
	if(Dummy[Tage[k]]==2){ /* dummy with age */
	cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(j1,k)]*cov[2];
	/* cov[++k1]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]cov[2]; /
	} else if(Dummy[Tage[k]]==3){ /* quantitative with age */
	printf("Internal IMaCh error, don't know which value for quantitative covariate with age, Tage[k]%d, k=%d, Tvar[Tage[k]]=V%d, age=%d\n",Tage[k],k ,Tvar[Tage[k]], (int)cov[2]);
	exit(1);
	/* cov[2+nagesqr+Tage[k]]=meanq[k]/idq[k]cov[2];/\ Using the mean of quantitative variable Tvar[Tage[k]] /\* Tqresult[nres][k]; \/ /
	/* cov[++k1]=Tqresult[nres][k]; */
	}
	/* cov[2+Tage[k]+nagesqr]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]cov[2]; /
	}
	for (k=1; k<=cptcovprod;k++){/* For product without age */
	if(Dummy[Tvard[k][1]==0]){
	if(Dummy[Tvard[k][2]==0]){
	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(j1,k)] * nbcode[Tvard[k][2]][codtabm(j1,k)];
	/* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
	}else{ /* Should we use the mean of the quantitative variables? */
	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(j1,k)] * Tqresult[nres][k];
	/* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k]; */
	}
	}else{
	if(Dummy[Tvard[k][2]==0]){
	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(j1,k)] * Tqinvresult[nres][Tvard[k][1]];
	/* cov[++k1]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]]; */
	}else{
	cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
	/* cov[++k1]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]]; */
	}
	}
	/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]nbcode[Tvard[k][2]][codtabm(ij,k)]; /
	}
	/* For each age and combination of dummy covariates we slightly move the parameters of delti in order to get the gradient*/
for(theta=1; theta <=npar; theta++){	for(theta=1; theta <=npar; theta++){
for(i=1; i<=npar; i++)	for(i=1; i<=npar; i++)
xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);	xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
Line 6964 To be simple, these graphs help to under	Line 7186 To be simple, these graphs help to under
} /* k12 */	} /* k12 */
} /l1 /	} /l1 /
}/* k1 */	}/* k1 */
	} /* loop on nres */
} /* loop on combination of covariates j1 */	} /* loop on combination of covariates j1 */
free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);	free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);	free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
Line 6986 void printinghtml(char fileresu[], char	Line 7209 void printinghtml(char fileresu[], char
double jprev1, double mprev1,double anprev1, double dateprev1, double dateprojd, double dateback1, \	double jprev1, double mprev1,double anprev1, double dateprev1, double dateprojd, double dateback1, \
double jprev2, double mprev2,double anprev2, double dateprev2, double dateprojf, double dateback2){	double jprev2, double mprev2,double anprev2, double dateprev2, double dateprojf, double dateback2){
int jj1, k1, i1, cpt, k4, nres;	int jj1, k1, i1, cpt, k4, nres;
	/* In fact some results are already printed in fichtm which is open */
fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \	fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
<li><a href='#secondorder'>Result files (second order (variance)</a>\n \	<li><a href='#secondorder'>Result files (second order (variance)</a>\n \
</ul>");	</ul>");
fprintf(fichtm,"<ul><li> model=1+age+%s\n \	/* fprintf(fichtm,"<ul><li> model=1+age+%s\n \ */
</ul>", model);	/* </ul>", model); */
fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");	fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",	fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",
jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));	jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
Line 7093 void printinghtml(char fileresu[], char	Line 7316 void printinghtml(char fileresu[], char
}	}

/* if(nqfveff+nqtveff 0) / / Test to be done */	/* if(nqfveff+nqtveff 0) / / Test to be done */
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");	fprintf(fichtm," (model=%s) ************\n<hr size=\"2\" color=\"#EC5E5E\">",model);
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);	fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
printf("\nCombination (%d) ignored because no cases \n",k1);	printf("\nCombination (%d) ignored because no cases \n",k1);
Line 7280 See page 'Matrix of variance-covariance	Line 7503 See page 'Matrix of variance-covariance
fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}

