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Diff for /imach/src/imach.c between versions 1.322 and 1.337

version 1.322, 2022/07/22 12:27:48	version 1.337, 2022/09/02 14:26:02
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	Revision 1.337 2022/09/02 14:26:02 brouard
	Summary: version 0.99r35

	* src/imach.c: Version 0.99r35 because it outputs same results with
	1+age+V1+V1*age for females and 1+age for females only
	(education=1 noweight)

	Revision 1.336 2022/08/31 09:52:36 brouard
	* empty log message *

	Revision 1.335 2022/08/31 08:23:16 brouard
	Summary: improvements...

	Revision 1.334 2022/08/25 09:08:41 brouard
	Summary: In progress for quantitative

	Revision 1.333 2022/08/21 09:10:30 brouard
	* src/imach.c (Module): Version 0.99r33 A lot of changes in
	reassigning covariates: my first idea was that people will always
	use the first covariate V1 into the model but in fact they are
	producing data with many covariates and can use an equation model
	with some of the covariate; it means that in a model V2+V3 instead
	of codtabm(k,Tvaraff[j]) which calculates for combination k, for
	three covariates (V1, V2, V3) the value of Tvaraff[j], but in fact
	the equation model is restricted to two variables only (V2, V3)
	and the combination for V2 should be codtabm(k,1) instead of
	(codtabm(k,2), and the code should be
	codtabm(k,TnsdVar[Tvaraff[j]]. Many many changes have been
	made. All of these should be simplified once a day like we did in
	hpxij() for example by using precov[nres] which is computed in
	decoderesult for each nres of each resultline. Loop should be done
	on the equation model globally by distinguishing only product with
	age (which are changing with age) and no more on type of
	covariates, single dummies, single covariates.

	Revision 1.332 2022/08/21 09:06:25 brouard
	Summary: Version 0.99r33

	* src/imach.c (Module): Version 0.99r33 A lot of changes in
	reassigning covariates: my first idea was that people will always
	use the first covariate V1 into the model but in fact they are
	producing data with many covariates and can use an equation model
	with some of the covariate; it means that in a model V2+V3 instead
	of codtabm(k,Tvaraff[j]) which calculates for combination k, for
	three covariates (V1, V2, V3) the value of Tvaraff[j], but in fact
	the equation model is restricted to two variables only (V2, V3)
	and the combination for V2 should be codtabm(k,1) instead of
	(codtabm(k,2), and the code should be
	codtabm(k,TnsdVar[Tvaraff[j]]. Many many changes have been
	made. All of these should be simplified once a day like we did in
	hpxij() for example by using precov[nres] which is computed in
	decoderesult for each nres of each resultline. Loop should be done
	on the equation model globally by distinguishing only product with
	age (which are changing with age) and no more on type of
	covariates, single dummies, single covariates.

	Revision 1.331 2022/08/07 05:40:09 brouard
	* empty log message *

	Revision 1.330 2022/08/06 07:18:25 brouard
	Summary: last 0.99r31

	* imach.c (Module): Version of imach using partly decoderesult to rebuild xpxij function

	Revision 1.329 2022/08/03 17:29:54 brouard
	* imach.c (Module): Many errors in graphs fixed with Vn*age covariates.

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

Line 866	Line 954

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 1045 Important routines	Line 1133 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 1171 typedef struct {	Line 1259 typedef struct {

#define GNUPLOTPROGRAM "gnuplot"	#define GNUPLOTPROGRAM "gnuplot"
/#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"/	/#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"/
#define FILENAMELENGTH 132	#define FILENAMELENGTH 256

#define GLOCK_ERROR_NOPATH -1 /* empty path */	#define GLOCK_ERROR_NOPATH -1 /* empty path */
#define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */	#define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
Line 1182 typedef struct {	Line 1270 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 1210 typedef struct {	Line 1298 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[]="September 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];
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 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=V2+V1+ V3age+V2V4 */	/* Number of covariates model (1)=V2+V1+ V3age+V2V4 */
int cptcovn=0; /*< cptcovn number of covariates added in the model (excepting constant and age and ageproduct) */	/* Model(2) V1 + V2 + V3 + V8 + V7V8 + V5V6 + V8age + V3age + ageage /
int cptcovt=0; /*< cptcovt number of covariates added in the model (excepting constant and age) /	int cptcovn=0; /*< cptcovn decodemodel: number of covariates k of the models excluding ageproducts =6 and ageage but including products /
int cptcovs=0; /*< cptcovs number of simple covariates in the model V2+V1 =2 /	int cptcovt=0; /*< cptcovt: total number of covariates of the model (2) nbocc(+)+1 = 8 excepting constant and age and ageage */
int cptcovsnq=0; /*< cptcovsnq number of simple covariates in the model but non quantitative V2+V1 =2 /	int cptcovs=0; /*< cptcovs number of SIMPLE covariates in the model V2+V1 =2 (dummy or quantit or time varying) /
	int cptcovsnq=0; /*< cptcovsnq number of SIMPLE covariates in the model but non quantitative V2+V1 =2 /
int cptcovage=0; /*< Number of covariates with age: V3age only =1 */	int cptcovage=0; /*< Number of covariates with age: V3age only =1 */
int cptcovprodnoage=0; /*< Number of covariate products without age /	int cptcovprodnoage=0; /*< Number of covariate products without age /
int cptcoveff=0; /* Total number of covariates to vary for printing results */	int cptcoveff=0; /* Total number of single dummy covariates (fixed or time varying) to vary for printing results (2*cptcoveff combinations of dummies)(computed in tricode as cptcov) /
int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */	int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */
int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */	int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */
int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */	int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */
Line 1234 int nqfveff=0; /**< nqfveff Number of Qu	Line 1323 int nqfveff=0; /**< nqfveff Number of Qu
int ntveff=0; /*< ntveff number of effective time varying variables /	int ntveff=0; /*< ntveff number of effective time varying variables /
int nqtveff=0; /*< ntqveff number of effective time varying quantitative variables /	int nqtveff=0; /*< ntqveff number of effective time varying quantitative variables /
int cptcov=0; /* Working variable */	int cptcov=0; /* Working variable */
	int firstobs=1, lastobs=10; /* nobs = lastobs-firstobs+1 declared globally ;*/
int nobs=10; /* Number of observations in the data lastobs-firstobs */	int nobs=10; /* Number of observations in the data lastobs-firstobs */
int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */	int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
int npar=NPARMAX; /* Number of parameters (nlstate+ndeath-1)nlstatencovmodel; */	int npar=NPARMAX; /* Number of parameters (nlstate+ndeath-1)nlstatencovmodel; */
Line 1373 int ncodemaxwundef; / ncodemax[j]= Nu	Line 1463 int ncodemaxwundef; / ncodemax[j]= Nu
double *agev,moisnais, annais, moisdc, andc,mint, *anint;	double *agev,moisnais, annais, moisdc, andc,mint, *anint;
double pmmij, probs; / Global pointer */	double pmmij, probs; / Global pointer */
double *mobaverage, mobaverages; / New global variable */	double *mobaverage, mobaverages; / New global variable */
	double *precov; / New global variable to store for each resultline, values of model covariates given by the resultlines (in order to speed up) */
double ageexmed,agecens;	double ageexmed,agecens;
double dateintmean=0;	double dateintmean=0;
double anprojd, mprojd, jprojd; /* For eventual projections */	double anprojd, mprojd, jprojd; /* For eventual projections */
Line 1397 int *nbcode, Tvar; /**< model=V2 => Tv	Line 1488 int *nbcode, Tvar; /**< model=V2 => Tv
* V1 V2 V3 V4 V5 V6 V7 V8 Weight ddb ddth d1st s1 V9 V10 V11 V12 s2 V9 V10 V11 V12	* 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	* < ncovcol=6 > nqv=2 (V7 V8) dv dv dv qtv dv dv dvv qtv
* ntv=3 nqtv=1	* ntv=3 nqtv=1
* cptcovn number of covariates (not including constant and age) = # of + plus 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][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][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[k,i], value of kth fixed covariate dummy or quanti :	* covar[Vk,i], value of the Vkth fixed covariate dummy or quanti 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)
* Model V2 + V1 + V3age + V3 + V5V6 + V7V8 + V8age + V8 + V9 + V9*age + V10	* 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	* k= 1 2 3 4 5 6 7 8 9 10 11
Line 1423 int *nbcode, Tvar; /**< model=V2 => Tv	Line 1514 int *nbcode, Tvar; /**< model=V2 => Tv
/* with age product, 3 quant with age product*/	/* with age product, 3 quant with age product*/
/Tvar[k]= 5 4 3 6 5 2 7 1 1 /	/Tvar[k]= 5 4 3 6 5 2 7 1 1 /
/* nsd 1 2 3 / / Counting single dummies covar fixed or tv */	/* nsd 1 2 3 / / Counting single dummies covar fixed or tv */
	/TnsdVar[Tvar] 1 2 3 /
	/Tvaraff[nsd] 4 3 1 / /* ID of single dummy cova fixed or timevary*/
/TvarsD[nsd] 4 3 1 / /* ID of single dummy cova fixed or timevary*/	/TvarsD[nsd] 4 3 1 / /* ID of single dummy cova fixed or timevary*/
/TvarsDind[k] 2 3 9 / /* position K of single dummy cova */	/TvarsDind[k] 2 3 9 / /* position K of single dummy cova */
/* nsq 1 2 / / Counting single quantit tv */	/* nsq 1 2 / / Counting single quantit tv */
Line 1432 int *nbcode, Tvar; /**< model=V2 => Tv	Line 1525 int *nbcode, Tvar; /**< model=V2 => Tv
/* cptcovage 1 2 / / Counting covage in the model equation /	/* cptcovage 1 2 / / Counting covage in the model equation /
/* Tage[cptcovage]=k 5 8 / / Position in the model of ith covage /	/* 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 */	/* Tvard[1][1]@4={4,3,1,2} V4V3 V1V2 / / Position in model of the ith prod without age */
	/* Tvardk[4][1]=4;Tvardk[4][2]=3;Tvardk[7][1]=1;Tvardk[7][2]=2 / / Variables of a prod at position in the model equation*/
/* 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 /	/* 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) */	/* TvarFind; TvarFind[1]=6, TvarFind[2]=7, TvarFind[3]=9 // Inverse V2(6) is first fixed (single or prod) */
/* Type */	/* Type */
Line 1440 int *nbcode, Tvar; /**< model=V2 => Tv	Line 1534 int *nbcode, Tvar; /**< model=V2 => Tv
/* D Q D D Q */	/* D Q D D Q */
/* */	/* */
int *TvarsD;	int *TvarsD;
	int *TnsdVar;
int *TvarsDind;	int *TvarsDind;
int *TvarsQ;	int *TvarsQ;
int *TvarsQind;	int *TvarsQind;
Line 1447 int *TvarsQind;	Line 1542 int *TvarsQind;
#define MAXRESULTLINESPONE 10+1	#define MAXRESULTLINESPONE 10+1
int nresult=0;	int nresult=0;
int parameterline=0; /* # of the parameter (type) line */	int parameterline=0; /* # of the parameter (type) line */
int TKresult[MAXRESULTLINESPONE];	int TKresult[MAXRESULTLINESPONE]; /* TKresult[nres]=k for each resultline nres give the corresponding combination of dummies */
int Tresult[MAXRESULTLINESPONE][NCOVMAX];/* For dummy variable , value (output) */	int resultmodel[MAXRESULTLINESPONE][NCOVMAX];/* resultmodel[k1]=k3: k1th position in the model corresponds to the k3 position in the resultline */
int Tinvresult[MAXRESULTLINESPONE][NCOVMAX];/* For dummy variable , value (output) */	int modelresult[MAXRESULTLINESPONE][NCOVMAX];/* modelresult[k3]=k1: k1th position in the model corresponds to the k3 position in the resultline */
int Tvresult[MAXRESULTLINESPONE][NCOVMAX]; /* For dummy variable , variable # (output) */	int Tresult[MAXRESULTLINESPONE][NCOVMAX];/* Tresult[nres][result_position]= value of the dummy variable at the result_position in the nres resultline */
double Tqresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , value (output) */	int Tinvresult[MAXRESULTLINESPONE][NCOVMAX];/* Tinvresult[nres][Name of a dummy variable]= value of the variable in the result line */
	double TinvDoQresult[MAXRESULTLINESPONE][NCOVMAX];/* TinvDoQresult[nres][Name of a Dummy or Q variable]= value of the variable in the result line */
	int Tvresult[MAXRESULTLINESPONE][NCOVMAX]; /* Tvresult[nres][result_position]= name of the dummy variable at the result_position in the nres resultline */
	double Tqresult[MAXRESULTLINESPONE][NCOVMAX]; /* Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline */
double Tqinvresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , value (output) */	double Tqinvresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , value (output) */
int Tvqresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , variable # (output) */	int Tvqresult[MAXRESULTLINESPONE][NCOVMAX]; /* Tvqresult[nres][result_position]= id of the variable at the result_position in the nres resultline */

/* 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
Line 1490 int TmodelInvQind; /* Tmodelqind[1]=1	Line 1588 int TmodelInvQind; /* Tmodelqind[1]=1
int Ndum; /* Freq of modality (tricode */	int Ndum; /* Freq of modality (tricode */
/* int *codtab;/ /*< codtab=imatrix(1,100,1,10); /	/* int *codtab;/ /*< codtab=imatrix(1,100,1,10); /
int **Tvard;	int **Tvard;
	int **Tvardk;
int Tprod;/< Gives the k position of the k1 product /	int Tprod;/< Gives the k position of the k1 product /
/* Tprod[k1=1]=3(=V1V4) for V2+V1+V1V4+ageV3 /	/* Tprod[k1=1]=3(=V1V4) for V2+V1+V1V4+ageV3 /
int Tposprod; /< Gives the k1 product from the k position /	int Tposprod; /< Gives the k1 product from the k position /
Line 2413 void powell(double p[], double **xi, int	Line 2512 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); /
	printf("\nPowell iter=%d -2LL=%.12f gain=%.3lg %ld sec. %ld sec.",iter,fret,fp-fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
	fprintf(ficlog,"\nPowell iter=%d -2LL=%.12f gain=%.3lg %ld sec. %ld sec.",iter,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 2748 void powell(double p[], double **xi, int	Line 2849 void powell(double p[], double **xi, int
/* 0.51326036147820708, 0.48673963852179264} */	/* 0.51326036147820708, 0.48673963852179264} */
/* If we start from prlim again, prlim tends to a constant matrix */	/* If we start from prlim again, prlim tends to a constant matrix */

int i, ii,j,k;	int i, ii,j,k, k1;
double min, max, *meandiff, maxmax,sumnew=0.;	double min, max, *meandiff, maxmax,sumnew=0.;
/* double *matprod2(); / /* test */	/* double *matprod2(); / /* test */
double out, cov[NCOVMAX+1], pmij(); /* *pmmij is a global variable feeded with oldms etc /	double out, cov[NCOVMAX+1], pmij(); /* *pmmij is a global variable feeded with oldms etc /
Line 2779 void powell(double p[], double **xi, int	Line 2880 void powell(double p[], double **xi, int
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 */	/* Model(2) V1 + V2 + V3 + V8 + V7V8 + V5V6 + V8age + V3age + ageage /
/* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */	/* total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and ageage /
cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];	for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */
/* cov[++k1]=nbcode[TvarsD[k]][codtabm(ij,k)]; */	if(Typevar[k1]==1){ /* A product with age */
/* 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)); */	cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
}	}else{
for (k=1; k<=nsq;k++) { /* For single varying covariates only */	cov[2+nagesqr+k1]=precov[nres][k1];
/* Here comes the value of quantitative after renumbering k with single quantitative covariates */	}
cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];	}/* End of loop on model equation */
/* 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]); */	/* Start of old code (replaced by a loop on position in the model equation */
}	/* for (k=1; k<=nsd;k++) { /\* For single dummy covariates only of the model \/ /
for (k=1; k<=cptcovage;k++){ /* For product with age */	/* /\* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates \/ /
if(Dummy[Tage[k]]==2){ /* dummy with age */	/* /\* cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,TvarsD[k])]; \/ /
cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];	/* cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,TnsdVar[TvarsD[k]])]; */
/* cov[++k1]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]cov[2]; /	/* /\* model = 1 +age + V1V3 + ageV1 + V2 + V1 + ageV2 + V3 + V3age + V1V2 /
} else if(Dummy[Tage[k]]==3){ /* quantitative with age */	/* * k 1 2 3 4 5 6 7 8 */
cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];	/* cov[] 1 2 3 4 5 6 7 8 9 10 /
/* cov[++k1]=Tqresult[nres][k]; */	/* TypeVar[k] 2 1 0 0 1 0 1 2 /
}	/* Dummy[k] 0 2 0 0 2 0 2 0 /
/* 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]); */	/* Tvar[k] 4 1 2 1 2 3 3 5 /
}	/* nsd=3 (1) (2) (3) /
for (k=1; k<=cptcovprod;k++){ /* For product without age */	/* TvarsD[nsd] [1]=2 1 3 /
/* printf("prevalim Prod ij=%d k=%d Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */	/* TnsdVar [2]=2 [1]=1 [3]=3 /
if(Dummy[Tvard[k][1]==0]){	/* TvarsDind[nsd](=k) [1]=3 [2]=4 [3]=6 /
if(Dummy[Tvard[k][2]==0]){	/* Tage[] [1]=1 [2]=2 [3]=3 /
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];	/* Tvard[] [1][1]=1 [2][1]=1 /
/* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */	/* * [1][2]=3 [2][2]=2 */
}else{	/* Tprod[](=k) [1]=1 [2]=8 /
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];	/* TvarsDp(=Tvar) [1]=1 [2]=2 [3]=3 [4]=5 /
/* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k]; */	/* TvarD (=k) [1]=1 [2]=3 [3]=4 [3]=6 [4]=6 /
}	/* TvarsDpType /
}else{	/* si model= 1 + age + V3 + V2age + V2 + V3age /
if(Dummy[Tvard[k][2]==0]){	/* * nsd=1 (1) (2) */
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];	/* TvarsD[nsd] 3 2 /
/* cov[++k1]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]]; */	/* TnsdVar (3)=1 (2)=2 /
}else{	/* TvarsDind[nsd](=k) [1]=1 [2]=3 /
cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];	/* Tage[] [1]=2 [2]= 3 /
/* cov[++k1]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]]; */	/* \/ /
}	/* /\* 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)); \/ /
}	/* } */
	/* for (k=1; k<=nsq;k++) { /\* For single quantitative varying covariates only of the model \/ /
	/* /\* Here comes the value of quantitative after renumbering k with single quantitative covariates \/ /
	/* /\* Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline \/ /
	/* /\* cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; \/ /
	/* cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][resultmodel[nres][k1]] */
	/* /\* 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]); \/ /
	/* } */
	/* 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(ij,Tvar[Tage[k]])]cov[2]; /
	/* /\* cov[++k1]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]cov[2]; \/ */
	/* } 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]); \/ /
	/* } */
	/* for (k=1; k<=cptcovprod;k++){ /\* For product without age \/ /
	/* /\* printf("prevalim Prod ij=%d k=%d Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); \/ /
	/* if(Dummy[Tvard[k][1]]==0){ */
	/* if(Dummy[Tvard[k][2]]==0){ */
	/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
	/* /\* cov[++k1]=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,Tvard[k][1])] * 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(ij,Tvard[k][2])] * 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]]; \/ /
	/* } */
	/* } */
	/* } /\* End product without age \/ /
	/* ENd of old code */
/printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);/	/printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);/
/printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);/	/printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);/
/printf("ij=%d cov[3]=%lf \n",ij, cov[3]);/	/printf("ij=%d cov[3]=%lf \n",ij, cov[3]);/
Line 2912 void powell(double p[], double **xi, int	Line 3052 void powell(double p[], double **xi, int
/* 0.51326036147820708, 0.48673963852179264} */	/* 0.51326036147820708, 0.48673963852179264} */
/* If we start from prlim again, prlim tends to a constant matrix */	/* If we start from prlim again, prlim tends to a constant matrix */

int i, ii,j,k;	int i, ii,j,k, k1;
int first=0;	int first=0;
double min, max, *meandiff, maxmax,sumnew=0.;	double min, max, *meandiff, maxmax,sumnew=0.;
/* double *matprod2(); / /* test */	/* double *matprod2(); / /* test */
Line 2952 void powell(double p[], double **xi, int	Line 3092 void powell(double p[], double **xi, int
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(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */
/* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */	if(Typevar[k1]==1){ /* A product with age */
cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];	cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
/* printf("bprevalim Dummy agefin=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agefin,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
}
/* for (k=1; k<=cptcovn;k++) { */
/* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; \/ /
/* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
/* /\* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); \/ /
/* } */
for (k=1; k<=nsq;k++) { /* For single varying covariates only */
/* Here comes the value of quantitative after renumbering k with single quantitative covariates */
cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
/* printf("prevalim Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
}
/* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]cov[2]; /
/* for (k=1; k<=cptcovprod;k++) /\* Useless \/ /
/* /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; \/ /
/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
for (k=1; k<=cptcovage;k++){ /* For product with age */
/* if(Dummy[Tvar[Tage[k]]]== 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];
} else if(Dummy[Tage[k]]== 3){ /* quantitative with age */
cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
}
/* printf("prevalim Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
}
for (k=1; k<=cptcovprod;k++){ /* For product without age */
/* printf("prevalim Prod ij=%d k=%d Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
if(Dummy[Tvard[k][1]==0]){
if(Dummy[Tvard[k][2]==0]){
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
}else{
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
}
}else{	}else{
if(Dummy[Tvard[k][2]==0]){	cov[2+nagesqr+k1]=precov[nres][k1];
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]];
}
}	}
}	}/* End of loop on model equation */

	/* Old code */

	/* 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 \/ /
	/* cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,TvarsD[k])]; */
	/* /\* printf("bprevalim Dummy agefin=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agefin,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); \/ /
	/* } */
	/* /\* for (k=1; k<=cptcovn;k++) { \/ /
	/* /\* /\\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; \\/ \/ */
	/* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; \/ /
	/* /\* /\\* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); \\/ \/ */
	/* /\* } \/ /
	/* for (k=1; k<=nsq;k++) { /\* For single varying covariates only \/ /
	/* /\* Here comes the value of quantitative after renumbering k with single quantitative covariates \/ /
	/* cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; */
	/* /\* printf("prevalim Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); \/ /
	/* } */
	/* /\* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]cov[2]; \/ */
	/* /\* for (k=1; k<=cptcovprod;k++) /\\* Useless \\/ \/ */
	/* /\* /\\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; \\/ \/ */
	/* /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; \/ /
	/* for (k=1; k<=cptcovage;k++){ /\* For product with age \/ /
	/* /\* if(Dummy[Tvar[Tage[k]]]== 2){ /\\* dummy with age \\/ ERROR ???\/ */
	/* if(Dummy[Tage[k]]== 2){ /\* dummy with age \/ /
	/* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]cov[2]; /
	/* } else if(Dummy[Tage[k]]== 3){ /\* quantitative with age \/ /
	/* cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; */
	/* } */
	/* /\* printf("prevalim Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); \/ /
	/* } */
	/* for (k=1; k<=cptcovprod;k++){ /\* For product without age \/ /
	/* /\* printf("prevalim Prod ij=%d k=%d Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); \/ /
	/* if(Dummy[Tvard[k][1]]==0){ */
	/* if(Dummy[Tvard[k][2]]==0){ */
	/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
	/* }else{ */
	/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * Tqresult[nres][k]; */
	/* } */
	/* }else{ */
	/* if(Dummy[Tvard[k][2]]==0){ */
	/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])] * Tqinvresult[nres][Tvard[k][1]]; */
	/* }else{ */
	/* cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]]; */
	/* } */
	/* } */
	/* } */

/printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);/	/printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);/
/printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);/	/printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);/
Line 3106 double pmij(double ps, double *cov,	Line 3256 double pmij(double ps, double *cov,
/* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */	/* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
}	}
ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */	ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
/* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */	/* printf("Debug pmij() i=%d j=%d nc=%d s1=%.17f, lnpijopii=%.17f\n",i,j,nc, s1,lnpijopii); */
}	}
for(j=i+1; j<=nlstate+ndeath;j++){	for(j=i+1; j<=nlstate+ndeath;j++){
for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){	for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
Line 3115 double pmij(double ps, double *cov,	Line 3265 double pmij(double ps, double *cov,
/* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */	/* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
}	}
ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */	ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
	/* printf("Debug pmij() i=%d j=%d nc=%d s1=%.17f, lnpijopii=%.17f\n",i,j,nc, s1,lnpijopii); */
}	}
}	}

Line 3122 double pmij(double ps, double *cov,	Line 3273 double pmij(double ps, double *cov,
s1=0;	s1=0;
for(j=1; j<i; j++){	for(j=1; j<i; j++){
s1+=exp(ps[i][j]); /* In fact sums pij/pii */	s1+=exp(ps[i][j]); /* In fact sums pij/pii */
/printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); /	/* printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
}	}
for(j=i+1; j<=nlstate+ndeath; j++){	for(j=i+1; j<=nlstate+ndeath; j++){
s1+=exp(ps[i][j]); /* In fact sums pij/pii */	s1+=exp(ps[i][j]); /* In fact sums pij/pii */
/printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); /	/* printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
}	}
/* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */	/* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
ps[i][i]=1./(s1+1.);	ps[i][i]=1./(s1+1.);
/* Computing other pijs */	/* Computing other pijs */
for(j=1; j<i; j++)	for(j=1; j<i; j++)
ps[i][j]= exp(ps[i][j])*ps[i][i];	ps[i][j]= exp(ps[i][j])ps[i][i];/ 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 3190 double pmij(double ps, double *cov,	Line 3341 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 3370 double matprod2(double out, double *	Line 3521 double matprod2(double out, double *

double *hpxij(double po, int nhstepm, double age, int hstepm, double x, int nlstate, int stepm, double oldm, double savm, int ij, int nres )	double *hpxij(double po, int nhstepm, double age, int hstepm, double x, int nlstate, int stepm, double oldm, double savm, int ij, int nres )
{	{
/* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over	/* Already optimized with precov.
	Computes the transition matrix starting at age 'age' and dummies values in each resultline (loop on ij to find the corresponding combination) to over
'nhstepmhstepmstepm' months (i.e. until	'nhstepmhstepmstepm' months (i.e. until
age (in years) age+nhstepmhstepmstepm/12) by multiplying	age (in years) age+nhstepmhstepmstepm/12) by multiplying
nhstepm*hstepm matrices.	nhstepm*hstepm matrices.
Line 3382 double *hpxij(double *po, int nhstep	Line 3534 double *hpxij(double *po, int nhstep

*/	*/

int i, j, d, h, k;	int i, j, d, h, k, k1;
double **out, cov[NCOVMAX+1];	double **out, cov[NCOVMAX+1];
double **newm;	double **newm;
double agexact;	double agexact;
Line 3405 double *hpxij(double *po, int nhstep	Line 3557 double *hpxij(double *po, int nhstep
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 */	/* Model(2) V1 + V2 + V3 + V8 + V7V8 + V5V6 + V8age + V3age + ageage /
/* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */	/* total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and ageage /
/* codtabm(ij,k) (1 & (ij-1) >> (k-1))+1 */	for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */
/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */	if(Typevar[k1]==1){ /* A product with age */
/* k 1 2 3 4 5 6 7 8 9 */	cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
/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)];
/* 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 */
/* Here comes the value of quantitative after renumbering k with single quantitative covariates */
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]); */
}
for (k=1; k<=cptcovage;k++){ /* For product with age V1+V1age +V4 +ageV3 */
/* 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];
} else if(Dummy[Tage[k]]== 3){ /* quantitative with age */
cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
}
/* printf("hPxij Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
}
for (k=1; k<=cptcovprod;k++){ /* 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]); */
/* 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{	}else{
if(Dummy[Tvard[k][2]==0]){	cov[2+nagesqr+k1]=precov[nres][k1];
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]];
}
}	}
}	}/* End of loop on model equation */
	/* Old code */
	/* if( Dummy[k1]==0 && Typevar[k1]==0 ){ /\* Single dummy \/ /
	/* /\* V(Tvarsel)=Tvalsel=Tresult[nres][pos](value); V(Tvresult[nres][pos] (variable): V(variable)=value) \/ /
	/* /\* 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 \\/ \/ */
	/* /\* 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)];or [codtabm(ij,TnsdVar[TvarsD[k]] \/ /
	/* cov[2+nagesqr+k1]=Tresult[nres][resultmodel[nres][k1]]; */
	/* /\* printf("hpxij Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,TnsdVar[TvarsD[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,TnsdVar[TvarsD[k]])],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,TnsdVar[TvarsD[k]])); \/ /
	/* printf("hpxij Dummy combi=%d k1=%d Tvar[%d]=V%d cov[2+%d+%d]=%lf resultmodel[nres][%d]=%d nres/nresult=%d/%d \n",ij,k1,k1, Tvar[k1],nagesqr,k1,cov[2+nagesqr+k1],k1,resultmodel[nres][k1],nres,nresult); */
	/* printf("hpxij new Dummy precov[nres=%d][k1=%d]=%.4f\n", nres, k1, precov[nres][k1]); */
	/* }else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /\* Single quantitative variables \/ /
	/* /\* resultmodel[nres][k1]=k3: k1th position in the model correspond to the k3 position in the resultline \/ /
	/* cov[2+nagesqr+k1]=Tqresult[nres][resultmodel[nres][k1]]; */
	/* /\* for (k=1; k<=nsq;k++) { /\\* For single varying covariates only \\/ \/ */
	/* /\* /\\* Here comes the value of quantitative after renumbering k with single quantitative covariates \\/ \/ */
	/* /\* cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; \/ /
	/* printf("hPxij Quantitative k1=%d resultmodel[nres][%d]=%d,Tqresult[%d][%d]=%f\n",k1,k1,resultmodel[nres][k1],nres,resultmodel[nres][k1],Tqresult[nres][resultmodel[nres][k1]]); */
	/* printf("hpxij new Quanti precov[nres=%d][k1=%d]=%.4f\n", nres, k1, precov[nres][k1]); */
	/* }else if( Dummy[k1]==2 ){ /\* For dummy with age product \/ /
	/* /\* Tvar[k1] Variable in the age product ageV1 is 1 \/ */
	/* /\* [Tinvresult[nres][V1] is its value in the resultline nres \/ /
	/* cov[2+nagesqr+k1]=TinvDoQresult[nres][Tvar[k1]]cov[2]; /
	/* printf("DhPxij Dummy with age k1=%d Tvar[%d]=%d TinvDoQresult[nres=%d][%d]=%.f age=%.2f,cov[2+%d+%d]=%.3f\n",k1,k1,Tvar[k1],nres,TinvDoQresult[nres][Tvar[k1]],cov[2],nagesqr,k1,cov[2+nagesqr+k1]); */
	/* printf("hpxij new Dummy with age product precov[nres=%d][k1=%d]=%.4f * age=%.2f\n", nres, k1, precov[nres][k1], cov[2]); */

	/* /\* cov[2+nagesqr+k1]=Tresult[nres][resultmodel[nres][k1]]; \/ /
	/* /\* for (k=1; k<=cptcovage;k++){ /\\* For product with age V1+V1age +V4 +ageV3 \\/ \/ */
	/* /\* 1+2 Tage[1]=2 TVar[2]=1 Dummy[2]=2, Tage[2]=4 TVar[4]=3 Dummy[4]=3 quant\/ /
	/* /\* \/ /
	/* /\* 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 \/ */
	/* /\cptcovage=2 1 2 \/ */
	/* /\Tage[k]= 5 8 \/ */
	/* }else if( Dummy[k1]==3 ){ /\* For quant with age product \/ /
	/* cov[2+nagesqr+k1]=Tresult[nres][resultmodel[nres][k1]]; */
	/* printf("QhPxij Quant with age k1=%d resultmodel[nres][%d]=%d,Tqresult[%d][%d]=%f\n",k1,k1,resultmodel[nres][k1],nres,resultmodel[nres][k1],Tqresult[nres][resultmodel[nres][k1]]); */
	/* printf("hpxij new Quanti with age product precov[nres=%d][k1=%d] * age=%.2f\n", nres, k1, precov[nres][k1], cov[2]); */
	/* /\* 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,TnsdVar[TvarsD[Tvar[Tage[k]]]])]cov[2]; \\/ \/ /
	/* /\* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,TnsdVar[TvarsD[Tvar[Tage[k]]]])]cov[2]; \/ */
	/* /\* printf("hPxij Age combi=%d k=%d cptcovage=%d Tage[%d]=%d Tvar[Tage[%d]]=V%d nbcode[Tvar[Tage[k]]][codtabm(ij,TnsdVar[Tvar[Tage[k]]]])]=%d nres=%d\n",ij,k,cptcovage,k,Tage[k],k,Tvar[Tage[k]], nbcode[Tvar[Tage[k]]][codtabm(ij,TnsdVar[Tvar[Tage[k]]])],nres); \/ /
	/* /\* } else if(Dummy[Tage[k]]== 3){ /\\* quantitative with age \\/ \/ */
	/* /\* 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]); \/ /
	/* }else if(Typevar[k1]==2 ){ /\* For product (not with age) \/ /
	/* /\* for (k=1; k<=cptcovprod;k++){ /\\* For product without age \\/ \/ */
	/* /\* /\\* 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 \\/ \/ /
	/* /\* /\\cptcovprod=1 1 2 \\/ \/ /
	/* /\* /\\Tprod[]= 4 7 \\/ \/ /
	/* /\* /\\Tvard[][1] 4 1 \\/ \/ /
	/* /\* /\\Tvard[][2] 3 2 \\/ \/ /

	/* /\* printf("hPxij Prod ij=%d k=%d Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]=%d nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][1])]=%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2],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+k1]=TinvDoQresult[nres][Tvardk[k1][1]] * TinvDoQresult[nres][Tvardk[k1][2]]; */
	/* printf("hPxij Prod ij=%d k1=%d cov[2+%d+%d]=%.5f Tvard[%d][1]=V%d * Tvard[%d][2]=V%d ; TinvDoQresult[nres][Tvardk[k1][1]]=%.4f * TinvDoQresult[nres][Tvardk[k1][1]]=%.4f\n",ij,k1,nagesqr,k1,cov[2+nagesqr+k1],k1,Tvardk[k1][1], k1,Tvardk[k1][2], TinvDoQresult[nres][Tvardk[k1][1]], TinvDoQresult[nres][Tvardk[k1][2]]); */
	/* printf("hpxij new Product no age product precov[nres=%d][k1=%d]=%.4f\n", nres, k1, precov[nres][k1]); */

	/* /\* if(Dummy[Tvardk[k1][1]]==0){ \/ /
	/* /\* if(Dummy[Tvardk[k1][2]]==0){ /\\* Product of dummies \\/ \/ */
	/* /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; \/ /
	/* /\* cov[2+nagesqr+k1]=Tinvresult[nres][Tvardk[k1][1]] * Tinvresult[nres][Tvardk[k1][2]]; \/ /
	/* /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,TnsdVar[Tvard[k][1]])] * nbcode[Tvard[k][2]][codtabm(ij,TnsdVar[Tvard[k][2]])]; \/ /
	/* /\* }else{ /\\* Product of dummy by quantitative \\/ \/ */
	/* /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,TnsdVar[Tvard[k][1]])] * Tqresult[nres][k]; \/ /
	/* /\* cov[2+nagesqr+k1]=Tresult[nres][Tinvresult[nres][Tvardk[k1][1]]] * Tqresult[nres][Tinvresult[nres][Tvardk[k1][2]]]; \/ /
	/* /\* } \/ /
	/* /\* }else{ /\\* Product of quantitative by...\\/ \/ */
	/* /\* if(Dummy[Tvard[k][2]]==0){ /\\* quant by dummy \\/ \/ */
	/* /\* /\\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,TnsdVar[Tvard[k][2]])] * Tqinvresult[nres][Tvard[k][1]]; \\/ \/ */
	/* /\* cov[2+nagesqr+k1]=Tqresult[nres][Tinvresult[nres][Tvardk[k1][1]]] * Tresult[nres][Tinvresult[nres][Tvardk[k1][2]]] ; \/ /
	/* /\* }else{ /\\* Product of two quant \\/ \/ */
	/* /\* /\\* cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]]; \\/ \/ */
	/* /\* cov[2+nagesqr+k1]=Tqresult[nres][Tinvresult[nres][Tvardk[k1][1]]] * Tqresult[nres][Tinvresult[nres][Tvardk[k1][2]]] ; \/ /
	/* /\* } \/ /
	/* /\* }/\\end of products quantitative \\/ \/ /
	/* }/\end of products \/ */
	/* } /\* End of loop on model equation \/ /
/* 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)]; */
/* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 \/ /	/* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 \/ /
Line 3495 double *hpxij(double *po, int nhstep	Line 3702 double *hpxij(double *po, int nhstep
/* double *hbxij(double po, int nhstepm, double age, int hstepm, double x, double *prevacurrent, int nlstate, int stepm, double oldm, double savm, double dnewm, double doldm, double dsavm, int ij ) */	/* double *hbxij(double po, int nhstepm, double age, int hstepm, double x, double *prevacurrent, int nlstate, int stepm, double oldm, double savm, double dnewm, double doldm, double dsavm, int ij ) */
double *hbxij(double po, int nhstepm, double age, int hstepm, double x, double ***prevacurrent, int nlstate, int stepm, int ij, int nres )	double *hbxij(double po, int nhstepm, double age, int hstepm, double x, double ***prevacurrent, int nlstate, int stepm, int ij, int nres )
{	{
/* For a combination of dummy covariate ij, computes the transition matrix starting at age 'age' over	/* For dummy covariates given in each resultline (for historical, computes the corresponding combination ij),
	computes the transition matrix starting at age 'age' over
'nhstepmhstepmstepm' months (i.e. until	'nhstepmhstepmstepm' months (i.e. until
age (in years) age+nhstepmhstepmstepm/12) by multiplying	age (in years) age+nhstepmhstepmstepm/12) by multiplying
nhstepm*hstepm matrices.	nhstepm*hstepm matrices.
Line 3507 double *hbxij(double *po, int nhstep	Line 3715 double *hbxij(double *po, int nhstep
The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output	The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output
*/	*/

int i, j, d, h, k;	int i, j, d, h, k, k1;
double out, cov[NCOVMAX+1], bmij();	double out, cov[NCOVMAX+1], bmij();
double newm, *newmm;	double newm, *newmm;
double agexact;	double agexact;
Line 3533 double *hbxij(double *po, int nhstep	Line 3741 double *hbxij(double *po, int nhstep
/* Debug */	/* Debug */
/* printf("hBxij age=%lf, agexact=%lf\n", age, agexact); */	/* printf("hBxij age=%lf, agexact=%lf\n", age, agexact); */
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++){	}
/* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */	/** New code */
/* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; \/ /	for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */
cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];	if(Typevar[k1]==1){ /* A product with age */
/* 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)); */	cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
}	}else{
for (k=1; k<=nsq;k++) { /* For single varying covariates only */	cov[2+nagesqr+k1]=precov[nres][k1];
/* Here comes the value of quantitative after renumbering k with single quantitative covariates */	}
cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];	}/* End of loop on model equation */
/* 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]); */	/** End of new code */
}	/** This was old code */
for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 // For product with age */	/* for (k=1; k<=nsd;k++){ /\* For single dummy covariates only \//\ cptcovn error \/ /
/* if(Dummy[Tvar[Tage[k]]]== 2){ /\* dummy with age error!!!\/ /	/* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; \/ /
if(Dummy[Tage[k]]== 2){ /* dummy with age */	/* /\* /\\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; \\/ \/ */
cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];	/* cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,TvarsD[k])];/\* Bug valgrind \/ /
} else if(Dummy[Tage[k]]== 3){ /* quantitative with age */	/* /\* 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)); \/ /
cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];	/* } */
}	/* for (k=1; k<=nsq;k++) { /\* For single varying covariates only \/ /
/* 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]); */	/* /\* Here comes the value of quantitative after renumbering k with single quantitative covariates \/ /
}	/* cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; */
for (k=1; k<=cptcovprod;k++){ /* Useless because included in cptcovn */	/* /\* printf("hPxij Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); \/ /
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];	/* } */
}	/* for (k=1; k<=cptcovage;k++){ /\* Should start at cptcovn+1 \//\ For product with age \/ /
/printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);/	/* /\* if(Dummy[Tvar[Tage[k]]]== 2){ /\\* dummy with age error!!!\\/ \/ */
/printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);/	/* if(Dummy[Tage[k]]== 2){ /\* dummy with age \/ /
	/* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]cov[2]; /
	/* } else if(Dummy[Tage[k]]== 3){ /\* quantitative with age \/ /
	/* 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]); \/ /
	/* } */
	/* for (k=1; k<=cptcovprod;k++){ /\* Useless because included in cptcovn \/ /
	/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; /
	/* if(Dummy[Tvard[k][1]]==0){ */
	/* if(Dummy[Tvard[k][2]]==0){ */
	/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][1])]; */
	/* }else{ */
	/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * Tqresult[nres][k]; */
	/* } */
	/* }else{ */
	/* if(Dummy[Tvard[k][2]]==0){ */
	/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])] * 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("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);\/ */
	/** End of old code */

/* Careful transposed matrix */	/* Careful transposed matrix */
/* age is in cov[2], prevacurrent at beginning of transition. */	/* age is in cov[2], prevacurrent at beginning of transition. */
/* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */	/* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
/* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */	/* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\	out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
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 3620 double *hbxij(double *po, int nhstep	Line 3853 double *hbxij(double *po, int nhstep
/************* log-likelihood ***********/	/************* log-likelihood ***********/
double func( double *x)	double func( double *x)
{	{
int i, ii, j, k, mi, d, kk;	int i, ii, j, k, mi, d, kk, kf=0;
int ioffset=0;	int ioffset=0;
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 */
int s1, s2;	int s1, s2;
int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */	int iv=0, iqv=0, itv=0, iqtv=0 ; /* Index of varying covariate, fixed quantitative cov, time varying covariate, quantitative time varying covariate */

double bbh, survp;	double bbh, survp;
long ipmx;
double agexact;	double agexact;
	double agebegin, ageend;
/extern weight /	/extern weight /
/* We are differentiating ll according to initial status */	/* We are differentiating ll according to initial status */
/* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/	/* for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
Line 3652 double func( double *x)	Line 3886 double func( double *x)
*/	*/
ioffset=2+nagesqr ;	ioffset=2+nagesqr ;
/* Fixed */	/* Fixed */
for (k=1; k<=ncovf;k++){ /* For each fixed covariate dummu or quant or prod */	for (kf=1; kf<=ncovf;kf++){ /* For each fixed covariate dummu 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 /
/* TvarFind; TvarFind[1]=6, TvarFind[2]=7, TvarFind[3]=9 // Inverse V2(6) is first fixed (single or prod) */	/* 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)*/	cov[ioffset+TvarFind[kf]]=covar[Tvar[TvarFind[kf]]][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 /	/* 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]
Line 3672 double func( double *x)	Line 3906 double func( double *x)
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]
*/	*/
for(mi=1; mi<= wav[i]-1; mi++){	for(mi=1; mi<= wav[i]-1; mi++){ /* Varying with waves */
	/* Wave varying (but not age varying) */
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*/	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]; 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];
Line 3682 double func( double *x)	Line 3917 double func( double *x)
oldm[ii][j]=(ii==j ? 1.0 : 0.0);	oldm[ii][j]=(ii==j ? 1.0 : 0.0);
savm[ii][j]=(ii==j ? 1.0 : 0.0);	savm[ii][j]=(ii==j ? 1.0 : 0.0);
}	}

	agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
	ageend=agev[mw[mi][i]][i] + (dh[mi][i])stepm/YEARM; / Age at end of effective wave and at the end of transition */
for(d=0; d<dh[mi][i]; d++){	for(d=0; d<dh[mi][i]; d++){
newm=savm;	newm=savm;
agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;	agexact=agev[mw[mi][i]][i]+d*stepm/YEARM;
Line 3772 double func( double *x)	Line 4010 double func( double *x)
/survp += out[s1][j]; /	/survp += out[s1][j]; /
lli= log(survp);	lli= log(survp);
}	}
else if (s2==-4) {	/* else if (s2==-4) { */
for (j=3,survp=0. ; j<=nlstate; j++)	/* for (j=3,survp=0. ; j<=nlstate; j++) */
survp += (1.+bbh)out[s1][j]- bbhsavm[s1][j];	/* survp += (1.+bbh)out[s1][j]- bbhsavm[s1][j]; */
lli= log(survp);	/* lli= log(survp); */
}	/* } */
else if (s2==-5) {	/* else if (s2==-5) { */
for (j=1,survp=0. ; j<=2; j++)	/* for (j=1,survp=0. ; j<=2; j++) */
survp += (1.+bbh)out[s1][j]- bbhsavm[s1][j];	/* survp += (1.+bbh)out[s1][j]- bbhsavm[s1][j]; */
lli= log(survp);	/* lli= log(survp); */
}	/* } */
else{	else{
lli= log((1.+bbh)out[s1][s2]- bbhsavm[s1][s2]); /* linear interpolation */	lli= log((1.+bbh)out[s1][s2]- bbhsavm[s1][s2]); /* linear interpolation */
/* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)out[s1][s2]- bbh(savm[s1][s2])):log((1.+bbh)out[s1][s2]));/ /* linear interpolation */	/* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)out[s1][s2]- bbh(savm[s1][s2])):log((1.+bbh)out[s1][s2]));/ /* linear interpolation */
Line 3956 double func( double *x)	Line 4194 double func( double *x)
double funcone( double *x)	double funcone( double *x)
{	{
/* Same as func but slower because of a lot of printf and if */	/* Same as func but slower because of a lot of printf and if */
int i, ii, j, k, mi, d, kk;	int i, ii, j, k, mi, d, kk, kf=0;
int ioffset=0;	int ioffset=0;
double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];	double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
double **out;	double **out;
Line 3979 double funcone( double *x)	Line 4217 double funcone( double *x)
for(k=1; k<=nlstate; k++) ll[k]=0.;	for(k=1; k<=nlstate; k++) ll[k]=0.;
ioffset=0;	ioffset=0;
for (i=1,ipmx=0, sw=0.; i<=imx; i++){	for (i=1,ipmx=0, sw=0.; i<=imx; i++){
	/* Computes the values of the ncovmodel covariates of the model
	depending if the covariates are fixed or varying (age dependent) and stores them in cov[]
	Then computes with function pmij which return a matrix p[i][j] giving the elementary probability
	to be observed in j being in i according to the model.
	*/
/* ioffset=2+nagesqr+cptcovage; */	/* ioffset=2+nagesqr+cptcovage; */
ioffset=2+nagesqr;	ioffset=2+nagesqr;
/* Fixed */	/* Fixed */
/* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */	/* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
/* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products \/ /	/* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products \/ /
for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products // Missing values are set to -1 but should be dropped */	for (kf=1; kf<=ncovf;kf++){ /* Simple and product fixed covariates without age* products // Missing values are set to -1 but should be dropped */
cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, only V1 is fixed (k=6)*/	cov[ioffset+TvarFind[kf]]=covar[Tvar[TvarFind[kf]]][i];/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, only V1 is fixed (k=6)*/
/* cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i]; */	/* cov[ioffset+TvarFind[1]]=covar[Tvar[TvarFind[1]]][i]; */
/* cov[2+6]=covar[Tvar[6]][i]; */	/* cov[2+6]=covar[Tvar[6]][i]; */
/* cov[2+6]=covar[2][i]; V2 */	/* cov[2+6]=covar[2][i]; V2 */
Line 3996 double funcone( double *x)	Line 4239 double funcone( double *x)
/* cov[2+9]=covar[Tvar[9]][i]; */	/* cov[2+9]=covar[Tvar[9]][i]; */
/* cov[2+9]=covar[1][i]; V1 */	/* cov[2+9]=covar[1][i]; V1 */
}	}
	/* In model V2+V1V4+ageV3+V3V2 Tvar[1] is V2, Tvar[2=V1V4]
	is 5, Tvar[3=ageV3] should not be computed because of age Tvar[4=V3V2]=6
	has been calculated etc */
	/* For an individual i, wav[i] gives the number of effective waves */
	/* We compute the contribution to Likelihood of each effective transition
	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];
	s2=s[mw[mi+1][i]][i];
	And the iv th varying covariate is the cotvar[mw[mi+1][i]][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 */
/* 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 \/ /
/* cov[++ioffset]=coqvar[TvarFQ[k]][i];/\* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, only V2 and V1V2 is fixed (k=6 and 7?)\/ */	/* cov[++ioffset]=coqvar[TvarFQ[k]][i];/\* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, only V2 and V1V2 is fixed (k=6 and 7?)\/ */
/* } */	/* } */
Line 4053 double funcone( double *x)	Line 4309 double funcone( double *x)
savm=oldm;	savm=oldm;
oldm=newm;	oldm=newm;
} /* end mult */	} /* end mult */
	/lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);/ /* Original formula */
	/* But now since version 0.9 we anticipate for bias at large stepm.
	* If stepm is larger than one month (smallest stepm) and if the exact delay
	* (in months) between two waves is not a multiple of stepm, we rounded to
	* the nearest (and in case of equal distance, to the lowest) interval but now
	* we keep into memory the bias bh[mi][i] and also the previous matrix product
	* (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
	* probability in order to take into account the bias as a fraction of the way
	* from savm to out if bh is negative or even beyond if bh is positive. bh varies
	* -stepm/2 to stepm/2 .
	* For stepm=1 the results are the same as for previous versions of Imach.
	* For stepm > 1 the results are less biased than in previous versions.
	*/
s1=s[mw[mi][i]][i];	s1=s[mw[mi][i]][i];
s2=s[mw[mi+1][i]][i];	s2=s[mw[mi+1][i]][i];
/* if(s2==-1){ */	/* if(s2==-1){ */
Line 4085 double funcone( double *x)	Line 4353 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("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("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])); */
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\ */
	/* %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, /
	/* 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); /
}	}
fprintf(ficresilk," %10.6f\n", -llt);	fprintf(ficresilk," %10.6f\n", -llt);
	/* printf(" %10.6f\n", -llt); */
}	}
} /* end of wave */	} /* end of wave */
} /* end of individual */	} /* end of individual */
for(k=1,l=0.; k<=nlstate; k++) l += ll[k];	for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
/* printf("l1=%f l2=%f ",ll[1],ll[2]); */	/* printf("l1=%f l2=%f ",ll[1],ll[2]); */
l= lipmx/sw; / To get the same order of magnitude as if weight=1 for every body */	l= lipmx/sw; / To get the same order of magnitude as if weight=1 for every body */
if(globpr==0){ /* First time we count the contributions and weights */	if(globpr==0){ /* First time we count the contributions and weights */
gipmx=ipmx;	gipmx=ipmx;
gsw=sw;	gsw=sw;
}	}
return -l;	return -l;
}	}

Line 4696 void freqsummary(char fileres[], double	Line 4970 void freqsummary(char fileres[], double
int Tvaraff, int invalidvarcomb, int *nbcode, int ncodemax,double mint,double anint, char strstart[], \	int Tvaraff, int invalidvarcomb, int *nbcode, int ncodemax,double mint,double anint, char strstart[], \
int firstpass, int lastpass, int stepm, int weightopt, char model[])	int firstpass, int lastpass, int stepm, int weightopt, char model[])
{ /* Some frequencies as well as proposing some starting values */	{ /* Some frequencies as well as proposing some starting values */
	/* Frequencies of any combination of dummy covariate used in the model equation */
int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1;	int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1;
int iind=0, iage=0;	int iind=0, iage=0;
int mi; /* Effective wave */	int mi; /* Effective wave */
Line 4764 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5038 Title=%s <br>Datafile=%s Firstpass=%d La
j1=0;	j1=0;

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


Line 4772 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5047 Title=%s <br>Datafile=%s Firstpass=%d La
reference=low_education V1=0,V2=0	reference=low_education V1=0,V2=0
med_educ V1=1 V2=0,	med_educ V1=1 V2=0,
high_educ V1=0 V2=1	high_educ V1=0 V2=1
Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff	Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcovn
*/	*/
dateintsum=0;	dateintsum=0;
k2cpt=0;	k2cpt=0;
Line 4809 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5084 Title=%s <br>Datafile=%s Firstpass=%d La
if(nj==1)	if(nj==1)
j=0; /* First pass for the constant */	j=0; /* First pass for the constant */
else{	else{
j=cptcoveff; /* Other passes for the covariate values */	j=cptcoveff; /* Other passes for the covariate values number of simple covariates in the model V2+V1 =2 (simple dummy fixed or time varying) */
}	}
first=1;	first=1;
for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on all covariates combination of the model, excluding quantitatives, V4=0, V3=0 for example, fixed or varying covariates */	for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on all dummy covariates combination of the model, ie excluding quantitatives, V4=0, V3=0 for example, fixed or varying covariates */
posproptt=0.;	posproptt=0.;
/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);	/*printf("cptcovn=%d Tvaraff=%d", cptcovn,Tvaraff[1]);
scanf("%d", i);*/	scanf("%d", i);*/
for (i=-5; i<=nlstate+ndeath; i++)	for (i=-5; i<=nlstate+ndeath; i++)
for (s2=-5; s2<=nlstate+ndeath; s2++)	for (s2=-5; s2<=nlstate+ndeath; s2++)
Line 4851 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5126 Title=%s <br>Datafile=%s Firstpass=%d La
/* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; \/ /	/* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; \/ /
/* }else if(Tvaraff[z1] ==-10){ */	/* }else if(Tvaraff[z1] ==-10){ */
/* /\* sumnew+=coqvar[z1][iind]; \/ /	/* /\* sumnew+=coqvar[z1][iind]; \/ /
/* }else */	/* }else / / TODO TODO codtabm(j1,z1) or codtabm(j1,Tvaraff[z1]]z1)*/
if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */	/* if( iind >=imx-3) printf("Searching error iind=%d Tvaraff[z1]=%d covar[Tvaraff[z1]][iind]=%.f TnsdVar[Tvaraff[z1]]=%d, cptcoveff=%d, cptcovs=%d \n",iind, Tvaraff[z1], covar[Tvaraff[z1]][iind],TnsdVar[Tvaraff[z1]],cptcoveff, cptcovs); */
	if(Tvaraff[z1]<1 \|\| Tvaraff[z1]>=NCOVMAX)
	printf("Error Tvaraff[z1]=%d<1 or >=%d, cptcoveff=%d model=%s\n",Tvaraff[z1],NCOVMAX, cptcoveff, model);
	if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]){ /* for combination j1 of covariates */
/* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */	/* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */
bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */	bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
/* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",	/* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n", */
bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),	/* bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),*/
j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/	/* j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
/* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/	/* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
} /* Onlyf fixed */	} /* Onlyf fixed */
} /* end z1 */	} /* end z1 */
} /* cptcovn > 0 */	} /* cptcoveff > 0 */
} /* end any */	} /* end any */
}/* end j==0 */	}/* end j==0 */
if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */	if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */
Line 4873 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5151 Title=%s <br>Datafile=%s Firstpass=%d La
for (z1=1; z1<=cptcoveff; z1++) {	for (z1=1; z1<=cptcoveff; z1++) {
if( Fixed[Tmodelind[z1]]==1){	if( Fixed[Tmodelind[z1]]==1){
iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;	iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality. If 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. */
bool=0; /* not selected */	bool=0; /* not selected */
}else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */	}else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {	/* i1=Tvaraff[z1]; */
	/* i2=TnsdVar[i1]; */
	/* i3=nbcode[i1][i2]; */
	/* i4=covar[i1][iind]; */
	/* if(i4 != i3){ */
	if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) { /* Bug valgrind */
bool=0;	bool=0;
}	}
}	}
Line 4906 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5189 Title=%s <br>Datafile=%s Firstpass=%d La
freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */	freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean on known values only */	for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean on known values only */
if(!isnan(covar[ncovcol+z1][iind])){	if(!isnan(covar[ncovcol+z1][iind])){
idq[z1]=idq[z1]+weight[iind];	idq[z1]=idq[z1]+weight[iind];
meanq[z1]+=covar[ncovcol+z1][iind]weight[iind]; / Computes mean of quantitative with selected filter */	meanq[z1]+=covar[ncovcol+z1][iind]weight[iind]; / Computes mean of quantitative with selected filter */
/* stdq[z1]+=covar[ncovcol+z1][iind]covar[ncovcol+z1][iind]weight[iind]weight[iind]; //error/	/* stdq[z1]+=covar[ncovcol+z1][iind]covar[ncovcol+z1][iind]weight[iind]weight[iind]; //error/
stdq[z1]+=covar[ncovcol+z1][iind]covar[ncovcol+z1][iind]weight[iind]; /* weight[iind];/ /* Computes mean of quantitative with selected filter */	stdq[z1]+=covar[ncovcol+z1][iind]covar[ncovcol+z1][iind]weight[iind]; /* weight[iind];/ /* Computes mean of quantitative with selected filter */
}	}
}	}
/* if((int)agev[m][iind] == 55) */	/* if((int)agev[m][iind] == 55) */
Line 4948 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5231 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<=cptcoveff; z1++){	for (z1=1; z1<=cptcovs; z1++){
if(!FixedV[Tvaraff[z1]]){	if(!FixedV[Tvaraff[z1]]){
printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,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,z1)]);	fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
}else{	}else{
printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
}	}
}	}
printf( "**********\n#");	printf( "**********\n#");
Line 4996 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5279 Title=%s <br>Datafile=%s Firstpass=%d La
fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");	fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
if((cptcoveff==0 && nj==1)\|\| nj==2 ) /* no covariate and first pass */	if((cptcoveff==0 && nj==1)\|\| nj==2 ) /* no covariate and first pass */
fprintf(ficresp, " Age");	fprintf(ficresp, " Age");
if(nj==2) for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " V%d=%d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	if(nj==2) for (z1=1; z1<=cptcoveff; z1++) {
	printf(" V%d=%d, z1=%d, Tvaraff[z1]=%d, j1=%d, TnsdVar[Tvaraff[%d]]=%d \|",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])], z1, Tvaraff[z1], j1,z1,TnsdVar[Tvaraff[z1]]);
	fprintf(ficresp, " V%d=%d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
	}
for(i=1; i<=nlstate;i++) {	for(i=1; i<=nlstate;i++) {
if((cptcoveff==0 && nj==1)\|\| nj==2 ) fprintf(ficresp," Prev(%d) N(%d) N ",i,i);	if((cptcoveff==0 && nj==1)\|\| nj==2 ) fprintf(ficresp," Prev(%d) N(%d) N ",i,i);
fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);	fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
Line 5076 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5362 Title=%s <br>Datafile=%s Firstpass=%d La
}else if( nj==2){	}else if( nj==2){
if( iage <= iagemax){	if( iage <= iagemax){
fprintf(ficresp," %d",iage);	fprintf(ficresp," %d",iage);
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
}	}
}	}
for(s1=1; s1 <=nlstate ; s1++){	for(s1=1; s1 <=nlstate ; s1++){
Line 5384 void prevalence(double ***probs, double	Line 5670 void prevalence(double ***probs, double
if (cptcovn<1) {j=1;ncodemax[1]=1;}	if (cptcovn<1) {j=1;ncodemax[1]=1;}

first=0;	first=0;
for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */	for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of simple dummy covariates */
for (i=1; i<=nlstate; i++)	for (i=1; i<=nlstate; i++)
for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)	for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
prop[i][iage]=0.0;	prop[i][iage]=0.0;
Line 5402 void prevalence(double ***probs, double	Line 5688 void prevalence(double ***probs, double
for (z1=1; z1<=cptcoveff; z1++){	for (z1=1; z1<=cptcoveff; z1++){
if( Fixed[Tmodelind[z1]]==1){	if( Fixed[Tmodelind[z1]]==1){
iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;	iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,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 */
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {	if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) {
bool=0;	bool=0;
}	}
}	}
Line 5708 void concatwav(int wav[], int **dh, int	Line 5994 void concatwav(int wav[], int **dh, int
nbcode[k][j]=0; /* Valgrind */	nbcode[k][j]=0; /* Valgrind */

/* 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++) { /* From model V1 + V2age + V3 + V3V4 keeps V1 + V3 = 2 only */	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;
if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */	if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
switch(Fixed[k]) {	switch(Fixed[k]) {
Line 5806 void concatwav(int wav[], int **dh, int	Line 6092 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){ /* Dummy covariate and not age product */	if(Dummy[k]==1 && Typevar[k] !=1){ /* 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){
	printf("Error k=%d \n",k);
	exit(1);
	}
if(isnan(covar[Tvar[k]][i])){	if(isnan(covar[Tvar[k]][i])){
printf("ERROR, IMaCh doesn't treat fixed quantitative covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);	printf("ERROR, IMaCh doesn't treat fixed quantitative covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);
fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);	fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);
Line 5815 void concatwav(int wav[], int **dh, int	Line 6105 void concatwav(int wav[], int **dh, int
exit(1);	exit(1);
}	}
}	}
}	} /* end Quanti */
} /* end of loop on model-covariate k. nbcode[Tvark][1]=-1, nbcode[Tvark][1]=0 and nbcode[Tvark][2]=1 sets the value of covariate k*/	} /* end of loop on model-covariate k. nbcode[Tvark][1]=-1, nbcode[Tvark][1]=0 and nbcode[Tvark][2]=1 sets the value of covariate k*/

for (k=-1; k< maxncov; k++) Ndum[k]=0;	for (k=-1; k< maxncov; k++) Ndum[k]=0;
Line 5829 void concatwav(int wav[], int **dh, int	Line 6119 void concatwav(int wav[], int **dh, int

ij=0;	ij=0;
/* for (i=0; i<= maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(ageV3), 5(V3V2) 6(V1V4) \/ */	/* for (i=0; i<= maxncov-1; i++) { /\* modmaxcovj is unknown here. Only Ndum[2(V2),3(ageV3), 5(V3V2) 6(V1V4) \/ */
for (k=1; k<= cptcovt; k++) { /* modmaxcovj is unknown here. Only Ndum[2(V2),3(ageV3), 5(V3V2) 6(V1V4) /	for (k=1; k<= cptcovt; k++) { /* cptcovt: total number of covariates of the model (2) nbocc(+)+1 = 8 excepting constant and age and ageage /
	/* modmaxcovj is unknown here. Only Ndum[2(V2),3(ageV3), 5(V3V2) 6(V1V4) /
/printf("Ndum[%d]=%d\n",i, Ndum[i]);/	/printf("Ndum[%d]=%d\n",i, Ndum[i]);/
/* if((Ndum[i]!=0) && (i<=ncovcol)){ /\* Tvar[i] <= ncovmodel ? \/ /	/* if((Ndum[i]!=0) && (i<=ncovcol)){ /\* Tvar[i] <= ncovmodel ? \/ /
if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){ /* Only Dummy and non empty in the model */	if(Ndum[Tvar[k]]!=0 && Dummy[k] == 0 && Typevar[k]==0){ /* Only Dummy simple and non empty in the model */
	/* Typevar[k] =0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */
	/* Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product*/
/* If product not in single variable we don't print results */	/* If product not in single variable we don't print results */
/printf("diff Ndum[%d]=%d\n",i, Ndum[i]);/	/printf("diff Ndum[%d]=%d\n",i, Ndum[i]);/
++ij;/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, */	++ij;/* V5 + V4 + V3 + V4V3 + V5age + V2 + V1V2 + V1age + V1, // V5 quanti, V2 quanti, V4, V3, V1 dummies */
	/* k= 1 2 3 4 5 6 7 8 9 */
	/* Tvar[k]= 5 4 3 6 5 2 7 1 1 */
	/* ij 1 2 3 */
	/* Tvaraff[ij]= 4 3 1 */
	/* Tmodelind[ij]=2 3 9 */
	/* TmodelInvind[ij]=2 1 1 */
Tvaraff[ij]=Tvar[k]; /* For printing combination // V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, Tvar {5, 4, 3, 6, 5, 2, 7, 1, 1} Tvaraff={4, 3, 1} V4, V3, V1*/	Tvaraff[ij]=Tvar[k]; /* For printing combination // V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, Tvar {5, 4, 3, 6, 5, 2, 7, 1, 1} Tvaraff={4, 3, 1} V4, V3, V1*/
Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */	Tmodelind[ij]=k; /* Tmodelind: index in model of dummies Tmodelind[1]=2 V4: pos=2; V3: pos=3, V1=9 {2, 3, 9, ?, ?,} */
TmodelInvind[ij]=Tvar[k]- ncovcol-nqv; /* Inverse TmodelInvind[2=V4]=2 second dummy varying cov (V4)4-1-1 {0, 2, 1, } TmodelInvind[3]=1 */	TmodelInvind[ij]=Tvar[k]- ncovcol-nqv; /* Inverse TmodelInvind[2=V4]=2 second dummy varying cov (V4)4-1-1 {0, 2, 1, } TmodelInvind[3]=1 */
Line 5851 void concatwav(int wav[], int **dh, int	Line 6150 void concatwav(int wav[], int **dh, int
} /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */	} /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
/* ij--; */	/* ij--; */
/* cptcoveff=ij; /\Number of total covariates\/ */	/* cptcoveff=ij; /\Number of total covariates\/ */
cptcov=ij; /Number of total real effective covariates: effective	cptcov=ij; / cptcov= Number of total real effective simple dummies (fixed or time arying) effective (used as cptcoveff in other functions)
* because they can be excluded from the model and real	* because they can be excluded from the model and real
* if in the model but excluded because missing values, but how to get k from ij?*/	* if in the model but excluded because missing values, but how to get k from ij?*/
for(j=ij+1; j<= cptcovt; j++){	for(j=ij+1; j<= cptcovt; j++){
Line 5872 void concatwav(int wav[], int **dh, int	Line 6171 void concatwav(int wav[], int **dh, int

{	{
/* Health expectancies, no variances */	/* Health expectancies, no variances */
	/* cij is the combination in the list of combination of dummy covariates */
	/* strstart is a string of time at start of computing */
int i, j, nhstepm, hstepm, h, nstepm;	int i, j, nhstepm, hstepm, h, nstepm;
int nhstepma, nstepma; /* Decreasing with age */	int nhstepma, nstepma; /* Decreasing with age */
double age, agelim, hf;	double age, agelim, hf;
Line 5940 void concatwav(int wav[], int **dh, int	Line 6241 void concatwav(int wav[], int **dh, int
/* If stepm=6 months */	/* If stepm=6 months */
/* Computed by stepm unit matrices, product of hstepma matrices, stored	/* Computed by stepm unit matrices, product of hstepma matrices, stored
in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */	in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
	/* printf("HELLO evsij Entering hpxij age=%d cij=%d hstepm=%d x[1]=%f nres=%d\n",(int) age, cij, hstepm, x[1], nres); */
hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);	hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);

hf=hstepmstepm/YEARM; / Duration of hstepm expressed in year unit. */	hf=hstepmstepm/YEARM; / Duration of hstepm expressed in year unit. */
Line 5982 void concatwav(int wav[], int **dh, int	Line 6283 void concatwav(int wav[], int **dh, int
/* Covariances of health expectancies eij and of total life expectancies according	/* Covariances of health expectancies eij and of total life expectancies according
to initial status i, ei. .	to initial status i, ei. .
*/	*/
	/* Very time consuming function, but already optimized with precov */
int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;	int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
int nhstepma, nstepma; /* Decreasing with age */	int nhstepma, nstepma; /* Decreasing with age */
double age, agelim, hf;	double age, agelim, hf;
Line 6250 void concatwav(int wav[], int **dh, int	Line 6552 void concatwav(int wav[], int **dh, int
pstamp(ficresprobmorprev);	pstamp(ficresprobmorprev);
fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1p1j+w2p2j+... stand dev in()\n",estepm);	fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1p1j+w2p2j+... stand dev in()\n",estepm);
fprintf(ficresprobmorprev,"# Selected quantitative variables and dummies");	fprintf(ficresprobmorprev,"# Selected quantitative variables and dummies");
for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	/* We use TinvDoQresult[nres][resultmodel[nres][j] we sort according to the equation model and the resultline: it is a choice */
	/* for (j=1; j<= nsq; j++){ /\* For each selected (single) quantitative value \/ /\ To be done\/ /
	/* 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*/
	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++) */
fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,j)]);	/* fprintf(ficresprobmorprev," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,TnsdVar[Tvaraff[j]])]); */
fprintf(ficresprobmorprev,"\n");	fprintf(ficresprobmorprev,"\n");

fprintf(ficresprobmorprev,"# Age cov=%-d",ij);	fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
Line 6794 void varprob(char optionfilefiname[], do	Line 7101 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 6881 To be simple, these graphs help to under	Line 7189 To be simple, these graphs help to under
tj = (int) pow(2,cptcoveff);	tj = (int) pow(2,cptcoveff);
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(nres=1;nres <=nresult; nres++){ /* For each resultline */
	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);
	if(tj != 1 && TKresult[nres]!= j1)
	continue;

