imach/src/imach.c - diff

Return to imach.c CVS log

Up to [Local Repository] / imach / src

Diff for /imach/src/imach.c between versions 1.335 and 1.358

version 1.335, 2022/08/31 08:23:16	version 1.358, 2023/06/14 14:57:02
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	Revision 1.358 2023/06/14 14:57:02 brouard
	* imach.c (Module): Testing if conjugate gradient could be quicker when lot of variables POWELLORIGINCONJUGATE

	Revision 1.357 2023/06/14 14:55:52 brouard
	* imach.c (Module): Testing if conjugate gradient could be quicker when lot of variables POWELLORIGINCONJUGATE

	Revision 1.356 2023/05/23 12:08:43 brouard
	Summary: 0.99r46

	* imach.c (Module): Fixed PROB_r

	Revision 1.355 2023/05/22 17:03:18 brouard
	Summary: 0.99r46

	* imach.c (Module): In the ILK....txt file, the number of columns
	before the covariates values is dependent of the number of states (16+nlstate): 0.99r46

	Revision 1.354 2023/05/21 05:05:17 brouard
	Summary: Temporary change for imachprax

	Revision 1.353 2023/05/08 18:48:22 brouard
	* empty log message *

	Revision 1.352 2023/04/29 10:46:21 brouard
	* empty log message *

	Revision 1.351 2023/04/29 10:43:47 brouard
	Summary: 099r45

	Revision 1.350 2023/04/24 11:38:06 brouard
	* empty log message *

	Revision 1.349 2023/01/31 09:19:37 brouard
	Summary: Improvements in models with ageVnVm

	Revision 1.347 2022/09/18 14:36:44 brouard
	Summary: version 0.99r42

	Revision 1.346 2022/09/16 13:52:36 brouard
	* src/imach.c (Module): 0.99r41 Was an error when product of timevarying and fixed. Using FixedV[of name] now. Thank you Feinuo

	Revision 1.345 2022/09/16 13:40:11 brouard
	Summary: Version 0.99r41

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

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

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

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

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

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

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

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

	After adding change in cotvar.

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

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

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

	* imach.c (Module): Many improvements for fixing products of fixed
	timevarying as well as fixed * fixed, and test with quantitative
	covariate.

	Revision 1.338 2022/09/04 17:40:33 brouard
	Summary: 0.99r36

	* imach.c (Module): Now the easy runs i.e. without result or
	model=1+age only did not work. The defautl combination should be 1
	and not 0 because everything hasn't been tranformed yet.

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

Line 1194 Important routines	Line 1298 Important routines
/* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test \/ /	/* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test \/ /
/* #define MNBRAKORIGINAL /\* Don't use mnbrak fix \/ /	/* #define MNBRAKORIGINAL /\* Don't use mnbrak fix \/ /
/* #define FLATSUP // Suppresses directions where likelihood is flat */	/* #define FLATSUP // Suppresses directions where likelihood is flat */
	#define POWELLORIGINCONJUGATE /* Don't use conjugate but biggest decrease if valuable */

#include <math.h>	#include <math.h>
#include <stdio.h>	#include <stdio.h>
Line 1245 typedef struct {	Line 1350 typedef struct {
/* #include <libintl.h> */	/* #include <libintl.h> */
/* #define _(String) gettext (String) */	/* #define _(String) gettext (String) */

#define MAXLINE 2048 /* Was 256 and 1024. Overflow with 312 with 2 states and 4 covariates. Should be ok */	#define MAXLINE 16384 /* Was 256 and 1024 and 2048. Overflow with 312 with 2 states and 4 covariates. Should be ok */

#define GNUPLOTPROGRAM "gnuplot"	#define GNUPLOTPROGRAM "gnuplot"
	#define GNUPLOTVERSION 5.1
	double gnuplotversion=GNUPLOTVERSION;
/#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"/	/#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"/
#define FILENAMELENGTH 256	#define FILENAMELENGTH 256

#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 */

#define MAXPARM 128 /*< Maximum number of parameters for the optimization /	#define MAXPARM 216 /*< Maximum number of parameters for the optimization was 128 /
#define NPARMAX 64 /*< (nlstate+ndeath-1)nlstatencovmodel /	#define NPARMAX 64 /*< (nlstate+ndeath-1)nlstatencovmodel /

#define NINTERVMAX 8	#define NINTERVMAX 8
Line 1288 typedef struct {	Line 1395 typedef struct {
/* $State$ */	/* $State$ */
#include "version.h"	#include "version.h"
char version[]=__IMACH_VERSION__;	char version[]=__IMACH_VERSION__;
char copyright[]="August 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[]="Testing conjugate April 2023,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 debugILK=0; /* debugILK is set by a #d in a comment line */
int nagesqr=0, nforce=0; /* nagesqr=1 if model is including ageage, number of forces /	int nagesqr=0, nforce=0; /* nagesqr=1 if model is including ageage, number of forces /
/* Number of covariates model (1)=V2+V1+ V3age+V2V4 */	/* Number of covariates model (1)=V2+V1+ V3age+V2V4 */
/* Model(2) V1 + V2 + V3 + V8 + V7V8 + V5V6 + V8age + V3age + ageage /	/* Model(2) V1 + V2 + V3 + V8 + V7V8 + V5V6 + V8age + V3age + ageage /
Line 1301 int cptcovt=0; /**< cptcovt: total numbe	Line 1409 int cptcovt=0; /**< cptcovt: total numbe
int cptcovs=0; /*< cptcovs number of SIMPLE covariates in the model V2+V1 =2 (dummy or quantit or time varying) /	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 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 cptcovprodage=0; /*< Number of fixed covariates with age: V3age or V2V3age 1 */
	int cptcovprodvage=0; /*< Number of varying covariates with age: V7age or V7V6age */
	int cptcovdageprod=0; /*< Number of doubleproducts with age, since 0.99r44 only: ageVnVm for gnuplot printing/
int cptcovprodnoage=0; /*< Number of covariate products without age /	int cptcovprodnoage=0; /*< Number of covariate products without age /
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 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 ncovvt=0; /* Total number of effective (wave) varying covariates (dummy or quantitative or products [without age]) in the model */
	int ncovvta=0; /* +ageV6 + ageV7+ ageV6V3 +ageV7V3 + ageV6V4 +ageV7V4 Total number of expandend products [with age]) in the model */
	int ncovta=0; /ageV3V2 +ageV2+agev3+ageV4 +ageV6 + ageV7+ ageV6V3 +ageV7V3 + ageV6V4 +ageV7V4 Total number of expandend products [with age]) in the model */
	int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (single or product, dummy or quantitative) in the model */
	int ncovva=0; /* +ageV6 + ageV7+geV6V3 +ageV7V3 + ageV6V4 +ageV7V4 Total number of effective (wave and stepm) varying with age covariates (single or product, dummy or quantitative) in the model */
int nsd=0; /*< Total number of single dummy variables (output) /	int nsd=0; /*< Total number of single dummy variables (output) /
int nsq=0; /*< Total number of single quantitative variables (output) /	int nsq=0; /*< Total number of single quantitative variables (output) /
int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */	int ncoveff=0; /* Total number of effective fixed dummy covariates in the model */
Line 1320 int npar=NPARMAX; /* Number of parameter	Line 1435 int npar=NPARMAX; /* Number of parameter
int nlstate=2; /* Number of live states */	int nlstate=2; /* Number of live states */
int ndeath=1; /* Number of dead states */	int ndeath=1; /* Number of dead states */
int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a121 +b12x ncovmodel=2 */	int ncovmodel=0, ncovcol=0; /* Total number of covariables including constant a121 +b12x ncovmodel=2 */
int nqv=0, ntv=0, nqtv=0; /* Total number of quantitative variables, time variable (dummy), quantitative and time variable */	int nqv=0, ntv=0, nqtv=0; /* Total number of quantitative variables, time variable (dummy), quantitative and time variable*/
	int ncovcolt=0; /* ncovcolt=ncovcol+nqv+ntv+nqtv; total of covariates in the data, not in the model equation*/
int popbased=0;	int popbased=0;

int wav; / Number of waves for this individuual 0 is possible */	int wav; / Number of waves for this individuual 0 is possible */
Line 1391 extern time_t time();	Line 1507 extern time_t time();

struct tm start_time, end_time, curr_time, last_time, forecast_time;	struct tm start_time, end_time, curr_time, last_time, forecast_time;
time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */	time_t rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
	time_t rlast_btime; /* raw time */
struct tm tm;	struct tm tm;

char strcurr[80], strfor[80];	char strcurr[80], strfor[80];
Line 1469 double covar; /< covar[j,i], value	Line 1586 double covar; /< covar[j,i], value
* covar=matrix(0,NCOVMAX,1,n);	* covar=matrix(0,NCOVMAX,1,n);
* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]age; /	* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]age; /
double *coqvar; / Fixed quantitative covariate nqv */	double *coqvar; / Fixed quantitative covariate nqv */
double **cotvar; / Time varying covariate ntv */	double **cotvar; / Time varying covariate start at ncovcol + nqv + (1 to ntv) */
double **cotqvar; / Time varying quantitative covariate itqv */	double **cotqvar; / Time varying quantitative covariate itqv */
double idx;	double idx;
int *nbcode, Tvar; /*< model=V2 => Tvar[1]= 2 /	int *nbcode, Tvar; /*< model=V2 => Tvar[1]= 2 /
Line 1481 int *nbcode, Tvar; /**< model=V2 => Tv	Line 1598 int *nbcode, Tvar; /**< model=V2 => Tv
* cptcovn number of covariates (not including constant and age or age*age) = number of plus sign + 1 = 10+1=11	* cptcovn number of covariates (not including constant and age or age*age) = number of plus sign + 1 = 10+1=11
* For time varying covariate, quanti or dummies	* For time varying covariate, quanti or dummies
* cotqvar[wav][iv(1 to nqtv)][i]= [1][12][i]=(V12) quanti	* cotqvar[wav][iv(1 to nqtv)][i]= [1][12][i]=(V12) quanti
* cotvar[wav][ntv+iv][i]= [3+(1 to nqtv)][i]=(V12) quanti	* cotvar[wav][ncovcol+nqv+ iv(1 to nqtv)][i]= [(1 to nqtv)][i]=(V12) quanti
* cotvar[wav][iv(1 to ntv)][i]= [1][1][i]=(V9) dummies at wav 1	* cotvar[wav][iv(1 to ntv)][i]= [1][1][i]=(V9) dummies at wav 1
* cotvar[wav][iv(1 to ntv)][i]= [1][2][i]=(V10) dummies at wav 1	* cotvar[wav][iv(1 to ntv)][i]= [1][2][i]=(V10) dummies at wav 1
* covar[Vk,i], value of the Vkth fixed covariate dummy or quanti for individual i:	* covar[Vk,i], value of the Vkth fixed covariate dummy or quanti for individual i:
Line 1494 int *nbcode, Tvar; /**< model=V2 => Tv	Line 1611 int *nbcode, Tvar; /**< model=V2 => Tv
# States 1=Coresidence, 2 Living alone, 3 Institution	# States 1=Coresidence, 2 Living alone, 3 Institution
# V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi	# V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi
*/	*/
/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */	/* V5+V4+ V3+V4V3 +V5age+V2 +V1V2+V1age+V1+V4V3age */
/* k 1 2 3 4 5 6 7 8 9 */	/* kmodel 1 2 3 4 5 6 7 8 9 10 */
/Typevar[k]= 0 0 0 2 1 0 2 1 0 //0 for simple covariate (dummy, quantitative,/	/Typevar[k]= 0 0 0 2 1 0 2 1 0 3 //0 for simple covariate (dummy, quantitative,/
/* fixed or varying), 1 for age product, 2 for*/	/* fixed or varying), 1 for age product, 2 for*/
/* product */	/* product without age, 3 for age and double product */
/Dummy[k]= 1 0 0 1 3 1 1 2 0 //Dummy[k] 0=dummy (0 1), 1 quantitative /	/Dummy[k]= 1 0 0 1 3 1 1 2 0 3 //Dummy[k] 0=dummy (0 1), 1 quantitative /
/(single or product without age), 2 dummy/	/(single or product without age), 2 dummy/
/* 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 6 /
/* 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 /	/TnsdVar[Tvar] 1 2 3 /
/TvarsD[nsd] 4 3 1 / /* ID of single dummy cova fixed or timevary*/	/Tvaraff[nsd] 4 3 1 / /* ID of single dummy cova fixed or timevary*/
/TvarsDind[k] 2 3 9 / /* position K of single dummy cova */	/TvarsD[nsd] 4 3 1 / /* ID of single dummy cova fixed or timevary*/
/* nsq 1 2 / / Counting single quantit tv */	/TvarsDind[nsd] 2 3 9 / /* position K of single dummy cova */
/* TvarsQ[k] 5 2 / / Number of single quantitative cova */	/* nsq 1 2 / / Counting single quantit tv */
/* TvarsQind 1 6 / / position K of single quantitative cova */	/* TvarsQ[k] 5 2 / / Number of single quantitative cova */
/* Tprod[i]=k 1 2 / / Position in model of the ith prod without age */	/* TvarsQind 1 6 / / position K of single quantitative cova */
/* cptcovage 1 2 / / Counting covage in the model equation /	/* Tprod[i]=k 1 2 / / Position in model of the ith prod without age */
/* Tage[cptcovage]=k 5 8 / / Position in the model of ith covage /	/* cptcovage 1 2 3 / / Counting covage in the model equation /
/* Tvard[1][1]@4={4,3,1,2} V4V3 V1V2 / / Position in model of the ith prod without age */	/* Tage[cptcovage]=k 5 8 10 / / Position in the model of ith covage /
	/* model="V2+V3+V4+V6+V7+V6V2+V7V2+V6V3+V7V3+V6V4+V7V4+ageV2+ageV3+ageV4+ageV6+ageV7+ageV6V2+ageV6V3+ageV7V3+ageV6V4+ageV7V4\r"/
	/* p Tvard[1][1]@21 = {6, 2, 7, 2, 6, 3, 7, 3, 6, 4, 7, 4, 0, 0, 0, 0, 0, 0, 0, 0, 0}*/
	/* p Tvard[2][1]@21 = {7, 2, 6, 3, 7, 3, 6, 4, 7, 4, 0 <repeats 11 times>} */
	/* p Tvardk[1][1]@24 = {0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 6, 2, 7, 2, 6, 3, 7, 3, 6, 4, 7, 4, 0, 0}*/
	/* p Tvardk[1][1]@22 = {0, 0, 0, 0, 0, 0, 0, 0, 6, 2, 7, 2, 6, 3, 7, 3, 6, 4, 7, 4, 0, 0} */
	/* 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*/	/* 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) */
Line 1561 int TvarVD; / TvarVD[1]=V5 in V5+V4+V3	Line 1684 int TvarVD; / TvarVD[1]=V5 in V5+V4+V3
int TvarVDind; / TvarVDind[1]=1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple fixed quantitative variable */	int TvarVDind; / TvarVDind[1]=1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple fixed quantitative variable */
int TvarVQ; / TvarVQ[1]=V5 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple time varying quantitative variable */	int TvarVQ; / TvarVQ[1]=V5 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple time varying quantitative variable */
int TvarVQind; / TvarVQind[1]=1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple time varying quantitative variable */	int TvarVQind; / TvarVQind[1]=1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple time varying quantitative variable */
	int TvarVV; / We count ncovvt time varying covariates (single or products without age) and put their name into TvarVV */
	int TvarVVind; / We count ncovvt time varying covariates (single or products without age) and put their name into TvarVV */
	int TvarVVA; / We count ncovvt time varying covariates (single or products with age) and put their name into TvarVVA */
	int TvarVVAind; / We count ncovvt time varying covariates (single or products without age) and put their name into TvarVV */
	int TvarAVVA; / We count ALL ncovta time varying covariates (single or products with age) and put their name into TvarVVA */
	int TvarAVVAind; / We count ALL ncovta time varying covariates (single or products without age) and put their name into TvarVV */
	/# ID V1 V2 weight birth death 1st s1 V3 V4 V5 2nd s2 /
	/* model V1+V3+ageV1+ageV3+V1V3 + V1V3age /
	/* Tvar={1, 3, 1, 3, 6, 6}, the 6 comes from the fact that there are already V1, V2, V3, V4, V5 native covariates */
	/* TvarVV={3,1,3,1,3}, for V3 and then the product V1V3 is decomposed into V1 and V3 /
	/* TvarVVind={2,5,5,6,6}, for V3 and then the product V1V3 is decomposed into V1 and V3 and V1V3age into 6,6 /
int Tvarsel; /< Selected covariates for output /	int Tvarsel; /< Selected covariates for output /
double Tvalsel; /< Selected modality value of covariate for output /	double Tvalsel; /< Selected modality value of covariate for output /
int Typevar; /< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product /	int Typevar; /< 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product, 3 ageVnVm /
int Fixed; /* Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */	int Fixed; /* Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age product */
int Dummy; /* Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */	int Dummy; /* Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product */
int DummyV; /* Dummy[v] 0=dummy (0 1), 1 quantitative */	int DummyV; /* Dummy[v] 0=dummy (0 1), 1 quantitative */
Line 1701 char trimbb(char out, char *in)	Line 1834 char trimbb(char out, char *in)
return s;	return s;
}	}

	char trimbtab(char out, char *in)
	{ /* Trim blanks or tabs in line but keeps first blanks if line starts with blanks */
	char *s;
	s=out;
	while (*in != '\0'){
	while( (in == ' ' \|\| in == '\t')){ /* && (in+1) != '\0'){/
	in++;
	}
	out++ = in++;
	}
	*out='\0';
	return s;
	}

/* char substrchaine(char out, char in, char chain) */	/* char substrchaine(char out, char in, char chain) */
/* { */	/* { */
/* /\* Substract chain 'chain' from 'in', return and output 'out' \/ /	/* /\* Substract chain 'chain' from 'in', return and output 'out' \/ /
Line 1727 char trimbb(char out, char *in)	Line 1874 char trimbb(char out, char *in)
char substrchaine(char out, char in, char chain)	char substrchaine(char out, char in, char chain)
{	{
/* Substract chain 'chain' from 'in', return and output 'out' */	/* Substract chain 'chain' from 'in', return and output 'out' */
/* in="V1+V1age+ageage+V2", chain="ageage" /	/* in="V1+V1age+ageage+V2", chain="+ageage" out="V1+V1age+V2" */

char *strloc;	char *strloc;

strcpy (out, in);	strcpy (out, in); /* out="V1+V1age+ageage+V2" */
strloc = strstr(out, chain); /* strloc points to out at ageage+V2 /	strloc = strstr(out, chain); /* strloc points to out at "+ageage+V2" /
printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out);	printf("Bef strloc=%s chain=%s out=%s \n", strloc, chain, out); /* strloc=+ageage+V2 chain="+ageage", out="V1+V1age+ageage+V2" */
if(strloc != NULL){	if(strloc != NULL){
/* will affect out / / strloc+strlenc(chain)=+V2 / / Will also work in Unicode */	/* will affect out / / strloc+strlen(chain)=\|+V2 = "V1+V1age+ageage\|+V2" / / Will also work in Unicodek */
memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1);	memmove(strloc,strloc+strlen(chain), strlen(strloc+strlen(chain))+1); /* move number of bytes corresponding to the length of "+V2" which is 3, plus one is 4 (including the null)*/
/* strcpy (strloc, strloc +strlen(chain));*/	/* equivalent to strcpy (strloc, strloc +strlen(chain)) if no overlap; Copies from "+V2" to V1+V1age+ /
}	}
printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out);	printf("Aft strloc=%s chain=%s in=%s out=%s \n", strloc, chain, in, out); /* strloc=+V2 chain="+ageage", in="V1+V1age+ageage+V2", out="V1+V1age+V2" */
return out;	return out;
}	}

Line 1747 char substrchaine(char out, char *in,	Line 1894 char substrchaine(char out, char *in,
char cutl(char blocc, char alocc, char in, char occ)	char cutl(char blocc, char alocc, char in, char occ)
{	{
/* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'	/* cuts string in into blocc and alocc where blocc ends before FIRST occurence of char 'occ'
and alocc starts after first occurence of char 'occ' : ex cutv(blocc,alocc,"abcdef2ghi2j",'2')	and alocc starts after first occurence of char 'occ' : ex cutl(blocc,alocc,"abcdef2ghi2j",'2')
gives alocc="abcdef" and blocc="ghi2j".	gives alocc="abcdef" and blocc="ghi2j".
If occ is not found blocc is null and alocc is equal to in. Returns blocc	If occ is not found blocc is null and alocc is equal to in. Returns blocc
*/	*/
Line 1813 int nbocc(char *s, char occ)	Line 1960 int nbocc(char *s, char occ)
return j;	return j;
}	}

	int nboccstr(char textin, char chain)
	{
	/* Counts the number of occurence of "chain" in string textin */
	/* in="+V7V4+ageV2+ageV3+ageV4" chain="age" */
	char *strloc;

	int i,j=0;

	i=0;

	strloc=textin; /* strloc points to "^+V7V4+age+..." in textin /
	for(;;) {
	strloc= strstr(strloc,chain); /* strloc points to first character of chain in textin if found. Example strloc points^ to "+V7V4+^age" in textin /
	if(strloc != NULL){
	strloc = strloc+strlen(chain); /* strloc points to "+V7V4+age^" in textin /
	j++;
	}else
	break;
	}
	return j;