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

if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);	fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
Line 7416 void printinggnuplot(char fileresu[], ch	Line 7639 void printinggnuplot(char fileresu[], ch
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 label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */	/* 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 title \"Alive state %d %s\" font \"Helvetica,12\"\n",cpt,gplotlabel);	fprintf(ficgp,"set title \"Alive state %d %s model=%s\" font \"Helvetica,12\"\n",cpt,gplotlabel,model);
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_"),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); */	/* 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*/	/* k1-1 error should be nres-1*/
Line 7837 set ter svg size 640, 480\nunset log y\n	Line 8060 set ter svg size 640, 480\nunset log y\n
fprintf(ficgp,", '' ");	fprintf(ficgp,", '' ");
/* l=(nlstate+ndeath)(i-1)+1; /	/* l=(nlstate+ndeath)(i-1)+1; /
l=(nlstate+ndeath)(cpt-1)+1; / fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2(nlstate+ndeath) /	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+i-1); /* To be verified */	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); */
Line 8188 set ter svg size 640, 480\nunset log y\n	Line 8411 set ter svg size 640, 480\nunset log y\n
for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */	for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
/* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */	/* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
if(cptcovage >0){ /* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, 2 V5 and V1 */	if(cptcovage >0){ /* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, 2 V5 and V1 */
if(j==Tage[ij]) { /* Product by age To be looked at!!*/	if(j==Tage[ij]) { /* Product by age To be looked at!!// Bug valgrind */
if(ij <=cptcovage) { /* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, 2 V5 and V1 */	if(ij <=cptcovage) { /* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, 2 V5 and V1 */
if(DummyV[j]==0){	if(DummyV[j]==0){/* Bug valgrind */
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 */
Line 9380 int readdata(char datafile[], int firsto	Line 9603 int readdata(char datafile[], int firsto

DummyV=ivector(1,NCOVMAX); /* 1 to 3 */	DummyV=ivector(1,NCOVMAX); /* 1 to 3 */
FixedV=ivector(1,NCOVMAX); /* 1 to 3 */	FixedV=ivector(1,NCOVMAX); /* 1 to 3 */
	for(v=1;v<NCOVMAX;v++){
	DummyV[v]=0;
	FixedV[v]=0;
	}