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

	/* Including quantitative variables of the resultline to be done */
	for (z1=1; z1<=cptcovs; z1++){ /* Loop on each variable of this resultline */
	printf("Varprob modelresult[%d][%d]=%d model=%s \n",nres, z1, modelresult[nres][z1], model);
	fprintf(ficlog,"Varprob modelresult[%d][%d]=%d model=%s \n",nres, z1, modelresult[nres][z1], model);
	/* fprintf(ficlog,"Varprob modelresult[%d][%d]=%d model=%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(Fixed[modelresult[nres][z1]]==0){ /* Fixed referenced to model equation */
	fprintf(ficresprob,"V%d=%d ",Tvresult[nres][z1],Tresult[nres][z1]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline */
	fprintf(ficresprobcov,"V%d=%d ",Tvresult[nres][z1],Tresult[nres][z1]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline */
	fprintf(ficgp,"V%d=%d ",Tvresult[nres][z1],Tresult[nres][z1]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline */
	fprintf(fichtmcov,"V%d=%d ",Tvresult[nres][z1],Tresult[nres][z1]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline */
	fprintf(ficresprobcor,"V%d=%d ",Tvresult[nres][z1],Tresult[nres][z1]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline */
	fprintf(ficresprob,"fixed ");
	fprintf(ficresprobcov,"fixed ");
	fprintf(ficgp,"fixed ");
	fprintf(fichtmcov,"fixed ");
	fprintf(ficresprobcor,"fixed ");
	}else{
	fprintf(ficresprob,"varyi ");
	fprintf(ficresprobcov,"varyi ");
	fprintf(ficgp,"varyi ");
	fprintf(fichtmcov,"varyi ");
	fprintf(ficresprobcor,"varyi ");
	}
	}else if(Dummy[modelresult[nres][z1]]==1){ /* Quanti variable */
	/* For each selected (single) quantitative value */
	fprintf(ficresprob," V%d=%lg ",Tvqresult[nres][z1],Tqresult[nres][z1]);
	if(Fixed[modelresult[nres][z1]]==0){ /* Fixed */
	fprintf(ficresprob,"fixed ");
	fprintf(ficresprobcov,"fixed ");
	fprintf(ficgp,"fixed ");
	fprintf(fichtmcov,"fixed ");
	fprintf(ficresprobcor,"fixed ");
	}else{
	fprintf(ficresprob,"varyi ");
	fprintf(ficresprobcov,"varyi ");
	fprintf(ficgp,"varyi ");
	fprintf(fichtmcov,"varyi ");
	fprintf(ficresprobcor,"varyi ");
	}
	}else{
	printf("Error in varprob() Dummy[modelresult[%d][%d]]=%d, modelresult[%d][%d]=V%d cptcovs=%d, cptcoveff=%d \n", nres, z1, Dummy[modelresult[nres][z1]],nres,z1,modelresult[nres][z1],cptcovs, cptcoveff); /* end if dummy or quanti */
	fprintf(ficlog,"Error in varprob() Dummy[modelresult[%d][%d]]=%d, modelresult[%d][%d]=V%d cptcovs=%d, cptcoveff=%d \n", nres, z1, Dummy[modelresult[nres][z1]],nres,z1,modelresult[nres][z1],cptcovs, cptcoveff); /* end if dummy or quanti */
	exit(1);
	}
	} /* End loop on variable of this resultline */
	/* for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]); */
	fprintf(ficresprob, "**********\n#\n");
fprintf(ficresprobcov, "**********\n#\n");	fprintf(ficresprobcov, "**********\n#\n");

fprintf(ficgp, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficgp, "**********\n#\n");	fprintf(ficgp, "**********\n#\n");


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(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 ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);
fprintf(ficresprobcor, "**********\n#");	fprintf(ficresprobcor, "**********\n#");
if(invalidvarcomb[j1]){	if(invalidvarcomb[j1]){
fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);	fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
Line 6913 To be simple, these graphs help to under	Line 7268 To be simple, these graphs help to under
trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);	trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
gp=vector(1,(nlstate)*(nlstate+ndeath));	gp=vector(1,(nlstate)*(nlstate+ndeath));
gm=vector(1,(nlstate)*(nlstate+ndeath));	gm=vector(1,(nlstate)*(nlstate+ndeath));
for (age=bage; age<=fage; age ++){	for (age=bage; age<=fage; age ++){ /* Fo each age we feed the model equation with covariates, using precov as in hpxij() ? */
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++) {	/* New code end of combination but for each resultline */
cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];	for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */
/cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];//* j1 1 2 3 4	if(Typevar[k1]==1){ /* A product with age */
* 1 1 1 1 1	cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
* 2 2 1 1 1	}else{
* 3 1 2 1 1	cov[2+nagesqr+k1]=precov[nres][k1];
*/	}
/* nbcode[1][1]=0 nbcode[1][2]=1;*/	}/* End of loop on model equation */
}	/* Old code */
/* V2+V1+V4+V3age Tvar[4]=3 ; V1+V2age Tvar[2]=2; V1+V1age Tvar[2]=1, Tage[1]=2 /	/* /\* for (k=1; k<=cptcovn;k++) { \/ /
/* ) p nbcode[Tvar[Tage[k]]][(1 & (ij-1) >> (k-1))+1] */	/* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)]; \/ /
/for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; */	/* for (k=1; k<=nsd;k++) { /\* For single dummy covariates only \/ /
for (k=1; k<=cptcovage;k++)	/* /\* Here comes the value of the covariate 'j1' after renumbering k with single dummy covariates \/ /
cov[2+Tage[k]+nagesqr]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];	/* cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(j1,TnsdVar[TvarsD[k]])]; */
for (k=1; k<=cptcovprod;k++)	/* /\cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];\//\* j1 1 2 3 4 */
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];	/* * 1 1 1 1 1 */
	/* * 2 2 1 1 1 */
	/* * 3 1 2 1 1 */
	/* \/ /
	/* /\* nbcode[1][1]=0 nbcode[1][2]=1;\/ /
	/* } */
	/* /\* V2+V1+V4+V3age Tvar[4]=3 ; V1+V2age Tvar[2]=2; V1+V1age Tvar[2]=1, Tage[1]=2 \/ */
	/* /\* ) p nbcode[Tvar[Tage[k]]][(1 & (ij-1) >> (k-1))+1] \/ /
	/* /\for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; \/ /
	/* for (k=1; k<=cptcovage;k++){ /\* For product with age \/ /
	/* if(Dummy[Tage[k]]==2){ /\* dummy with age \/ /
	/* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(j1,TnsdVar[Tvar[Tage[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]); */
	/* /\* cov[2+nagesqr+Tage[k]]=meanq[k]/idq[k]cov[2];/\\ Using the mean of quantitative variable Tvar[Tage[k]] /\\* Tqresult[nres][k]; \\/ \/ */
	/* /\* exit(1); \/ /
	/* /\* 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,TnsdVar[Tvard[k][1]])] * nbcode[Tvard[k][2]][codtabm(j1,TnsdVar[Tvard[k][2]])]; */
	/* /\* 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,TnsdVar[Tvard[k][1]])] * Tqresult[nres][resultmodel[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,TnsdVar[Tvard[k][2]])] * Tqinvresult[nres][TnsdVar[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][TnsdVar[Tvard[k][1]]]* Tqinvresult[nres][TnsdVar[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 7120 To be simple, these graphs help to under	Line 7514 To be simple, these graphs help to under
} /l1 /	} /l1 /
}/* k1 */	}/* k1 */
} /* loop on combination of covariates j1 */	} /* loop on combination of covariates j1 */
	} /* loop on nres */
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);
free_matrix(doldm,1,(nlstate)(nlstate+ndeath),1,(nlstate)(nlstate+ndeath));	free_matrix(doldm,1,(nlstate)(nlstate+ndeath),1,(nlstate)(nlstate+ndeath));
Line 7150 void printinghtml(char fileresu[], char	Line 7545 void printinghtml(char fileresu[], char
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"));
fprintf(fichtm,"<li> - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file) ",	fprintf(fichtm,"<li> - Observed prevalence (cross-sectional prevalence) in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file) ",
jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));	jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));	fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
fprintf(fichtm,"\	fprintf(fichtm,"\
Line 7184 void printinghtml(char fileresu[], char	Line 7579 void printinghtml(char fileresu[], char
jj1=0;	jj1=0;

fprintf(fichtm," \n<ul>");	fprintf(fichtm," \n<ul>");
for(nres=1; nres <= nresult; nres++) /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
for(k1=1; k1<=m;k1++){ /* For each combination of covariate */	/* k1=nres; */
if(m != 1 && TKresult[nres]!= k1)	k1= TKresult[nres];
continue;	/* for(k1=1; k1<=m;k1++){ /\* For each combination of covariate \/ /
	/* if(m != 1 && TKresult[nres]!= k1) */
	/* continue; */
jj1++;	jj1++;
if (cptcovn > 0) {	if (cptcovn > 0) {
fprintf(fichtm,"\n<li><a size=\"1\" color=\"#EC5E5E\" href=\"#rescov");	fprintf(fichtm,"\n<li><a size=\"1\" color=\"#EC5E5E\" href=\"#rescov");
for (cpt=1; cpt<=cptcoveff;cpt++){	for (cpt=1; cpt<=cptcovs;cpt++){ /*< cptcovs number of SIMPLE covariates in the model V2+V1 =2 (dummy or quantit or time varying) /
fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);	fprintf(fichtm,"_V%d=%lg_",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}
	/* for (cpt=1; cpt<=cptcoveff;cpt++){ */
	/* fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]); */
	/* } */
	/* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value \/ /
	/* fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]); */
	/* } */
fprintf(fichtm,"\">");	fprintf(fichtm,"\">");

/* if(nqfveff+nqtveff 0) / / Test to be done */	/* if(nqfveff+nqtveff 0) / / Test to be done */
fprintf(fichtm,"************ Results for covariates");	fprintf(fichtm,"************ Results for covariates");
for (cpt=1; cpt<=cptcoveff;cpt++){	for (cpt=1; cpt<=cptcovs;cpt++){
fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);	fprintf(fichtm," V%d=%lg ",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}
	/* fprintf(fichtm,"************ Results for covariates"); */
	/* for (cpt=1; cpt<=cptcoveff;cpt++){ */
	/* fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]); */
	/* } */
	/* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value \/ /
	/* fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
	/* } */
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1);	fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1);
continue;	continue;
Line 7218 void printinghtml(char fileresu[], char	Line 7622 void printinghtml(char fileresu[], char

jj1=0;	jj1=0;

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

/* for(i1=1; i1<=ncodemax[k1];i1++){ */	/* for(i1=1; i1<=ncodemax[k1];i1++){ */
jj1++;	jj1++;
if (cptcovn > 0) {	if (cptcovn > 0) {
fprintf(fichtm,"\n<p><a name=\"rescov");	fprintf(fichtm,"\n<p><a name=\"rescov");
for (cpt=1; cpt<=cptcoveff;cpt++){	for (cpt=1; cpt<=cptcovs;cpt++){
fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);	fprintf(fichtm,"_V%d=%lg_",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}
	/* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value \/ /
	/* fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]); */
	/* } */
fprintf(fichtm,"\"</a>");	fprintf(fichtm,"\"</a>");

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

/* if(nqfveff+nqtveff 0) / / Test to be done */	/* if(nqfveff+nqtveff 0) / / Test to be done */
fprintf(fichtm," (model=%s) ************\n<hr size=\"2\" color=\"#EC5E5E\">",model);	fprintf(fichtm," (model=%s) ************\n<hr size=\"2\" color=\"#EC5E5E\">",model);
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
Line 7269 divided by h: <sub>h</sub>P<sub>ij</sub>	Line 7670 divided by h: <sub>h</sub>P<sub>ij</sub>
<img src=\"%s_%d-3-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);	<img src=\"%s_%d-3-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);
/* Survival functions (period) in state j */	/* Survival functions (period) in state j */
for(cpt=1; cpt<=nlstate;cpt++){	for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"<br>\n- Survival functions in state %d. And probability to be observed in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \	fprintf(fichtm,"<br>\n- Survival functions in state %d. And probability to be observed in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br>", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
<img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);	fprintf(fichtm," (data from text file <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"PIJ_"),subdirf2(optionfilefiname,"PIJ_"));
	fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
}	}
/* State specific survival functions (period) */	/* State specific survival functions (period) */
for(cpt=1; cpt<=nlstate;cpt++){	for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"<br>\n- Survival functions in state %d and in any other live state (total).\	fprintf(fichtm,"<br>\n- Survival functions in state %d and in any other live state (total).\
And probability to be observed in various states (up to %d) being in state %d at different ages. \	And probability to be observed in various states (up to %d) being in state %d at different ages. \
<a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);	<a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> ", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
	fprintf(fichtm," (data from text file <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"PIJ_"),subdirf2(optionfilefiname,"PIJ_"));
	fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
}	}
/* Period (forward stable) prevalence in each health state */	/* Period (forward stable) prevalence in each health state */
for(cpt=1; cpt<=nlstate;cpt++){	for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability for a person being in state (1 to %d) at different ages, to be in state %d some years after. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \	fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability for a person being in state (1 to %d) at different ages, to be in state %d some years after. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br>", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
<img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);	fprintf(fichtm," (data from text file <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"P_"),subdirf2(optionfilefiname,"P_"));
	fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">" ,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
}	}
if(prevbcast==1){	if(prevbcast==1){
/* Backward prevalence in each health state */	/* Backward prevalence in each health state */
Line 7317 with weights corresponding to observed p	Line 7722 with weights corresponding to observed p
fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">", subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres );	fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">", subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres );
}	}
/* } /\* end i1 \/ /	/* } /\* end i1 \/ /
}/* End k1 */	}/* End k1=nres */
fprintf(fichtm,"</ul>");	fprintf(fichtm,"</ul>");

fprintf(fichtm,"\	fprintf(fichtm,"\
Line 7375 See page 'Matrix of variance-covariance	Line 7780 See page 'Matrix of variance-covariance
jj1=0;	jj1=0;

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

/* if(nqfveff+nqtveff 0) / / Test to be done */	/* if(nqfveff+nqtveff 0) / / Test to be done */
fprintf(fichtm,"************ Results for covariates");	fprintf(fichtm,"************ Results for covariates");
for (cpt=1; cpt<=cptcoveff;cpt++){	for (cpt=1; cpt<=cptcovs;cpt++){
fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);	fprintf(fichtm," V%d=%lg ",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(fichtm," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1);	fprintf(fichtm," Warning Combination (%d) ignored because no cases ",k1);
Line 7404 See page 'Matrix of variance-covariance	Line 7805 See page 'Matrix of variance-covariance
}	}
fprintf(fichtm,"</a></li>");	fprintf(fichtm,"</a></li>");
} /* cptcovn >0 */	} /* cptcovn >0 */
}	} /* End nres */
fprintf(fichtm," \n</ul>");	fprintf(fichtm," \n</ul>");

jj1=0;	jj1=0;

for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
for(k1=1; k1<=m;k1++){	/* k1=nres; */
if(m != 1 && TKresult[nres]!= k1)	k1= TKresult[nres];
continue;	/* for(k1=1; k1<=m;k1++){ */
	/* if(m != 1 && TKresult[nres]!= k1) */
	/* continue; */
/* for(i1=1; i1<=ncodemax[k1];i1++){ */	/* for(i1=1; i1<=ncodemax[k1];i1++){ */
jj1++;	jj1++;
if (cptcovn > 0) {	if (cptcovn > 0) {
fprintf(fichtm,"\n<p><a name=\"rescovsecond");	fprintf(fichtm,"\n<p><a name=\"rescovsecond");
for (cpt=1; cpt<=cptcoveff;cpt++){	for (cpt=1; cpt<=cptcovs;cpt++){
fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);	fprintf(fichtm,"_V%d=%lg_",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);
}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}
fprintf(fichtm,"\"</a>");	fprintf(fichtm,"\"</a>");

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

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

Line 7441 See page 'Matrix of variance-covariance	Line 7838 See page 'Matrix of variance-covariance
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);
continue;	continue;
}	}
}	} /* If cptcovn >0 */
for(cpt=1; cpt<=nlstate;cpt++) {	for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \	fprintf(fichtm,"\n<br>- Observed (cross-sectional with mov_average=%d) and period (incidence based) \
prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d-%d.svg\"> %s_%d-%d-%d.svg</a>",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);	prevalence (with 95%% confidence interval) in state (%d): <a href=\"%s_%d-%d-%d.svg\"> %s_%d-%d-%d.svg</a>",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
Line 7456 true period expectancies (those weighted	Line 7853 true period expectancies (those weighted
fprintf(fichtm," (data from text file <a href=\"%s.txt\">%s.txt</a>) \n<br>",subdirf2(optionfilefiname,"T_"),subdirf2(optionfilefiname,"T_"));	fprintf(fichtm," (data from text file <a href=\"%s.txt\">%s.txt</a>) \n<br>",subdirf2(optionfilefiname,"T_"),subdirf2(optionfilefiname,"T_"));
fprintf(fichtm,"<img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres);	fprintf(fichtm,"<img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres);
/* } /\* end i1 \/ /	/* } /\* end i1 \/ /
}/* End k1 */
}/* End nres */	}/* End nres */
fprintf(fichtm,"</ul>");	fprintf(fichtm,"</ul>");
fflush(fichtm);	fflush(fichtm);
Line 7534 void printinggnuplot(char fileresu[], ch	Line 7930 void printinggnuplot(char fileresu[], ch
strcpy(optfileres,"vpl");	strcpy(optfileres,"vpl");
/* 1eme*/	/* 1eme*/
for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */	for (cpt=1; cpt<= nlstate ; cpt ++){ /* For each live state */
for (k1=1; k1<= m ; k1 ++){ /* For each valid combination of covariate */	/* for (k1=1; k1<= m ; k1 ++){ /\* For each valid combination of covariate \/ /
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
	k1=TKresult[nres];
/* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */	/* plot [100000000000000000000:-100000000000000000000] "mysbiaspar/vplrmysbiaspar.txt to check */
if(m != 1 && TKresult[nres]!= k1)	/* if(m != 1 && TKresult[nres]!= k1) */
continue;	/* continue; */
/* We are interested in selected combination by the resultline */	/* We are interested in selected combination by the resultline */
/* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */	/* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
fprintf(ficgp,"\n# 1st: Forward (stable period) prevalence with CI: 'VPL_' files and live state =%d ", cpt);	fprintf(ficgp,"\n# 1st: Forward (stable period) prevalence with CI: 'VPL_' files and live state =%d ", cpt);
strcpy(gplotlabel,"(");	strcpy(gplotlabel,"(");
for (k=1; k<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */	for (k=1; k<=cptcovs; k++){ /* For each covariate k get corresponding value lv for combination k1 */
lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */	fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* for (k=1; k<=cptcoveff; k++){ /\* For each covariate k get corresponding value lv for combination k1 \/ /
vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */	/* /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the value of the covariate corresponding to k1 combination \\/ \/ */
/* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */	/* lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
/* printf(" V%d=%d ",Tvaraff[k],vlv); */	/* /\* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 \/ /
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	/* /\* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 \/ /
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);	/* /\* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 \/ /
}	/* vlv= nbcode[Tvaraff[k]][lv]; /\* vlv is the value of the covariate lv, 0 or 1 \/ /
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	/* /\* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv \/ /
/* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */	/* /\* printf(" V%d=%d ",Tvaraff[k],vlv); \/ /
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	/* fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	/* sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
	/* } */
	/* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value \/ /
	/* /\* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); \/ /
	/* fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
	/* sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
}	}
strcpy(gplotlabel+strlen(gplotlabel),")");	strcpy(gplotlabel+strlen(gplotlabel),")");
/* printf("\n#\n"); */	/* printf("\n#\n"); */
Line 7597 void printinggnuplot(char fileresu[], ch	Line 7999 void printinggnuplot(char fileresu[], ch
}else{	}else{
kl=0;	kl=0;
for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */	for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */	/* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to k1 combination and kth covariate \/ /
	lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
Line 7625 void printinggnuplot(char fileresu[], ch	Line 8028 void printinggnuplot(char fileresu[], ch
}else{	}else{
kl=0;	kl=0;
for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */	for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */	/* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to k1 combination and kth covariate \/ /
	lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];	/* vlv= nbcode[Tvaraff[k]][lv]; */
	vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];
kl++;	kl++;
/* kl=6+(cpt-1)(nlstate+1)+1+(i-1); /\ 6+(1-1)(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 \/ */	/* kl=6+(cpt-1)(nlstate+1)+1+(i-1); /\ 6+(1-1)(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 \/ */
/6+(cpt-1)(nlstate+1)+1+(i-1)+(nlstate+1)nlstate; 6+(1-1)(2+1)+1+(1-1) +(2+1)2=13 /	/6+(cpt-1)(nlstate+1)+1+(i-1)+(nlstate+1)nlstate; 6+(1-1)(2+1)+1+(1-1) +(2+1)2=13 /
Line 7639 void printinggnuplot(char fileresu[], ch	Line 8044 void printinggnuplot(char fileresu[], ch
fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \	fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
2+cptcoveff2+(cpt-1), cpt ); / 4 or 6 ?*/	2+cptcoveff2+(cpt-1), cpt ); / 4 or 6 ?*/
}else{	}else{
fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);	fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]);
kl++;	kl++;
}	}
} /* end covariate */	} /* end covariate */
Line 7667 void printinggnuplot(char fileresu[], ch	Line 8072 void printinggnuplot(char fileresu[], ch
/* fprintf(ficgp,"\nset out ;unset label;\n"); */	/* fprintf(ficgp,"\nset out ;unset label;\n"); */
fprintf(ficgp,"\nset out ;unset title;\n");	fprintf(ficgp,"\nset out ;unset title;\n");
} /* nres */	} /* nres */
} /* k1 */	/* } /\* k1 \/ /
} /* cpt */	} /* cpt */