	}
/* void cutv(char u,char v, chart, char occ) /	/* void cutv(char u,char v, chart, char occ) /
/* { */	/* { */
/* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */	/* /\* cuts string t into u and v where u ends before last occurence of char 'occ' */
Line 2492 void powell(double p[], double **xi, int	Line 2661 void powell(double p[], double **xi, int
double fp,fptt;	double fp,fptt;
double *xits;	double *xits;
int niterf, itmp;	int niterf, itmp;
	int Bigter=0, nBigterf=1;

pt=vector(1,n);	pt=vector(1,n);
ptt=vector(1,n);	ptt=vector(1,n);
xit=vector(1,n);	xit=vector(1,n);
xits=vector(1,n);	xits=vector(1,n);
fret=(func)(p);	fret=(func)(p);
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);
	fp=(fret); / Initialisation */
for (iter=1;;++(iter)) {	for (iter=1;;++(iter)) {
ibig=0;	ibig=0;
del=0.0;	del=0.0;
rlast_time=rcurr_time;	rlast_time=rcurr_time;
	rlast_btime=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 gain=%.12f=%.3g %ld sec. %ld sec.",iter,fret, fp-fret,fp-*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 gain=%.12f=%.3g %ld sec. %ld sec.",iter,fret, fp-fret,fp-*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);	/* fprintf(ficlog,"\nPowell iter=%d -2LL=%.12f gain=%.12f=%.3g %ld sec. %ld sec.",iter,fret, fp-fret,fp-fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog); /
/* fprintf(ficrespow,"%d %.12f %ld",iter,fret,curr_time.tm_sec-start_time.tm_sec); */	Bigter=(iter - iter % ncovmodel)/ncovmodel +1; /* Big iteration, i.e on ncovmodel cycle */
	printf("\nPowell iter=%d Big Iter=%d -2LL=%.12f gain=%.3lg %ld sec. %ld sec.",iter,Bigter,fret,fp-fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
	fprintf(ficlog,"\nPowell iter=%d Big Iter=%d -2LL=%.12f gain=%.3lg %ld sec. %ld sec.",iter,Bigter,fret,fp-fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
	fprintf(ficrespow,"%d %d %.12f %d",iter,Bigter, fret,curr_time.tm_sec-start_time.tm_sec);
fp=(fret); / From former iteration or initial value */	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 2531 void powell(double p[], double **xi, int	Line 2706 void powell(double p[], double **xi, int
}else if(Typevar[j]==2) {	}else if(Typevar[j]==2) {
printf(" + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);	printf(" + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
fprintf(ficlog," + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);	fprintf(ficlog," + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
	}else if(Typevar[j]==3) {
	printf(" + V%dV%dage ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
	fprintf(ficlog," + V%dV%dage ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
}	}
}	}
printf("\n");	printf("\n");
Line 2561 void powell(double p[], double **xi, int	Line 2739 void powell(double p[], double **xi, int
strcurr[itmp-1]='\0';	strcurr[itmp-1]='\0';
printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);	printf("\nConsidering the time needed for the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);	fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
for(niterf=10;niterf<=30;niterf+=10){	for(nBigterf=1;nBigterf<=31;nBigterf+=10){
	niterf=nBigterf*ncovmodel;
	/* rforecast_time=rcurr_time+(niterf-iter)(rcurr_time-rlast_time); */
rforecast_time=rcurr_time+(niterf-iter)(rcurr_time-rlast_time);	rforecast_time=rcurr_time+(niterf-iter)(rcurr_time-rlast_time);
forecast_time = *localtime(&rforecast_time);	forecast_time = *localtime(&rforecast_time);
strcpy(strfor,asctime(&forecast_time));	strcpy(strfor,asctime(&forecast_time));
itmp = strlen(strfor);	itmp = strlen(strfor);
if(strfor[itmp-1]=='\n')	if(strfor[itmp-1]=='\n')
strfor[itmp-1]='\0';	strfor[itmp-1]='\0';
printf(" - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);	printf(" - if your program needs %d BIG iterations (%d iterations) to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",nBigterf, niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
fprintf(ficlog," - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);	fprintf(ficlog," - if your program needs %d BIG iterations (%d iterations) to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",nBigterf, niterf, asc_diff_time(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
}	}
}	}
for (i=1;i<=n;i++) { /* For each direction i */	for (i=1;i<=n;i++) { /* For each direction i */
Line 2582 void powell(double p[], double **xi, int	Line 2762 void powell(double p[], double **xi, int
printf("%d",i);fflush(stdout); /* print direction (parameter) i */	printf("%d",i);fflush(stdout); /* print direction (parameter) i */
fprintf(ficlog,"%d",i);fflush(ficlog);	fprintf(ficlog,"%d",i);fflush(ficlog);
#ifdef LINMINORIGINAL	#ifdef LINMINORIGINAL
linmin(p,xit,n,fret,func); /* Point p[n]. xit[n] has been loaded for direction i as input.*/	linmin(p,xit,n,fret,func); /* New point i minimizing in direction i has coordinates p[j].*/
	/* xit[j] gives the n coordinates of direction i as input.*/
	/* fret gives the maximum value on direction xit /
#else	#else
linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/	linmin(p,xit,n,fret,func,&flat); /* Point p[n]. xit[n] has been loaded for direction i as input.*/
flatdir[i]=flat; /* Function is vanishing in that direction i */	flatdir[i]=flat; /* Function is vanishing in that direction i */
Line 2612 void powell(double p[], double **xi, int	Line 2794 void powell(double p[], double **xi, int
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
#endif	#endif
} /* end loop on each direction i */	} /* end loop on each direction i */
/* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */	/* Convergence test will use last linmin estimation (fret) and compare to former iteration (fp) */
/* But p and xit have been updated at the end of linmin, fret corresponds to new p, xit /	/* But p and xit have been updated at the end of linmin, fret corresponds to new p, xit /
/* New value of last point Pn is not computed, P(n-1) */
for(j=1;j<=n;j++) {	for(j=1;j<=n;j++) {
if(flatdir[j] >0){	if(flatdir[j] >0){
printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);	printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
Line 2752 void powell(double p[], double **xi, int	Line 2933 void powell(double p[], double **xi, int
}	}
}	}
#endif	#endif
	#ifdef POWELLORIGINCONJUGATE
for (j=1;j<=n;j++) {	for (j=1;j<=n;j++) {
xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */	xi[j][ibig]=xi[j][n]; /* Replace direction with biggest decrease by last direction n */
xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */	xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
}	}
	#else
	for (j=1;j<=n-1;j++) {
	xi[j][1]=xi[j][j+1]; /* Standard method of conjugate directions */
	xi[j][n]=xit[j]; /* and this nth direction by the by the average p_0 p_n */
	}
	#endif
#ifdef LINMINORIGINAL	#ifdef LINMINORIGINAL
#else	#else
for (j=1, flatd=0;j<=n;j++) {	for (j=1, flatd=0;j<=n;j++) {
Line 2784 void powell(double p[], double **xi, int	Line 2972 void powell(double p[], double **xi, int
#endif	#endif
printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);	printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);	fprintf(ficlog,"Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
	/* The minimization in direction $\xi_1$ gives $P_1$. From $P_1$ minimization in direction $\xi_2$ gives */
	/* $P_2$. Minimization of line $P_2-P_1$ gives new starting point $P^{(1)}_0$ and direction $\xi_1$ is dropped and replaced by second */
	/* direction $\xi_1^{(1)}=\xi_2$. Also second direction is replaced by new direction $\xi^{(1)}_2=P_2-P_0$. */

	/* At the second iteration, starting from $P_0^{(1)}$, minimization amongst $\xi^{(1)}_1$ gives point $P^{(1)}_1$. */
	/* Minimization amongst $\xi^{(1)}_2=(P_2-P_0)$ gives point $P^{(1)}_2$. As $P^{(2)}_1$ and */
	/* $P^{(1)}_0$ are minimizing in the same direction $P^{(1)}_2 - P^{(1)}_1= P_2-P_0$, directions $P^{(1)}_2-P^{(1)}_0$ */
	/* and $P_2-P_0$ (parallel to $\xi$ and $\xi^c$) are conjugate. } */


#ifdef DEBUG	#ifdef DEBUG
printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);	printf("Direction changed last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
Line 2811 void powell(double p[], double **xi, int	Line 3008 void powell(double p[], double **xi, int

double prevalim(double prlim, int nlstate, double x[], double age, double oldm, double savm, double ftolpl, int *ncvyear, int ij, int nres)	double prevalim(double prlim, int nlstate, double x[], double age, double oldm, double savm, double ftolpl, int *ncvyear, int ij, int nres)
{	{
/**< Computes the prevalence limit in each live state at age x and for covariate combination ij	/**< Computes the prevalence limit in each live state at age x and for covariate combination ij . Nicely done
* (and selected quantitative values in nres)	* (and selected quantitative values in nres)
* by left multiplying the unit	* by left multiplying the unit
* matrix by transitions matrix until convergence is reached with precision ftolpl	* matrix by transitions matrix until convergence is reached with precision ftolpl
Line 2870 void powell(double p[], double **xi, int	Line 3067 void powell(double p[], double **xi, int
/* Model(2) V1 + V2 + V3 + V8 + V7V8 + V5V6 + V8age + V3age + ageage /	/* Model(2) V1 + V2 + V3 + V8 + V7V8 + V5V6 + V8age + V3age + ageage /
/* total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and ageage /	/* total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and ageage /
for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */	for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */
if(Typevar[k1]==1){ /* A product with age */	if(Typevar[k1]==1 \|\| Typevar[k1]==3){ /* A product with age */
cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];	cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
}else{	}else{
cov[2+nagesqr+k1]=precov[nres][k1];	cov[2+nagesqr+k1]=precov[nres][k1];
Line 3080 void powell(double p[], double **xi, int	Line 3277 void powell(double p[], double **xi, int
cov[3]= agefin*agefin;;	cov[3]= agefin*agefin;;
}	}
for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */	for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */
if(Typevar[k1]==1){ /* A product with age */	if(Typevar[k1]==1 \|\| Typevar[k1]==3){ /* A product with age */
cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];	cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
}else{	}else{
cov[2+nagesqr+k1]=precov[nres][k1];	cov[2+nagesqr+k1]=precov[nres][k1];
Line 3259 double pmij(double ps, double *cov,	Line 3456 double pmij(double ps, double *cov,
for(i=1; i<= nlstate; i++){	for(i=1; i<= nlstate; i++){
s1=0;	s1=0;
for(j=1; j<i; j++){	for(j=1; j<i; j++){
	/* printf("debug1 %d %d ps=%lf exp(ps)=%lf \n",i,j,ps[i][j],exp(ps[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); */
}	}
for(j=i+1; j<=nlstate+ndeath; j++){	for(j=i+1; j<=nlstate+ndeath; j++){
	/* printf("debug2 %d %d ps=%lf exp(ps)=%lf \n",i,j,ps[i][j],exp(ps[i][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); */
}	}
/* 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.);
Line 3508 double matprod2(double out, double *	Line 3705 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 dummies values in each resultline (loop on ij to find the corresponding combination) to 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 3546 double *hpxij(double *po, int nhstep	Line 3744 double *hpxij(double *po, int nhstep
/* Model(2) V1 + V2 + V3 + V8 + V7V8 + V5V6 + V8age + V3age + ageage /	/* Model(2) V1 + V2 + V3 + V8 + V7V8 + V5V6 + V8age + V3age + ageage /
/* total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and ageage /	/* total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and ageage /
for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */	for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */
if(Typevar[k1]==1){ /* A product with age */	if(Typevar[k1]==1 \|\| Typevar[k1]==3){ /* A product with age */
cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];	cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
}else{	}else{
cov[2+nagesqr+k1]=precov[nres][k1];	cov[2+nagesqr+k1]=precov[nres][k1];
Line 3732 double *hbxij(double *po, int nhstep	Line 3930 double *hbxij(double *po, int nhstep
}	}
/** New code */	/** New code */
for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */	for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */
if(Typevar[k1]==1){ /* A product with age */	if(Typevar[k1]==1 \|\| Typevar[k1]==3){ /* A product with age */
cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];	cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
}else{	}else{
cov[2+nagesqr+k1]=precov[nres][k1];	cov[2+nagesqr+k1]=precov[nres][k1];
Line 3839 double *hbxij(double *po, int nhstep	Line 4037 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;
	int ipos=0,iposold=0,ncovv=0;

	double cotvarv, cotvarvold;
double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];	double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
double **out;	double **out;
double lli; /* Individual log likelihood */	double lli; /* Individual log likelihood */
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 3871 double func( double *x)	Line 4073 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 dummy or quant or prod */
/* # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi */	/* # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi */
/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */	/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
/* TvarF[1]=Tvar[6]=2, TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1 ID of fixed covariates or product V2, V1V2, V1 /	/* TvarF[1]=Tvar[6]=2, TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1 ID of fixed covariates or product V2, V1V2, V1 /
/* 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 3887 double func( double *x)	Line 4089 double func( double *x)
mw[mi][i] is real wave of the mi th effectve wave */	mw[mi][i] is real wave of the mi th effectve wave */
/* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];	/* Then statuses are computed at each begin and end of an effective wave s1=s[ mw[mi][i] ][i];
s2=s[mw[mi+1][i]][i];	s2=s[mw[mi+1][i]][i];
And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i]	And the iv th varying covariate is the cotvar[mw[mi+1][i]][iv][i] because now is moved after nvocol+nqv
But if the variable is not in the model TTvar[iv] is the real variable effective in the model:	But if the variable is not in the model TTvar[iv] is the real variable effective in the model:
meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]	meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
*/	*/
for(mi=1; mi<= wav[i]-1; mi++){	for(mi=1; mi<= wav[i]-1; mi++){ /* Varying with waves */
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*/	/* Wave varying (but not age varying) */
/* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; but where is the crossproduct? */	/* 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]]-ncovcol-nqv][i];	/* /\* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; but where is the crossproduct? \/ /
	/* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i]; */
	/* } */
	for(ncovv=1, iposold=0; ncovv <= ncovvt ; ncovv++){ /* Varying covariates (single and product but no age )*/
	itv=TvarVV[ncovv]; /* TvarVV={3, 1, 3} gives the name of each varying covariate */
	ipos=TvarVVind[ncovv]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate*/
	if(FixedV[itv]!=0){ /* Not a fixed covariate */
	cotvarv=cotvar[mw[mi][i]][TvarVV[ncovv]][i]; /* cotvar[wav][ncovcol+nqv+iv][i] */
	}else{ /* fixed covariate */
	cotvarv=covar[itv][i]; /* Error: TvarFind gives the name, that is the true column of fixed covariates, but Tvar of the model */
	}
	if(ipos!=iposold){ /* Not a product or first of a product */
	cotvarvold=cotvarv;
	}else{ /* A second product */
	cotvarv=cotvarv*cotvarvold;
	}
	iposold=ipos;
	cov[ioffset+ipos]=cotvarv;
}	}
	/* for products of time varying to be done */
for (ii=1;ii<=nlstate+ndeath;ii++)	for (ii=1;ii<=nlstate+ndeath;ii++)
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
oldm[ii][j]=(ii==j ? 1.0 : 0.0);	oldm[ii][j]=(ii==j ? 1.0 : 0.0);
savm[ii][j]=(ii==j ? 1.0 : 0.0);	savm[ii][j]=(ii==j ? 1.0 : 0.0);
}	}

	agebegin=agev[mw[mi][i]][i]; /* Age at beginning of effective wave */
	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;
cov[2]=agexact;	cov[2]=agexact;
if(nagesqr==1)	if(nagesqr==1)
cov[3]= agexactagexact; / Should be changed here */	cov[3]= agexactagexact; / Should be changed here */
for (kk=1; kk<=cptcovage;kk++) {	/* for (kk=1; kk<=cptcovage;kk++) { */
if(!FixedV[Tvar[Tage[kk]]])	/* if(!FixedV[Tvar[Tage[kk]]]) */
cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]agexact; / Tage[kk] gives the data-covariate associated with age */	/* cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]agexact; /\ Tage[kk] gives the data-covariate associated with age \/ /
else	/* else */
cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;	/* cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]][i]agexact; /\ because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) \/ /
	/* } */
	for(ncovva=1, iposold=0; ncovva <= ncovta ; ncovva++){ /* Time varying covariates with age including individual from products, product is computed dynamically */
	itv=TvarAVVA[ncovva]; /* TvarVV={3, 1, 3} gives the name of each varying covariate, exploding product VnVm into Vn and then Vm /
	ipos=TvarAVVAind[ncovva]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate*/
	if(FixedV[itv]!=0){ /* Not a fixed covariate? Could be a fixed covariate of a product with a higher than ncovcol+nqv, itv */
	cotvarv=cotvar[mw[mi][i]][TvarAVVA[ncovva]][i]; /* because cotvar starts now at first ncovcol+nqv+ntv+nqtv (1 to nqtv) */
	}else{ /* fixed covariate */
	cotvarv=covar[itv][i]; /* Error: TvarFind gives the name, that is the true column of fixed covariates, but Tvar of the model */
	}
	if(ipos!=iposold){ /* Not a product or first of a product */
	cotvarvold=cotvarv;
	}else{ /* A second product */
	cotvarv=cotvarv*cotvarvold;
	}
	iposold=ipos;
	cov[ioffset+ipos]=cotvarv*agexact;
	/* For products */
}	}

out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));	1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
savm=oldm;	savm=oldm;
Line 3991 double func( double *x)	Line 4232 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 */
}	}
/lli=(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]);/	/lli=(1.+bbh)log(out[s1][s2])- bbhlog(savm[s1][s2]);/
/if(lli ==000.0)/	/if(lli ==000.0)/
/printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); /	/* printf("num[i], i=%d, bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
ipmx +=1;	ipmx +=1;
sw += weight[i];	sw += weight[i];
ll[s[mw[mi][i]][i]] += 2weight[i]lli;	ll[s[mw[mi][i]][i]] += 2weight[i]lli;
Line 4024 double func( double *x)	Line 4265 double func( double *x)
cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];	cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];
for(mi=1; mi<= wav[i]-1; mi++){	for(mi=1; mi<= wav[i]-1; mi++){
for(k=1; k <= ncovv ; k++){	for(k=1; k <= ncovv ; k++){
cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];	cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; /* because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) */
}	}
for (ii=1;ii<=nlstate+ndeath;ii++)	for (ii=1;ii<=nlstate+ndeath;ii++)
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
Line 4071 double func( double *x)	Line 4312 double func( double *x)
if(nagesqr==1)	if(nagesqr==1)
cov[3]= agexact*agexact;	cov[3]= agexact*agexact;
for (kk=1; kk<=cptcovage;kk++) {	for (kk=1; kk<=cptcovage;kk++) {
cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;	if(!FixedV[Tvar[Tage[kk]]])
	cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]agexact; / Tage[kk] gives the data-covariate associated with age */
	else
	cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]][i]agexact; / because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) */
}	}
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));	1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
Line 4127 double func( double *x)	Line 4371 double func( double *x)
ipmx +=1;	ipmx +=1;
sw += weight[i];	sw += weight[i];
ll[s[mw[mi][i]][i]] += 2weight[i]lli;	ll[s[mw[mi][i]][i]] += 2weight[i]lli;
/* printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */	/* printf("num[i]=%09ld, i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2])); */
} /* end of wave */	} /* end of wave */
} /* end of individual */	} /* end of individual */
}else{ /* ml=5 no inter-extrapolation no jackson =0.8a */	}else{ /* ml=5 no inter-extrapolation no jackson =0.8a */
Line 4146 double func( double *x)	Line 4390 double func( double *x)
if(nagesqr==1)	if(nagesqr==1)
cov[3]= agexact*agexact;	cov[3]= agexact*agexact;
for (kk=1; kk<=cptcovage;kk++) {	for (kk=1; kk<=cptcovage;kk++) {
cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;	if(!FixedV[Tvar[Tage[kk]]])
	cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]agexact; / Tage[kk] gives the data-covariate associated with age */
	else
	cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]][i]agexact; / because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) */
}	}

out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
Line 4175 double func( double *x)	Line 4422 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, kf=0;	int i, ii, j, k, mi, d, kk, kv=0, kf=0;
int ioffset=0;	int ioffset=0;
	int ipos=0,iposold=0,ncovv=0;

	double cotvarv, cotvarvold;
double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];	double l, ll[NLSTATEMAX+1], cov[NCOVMAX+1];
double **out;	double **out;
double lli; /* Individual log likelihood */	double lli; /* Individual log likelihood */
Line 4198 double funcone( double *x)	Line 4448 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 (kf=1; kf<=ncovf;kf++){ /* Simple and product fixed covariates without age* products // Missing values are set to -1 but should be dropped */	for (kf=1; kf<=ncovf;kf++){ /* V2 + V3 + V4 Simple and product fixed covariates without age* products // Missing values are set to -1 but should be dropped */
	/* printf("Debug3 TvarFind[%d]=%d",kf, TvarFind[kf]); */
	/* printf(" Tvar[TvarFind[kf]]=%d", Tvar[TvarFind[kf]]); */
	/* printf(" i=%d covar[Tvar[TvarFind[kf]]][i]=%f\n",i,covar[Tvar[TvarFind[kf]]][i]); */
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[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]; */
Line 4215 double funcone( double *x)	Line 4473 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 in the DATA is the cotvar[mw[mi+1][i]][ncovcol+nqv+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 4224 double funcone( double *x)	Line 4493 double funcone( double *x)