for(v=1; v <=ncovcol;v++){	for(v=1; v <=ncovcol;v++){
DummyV[v]=0;	DummyV[v]=0;
Line 9520 int readdata(char datafile[], int firsto	Line 9747 int readdata(char datafile[], int firsto
}	}
if(lval <-1 \|\| lval >1){	if(lval <-1 \|\| lval >1){
printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \	printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \	Should be a value of %d(nth) covariate of wave %d (0 should be the value for the reference and 1\n \
for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \	for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
For example, for multinomial values like 1, 2 and 3,\n \	For example, for multinomial values like 1, 2 and 3,\n \
build V1=0 V2=0 for the reference value (1),\n \	build V1=0 V2=0 for the reference value (1),\n \
V1=1 V2=0 for (2) \n \	V1=1 V2=0 for (2) \n \
and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \	and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
output of IMaCh is often meaningless.\n \	output of IMaCh is often meaningless.\n \
Exiting.\n",lval,linei, i,line,j);	Exiting.\n",lval,linei, i,line,iv,j);
fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \	fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \	Should be a value of %d(nth) covariate of wave %d (0 should be the value for the reference and 1\n \
for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \	for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
For example, for multinomial values like 1, 2 and 3,\n \	For example, for multinomial values like 1, 2 and 3,\n \
build V1=0 V2=0 for the reference value (1),\n \	build V1=0 V2=0 for the reference value (1),\n \
V1=1 V2=0 for (2) \n \	V1=1 V2=0 for (2) \n \
and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \	and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
output of IMaCh is often meaningless.\n \	output of IMaCh is often meaningless.\n \
Exiting.\n",lval,linei, i,line,j);fflush(ficlog);	Exiting.\n",lval,linei, i,line,iv,j);fflush(ficlog);
return 1;	return 1;
}	}
cotvar[j][iv][i]=(double)(lval);	cotvar[j][iv][i]=(double)(lval);
Line 9875 int decodemodel( char model[], int lasto	Line 10102 int decodemodel( char model[], int lasto
* - cptcovs number of simple covariates	* - cptcovs number of simple covariates
* - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10	* - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
* which is a new column after the 9 (ncovcol) variables.	* which is a new column after the 9 (ncovcol) variables.
* - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual	* - if k is a product Vn*Vm, covar[k][i] is filled with correct values for each individual
* - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage	* - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
* Tprod[1]@2 {5, 6}: position of first product V7V8 is 5, and second V5V6 is 6.	* Tprod[1]@2 {5, 6}: position of first product V7V8 is 5, and second V5V6 is 6.
* - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7V8 and V5V6 .	* - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7V8 and V5V6 .
*/	*/
	/* V2+V1+V4+V3age Tvar[4]=3 ; V1+V2age Tvar[2]=2; V1+V1age Tvar[2]=1, Tage[1]=2 /
{	{
int i, j, k, ks, v;	int i, j, k, ks, v;
int j1, k1, k2, k3, k4;	int j1, k1, k2, k3, k4;
Line 9957 int decodemodel( char model[], int lasto	Line 10185 int decodemodel( char model[], int lasto
* 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	* Tvar[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, 11, 10, 8, 8, 7, 8, 5, 6}
* 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
* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];	* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
*How to reorganize?	*How to reorganize? Tvars(orted)
* Model V1 + V2 + V3 + V8 + V5V6 + V7V8 + V3age + V8age	* Model V1 + V2 + V3 + V8 + V5V6 + V7V8 + V3age + V8age
* Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}	* Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
* {2, 1, 4, 8, 5, 6, 3, 7}	* {2, 1, 4, 8, 5, 6, 3, 7}
Line 9987 int decodemodel( char model[], int lasto	Line 10215 int decodemodel( char model[], int lasto
Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;	Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
}	}
cptcovage=0;	cptcovage=0;
for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */	for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model line */
cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'	cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' cutl from left to right
modelsav==V2+V1+V4+V3age strb=V3age stra=V2+V1+V4 */	modelsav==V2+V1+V5age+V4+V3age strb=V3age stra=V2+V1V5age+V4 / / <model> "V5+V4+V3+V4V3+V5age+V1age+V1" strb="V5" stra="V4+V3+V4V3+V5age+V1age+V1" */
if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */	if (nbocc(modelsav,'+')==0)
	strcpy(strb,modelsav); /* and analyzes it */
/* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/	/* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
/scanf("%d",i);/	/scanf("%d",i);/