/2 eme/	/2 eme/
for (k1=1; k1<= m ; k1 ++){	/* for (k1=1; k1<= m ; k1 ++){ */
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
if(m != 1 && TKresult[nres]!= k1)	k1=TKresult[nres];
continue;	/* if(m != 1 && TKresult[nres]!= k1) */
	/* continue; */
fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");	fprintf(ficgp,"\n# 2nd: Total life expectancy with CI: 't' files ");
strcpy(gplotlabel,"(");	strcpy(gplotlabel,"(");
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	for (k=1; k<=cptcovs; k++){ /* For each covariate k get corresponding value lv for combination k1 */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* for (k=1; k<=cptcoveff; k++){ /\* For each covariate and each value \/ /
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination \\/ \/ */
vlv= nbcode[Tvaraff[k]][lv];	/* lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	/* /\* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 \/ /
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);	/* /\* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 \/ /
}	/* /\* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 \/ /
/* for(k=1; k <= ncovds; k++){ */	/* /\* vlv= nbcode[Tvaraff[k]][lv]; \/ /
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	/* vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	/* fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	/* sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	/* } */
	/* /\* for(k=1; k <= ncovds; k++){ \/ /
	/* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value \/ /
	/* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
	/* fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
	/* sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
}	}
strcpy(gplotlabel+strlen(gplotlabel),")");	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
Line 7733 void printinggnuplot(char fileresu[], ch	Line 8144 void printinggnuplot(char fileresu[], ch
} /* vpopbased */	} /* vpopbased */
fprintf(ficgp,"\nset out;set out \"%s_%d-%d.svg\"; replot; set out; unset label;\n",subdirf2(optionfilefiname,"E_"),k1,nres); /* Buggy gnuplot */	fprintf(ficgp,"\nset out;set out \"%s_%d-%d.svg\"; replot; set out; unset label;\n",subdirf2(optionfilefiname,"E_"),k1,nres); /* Buggy gnuplot */
} /* end nres */	} /* end nres */
} /* k1 end 2 eme*/	/* } /\* k1 end 2 eme\/ /


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

for (cpt=1; cpt<= nlstate ; cpt ++) {	for (cpt=1; cpt<= nlstate ; cpt ++) { /* Fragile no verification of covariate values */
fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files: combination=%d state=%d",k1, cpt);	fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files: combination=%d state=%d",k1, cpt);
strcpy(gplotlabel,"(");	strcpy(gplotlabel,"(");
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	for (k=1; k<=cptcovs; k++){ /* For each covariate k get corresponding value lv for combination k1 */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* for (k=1; k<=cptcoveff; k++){ /\* For each covariate and each value \/ /
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination \\/ \/ */
vlv= nbcode[Tvaraff[k]][lv];	/* lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /\* Should be the covariate value corresponding to combination k1 and covariate k \/ /
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	/* /\* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 \/ /
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);	/* /\* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 \/ /
}	/* /\* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 \/ /
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	/* /\* vlv= nbcode[Tvaraff[k]][lv]; \/ /
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	/* vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	/* fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
}	/* sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
	/* } */
	/* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value \/ /
	/* fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][resultmodel[nres][k4]]); */
	/* sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][resultmodel[nres][k4]]); */
	}
strcpy(gplotlabel+strlen(gplotlabel),")");	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
Line 7788 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 8205 plot [%.f:%.f] \"%s\" every :::%d::%d u
}	}
fprintf(ficgp,"\nunset label;\n");	fprintf(ficgp,"\nunset label;\n");
} /* end nres */	} /* end nres */
} /* end kl 3eme */	/* } /\* end kl 3eme \/ /

/* 4eme */	/* 4eme */
/* Survival functions (period) from state i in state j by initial state i */	/* Survival functions (period) from state i in state j by initial state i */
for (k1=1; k1<=m; k1++){ /* For each covariate and each value */	/* for (k1=1; k1<=m; k1++){ /\* For each covariate and each value \/ /
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
if(m != 1 && TKresult[nres]!= k1)	k1=TKresult[nres];
continue;	/* if(m != 1 && TKresult[nres]!= k1) */
	/* continue; */
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state cpt*/
strcpy(gplotlabel,"(");	strcpy(gplotlabel,"(");
fprintf(ficgp,"\n#\n#\n# Survival functions in state j : 'LIJ_' files, cov=%d state=%d",k1, cpt);	fprintf(ficgp,"\n#\n#\n# Survival functions in state %d : 'LIJ_' files, cov=%d state=%d", cpt, k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	for (k=1; k<=cptcovs; k++){ /* For each covariate k get corresponding value lv for combination k1 */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* for (k=1; k<=cptcoveff; k++){ /\* For each covariate and each value \/ /
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
vlv= nbcode[Tvaraff[k]][lv];	/* /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination \\/ \/ */
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	/* /\* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 \/ /
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);	/* /\* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 \/ /
}	/* /\* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 \/ /
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	/* /\* vlv= nbcode[Tvaraff[k]][lv]; \/ /
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	/* vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	/* fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
	/* sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
	/* } */
	/* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value \/ /
	/* fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
	/* sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
}	}
strcpy(gplotlabel+strlen(gplotlabel),")");	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
Line 7839 set ter svg size 640, 480\nunset log y\n	Line 8262 set ter svg size 640, 480\nunset log y\n
fprintf(ficgp,"\nset out; unset label;\n");	fprintf(ficgp,"\nset out; unset label;\n");
} /* end cpt state*/	} /* end cpt state*/
} /* end nres */	} /* end nres */
} /* end covariate k1 */	/* } /\* end covariate k1 \/ /

/* 5eme */	/* 5eme */
/* Survival functions (period) from state i in state j by final state j */	/* Survival functions (period) from state i in state j by final state j */
for (k1=1; k1<= m ; k1++){ /* For each covariate combination if any */	/* for (k1=1; k1<= m ; k1++){ /\* For each covariate combination if any \/ /
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
if(m != 1 && TKresult[nres]!= k1)	k1=TKresult[nres];
continue;	/* if(m != 1 && TKresult[nres]!= k1) */
	/* continue; */
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each inital state */
strcpy(gplotlabel,"(");	strcpy(gplotlabel,"(");
fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);	fprintf(ficgp,"\n#\n#\n# Survival functions in state j and all livestates from state i by final state j: 'lij' files, cov=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	for (k=1; k<=cptcovs; k++){ /* For each covariate k get corresponding value lv for combination k1 */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* for (k=1; k<=cptcoveff; k++){ /\* For each covariate and each value \/ /
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
vlv= nbcode[Tvaraff[k]][lv];	/* /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination \\/ \/ */
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	/* /\* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 \/ /
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);	/* /\* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 \/ /
}	/* /\* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 \/ /
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	/* /\* vlv= nbcode[Tvaraff[k]][lv]; \/ /
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	/* vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	/* fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
	/* sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
	/* } */
	/* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value \/ /
	/* fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
	/* sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
}	}
strcpy(gplotlabel+strlen(gplotlabel),")");	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
Line 7897 set ter svg size 640, 480\nunset log y\n	Line 8326 set ter svg size 640, 480\nunset log y\n
}	}
fprintf(ficgp,"\nset out; unset label;\n");	fprintf(ficgp,"\nset out; unset label;\n");
} /* end cpt state*/	} /* end cpt state*/
} /* end covariate */	/* } /\* end covariate \/ /
} /* end nres */	} /* end nres */

/* 6eme */	/* 6eme */
/* CV preval stable (period) for each covariate */	/* CV preval stable (period) for each covariate */
for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */	/* for (k1=1; k1<= m ; k1 ++) /\* For each covariate combination if any \/ /
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
if(m != 1 && TKresult[nres]!= k1)	k1=TKresult[nres];
continue;	/* if(m != 1 && TKresult[nres]!= k1) */
	/* continue; */
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state of arrival */
strcpy(gplotlabel,"(");	strcpy(gplotlabel,"(");
fprintf(ficgp,"\n#\n#\n#CV preval stable (forward): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);	fprintf(ficgp,"\n#\n#\n#CV preval stable (forward): 'pij' files, covariatecombination#=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	for (k=1; k<=cptcovs; k++){ /* For each covariate k get corresponding value lv for combination k1 */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* for (k=1; k<=cptcoveff; k++){ /\* For each covariate and each value \/ /
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination \\/ \/ */
vlv= nbcode[Tvaraff[k]][lv];	/* lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	/* /\* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 \/ /
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);	/* /\* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 \/ /
}	/* /\* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 \/ /
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	/* /\* vlv= nbcode[Tvaraff[k]][lv]; \/ /
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	/* vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	/* fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
	/* sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
	/* } */
	/* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value \/ /
	/* fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
	/* sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
}	}
strcpy(gplotlabel+strlen(gplotlabel),")");	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
Line 7953 set ter svg size 640, 480\nunset log y\n	Line 8388 set ter svg size 640, 480\nunset log y\n
/* 7eme */	/* 7eme */
if(prevbcast == 1){	if(prevbcast == 1){
/* CV backward prevalence for each covariate */	/* CV backward prevalence for each covariate */
for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */	/* for (k1=1; k1<= m ; k1 ++) /\* For each covariate combination if any \/ /
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
if(m != 1 && TKresult[nres]!= k1)	k1=TKresult[nres];
continue;	/* if(m != 1 && TKresult[nres]!= k1) */
	/* continue; */
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life origin state */
strcpy(gplotlabel,"(");	strcpy(gplotlabel,"(");
fprintf(ficgp,"\n#\n#\n#CV Backward stable prevalence: 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);	fprintf(ficgp,"\n#\n#\n#CV Backward stable prevalence: 'pijb' files, covariatecombination#=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	for (k=1; k<=cptcovs; k++){ /* For each covariate k get corresponding value lv for combination k1 */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* for (k=1; k<=cptcoveff; k++){ /\* For each covariate and each value \/ /
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination \\/ \/ */
vlv= nbcode[Tvaraff[k]][lv];	/* lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	/* /\* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 \/ /
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);	/* /\* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 \/ /
}	/* /\* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 \/ /
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	/* /\* vlv= nbcode[Tvaraff[k]][lv]; \/ /
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	/* vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	/* fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
	/* sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
	/* } */
	/* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value \/ /
	/* fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
	/* sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
}	}
strcpy(gplotlabel+strlen(gplotlabel),")");	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
Line 7992 set ter svg size 640, 480\nunset log y\n	Line 8433 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 8009 set ter svg size 640, 480\nunset log y\n	Line 8450 set ter svg size 640, 480\nunset log y\n
if(prevfcast==1){	if(prevfcast==1){
/* Projection from cross-sectional to forward stable (period) prevalence for each covariate */	/* Projection from cross-sectional to forward stable (period) prevalence for each covariate */

for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */	/* for (k1=1; k1<= m ; k1 ++) /\* For each covariate combination if any \/ /
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
if(m != 1 && TKresult[nres]!= k1)	k1=TKresult[nres];
continue;	/* if(m != 1 && TKresult[nres]!= k1) */
	/* continue; */
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
strcpy(gplotlabel,"(");	strcpy(gplotlabel,"(");
fprintf(ficgp,"\n#\n#\n#Projection of prevalence to forward stable prevalence (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);	fprintf(ficgp,"\n#\n#\n#Projection of prevalence to forward stable prevalence (period): 'PROJ_' files, covariatecombination#=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */	for (k=1; k<=cptcovs; k++){ /* For each covariate k get corresponding value lv for combination k1 */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */	fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* for (k=1; k<=cptcoveff; k++){ /\* For each correspondig covariate value \/ /
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate value corresponding to k1 combination and kth covariate \\/ \/ */
vlv= nbcode[Tvaraff[k]][lv];	/* lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	/* /\* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 \/ /
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);	/* /\* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 \/ /
}	/* /\* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 \/ /
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	/* /\* vlv= nbcode[Tvaraff[k]][lv]; \/ /
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	/* vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	/* fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
	/* sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
	/* } */
	/* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value \/ /
	/* fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
	/* sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
}	}
strcpy(gplotlabel+strlen(gplotlabel),")");	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
Line 8083 set ter svg size 640, 480\nunset log y\n	Line 8530 set ter svg size 640, 480\nunset log y\n
kl=0;	kl=0;
strcpy(gplotcondition,"(");	strcpy(gplotcondition,"(");
for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */	for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */	/* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to combination k1 and covariate k \/ /
	lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */	/* vlv= nbcode[Tvaraff[k]][lv]; /\* Value of the modality of Tvaraff[k] \/ /
	vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];
kl++;	kl++;
sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);	sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
kl++;	kl++;
Line 8122 set ter svg size 640, 480\nunset log y\n	Line 8571 set ter svg size 640, 480\nunset log y\n
if(prevbcast==1){	if(prevbcast==1){
/* Back projection from cross-sectional to stable (mixed) for each covariate */	/* Back projection from cross-sectional to stable (mixed) for each covariate */

for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */	/* for (k1=1; k1<= m ; k1 ++) /\* For each covariate combination if any \/ /
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
if(m != 1 && TKresult[nres]!= k1)	k1=TKresult[nres];
continue;	/* if(m != 1 && TKresult[nres]!= k1) */
	/* continue; */
for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
strcpy(gplotlabel,"(");	strcpy(gplotlabel,"(");
fprintf(ficgp,"\n#\n#\n#Back projection of prevalence to stable (mixed) back prevalence: 'BPROJ_' files, covariatecombination#=%d originstate=%d",k1, cpt);	fprintf(ficgp,"\n#\n#\n#Back projection of prevalence to stable (mixed) back prevalence: 'BPROJ_' files, covariatecombination#=%d originstate=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */	for (k=1; k<=cptcovs; k++){ /* For each covariate k get corresponding value lv for combination k1 */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */	fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* for (k=1; k<=cptcoveff; k++){ /\* For each correspondig covariate value \/ /
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate value corresponding to k1 combination and kth covariate \\/ \/ */
vlv= nbcode[Tvaraff[k]][lv];	/* lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /\* Should be the covariate value corresponding to combination k1 and covariate k \/ /
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	/* /\* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 \/ /
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);	/* /\* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 \/ /
}	/* /\* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 \/ /
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	/* /\* vlv= nbcode[Tvaraff[k]][lv]; \/ /
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	/* vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	/* fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
	/* sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
	/* } */
	/* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value \/ /
	/* fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
	/* sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
}	}
strcpy(gplotlabel+strlen(gplotlabel),")");	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
Line 8195 set ter svg size 640, 480\nunset log y\n	Line 8650 set ter svg size 640, 480\nunset log y\n
fprintf(ficgp," u %d:(",ioffset);	fprintf(ficgp," u %d:(",ioffset);
kl=0;	kl=0;
strcpy(gplotcondition,"(");	strcpy(gplotcondition,"(");
for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */	for (k=1; k<=cptcovs; k++){ /* For each covariate k of the resultline, get corresponding value lv for combination k1 */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */	if(Dummy[Tvresult[nres][k]]==0){ /* To be verified */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* for (k=1; k<=cptcoveff; k++){ /\* For each covariate writing the chain of conditions \/ /
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to combination k1 and covariate k \/ /
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /\* Should be the covariate value corresponding to combination k1 and covariate k \/ /
vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */	lv=Tvresult[nres][k];
kl++;	vlv=TinvDoQresult[nres][Tvresult[nres][k]];
sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
kl++;	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
if(k <cptcoveff && cptcoveff>1)	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
sprintf(gplotcondition+strlen(gplotcondition)," && ");	/* vlv= nbcode[Tvaraff[k]][lv]; /\* Value of the modality of Tvaraff[k] \/ /
	/* vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
	kl++;
	/* sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]); */
	sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%lg " ,kl,Tvresult[nres][k], kl+1,TinvDoQresult[nres][Tvresult[nres][k]]);
	kl++;
	if(k <cptcoveff && cptcoveff>1)
	sprintf(gplotcondition+strlen(gplotcondition)," && ");
	}
}	}
strcpy(gplotcondition+strlen(gplotcondition),")");	strcpy(gplotcondition+strlen(gplotcondition),")");
/* kl=6+(cpt-1)(nlstate+1)+1+(i-1); /\ 6+(1-1)(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 \/ */	/* kl=6+(cpt-1)(nlstate+1)+1+(i-1); /\ 6+(1-1)(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 \/ */
Line 8273 set ter svg size 640, 480\nunset log y\n	Line 8736 set ter svg size 640, 480\nunset log y\n
fprintf(ficgp,"#model=%s \n",model);	fprintf(ficgp,"#model=%s \n",model);
fprintf(ficgp,"# Type of graphic ng=%d\n",ng);	fprintf(ficgp,"# Type of graphic ng=%d\n",ng);
fprintf(ficgp,"# k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */	fprintf(ficgp,"# k1=1 to 2^%d=%d\n",cptcoveff,m);/* to be checked */
for(k1=1; k1 <=m; k1++) /* For each combination of covariate */	/* for(k1=1; k1 <=m; k1++) /\* For each combination of covariate \/ /
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
if(m != 1 && TKresult[nres]!= k1)	/* k1=nres; */
continue;	k1= TKresult[nres];
fprintf(ficgp,"\n\n# Combination of dummy k1=%d which is ",k1);	fprintf(ficgp,"\n\n# Resultline k1=%d ",k1);
strcpy(gplotlabel,"(");	strcpy(gplotlabel,"(");
/sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);/	/sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);/
for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */	for (k=1; k<=cptcovs; k++){ /*< cptcovs number of SIMPLE covariates in the model V2+V1 =2 (dummy or quantit or time varying) /
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */	/* for each resultline nres, and position k, Tvresult[nres][k] gives the name of the variable and
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	TinvDoQresult[nres][Tvresult[nres][k]] gives its value double or integer) */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
vlv= nbcode[Tvaraff[k]][lv];	}
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	/* if(m != 1 && TKresult[nres]!= k1) */
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);	/* continue; */
}	/* fprintf(ficgp,"\n\n# Combination of dummy k1=%d which is ",k1); */
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	/* strcpy(gplotlabel,"("); */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	/* /\sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);\/ */
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	/* for (k=1; k<=cptcoveff; k++){ /\* For each correspondig covariate value \/ /
}	/* /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate value corresponding to k1 combination and kth covariate \\/ \/ */
	/* lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /\* Should be the covariate value corresponding to combination k1 and covariate k \/ /
	/* /\* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 \/ /
	/* /\* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 \/ /
	/* /\* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 \/ /
	/* /\* vlv= nbcode[Tvaraff[k]][lv]; \/ /
	/* vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
	/* fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
	/* sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
	/* } */
	/* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value \/ /
	/* fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
	/* sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]); */
	/* } */
strcpy(gplotlabel+strlen(gplotlabel),")");	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);
Line 8342 set ter svg size 640, 480\nunset log y\n	Line 8818 set ter svg size 640, 480\nunset log y\n
/* for(j=3; j <=ncovmodel-nagesqr; j++) { */	/* for(j=3; j <=ncovmodel-nagesqr; j++) { */
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 */	switch(Typevar[j]){
if(j==Tage[ij]) { /* Product by age To be looked at!!*/	case 1:
if(ij <=cptcovage) { /* 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(DummyV[j]==0){	if(j==Tage[ij]) { /* Product by age To be looked at!!// Bug valgrind */
fprintf(ficgp,"+p%d%dx",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;	if(ij <=cptcovage) { /* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, 2 V5 and V1 */
}else{ /* quantitative */	if(DummyV[j]==0){/* Bug valgrind */
fprintf(ficgp,"+p%d%fx",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */	fprintf(ficgp,"+p%d%dx",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
/* fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */	}else{ /* quantitative */
	fprintf(ficgp,"+p%d%fx",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
	/* fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
	}
	ij++;
}	}
ij++;
}	}
}	}
}else if(cptcovprod >0){	break;
if(j==Tprod[ijp]) { /* */	case 2:
/* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */	if(cptcovprod >0){
if(ijp <=cptcovprod) { /* Product */	if(j==Tprod[ijp]) { /* */
if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */	/* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */	if(ijp <=cptcovprod) { /* Product */
/* fprintf(ficgp,"+p%d%d%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */	if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
fprintf(ficgp,"+p%d%d%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);	if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
}else{ /* Vn is dummy and Vm is quanti */	/* fprintf(ficgp,"+p%d%d%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */
/* fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */	fprintf(ficgp,"+p%d%d%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);	}else{ /* Vn is dummy and Vm is quanti */
}	/* fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
}else{ /* VnVm Vn is quanti /	fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
if(DummyV[Tvard[ijp][2]]==0){	}
fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);	}else{ /* VnVm Vn is quanti /
}else{ /* Both quanti */	if(DummyV[Tvard[ijp][2]]==0){
fprintf(ficgp,"+p%d%f%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);	fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
	}else{ /* Both quanti */
	fprintf(ficgp,"+p%d%f%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
	}
}	}
	ijp++;
}	}
ijp++;	} /* end Tprod */
}	}
} /* end Tprod */	break;
} else{ /* simple covariate */	case 0:
	/* simple covariate */
/* fprintf(ficgp,"+p%d%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\ Valgrind bug nbcode \/ /	/* fprintf(ficgp,"+p%d%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\ Valgrind bug nbcode \/ /
if(Dummy[j]==0){	if(Dummy[j]==0){
fprintf(ficgp,"+p%d%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); / */	fprintf(ficgp,"+p%d%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); / */
Line 8384 set ter svg size 640, 480\nunset log y\n	Line 8868 set ter svg size 640, 480\nunset log y\n
fprintf(ficgp,"+p%d%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); / */	fprintf(ficgp,"+p%d%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); / */
/* fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */	/* fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
}	}
} /* end simple */	/* end simple */
	break;
	default:
	break;
	} /* end switch */
} /* end j */	} /* end j */
}else{	}else{ /* k=k2 */
i=i-ncovmodel;	if(ng !=1 ){ /* For logit formula of log p11 is more difficult to get */
if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */	fprintf(ficgp," (1.");i=i-ncovmodel;
fprintf(ficgp," (1.");	}else
	i=i-ncovmodel;
}	}

if(ng != 1){	if(ng != 1){
Line 8402 set ter svg size 640, 480\nunset log y\n	Line 8891 set ter svg size 640, 480\nunset log y\n
fprintf(ficgp,"+exp(p%d+p%dx+p%dxx",k3+(cpt-1)ncovmodel,k3+(cpt-1)ncovmodel+1,k3+(cpt-1)ncovmodel+1+nagesqr);	fprintf(ficgp,"+exp(p%d+p%dx+p%dxx",k3+(cpt-1)ncovmodel,k3+(cpt-1)ncovmodel+1,k3+(cpt-1)ncovmodel+1+nagesqr);