for(mi=1; mi<= wav[i]-1; mi++){ /* Varying with waves */	for(mi=1; mi<= wav[i]-1; mi++){ /* Varying with waves */
/* Wave varying (but not age varying) */	/* Wave varying (but not age varying) // V1+V3+ageV1+ageV3+V1V3 with V4 tv and V5 tvq k= 1 to 5 and extra at V(5+1)=6 for V1V3 */
for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/	/* for(k=1; k <= ncovv ; k++){ /\* Varying covariates (single and product but no age )\/ /
/* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */	/* /\* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; \/ /
cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];	/* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i]; */
}	/* } */
/* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates (single??)\/ /
/* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; /\* Counting the # varying covariate from 1 to ntveff \/ /	/# ID V1 V2 weight birth death 1st s1 V3 V4 V5 2nd s2 /
/* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; */	/* model V1+V3+ageV1+ageV3+V1V3 /
/* k=ioffset-2-nagesqr-cptcovage+itv; /\* position in simple model \/ /	/* Tvar={1, 3, 1, 3, 6}, the 6 comes from the fact that there are already V1, V2, V3, V4, V5 native covariates */
/* cov[ioffset+itv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; */	/* TvarVV[1]=V3 (first time varying in the model equation, TvarVV[2]=V1 (in V1V3) TvarVV[3]=3(V3) /
/* printf(" i=%d,mi=%d,itv=%d,TmodelInvind[itv]=%d,cotvar[mw[mi][i]][TmodelInvind[itv]][i]=%f\n", i, mi, itv, TmodelInvind[itv],cotvar[mw[mi][i]][TmodelInvind[itv]][i]); */	/* We need the position of the time varying or product in the model */
	/* TvarVVind={2,5,5}, for V3 at position 2 and then the product V1V3 is decomposed into V1 and V3 but at same position 5 /
	/* TvarVV gives the variable name */
	/* Other example V1 + V3 + V5 + ageV1 + ageV3 + ageV5 + V1V3 + V3V5 + V1V5
	* k= 1 2 3 4 5 6 7 8 9
	* varying 1 2 3 4 5
	* ncovv 1 2 3 4 5 6 7 8
	* TvarVV[ncovv] V3 5 1 3 3 5 1 5
	* TvarVVind 2 3 7 7 8 8 9 9
	* TvarFind[k] 1 0 0 0 0 0 0 0 0
	*/
	/* Other model ncovcol=5 nqv=0 ntv=3 nqtv=0 nlstate=3
	* V2 V3 V4 are fixed V6 V7 are timevarying so V8 and V5 are not in the model and product column will start at 9 Tvar[(v6*V2)6]=9
	* FixedV[ncovcol+qv+ntv+nqtv] V5
	* 3 V1 V2 V3 V4 V5 V6 V7 V8 V3V2 V7V2 V6V3 V7V3 V6V4 V7V4
	* 0 0 0 0 0 1 1 1 0, 0, 1,1, 1, 0, 1, 0, 1, 0, 1, 0}
	* 3 0 0 0 0 0 1 1 1 0, 1 1 1 1 1}
	* model= V2 + V3 + V4 + V6 + V7 + V6V2 + V7V2 + V6V3 + V7V3 + V6V4 + V7V4
	* +ageV2 +ageV3 +ageV4 +ageV6 + age*V7
	* +ageV6V2 + ageV6V3 +ageV7V3 + ageV6V4 +ageV7V4
	* model2= V2 + V3 + V4 + V6 + V7 + V3V2 + V7V2 + V6V3 + V7V3 + V6V4 + V7V4
	* +ageV2 +ageV3 +ageV4 +ageV6 + age*V7
	* +ageV3V2 + ageV6V3 +ageV7V3 + ageV6V4 +ageV7V4
	* model3= V2 + V3 + V4 + V6 + V7 + ageV3V2 + V7V2 + V6V3 + V7V3 + V6V4 + V7*V4
	* +ageV2 +ageV3 +ageV4 +ageV6 + age*V7
	* +V3V2 + ageV6V3 +ageV7V3 + ageV6V4 +ageV7*V4
	* kmodel 1 2 3 4 5 6 7 8 9 10 11
	* 12 13 14 15 16
	* 17 18 19 20 21
	* Tvar[kmodel] 2 3 4 6 7 9 10 11 12 13 14
	* 2 3 4 6 7
	* 9 11 12 13 14
	* cptcovage=5+5 total of covariates with age
	* Tage[cptcovage] age*V2=12 13 14 15 16
	*1 17 18 19 20 21 gives the position in model of covariates associated with age
	3 Tage[cptcovage] ageV3*V2=6
	3 ageV2=12 13 14 15 16
	3 ageV6*V3=18 19 20 21
	* Tvar[Tage[cptcovage]] Tvar[12]=2 3 4 6 Tvar[16]=7(age*V7)
	* Tvar[17]ageV6V2=9 Tvar[18]ageV6V3=11 ageV7V3=12 ageV6V4=13 Tvar[21]ageV7V4=14
	* 2 Tvar[17]ageV3V2=9 Tvar[18]ageV6V3=11 ageV7V3=12 ageV6V4=13 Tvar[21]ageV7V4=14
	* 3 Tvar[Tage[cptcovage]] Tvar[6]=9 Tvar[12]=2 3 4 6 Tvar[16]=7(age*V7)
	* 3 Tvar[18]ageV6V3=11 ageV7V3=12 ageV6V4=13 Tvar[21]ageV7V4=14
	* 3 Tage[cptcovage] ageV3V2=6 ageV2=12 ageV3 13 14 15 16
	* ageV6V3=18 19 20 21 gives the position in model of covariates associated with age
	* 3 Tvar[17]ageV3V2=9 Tvar[18]ageV6V3=11 ageV7V3=12 ageV6V4=13 Tvar[21]ageV7V4=14
	* Tvar= {2, 3, 4, 6, 7,
	* 9, 10, 11, 12, 13, 14,
	* Tvar[12]=2, 3, 4, 6, 7,
	* Tvar[17]=9, 11, 12, 13, 14}
	* Typevar[1]@21 = {0, 0, 0, 0, 0,
	* 2, 2, 2, 2, 2, 2,
	* 3 3, 2, 2, 2, 2, 2,
	* 1, 1, 1, 1, 1,
	* 3, 3, 3, 3, 3}
	* 3 2, 3, 3, 3, 3}
	* p Tposprod[1]@21 {0, 0, 0, 0, 0, 1, 2, 3, 4, 5, 6, 0, 0, 0, 0, 0, 1, 3, 4, 5, 6} Id of the prod at position k in the model
	* p Tprod[1]@21 {6, 7, 8, 9, 10, 11, 0 <repeats 15 times>}
	* 3 Tposprod[1]@21 {0, 0, 0, 0, 0, 1, 2, 3, 4, 5, 6, 0, 0, 0, 0, 0, 1, 3, 4, 5, 6}
	* 3 Tprod[1]@21 {17, 7, 8, 9, 10, 11, 0 <repeats 15 times>}
	* cptcovprod=11 (6+5)
	* FixedV[Tvar[Tage[cptcovage]]]] FixedV[2]=0 FixedV[3]=0 0 1 (age*V7)Tvar[16]=1 FixedV[absolute] not [kmodel]
	* FixedV[Tvar[17]=FixedV[ageV6V2]=FixedV[9]=1 1 1 1 1
	* 3 FixedV[Tvar[17]=FixedV[ageV3V2]=FixedV[9]=0 [11]=1 1 1 1
	* FixedV[] V1=0 V2=0 V3=0 v4=0 V5=0 V6=1 V7=1 v8=1 OK then model dependent
	* 9=1 [V7*V2]=[10]=1 11=1 12=1 13=1 14=1
	* 3 9=0 [V7*V2]=[10]=1 11=1 12=1 13=1 14=1
	* cptcovdageprod=5 for gnuplot printing
	* cptcovprodvage=6
	* ncova=15 1 2 3 4 5
	* 6 7 8 9 10 11 12 13 14 15
	* TvarA 2 3 4 6 7
	* 6 2 6 7 7 3 6 4 7 4
	* TvaAind 12 12 13 13 14 14 15 15 16 16
	* ncovf 1 2 3
	* V6 V7 V6V2 V7V2 V6V3 V7V3 V6V4 V7V4
	* ncovvt=14 1 2 3 4 5 6 7 8 9 10 11 12 13 14
	* TvarVV[1]@14 = itv {V6=6, 7, V6*V2=6, 2, 7, 2, 6, 3, 7, 3, 6, 4, 7, 4}
	* TvarVVind[1]@14= {4, 5, 6, 6, 7, 7, 8, 8, 9, 9, 10, 10, 11, 11}
	* 3 ncovvt=12 V6 V7 V7V2 V6V3 V7V3 V6V4 V7*V4
	* 3 TvarVV[1]@12 = itv {6, 7, V7*V2=7, 2, 6, 3, 7, 3, 6, 4, 7, 4}
	* 3 1 2 3 4 5 6 7 8 9 10 11 12
	* TvarVVind[1]@12= {V6 is in k=4, 5, 7,(4isV2)=7, 8, 8, 9, 9, 10,10, 11,11}TvarVVind[12]=k=11
	* TvarV 6, 7, 9, 10, 11, 12, 13, 14
	* 3 cptcovprodvage=6
	* 3 ncovta=15 +ageV3V2+ageV2+agev3+ageV4 +ageV6 + ageV7 + ageV6V3 +ageV7V3 + ageV6V4 +ageV7*V4
	* 3 TvarAVVA[1]@15= itva 3 2 2 3 4 6 7 6 3 7 3 6 4 7 4
	* 3 ncovta 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
	*?TvarAVVAind[1]@15= V3 is in k=2 1 1 2 3 4 5 4,2 5,2, 4,3 5 3}TvarVVAind[]
	* TvarAVVAind[1]@15= V3 is in k=6 6 12 13 14 15 16 18 18 19,19, 20,20 21,21}TvarVVAind[]
	* 3 ncovvta=10 +ageV6 + ageV7 + ageV6V3 +ageV7V3 + ageV6V4 +ageV7V4
	* 3 we want to compute =cotvar[mw[mi][i]][TvarVVA[ncovva]][i] at position TvarVVAind[ncovva]
	* 3 TvarVVA[1]@10= itva 6 7 6 3 7 3 6 4 7 4
	* 3 ncovva 1 2 3 4 5 6 7 8 9 10
	* TvarVVAind[1]@10= V6 is in k=4 5 8,8 9, 9, 10,10 11 11}TvarVVAind[]
	* TvarVVAind[1]@10= 15 16 18,18 19,19, 20,20 21 21}TvarVVAind[]
	* TvarVA V3*V2=6 6 , 1, 2, 11, 12, 13, 14
	* TvarFind[1]@14= {1, 2, 3, 0 <repeats 12 times>}
	* Tvar[1]@21= {2, 3, 4, 6, 7, 9, 10, 11, 12, 13, 14,
	* 2, 3, 4, 6, 7,
	* 6, 8, 9, 10, 11}
	* TvarFind[itv] 0 0 0
	* FixedV[itv] 1 1 1 0 1 0 1 0 1 0 0
	*? FixedV[itv] 1 1 1 0 1 0 1 0 1 0 1 0 1 0
	* Tvar[TvarFind[ncovf]]=[1]=2 [2]=3 [4]=4
	* Tvar[TvarFind[itv]] [0]=? ?ncovv 1 à ncovvt]
	* Not a fixed cotvar[mw][itv][i] 6 7 6 2 7, 2, 6, 3, 7, 3, 6, 4, 7, 4}
	* fixed covar[itv] [6] [7] [6][2]
	*/

	for(ncovv=1, iposold=0; ncovv <= ncovvt ; ncovv++){ /* V6 V7 V7V2 V6V3 V7V3 V6V4 V7V4 Time varying covariates (single and extended product but no age) including individual from products, product is computed dynamically /
	itv=TvarVV[ncovv]; /* TvarVV={3, 1, 3} gives the name of each varying covariate, or fixed covariate of a varying product after exploding product VnVm into Vn and then Vm /
	ipos=TvarVVind[ncovv]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate*/
	/* if(TvarFind[itv]==0){ /\* Not a fixed covariate? Could be a fixed covariate of a product with a higher than ncovcol+nqv, itv \/ /
	if(FixedV[itv]!=0){ /* Not a fixed covariate? Could be a fixed covariate of a product with a higher than ncovcol+nqv, itv */
	/* printf("DEBUG ncovv=%d, Varying TvarVV[ncovv]=%d\n",ncovv, TvarVV[ncovv]); */
	cotvarv=cotvar[mw[mi][i]][TvarVV[ncovv]][i]; /* because cotvar starts now at first ncovcol+nqv+ntv+nqtv (1 to nqtv) */
	/* printf("DEBUG Varying cov[ioffset+ipos=%d]=%g \n",ioffset+ipos,cotvarv); */
	}else{ /* fixed covariate */
	/* cotvarv=covar[Tvar[TvarFind[itv]]][i]; /\* Error: TvarFind gives the name, that is the true column of fixed covariates, but Tvar of the model \/ /
	/* printf("DEBUG ncovv=%d, Fixed TvarVV[ncovv]=%d\n",ncovv, TvarVV[ncovv]); */
	cotvarv=covar[itv][i]; /* Good: In V6V3, 3 is fixed at position of the data /
	/* printf("DEBUG Fixed cov[ioffset+ipos=%d]=%g \n",ioffset+ipos,cotvarv); */
	}
	if(ipos!=iposold){ /* Not a product or first of a product */
	cotvarvold=cotvarv;
	}else{ /* A second product */
	cotvarv=cotvarv*cotvarvold;
	}
	iposold=ipos;
	cov[ioffset+ipos]=cotvarv;
	/* printf("DEBUG Product cov[ioffset+ipos=%d] \n",ioffset+ipos); */
	/* For products */
	}
	/* for(itv=1; itv <= ntveff; itv++){ /\* Varying dummy covariates single \/ /
	/* iv=TvarVDind[itv]; /\* iv, position in the model equation of time varying covariate itv \/ /
	/* /\* "V1+V3+ageV1+ageV3+V1V3" with V3 time varying \/ */
	/* /\* 1 2 3 4 5 \/ /
	/* /\itv 1 \/ */
	/* /\* TvarVInd[1]= 2 \/ /
	/* /\* iv= Tvar[Tmodelind[itv]]-ncovcol-nqv; /\\* Counting the # varying covariate from 1 to ntveff \\/ \/ */
	/* /\* iv= Tvar[Tmodelind[ioffset-2-nagesqr-cptcovage+itv]]-ncovcol-nqv; \/ /
	/* /\* cov[ioffset+iv]=cotvar[mw[mi][i]][iv][i]; \/ /
	/* /\* k=ioffset-2-nagesqr-cptcovage+itv; /\\* position in simple model \\/ \/ */
	/* /\* cov[ioffset+iv]=cotvar[mw[mi][i]][TmodelInvind[itv]][i]; \/ /
	/* cov[ioffset+iv]=cotvar[mw[mi][i]][itv][i]; */
	/* /\* printf(" i=%d,mi=%d,itv=%d,TmodelInvind[itv]=%d,cotvar[mw[mi][i]][itv][i]=%f\n", i, mi, itv, TvarVDind[itv],cotvar[mw[mi][i]][itv][i]); \/ /
	/* } */
/* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates \/ /	/* for(iqtv=1; iqtv <= nqtveff; iqtv++){ /\* Varying quantitatives covariates \/ /
/* iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff \/ /	/* iv=TmodelInvQind[iqtv]; /\* Counting the # varying covariate from 1 to ntveff \/ /
/* /\* printf(" i=%d,mi=%d,iqtv=%d,TmodelInvQind[iqtv]=%d,cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]=%f\n", i, mi, iqtv, TmodelInvQind[iqtv],cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]); \/ /	/* /\* printf(" i=%d,mi=%d,iqtv=%d,TmodelInvQind[iqtv]=%d,cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]=%f\n", i, mi, iqtv, TmodelInvQind[iqtv],cotqvar[mw[mi][i]][TmodelInvQind[iqtv]][i]); \/ /
Line 4257 double funcone( double *x)	Line 4673 double funcone( double *x)
cov[2]=agexact;	cov[2]=agexact;
if(nagesqr==1)	if(nagesqr==1)
cov[3]= agexact*agexact;	cov[3]= agexact*agexact;
for (kk=1; kk<=cptcovage;kk++) {	for(ncovva=1, iposold=0; ncovva <= ncovta ; ncovva++){ /* Time varying covariates with age including individual from products, product is computed dynamically */
if(!FixedV[Tvar[Tage[kk]]])	itv=TvarAVVA[ncovva]; /* TvarVV={3, 1, 3} gives the name of each varying covariate, exploding product VnVm into Vn and then Vm /
cov[Tage[kk]+2+nagesqr]=covar[Tvar[Tage[kk]]][i]*agexact;	ipos=TvarAVVAind[ncovva]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate*/
else	/* if(TvarFind[itv]==0){ /\* Not a fixed covariate? Could be a fixed covariate of a product with a higher than ncovcol+nqv, itv \/ /
cov[Tage[kk]+2+nagesqr]=cotvar[mw[mi][i]][Tvar[Tage[kk]]-ncovcol-nqv][i]*agexact;	if(FixedV[itv]!=0){ /* Not a fixed covariate? Could be a fixed covariate of a product with a higher than ncovcol+nqv, itv */
	/* printf("DEBUG ncovva=%d, Varying TvarAVVA[ncovva]=%d\n", ncovva, TvarAVVA[ncovva]); */
	cotvarv=cotvar[mw[mi][i]][TvarAVVA[ncovva]][i]; /* because cotvar starts now at first ncovcol+nqv+ntv+nqtv (1 to nqtv) */
	}else{ /* fixed covariate */
	/* cotvarv=covar[Tvar[TvarFind[itv]]][i]; /\* Error: TvarFind gives the name, that is the true column of fixed covariates, but Tvar of the model \/ /
	/* printf("DEBUG ncovva=%d, Fixed TvarAVVA[ncovva]=%d\n", ncovva, TvarAVVA[ncovva]); */
	cotvarv=covar[itv][i]; /* Error: TvarFind gives the name, that is the true column of fixed covariates, but Tvar of the model */
	}
	if(ipos!=iposold){ /* Not a product or first of a product */
	cotvarvold=cotvarv;
	}else{ /* A second product */
	/* printf("DEBUG * \n"); */
	cotvarv=cotvarv*cotvarvold;
	}
	iposold=ipos;
	/* printf("DEBUG Product cov[ioffset+ipos=%d] \n",ioffset+ipos); */
	cov[ioffset+ipos]=cotvarv*agexact;
	/* For products */
}	}

/* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */	/* printf("i=%d,mi=%d,d=%d,mw[mi][i]=%d\n",i, mi,d,mw[mi][i]); */
/* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */	/* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
Line 4272 double funcone( double *x)	Line 4706 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 4304 double funcone( double *x)	Line 4750 double funcone( double *x)
ipmx +=1;	ipmx +=1;
sw += weight[i];	sw += weight[i];
ll[s[mw[mi][i]][i]] += 2weight[i]lli;	ll[s[mw[mi][i]][i]] += 2weight[i]lli;
/* printf("Funcone i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2])); */	/* Printing covariates values for each contribution for checking */
	/* printf("num[i]=%09ld, i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2])); */
if(globpr){	if(globpr){
fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\	fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
%11.6f %11.6f %11.6f ", \	%11.6f %11.6f %11.6f ", \
num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,	num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
2weight[i]lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2]));	2weight[i]lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2]));
/* printf("%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\ */	/* printf("%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\ */
/* %11.6f %11.6f %11.6f ", \ */	/* %11.6f %11.6f %11.6f ", \ */
/* num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]gipmx/gsw, /	/* num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]gipmx/gsw, /
/* 2weight[i]lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2])); */	/* 2weight[i]lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2])); */
for(k=1,llt=0.,l=0.; k<=nlstate; k++){	for(k=1,llt=0.,l=0.; k<=nlstate; k++){
llt +=ll[k]*gipmx/gsw;	llt +=ll[k]*gipmx/gsw;
fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);	fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
/* printf(" %10.6f",-ll[k]gipmx/gsw); /	/* printf(" %10.6f",-ll[k]gipmx/gsw); /
}	}
fprintf(ficresilk," %10.6f\n", -llt);	fprintf(ficresilk," %10.6f ", -llt);
/* printf(" %10.6f\n", -llt); */	/* printf(" %10.6f\n", -llt); */
}	/* if(debugILK){ /\* debugILK is set by a #d in a comment line \/ /
	/* fprintf(ficresilk,"%09ld ", num[i]); / / not necessary */
	for (kf=1; kf<=ncovf;kf++){ /* Simple and product fixed covariates without age* products // Missing values are set to -1 but should be dropped */
	fprintf(ficresilk," %g",covar[Tvar[TvarFind[kf]]][i]);
	}
	for(ncovv=1, iposold=0; ncovv <= ncovvt ; ncovv++){ /* Varying covariates (single and product but no age) including individual from products */
	ipos=TvarVVind[ncovv]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate*/
	if(ipos!=iposold){ /* Not a product or first of a product */
	fprintf(ficresilk," %g",cov[ioffset+ipos]);
	/* printf(" %g",cov[ioffset+ipos]); */
	}else{
	fprintf(ficresilk,"*");
	/* printf(""); /
	}
	iposold=ipos;
	}
	/* for (kk=1; kk<=cptcovage;kk++) { */
	/* if(!FixedV[Tvar[Tage[kk]]]){ */
	/* fprintf(ficresilk," %gage",covar[Tvar[Tage[kk]]][i]); /
	/* /\* printf(" %gage",covar[Tvar[Tage[kk]]][i]); \/ */
	/* }else{ */
	/* fprintf(ficresilk," %gage",cotvar[mw[mi][i]][Tvar[Tage[kk]]][i]);/\ because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) \/ /
	/* /\* printf(" %gage",cotvar[mw[mi][i]][Tvar[Tage[kk]]][i]);/\\ because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) \\/ \/ */
	/* } */
	/* } */
	for(ncovva=1, iposold=0; ncovva <= ncovta ; ncovva++){ /* Time varying covariates with age including individual from products, product is computed dynamically */
	itv=TvarAVVA[ncovva]; /* TvarVV={3, 1, 3} gives the name of each varying covariate, exploding product VnVm into Vn and then Vm /
	ipos=TvarAVVAind[ncovva]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate*/
	/* if(TvarFind[itv]==0){ /\* Not a fixed covariate? Could be a fixed covariate of a product with a higher than ncovcol+nqv, itv \/ /
	if(FixedV[itv]!=0){ /* Not a fixed covariate? Could be a fixed covariate of a product with a higher than ncovcol+nqv, itv */
	/* printf("DEBUG ncovva=%d, Varying TvarAVVA[ncovva]=%d\n", ncovva, TvarAVVA[ncovva]); */
	cotvarv=cotvar[mw[mi][i]][TvarAVVA[ncovva]][i]; /* because cotvar starts now at first ncovcol+nqv+ntv+nqtv (1 to nqtv) */
	}else{ /* fixed covariate */
	/* cotvarv=covar[Tvar[TvarFind[itv]]][i]; /\* Error: TvarFind gives the name, that is the true column of fixed covariates, but Tvar of the model \/ /
	/* printf("DEBUG ncovva=%d, Fixed TvarAVVA[ncovva]=%d\n", ncovva, TvarAVVA[ncovva]); */
	cotvarv=covar[itv][i]; /* Error: TvarFind gives the name, that is the true column of fixed covariates, but Tvar of the model */
	}
	if(ipos!=iposold){ /* Not a product or first of a product */
	cotvarvold=cotvarv;
	}else{ /* A second product */
	/* printf("DEBUG * \n"); */
	cotvarv=cotvarv*cotvarvold;
	}
	cotvarv=cotvarv*agexact;
	fprintf(ficresilk," %g*age",cotvarv);
	iposold=ipos;
	/* printf("DEBUG Product cov[ioffset+ipos=%d] \n",ioffset+ipos); */
	cov[ioffset+ipos]=cotvarv;
	/* For products */
	}
	/* printf("\n"); */
	/* } /\* End debugILK \/ /
	fprintf(ficresilk,"\n");
	} /* End if globpr */
} /* end of wave */	} /* end of wave */
} /* end of individual */	} /* end of individual */
for(k=1,l=0.; k<=nlstate; k++) l += ll[k];	for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
Line 4331 double funcone( double *x)	Line 4831 double funcone( double *x)
gipmx=ipmx;	gipmx=ipmx;
gsw=sw;	gsw=sw;
}	}
return -l;	return -l;
}	}