if (strchr(strb,'')) { /< Model includes a product V2+V1+V4+V3age strb=V3age /	if (strchr(strb,'')) { /< Model includes a product V2+V1+V5age+ V4+V3age strb=V3age */
cutl(strc,strd,strb,''); /< strdstrc VmVn: strb=V3age(input) strc=age strd=V3 ; V3V2 strc=V2, strd=V3 /	cutl(strc,strd,strb,''); /< k=1 strdstrc VmVn: strb=V3age(input) strc=age strd=V3 ; V3V2 strc=V2, strd=V3 /
if (strcmp(strc,"age")==0) { /*< Model includes age: Vnage */	if (strcmp(strc,"age")==0) { /*< Model includes age: Vnage */
/* covar is not filled and then is empty */	/* covar is not filled and then is empty */
cptcovprod--;	cptcovprod--;
cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */	cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
Tvar[k]=atoi(stre); /* V2+V1+V4+V3age Tvar[4]=3 ; V1+V2age Tvar[2]=2; V1+V1age Tvar[2]=1 /	Tvar[k]=atoi(stre); /* V2+V1+V5age+V4+V3age Tvar[5]=3 ; V1+V2age Tvar[2]=2; V1+V1age Tvar[2]=1 */
Typevar[k]=1; /* 1 for age product */	Typevar[k]=1; /* 1 for age product */
cptcovage++; /* Sums the number of covariates which include age as a product */	cptcovage++; /* Counts the number of covariates which include age as a product */
Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1age Tvar[2]=1, Tage[1]=2 /	Tage[cptcovage]=k; /* V2+V1+V4+V3age Tvar[4]=3, Tage[1] = 4 or V1+V1age Tvar[2]=1, Tage[1]=2 */
/printf("stre=%s ", stre);/	/printf("stre=%s ", stre);/
} else if (strcmp(strd,"age")==0) { /* or ageVn /	} else if (strcmp(strd,"age")==0) { /* or ageVn /
cptcovprod--;	cptcovprod--;
Line 10019 int decodemodel( char model[], int lasto	Line 10248 int decodemodel( char model[], int lasto
Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but	Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
because this model-covariate is a construction we invent a new column	because this model-covariate is a construction we invent a new column
which is after existing variables ncovcol+nqv+ntv+nqtv + k1	which is after existing variables ncovcol+nqv+ntv+nqtv + k1
If already ncovcol=4 and model=V2+V1+V1V4+ageV3+V3*V2	If already ncovcol=4 and model=V2 + V1 +V1V4 +ageV3 +V3*V2
Tvar[3=V1V4]=4+1 Tvar[5=V3V2]=4 + 2= 6, etc */	thus after V4 we invent V5 and V6 because age*V3 will be computed in 4
	Tvar[3=V1V4]=4+1=5 Tvar[5=V3V2]=4 + 2= 6, Tvar[4=ageV3]=4 etc /
Typevar[k]=2; /* 2 for double fixed dummy covariates */	Typevar[k]=2; /* 2 for double fixed dummy covariates */
cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */	cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
Tprod[k1]=k; /* Tprod[1]=3(=V1V4) for V2+V1+V1V4+ageV3+V3V2 */	Tprod[k1]=k; /* Tprod[1]=3(=V1V4) for V2+V1+V1V4+ageV3+V3V2 */
Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */	Tposprod[k]=k1; /* Tposprod[3]=1, Tposprod[2]=5 */
Tvard[k1][1] =atoi(strc); /* m 1 for V1*/	Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
Tvard[k1][2] =atoi(stre); /* n 4 for V4*/	Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in VnVm at the end of Tvar /	k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in VnVm at the end of Tvar /
Line 10039 int decodemodel( char model[], int lasto	Line 10269 int decodemodel( char model[], int lasto
}	}
} /* End age is not in the model */	} /* End age is not in the model */
} /* End if model includes a product */	} /* End if model includes a product */
else { /* no more sum */	else { /* not a product */
/printf("d=%s c=%s b=%s\n", strd,strc,strb);/	/printf("d=%s c=%s b=%s\n", strd,strc,strb);/
/* scanf("%d",i);*/	/* scanf("%d",i);*/
cutl(strd,strc,strb,'V');	cutl(strd,strc,strb,'V');
Line 10070 int decodemodel( char model[], int lasto	Line 10300 int decodemodel( char model[], int lasto
model= V5 + V4 +V3 + V4V3 + V5age + V2 + V1V2 + V1age + V5*age, V1 is not used saving its place	model= V5 + V4 +V3 + V4V3 + V5age + V2 + V1V2 + V1age + V5*age, V1 is not used saving its place
k = 1 2 3 4 5 6 7 8 9	k = 1 2 3 4 5 6 7 8 9
Tvar[k]= 5 4 3 1+1+2+1+1=6 5 2 7 1 5	Tvar[k]= 5 4 3 1+1+2+1+1=6 5 2 7 1 5
Typevar[k]= 0 0 0 2 1 0 2 1 1	Typevar[k]= 0 0 0 2 1 0 2 1 0
Fixed[k] 1 1 1 1 3 0 0 or 2 2 3	Fixed[k] 1 1 1 1 3 0 0 or 2 2 3
Dummy[k] 1 0 0 0 3 1 1 2 3	Dummy[k] 1 0 0 0 3 1 1 2 3
Tmodelind[combination of covar]=k;	Tmodelind[combination of covar]=k;
Line 10150 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 10380 Dummy[k] 0=dummy (0 1), 1 quantitative (
modell[k].subtype= VQ;	modell[k].subtype= VQ;
ncovv++; /* Only simple time varying variables */	ncovv++; /* Only simple time varying variables */
nsq++;	nsq++;
TvarsQ[nsq]=Tvar[k];	TvarsQ[nsq]=Tvar[k]; /* k=1 Tvar=5 nsq=1 TvarsQ[1]=5 */
TvarsQind[nsq]=k;	TvarsQind[nsq]=k;
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k; /* TvarVind[1]=1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Any time varying singele */	TvarVind[ncovv]=k; /* TvarVind[1]=1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Any time varying singele */
Line 11016 int hPijx(double *p, int bage, int fage)	Line 11246 int hPijx(double *p, int bage, int fage)