ij=1;	ij=1;
for(j=3; j <=ncovmodel-nagesqr; j++){	ijp=1;
if(cptcovage >0){	/* for(j=3; j <=ncovmodel-nagesqr; j++){ */
if((j-2)==Tage[ij]) { /* Bug valgrind */	for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
if(ij <=cptcovage) { /* Bug valgrind */	switch(Typevar[j]){
fprintf(ficgp,"+p%d%dx",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);	case 1:
/* fprintf(ficgp,"+p%d%dx",k3+(cpt-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); /	if(cptcovage >0){
ij++;	if(j==Tage[ij]) { /* Bug valgrind */
}	if(ij <=cptcovage) { /* Bug valgrind */
}	if(DummyV[j]==0){/* Bug valgrind */
}else	/* fprintf(ficgp,"+p%d%dx",k3+(cpt-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]); /
fprintf(ficgp,"+p%d%d",k3+(cpt-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);/* Valgrind bug nbcode */	/* fprintf(ficgp,"+p%d%dx",k3+(cpt-1)ncovmodel+1+j+nagesqr,nbcode[Tvar[j]][codtabm(k1,j)]); /
	fprintf(ficgp,"+p%d%dx",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvar[j]]);
	/* fprintf(ficgp,"+p%d%dx",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);; */
	/* fprintf(ficgp,"+p%d%dx",k3+(cpt-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); /
	}else{ /* quantitative */
	/* fprintf(ficgp,"+p%d%fx",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /\* Tqinvresult in decoderesult \/ /
	fprintf(ficgp,"+p%d%fx",k3+(cpt-1)ncovmodel+1+j+nagesqr,Tqinvresult[nres][Tvar[j]]); / Tqinvresult in decoderesult */
	/* fprintf(ficgp,"+p%d%fx",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /\* Tqinvresult in decoderesult \/ /
	/* fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
	}
	ij++;
	}
	}
	}
	break;
	case 2:
	if(cptcovprod >0){
	if(j==Tprod[ijp]) { /* */
	/* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
	if(ijp <=cptcovprod) { /* Product */
	if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
	if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
	/* fprintf(ficgp,"+p%d%d%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */
	fprintf(ficgp,"+p%d%d%d",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
	/* fprintf(ficgp,"+p%d%d%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]); */
	}else{ /* Vn is dummy and Vm is quanti */
	/* fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
	fprintf(ficgp,"+p%d%d%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
	/* fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); */
	}
	}else{ /* VnVm Vn is quanti /
	if(DummyV[Tvard[ijp][2]]==0){
	fprintf(ficgp,"+p%d%d%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
	/* fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]); */
	}else{ /* Both quanti */
	fprintf(ficgp,"+p%d%f%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
	/* fprintf(ficgp,"+p%d%f%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); */
	}
	}
	ijp++;
	}
	} /* end Tprod */
	} /* end if */
	break;
	case 0:
	/* simple covariate */
	/* fprintf(ficgp,"+p%d%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\ Valgrind bug nbcode \/ /
	if(Dummy[j]==0){
	/* fprintf(ficgp,"+p%d%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /\ \/ /
	fprintf(ficgp,"+p%d%d",k3+(cpt-1)ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvar[j]]); /* */
	/* fprintf(ficgp,"+p%d%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /\ \/ /
	}else{ /* quantitative */
	fprintf(ficgp,"+p%d%f",k3+(cpt-1)ncovmodel+1+j+nagesqr,Tqinvresult[nres][Tvar[j]]); /* */
	/* fprintf(ficgp,"+p%d%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /\ \/ /
	/* fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
	}
	/* end simple */
	/* fprintf(ficgp,"+p%d%d",k3+(cpt-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);/\* Valgrind bug nbcode \/ /
	break;
	default:
	break;
	} /* end switch */
}	}
fprintf(ficgp,")");	fprintf(ficgp,")");
}	}
Line 8421 set ter svg size 640, 480\nunset log y\n	Line 8971 set ter svg size 640, 480\nunset log y\n
fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"p%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);	fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"p%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
else /* ng= 3 */	else /* ng= 3 */
fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"i%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);	fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"i%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
}else{ /* end ng <> 1 */	}else{ /* end ng <> 1 */
if( k !=k2) /* logit p11 is hard to draw */	if( k !=k2) /* logit p11 is hard to draw */
fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"logit(p%d%d)\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);	fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"logit(p%d%d)\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
}	}
Line 8434 set ter svg size 640, 480\nunset log y\n	Line 8984 set ter svg size 640, 480\nunset log y\n
} /* end k2 */	} /* end k2 */
/* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */	/* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */
fprintf(ficgp,"\n set out; unset title;set key default;\n");	fprintf(ficgp,"\n set out; unset title;set key default;\n");
} /* end k1 */	} /* end resultline */
} /* end ng */	} /* end ng */
/* avoid: */	/* avoid: */
fflush(ficgp);	fflush(ficgp);
Line 8757 void prevforecast(char fileres[], double	Line 9307 void prevforecast(char fileres[], double

/* if (h==(int)(YEARMyearp)){ /	/* if (h==(int)(YEARMyearp)){ /
for(nres=1; nres <= nresult; nres++) /* For each resultline */	for(nres=1; nres <= nresult; nres++) /* For each resultline */
for(k=1; k<=i1;k++){	for(k=1; k<=i1;k++){ /* We want to find the combination k corresponding to the values of the dummies given in this resut line (to be cleaned one day) */
if(i1 != 1 && TKresult[nres]!= k)	if(i1 != 1 && TKresult[nres]!= k)
continue;	continue;
if(invalidvarcomb[k]){	if(invalidvarcomb[k]){
Line 8766 void prevforecast(char fileres[], double	Line 9316 void prevforecast(char fileres[], double
}	}
fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");	fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcoveff;j++) {
fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	/* fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); */
	fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
Line 8796 void prevforecast(char fileres[], double	Line 9347 void prevforecast(char fileres[], double
}	}
fprintf(ficresf,"\n");	fprintf(ficresf,"\n");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	/* fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); /\* Tvaraff not correct \/ /
	fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); /* TnsdVar[Tvaraff] correct */
fprintf(ficresf,"%.f %.f ",anprojd+yearp,agec+hhstepm/YEARMstepm);	fprintf(ficresf,"%.f %.f ",anprojd+yearp,agec+hhstepm/YEARMstepm);

for(j=1; j<=nlstate+ndeath;j++) {	for(j=1; j<=nlstate+ndeath;j++) {
Line 8906 void prevforecast(char fileres[], double	Line 9458 void prevforecast(char fileres[], double
}	}
fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");	fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcoveff;j++) {
fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
Line 8942 void prevforecast(char fileres[], double	Line 9494 void prevforecast(char fileres[], double
}	}
fprintf(ficresfb,"\n");	fprintf(ficresfb,"\n");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
fprintf(ficresfb,"%.f %.f ",anbackd+yearp,agec-hhstepm/YEARMstepm);	fprintf(ficresfb,"%.f %.f ",anbackd+yearp,agec-hhstepm/YEARMstepm);
for(i=1; i<=nlstate+ndeath;i++) {	for(i=1; i<=nlstate+ndeath;i++) {
ppij=0.;ppi=0.;	ppij=0.;ppi=0.;
Line 9001 void prevforecast(char fileres[], double	Line 9553 void prevforecast(char fileres[], double
i1=pow(2,cptcoveff);	i1=pow(2,cptcoveff);
if (cptcovn < 1){i1=1;}	if (cptcovn < 1){i1=1;}

for(nres=1; nres <= nresult; nres++) /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
for(k=1; k<=i1;k++){	k=TKresult[nres];
	/* for(k=1; k<=i1;k++){ /\* We find the combination equivalent to result line values of dummies \/ /
if(i1 != 1 && TKresult[nres]!= k)	if(i1 != 1 && TKresult[nres]!= k)
continue;	continue;
fprintf(ficresvpl,"\n#****** ");	fprintf(ficresvpl,"\n#****** ");
printf("\n#****** ");	printf("\n#****** ");
fprintf(ficlog,"\n#****** ");	fprintf(ficlog,"\n#****** ");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcovs;j++) {
fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresvpl,"V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficlog,"V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	printf("V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
}	/* fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */	/* printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	}
fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	/* for (j=1; j<= nsq; j++){ /\* For each selected (single) quantitative value \/ /
fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	/* printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
}	/* fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
	/* fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
	/* } */
fprintf(ficresvpl,"******\n");	fprintf(ficresvpl,"******\n");
printf("******\n");	printf("******\n");
fprintf(ficlog,"******\n");	fprintf(ficlog,"******\n");
Line 9058 void prevforecast(char fileres[], double	Line 9613 void prevforecast(char fileres[], double
i1=pow(2,cptcoveff);	i1=pow(2,cptcoveff);
if (cptcovn < 1){i1=1;}	if (cptcovn < 1){i1=1;}

for(nres=1; nres <= nresult; nres++) /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
for(k=1; k<=i1;k++){	k=TKresult[nres];
if(i1 != 1 && TKresult[nres]!= k)	/* for(k=1; k<=i1;k++){ */
continue;	/* if(i1 != 1 && TKresult[nres]!= k) */
	/* continue; */
fprintf(ficresvbl,"\n#****** ");	fprintf(ficresvbl,"\n#****** ");
printf("\n#****** ");	printf("\n#****** ");
fprintf(ficlog,"\n#****** ");	fprintf(ficlog,"\n#****** ");
for(j=1;j<=cptcoveff;j++) {	for (j=1; j<= cptcovs; j++){ /* For each selected (single) quantitative value */
fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	printf(" V%d=%lg ",Tvqresult[nres][j],TinvDoQresult[nres][resultmodel[nres][j]]);
fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresvbl," V%d=%lg ",Tvqresult[nres][j],TinvDoQresult[nres][resultmodel[nres][j]]);
printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficlog," V%d=%lg ",Tvqresult[nres][j],TinvDoQresult[nres][resultmodel[nres][j]]);
}	/* for(j=1;j<=cptcoveff;j++) { */
for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */	/* fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	/* fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	/* printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	/* } */
	/* for (j=1; j<= nsq; j++){ /\* For each selected (single) quantitative value \/ /
	/* printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
	/* fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
	/* fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
}	}
fprintf(ficresvbl,"******\n");	fprintf(ficresvbl,"******\n");
printf("******\n");	printf("******\n");
Line 9535 int readdata(char datafile[], int firsto	Line 10095 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 9894 void removefirstspace(char *stri){/, c	Line 10458 void removefirstspace(char *stri){/, c
*stri=p2;	*stri=p2;
}	}

int decoderesult ( char resultline[], int nres)	int decoderesult( char resultline[], int nres)
/< This routine decode one result line and returns the combination # of dummy covariates only /	/< This routine decode one result line and returns the combination # of dummy covariates only /
{	{
int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;	int j=0, k=0, k1=0, k2=0, k3=0, k4=0, match=0, k2q=0, k3q=0, k4q=0;
char resultsav[MAXLINE];	char resultsav[MAXLINE];
int resultmodel[MAXLINE];	/* int resultmodel[MAXLINE]; */
int modelresult[MAXLINE];	/* int modelresult[MAXLINE]; */
char stra[80], strb[80], strc[80], strd[80],stre[80];	char stra[80], strb[80], strc[80], strd[80],stre[80];

removefirstspace(&resultline);	removefirstspace(&resultline);
	printf("decoderesult:%s\n",resultline);

if (strstr(resultline,"v") !=0){	strcpy(resultsav,resultline);
printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);	printf("Decoderesult resultsav=\"%s\" resultline=\"%s\"\n", resultsav, resultline);
fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog);
return 1;
}
trimbb(resultsav, resultline);
if (strlen(resultsav) >1){	if (strlen(resultsav) >1){
j=nbocc(resultsav,'='); /*< j=Number of covariate values'=' /	j=nbocc(resultsav,'='); /*< j=Number of covariate values'=' in this resultline /
}	}
if(j == 0){ /* Resultline but no = */	if(j == 0){ /* Resultline but no = */
TKresult[nres]=0; /* Combination for the nresult and the model */	TKresult[nres]=0; /* Combination for the nresult and the model */
return (0);	return (0);
}	}
if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */	if( j != cptcovs ){ /* Be careful if a variable is in a product but not single */
printf("ERROR: the number of variables in this result line, %d, differs from the number of variables used in the model line, %d.\n",j, cptcovs);	printf("ERROR: the number of variables in the resultline which is %d, differs from the number %d of single variables used in the model line, %s.\n",j, cptcovs, model);
fprintf(ficlog,"ERROR: the number of variables in the resultline, %d, differs from the number of variables used in the model line, %d.\n",j, cptcovs);	fprintf(ficlog,"ERROR: the number of variables in the resultline which is %d, differs from the number %d of single variables used in the model line, %s.\n",j, cptcovs, model);
	/* return 1;*/
}	}
for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */	for(k=1; k<=j;k++){ /* Loop on any covariate of the RESULT LINE */
if(nbocc(resultsav,'=') >1){	if(nbocc(resultsav,'=') >1){
cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' ' (stra is the rest of the resultline to be analyzed in the next loop // resultsav= "V4=1 V5=25.1 V3=0" stra= "V5=25.1 V3=0" strb= "V4=1" */	cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' ' (stra is the rest of the resultline to be analyzed in the next loop // resultsav= "V4=1 V5=25.1 V3=0" stra= "V5=25.1 V3=0" strb= "V4=1" */
	/* If resultsav= "V4= 1 V5=25.1 V3=0" with a blank then strb="V4=" and stra="1 V5=25.1 V3=0" */
cutl(strc,strd,strb,'='); /* strb:"V4=1" strc="1" strd="V4" */	cutl(strc,strd,strb,'='); /* strb:"V4=1" strc="1" strd="V4" */
	/* If a blank, then strc="V4=" and strd='\0' */
	if(strc[0]=='\0'){
	printf("Error in resultline, probably a blank after the \"%s\", \"result:%s\", stra=\"%s\" resultsav=\"%s\"\n",strb,resultline, stra, resultsav);
	fprintf(ficlog,"Error in resultline, probably a blank after the \"V%s=\", resultline=%s\n",strb,resultline);
	return 1;
	}
}else	}else
cutl(strc,strd,resultsav,'=');	cutl(strc,strd,resultsav,'=');
Tvalsel[k]=atof(strc); /* 1 / / Tvalsel of k is the float value of the kth covariate appearing in this result line */	Tvalsel[k]=atof(strc); /* 1 / / Tvalsel of k is the float value of the kth covariate appearing in this result line */
Line 9938 int decoderesult ( char resultline[], in	Line 10507 int decoderesult ( char resultline[], in
strcpy(resultsav,stra); /* and analyzes it */	strcpy(resultsav,stra); /* and analyzes it */
}	}
/* Checking for missing or useless values in comparison of current model needs */	/* Checking for missing or useless values in comparison of current model needs */
for(k1=1; k1<= cptcovt ;k1++){ /* Loop on model. model line V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */	/* Feeds resultmodel[nres][k1]=k2 for k1th product covariate with age in the model equation fed by the index k2 of the resutline*/
if(Typevar[k1]==0){ /* Single covariate in model //0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */	for(k1=1; k1<= cptcovt ;k1++){ /* Loop on MODEL LINE V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
	if(Typevar[k1]==0){ /* Single covariate in model */
	/* 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */
match=0;	match=0;
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(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[k2]=k1;/* modelresult[2]=1 modelresult[1]=2 modelresult[3]=3 modelresult[6]=4 modelresult[9]=5 */	modelresult[nres][k2]=k1;/* modelresult[2]=1 modelresult[1]=2 modelresult[3]=3 modelresult[6]=4 modelresult[9]=5 */
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;
}	}
}	}
if(match == 0){	if(match == 0){
printf("Error in result line: V%d is missing in result: %s according to model=%s\n",k1, resultline, model);	printf("Error in result line (Dummy single): V%d is missing in result: %s according to model=%s. Tvar[k1=%d]=%d is different from Tvarsel[k2=%d]=%d.\n",Tvar[k1], resultline, model,k1, Tvar[k1], k2, Tvarsel[k2]);
fprintf(ficlog,"Error in result line: V%d is missing in result: %s according to model=%s\n",k1, resultline, model);	fprintf(ficlog,"Error in result line (Dummy single): V%d is missing in result: %s according to model=%s\n",Tvar[k1], resultline, model);
return 1;	return 1;
}	}
}	}else if(Typevar[k1]==1){ /* Product with age We want to get the position k2 in the resultline of the product k1 in the model line*/
}	/* We feed resultmodel[k1]=k2; */
	match=0;
	for(k2=1; k2 <=j;k2++){/* Loop on resultline. jth occurence of = signs in the result line. In result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
	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 /
	resultmodel[nres][k1]=k2; /* Added here */
	printf("Decoderesult first modelresult[k2=%d]=%d (k1) V%d*AGE\n",k2,k1,Tvar[k1]);
	match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
	break;
	}
	}
	if(match == 0){
	printf("Error in result line (Product with age): V%d is missing in result: %s according to model=%s (Tvarsel[k2=%d]=%d)\n",Tvar[k1], resultline, model, k2, Tvarsel[k2]);
	fprintf(ficlog,"Error in result line (Product with age): V%d is missing in result: %s according to model=%s (Tvarsel[k2=%d]=%d)\n",Tvar[k1], resultline, model, k2, Tvarsel[k2]);
	return 1;
	}
	}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] */
	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]);
	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 */
	/* modelresult[k2]=k1; */
	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 */
	}
	}
	if(match == 0){
	printf("Error in result line (Product without age first variable): V%d is missing in result: %s according to model=%s\n",Tvardk[k1][1], resultline, model);
	fprintf(ficlog,"Error in result line (Product without age first variable): V%d is missing in result: %s according to model=%s\n",Tvardk[k1][1], resultline, model);
	return 1;
	}
	match=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 */
	/* modelresult[k2]=k1;*/
	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 */
	break;
	}
	}
	if(match == 0){
	printf("Error in result line (Product without age second variable): V%d is missing in result: %s according to model=%s\n",Tvardk[k1][2], resultline, model);
	fprintf(ficlog,"Error in result line (Product without age second variable): V%d is missing in result : %s according to model=%s\n",Tvardk[k1][2], resultline, model);
	return 1;
	}
	}/* End of testing */
	}/* End loop cptcovt */
/* Checking for missing or useless values in comparison of current model needs */	/* Checking for missing or useless values in comparison of current model needs */
for(k2=1; k2 <=j;k2++){ /* Loop on resultline variables: result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */	/* Feeds resultmodel[nres][k1]=k2 for single covariate (k1) in the model equation */
	for(k2=1; k2 <=j;k2++){ /* j or cptcovs is the number of single covariates used either in the model line as well as in the result line (dummy or quantitative)
	* Loop on resultline variables: result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
match=0;	match=0;
for(k1=1; k1<= cptcovt ;k1++){ /* loop on model: model line V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */	for(k1=1; k1<= cptcovt ;k1++){ /* loop on model: model line V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
if(Typevar[k1]==0){ /* Single */	if(Typevar[k1]==0){ /* Single only */
if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4 */	if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4 */
resultmodel[k1]=k2; /* k2th variable of the model corresponds to k1 variable of the model. resultmodel[2]=1 resultmodel[1]=2 resultmodel[3]=3 resultmodel[6]=4 resultmodel[9]=5 */	resultmodel[nres][k1]=k2; /* k1th position in the model equation corresponds to k2th position in the result line. resultmodel[2]=1 resultmodel[1]=2 resultmodel[3]=3 resultmodel[6]=4 resultmodel[9]=5 */
	modelresult[nres][k2]=k1; /* k1th position in the model equation corresponds to k2th position in the result line. modelresult[1]=2 modelresult[2]=1 modelresult[3]=3 remodelresult[4]=6 modelresult[5]=9 */
++match;	++match;
}	}
}	}
}	}
if(match == 0){	if(match == 0){
printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);	printf("Error in result line: variable V%d is missing in model; result: %s, model=%s\n",Tvarsel[k2], resultline, model);
fprintf(ficlog,"Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);	fprintf(ficlog,"Error in result line: variable V%d is missing in model; result: %s, model=%s\n",Tvarsel[k2], resultline, model);
return 1;	return 1;
}else if(match > 1){	}else if(match > 1){
printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);	printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
Line 9976 int decoderesult ( char resultline[], in	Line 10597 int decoderesult ( char resultline[], in
return 1;	return 1;
}	}
}	}
	/* cptcovres=j /\* Number of variables in the resultline is equal to cptcovs and thus useless \/ /
/* We need to deduce which combination number is chosen and save quantitative values */	/* We need to deduce which combination number is chosen and save quantitative values */
/* model line V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */	/* model line V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
/* result line V4=1 V5=25.1 V3=0 V2=8 V1=1 */	/* nres=1st result line: V4=1 V5=25.1 V3=0 V2=8 V1=1 */
/* should give a combination of dummy V4=1, V3=0, V1=1 => V42(0) + V32*(1) + V12*(2) = 5 + (1offset) = 6/	/* should correspond to the combination 6 of dummy: V4=1, V3=0, V1=1 => V42(0) + V32*(1) + V12*(2) = 11 + 02 + 14 = 5 + (1offset) = 6*/
/* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */	/* nres=2nd result line: V4=1 V5=24.1 V3=1 V2=8 V1=0 */
/* should give a combination of dummy V4=1, V3=1, V1=0 => V42(0) + V32*(1) + V12*(2) = 3 + (1offset) = 4/	/* should give a combination of dummy V4=1, V3=1, V1=0 => V42(0) + V32*(1) + V12*(2) = 3 + (1offset) = 4/
/* 1 0 0 0 */	/* 1 0 0 0 */
/* 2 1 0 0 */	/* 2 1 0 0 */
/* 3 0 1 0 */	/* 3 0 1 0 */
/* 4 1 1 0 / / V4=1, V3=1, V1=0 */	/* 4 1 1 0 / / V4=1, V3=1, V1=0 (nres=2)*/
/* 5 0 0 1 */	/* 5 0 0 1 */
/* 6 1 0 1 / / V4=1, V3=0, V1=1 */	/* 6 1 0 1 / / V4=1, V3=0, V1=1 (nres=1)*/
/* 7 0 1 1 */	/* 7 0 1 1 */
/* 8 1 1 1 */	/* 8 1 1 1 */
/* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */	/* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */
/* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */	/* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */
/* V5age V5 known which value for nres? /	/* V5age V5 known which value for nres? /
/* Tqinvresult[2]=8 Tqinvresult[1]=25.1 */	/* Tqinvresult[2]=8 Tqinvresult[1]=25.1 */
for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* loop on model line */	for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* cptcovt number of covariates (excluding 1 and age or age*age) in the MODEL equation.
if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */	* loop on position k1 in the MODEL LINE */
k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */	/* k counting number of combination of single dummies in the equation model */
k2=(int)Tvarsel[k3]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */	/* k4 counting single dummies in the equation model */
k+=Tvalsel[k3]pow(2,k4); / Tvalsel[1]=1 */	/* k4q counting single quantitatives in the equation model */
Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1) Tresult[nres][2]=0(V3=0) */	if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Dummy and Single, k1 is sorting according to MODEL, but k3 to resultline */
Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */	/* 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)*/
	/* Value in the (current nres) resultline of the variable at the k1th position in the model equation resultmodel[nres][k1]= k3 */
	/* resultmodel[nres][k1]=k3: k1th position in the model correspond to the k3 position in the resultline */
	/* k3 is the position in the nres result line of the k1th variable of the model equation */
	/* Tvarsel[k3]: Name of the variable at the k3th position in the result line. */
	/* Tvalsel[k3]: Value of the variable at the k3th position in the result line. */
	/* Tresult[nres][result_position]= value of the dummy variable at the result_position in the nres resultline */
	/* Tvresult[nres][result_position]= name of the dummy variable at the result_position in the nres resultline */
	/* Tinvresult[nres][Name of a dummy variable]= value of the variable in the result line */
	/* TinvDoQresult[nres][Name of a Dummy or Q variable]= value of the variable in the result line */
	k3= resultmodel[nres][k1]; /* From position k1 in model get position k3 in result line */
	/* nres=1 k1=2 resultmodel[2(V4)] = 1=k3 ; k1=3 resultmodel[3(V3)] = 2=k3*/
	k2=(int)Tvarsel[k3]; /* from position k3 in resultline get name k2: nres=1 k1=2=>k3=1 Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 (V4); k1=3=>k3=2 Tvarsel[2]=3 (V3)*/
	k+=Tvalsel[k3]pow(2,k4); / nres=1 k1=2 Tvalsel[1]=1 (V4=1); k1=3 k3=2 Tvalsel[2]=0 (V3=0) */
	TinvDoQresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* TinvDoQresult[nres][Name]=Value; stores the value into the name of the variable. */
	/* Tinvresult[nres][4]=1 */
	/* Tresult[nres][k4+1]=Tvalsel[k3];/\* Tresult[nres=2][1]=1(V4=1) Tresult[nres=2][2]=0(V3=0) \/ /
	Tresult[nres][k3]=Tvalsel[k3];/* Tresult[nres=2][1]=1(V4=1) Tresult[nres=2][2]=0(V3=0) */
	/* Tvresult[nres][k4+1]=(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 */
printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);	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);
k4++;;	k4++;;
} else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */	}else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Quantitative and single */
k3q= resultmodel[k1]; /* resultmodel[1(V5)] = 25.1=k3q */	/* Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline */
k2q=(int)Tvarsel[k3q]; /* Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */	/* Tvqresult[nres][result_position]= id of the variable at the result_position in the nres resultline */
Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */	/* Tqinvresult[nres][Name of a quantitative variable]= value of the variable in the result line */
Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */	k3q= resultmodel[nres][k1]; /* resultmodel[1(V5)] = 5 =k3q */
	k2q=(int)Tvarsel[k3q]; /* Name of variable at k3q th position in the resultline */
	/* Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */
	/* Tqresult[nres][k4q+1]=Tvalsel[k3q]; /\* Tqresult[nres][1]=25.1 \/ /
	/* Tvresult[nres][k4q+1]=(int)Tvarsel[k3q];/\* Tvresult[nres][1]=4 Tvresult[nres][3]=1 \/ /
	/* Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /\* Tvqresult[nres][1]=5 \/ /
	Tqresult[nres][k3q]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
	Tvresult[nres][k3q]=(int)Tvarsel[k3q];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
	Tvqresult[nres][k3q]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */	Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);	TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
	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]);
k4q++;;	k4q++;;
	}else if( Dummy[k1]==2 ){ /* For dummy with age product */
	/* Tvar[k1]; / / Age variable */
	/* Wrong we want the value of variable name Tvar[k1] */

	k3= resultmodel[nres][k1]; /* nres=1 k1=2 resultmodel[2(V4)] = 1=k3 ; k1=3 resultmodel[3(V3)] = 2=k3*/
	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 */
	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]);
	}else if( Dummy[k1]==3 ){ /* For quant with age product */
	k3q= resultmodel[nres][k1]; /* resultmodel[1(V5)] = 25.1=k3q */
	k2q=(int)Tvarsel[k3q]; /* Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */
	TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* TinvDoQresult[nres][5]=25.1 */
	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]);
	}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]];
	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{
	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]);
}	}
}	}