Line 4342 void likelione(FILE *ficres,double p[],	Line 4842 void likelione(FILE *ficres,double p[],
the selection of individuals/waves and	the selection of individuals/waves and
to check the exact contribution to the likelihood.	to check the exact contribution to the likelihood.
Plotting could be done.	Plotting could be done.
*/	*/
int k;	void pstamp(FILE *ficres);
	int k, kf, kk, kvar, ncovv, iposold, ipos;

if(globpri !=0){ / Just counts and sums, no printings */	if(globpri !=0){ / Just counts and sums, no printings */
strcpy(fileresilk,"ILK_");	strcpy(fileresilk,"ILK_");
Line 4352 void likelione(FILE *ficres,double p[],	Line 4853 void likelione(FILE *ficres,double p[],
printf("Problem with resultfile: %s\n", fileresilk);	printf("Problem with resultfile: %s\n", fileresilk);
fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);	fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
}	}
	pstamp(ficresilk);fprintf(ficresilk,"# model=1+age+%s\n",model);
fprintf(ficresilk, "#individual(line's_record) count ageb ageend s1 s2 wave# effective_wave# number_of_matrices_product pij weight weight/gpw -2ln(pij)weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2llweightXnumber_of_contribs/sum_of_weights) and_total\n");	fprintf(ficresilk, "#individual(line's_record) count ageb ageend s1 s2 wave# effective_wave# number_of_matrices_product pij weight weight/gpw -2ln(pij)weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2llweightXnumber_of_contribs/sum_of_weights) and_total\n");
fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");	fprintf(ficresilk, "#num_i ageb agend i s1 s2 mi mw dh likeli weight %%weight 2wlli out sav ");
/* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2weight[i]lli,out[s1][s2],savm[s1][s2]); */	/* i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2weight[i]lli,out[s1][s2],savm[s1][s2]); */
for(k=1; k<=nlstate; k++)	for(k=1; k<=nlstate; k++)
fprintf(ficresilk," -2gipw/gswweight*ll[%d]++",k);	fprintf(ficresilk," -2gipw/gswweight*ll[%d]++",k);
fprintf(ficresilk," -2gipw/gswweight*ll(total)\n");	fprintf(ficresilk," -2gipw/gswweight*ll(total) ");
}
	/* if(debugILK){ /\* debugILK is set by a #d in a comment line \/ /
	for(kf=1;kf <= ncovf; kf++){
	fprintf(ficresilk,"V%d",Tvar[TvarFind[kf]]);
	/* printf("V%d",Tvar[TvarFind[kf]]); */
	}
	for(ncovv=1, iposold=0; ncovv <= ncovvt ; ncovv++){
	ipos=TvarVVind[ncovv]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate */
	if(ipos!=iposold){ /* Not a product or first of a product */
	/* printf(" %d",ipos); */
	fprintf(ficresilk," V%d",TvarVV[ncovv]);
	}else{
	/* printf(""); /
	fprintf(ficresilk,"*");
	}
	iposold=ipos;
	}
	for (kk=1; kk<=cptcovage;kk++) {
	if(!FixedV[Tvar[Tage[kk]]]){
	/* printf(" %dage(Fixed)",Tvar[Tage[kk]]); /
	fprintf(ficresilk," %d*age(Fixed)",Tvar[Tage[kk]]);
	}else{
	fprintf(ficresilk," %dage(Varying)",Tvar[Tage[kk]]);/ because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) */
	/* printf(" %dage(Varying)",Tvar[Tage[kk]]);/\ because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) \/ /
	}
	}
	/* } /\* End if debugILK \/ /
	/* printf("\n"); */
	fprintf(ficresilk,"\n");
	} /* End glogpri */

fretone=(func)(p);	fretone=(func)(p);
if(*globpri !=0){	if(*globpri !=0){
Line 4370 void likelione(FILE *ficres,double p[],	Line 4901 void likelione(FILE *ficres,double p[],
fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));	fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
fprintf(fichtm,"\n<br>Equation of the model: <b>model=1+age+%s</b><br>\n",model);	fprintf(fichtm,"\n<br>Equation of the model: <b>model=1+age+%s</b><br>\n",model);

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

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

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

Line 4393 void mlikeli(FILE *ficres,double p[], in	Line 4977 void mlikeli(FILE *ficres,double p[], in
double fret;	double fret;
double fretone; /* Only one call to likelihood */	double fretone; /* Only one call to likelihood */
/* char filerespow[FILENAMELENGTH];*/	/* char filerespow[FILENAMELENGTH];*/

	double * p1; /* Shifted parameters from 0 instead of 1 */
#ifdef NLOPT	#ifdef NLOPT
int creturn;	int creturn;
nlopt_opt opt;	nlopt_opt opt;
/* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds \/ /	/* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds \/ /
double *lb;	double *lb;
double minf; /* the minimum objective value, upon return */	double minf; /* the minimum objective value, upon return */
double * p1; /* Shifted parameters from 0 instead of 1 */
myfunc_data dinst, *d = &dinst;	myfunc_data dinst, *d = &dinst;
#endif	#endif


xi=matrix(1,npar,1,npar);	xi=matrix(1,npar,1,npar);
for (i=1;i<=npar;i++)	for (i=1;i<=npar;i++) /* Starting with canonical directions j=1,n xi[i=1,n][j] */
for (j=1;j<=npar;j++)	for (j=1;j<=npar;j++)
xi[i][j]=(i==j ? 1.0 : 0.0);	xi[i][j]=(i==j ? 1.0 : 0.0);
printf("Powell\n"); fprintf(ficlog,"Powell\n");	printf("Powell\n"); fprintf(ficlog,"Powell\n");
Line 4735 double hessij( double x[], double **hess	Line 5320 double hessij( double x[], double **hess
kmax=kmax+10;	kmax=kmax+10;
}	}
if(kmax >=10 \|\| firstime ==1){	if(kmax >=10 \|\| firstime ==1){
	/* What are the thetai and thetaj? thetai/ncovmodel thetai=(thetai-thetai%ncovmodel)/ncovmodel +thetai%ncovmodel=(line,pos) */
printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol);	printf("Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol);
fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol);	fprintf(ficlog,"Warning: directions %d-%d, you are not estimating the Hessian at the exact maximum likelihood; you could increase ftol=%.2e\n",thetai,thetaj, ftol);
printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e deltik=%.12e deltjk=%.12e, xi-dek=%.12e xj-dek=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);	printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e deltik=%.12e deltjk=%.12e, xi-dek=%.12e xj-dek=%.12e res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
Line 5080 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5666 Title=%s <br>Datafile=%s Firstpass=%d La
/* }else / / TODO TODO codtabm(j1,z1) or codtabm(j1,Tvaraff[z1]]z1)*/	/* }else / / TODO TODO codtabm(j1,z1) or codtabm(j1,Tvaraff[z1]]z1)*/
/* 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( 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)	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);	printf("Error Tvaraff[z1]=%d<1 or >=%d, cptcoveff=%d model=1+age+%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 */	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 */
Line 5101 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5687 Title=%s <br>Datafile=%s Firstpass=%d La
if(anyvaryingduminmodel==1){ /* Some are varying covariates */	if(anyvaryingduminmodel==1){ /* Some are varying covariates */
for (z1=1; z1<=cptcoveff; z1++) {	for (z1=1; z1<=cptcoveff; z1++) {
if( Fixed[Tmodelind[z1]]==1){	if( Fixed[Tmodelind[z1]]==1){
iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;	/* iv= Tvar[Tmodelind[z1]]-ncovcol-nqv; /\* Good \/ /
	iv= Tvar[Tmodelind[z1]]; /* Good // because cotvar starts now at first at ncovcol+nqv+ntv */
if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) /* iv=1 to ntv, right modality. If covariate's	if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) /* iv=1 to ntv, right modality. If covariate's
value is -1, we don't select. It differs from the	value is -1, we don't select. It differs from the
constant and age model which counts them. */	constant and age model which counts them. */
Line 5182 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5769 Title=%s <br>Datafile=%s Firstpass=%d La
fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");	fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");	fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
fprintf(ficlog, "\n#********** Variable ");	fprintf(ficlog, "\n#********** Variable ");
for (z1=1; z1<=cptcovs; z1++){	for (z1=1; z1<=cptcoveff; z1++){
if(!FixedV[Tvaraff[z1]]){	if(!FixedV[Tvaraff[z1]]){
printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);	printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);	fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
Line 5390 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5977 Title=%s <br>Datafile=%s Firstpass=%d La
printf("# This combination (%d) is not valid and no result will be produced\n",j1);	printf("# This combination (%d) is not valid and no result will be produced\n",j1);
invalidvarcomb[j1]=1;	invalidvarcomb[j1]=1;
}else{	}else{
fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced.</p>",j1);	fprintf(ficresphtm,"\n <p> This combination (%d) is valid and result will be produced (or no resultline).</p>",j1);
invalidvarcomb[j1]=0;	invalidvarcomb[j1]=0;
}	}
fprintf(ficresphtmfr,"</table>\n");	fprintf(ficresphtmfr,"</table>\n");
Line 5638 void prevalence(double ***probs, double	Line 6225 void prevalence(double ***probs, double
/* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */	/* Tvar[Tmodelind[z1]] is the n of Vn; n-ncovcol-nqv is the first time varying covariate or iv */
for (z1=1; z1<=cptcoveff; z1++){	for (z1=1; z1<=cptcoveff; z1++){
if( Fixed[Tmodelind[z1]]==1){	if( Fixed[Tmodelind[z1]]==1){
iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;	iv= Tvar[Tmodelind[z1]];/* because cotvar starts now at first ncovcol+nqv+ (1 to nqtv) */
if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) /* iv=1 to ntv, right modality */	if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) /* iv=1 to ntv, right modality */
bool=0;	bool=0;
}else if( Fixed[Tmodelind[z1]]== 0) /* fixed */	}else if( Fixed[Tmodelind[z1]]== 0) /* fixed */
Line 5947 void concatwav(int wav[], int **dh, int	Line 6534 void concatwav(int wav[], int **dh, int
/* Loop on covariates without age and products and no quantitative variable */	/* Loop on covariates without age and products and no quantitative variable */
for (k=1; k<=cptcovt; k++) { /* cptcovt: total number of covariates of the model (2) nbocc(+)+1 = 8 excepting constant and age and ageage /	for (k=1; k<=cptcovt; k++) { /* cptcovt: total number of covariates of the model (2) nbocc(+)+1 = 8 excepting constant and age and ageage /
for (j=-1; (j < maxncov); j++) Ndum[j]=0;	for (j=-1; (j < maxncov); j++) Ndum[j]=0;
if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */	/* printf("Testing k=%d, cptcovt=%d\n",k, cptcovt); */
	if(Dummy[k]==0 && Typevar[k] !=1 && Typevar[k] != 3 && Typevar[k] != 2){ /* Dummy covariate and not age product nor fixed product */
switch(Fixed[k]) {	switch(Fixed[k]) {
case 0: /* Testing on fixed dummy covariate, simple or product of fixed */	case 0: /* Testing on fixed dummy covariate, simple or product of fixed */
modmaxcovj=0;	modmaxcovj=0;
modmincovj=0;	modmincovj=0;
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*/
	/* printf("Waiting for error tricode Tvar[%d]=%d i=%d (int)(covar[Tvar[k]][i]=%d\n",k,Tvar[k], i, (int)(covar[Tvar[k]][i])); */
ij=(int)(covar[Tvar[k]][i]);	ij=(int)(covar[Tvar[k]][i]);
/* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i	/* ij=0 or 1 or -1. Value of the covariate Tvar[j] for individual i
* If product of VnVm, still boolean :	* If product of VnVm, still boolean :
Line 6043 void concatwav(int wav[], int **dh, int	Line 6632 void concatwav(int wav[], int **dh, int
break;	break;
} /* end switch */	} /* end switch */
} /* end dummy test */	} /* end dummy test */
if(Dummy[k]==1 && Typevar[k] !=1){ /* Quantitative covariate and not age product */	if(Dummy[k]==1 && Typevar[k] !=1 && Typevar[k] !=3 && Fixed ==0){ /* Fixed Quantitative covariate and not age product */
for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the modality of this covariate Vj*/	for (i=1; i<=imx; i++) { /* Loop on individuals: reads the data file to get the maximum value of the modality of this covariate Vj*/
if(Tvar[k]<=0 \|\| Tvar[k]>=NCOVMAX){	if(Tvar[k]<=0 \|\| Tvar[k]>=NCOVMAX){
printf("Error k=%d \n",k);	printf("Error k=%d \n",k);
Line 6234 void concatwav(int wav[], int **dh, int	Line 6823 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 6502 void concatwav(int wav[], int **dh, int	Line 7092 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 / / To be done*/
fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[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]]); */
	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,TnsdVar[Tvaraff[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 7062 void varprob(char optionfilefiname[], do	Line 7658 void varprob(char optionfilefiname[], do
double ***varpij;	double ***varpij;

strcpy(fileresprob,"PROB_");	strcpy(fileresprob,"PROB_");
strcat(fileresprob,fileres);	strcat(fileresprob,fileresu);
if((ficresprob=fopen(fileresprob,"w"))==NULL) {	if((ficresprob=fopen(fileresprob,"w"))==NULL) {
printf("Problem with resultfile: %s\n", fileresprob);	printf("Problem with resultfile: %s\n", fileresprob);
fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);	fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
Line 7137 To be simple, these graphs help to under	Line 7733 To be simple, these graphs help to under

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

Line 7153 To be simple, these graphs help to under	Line 7749 To be simple, these graphs help to under

/* Including quantitative variables of the resultline to be done */	/* Including quantitative variables of the resultline to be done */
for (z1=1; z1<=cptcovs; z1++){ /* Loop on each variable of this resultline */	for (z1=1; z1<=cptcovs; z1++){ /* Loop on each variable of this resultline */
printf("Varprob modelresult[%d][%d]=%d model=%s \n",nres, z1, modelresult[nres][z1], model);	/* printf("Varprob modelresult[%d][%d]=%d model=1+age+%s \n",nres, z1, modelresult[nres][z1], model); */
fprintf(ficlog,"Varprob modelresult[%d][%d]=%d model=%s \n",nres, z1, modelresult[nres][z1], model);	fprintf(ficlog,"Varprob modelresult[%d][%d]=%d model=1+age+%s \n",nres, z1, modelresult[nres][z1], model);
/* fprintf(ficlog,"Varprob modelresult[%d][%d]=%d model=%s resultline[%d]=%s \n",nres, z1, modelresult[nres][z1], model, nres, resultline[nres]); */	/* fprintf(ficlog,"Varprob modelresult[%d][%d]=%d model=1+age+%s resultline[%d]=%s \n",nres, z1, modelresult[nres][z1], model, nres, resultline[nres]); */
if(Dummy[modelresult[nres][z1]]==0){/* Dummy variable of the variable in position modelresult in the model corresponding to z1 in resultline */	if(Dummy[modelresult[nres][z1]]==0){/* Dummy variable of the variable in position modelresult in the model corresponding to z1 in resultline */
if(Fixed[modelresult[nres][z1]]==0){ /* Fixed referenced to model equation */	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(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 */
Line 7177 To be simple, these graphs help to under	Line 7773 To be simple, these graphs help to under
}	}
}else if(Dummy[modelresult[nres][z1]]==1){ /* Quanti variable */	}else if(Dummy[modelresult[nres][z1]]==1){ /* Quanti variable */
/* For each selected (single) quantitative value */	/* For each selected (single) quantitative value */
fprintf(ficresprob," V%d=%f ",Tvqresult[nres][z1],Tqresult[nres][z1]);	fprintf(ficresprob," V%d=%lg ",Tvqresult[nres][z1],Tqresult[nres][z1]);
if(Fixed[modelresult[nres][z1]]==0){ /* Fixed */	if(Fixed[modelresult[nres][z1]]==0){ /* Fixed */
fprintf(ficresprob,"fixed ");	fprintf(ficresprob,"fixed ");
fprintf(ficresprobcov,"fixed ");	fprintf(ficresprobcov,"fixed ");
Line 7219 To be simple, these graphs help to under	Line 7815 To be simple, these graphs help to under
cov[3]= age*age;	cov[3]= age*age;
/* New code end of combination but for each resultline */	/* New code end of combination but for each resultline */
for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */	for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */
if(Typevar[k1]==1){ /* A product with age */	if(Typevar[k1]==1 \|\| Typevar[k1] ==3){ /* A product with age */
cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];	cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
}else{	}else{
cov[2+nagesqr+k1]=precov[nres][k1];	cov[2+nagesqr+k1]=precov[nres][k1];
Line 7524 void printinghtml(char fileresu[], char	Line 8120 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;	if(TKresult[nres]==0)k1=1; /* To be checked for no result */
	/* 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 7558 void printinghtml(char fileresu[], char	Line 8164 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;	if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
	/* 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=1+age+%s) ************\n<hr size=\"2\" color=\"#EC5E5E\">",model);
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);	fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
printf("\nCombination (%d) ignored because no cases \n",k1);	printf("\nCombination (%d) ignored because no cases \n",k1);
Line 7624 divided by h: <sub>h</sub>P<sub>ij</sub>	Line 8228 divided by h: <sub>h</sub>P<sub>ij</sub>
/* 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>", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);	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);
fprintf(fichtm," (data from text file <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"P_"),subdirf2(optionfilefiname,"P_"));	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,"P_"),cpt,k1,nres);	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 */
for(cpt=1; cpt<=nlstate;cpt++){	for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"<br>\n- Convergence to mixed (stable) back prevalence in state %d. Or probability for a person to be in state %d at a younger age, knowing that she/he was in state (1 to %d) at different older ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \	fprintf(fichtm,"<br>\n- Convergence to mixed (stable) back prevalence in state %d. Or probability for a person to be in state %d at a younger age, knowing that she/he was in state (1 to %d) at different older ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br>", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
<img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);	fprintf(fichtm," (data from text file <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"PIJB_"),subdirf2(optionfilefiname,"PIJB_"));
	fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">" ,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
}	}
}	}
if(prevfcast==1){	if(prevfcast==1){
Line 7661 with weights corresponding to observed p	Line 8266 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 7708 See page 'Matrix of variance-covariance	Line 8313 See page 'Matrix of variance-covariance
/* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */	/* - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
/* <br>",fileres,fileres,fileres,fileres); */	/* <br>",fileres,fileres,fileres,fileres); */
/* else */	/* else */
/* fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */	/* fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=1+age+%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
fflush(fichtm);	fflush(fichtm);

m=pow(2,cptcoveff);	m=pow(2,cptcoveff);
Line 7719 See page 'Matrix of variance-covariance	Line 8324 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 7748 See page 'Matrix of variance-covariance	Line 8349 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;	if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
	/* 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=1+age+%s) ************\n<hr size=\"2\" color=\"#EC5E5E\">",model);

if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);	fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
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 7800 true period expectancies (those weighted	Line 8398 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 7809 true period expectancies (those weighted	Line 8406 true period expectancies (those weighted
/***************** Gnuplot file ************/	/***************** Gnuplot file ************/
void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double bage, double fage , int prevfcast, int prevbcast, char pathc[], double p[], int offyear, int offbyear){	void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double bage, double fage , int prevfcast, int prevbcast, char pathc[], double p[], int offyear, int offbyear){

char dirfileres[132],optfileres[132];	char dirfileres[256],optfileres[256];
char gplotcondition[132], gplotlabel[132];	char gplotcondition[256], gplotlabel[256];
int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,k4=0,ij=0, ijp=0, l=0;	int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,k4=0,kf=0,kvar=0,kk=0,ipos=0,iposold=0,ij=0, ijp=0, l=0;
int lv=0, vlv=0, kl=0;	int lv=0, vlv=0, kl=0;
int ng=0;	int ng=0;
int vpopbased;	int vpopbased;
Line 7837 void printinggnuplot(char fileresu[], ch	Line 8434 void printinggnuplot(char fileresu[], ch
fprintf(ficgp,"yoff=(%d > 2? 0:1);\n",nlstate);	fprintf(ficgp,"yoff=(%d > 2? 0:1);\n",nlstate);
fprintf(ficgp,"\n#Peripheral arrows\nset for [i=1:%d] for [j=1:%d] arrow i10+j from cos(pi((1-(%d/2)2./%d)/2+(i-1)2./%d))-(i!=j?(i-j)/abs(i-j)delta:0), yoff +sin(pi((1-(%d/2)2./%d)/2+(i-1)2./%d)) + (i!=j?(i-j)/abs(i-j)delta:0) rto -0.95(cos(pi((1-(%d/2)2./%d)/2+(i-1)2./%d))+(i!=j?(i-j)/abs(i-j)delta:0) - cos(pi((1-(%d/2)2./%d)/2+(j-1)2./%d)) + (i!=j?(i-j)/abs(i-j)delta2:0)), -0.95(sin(pi((1-(%d/2)2./%d)/2+(i-1)2./%d)) + (i!=j?(i-j)/abs(i-j)delta:0) - sin(pi((1-(%d/2)2./%d)/2+(j-1)2./%d))+( i!=j?(i-j)/abs(i-j)*delta2:0)) ls (i < j? 1:2)\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);	fprintf(ficgp,"\n#Peripheral arrows\nset for [i=1:%d] for [j=1:%d] arrow i10+j from cos(pi((1-(%d/2)2./%d)/2+(i-1)2./%d))-(i!=j?(i-j)/abs(i-j)delta:0), yoff +sin(pi((1-(%d/2)2./%d)/2+(i-1)2./%d)) + (i!=j?(i-j)/abs(i-j)delta:0) rto -0.95(cos(pi((1-(%d/2)2./%d)/2+(i-1)2./%d))+(i!=j?(i-j)/abs(i-j)delta:0) - cos(pi((1-(%d/2)2./%d)/2+(j-1)2./%d)) + (i!=j?(i-j)/abs(i-j)delta2:0)), -0.95(sin(pi((1-(%d/2)2./%d)/2+(i-1)2./%d)) + (i!=j?(i-j)/abs(i-j)delta:0) - sin(pi((1-(%d/2)2./%d)/2+(j-1)2./%d))+( i!=j?(i-j)/abs(i-j)*delta2:0)) ls (i < j? 1:2)\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);

fprintf(ficgp,"\n#Centripete arrows (turning in other direction (1-i) instead of (i-1)) \nset for [i=1:%d] arrow (%d+1)10+i from cos(pi((1-(%d/2)2./%d)/2+(1-i)2./%d))-(i!=j?(i-j)/abs(i-j)delta:0), yoff +sin(pi((1-(%d/2)2./%d)/2+(1-i)2./%d)) + (i!=j?(i-j)/abs(i-j)delta:0) rto -0.80(cos(pi((1-(%d/2)2./%d)/2+(1-i)2./%d))+(i!=j?(i-j)/abs(i-j)delta:0) ), -0.80(sin(pi((1-(%d/2)2./%d)/2+(1-i)2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) + yoff ) ls 4\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);	fprintf(ficgp,"\n#Centripete arrows (turning in other direction (1-i) instead of (i-1)) \nset for [i=1:%d] for [j=1:%d] arrow (%d+1)10+i from cos(pi((1-(%d/2)2./%d)/2+(1-i)2./%d))-(i!=j?(i-j)/abs(i-j)delta:0), yoff +sin(pi((1-(%d/2)2./%d)/2+(1-i)2./%d)) + (i!=j?(i-j)/abs(i-j)delta:0) rto -0.80(cos(pi((1-(%d/2)2./%d)/2+(1-i)2./%d))+(i!=j?(i-j)/abs(i-j)delta:0) ), -0.80(sin(pi((1-(%d/2)2./%d)/2+(1-i)2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) + yoff ) ls 4\n",nlstate, nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
fprintf(ficgp,"\n#show arrow\nunset label\n");	fprintf(ficgp,"\n#show arrow\nunset label\n");
fprintf(ficgp,"\n#States labels, starting from 2 (2-i) instead of (1-i), was (i-1)\nset for [i=1:%d] label i sprintf(\"State %%d\",i) center at cos(pi((1-(%d/2)2./%d)/2+(2-i)2./%d)), yoff+sin(pi((1-(%d/2)2./%d)/2+(2-i)2./%d)) font \"helvetica, 16\" tc rgbcolor \"blue\"\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);	fprintf(ficgp,"\n#States labels, starting from 2 (2-i) instead of (1-i), was (i-1)\nset for [i=1:%d] label i sprintf(\"State %%d\",i) center at cos(pi((1-(%d/2)2./%d)/2+(2-i)2./%d)), yoff+sin(pi((1-(%d/2)2./%d)/2+(2-i)2./%d)) font \"helvetica, 16\" tc rgbcolor \"blue\"\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
fprintf(ficgp,"\nset label %d+1 sprintf(\"State %%d\",%d+1) center at 0.,0. font \"helvetica, 16\" tc rgbcolor \"red\"\n",nlstate,nlstate);	fprintf(ficgp,"\nset label %d+1 sprintf(\"State %%d\",%d+1) center at 0.,0. font \"helvetica, 16\" tc rgbcolor \"red\"\n",nlstate,nlstate);
Line 7874 void printinggnuplot(char fileresu[], ch	Line 8471 void printinggnuplot(char fileresu[], ch
fprintf(ficgp,"\nset out;unset log\n");	fprintf(ficgp,"\nset out;unset log\n");
/* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */	/* fprintf(ficgp,"\nset out \"%s.svg\"; replot; set out; # bug gnuplot",subdirf2(optionfilefiname,"ILK_")); */