/* 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, nres);	hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);/* Bug valgrind */
/* 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 hbijx 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++)
Line 11029 int hPijx(double *p, int bage, int fage)	Line 11259 int hPijx(double *p, int bage, int fage)
/* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + hhstepm/YEARMstepm ); */	/* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + hhstepm/YEARMstepm ); */
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate+ndeath;j++)	for(j=1; j<=nlstate+ndeath;j++)
fprintf(ficrespijb," %.5f", p3mat[i][j][h]);	fprintf(ficrespijb," %.5f", p3mat[i][j][h]);/* Bug valgrind */
fprintf(ficrespijb,"\n");	fprintf(ficrespijb,"\n");
}	}
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
Line 11082 int main(int argc, char *argv[])	Line 11312 int main(int argc, char *argv[])
double dum=0.; /* Dummy variable */	double dum=0.; /* Dummy variable */
double ***p3mat;	double ***p3mat;
/* double **mobaverage; /	/* double **mobaverage; /
	double wald;

char line[MAXLINE];	char line[MAXLINE];
char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];	char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];
Line 11713 Please run with mle=-1 to get a correct	Line 11944 Please run with mle=-1 to get a correct
}	}
mint=matrix(1,maxwav,firstobs,lastobs);	mint=matrix(1,maxwav,firstobs,lastobs);
anint=matrix(1,maxwav,firstobs,lastobs);	anint=matrix(1,maxwav,firstobs,lastobs);
s=imatrix(1,maxwav+1,firstobs,lastobs); /* s[i][j] health state for wave i and individual j */	s=imatrix(1,maxwav+1,firstobs,lastobs); /* s[i][j] health state for wave i and individual j */
	printf("BUG ncovmodel=%d NCOVMAX=%d 2**ncovmodel=%f BUG\n",ncovmodel,NCOVMAX,pow(2,ncovmodel));
tab=ivector(1,NCOVMAX);	tab=ivector(1,NCOVMAX);
ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2*ncov; V1+V2+V3+V4=>16 /	ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2*ncov; V1+V2+V3+V4=>16 /
ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2*ncov; V1+V2+V3+V4=>16 /	ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2*ncov; V1+V2+V3+V4=>16 /
Line 11777 Please run with mle=-1 to get a correct	Line 12009 Please run with mle=-1 to get a correct
Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + ageV4 + V3age	Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + ageV4 + V3age
4 covariates (3 plus signs)	4 covariates (3 plus signs)
Tage[1=V3age]= 4; Tage[2=ageV4] = 3	Tage[1=V3age]= 4; Tage[2=ageV4] = 3
*/	*/
	for(i=1;i<NCOVMAX;i++)
	Tage[i]=0;
Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an	Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
* individual dummy, fixed or varying:	* individual dummy, fixed or varying:
* Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,	* Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
Line 11990 Title=%s <br>Datafile=%s Firstpass=%d La	Line 12224 Title=%s <br>Datafile=%s Firstpass=%d La
optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);	optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
}	}