TKresult[nres]=++k; /* Combination for the nresult and the model */	TKresult[nres]=++k; /* Number of combinations of dummies for the nresult and the model =Tvalsel[k3]pow(2,k4) + 1/
return (0);	return (0);
}	}

Line 10176 int decodemodel( char model[], int lasto	Line 10849 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
thus after V4 we invent V5 and V6 because age*V3 will be computed in 4	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 /	Tvar[3=V1V4]=4+1=5 Tvar[5=V3V2]=4 + 2= 6, Tvar[4=ageV3]=4 etc /
	/* Please remark that the new variables are model dependent */
	/* If we have 4 variable but the model uses only 3, like in
	* model= V1 + ageV1 + V2 + V3 + ageV2 + ageV3 + V1V2 + V1*V3
	* k= 1 2 3 4 5 6 7 8
	* Tvar[k]=1 1 2 3 2 3 (5 6) (and not 4 5 because of V4 missing)
	* Tage[kk] [1]= 2 [2]=5 [3]=6 kk=1 to cptcovage=3
	* Tvar[Tage[kk]][1]=2 [2]=2 [3]=3
	*/
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; /* Tposprod[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*/
	Tvardk[k][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*/
	Tvardk[k][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 /
/* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) \/ /	/* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) \/ /
/* Tvar[cptcovt+k2+1]=Tvard[k1][2]; /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) \/ /	/* Tvar[cptcovt+k2+1]=Tvard[k1][2]; /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) \/ /
Line 10256 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 10939 Dummy[k] 0=dummy (0 1), 1 quantitative (
modell[k].maintype= FTYPE;	modell[k].maintype= FTYPE;
TvarsD[nsd]=Tvar[k];	TvarsD[nsd]=Tvar[k];
TvarsDind[nsd]=k;	TvarsDind[nsd]=k;
	TnsdVar[Tvar[k]]=nsd;
TvarF[ncovf]=Tvar[k];	TvarF[ncovf]=Tvar[k];
TvarFind[ncovf]=k;	TvarFind[ncovf]=k;
TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */	TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
Line 10267 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 10951 Dummy[k] 0=dummy (0 1), 1 quantitative (
ncovf++;	ncovf++;
modell[k].maintype= FTYPE;	modell[k].maintype= FTYPE;
TvarF[ncovf]=Tvar[k];	TvarF[ncovf]=Tvar[k];
	/* TnsdVar[Tvar[k]]=nsd; / / To be done */
TvarFind[ncovf]=k;	TvarFind[ncovf]=k;
TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */	TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */	TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
Line 10277 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 10962 Dummy[k] 0=dummy (0 1), 1 quantitative (
modell[k].maintype= FTYPE;	modell[k].maintype= FTYPE;
modell[k].subtype= FQ;	modell[k].subtype= FQ;
nsq++;	nsq++;
TvarsQ[nsq]=Tvar[k];	TvarsQ[nsq]=Tvar[k]; /* Gives the variable name (extended to products) of first nsq simple quantitative covariates (fixed or time vary see below */
TvarsQind[nsq]=k;	TvarsQind[nsq]=k; /* Gives the position in the model equation of the first nsq simple quantitative covariates (fixed or time vary) */
ncovf++;	ncovf++;
TvarF[ncovf]=Tvar[k];	TvarF[ncovf]=Tvar[k];
TvarFind[ncovf]=k;	TvarFind[ncovf]=k;
Line 10293 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 10978 Dummy[k] 0=dummy (0 1), 1 quantitative (
nsd++;	nsd++;
TvarsD[nsd]=Tvar[k];	TvarsD[nsd]=Tvar[k];
TvarsDind[nsd]=k;	TvarsDind[nsd]=k;
	TnsdVar[Tvar[k]]=nsd; /* To be verified */
ncovv++; /* Only simple time varying variables */	ncovv++; /* Only simple time varying variables */
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k; /* TvarVind[2]=2 TvarVind[3]=3 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Any time varying singele */	TvarVind[ncovv]=k; /* TvarVind[2]=2 TvarVind[3]=3 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Any time varying singele */
Line 10308 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 10994 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]; /* k=1 Tvar=5 nsq=1 TvarsQ[1]=5 */	TvarsQ[nsq]=Tvar[k]; /* k=1 Tvar=5 nsq=1 TvarsQ[1]=5 / / Gives the variable name (extended to products) of first nsq simple quantitative covariates (fixed or time vary here) */
TvarsQind[nsq]=k;	TvarsQind[nsq]=k; /* For single quantitative covariate gives the model position of each single quantitative covariate // Gives the position in the model equation of the first nsq simple quantitative covariates (fixed or time vary) */
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 */
TvarVQ[nqtveff]=Tvar[k]; /* TvarVQ[1]=V5 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple time varying quantitative variable */	TvarVQ[nqtveff]=Tvar[k]; /* TvarVQ[1]=V5 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple time varying quantitative variable */
Line 10835 void syscompilerinfo(int logged)	Line 11521 void syscompilerinfo(int logged)

int prevalence_limit(double p, double prlim, double ageminpar, double agemaxpar, double ftolpl, int ncvyearp){	int prevalence_limit(double p, double prlim, double ageminpar, double agemaxpar, double ftolpl, int ncvyearp){
/--------------- Prevalence limit (forward period or forward stable prevalence) --------------/	/--------------- Prevalence limit (forward period or forward stable prevalence) --------------/
	/* Computes the prevalence limit for each combination of the dummy covariates */
int i, j, k, i1, k4=0, nres=0 ;	int i, j, k, i1, k4=0, nres=0 ;
/* double ftolpl = 1.e-10; */	/* double ftolpl = 1.e-10; */
double age, agebase, agelim;	double age, agebase, agelim;
Line 10863 int prevalence_limit(double p, double	Line 11550 int prevalence_limit(double p, double
i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */	i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
if (cptcovn < 1){i1=1;}	if (cptcovn < 1){i1=1;}

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

/* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */	/* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
/* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */	/* for(cptcov=1,k=0;cptcov<=1;cptcov++){ */
//for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){	//for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
/* k=k+1; */	/* k=k+1; */
/* to clean */	/* to clean */
//printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));	/printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));/
fprintf(ficrespl,"#******");	fprintf(ficrespl,"#******");
printf("#******");	printf("#******");
fprintf(ficlog,"#******");	fprintf(ficlog,"#******");
for(j=1;j<=cptcoveff ;j++) {/* all covariates */	for(j=1;j<=cptcovs ;j++) {/*< cptcovs number of SIMPLE covariates in the model or resultline V2+V1 =2 (dummy or quantit or time varying) /
fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/	/* fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); /\* Here problem for varying dummy\/ /
printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	/* printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	/* fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
}	fprintf(ficrespl," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	printf(" V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficlog," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	}
fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	/* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value \/ /
}	/* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
	/* fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
	/* fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
	/* } */
fprintf(ficrespl,"******\n");	fprintf(ficrespl,"******\n");
printf("******\n");	printf("******\n");
fprintf(ficlog,"******\n");	fprintf(ficlog,"******\n");
Line 10898 int prevalence_limit(double p, double	Line 11589 int prevalence_limit(double p, double
}	}

fprintf(ficrespl,"#Age ");	fprintf(ficrespl,"#Age ");
for(j=1;j<=cptcoveff;j++) {	/* for(j=1;j<=cptcoveff;j++) { */
fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	/* fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
	/* } */
	for(j=1;j<=cptcovs;j++) { /* New the quanti variable is added */
	fprintf(ficrespl,"V%d %lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
}	}
for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);	for(i=1; i<=nlstate;i++) fprintf(ficrespl," %d-%d ",i,i);
fprintf(ficrespl,"Total Years_to_converge\n");	fprintf(ficrespl,"Total Years_to_converge\n");

for (age=agebase; age<=agelim; age++){	for (age=agebase; age<=agelim; age++){
/* for (age=agebase; age<=agebase; age++){ */	/* for (age=agebase; age<=agebase; age++){ */
prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);	/*< Computes the prevalence limit in each live state at age x and for covariate combination (k and) nres /
	prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres); /* Nicely done */
fprintf(ficrespl,"%.0f ",age );	fprintf(ficrespl,"%.0f ",age );
for(j=1;j<=cptcoveff;j++)	/* for(j=1;j<=cptcoveff;j++) */
fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	/* fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
	for(j=1;j<=cptcovs;j++)
	fprintf(ficrespl,"%d %lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
tot=0.;	tot=0.;
for(i=1; i<=nlstate;i++){	for(i=1; i<=nlstate;i++){
tot += prlim[i][i];	tot += prlim[i][i];
Line 10918 int prevalence_limit(double p, double	Line 11615 int prevalence_limit(double p, double
fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);	fprintf(ficrespl," %.3f %d\n", tot, *ncvyearp);
} /* Age */	} /* Age */
/* was end of cptcod */	/* was end of cptcod */
} /* cptcov */	} /* nres */
} /* nres */	/* } /\* for each combination \/ /
return 0;	return 0;
}	}

Line 10964 int back_prevalence_limit(double *p, dou	Line 11661 int back_prevalence_limit(double *p, dou
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("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));	/printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));/
fprintf(ficresplb,"#******");	fprintf(ficresplb,"#******");
printf("#******");	printf("#******");
fprintf(ficlog,"#******");	fprintf(ficlog,"#******");
for(j=1;j<=cptcoveff ;j++) {/* all covariates */	for(j=1;j<=cptcoveff ;j++) {/* all covariates */
fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
}	}
for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */	for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
}	}
fprintf(ficresplb,"******\n");	fprintf(ficresplb,"******\n");
printf("******\n");	printf("******\n");
Line 10990 int back_prevalence_limit(double *p, dou	Line 11687 int back_prevalence_limit(double *p, dou

fprintf(ficresplb,"#Age ");	fprintf(ficresplb,"#Age ");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcoveff;j++) {
fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
}	}
for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);	for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);
fprintf(ficresplb,"Total Years_to_converge\n");	fprintf(ficresplb,"Total Years_to_converge\n");
Line 11014 int back_prevalence_limit(double *p, dou	Line 11711 int back_prevalence_limit(double *p, dou
}	}
fprintf(ficresplb,"%.0f ",age );	fprintf(ficresplb,"%.0f ",age );
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
tot=0.;	tot=0.;
for(i=1; i<=nlstate;i++){	for(i=1; i<=nlstate;i++){
tot += bprlim[i][i];	tot += bprlim[i][i];
Line 11034 int back_prevalence_limit(double *p, dou	Line 11731 int back_prevalence_limit(double *p, dou

int hPijx(double *p, int bage, int fage){	int hPijx(double *p, int bage, int fage){
/------------- h Pij x at various ages ------------/	/------------- h Pij x at various ages ------------/
	/* to be optimized with precov */
int stepsize;	int stepsize;
int agelim;	int agelim;
int hstepm;	int hstepm;
Line 11044 int hPijx(double *p, int bage, int fage)	Line 11741 int hPijx(double *p, int bage, int fage)
double agedeb;	double agedeb;
double ***p3mat;	double ***p3mat;

strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);	strcpy(filerespij,"PIJ_"); strcat(filerespij,fileresu);
if((ficrespij=fopen(filerespij,"w"))==NULL) {	if((ficrespij=fopen(filerespij,"w"))==NULL) {
printf("Problem with Pij resultfile: %s\n", filerespij); return 1;	printf("Problem with Pij resultfile: %s\n", filerespij); return 1;
fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;	fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij); return 1;
}	}
printf("Computing pij: result on file '%s' \n", filerespij);	printf("Computing pij: result on file '%s' \n", filerespij);
fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);	fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);

stepsize=(int) (stepm+YEARM-1)/YEARM;	stepsize=(int) (stepm+YEARM-1)/YEARM;
/if (stepm<=24) stepsize=2;/	/if (stepm<=24) stepsize=2;/

agelim=AGESUP;	agelim=AGESUP;
hstepm=stepsizeYEARM; / Every year of age */	hstepm=stepsizeYEARM; / Every year of age */
hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */	hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */

/* hstepm=1; aff par mois*/	/* hstepm=1; aff par mois*/
pstamp(ficrespij);	pstamp(ficrespij);
fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");	fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
i1= pow(2,cptcoveff);	i1= pow(2,cptcoveff);
/* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */	/* for(cptcov=1,k=0;cptcov<=i1;cptcov++){ */
/* /\for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){\/ */	/* /\for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){\/ */
/* k=k+1; */	/* k=k+1; */
for(nres=1; nres <= nresult; nres++) /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
for(k=1; k<=i1;k++){	k=TKresult[nres];
if(i1 != 1 && TKresult[nres]!= k)	/* for(k=1; k<=i1;k++){ */
continue;	/* if(i1 != 1 && TKresult[nres]!= k) */
fprintf(ficrespij,"\n#****** ");	/* continue; */
for(j=1;j<=cptcoveff;j++)	fprintf(ficrespij,"\n#****** ");
fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	for(j=1;j<=cptcovs;j++){
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	fprintf(ficrespij," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	/* fprintf(ficrespij,"@wV%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	/* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value \/ /
}	/* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
fprintf(ficrespij,"******\n");	/* fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
	}
for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */	fprintf(ficrespij,"******\n");
nhstepm=(int) rint((agelim-agedeb)YEARM/stepm); / Typically 20 years = 2012/6=40 /
nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */	for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
	nhstepm=(int) rint((agelim-agedeb)YEARM/stepm); / Typically 20 years = 2012/6=40 /
/* nhstepm=nhstepmYEARM; aff par mois/	nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */

p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	/* nhstepm=nhstepmYEARM; aff par mois/
oldm=oldms;savm=savms;
hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);	p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");	oldm=oldms;savm=savms;
	hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
	fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
	for(i=1; i<=nlstate;i++)
	for(j=1; j<=nlstate+ndeath;j++)
	fprintf(ficrespij," %1d-%1d",i,j);
	fprintf(ficrespij,"\n");
	for (h=0; h<=nhstepm; h++){
	/agedebphstep = agedeb + hhstepm/YEARMstepm;/
	fprintf(ficrespij,"%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(ficrespij," %1d-%1d",i,j);	fprintf(ficrespij," %.5f", p3mat[i][j][h]);
fprintf(ficrespij,"\n");
for (h=0; h<=nhstepm; h++){
/agedebphstep = agedeb + hhstepm/YEARMstepm;/
fprintf(ficrespij,"%d %3.f %3.f",k, agedeb, agedeb + hhstepm/YEARMstepm );
for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate+ndeath;j++)
fprintf(ficrespij," %.5f", p3mat[i][j][h]);
fprintf(ficrespij,"\n");
}
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
fprintf(ficrespij,"\n");	fprintf(ficrespij,"\n");
}	}
/}/	free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
	fprintf(ficrespij,"\n");
}	}
return 0;	}
	/}/
	return 0;
}	}

int hBijx(double p, int bage, int fage, double **prevacurrent){	int hBijx(double p, int bage, int fage, double **prevacurrent){
/------------- h Bij x at various ages ------------/	/------------- h Bij x at various ages ------------/
	/* To be optimized with precov */
int stepsize;	int stepsize;
/* int agelim; */	/* int agelim; */
int ageminl;	int ageminl;
Line 11146 int hPijx(double *p, int bage, int fage)	Line 11845 int hPijx(double *p, int bage, int fage)
/* /\for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){\/ */	/* /\for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){\/ */
/* k=k+1; */	/* k=k+1; */
for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */	k=TKresult[nres];
if(i1 != 1 && TKresult[nres]!= k)	/* for(k=1; k<=i1;k++){ /\* For any combination of dummy covariates, fixed and varying \/ /
continue;	/* if(i1 != 1 && TKresult[nres]!= k) */
fprintf(ficrespijb,"\n#****** ");	/* continue; */
for(j=1;j<=cptcoveff;j++)	fprintf(ficrespijb,"\n#****** ");
fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	for(j=1;j<=cptcovs;j++){
for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */	fprintf(ficrespij," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	/* for(j=1;j<=cptcoveff;j++) */
}	/* fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
fprintf(ficrespijb,"******\n");	/* for (j=1; j<= nsq; j++){ /\* For each selected (single) quantitative value \/ /
if(invalidvarcomb[k]){ /* Is it necessary here? */	/* fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);	}
continue;	fprintf(ficrespijb,"******\n");
}	if(invalidvarcomb[k]){ /* Is it necessary here? */
	fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
/* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months \/ /	continue;
for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */	}
/* nhstepm=(int) rint((agelim-agedeb)YEARM/stepm); /\ Typically 20 years = 2012/6=40 \/ */
nhstepm=(int) rint((agedeb-ageminl)YEARM/stepm+0.1)-1; / Typically 20 years = 2012/6=40 or 5512/24=27.5-1.1=>27 */	/* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months \/ /
nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 or 28*/	for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
	/* nhstepm=(int) rint((agelim-agedeb)YEARM/stepm); /\ Typically 20 years = 2012/6=40 \/ */
/* nhstepm=nhstepmYEARM; aff par mois/	nhstepm=(int) rint((agedeb-ageminl)YEARM/stepm+0.1)-1; / Typically 20 years = 2012/6=40 or 5512/24=27.5-1.1=>27 */
	nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 or 28*/
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
/* and memory limitations if stepm is small */	/* nhstepm=nhstepmYEARM; aff par mois/

/* oldm=oldms;savm=savms; */	p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
/* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */	/* and memory limitations if stepm is small */
hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
/* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */	/* oldm=oldms;savm=savms; */
fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");	/* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
	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); */
	fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
	for(i=1; i<=nlstate;i++)
	for(j=1; j<=nlstate+ndeath;j++)
	fprintf(ficrespijb," %1d-%1d",i,j);
	fprintf(ficrespijb,"\n");
	for (h=0; h<=nhstepm; h++){
	/agedebphstep = agedeb + hhstepm/YEARMstepm;/
	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," %1d-%1d",i,j);	fprintf(ficrespijb," %.5f", p3mat[i][j][h]);/* Bug valgrind */
fprintf(ficrespijb,"\n");
for (h=0; h<=nhstepm; h++){
/agedebphstep = agedeb + hhstepm/YEARMstepm;/
fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb - hhstepm/YEARMstepm );
/* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + hhstepm/YEARMstepm ); */
for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate+ndeath;j++)
fprintf(ficrespijb," %.5f", p3mat[i][j][h]);
fprintf(ficrespijb,"\n");
}
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
fprintf(ficrespijb,"\n");	fprintf(ficrespijb,"\n");
} /* end age deb */	}
} /* end combination */	free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
	fprintf(ficrespijb,"\n");
	} /* end age deb */
	/* } /\* end combination \/ /
} /* end nres */	} /* end nres */
return 0;	return 0;
} /* hBijx */	} /* hBijx */
Line 11246 int main(int argc, char *argv[])	Line 11948 int main(int argc, char *argv[])
char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];	char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];

char modeltemp[MAXLINE];	char modeltemp[MAXLINE];
char resultline[MAXLINE];	char resultline[MAXLINE], resultlineori[MAXLINE];

char pathr[MAXLINE], pathimach[MAXLINE];	char pathr[MAXLINE], pathimach[MAXLINE];
char tok, val; /* pathtot */	char tok, val; /* pathtot */
int firstobs=1, lastobs=10; /* nobs = lastobs-firstobs declared globally ;*/	/* int firstobs=1, lastobs=10; /\* nobs = lastobs-firstobs declared globally ;\/ /
int c, h , cpt, c2;	int c, h , cpt, c2;
int jl=0;	int jl=0;
int i1, j1, jk, stepsize=0;	int i1, j1, jk, stepsize=0;
Line 11872 Please run with mle=-1 to get a correct	Line 12574 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 11891 Please run with mle=-1 to get a correct	Line 12594 Please run with mle=-1 to get a correct

Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */	Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
TvarsDind=ivector(1,NCOVMAX); /* */	TvarsDind=ivector(1,NCOVMAX); /* */
	TnsdVar=ivector(1,NCOVMAX); /* */
	/* for(i=1; i<=NCOVMAX;i++) TnsdVar[i]=3; */
TvarsD=ivector(1,NCOVMAX); /* */	TvarsD=ivector(1,NCOVMAX); /* */
TvarsQind=ivector(1,NCOVMAX); /* */	TvarsQind=ivector(1,NCOVMAX); /* */
TvarsQ=ivector(1,NCOVMAX); /* */	TvarsQ=ivector(1,NCOVMAX); /* */
Line 11933 Please run with mle=-1 to get a correct	Line 12638 Please run with mle=-1 to get a correct
Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1] and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm	Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1] and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
* For V3V2 (in V2+V1+V1V4+ageV3+V3V2), V3*V2 position is 2nd.	* For V3V2 (in V2+V1+V1V4+ageV3+V3V2), V3*V2 position is 2nd.
* Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */	* Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
	Tvardk=imatrix(1,NCOVMAX,1,2);
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 12010 Please run with mle=-1 to get a correct	Line 12718 Please run with mle=-1 to get a correct
Ndum =ivector(-1,NCOVMAX);	Ndum =ivector(-1,NCOVMAX);
cptcoveff=0;	cptcoveff=0;
if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and ageage /	if (ncovmodel-nagesqr > 2 ){ /* That is if covariate other than cst, age and ageage /
tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /*< Fills nbcode[Tvar[j]][l]; /	tricode(&cptcoveff,Tvar,nbcode,imx, Ndum); /*< Fills nbcode[Tvar[j]][l]; as well as calculate cptcoveff or number of total effective dummy covariates/
}	}

ncovcombmax=pow(2,cptcoveff);	ncovcombmax=pow(2,cptcoveff);
Line 12040 Please run with mle=-1 to get a correct	Line 12748 Please run with mle=-1 to get a correct
* For k=4 covariates, h goes from 1 to m=2**k	* For k=4 covariates, h goes from 1 to m=2**k
* codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;	* codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
* #define codtabm(h,k) (1 & (h-1) >> (k-1))+1	* #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
* h\k 1 2 3 4	* h\k 1 2 3 4 * h-1\k-1 4 3 2 1
*______________________________	______________________________ ______________________
* 1 i=1 1 i=1 1 i=1 1 i=1 1	* 1 i=1 1 i=1 1 i=1 1 i=1 1 * 0 0 0 0 0
* 2 2 1 1 1	* 2 2 1 1 1 * 1 0 0 0 1
* 3 i=2 1 2 1 1	* 3 i=2 1 2 1 1 * 2 0 0 1 0
* 4 2 2 1 1	* 4 2 2 1 1 * 3 0 0 1 1
* 5 i=3 1 i=2 1 2 1	* 5 i=3 1 i=2 1 2 1 * 4 0 1 0 0
* 6 2 1 2 1	* 6 2 1 2 1 * 5 0 1 0 1
* 7 i=4 1 2 2 1	* 7 i=4 1 2 2 1 * 6 0 1 1 0
* 8 2 2 2 1	* 8 2 2 2 1 * 7 0 1 1 1
* 9 i=5 1 i=3 1 i=2 1 2	* 9 i=5 1 i=3 1 i=2 1 2 * 8 1 0 0 0
* 10 2 1 1 2	* 10 2 1 1 2 * 9 1 0 0 1
* 11 i=6 1 2 1 2	* 11 i=6 1 2 1 2 * 10 1 0 1 0
* 12 2 2 1 2	* 12 2 2 1 2 * 11 1 0 1 1
* 13 i=7 1 i=4 1 2 2	* 13 i=7 1 i=4 1 2 2 * 12 1 1 0 0
* 14 2 1 2 2	* 14 2 1 2 2 * 13 1 1 0 1
* 15 i=8 1 2 2 2	* 15 i=8 1 2 2 2 * 14 1 1 1 0
* 16 2 2 2 2	* 16 2 2 2 2 * 15 1 1 1 1
*/	*/
/* How to do the opposite? From combination h (=1 to 2*k) how to get the value on the covariates? /	/* How to do the opposite? From combination h (=1 to 2*k) how to get the value on the covariates? /
/* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4	/* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
* and the value of each covariate?	* and the value of each covariate?
Line 12149 Title=%s <br>Datafile=%s Firstpass=%d La	Line 12857 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<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n\
<hr size=\"2\" color=\"#EC5E5E\"> \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-2013-2022-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> \n", optionfilehtm);

	fprintf(fichtm,"<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\
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\	This file: <a href=\"%s\">%s</a></br>Title=%s <br>Datafile=<a href=\"%s\">%s</a> Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n\
\n\	\n\
<hr size=\"2\" color=\"#EC5E5E\">\	<hr size=\"2\" color=\"#EC5E5E\">\
<ul><li><h4>Parameter files</h4>\n\	<ul><li><h4>Parameter files</h4>\n\
Line 12162 Title=%s <br>Datafile=%s Firstpass=%d La	Line 12877 Title=%s <br>Datafile=%s Firstpass=%d La
- Log file of the run: <a href=\"%s\">%s</a><br>\n\	- Log file of the run: <a href=\"%s\">%s</a><br>\n\
- Gnuplot file name: <a href=\"%s\">%s</a><br>\n\	- Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
- Date and time at start: %s</ul>\n",\	- Date and time at start: %s</ul>\n",\
optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\	version,fullversion,optionfilehtm,optionfilehtm,title,datafile,datafile,firstpass,lastpass,stepm, weightopt, model, \
optionfilefiname,optionfilext,optionfilefiname,optionfilext,\	optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
fileres,fileres,\	fileres,fileres,\
filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);	filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
Line 12476 Please run with mle=-1 to get a correct	Line 13191 Please run with mle=-1 to get a correct
globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */	globpr=1; /* again, to print the individual contributions using computed gpimx and gsw */
likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */	likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);	printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
	/* exit(0); */
for (k=1; k<=npar;k++)	for (k=1; k<=npar;k++)
printf(" %d %8.5f",k,p[k]);	printf(" %d %8.5f",k,p[k]);
printf("\n");	printf("\n");
Line 12590 Please run with mle=-1 to get a correct	Line 13306 Please run with mle=-1 to get a correct
fprintf(fichtm, "<td>%1d%1d</td>",i,k);	fprintf(fichtm, "<td>%1d%1d</td>",i,k);
for(j=1; j <=ncovmodel; j++){	for(j=1; j <=ncovmodel; j++){
wald=p[jk]/sqrt(matcov[jk][jk]);	wald=p[jk]/sqrt(matcov[jk][jk]);
printf("%12.7f(%12.7f) sqrt(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]));	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) sqrt(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){	if(fabs(wald) > 1.96){
fprintf(fichtm, "<td><b>%12.7f</b></br> (%12.7f)</br>",p[jk],sqrt(matcov[jk][jk]));	fprintf(fichtm, "<td><b>%12.7f</b></br> (%12.7f)</br>",p[jk],sqrt(matcov[jk][jk]));
}else{	}else{
fprintf(fichtm, "<td>%12.7f (%12.7f)</br>",p[jk],sqrt(matcov[jk][jk]));	fprintf(fichtm, "<td>%12.7f (%12.7f)</br>",p[jk],sqrt(matcov[jk][jk]));
}	}
fprintf(fichtm,"sqrt(W)=%8.3f</br>",wald);	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]));	fprintf(fichtm,"[%12.7f;%12.7f]</br></td>", p[jk]-1.96sqrt(matcov[jk][jk]),p[jk]+1.96sqrt(matcov[jk][jk]));
jk++;	jk++;
}	}
Line 12820 Please run with mle=-1 to get a correct	Line 13536 Please run with mle=-1 to get a correct
}	}

/* Results */	/* Results */
	/* Value of covariate in each resultine will be compututed (if product) and sorted according to model rank */
	/* It is precov[] because we need the varying age in order to compute the real cov[] of the model equation */
	precov=matrix(1,MAXRESULTLINESPONE,1,NCOVMAX+1);
endishere=0;	endishere=0;
nresult=0;	nresult=0;
parameterline=0;	parameterline=0;
Line 12893 Please run with mle=-1 to get a correct	Line 13612 Please run with mle=-1 to get a correct
}	}
break;	break;
case 13:	case 13:
num_filled=sscanf(line,"result:%[^\n]\n",resultline);	num_filled=sscanf(line,"result:%[^\n]\n",resultlineori);
nresult++; /* Sum of resultlines */	nresult++; /* Sum of resultlines */
printf("Result %d: result:%s\n",nresult, resultline);	printf("Result %d: result:%s\n",nresult, resultlineori);
	/* removefirstspace(&resultlineori); */

	if(strstr(resultlineori,"v") !=0){
	printf("Error. 'v' must be in upper case 'V' result: %s ",resultlineori);
	fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultlineori);fflush(ficlog);
	return 1;
	}
	trimbb(resultline, resultlineori); /* Suppressing double blank in the resultline */
	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);
goto end;	goto end;
}	}

if(!decoderesult(resultline, nresult)){ /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */	if(!decoderesult(resultline, nresult)){ /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
fprintf(ficparo,"result: %s\n",resultline);	fprintf(ficparo,"result: %s\n",resultline);
fprintf(ficres,"result: %s\n",resultline);	fprintf(ficres,"result: %s\n",resultline);
Line 13004 Please run with mle=-1 to get a correct	Line 13733 Please run with mle=-1 to get a correct
/--------------- Prevalence limit (period or stable prevalence) --------------/	/--------------- Prevalence limit (period or stable prevalence) --------------/
/#include "prevlim.h"/ /* Use ficrespl, ficlog */	/#include "prevlim.h"/ /* Use ficrespl, ficlog */
prlim=matrix(1,nlstate,1,nlstate);	prlim=matrix(1,nlstate,1,nlstate);
	/* Computes the prevalence limit for each combination k of the dummy covariates by calling prevalim(k) */
prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);	prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
fclose(ficrespl);	fclose(ficrespl);

/------------- h Pij x at various ages ------------/	/------------- h Pij x at various ages ------------/
/#include "hpijx.h"/	/#include "hpijx.h"/
	/** h Pij x Probability to be in state j at age x+h being in i at x, for each combination k of dummies in the model line or to nres?*/
	/* calls hpxij with combination k */
hPijx(p, bage, fage);	hPijx(p, bage, fage);
fclose(ficrespij);	fclose(ficrespij);

/* ncovcombmax= pow(2,cptcoveff); */	/* ncovcombmax= pow(2,cptcoveff); */
/-------------- Variance of one-step probabilities---/	/-------------- Variance of one-step probabilities for a combination ij or for nres ?---/
k=1;	k=1;
varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);	varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);

Line 13134 Please run with mle=-1 to get a correct	Line 13866 Please run with mle=-1 to get a correct
fprintf(ficreseij,"\n#****** ");	fprintf(ficreseij,"\n#****** ");
printf("\n#****** ");	printf("\n#****** ");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcoveff;j++) {
fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
}	}
for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */	for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	printf(" V%d=%lg ",TvarsQ[j], TinvDoQresult[nres][TvarsQ[j]]); /* TvarsQ[j] gives the name of the jth quantitative (fixed or time v) */
fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	fprintf(ficreseij,"V%d=%lg ",TvarsQ[j], TinvDoQresult[nres][TvarsQ[j]]);
}	}
fprintf(ficreseij,"******\n");	fprintf(ficreseij,"******\n");
printf("******\n");	printf("******\n");

eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);	eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
oldm=oldms;savm=savms;	oldm=oldms;savm=savms;
	/* printf("HELLO Entering evsij bage=%d fage=%d k=%d estepm=%d nres=%d\n",(int) bage, (int)fage, k, estepm, nres); */
evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);	evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart, nres);

free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);	free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
Line 13156 Please run with mle=-1 to get a correct	Line 13889 Please run with mle=-1 to get a correct


/---------- State-specific expectancies and variances ------------/	/---------- State-specific expectancies and variances ------------/
	/* Should be moved in a function */
strcpy(filerest,"T_");	strcpy(filerest,"T_");
strcat(filerest,fileresu);	strcat(filerest,fileresu);
if((ficrest=fopen(filerest,"w"))==NULL) {	if((ficrest=fopen(filerest,"w"))==NULL) {
Line 13195 Please run with mle=-1 to get a correct	Line 13928 Please run with mle=-1 to get a correct
i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */	i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
if (cptcovn < 1){i1=1;}	if (cptcovn < 1){i1=1;}

for(nres=1; nres <= nresult; nres++) /* For each resultline */	for(nres=1; nres <= nresult; nres++) /* For each resultline, find the combination and output results according to the values of dummies and then quanti. */
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. For each nres and each value at position k
if(i1 != 1 && TKresult[nres]!= k)	* we know Tresult[nres][result_position]= value of the dummy variable at the result_position in the nres resultline
	* Tvqresult[nres][result_position]= id of the variable at the result_position in the nres resultline
	* and Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline */
	/* */
	if(i1 != 1 && TKresult[nres]!= k) /* TKresult[nres] is the combination of this nres resultline. All the i1 combinations are not output */
continue;	continue;
printf("\n# model %s \n#****** Result for:", model);	printf("\n# model %s \n#****** Result for:", model);
fprintf(ficrest,"\n# model %s \n#****** Result for:", model);	fprintf(ficrest,"\n# model %s \n#****** Result for:", model);
fprintf(ficlog,"\n# model %s \n#****** Result for:", model);	fprintf(ficlog,"\n# model %s \n#****** Result for:", model);
for(j=1;j<=cptcoveff;j++){	/* It might not be a good idea to mix dummies and quantitative */
printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	/* for(j=1;j<=cptcoveff;j++){ /\* j=resultpos. Could be a loop on cptcovs: number of single dummy covariate in the result line as well as in the model \/ /
fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	for(j=1;j<=cptcovs;j++){ /* j=resultpos. Could be a loop on cptcovs: number of single covariate (dummy or quantitative) in the result line as well as in the model */
fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	/* printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); /\* Output by variables in the resultline \/ /
}	/* Tvaraff[j] is the name of the dummy variable in position j in the equation model:
for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */	* Tvaraff[1]@9={4, 3, 0, 0, 0, 0, 0, 0, 0}, in model=V5+V4+V3+V4V3+V5age
printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	* (V5 is quanti) V4 and V3 are dummies
fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	* TnsdVar[4] is the position 1 and TnsdVar[3]=2 in codtabm(k,l)(V4 V3)=V4 V3
fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	* l=1 l=2
}	* k=1 1 1 0 0
	* k=2 2 1 1 0
	* k=3 [1] [2] 0 1
	* k=4 2 2 1 1
	* If nres=1 result: V3=1 V4=0 then k=3 and outputs
	* If nres=2 result: V4=1 V3=0 then k=2 and outputs
	* nres=1 =>k=3 j=1 V4= nbcode[4][codtabm(3,1)=1)=0; j=2 V3= nbcode[3][codtabm(3,2)=2]=1
	* nres=2 =>k=2 j=1 V4= nbcode[4][codtabm(2,1)=2)=1; j=2 V3= nbcode[3][codtabm(2,2)=1]=0
	*/
	/* 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 */
	/* 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(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 */
	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 */
	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 */
	if(Fixed[modelresult[nres][j]]==0){ /* Fixed */
	printf("fixed ");fprintf(ficlog,"fixed ");fprintf(ficrest,"fixed ");
	}else{
	printf("varyi ");fprintf(ficlog,"varyi ");fprintf(ficrest,"varyi ");
	}
	/* fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
	/* fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
	}else if(Dummy[modelresult[nres][j]]==1){ /* Quanti variable */
	/* For each selected (single) quantitative value */
	printf(" V%d=%lg ",Tvqresult[nres][j],Tqresult[nres][j]);
	fprintf(ficlog," V%d=%lg ",Tvqresult[nres][j],Tqresult[nres][j]);
	fprintf(ficrest," V%d=%lg ",Tvqresult[nres][j],Tqresult[nres][j]);
	if(Fixed[modelresult[nres][j]]==0){ /* Fixed */
	printf("fixed ");fprintf(ficlog,"fixed ");fprintf(ficrest,"fixed ");
	}else{
	printf("varyi ");fprintf(ficlog,"varyi ");fprintf(ficrest,"varyi ");
	}
	}else{
	printf("Error in computing T_ Dummy[modelresult[%d][%d]]=%d, modelresult[%d][%d]=%d cptcovs=%d, cptcoveff=%d \n", nres, j, Dummy[modelresult[nres][j]],nres,j,modelresult[nres][j],cptcovs, cptcoveff); /* end if dummy or quanti */
	fprintf(ficlog,"Error in computing T_ Dummy[modelresult[%d][%d]]=%d, modelresult[%d][%d]=%d cptcovs=%d, cptcoveff=%d \n", nres, j, Dummy[modelresult[nres][j]],nres,j,modelresult[nres][j],cptcovs, cptcoveff); /* end if dummy or quanti */
	exit(1);
	}
	} /* End loop for each variable in the resultline */
	/* for (j=1; j<= nsq; j++){ /\* For each selected (single) quantitative value \/ /
	/* printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); /\* Wrong j is not in the equation model \/ /
	/* fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
	/* fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
	/* } */
fprintf(ficrest,"******\n");	fprintf(ficrest,"******\n");
fprintf(ficlog,"******\n");	fprintf(ficlog,"******\n");
printf("******\n");	printf("******\n");

fprintf(ficresstdeij,"\n#****** ");	fprintf(ficresstdeij,"\n#****** ");
fprintf(ficrescveij,"\n#****** ");	fprintf(ficrescveij,"\n#****** ");
	/* It could have been: for(j=1;j<=cptcoveff;j++) {printf("V=%d=%lg",Tvresult[nres][cpt],TinvDoQresult[nres][Tvresult[nres][cpt]]);} */
	/* But it won't be sorted and depends on how the resultline is ordered */
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcoveff;j++) {
fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresstdeij,"V%d=%d ",Tvresult[nres][j],Tresult[nres][j]);
fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	/* fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
}	/* fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */	}
fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value, TvarsQind gives the position of a quantitative in model equation */
fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	fprintf(ficresstdeij," V%d=%lg ",Tvar[TvarsQind[j]],Tqresult[nres][resultmodel[nres][TvarsQind[j]]]);
	fprintf(ficrescveij," V%d=%lg ",Tvar[TvarsQind[j]],Tqresult[nres][resultmodel[nres][TvarsQind[j]]]);
}	}
fprintf(ficresstdeij,"******\n");	fprintf(ficresstdeij,"******\n");
fprintf(ficrescveij,"******\n");	fprintf(ficrescveij,"******\n");
Line 13232 Please run with mle=-1 to get a correct	Line 14017 Please run with mle=-1 to get a correct
fprintf(ficresvij,"\n#****** ");	fprintf(ficresvij,"\n#****** ");
/* pstamp(ficresvij); */	/* pstamp(ficresvij); */
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresvij,"V%d=%d ",Tvresult[nres][j],Tresult[nres][j]);
	/* fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[TnsdVar[Tvaraff[j]]])]); */
for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */	for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	/* fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); /\* To solve \/ /
	fprintf(ficresvij," V%d=%lg ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); /* Solved */
}	}
fprintf(ficresvij,"******\n");	fprintf(ficresvij,"******\n");

Line 13265 Please run with mle=-1 to get a correct	Line 14052 Please run with mle=-1 to get a correct
fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);	fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
else	else
fprintf(ficrest,"the age specific forward period (stable) prevalences in each health state \n");	fprintf(ficrest,"the age specific forward period (stable) prevalences in each health state \n");
fprintf(ficrest,"# Age popbased mobilav e.. (std) ");	fprintf(ficrest,"# Age popbased mobilav e.. (std) "); /* Adding covariate values? */
for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);	for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
fprintf(ficrest,"\n");	fprintf(ficrest,"\n");
/* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */	/* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
Line 13312 Please run with mle=-1 to get a correct	Line 14099 Please run with mle=-1 to get a correct
printf("done selection\n");fflush(stdout);	printf("done selection\n");fflush(stdout);
fprintf(ficlog,"done selection\n");fflush(ficlog);	fprintf(ficlog,"done selection\n");fflush(ficlog);

} /* End k selection */	} /* End k selection or end covariate selection for nres */

printf("done State-specific expectancies\n");fflush(stdout);	printf("done State-specific expectancies\n");fflush(stdout);
fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);	fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);

/* variance-covariance of forward period prevalence*/	/* variance-covariance of forward period prevalence */
varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);	varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);


free_vector(weight,firstobs,lastobs);	free_vector(weight,firstobs,lastobs);
	free_imatrix(Tvardk,1,NCOVMAX,1,2);
free_imatrix(Tvard,1,NCOVMAX,1,2);	free_imatrix(Tvard,1,NCOVMAX,1,2);
free_imatrix(s,1,maxwav+1,firstobs,lastobs);	free_imatrix(s,1,maxwav+1,firstobs,lastobs);
free_matrix(anint,1,maxwav,firstobs,lastobs);	free_matrix(anint,1,maxwav,firstobs,lastobs);
Line 13369 Please run with mle=-1 to get a correct	Line 14157 Please run with mle=-1 to get a correct
free_ivector(TvarsQ,1,NCOVMAX);	free_ivector(TvarsQ,1,NCOVMAX);
free_ivector(TvarsQind,1,NCOVMAX);	free_ivector(TvarsQind,1,NCOVMAX);
free_ivector(TvarsD,1,NCOVMAX);	free_ivector(TvarsD,1,NCOVMAX);
	free_ivector(TnsdVar,1,NCOVMAX);
free_ivector(TvarsDind,1,NCOVMAX);	free_ivector(TvarsDind,1,NCOVMAX);
free_ivector(TvarFD,1,NCOVMAX);	free_ivector(TvarFD,1,NCOVMAX);
free_ivector(TvarFDind,1,NCOVMAX);	free_ivector(TvarFDind,1,NCOVMAX);
Line 13394 Please run with mle=-1 to get a correct	Line 14183 Please run with mle=-1 to get a correct
free_ivector(Tmodelind,1,NCOVMAX);	free_ivector(Tmodelind,1,NCOVMAX);
free_ivector(TmodelInvind,1,NCOVMAX);	free_ivector(TmodelInvind,1,NCOVMAX);
free_ivector(TmodelInvQind,1,NCOVMAX);	free_ivector(TmodelInvQind,1,NCOVMAX);

	free_matrix(precov, 1,MAXRESULTLINESPONE,1,NCOVMAX+1); /* Could be elsewhere ?*/

free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);	free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
/* free_imatrix(codtab,1,100,1,10); */	/* free_imatrix(codtab,1,100,1,10); */
fflush(fichtm);	fflush(fichtm);

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

Removed from v.1.322
changed lines
	Added in v.1.337