	/* Plot the probability implied in the likelihood by covariate value */
	fprintf(ficgp,"\nset ter pngcairo size 640, 480");
	/* if(debugILK==1){ */
	for(kf=1; kf <= ncovf; kf++){ /* For each simple dummy covariate of the model */
	kvar=Tvar[TvarFind[kf]]; /* variable name */
	/* k=18+Tvar[TvarFind[kf]];/\offset because there are 18 columns in the ILK_ file but could be placed else where \/ */
	/* k=18+kf;/\offset because there are 18 columns in the ILK_ file \/ */
	/* k=19+kf;/\offset because there are 19 columns in the ILK_ file \/ */
	k=16+nlstate+kf;/offset because there are 19 columns in the ILK_ file, first cov Vn on col 21 with 4 living states /
	for (i=1; i<= nlstate ; i ++) {
	fprintf(ficgp,"\nset out \"%s-p%dj-%d.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i,kvar);
	fprintf(ficgp,"unset log;\n# For each simple dummy covariate of the model \n plot \"%s\"",subdirf(fileresilk));
	if(gnuplotversion >=5.2){ /* Former gnuplot versions do not have variable pointsize!! */
	fprintf(ficgp," u 2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? 7 : 9):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt variable ps 0.4 lc variable \\\n",i,1,k,k,i,1,kvar);
	for (j=2; j<= nlstate+ndeath ; j ++) {
	fprintf(ficgp,",\\\n \"\" u 2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? 7 : 9):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt variable ps 0.4 lc variable ",i,j,k,k,i,j,kvar);
	}
	}else{
	fprintf(ficgp," u 2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt 7 ps 0.4 lc variable \\\n",i,1,k,i,1,kvar);
	for (j=2; j<= nlstate+ndeath ; j ++) {
	fprintf(ficgp,",\\\n \"\" u 2:($5 == %d && $6==%d ? $10 : 1/0):($%d==0 ? $6 : $6+4) t \"p%d%d V%d\" with points pt 7 ps 0.4 lc variable ",i,j,k,i,j,kvar);
	}
	}
	fprintf(ficgp,";\nset out; unset ylabel;\n");
	}
	} /* End of each covariate dummy */
	for(ncovv=1, iposold=0, kk=0; ncovv <= ncovvt ; ncovv++){
	/* Other example V1 + V3 + V5 + ageV1 + ageV3 + ageV5 + V1V3 + V3V5 + V1V5
	* kmodel = 1 2 3 4 5 6 7 8 9
	* varying 1 2 3 4 5
	* ncovv 1 2 3 4 5 6 7 8
	* TvarVV[ncovv] V3 5 1 3 3 5 1 5
	* TvarVVind[ncovv]=kmodel 2 3 7 7 8 8 9 9
	* TvarFind[kmodel] 1 0 0 0 0 0 0 0 0
	* kdata ncovcol=[V1 V2] nqv=0 ntv=[V3 V4] nqtv=V5
	* Dummy[kmodel] 0 0 1 2 2 3 1 1 1
	*/
	ipos=TvarVVind[ncovv]; /* TvarVVind={2, 5, 5] gives the position in the model of the ncovv th varying covariate */
	kvar=TvarVV[ncovv]; /* TvarVV={3, 1, 3} gives the name of each varying covariate */
	/* printf("DebugILK ficgp ncovv=%d, kvar=TvarVV[ncovv]=%d, ipos=TvarVVind[ncovv]=%d, Dummy[ipos]=%d, Typevar[ipos]=%d\n", ncovv,kvar,ipos,Dummy[ipos],Typevar[ipos]); */
	if(ipos!=iposold){ /* Not a product or first of a product */
	/* printf(" %d",ipos); */
	/* fprintf(ficresilk," V%d",TvarVV[ncovv]); */
	/* printf(" DebugILK ficgp suite ipos=%d != iposold=%d\n", ipos, iposold); */
	kk++; /* Position of the ncovv column in ILK_ */
	k=18+ncovf+kk; /offset because there are 18 columns in the ILK_ file plus ncovf fixed covariate /
	if(Dummy[ipos]==0 && Typevar[ipos]==0){ /* Only if dummy time varying: Dummy(0, 1=quant singor prod without age,2 dummyage, 3quantage) Typevar (0 single, 1=age,2=Vnvm) */
	for (i=1; i<= nlstate ; i ++) {
	fprintf(ficgp,"\nset out \"%s-p%dj-%d.png\";set ylabel \"Probability for each individual/wave\";",subdirf2(optionfilefiname,"ILK_"),i,kvar);
	fprintf(ficgp,"unset log;\n# For each simple dummy covariate of the model \n plot \"%s\"",subdirf(fileresilk));

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



strcpy(dirfileres,optionfilefiname);	strcpy(dirfileres,optionfilefiname);
strcpy(optfileres,"vpl");	strcpy(optfileres,"vpl");
/* 1eme*/	/* 1eme*/
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];
	if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
/* 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]]);
lv=codtabm(k1,TnsdVar[Tvaraff[k]]);	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][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 */	/* for (k=1; k<=cptcoveff; k++){ /\* For each covariate k get corresponding value lv for combination k1 \/ /
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the value of the covariate corresponding to k1 combination \\/ \/ */
vlv= nbcode[Tvaraff[k]][lv]; /* vlv is the value of the covariate lv, 0 or 1 */	/* lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
/* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv */	/* /\* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 \/ /
/* printf(" V%d=%d ",Tvaraff[k],vlv); */	/* /\* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 \/ /
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	/* /\* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 \/ /
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);	/* vlv= nbcode[Tvaraff[k]][lv]; /\* vlv is the value of the covariate lv, 0 or 1 \/ /
}	/* /\* For each combination of covariate k1 (V1=1, V3=0), we printed the current covariate k and its value vlv \/ /
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	/* /\* printf(" V%d=%d ",Tvaraff[k],vlv); \/ /
/* 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 (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 7916 void printinggnuplot(char fileresu[], ch	Line 8602 void printinggnuplot(char fileresu[], ch
fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);	fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
/* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */	/* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
fprintf(ficgp,"set title \"Alive state %d %s model=%s\" font \"Helvetica,12\"\n",cpt,gplotlabel,model);	fprintf(ficgp,"set title \"Alive state %d %s model=1+age+%s\" font \"Helvetica,12\"\n",cpt,gplotlabel,model);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
/* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */	/* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */
/* k1-1 error should be nres-1*/	/* k1-1 error should be nres-1*/
Line 8015 void printinggnuplot(char fileresu[], ch	Line 8701 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(TKresult[nres]==0) k1=1; /* To be checked for noresult */
	/* 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]]);
lv=codtabm(k1,TnsdVar[Tvaraff[k]]);	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* for (k=1; k<=cptcoveff; k++){ /\* For each covariate and each value \/ /
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination \\/ \/ */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
/* vlv= nbcode[Tvaraff[k]][lv]; */	/* /\* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 \/ /
vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];	/* /\* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 \/ /
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	/* /\* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 \/ /
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);	/* /\* vlv= nbcode[Tvaraff[k]][lv]; \/ /
}	/* vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
/* for(k=1; k <= ncovds; k++){ */	/* fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	/* sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	/* } */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	/* /\* for(k=1; k <= ncovds; k++){ \/ /
sprintf(gplotlabel+strlen(gplotlabel)," 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(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 8083 void printinggnuplot(char fileresu[], ch	Line 8774 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(TKresult[nres]==0) k1=1; /* To be checked for noresult */
	/* if(m != 1 && TKresult[nres]!= k1) */
	/* continue; */

for (cpt=1; cpt<= nlstate ; cpt ++) { /* Fragile no verification of covariate values */	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]]);
lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /* Should be the covariate value corresponding to combination k1 and covariate k */	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* for (k=1; k<=cptcoveff; k++){ /\* For each covariate and each value \/ /
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination \\/ \/ */
/* 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]; */	/* /\* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 \/ /
vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];	/* /\* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 \/ /
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	/* /\* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 \/ /
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);	/* /\* vlv= nbcode[Tvaraff[k]][lv]; \/ /
}	/* vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	/* fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][resultmodel[nres][k4]]);	/* sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][resultmodel[nres][k4]]);	/* } */
}	/* 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 8140 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 8836 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(TKresult[nres]==0) k1=1; /* To be checked for noresult */
	/* 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=codtabm(k1,TnsdVar[Tvaraff[k]]);	fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
/* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate number corresponding to k1 combination \/ /	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* for (k=1; k<=cptcoveff; k++){ /\* For each covariate and each value \/ /
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
/* 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]; */	/* /\* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 \/ /
vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];	/* /\* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 \/ /
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	/* /\* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 \/ /
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);	/* /\* vlv= nbcode[Tvaraff[k]][lv]; \/ /
}	/* vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	/* fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);	/* sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);	/* } */
	/* 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 8193 set ter svg size 640, 480\nunset log y\n	Line 8894 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(TKresult[nres]==0) k1=1; /* To be checked for noresult */
	/* 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=codtabm(k1,TnsdVar[Tvaraff[k]]);	fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
/* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate number corresponding to k1 combination \/ /	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* for (k=1; k<=cptcoveff; k++){ /\* For each covariate and each value \/ /
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
/* 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]; */	/* /\* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 \/ /
vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];	/* /\* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 \/ /
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	/* /\* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 \/ /
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);	/* /\* vlv= nbcode[Tvaraff[k]][lv]; \/ /
}	/* vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	/* fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);	/* sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);	/* } */
	/* 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 8253 set ter svg size 640, 480\nunset log y\n	Line 8959 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(TKresult[nres]==0) k1=1; /* To be checked for noresult */
	/* 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]]);
lv=codtabm(k1,TnsdVar[Tvaraff[k]]);	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* for (k=1; k<=cptcoveff; k++){ /\* For each covariate and each value \/ /
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination \\/ \/ */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
/* vlv= nbcode[Tvaraff[k]][lv]; */	/* /\* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 \/ /
vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];	/* /\* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 \/ /
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	/* /\* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 \/ /
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);	/* /\* vlv= nbcode[Tvaraff[k]][lv]; \/ /
}	/* vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	/* fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);	/* sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);	/* } */
	/* 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 8311 set ter svg size 640, 480\nunset log y\n	Line 9022 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(TKresult[nres]==0) k1=1; /* To be checked for noresult */
	/* 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]]);
lv=codtabm(k1,TnsdVar[Tvaraff[k]]);	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* for (k=1; k<=cptcoveff; k++){ /\* For each covariate and each value \/ /
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate number corresponding to k1 combination \\/ \/ */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
/* vlv= nbcode[Tvaraff[k]][lv]; */	/* /\* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 \/ /
vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];	/* /\* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 \/ /
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	/* /\* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 \/ /
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);	/* /\* vlv= nbcode[Tvaraff[k]][lv]; \/ /
}	/* vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	/* fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);	/* sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);	/* } */
	/* 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 8369 set ter svg size 640, 480\nunset log y\n	Line 9085 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(TKresult[nres]==0) k1=1; /* To be checked for noresult */
	/* 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]]);
lv=codtabm(k1,TnsdVar[Tvaraff[k]]);	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* for (k=1; k<=cptcoveff; k++){ /\* For each correspondig covariate value \/ /
/* 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 k1 combination and kth covariate \\/ \/ */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
/* vlv= nbcode[Tvaraff[k]][lv]; */	/* /\* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 \/ /
vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];	/* /\* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 \/ /
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	/* /\* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 \/ /
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);	/* /\* vlv= nbcode[Tvaraff[k]][lv]; \/ /
}	/* vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	/* fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);	/* sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);	/* } */
	/* 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 8444 set ter svg size 640, 480\nunset log y\n	Line 9165 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<=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]]);	for (k=1; k<=cptcovs; k++){ /* For each covariate k get corresponding value lv for combination k1 */
	/* lv=codtabm(k1,TnsdVar[Tvaraff[k]]); */
	lv=Tvresult[nres][k];
	vlv=TinvDoQresult[nres][Tvresult[nres][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]])];	/* 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 && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]); */
	sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,lv, kl+1, vlv );
kl++;	kl++;
if(k <cptcoveff && cptcoveff>1)	if(k <cptcovs && cptcovs>1)
sprintf(gplotcondition+strlen(gplotcondition)," && ");	sprintf(gplotcondition+strlen(gplotcondition)," && ");
}	}
strcpy(gplotcondition+strlen(gplotcondition),")");	strcpy(gplotcondition+strlen(gplotcondition),")");
Line 8486 set ter svg size 640, 480\nunset log y\n	Line 9211 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(TKresult[nres]==0) k1=1; /* To be checked for noresult */
	/* 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]]);
lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /* Should be the covariate value corresponding to combination k1 and covariate k */	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* for (k=1; k<=cptcoveff; k++){ /\* For each correspondig covariate value \/ /
/* 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 k1 combination and kth covariate \\/ \/ */
/* 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]; */	/* /\* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 \/ /
vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];	/* /\* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 \/ /
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	/* /\* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 \/ /
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);	/* /\* vlv= nbcode[Tvaraff[k]][lv]; \/ /
}	/* vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	/* fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv); */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);	/* sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv); */
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);	/* } */
	/* 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 8534 set ter svg size 640, 480\nunset log y\n	Line 9264 set ter svg size 640, 480\nunset log y\n
}else{	}else{
fprintf(ficgp,",\\\n '' ");	fprintf(ficgp,",\\\n '' ");
}	}
if(cptcoveff ==0){ /* No covariate */	/* if(cptcoveff ==0){ /\* No covariate \/ /
	if(cptcovs ==0){ /* No covariate */
ioffset=2; /* Age is in 2 */	ioffset=2; /* Age is in 2 */
/# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4/	/# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4/
/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 /	/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 /
Line 8561 set ter svg size 640, 480\nunset log y\n	Line 9292 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[modelresult[nres][k]]==0){ /* To be verified */
lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /* Should be the covariate value corresponding to combination k1 and covariate k */	/* for (k=1; k<=cptcoveff; k++){ /\* For each covariate writing the chain of conditions \/ /
/* decodtabm(1,1,4) = 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(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /\* 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=Tvresult[nres][k];
/* vlv= nbcode[Tvaraff[k]][lv]; /\* Value of the modality of Tvaraff[k] \/ /	vlv=TinvDoQresult[nres][Tvresult[nres][k]];
vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];	/* 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 */
sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
kl++;	/* vlv= nbcode[Tvaraff[k]][lv]; /\* Value of the modality of Tvaraff[k] \/ /
if(k <cptcoveff && cptcoveff>1)	/* vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]; */
sprintf(gplotcondition+strlen(gplotcondition)," && ");	kl++;
	/* sprintf(gplotcondition+strlen(gplotcondition),"$%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 <cptcovs && cptcovs>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 8638 set ter svg size 640, 480\nunset log y\n	Line 9375 set ter svg size 640, 480\nunset log y\n
fprintf(ficgp,"#\n");	fprintf(ficgp,"#\n");
for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/	for(ng=1; ng<=3;ng++){ /* Number of graphics: first is logit, 2nd is probabilities, third is incidences per year*/
fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");	fprintf(ficgp,"#Number of graphics: first is logit, 2nd is probabilities, third is incidences per year\n");
fprintf(ficgp,"#model=%s \n",model);	fprintf(ficgp,"#model=1+age+%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 */	fprintf(ficgp,"# k1=1 to 2^%d=%d\n",cptcovs,m);/* to be checked */
	/* 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);	if(TKresult[nres]==0) k1=1; /* To be checked for noresult */
	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
lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /* Should be the covariate value corresponding to combination k1 and covariate k */	TinvDoQresult[nres][Tvresult[nres][k]] gives its value double or integer) */
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	fprintf(ficgp," V%d=%lg ",Tvresult[nres][k],TinvDoQresult[nres][Tvresult[nres][k]]);
/* decodtabm(1,2,4) = 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(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	}
/* vlv= nbcode[Tvaraff[k]][lv]; */	/* if(m != 1 && TKresult[nres]!= k1) */
vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];	/* continue; */
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	/* fprintf(ficgp,"\n\n# Combination of dummy k1=%d which is ",k1); */
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);	/* strcpy(gplotlabel,"("); */
}	/* /\sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);\/ */
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	/* for (k=1; k<=cptcoveff; k++){ /\* For each correspondig covariate value \/ /
fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);	/* /\* lv= decodtabm(k1,k,cptcoveff); /\\* Should be the covariate value corresponding to k1 combination and kth covariate \\/ \/ */
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);	/* 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 8753 set ter svg size 640, 480\nunset log y\n	Line 9503 set ter svg size 640, 480\nunset log y\n
} /* end Tprod */	} /* end Tprod */
}	}
break;	break;
	case 3:
	if(cptcovdageprod >0){
	/* if(j==Tprod[ijp]) { / / not necessary */
	/* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
	if(ijp <=cptcovprod) { /* Product VnVm and ageVNVm/
	if(DummyV[Tvardk[ijp][1]]==0){/* Vn is dummy */
	if(DummyV[Tvardk[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*x",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*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvardk[ijp][1]],Tqinvresult[nres][Tvardk[ijp][2]]);
	}
	}else{ /* age* VnVm Vn is quanti HERE /
	if(DummyV[Tvard[ijp][2]]==0){
	fprintf(ficgp,"+p%d%d%f*x",i+j+2+nagesqr-1,Tinvresult[nres][Tvardk[ijp][2]],Tqinvresult[nres][Tvardk[ijp][1]]);
	}else{ /* Both quanti */
	fprintf(ficgp,"+p%d%f%f*x",i+j+2+nagesqr-1,Tqinvresult[nres][Tvardk[ijp][1]],Tqinvresult[nres][Tvardk[ijp][2]]);
	}
	}
	ijp++;
	}
	/* } / / end Tprod */
	}
	break;
case 0:	case 0:
/* simple covariate */	/* 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 \/ /
Line 8839 set ter svg size 640, 480\nunset log y\n	Line 9614 set ter svg size 640, 480\nunset log y\n
} /* end Tprod */	} /* end Tprod */
} /* end if */	} /* end if */
break;	break;
	case 3:
	if(cptcovdageprod >0){
	/* if(j==Tprod[ijp]) { /\* \/ /
	/* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
	if(ijp <=cptcovprod) { /* Product */
	if(DummyV[Tvardk[ijp][1]]==0){/* Vn is dummy */
	if(DummyV[Tvardk[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%dx",k3+(cpt-1)ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvardk[ijp][1]],Tinvresult[nres][Tvardk[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%fx",k3+(cpt-1)ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvardk[ijp][1]],Tqinvresult[nres][Tvardk[ijp][2]]);
	/* fprintf(ficgp,"+p%d%d%fx",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); /
	}
	}else{ /* VnVm Vn is quanti /
	if(DummyV[Tvardk[ijp][2]]==0){
	fprintf(ficgp,"+p%d%d%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvardk[ijp][2]],Tqinvresult[nres][Tvardk[ijp][1]]);
	/* fprintf(ficgp,"+p%d%d%fx",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][Tvardk[ijp][1]],Tqinvresult[nres][Tvardk[ijp][2]]);
	/* fprintf(ficgp,"+p%d%f%fx",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); /
	}
	}
	ijp++;
	}
	/* } /\* end Tprod \/ /
	} /* end if */
	break;
case 0:	case 0:
/* simple covariate */	/* 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 \/ /
Line 8878 set ter svg size 640, 480\nunset log y\n	Line 9682 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 9192 void prevforecast(char fileres[], double	Line 9996 void prevforecast(char fileres[], double
/* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */	/* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */
/* date2dmy(dateprojd,&jprojd, &mprojd, &anprojd); */	/* date2dmy(dateprojd,&jprojd, &mprojd, &anprojd); */
/* date2dmy(dateprojf,&jprojf, &mprojf, &anprojf); */	/* date2dmy(dateprojf,&jprojf, &mprojf, &anprojf); */
i1=pow(2,cptcoveff);	/* i1=pow(2,cptcoveff); */
if (cptcovn < 1){i1=1;}	/* if (cptcovn < 1){i1=1;} */

fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);	fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);

fprintf(ficresf,"#**** Routine prevforecast \n");	fprintf(ficresf,"#**** Routine prevforecast \n");

/* if (h==(int)(YEARMyearp)){ /	/* if (h==(int)(YEARMyearp)){ /
for(nres=1; nres <= nresult; nres++) /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
for(k=1; k<=i1;k++){ /* We want to find the combination k corresponding to the values of the dummies given in this resut line (to be cleaned one day) */	k=TKresult[nres];
if(i1 != 1 && TKresult[nres]!= k)	if(TKresult[nres]==0) k=1; /* To be checked for noresult */
continue;	/* 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(invalidvarcomb[k]){	/* if(i1 != 1 && TKresult[nres]!= k) */
printf("\nCombination (%d) projection ignored because no cases \n",k);	/* continue; */
continue;	/* if(invalidvarcomb[k]){ */
}	/* printf("\nCombination (%d) projection ignored because no cases \n",k); */
	/* continue; */
	/* } */
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<=cptcovs;j++){
/* fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); */	/* for(j=1;j<=cptcoveff;j++) { */
fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[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 */	/* } */
fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	/* 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=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
}	}

fprintf(ficresf," yearproj age");	fprintf(ficresf," yearproj age");
for(j=1; j<=nlstate+ndeath;j++){	for(j=1; j<=nlstate+ndeath;j++){
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
Line 9240 void prevforecast(char fileres[], double	Line 10050 void prevforecast(char fileres[], double
}	}
}	}
fprintf(ficresf,"\n");	fprintf(ficresf,"\n");
for(j=1;j<=cptcoveff;j++)	/* for(j=1;j<=cptcoveff;j++) */
	for(j=1;j<=cptcovs;j++)
	fprintf(ficresf,"%d %lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][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,Tvaraff[j])]); /\* Tvaraff not correct \/ /
fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); /* TnsdVar[Tvaraff] 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 9334 void prevforecast(char fileres[], double	Line 10146 void prevforecast(char fileres[], double
/* if(jintmean==0) jintmean=1; */	/* if(jintmean==0) jintmean=1; */
/* if(mintmean==0) jintmean=1; */	/* if(mintmean==0) jintmean=1; */

i1=pow(2,cptcoveff);	/* i1=pow(2,cptcoveff); */
if (cptcovn < 1){i1=1;}	/* if (cptcovn < 1){i1=1;} */

fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);	fprintf(ficresfb,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);
printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);	printf("# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jintmean,mintmean,aintmean,dateintmean,dateprev1,dateprev2);

fprintf(ficresfb,"#**** Routine prevbackforecast \n");	fprintf(ficresfb,"#**** Routine prevbackforecast \n");