fprintf(fichtm,"<html><head>\n<head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n<title>IMaCh %s</title></head>\n <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n<font size=\"3\">Sponsored by Copyright (C) 2002-2015 <a href=http://www.ined.fr>INED</a>-EUROREVES-Institut de longévité-2013-2016-Japan Society for the Promotion of Sciences 日本学術振興会 (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - <a href=https://software.intel.com/en-us>Intel Software 2015-2018</a></font><br> \	fprintf(fichtm,"<html><head>\n<head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n<title>IMaCh %s</title></head>\n <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n<font size=\"3\">Sponsored by Copyright (C) 2002-2015 <a href=http://www.ined.fr>INED</a>-EUROREVES-Institut de longévité-2013-2016-Japan Society for the Promotion of Sciences 日本学術振興会 (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - <a href=https://software.intel.com/en-us>Intel Software 2015-2018</a></font><br> \
<hr size=\"2\" color=\"#EC5E5E\"> \n\	<hr size=\"2\" color=\"#EC5E5E\"> \n\
<font size=\"2\">IMaCh-%s <br> %s</font> \	<font size=\"2\">IMaCh-%s <br> %s</font> \
<hr size=\"2\" color=\"#EC5E5E\"> \n\	<hr size=\"2\" color=\"#EC5E5E\"> \n\
Line 12326 Please run with mle=-1 to get a correct	Line 12560 Please run with mle=-1 to get a correct


fprintf(ficres,"# Parameters nlstatenlstatencov a121 + b12 age + ...\n");	fprintf(ficres,"# Parameters nlstatenlstatencov a121 + b12 age + ...\n");
printf("# Parameters nlstatenlstatencov a121 + b12 age + ...\n");	printf("# Parameters nlstatenlstatencov a121 + b12 age + ...\n"); /* Printing model equation */
fprintf(ficlog,"# Parameters nlstatenlstatencov a121 + b12 age + ...\n");	fprintf(ficlog,"# Parameters nlstatenlstatencov a121 + b12 age + ...\n");

	printf("#model= 1 + age ");
	fprintf(ficres,"#model= 1 + age ");
	fprintf(ficlog,"#model= 1 + age ");
	fprintf(fichtm,"\n<ul><li> model=1+age+%s\n \
	</ul>", model);

	fprintf(fichtm,"\n<table style=\"text-align:center; border: 1px solid\">\n");
	fprintf(fichtm, "<tr><th>Model=</th><th>1</th><th>+ age</th>");
	if(nagesqr==1){
	printf(" + age*age ");
	fprintf(ficres," + age*age ");
	fprintf(ficlog," + age*age ");
	fprintf(fichtm, "<th>+ age*age</th>");
	}
	for(j=1;j <=ncovmodel-2;j++){
	if(Typevar[j]==0) {
	printf(" + V%d ",Tvar[j]);
	fprintf(ficres," + V%d ",Tvar[j]);
	fprintf(ficlog," + V%d ",Tvar[j]);
	fprintf(fichtm, "<th>+ V%d</th>",Tvar[j]);
	}else if(Typevar[j]==1) {
	printf(" + V%d*age ",Tvar[j]);
	fprintf(ficres," + V%d*age ",Tvar[j]);
	fprintf(ficlog," + V%d*age ",Tvar[j]);
	fprintf(fichtm, "<th>+ V%d*age</th>",Tvar[j]);
	}else if(Typevar[j]==2) {
	printf(" + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
	fprintf(ficres," + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
	fprintf(ficlog," + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
	fprintf(fichtm, "<th>+ V%d*V%d</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
	}
	}
	printf("\n");
	fprintf(ficres,"\n");
	fprintf(ficlog,"\n");
	fprintf(fichtm, "</tr>");
	fprintf(fichtm, "\n");