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)	if(TKresult[nres]==0) k=1; /* To be checked for noresult */
continue;	/* for(k=1; k<=i1;k++){ */
if(invalidvarcomb[k]){	/* if(i1 != 1 && TKresult[nres]!= k) */
printf("\nCombination (%d) projection ignored because no cases \n",k);	/* continue; */
continue;	/* if(invalidvarcomb[k]){ */
}	/* printf("\nCombination (%d) projection ignored because no cases \n",k); */
	/* continue; */
	/* } */
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<=cptcovs;j++){
fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);	/* for(j=1;j<=cptcoveff;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 */	/* } */
fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficresfb," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
}	}
	/* fprintf(ficrespij,"*****\n"); /
	/* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value \/ /
	/* fprintf(ficresfb," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
	/* } */
fprintf(ficresfb," yearbproj age");	fprintf(ficresfb," yearbproj age");
for(j=1; j<=nlstate+ndeath;j++){	for(j=1; j<=nlstate+ndeath;j++){
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
Line 9387 void prevforecast(char fileres[], double	Line 10205 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,TnsdVar[Tvaraff[j]])]);	for(j=1;j<=cptcovs;j++)
	fprintf(ficresfb,"%d %lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][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 9447 void prevforecast(char fileres[], double	Line 10267 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++){ /* We find the combination equivalent to result line values of dummies */	k=TKresult[nres];
	if(TKresult[nres]==0) k=1; /* To be checked for noresult */
	/* 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,TnsdVar[Tvaraff[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,TnsdVar[Tvaraff[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,TnsdVar[Tvaraff[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]])]); */
	/* 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][resultmodel[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(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(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 9504 void prevforecast(char fileres[], double	Line 10328 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)	if(TKresult[nres]==0) k=1; /* To be checked for noresult */
continue;	/* for(k=1; k<=i1;k++){ */
	/* 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,TnsdVar[Tvaraff[j]])]);	printf(" V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][resultmodel[nres][j]]);
fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);	fprintf(ficresvbl," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][resultmodel[nres][j]]);
printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);	fprintf(ficlog," V%d=%lg ",Tvresult[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][resultmodel[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][resultmodel[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][resultmodel[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 9979 int readdata(char datafile[], int firsto	Line 10809 int readdata(char datafile[], int firsto
char stra[MAXLINE], strb[MAXLINE];	char stra[MAXLINE], strb[MAXLINE];
char *stratrunc;	char *stratrunc;

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;	ncovcolt=ncovcol+nqv+ntv+nqtv; /* total of covariates in the data, not in the model equation */
FixedV[v]=0;
}

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

if((fic=fopen(datafile,"r"))==NULL) {	if((fic=fopen(datafile,"r"))==NULL) {
printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);	printf("Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(stdout);
fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;	fprintf(ficlog,"Problem while opening datafile: %s with errno='%s'\n", datafile,strerror(errno));fflush(ficlog);return 1;
Line 10084 int readdata(char datafile[], int firsto	Line 10891 int readdata(char datafile[], int firsto
if(strb[0]=='.') { /* Missing value */	if(strb[0]=='.') { /* Missing value */
lval=-1;	lval=-1;
cotqvar[j][iv][i]=-1; /* 0.0/0.0 */	cotqvar[j][iv][i]=-1; /* 0.0/0.0 */
cotvar[j][ntv+iv][i]=-1; /* For performance reasons */	cotvar[j][ncovcol+nqv+ntv+iv][i]=-1; /* For performance reasons */
if(isalpha(strb[1])) { /* .m or .d Really Missing value */	if(isalpha(strb[1])) { /* .m or .d Really Missing value */
printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value. Exiting.\n", strb, linei,i,line,iv, nqtv, j);	printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value. Exiting.\n", strb, linei,i,line,iv, nqtv, j);
fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value. Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog);	fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be the %d th quantitative value out of %d measured at wave %d. If missing, you should remove this individual or impute a value. Exiting.\n", strb, linei,i,line,iv, nqtv, j);fflush(ficlog);
Line 10104 int readdata(char datafile[], int firsto	Line 10911 int readdata(char datafile[], int firsto
return 1;	return 1;
}	}
cotqvar[j][iv][i]=dval;	cotqvar[j][iv][i]=dval;
cotvar[j][ntv+iv][i]=dval;	cotvar[j][ncovcol+nqv+ntv+iv][i]=dval; /* because cotvar starts now at first ntv */
}	}
strcpy(line,stra);	strcpy(line,stra);
}/* end loop ntqv */	}/* end loop ntqv */
Line 10144 int readdata(char datafile[], int firsto	Line 10951 int readdata(char datafile[], int firsto
Exiting.\n",lval,linei, i,line,iv,j);fflush(ficlog);	Exiting.\n",lval,linei, i,line,iv,j);fflush(ficlog);
return 1;	return 1;
}	}
cotvar[j][iv][i]=(double)(lval);	cotvar[j][ncovcol+nqv+iv][i]=(double)(lval);
strcpy(line,stra);	strcpy(line,stra);
}/* end loop ntv */	}/* end loop ntv */

Line 10156 int readdata(char datafile[], int firsto	Line 10963 int readdata(char datafile[], int firsto
errno=0;	errno=0;
lval=strtol(strb,&endptr,10);	lval=strtol(strb,&endptr,10);
/* if (errno == ERANGE && (lval == LONG_MAX \|\| lval == LONG_MIN))*/	/* if (errno == ERANGE && (lval == LONG_MAX \|\| lval == LONG_MIN))*/
if( strb[0]=='\0' \|\| (*endptr != '\0')){	if( strb[0]=='\0' \|\| (*endptr != '\0' )){
printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);	printf("Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);
fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);	fprintf(ficlog,"Error reading data around '%s' at line number %d for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);fflush(ficlog);
	return 1;
	}else if( lval==0 \|\| lval > nlstate+ndeath){
	printf("Error in data around '%s' at line number %d for individual %d, '%s'\n Should be a state at wave %d. A state should be 1 to %d and not %ld.\n Fix your data file '%s'! Exiting.\n", strb, linei,i,line,j,nlstate+ndeath, lval, datafile);fflush(stdout);
	fprintf(ficlog,"Error in data around '%s' at line number %d for individual %d, '%s'\n Should be a state at wave %d. A state should be 1 to %d and not %ld.\n Fix your data file '%s'! Exiting.\n", strb, linei,i,line,j,nlstate+ndeath, lval, datafile); fflush(ficlog);
return 1;	return 1;
}	}
}	}
Line 10357 int decoderesult( char resultline[], int	Line 11168 int decoderesult( char resultline[], int
printf("decoderesult:%s\n",resultline);	printf("decoderesult:%s\n",resultline);

strcpy(resultsav,resultline);	strcpy(resultsav,resultline);
printf("Decoderesult resultsav=\"%s\" resultline=\"%s\"\n", resultsav, resultline);	/* printf("Decoderesult resultsav=\"%s\" resultline=\"%s\"\n", resultsav, resultline); */
if (strlen(resultsav) >1){	if (strlen(resultsav) >1){
j=nbocc(resultsav,'='); /*< j=Number of covariate values'=' in this resultline /	j=nbocc(resultsav,'='); /*< j=Number of covariate values'=' in this resultline /
}	}
if(j == 0){ /* Resultline but no = */	if(j == 0 && cptcovs== 0){ /* Resultline but no = and no covariate in the model */
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 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 which is %d, differs from the number %d of single variables used in the model line, 1+age+%s.\n",j, cptcovs, model);fflush(ficlog);
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);	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, 1+age+%s.\n",j, cptcovs, model);fflush(stdout);
/* return 1;*/	if(j==0)
	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){
Line 10406 int decoderesult( char resultline[], int	Line 11218 int decoderesult( char resultline[], int
}	}
}	}
if(match == 0){	if(match == 0){
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]);	printf("Error in result line (Dummy single): V%d is missing in result: %s according to model=1+age+%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 (Dummy single): V%d is missing in result: %s according to model=%s\n",Tvar[k1], resultline, model);	fprintf(ficlog,"Error in result line (Dummy single): V%d is missing in result: %s according to model=1+age+%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*/	}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*/
Line 10417 int decoderesult( char resultline[], int	Line 11229 int decoderesult( char resultline[], int
if(Tvar[k1]==Tvarsel[k2]) {/* Tvar is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5 */	if(Tvar[k1]==Tvarsel[k2]) {/* Tvar is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5 */
modelresult[nres][k2]=k1;/* we found a Vn=1 corrresponding to Vnage in the model modelresult[2]=1 modelresult[1]=2 modelresult[3]=3 modelresult[6]=4 modelresult[9]=5 /	modelresult[nres][k2]=k1;/* we found a Vn=1 corrresponding to Vnage in the model modelresult[2]=1 modelresult[1]=2 modelresult[3]=3 modelresult[6]=4 modelresult[9]=5 /
resultmodel[nres][k1]=k2; /* Added here */	resultmodel[nres][k1]=k2; /* Added here */
printf("Decoderesult first modelresult[k2=%d]=%d (k1) V%d*AGE\n",k2,k1,Tvar[k1]);	/* printf("Decoderesult first modelresult[k2=%d]=%d (k1) V%dAGE\n",k2,k1,Tvar[k1]); /
match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */	match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
break;	break;
}	}
}	}
if(match == 0){	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]);	printf("Error in result line (Product with age): V%d is missing in result: %s according to model=1+age+%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]);	fprintf(ficlog,"Error in result line (Product with age): V%d is missing in result: %s according to model=1+age+%s (Tvarsel[k2=%d]=%d)\n",Tvar[k1], resultline, model, k2, Tvarsel[k2]);
return 1;	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*/	}else if(Typevar[k1]==2 \|\| Typevar[k1]==3){ /* Product with or without age. We want to get the position in the resultline of the product in the model line*/
/* resultmodel[nres][of such a Vn * Vm product k1] is not unique, so can't exist, we feed Tvard[k1][1] and [2] */	/* resultmodel[nres][of such a Vn * Vm product k1] is not unique, so can't exist, we feed Tvard[k1][1] and [2] */
match=0;	match=0;
printf("Decoderesult very first Product Tvardk[k1=%d][1]=%d Tvardk[k1=%d][2]=%d V%d * V%d\n",k1,Tvardk[k1][1],k1,Tvardk[k1][2],Tvardk[k1][1],Tvardk[k1][2]);	/* printf("Decoderesult very first Product Tvardk[k1=%d][1]=%d Tvardk[k1=%d][2]=%d V%d * V%d\n",k1,Tvardk[k1][1],k1,Tvardk[k1][2],Tvardk[k1][1],Tvardk[k1][2]); */
for(k2=1; k2 <=j;k2++){/* Loop on resultline. In result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */	for(k2=1; k2 <=j;k2++){/* Loop on resultline. In result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
if(Tvardk[k1][1]==Tvarsel[k2]) {/* Tvardk is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5 */	if(Tvardk[k1][1]==Tvarsel[k2]) {/* Tvardk is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5 */
/* modelresult[k2]=k1; */	/* modelresult[k2]=k1; */
printf("Decoderesult first Product modelresult[k2=%d]=%d (k1) V%d * \n",k2,k1,Tvarsel[k2]);	/* printf("Decoderesult first Product modelresult[k2=%d]=%d (k1) V%d * \n",k2,k1,Tvarsel[k2]); */
match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */	match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
}	}
}	}
if(match == 0){	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);	printf("Error in result line (Product without age first variable or double product with age): V%d is missing in result: %s according to model=1+age+%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);	fprintf(ficlog,"Error in result line (Product without age first variable or double product with age): V%d is missing in result: %s according to model=1+age+%s\n",Tvardk[k1][1], resultline, model);
return 1;	return 1;
}	}
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(Tvardk[k1][2]==Tvarsel[k2]) {/* Tvardk is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5 */	if(Tvardk[k1][2]==Tvarsel[k2]) {/* Tvardk is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5 */
/* modelresult[k2]=k1;*/	/* modelresult[k2]=k1;*/
printf("Decoderesult second Product modelresult[k2=%d]=%d (k1) * V%d \n ",k2,k1,Tvarsel[k2]);	/* printf("Decoderesult second Product modelresult[k2=%d]=%d (k1) * V%d \n ",k2,k1,Tvarsel[k2]); */
match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */	match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
break;	break;
}	}
}	}
if(match == 0){	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);	printf("Error in result line (Product without age second variable or double product with age): V%d is missing in result: %s according to model=1+age+%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);	fprintf(ficlog,"Error in result line (Product without age second variable or double product with age): V%d is missing in result : %s according to model=1+age+%s\n",Tvardk[k1][2], resultline, model);
return 1;	return 1;
}	}
}/* End of testing */	}/* End of testing */
Line 10466 int decoderesult( char resultline[], int	Line 11278 int decoderesult( char resultline[], int
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 only */	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 What if a product? */
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 */	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 */	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;
Line 10474 int decoderesult( char resultline[], int	Line 11286 int decoderesult( char resultline[], int
}	}
}	}
if(match == 0){	if(match == 0){
printf("Error in result line: variable V%d is missing in model; result: %s, model=%s\n",Tvarsel[k2], resultline, model);	printf("Error in result line: variable V%d is missing in model; result: %s, model=1+age+%s\n",Tvarsel[k2], resultline, model);
fprintf(ficlog,"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: variable V%d is missing in model; result: %s, model=1+age+%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=1+age+%s\n",k2, resultline, model);
fprintf(ficlog,"Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);	fprintf(ficlog,"Error in result line: %d doubled; result: %s, model=1+age+%s\n",k2, resultline, model);
return 1;	return 1;
}	}
}	}
Line 10507 int decoderesult( char resultline[], int	Line 11319 int decoderesult( char resultline[], int
/* k counting number of combination of single dummies in the equation model */	/* k counting number of combination of single dummies in the equation model */
/* k4 counting single dummies in the equation model */	/* k4 counting single dummies in the equation model */
/* k4q counting single quantitatives in the equation model */	/* k4q counting single quantitatives in the equation model */
if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Dummy and Single, k1 is sorting according to MODEL, but k3 to resultline */	if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Dummy and Single, fixed or timevarying, k1 is sorting according to MODEL, but k3 to resultline */
/* k4+1= (not always if quant in model) position in the resultline V(Tvarsel)=Tvalsel=Tresult[nres][pos](value); V(Tvresult[nres][pos] (variable): V(variable)=value) */	/* k4+1= (not always if quant in model) position in the resultline V(Tvarsel)=Tvalsel=Tresult[nres][pos](value); V(Tvresult[nres][pos] (variable): V(variable)=value) */
/* modelresult[k3]=k1: k3th position in the result line corresponds to the k1 position in the model line (doesn't work with products)*/	/* modelresult[k3]=k1: k3th position in the result line corresponds to the k1 position in the model line (doesn't work with products)*/
/* Value in the (current nres) resultline of the variable at the k1th position in the model equation resultmodel[nres][k1]= k3 */	/* Value in the (current nres) resultline of the variable at the k1th position in the model equation resultmodel[nres][k1]= k3 */
Line 10531 int decoderesult( char resultline[], int	Line 11343 int decoderesult( char resultline[], int
Tvresult[nres][k3]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */	Tvresult[nres][k3]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */	Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
precov[nres][k1]=Tvalsel[k3]; /* Value from resultline of the variable at the k1 position in the model */	precov[nres][k1]=Tvalsel[k3]; /* Value from resultline of the variable at the k1 position in the model */
printf("Decoderesult Dummy k=%d, k1=%d precov[nres=%d][k1=%d]=%.f V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k1, nres, k1,precov[nres][k1], k2, k3, (int)Tvalsel[k3], k4);	/* printf("Decoderesult Dummy k=%d, k1=%d precov[nres=%d][k1=%d]=%.f V(k2=V%d)= Tvalsel[%d]=%d, 2*(%d)\n",k, k1, nres, k1,precov[nres][k1], k2, k3, (int)Tvalsel[k3], k4); /
k4++;;	k4++;;
}else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Quantitative and single */	}else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Quantitative and single */
/* Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline */	/* Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline */
Line 10549 int decoderesult( char resultline[], int	Line 11361 int decoderesult( char resultline[], int
Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */	Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */	TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
precov[nres][k1]=Tvalsel[k3q];	precov[nres][k1]=Tvalsel[k3q];
printf("Decoderesult Quantitative nres=%d,precov[nres=%d][k1=%d]=%.f V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, nres, k1,precov[nres][k1], k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);	/* printf("Decoderesult Quantitative nres=%d,precov[nres=%d][k1=%d]=%.f V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, nres, k1,precov[nres][k1], k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]); */
k4q++;;	k4q++;;
}else if( Dummy[k1]==2 ){ /* For dummy with age product */	}else if( Dummy[k1]==2 ){ /* For dummy with age product "V2+V3+V4+V6+V7+V6V2+V7V2+V6V3+V7V3+V6V4+V7V4+ageV2+ageV3+ageV4+ageV6+ageV7+ageV6V2+ageV6V3+ageV7V3+ageV6V4+ageV7V4\r"/
/* Tvar[k1]; / / Age variable */	/* Tvar[k1]; / / Age variable / / 17 ageV6V2 ?*/
/* Wrong we want the value of variable name Tvar[k1] */	/* Wrong we want the value of variable name Tvar[k1] */
	if(Typevar[k1]==2 \|\| Typevar[k1]==3 ){ /* For product quant or dummy (with or without age) */
k3= resultmodel[nres][k1]; /* nres=1 k1=2 resultmodel[2(V4)] = 1=k3 ; k1=3 resultmodel[3(V3)] = 2=k3*/	precov[nres][k1]=TinvDoQresult[nres][Tvardk[k1][1]] * TinvDoQresult[nres][Tvardk[k1][2]];
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)*/	/* 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]]); */
TinvDoQresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* TinvDoQresult[nres][4]=1 */	}else{
precov[nres][k1]=Tvalsel[k3];	k3= resultmodel[nres][k1]; /* nres=1 k1=2 resultmodel[2(V4)] = 1=k3 ; k1=3 resultmodel[3(V3)] = 2=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]);	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 */	}else if( Dummy[k1]==3 ){ /* For quant with age product */
k3q= resultmodel[nres][k1]; /* resultmodel[1(V5)] = 25.1=k3q */	if(Typevar[k1]==2 \|\| Typevar[k1]==3 ){ /* For product quant or dummy (with or without age) */
k2q=(int)Tvarsel[k3q]; /* Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */	precov[nres][k1]=TinvDoQresult[nres][Tvardk[k1][1]] * TinvDoQresult[nres][Tvardk[k1][2]];
TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* TinvDoQresult[nres][5]=25.1 */	/* 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]]); */
precov[nres][k1]=Tvalsel[k3q];	}else{
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]);	k3q= resultmodel[nres][k1]; /* resultmodel[1(V5)] = 25.1=k3q */
}else if(Typevar[k1]==2 ){ /* For product quant or dummy (not with age) */	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 \|\| Typevar[k1]==3 ){ /* For product quant or dummy (with or without age) */
precov[nres][k1]=TinvDoQresult[nres][Tvardk[k1][1]] * TinvDoQresult[nres][Tvardk[k1][2]];	precov[nres][k1]=TinvDoQresult[nres][Tvardk[k1][1]] * TinvDoQresult[nres][Tvardk[k1][2]];
printf("Decoderesult Quantitative or Dummy (not with age) nres=%d k1=%d precov[nres=%d][k1=%d]=%.f V%d(=%.f) * V%d(=%.f) \n",nres, k1, nres, k1,precov[nres][k1], Tvardk[k1][1], TinvDoQresult[nres][Tvardk[k1][1]], Tvardk[k1][2], TinvDoQresult[nres][Tvardk[k1][2]]);	/* printf("Decoderesult Quantitative or Dummy (not with age) nres=%d k1=%d precov[nres=%d][k1=%d]=%.f V%d(=%.f) * V%d(=%.f) \n",nres, k1, nres, k1,precov[nres][k1], Tvardk[k1][1], TinvDoQresult[nres][Tvardk[k1][1]], Tvardk[k1][2], TinvDoQresult[nres][Tvardk[k1][2]]); */
}else{	}else{
printf("Error Decoderesult probably a product Dummy[%d]==%d && Typevar[%d]==%d\n", k1, Dummy[k1], k1, Typevar[k1]);	printf("Error Decoderesult probably a product Dummy[%d]==%d && Typevar[%d]==%d\n", k1, Dummy[k1], k1, Typevar[k1]);
fprintf(ficlog,"Error Decoderesult probably a product Dummy[%d]==%d && Typevar[%d]==%d\n", k1, Dummy[k1], k1, Typevar[k1]);	fprintf(ficlog,"Error Decoderesult probably a product Dummy[%d]==%d && Typevar[%d]==%d\n", k1, Dummy[k1], k1, Typevar[k1]);
Line 10587 int decodemodel( char model[], int lasto	Line 11408 int decodemodel( char model[], int lasto
* - cptcovn or number of covariates k of the models excluding ageproducts =6 and ageage	* - cptcovn or number of covariates k of the models excluding ageproducts =6 and ageage
* - cptcovage number of covariates with age*products =2	* - cptcovage number of covariates with age*products =2
* - cptcovs number of simple covariates	* - cptcovs number of simple covariates
	* ncovcolt=ncovcol+nqv+ntv+nqtv total of covariates in the data, not in the model equation
* - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10	* - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
* which is a new column after the 9 (ncovcol) variables.	* which is a new column after the 9 (ncovcol+nqv+ntv+nqtv) variables.
* - if k is a product Vn*Vm, covar[k][i] is filled with correct values for each individual	* - if k is a product Vn*Vm, covar[k][i] is filled with correct values for each individual
* - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage	* - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
* Tprod[1]@2 {5, 6}: position of first product V7V8 is 5, and second V5V6 is 6.	* Tprod[1]@2 {5, 6}: position of first product V7V8 is 5, and second V5V6 is 6.
Line 10597 int decodemodel( char model[], int lasto	Line 11419 int decodemodel( char model[], int lasto
/* V2+V1+V4+V3age Tvar[4]=3 ; V1+V2age Tvar[2]=2; V1+V1age Tvar[2]=1, Tage[1]=2 /	/* V2+V1+V4+V3age Tvar[4]=3 ; V1+V2age Tvar[2]=2; V1+V1age Tvar[2]=1, Tage[1]=2 /
{	{
int i, j, k, ks, v;	int i, j, k, ks, v;
int j1, k1, k2, k3, k4;	int n,m;
char modelsav[80];	int j1, k1, k11, k12, k2, k3, k4;
char stra[80], strb[80], strc[80], strd[80],stre[80];	char modelsav[300];
	char stra[300], strb[300], strc[300], strd[300],stre[300],strf[300];
char *strpt;	char *strpt;
	int **existcomb;

	existcomb=imatrix(1,NCOVMAX,1,NCOVMAX);
	for(i=1;i<=NCOVMAX;i++)
	for(j=1;j<=NCOVMAX;j++)
	existcomb[i][j]=0;

/removespace(model);/	/removespace(model);/
if (strlen(model) >1){ /* If there is at least 1 covariate */	if (strlen(model) >1){ /* If there is at least 1 covariate */
j=0, j1=0, k1=0, k2=-1, ks=0, cptcovn=0;	j=0, j1=0, k1=0, k12=0, k2=-1, ks=0, cptcovn=0;
if (strstr(model,"AGE") !=0){	if (strstr(model,"AGE") !=0){
printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);	printf("Error. AGE must be in lower case 'age' model=1+age+%s. ",model);
fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);	fprintf(ficlog,"Error. AGE must be in lower case model=1+age+%s. ",model);fflush(ficlog);
return 1;	return 1;
}	}
if (strstr(model,"v") !=0){	if (strstr(model,"v") !=0){
printf("Error. 'v' must be in upper case 'V' model=%s ",model);	printf("Error. 'v' must be in upper case 'V' model=1+age+%s ",model);
fprintf(ficlog,"Error. 'v' must be in upper case model=%s ",model);fflush(ficlog);	fprintf(ficlog,"Error. 'v' must be in upper case model=1+age+%s ",model);fflush(ficlog);
return 1;	return 1;
}	}
strcpy(modelsav,model);	strcpy(modelsav,model);
if ((strpt=strstr(model,"age*age")) !=0){	if ((strpt=strstr(model,"age*age")) !=0){
printf(" strpt=%s, model=%s\n",strpt, model);	printf(" strpt=%s, model=1+age+%s\n",strpt, model);
if(strpt != model){	if(strpt != model){
printf("Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \	printf("Error in model: 'model=1+age+%s'; 'age*age' should in first place before other covariates\n \
'model=1+age+ageage+V1.' or 'model=1+age+ageage+V1+V1*age.', please swap as well as \n \	'model=1+age+ageage+V1.' or 'model=1+age+ageage+V1+V1*age.', please swap as well as \n \
corresponding column of parameters.\n",model);	corresponding column of parameters.\n",model);
fprintf(ficlog,"Error in model: 'model=%s'; 'age*age' should in first place before other covariates\n \	fprintf(ficlog,"Error in model: 'model=1+age+%s'; 'age*age' should in first place before other covariates\n \
'model=1+age+ageage+V1.' or 'model=1+age+ageage+V1+V1*age.', please swap as well as \n \	'model=1+age+ageage+V1.' or 'model=1+age+ageage+V1+V1*age.', please swap as well as \n \
corresponding column of parameters.\n",model); fflush(ficlog);	corresponding column of parameters.\n",model); fflush(ficlog);
return 1;	return 1;
Line 10636 int decodemodel( char model[], int lasto	Line 11465 int decodemodel( char model[], int lasto
substrchaine(modelsav, model, "age*age");	substrchaine(modelsav, model, "age*age");
}else	}else
nagesqr=0;	nagesqr=0;
if (strlen(modelsav) >1){	if (strlen(modelsav) >1){ /* V2 +V3 +V4 +V6 +V7 +V6V2 +V7V2 +V6V3 +V7V3 +V6V4 +V7V4 +ageV2 +ageV3 +ageV4 +ageV6 +ageV7 +ageV6V2 +V7V2 +ageV6V3 +ageV7V3 +ageV6V4 +ageV7V4 */
j=nbocc(modelsav,'+'); /*< j=Number of '+' /	j=nbocc(modelsav,'+'); /*< j=Number of '+' /
j1=nbocc(modelsav,''); /< j1=Number of '' */	j1=nbocc(modelsav,''); /< j1=Number of '' */
cptcovs=j+1-j1; /*< Number of simple covariates V1+V1age+V3 +V3V4+ageage=> V1 + V3 =5-3=2 */	cptcovs=0; /*< Number of simple covariates V1 +V1age +V3 +V3V4 +ageage => V1 + V3 =4+1-3=2 Wrong */
cptcovt= j+1; /* Number of total covariates in the model, not including	cptcovt= j+1; /* Number of total covariates in the model, not including
* cst, age and age*age	* cst, age and age*age
* V1+V1age+ V3 + V3V4+ageage=> 3+1=4/	* V1+V1age+ V3 + V3V4+ageage=> 3+1=4/
/* including age products which are counted in cptcovage.	/* including age products which are counted in cptcovage.
* but the covariates which are products must be treated	* but the covariates which are products must be treated
* separately: ncovn=4- 2=2 (V1+V3). */	* separately: ncovn=4- 2=2 (V1+V3). */
cptcovprod=j1; /*< Number of products V1V2 +v3age = 2 /	cptcovprod=0; /*< Number of products V1V2 +v3age = 2 /
	cptcovdageprod=0; /* Number of doouble products with age ageVnVM or VnageVm or VnVmage */
cptcovprodnoage=0; /*< Number of covariate products without age: V3V4 =1 */	cptcovprodnoage=0; /*< Number of covariate products without age: V3V4 =1 */
	cptcovprodage=0;
	/* cptcovprodage=nboccstr(modelsav,"age");*/

/* Design	/* Design
* V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight	* V1 V2 V3 V4 V5 V6 V7 V8 V9 Weight
Line 10656 int decodemodel( char model[], int lasto	Line 11487 int decodemodel( char model[], int lasto
* Model V2 + V1 + V3age + V3 + V5V6 + V7V8 + V8age + V8	* Model V2 + V1 + V3age + V3 + V5V6 + V7V8 + V8age + V8
* k= 1 2 3 4 5 6 7 8	* k= 1 2 3 4 5 6 7 8
* cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8	* cptcovn number of covariates (not including constant and age ) = # of + plus 1 = 7+1=8
* covar[k,i], value of kth covariate if not including age for individual i:	* covar[k,i], are for fixed covariates, value of kth covariate if not including age for individual i:
* covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)	* covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
* Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[2]=1 Tvar[4]=3 Tvar[8]=8	* Tvar[k] # of the kth covariate: Tvar[1]=2 Tvar[2]=1 Tvar[4]=3 Tvar[8]=8
* if multiplied by age: V3age Tvar[3=V3age]=3 (V3) Tvar[7]=8 and	* if multiplied by age: V3age Tvar[3=V3age]=3 (V3) Tvar[7]=8 and
* Tage[++cptcovage]=k	* Tage[++cptcovage]=k
* if products, new covar are created after ncovcol with k1	* if products, new covar are created after ncovcol + nqv (quanti fixed) with k1
* Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11	* Tvar[k]=ncovcol+k1; # of the kth covariate product: Tvar[5]=ncovcol+1=10 Tvar[6]=ncovcol+1=11
* Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product	* Tprod[k1]=k; Tprod[1]=5 Tprod[2]= 6; gives the position of the k1th product
* Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8	* Tvard[k1][1]=m Tvard[k1][2]=m; Tvard[1][1]=5 (V5) Tvard[1][2]=6 Tvard[2][1]=7 (V7) Tvard[2][2]=8
* Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];	* Tvar[cptcovn+k2]=Tvard[k1][1];Tvar[cptcovn+k2+1]=Tvard[k1][2];
* Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted	* Tvar[8+1]=5;Tvar[8+2]=6;Tvar[8+3]=7;Tvar[8+4]=8 inverted
* V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11	* V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11
* < ncovcol=8 >	* < ncovcol=8 8 fixed covariate. Additional starts at 9 (V5V6) and 10(V7V8) >
* Model V2 + V1 + V3age + V3 + V5V6 + V7V8 + V8age + V8 d1 d1 d2 d2	* Model V2 + V1 + V3age + V3 + V5V6 + V7V8 + V8age + V8 d1 d1 d2 d2
* k= 1 2 3 4 5 6 7 8 9 10 11 12	* k= 1 2 3 4 5 6 7 8 9 10 11 12
* Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8	* Tvard[k]= 2 1 3 3 10 11 8 8 5 6 7 8
* p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}	* p Tvar[1]@12={2, 1, 3, 3, 9, 10, 8, 8}
* p Tprod[1]@2={ 6, 5}	* p Tprod[1]@2={ 6, 5}
*p Tvard[1][1]@4= {7, 8, 5, 6}	*p Tvard[1][1]@4= {7, 8, 5, 6}
* covar[k][i]= V2 V1 ? V3 V5V6? V7V8? ? V8	* covar[k][i]= V2 V1 ? V3 V5V6? V7V8? ? V8
Line 10702 int decodemodel( char model[], int lasto	Line 11533 int decodemodel( char model[], int lasto
Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;	Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
}	}
cptcovage=0;	cptcovage=0;

	/* First loop in order to calculate */
	/* for ageVNVm
	* Provides, Typevar[k], Tage[cptcovage], existcomb[n][m], FixedV[ncovcolt+k12]
	* Tprod[k1]=k Tposprod[k]=k1; Tvard[k1][1] =m;
	*/
	/* Needs FixedV[Tvardk[k][1]] */
	/* For others:
	* Sets Typevar[k];
	* Tvar[k]=ncovcol+nqv+ntv+nqtv+k11;
	* Tposprod[k]=k11;
	* Tprod[k11]=k;
	* Tvardk[k][1] =m;
	* Needs FixedV[Tvardk[k][1]] == 0
	*/

for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model line */	for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model line */
cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' cutl from left to right	cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' cutl from left to right
modelsav==V2+V1+V5age+V4+V3age strb=V3age stra=V2+V1V5age+V4 / / <model> "V5+V4+V3+V4V3+V5age+V1age+V1" strb="V5" stra="V4+V3+V4V3+V5age+V1age+V1" */	modelsav==V2+V1+V5age+V4+V3age strb=V3age stra=V2+V1V5age+V4 / / <model> "V5+V4+V3+V4V3+V5age+V1age+V1" strb="V5" stra="V4+V3+V4V3+V5age+V1age+V1" */
Line 10709 int decodemodel( char model[], int lasto	Line 11556 int decodemodel( char model[], int lasto
strcpy(strb,modelsav); /* and analyzes it */	strcpy(strb,modelsav); /* and analyzes it */
/* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/	/* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
/scanf("%d",i);/	/scanf("%d",i);/
if (strchr(strb,'')) { /< Model includes a product V2+V1+V5age+ V4+V3age strb=V3age */	if (strchr(strb,'')) { /< Model includes a product V2+V1+V5age+ V4+V3age strb=V3age OR double product with age strb=ageV6V2 or V6V2age or V6ageV2 */
cutl(strc,strd,strb,''); /< k=1 strdstrc VmVn: strb=V3age(input) strc=age strd=V3 ; V3V2 strc=V2, strd=V3 /	cutl(strc,strd,strb,''); /< k=1 strdstrc VmVn: strb=V3age(input) strc=age strd=V3 ; V3V2 strc=V2, strd=V3 OR strb=ageV6V2 strc=V6V2 strd=age OR c=V2age OR c=ageV2 */
if (strcmp(strc,"age")==0) { /*< Model includes age: Vnage */	if(strchr(strc,'')) { /< Model with age and DOUBLE product: allowed since 0.99r44, strc=V6V2 or V2age or ageV2, strd=age or V6 or V6 */
/* covar is not filled and then is empty */	Typevar[k]=3; /* 3 for age and double product ageVnVm varying of fixed */
cptcovprod--;	if(strstr(strc,"age")!=0) { /* It means that strc=V2age or ageV2 and thus that strd=Vn */
cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */	cutl(stre,strf,strc,'') ; / strf=age or Vm, stre=Vm or age. If strc=V6V2 then strf=V6 and stre=V2 /
Tvar[k]=atoi(stre); /* V2+V1+V5age+V4+V3age Tvar[5]=3 ; V1+V2age Tvar[2]=2; V1+V1age Tvar[2]=1 */	strcpy(strc,strb); /* save strb(=ageVnVm) into strc */
Typevar[k]=1; /* 1 for age product */	/* We want strb=VnVm /
cptcovage++; /* Counts the number of covariates which include age as a product */	if(strcmp(strf,"age")==0){ /* strf is "age" so that stre=Vm =V2 . */
Tage[cptcovage]=k; /* V2+V1+V4+V3age Tvar[4]=3, Tage[1] = 4 or V1+V1age Tvar[2]=1, Tage[1]=2 */	strcpy(strb,strd);
/printf("stre=%s ", stre);/	strcat(strb,"*");
} else if (strcmp(strd,"age")==0) { /* or ageVn /	strcat(strb,stre);
cptcovprod--;	}else{ /* strf=Vm If strf=V6 then stre=V2 */
cutl(stre,strb,strc,'V');	strcpy(strb,strf);
Tvar[k]=atoi(stre);	strcat(strb,"*");
Typevar[k]=1; /* 1 for age product */	strcat(strb,stre);
cptcovage++;	strcpy(strd,strb); /* in order for strd to not be "age" for next test (will be VnVm /
Tage[cptcovage]=k;	}
} else { /* Age is not in the model product V2+V1+V1V4+V3age+V3V2 strb=V3V2*/	/* printf("DEBUG FIXED k=%d, Tage[k]=%d, Tvar[Tage[k]=%d,FixedV[Tvar[Tage[k]]]=%d\n",k,Tage[k],Tvar[Tage[k]],FixedV[Tvar[Tage[k]]]); */
/* loops on k1=1 (V3V2) and k1=2 V4V3 */	/* FixedV[Tvar[Tage[k]]]=0; /\* HERY not sure if V7V4age Fixed might not exist yet\/ /
cptcovn++;	}else{ /* strc=VnVm (and strd=age) and should be strb=VnVm but want to keep original strb double product */
cptcovprodnoage++;k1++;	strcpy(stre,strb); /* save full b in stre */
	strcpy(strb,strc); /* save short c in new short b for next block strb=VnVm/
	strcpy(strf,strc); /* save short c in new short f */
	cutl(strc,strd,strf,''); / We get strd=Vn and strc=Vm for next block (strb=VnVm)/
	/* strcpy(strc,stre);/ / save full e in c for future */
	}
	cptcovdageprod++; /* double product with age Which product is it? */
	/* strcpy(strb,strc); /\* strb was ageV6V2 or V6V2age or V6ageV2 IS now V6V2 or V2age or ageV2 \/ */
	/* cutl(strc,strd,strb,''); /\ strd= V6 or V2 or age and strc= V2 or age or V2 \/ /
cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3V2 stre=3 strc=/	cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3V2 stre=3 strc=/
Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but	n=atoi(stre);
because this model-covariate is a construction we invent a new column
which is after existing variables ncovcol+nqv+ntv+nqtv + k1
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
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 */
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 */	m=atoi(strc);
Tposprod[k]=k1; /* Tposprod[3]=1, Tposprod[2]=5 */	cptcovage++; /* Counts the number of covariates which include age as a product */
Tvard[k1][1] =atoi(strc); /* m 1 for V1*/	Tage[cptcovage]=k; /* For ageV3V2 gives the position in model of covariates associated with age Tage[1]=6 HERY too*/
Tvardk[k][1] =atoi(strc); /* m 1 for V1*/	if(existcomb[n][m] == 0){
Tvard[k1][2] =atoi(stre); /* n 4 for V4*/	/* r /home/brouard/Documents/Recherches/REVES/Zachary/Zach-2022/Feinuo_Sun/Feinuo-threeway/femV12V15_3wayintNBe.imach */
Tvardk[k][2] =atoi(stre); /* n 4 for V4*/	printf("Warning in model combination V%dV%d should exist in the model before adding V%dV%d*age !\n",n,m,n,m);
k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in VnVm at the end of Tvar /	fprintf(ficlog,"Warning in model combination V%dV%d should exist in the model before adding V%dV%d*age !\n",n,m,n,m);
/* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) \/ /	fflush(ficlog);
/* Tvar[cptcovt+k2+1]=Tvard[k1][2]; /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) \/ /	k1++; /* The combination VnVm will be in the model so we create it at k1 /
/ncovcol=4 and model=V2+V1+V1V4+ageV3+V3V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */	k12++;
/* 1 2 3 4 5 \| Tvar[5+1)=1, Tvar[7]=2 */	existcomb[n][m]=k1;
for (i=1; i<=lastobs;i++){	existcomb[m][n]=k1;
/* Computes the new covariate which is a product of	Tvar[k]=ncovcol+nqv+ntv+nqtv+k1;
covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */	Tprod[k1]=k; /* Tprod[1]=3(=V1V4) for V2+V1+V1V4+ageV3+V3V2+ ageV6V3 Gives the k position of the k1 double product VnVm or ageVnVm/
covar[ncovcol+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];	Tposprod[k]=k1; /* Tposprod[3]=1, Tposprod[2]=5 Gives the k1 double product VnVm or ageVnVm at the k position /
	Tvard[k1][1] =m; /* m 1 for V1*/
	Tvardk[k][1] =m; /* m 1 for V1*/
	Tvard[k1][2] =n; /* n 4 for V4*/
	Tvardk[k][2] =n; /* n 4 for V4*/
	/* Tvar[Tage[cptcovage]]=k1;/ / Tvar[6=ageV3V2]=9 (new fixed covariate) / / We don't know about Fixed yet HERE */
	if( FixedV[Tvardk[k][1]] == 0 && FixedV[Tvardk[k][2]] == 0){ /* If the product is a fixed covariate then we feed the new column with VnVm /
	for (i=1; i<=lastobs;i++){/* For fixed product */
	/* Computes the new covariate which is a product of
	covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
	covar[ncovcolt+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
	}
	cptcovprodage++; /* Counting the number of fixed covariate with age */
	FixedV[ncovcolt+k12]=0; /* We expand VnVm /
	k12++;
	FixedV[ncovcolt+k12]=0;
	}else{ /End of FixedV /
	cptcovprodvage++; /* Counting the number of varying covariate with age */
	FixedV[ncovcolt+k12]=1; /* We expand VnVm /
	k12++;
	FixedV[ncovcolt+k12]=1;
	}
	}else{ /* k1 VnVm already exists /
	k11=existcomb[n][m];
	Tposprod[k]=k11; /* OK */
	Tvar[k]=Tvar[Tprod[k11]]; /* HERY */
	Tvardk[k][1]=m;
	Tvardk[k][2]=n;
	if( FixedV[Tvardk[k][1]] == 0 && FixedV[Tvardk[k][2]] == 0){ /* If the product is a fixed covariate then we feed the new column with VnVm /
	/cptcovage++;/ /* Counts the number of covariates which include age as a product */
	cptcovprodage++; /* Counting the number of fixed covariate with age */
	/Tage[cptcovage]=k;/ /* For ageV3V2 Tage[1]=V3V3=9 HERY too/
	Tvar[Tage[cptcovage]]=k1;
	FixedV[ncovcolt+k12]=0; /* We expand VnVm /
	k12++;
	FixedV[ncovcolt+k12]=0;
	}else{ /* Already exists but time varying (and age) */
	/cptcovage++;/ /* Counts the number of covariates which include age as a product */
	/Tage[cptcovage]=k;/ /* For ageV3V2 Tage[1]=V3V3=9 HERY too/
	/* Tvar[Tage[cptcovage]]=k1; */
	cptcovprodvage++;
	FixedV[ncovcolt+k12]=1; /* We expand VnVm /
	k12++;
	FixedV[ncovcolt+k12]=1;
	}
}	}
} /* End age is not in the model */	/* Tage[cptcovage]=k; /\* V2+V1+V4+V3age Tvar[4]=3, Tage[1] = 4 or V1+V1age Tvar[2]=1, Tage[1]=2 \/ /
} /* End if model includes a product */	/* Tvar[k]=k11; /\* HERY \/ /
else { /* not a product */	} else {/* simple product strb=ageVn so that c=Vn and d=age, or strb=Vnage so that c=age and d=Vn, or b=VnVm so that c=Vm and d=Vn /
	cptcovprod++;
	if (strcmp(strc,"age")==0) { /*< Model includes age: strb= Vnage c=age d=Vn*/
	/* covar is not filled and then is empty */
	cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
	Tvar[k]=atoi(stre); /* V2+V1+V5age+V4+V3age Tvar[5]=3 ; V1+V2age Tvar[2]=2; V1+V1age Tvar[2]=1 */
	Typevar[k]=1; /* 1 for age product */
	cptcovage++; /* Counts the number of covariates which include age as a product */
	Tage[cptcovage]=k; /* V2+V1+V4+V3age Tvar[4]=3, Tage[1] = 4 or V1+V1age Tvar[2]=1, Tage[1]=2 */
	if( FixedV[Tvar[k]] == 0){
	cptcovprodage++; /* Counting the number of fixed covariate with age */
	}else{
	cptcovprodvage++; /* Counting the number of fixedvarying covariate with age */
	}
	/printf("stre=%s ", stre);/
	} else if (strcmp(strd,"age")==0) { /* strb= ageVn c=Vn /
	cutl(stre,strb,strc,'V');
	Tvar[k]=atoi(stre);
	Typevar[k]=1; /* 1 for age product */
	cptcovage++;
	Tage[cptcovage]=k;
	if( FixedV[Tvar[k]] == 0){
	cptcovprodage++; /* Counting the number of fixed covariate with age */
	}else{
	cptcovprodvage++; /* Counting the number of fixedvarying covariate with age */
	}
	}else{ /* for product VnVm /
	Typevar[k]=2; /* 2 for product VnVm /
	cutl(stre,strb,strc,'V'); /* strc= Vn, stre is n; strb=V3V2 stre=3 strc=/
	n=atoi(stre);
	cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
	m=atoi(strc);
	k1++;
	cptcovprodnoage++;
	if(existcomb[n][m] != 0 \|\| existcomb[m][n] != 0){
	printf("Warning in model combination V%d*V%d already exists in the model in position k1=%d!\n",n,m,existcomb[n][m]);
	fprintf(ficlog,"Warning in model combination V%d*V%d already exists in the model in position k1=%d!\n",n,m,existcomb[n][m]);
	fflush(ficlog);
	k11=existcomb[n][m];
	Tvar[k]=ncovcol+nqv+ntv+nqtv+k11;
	Tposprod[k]=k11;
	Tprod[k11]=k;
	Tvardk[k][1] =m; /* m 1 for V1*/
	/* Tvard[k11][1] =m; /\* n 4 for V4\/ /
	Tvardk[k][2] =n; /* n 4 for V4*/
	/* Tvard[k11][2] =n; /\* n 4 for V4\/ /
	}else{ /* combination VnVm doesn't exist we create it (no age)/
	existcomb[n][m]=k1;
	existcomb[m][n]=k1;
	Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* ncovcolt+k1; For model-covariate k tells which data-covariate to use but
	because this model-covariate is a construction we invent a new column
	which is after existing variables ncovcol+nqv+ntv+nqtv + k1
	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
	Tvar[3=V1V4]=4+1=5 Tvar[5=V3V2]=4 + 2= 6, Tvar[4=ageV3]=3 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
	*/
	/* We need to feed some variables like TvarVV, but later on next loop because of ncovv (k2) is not correct */
	Tprod[k1]=k; /* Tprod[1]=3(=V1V4) for V2+V1+V1V4+ageV3+V3V2 +V6V2age */
	Tposprod[k]=k1; /* Tposprod[3]=1, Tposprod[2]=5 */
	Tvard[k1][1] =m; /* m 1 for V1*/
	Tvardk[k][1] =m; /* m 1 for V1*/
	Tvard[k1][2] =n; /* n 4 for V4*/
	Tvardk[k][2] =n; /* 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 /
	/* 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) \/ /
	/ncovcol=4 and model=V2+V1+V1V4+ageV3+V3V2, Tvar[3]=5, Tvar[4]=6, cptcovt=5 */
	/* 1 2 3 4 5 \| Tvar[5+1)=1, Tvar[7]=2 */
	if( FixedV[Tvardk[k][1]] == 0 && FixedV[Tvardk[k][2]] == 0){ /* If the product is a fixed covariate then we feed the new column with VnVm /
	for (i=1; i<=lastobs;i++){/* For fixed product */
	/* Computes the new covariate which is a product of
	covar[n][i]* covar[m][i] and stores it at ncovol+k1 May not be defined */
	covar[ncovcolt+k1][i]=covar[atoi(stre)][i]*covar[atoi(strc)][i];
	}
	/* TvarVV[k2]=n; */
	/* FixedV[ncovcolt+k2]=0; /\* or FixedV[Tvar[k]]=0; FixedV[TvarVV[ncovv]]=0 HERE \/ /
	/* TvarVV[k2+1]=m; */
	/* FixedV[ncovcolt+k2]=0; /\* or FixedV[Tvar[k]]=0; FixedV[TvarVV[ncovv]]=0 HERE \/ /
	}else{ /* not FixedV */
	/* TvarVV[k2]=n; */
	/* FixedV[ncovcolt+k2]=0; /\* or FixedV[Tvar[k]]=0; FixedV[TvarVV[ncovv]]=0 HERE \/ /
	/* TvarVV[k2+1]=m; */
	/* FixedV[ncovcolt+k2]=0; /\* or FixedV[Tvar[k]]=0; FixedV[TvarVV[ncovv]]=0 HERE \/ /
	}
	} /* End of creation of VnVm if not created by ageVnVm earlier /
	} /* End of product VnVm /
	} /* End of agedouble product or simple product /
	}else { /* not a product */
/printf("d=%s c=%s b=%s\n", strd,strc,strb);/	/printf("d=%s c=%s b=%s\n", strd,strc,strb);/
/* scanf("%d",i);*/	/* scanf("%d",i);*/
cutl(strd,strc,strb,'V');	cutl(strd,strc,strb,'V');
Line 10779 int decodemodel( char model[], int lasto	Line 11758 int decodemodel( char model[], int lasto
/*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);	/*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
scanf("%d",i);*/	scanf("%d",i);*/
} /* end of loop + on total covariates */	} /* end of loop + on total covariates */