for(i=1,jk=1; i <=nlstate; i++){	for(i=1,jk=1; i <=nlstate; i++){
for(k=1; k <=(nlstate+ndeath); k++){	for(k=1; k <=(nlstate+ndeath); k++){
if (k != i) {	if (k != i) {
	fprintf(fichtm, "<tr>");
printf("%d%d ",i,k);	printf("%d%d ",i,k);
fprintf(ficlog,"%d%d ",i,k);	fprintf(ficlog,"%d%d ",i,k);
fprintf(ficres,"%1d%1d ",i,k);	fprintf(ficres,"%1d%1d ",i,k);
	fprintf(fichtm, "<td>%1d%1d</td>",i,k);
for(j=1; j <=ncovmodel; j++){	for(j=1; j <=ncovmodel; j++){
printf("%12.7f ",p[jk]);	printf("%12.7f ",p[jk]);
fprintf(ficlog,"%12.7f ",p[jk]);	fprintf(ficlog,"%12.7f ",p[jk]);
fprintf(ficres,"%12.7f ",p[jk]);	fprintf(ficres,"%12.7f ",p[jk]);
	fprintf(fichtm, "<td>%12.7f</td>",p[jk]);
jk++;	jk++;
}	}
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
fprintf(ficres,"\n");	fprintf(ficres,"\n");
	fprintf(fichtm, "</tr>\n");
}	}
}	}
}	}
	/* fprintf(fichtm,"</tr>\n"); */
	fprintf(fichtm,"</table>\n");
	fprintf(fichtm, "\n");

if(mle != 0){	if(mle != 0){
/* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */	/* Computing hessian and covariance matrix only at a peak of the Likelihood, that is after optimization */
ftolhess=ftol; /* Usually correct */	ftolhess=ftol; /* Usually correct */
hesscov(matcov, hess, p, npar, delti, ftolhess, func);	hesscov(matcov, hess, p, npar, delti, ftolhess, func);
printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");	printf("Parameters and 95%% confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W .\n But be careful that parameters are highly correlated because incidence of disability is highly correlated to incidence of recovery.\n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");	fprintf(ficlog, "Parameters, Wald tests and Wald-based confidence intervals\n W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n And Wald-based confidence intervals plus and minus 1.96 * W \n It might be better to visualize the covariance matrix. See the page 'Matrix of variance-covariance of one-step probabilities' and its graphs.\n");
	fprintf(fichtm, "\n<p>The Wald test results are output only if the maximimzation of the Likelihood is performed (mle=1)\n</br>Parameters, Wald tests and Wald-based confidence intervals\n</br> W is simply the result of the division of the parameter by the square root of covariance of the parameter.\n</br> And Wald-based confidence intervals plus and minus 1.96 * W \n </br> It might be better to visualize the covariance matrix. See the page '<a href=\"%s\">Matrix of variance-covariance of one-step probabilities and its graphs</a>'.\n</br>",optionfilehtmcov);
	fprintf(fichtm,"\n<table style=\"text-align:center; border: 1px solid\">");
	fprintf(fichtm, "\n<tr><th>Model=</th><th>1</th><th>+ age</th>");
	if(nagesqr==1){
	printf(" + age*age ");
	fprintf(ficres," + age*age ");
	fprintf(ficlog," + age*age ");
	fprintf(fichtm, "<th>+ age*age</th>");
	}
	for(j=1;j <=ncovmodel-2;j++){
	if(Typevar[j]==0) {
	printf(" + V%d ",Tvar[j]);
	fprintf(fichtm, "<th>+ V%d</th>",Tvar[j]);
	}else if(Typevar[j]==1) {
	printf(" + V%d*age ",Tvar[j]);
	fprintf(fichtm, "<th>+ V%d*age</th>",Tvar[j]);
	}else if(Typevar[j]==2) {
	fprintf(fichtm, "<th>+ V%d*V%d</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
	}
	}
	fprintf(fichtm, "</tr>\n");

for(i=1,jk=1; i <=nlstate; i++){	for(i=1,jk=1; i <=nlstate; i++){
for(k=1; k <=(nlstate+ndeath); k++){	for(k=1; k <=(nlstate+ndeath); k++){
if (k != i) {	if (k != i) {
	fprintf(fichtm, "<tr valign=top>");
printf("%d%d ",i,k);	printf("%d%d ",i,k);
fprintf(ficlog,"%d%d ",i,k);	fprintf(ficlog,"%d%d ",i,k);
	fprintf(fichtm, "<td>%1d%1d</td>",i,k);
for(j=1; j <=ncovmodel; j++){	for(j=1; j <=ncovmodel; j++){
printf("%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96sqrt(matcov[jk][jk]),p[jk]+1.96sqrt(matcov[jk][jk]));	wald=p[jk]/sqrt(matcov[jk][jk]);
fprintf(ficlog,"%12.7f W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk], p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96sqrt(matcov[jk][jk]),p[jk]+1.96sqrt(matcov[jk][jk]));	printf("%12.7f(%12.7f) W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk],sqrt(matcov[jk][jk]), p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96sqrt(matcov[jk][jk]),p[jk]+1.96sqrt(matcov[jk][jk]));
	fprintf(ficlog,"%12.7f(%12.7f) W=%8.3f CI=[%12.7f ; %12.7f] ",p[jk],sqrt(matcov[jk][jk]), p[jk]/sqrt(matcov[jk][jk]), p[jk]-1.96sqrt(matcov[jk][jk]),p[jk]+1.96sqrt(matcov[jk][jk]));
	if(fabs(wald) > 1.96){
	fprintf(fichtm, "<td><b>%12.7f</b></br> (%12.7f)</br>",p[jk],sqrt(matcov[jk][jk]));
	}else{
	fprintf(fichtm, "<td>%12.7f (%12.7f)</br>",p[jk],sqrt(matcov[jk][jk]));
	}
	fprintf(fichtm,"W=%8.3f</br>",wald);
	fprintf(fichtm,"[%12.7f;%12.7f]</br></td>", p[jk]-1.96sqrt(matcov[jk][jk]),p[jk]+1.96sqrt(matcov[jk][jk]));
jk++;	jk++;
}	}
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
	fprintf(fichtm, "</tr>\n");
}	}
}	}
}	}
} /* end of hesscov and Wald tests */	} /* end of hesscov and Wald tests */
	fprintf(fichtm,"</table>\n");

/* */	/* */
fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");	fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
Line 12958 Please run with mle=-1 to get a correct	Line 13274 Please run with mle=-1 to get a correct
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(i1 != 1 && TKresult[nres]!= k)	if(i1 != 1 && TKresult[nres]!= k)
continue;	continue;
printf("\n#****** Result for:");	printf("\n# model %s \n#****** Result for:", model);
fprintf(ficrest,"\n#****** Result for:");	fprintf(ficrest,"\n# model %s \n#****** Result for:", model);
fprintf(ficlog,"\n#****** Result for:");	fprintf(ficlog,"\n# model %s \n#****** Result for:", model);
for(j=1;j<=cptcoveff;j++){	for(j=1;j<=cptcoveff;j++){
printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);

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

Removed from v.1.318
changed lines
	Added in v.1.328