} /* end if strlen(modelsave == 0) ageage might exist /	} /* end if strlen(modelsave == 0) ageage might exist /
} /* end if strlen(model == 0) */	} /* end if strlen(model == 0) */
	cptcovs=cptcovt - cptcovdageprod - cptcovprod;/*< Number of simple covariates V1 +V1age +V3 +V3V4 +ageage + agev4V3=> V1 + V3 =4+1-3=2 */

/*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.	/*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
If model=V1+V1age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0/	If model=V1+V1age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0/

Line 10807 int decodemodel( char model[], int lasto	Line 11789 int decodemodel( char model[], int lasto
/* Tvar[k] is the value n of Vn with n varying for 1 to nvcol, or p Vp=VnVm for product /	/* Tvar[k] is the value n of Vn with n varying for 1 to nvcol, or p Vp=VnVm for product /
/* Computing effective variables, ie used by the model, that is from the cptcovt variables */	/* Computing effective variables, ie used by the model, that is from the cptcovt variables */
printf("Model=1+age+%s\n\	printf("Model=1+age+%s\n\
Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\	Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product, 3 for double product with age \n\
Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\	Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);	Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
fprintf(ficlog,"Model=1+age+%s\n\	fprintf(ficlog,"Model=1+age+%s\n\
Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\	Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product, 3 for double product with age \n\
Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\	Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);	Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
for(k=-1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}	for(k=-1;k<=NCOVMAX; k++){ Fixed[k]=0; Dummy[k]=0;}
for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */	for(k=1;k<=NCOVMAX; k++){TvarFind[k]=0; TvarVind[k]=0;}


	/* Second loop for calculating Fixed[k], Dummy[k]*/


	for(k=1, ncovf=0, nsd=0, nsq=0, ncovv=0,ncovva=0,ncovvta=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0, ncovvt=0;k<=cptcovt; k++){ /* or cptocvt loop on k from model */
if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */	if (Tvar[k] <=ncovcol && Typevar[k]==0 ){ /* Simple fixed dummy (<=ncovcol) covariates */
Fixed[k]= 0;	Fixed[k]= 0;
Dummy[k]= 0;	Dummy[k]= 0;
Line 10830 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 11818 Dummy[k] 0=dummy (0 1), 1 quantitative (
TvarFind[ncovf]=k;	TvarFind[ncovf]=k;
TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */	TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */	TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
}else if( Tvar[k] <=ncovcol && Typevar[k]==2){ /* Product of fixed dummy (<=ncovcol) covariates */	/* }else if( Tvar[k] <=ncovcol && Typevar[k]==2){ /\* Product of fixed dummy (<=ncovcol) covariates For a fixed product k is higher than ncovcol \/ /
Fixed[k]= 0;
Dummy[k]= 0;
ncoveff++;
ncovf++;
modell[k].maintype= FTYPE;
TvarF[ncovf]=Tvar[k];
/* TnsdVar[Tvar[k]]=nsd; / / To be done */
TvarFind[ncovf]=k;
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 */
}else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){/* Remind that product VnVm are added in k Only simple fixed quantitative variable /	}else if( Tvar[k] <=ncovcol+nqv && Typevar[k]==0){/* Remind that product VnVm are added in k Only simple fixed quantitative variable /
Fixed[k]= 0;	Fixed[k]= 0;
Dummy[k]= 1;	Dummy[k]= 1;
Line 10856 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 11834 Dummy[k] 0=dummy (0 1), 1 quantitative (
TvarFQ[nqfveff]=Tvar[k]-ncovcol; /* TvarFQ[1]=V2-1=1st in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple fixed quantitative variable */	TvarFQ[nqfveff]=Tvar[k]-ncovcol; /* TvarFQ[1]=V2-1=1st in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple fixed quantitative variable */
TvarFQind[nqfveff]=k; /* TvarFQind[1]=6 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple fixed quantitative variable */	TvarFQind[nqfveff]=k; /* TvarFQind[1]=6 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple fixed quantitative variable */
}else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying dummy variables */	}else if( Tvar[k] <=ncovcol+nqv+ntv && Typevar[k]==0){/* Only simple time varying dummy variables */
	/# ID V1 V2 weight birth death 1st s1 V3 V4 V5 2nd s2 /
	/* model V1+V3+ageV1+ageV3+V1V3 /
	/* Tvar={1, 3, 1, 3, 6}, the 6 comes from the fact that there are already V1, V2, V3, V4, V5 native covariates */
	ncovvt++;
	TvarVV[ncovvt]=Tvar[k]; /* TvarVV[1]=V3 (first time varying in the model equation */
	TvarVVind[ncovvt]=k; /* TvarVVind[1]=2 (second position in the model equation */

Fixed[k]= 1;	Fixed[k]= 1;
Dummy[k]= 0;	Dummy[k]= 0;
ntveff++; /* Only simple time varying dummy variable */	ntveff++; /* Only simple time varying dummy variable */
Line 10873 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 11858 Dummy[k] 0=dummy (0 1), 1 quantitative (
printf("Quasi Tmodelind[%d]=%d,Tvar[Tmodelind[%d]]=V%d, ncovcol=%d, nqv=%d,Tvar[k]- ncovcol-nqv=%d\n",ntveff,k,ntveff,Tvar[k], ncovcol, nqv,Tvar[k]- ncovcol-nqv);	printf("Quasi Tmodelind[%d]=%d,Tvar[Tmodelind[%d]]=V%d, ncovcol=%d, nqv=%d,Tvar[k]- ncovcol-nqv=%d\n",ntveff,k,ntveff,Tvar[k], ncovcol, nqv,Tvar[k]- ncovcol-nqv);
printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);	printf("Quasi TmodelInvind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv);
}else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/	}else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv && Typevar[k]==0){ /* Only simple time varying quantitative variable V5*/
	/# ID V1 V2 weight birth death 1st s1 V3 V4 V5 2nd s2 /
	/* model V1+V3+ageV1+ageV3+V1V3 /
	/* Tvar={1, 3, 1, 3, 6}, the 6 comes from the fact that there are already V1, V2, V3, V4, V5 native covariates */
	ncovvt++;
	TvarVV[ncovvt]=Tvar[k]; /* TvarVV[1]=V3 (first time varying in the model equation */
	TvarVVind[ncovvt]=k; /* TvarVV[1]=V3 (first time varying in the model equation */

Fixed[k]= 1;	Fixed[k]= 1;
Dummy[k]= 1;	Dummy[k]= 1;
nqtveff++;	nqtveff++;
Line 10888 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 11880 Dummy[k] 0=dummy (0 1), 1 quantitative (
TvarVQind[nqtveff]=k; /* TvarVQind[1]=1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple time varying quantitative variable */	TvarVQind[nqtveff]=k; /* TvarVQind[1]=1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple time varying quantitative variable */
TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */	TmodelInvQind[nqtveff]=Tvar[k]- ncovcol-nqv-ntv;/* Only simple time varying quantitative variable */
/* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable \/ /	/* Tmodeliqind[k]=nqtveff;/\* Only simple time varying quantitative variable \/ /
printf("Quasi TmodelQind[%d]=%d,Tvar[TmodelQind[%d]]=V%d, ncovcol=%d, nqv=%d, ntv=%d,Tvar[k]- ncovcol-nqv-ntv=%d\n",nqtveff,k,nqtveff,Tvar[k], ncovcol, nqv, ntv, Tvar[k]- ncovcol-nqv-ntv);	/* printf("Quasi TmodelQind[%d]=%d,Tvar[TmodelQind[%d]]=V%d, ncovcol=%d, nqv=%d, ntv=%Ad,Tvar[k]- ncovcol-nqv-ntv=%d\n",nqtveff,k,nqtveff,Tvar[k], ncovcol, nqv, ntv, Tvar[k]- ncovcol-nqv-ntv); */
printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv);	/* printf("Quasi TmodelInvQind[%d]=%d\n",k,Tvar[k]- ncovcol-nqv-ntv); */
}else if (Typevar[k] == 1) { /* product with age */	}else if (Typevar[k] == 1) { /* product with age */
ncova++;	ncova++;
TvarA[ncova]=Tvar[k];	TvarA[ncova]=Tvar[k];
TvarAind[ncova]=k;	TvarAind[ncova]=k;
	/** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age 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 (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */	if (Tvar[k] <=ncovcol ){ /* Product age with fixed dummy covariatee */
Fixed[k]= 2;	Fixed[k]= 2;
Dummy[k]= 2;	Dummy[k]= 2;
modell[k].maintype= ATYPE;	modell[k].maintype= ATYPE;
modell[k].subtype= APFD;	modell[k].subtype= APFD;
	ncovta++;
	TvarAVVA[ncovta]=Tvar[k]; /* (2)ageV3 /
	TvarAVVAind[ncovta]=k;
/* ncoveff++; */	/* ncoveff++; */
}else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product VnVm are added in k/	}else if( Tvar[k] <=ncovcol+nqv) { /* Remind that product VnVm are added in k/
Fixed[k]= 2;	Fixed[k]= 2;
Dummy[k]= 3;	Dummy[k]= 3;
modell[k].maintype= ATYPE;	modell[k].maintype= ATYPE;
modell[k].subtype= APFQ; /* Product age * fixed quantitative */	modell[k].subtype= APFQ; /* Product age * fixed quantitative */
	ncovta++;
	TvarAVVA[ncovta]=Tvar[k]; /* */
	TvarAVVAind[ncovta]=k;
/* nqfveff++; /\* Only simple fixed quantitative variable \/ /	/* nqfveff++; /\* Only simple fixed quantitative variable \/ /
}else if( Tvar[k] <=ncovcol+nqv+ntv ){	}else if( Tvar[k] <=ncovcol+nqv+ntv ){
Fixed[k]= 3;	Fixed[k]= 3;
Dummy[k]= 2;	Dummy[k]= 2;
modell[k].maintype= ATYPE;	modell[k].maintype= ATYPE;
modell[k].subtype= APVD; /* Product age * varying dummy */	modell[k].subtype= APVD; /* Product age * varying dummy */
	ncovva++;
	TvarVVA[ncovva]=Tvar[k]; /* (1)+ageV6 + (2)ageV7 */
	TvarVVAind[ncovva]=k;
	ncovta++;
	TvarAVVA[ncovta]=Tvar[k]; /* */
	TvarAVVAind[ncovta]=k;
/* ntveff++; /\* Only simple time varying dummy variable \/ /	/* ntveff++; /\* Only simple time varying dummy variable \/ /
}else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){	}else if( Tvar[k] <=ncovcol+nqv+ntv+nqtv){
Fixed[k]= 3;	Fixed[k]= 3;
Dummy[k]= 3;	Dummy[k]= 3;
modell[k].maintype= ATYPE;	modell[k].maintype= ATYPE;
modell[k].subtype= APVQ; /* Product age * varying quantitative */	modell[k].subtype= APVQ; /* Product age * varying quantitative */
	ncovva++;
	TvarVVA[ncovva]=Tvar[k]; /* */
	TvarVVAind[ncovva]=k;
	ncovta++;
	TvarAVVA[ncovta]=Tvar[k]; /* (1)+ageV6 + (2)ageV7 */
	TvarAVVAind[ncovta]=k;
/* nqtveff++;/\* Only simple time varying quantitative variable \/ /	/* nqtveff++;/\* Only simple time varying quantitative variable \/ /
}	}
}else if (Typevar[k] == 2) { /* product without age */	}else if( Tposprod[k]>0 && Typevar[k]==2){ /* Detects if fixed product no age VmVn /
k1=Tposprod[k];	printf("MEMORY ERRORR k=%d Tposprod[k]=%d, Typevar[k]=%d\n ",k, Tposprod[k], Typevar[k]);
if(Tvard[k1][1] <=ncovcol){	if(FixedV[Tvardk[k][1]] == 0 && FixedV[Tvardk[k][2]] == 0){ /* Needs a fixed product Product of fixed dummy (<=ncovcol) covariates For a fixed product k is higher than ncovcol V3V2 /
if(Tvard[k1][2] <=ncovcol){	printf("MEMORY ERRORR k=%d Tvardk[k][1]=%d, Tvardk[k][2]=%d, FixedV[Tvardk[k][1]]=%d,FixedV[Tvardk[k][2]]=%d\n ",k,Tvardk[k][1],Tvardk[k][2],FixedV[Tvardk[k][1]],FixedV[Tvardk[k][2]]);
Fixed[k]= 1;	Fixed[k]= 0;
Dummy[k]= 0;	Dummy[k]= 0;
	ncoveff++;
	ncovf++;
	/* ncovv++; */
	/* TvarVV[ncovv]=Tvardk[k][1]; */
	/* FixedV[ncovcolt+ncovv]=0; /\* or FixedV[TvarVV[ncovv]]=0 HERE \/ /
	/* ncovv++; */
	/* TvarVV[ncovv]=Tvardk[k][2]; */
	/* FixedV[ncovcolt+ncovv]=0; /\* or FixedV[TvarVV[ncovv]]=0 HERE \/ /
	modell[k].maintype= FTYPE;
	TvarF[ncovf]=Tvar[k];
	/* TnsdVar[Tvar[k]]=nsd; / / To be done */
	TvarFind[ncovf]=k;
	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 */
	}else{/* product varying Vn * Vm without age, V1+V3+ageV1+ageV3+V1V3 looking at V1V3, Typevar={0, 0, 1, 1, 2}, k=5, V1 is fixed, V3 is timevary, V5 is a product */
	/# ID V1 V2 weight birth death 1st s1 V3 V4 V5 2nd s2 /
	/* model V1+V3+ageV1+ageV3+V1V3 + V1V3age/
	/* Tvar={1, 3, 1, 3, 6, 6}, the 6 comes from the fact that there are already V1, V2, V3, V4, V5 native covariates */
	k1=Tposprod[k]; /* Position in the products of product k, Tposprod={0, 0, 0, 0, 1, 1} k1=1 first product but second time varying because of V3 */
	ncovvt++;
	TvarVV[ncovvt]=Tvard[k1][1]; /* TvarVV[2]=V1 (because TvarVV[1] was V3, first time varying covariates */
	TvarVVind[ncovvt]=k; /* TvarVVind[2]=5 (because TvarVVind[2] was V1V3 at position 5 /
	ncovvt++;
	TvarVV[ncovvt]=Tvard[k1][2]; /* TvarVV[3]=V3 */
	TvarVVind[ncovvt]=k; /* TvarVVind[2]=5 (because TvarVVind[2] was V1V3 at position 5 /

	/** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age 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(Tvard[k1][1] <=ncovcol){ /* Vn is dummy fixed, (Tvard[1][1]=V1), (Tvard[1][1]=V3 time varying) */
	if(Tvard[k1][2] <=ncovcol){ /* Vm is dummy fixed */
	Fixed[k]= 1;
	Dummy[k]= 0;
	modell[k].maintype= FTYPE;
	modell[k].subtype= FPDD; /* Product fixed dummy * fixed dummy */
	ncovf++; /* Fixed variables without age */
	TvarF[ncovf]=Tvar[k];
	TvarFind[ncovf]=k;
	}else if(Tvard[k1][2] <=ncovcol+nqv){ /* Vm is quanti fixed */
	Fixed[k]= 0; /* Fixed product */
	Dummy[k]= 1;
	modell[k].maintype= FTYPE;
	modell[k].subtype= FPDQ; /* Product fixed dummy * fixed quantitative */
	ncovf++; /* Varying variables without age */
	TvarF[ncovf]=Tvar[k];
	TvarFind[ncovf]=k;
	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ /* Vm is a time varying dummy covariate */
	Fixed[k]= 1;
	Dummy[k]= 0;
	modell[k].maintype= VTYPE;
	modell[k].subtype= VPDD; /* Product fixed dummy * varying dummy */
	ncovv++; /* Varying variables without age */
	TvarV[ncovv]=Tvar[k]; /* TvarV[1]=Tvar[5]=5 because there is a V4 */
	TvarVind[ncovv]=k;/* TvarVind[1]=5 */
	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ /* Vm is a time varying quantitative covariate */
	Fixed[k]= 1;
	Dummy[k]= 1;
	modell[k].maintype= VTYPE;
	modell[k].subtype= VPDQ; /* Product fixed dummy * varying quantitative */
	ncovv++; /* Varying variables without age */
	TvarV[ncovv]=Tvar[k];
	TvarVind[ncovv]=k;
	}
	}else if(Tvard[k1][1] <=ncovcol+nqv){ /* Vn is fixed quanti */
	if(Tvard[k1][2] <=ncovcol){ /* Vm is fixed dummy */
	Fixed[k]= 0; /* Fixed product */
	Dummy[k]= 1;
	modell[k].maintype= FTYPE;
	modell[k].subtype= FPDQ; /* Product fixed quantitative * fixed dummy */
	ncovf++; /* Fixed variables without age */
	TvarF[ncovf]=Tvar[k];
	TvarFind[ncovf]=k;
	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ /* Vm is time varying */
	Fixed[k]= 1;
	Dummy[k]= 1;
	modell[k].maintype= VTYPE;
	modell[k].subtype= VPDQ; /* Product fixed quantitative * varying dummy */
	ncovv++; /* Varying variables without age */
	TvarV[ncovv]=Tvar[k];
	TvarVind[ncovv]=k;
	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ /* Vm is time varying quanti */
	Fixed[k]= 1;
	Dummy[k]= 1;
	modell[k].maintype= VTYPE;
	modell[k].subtype= VPQQ; /* Product fixed quantitative * varying quantitative */
	ncovv++; /* Varying variables without age */
	TvarV[ncovv]=Tvar[k];
	TvarVind[ncovv]=k;
	ncovv++; /* Varying variables without age */
	TvarV[ncovv]=Tvar[k];
	TvarVind[ncovv]=k;
	}
	}else if(Tvard[k1][1] <=ncovcol+nqv+ntv){ /* Vn is time varying dummy */
	if(Tvard[k1][2] <=ncovcol){
	Fixed[k]= 1;
	Dummy[k]= 1;
	modell[k].maintype= VTYPE;
	modell[k].subtype= VPDD; /* Product time varying dummy * fixed dummy */
	ncovv++; /* Varying variables without age */
	TvarV[ncovv]=Tvar[k];
	TvarVind[ncovv]=k;
	}else if(Tvard[k1][2] <=ncovcol+nqv){
	Fixed[k]= 1;
	Dummy[k]= 1;
	modell[k].maintype= VTYPE;
	modell[k].subtype= VPDQ; /* Product time varying dummy * fixed quantitative */
	ncovv++; /* Varying variables without age */
	TvarV[ncovv]=Tvar[k];
	TvarVind[ncovv]=k;
	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
	Fixed[k]= 1;
	Dummy[k]= 0;
	modell[k].maintype= VTYPE;
	modell[k].subtype= VPDD; /* Product time varying dummy * time varying dummy */
	ncovv++; /* Varying variables without age */
	TvarV[ncovv]=Tvar[k];
	TvarVind[ncovv]=k;
	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
	Fixed[k]= 1;
	Dummy[k]= 1;
	modell[k].maintype= VTYPE;
	modell[k].subtype= VPDQ; /* Product time varying dummy * time varying quantitative */
	ncovv++; /* Varying variables without age */
	TvarV[ncovv]=Tvar[k];
	TvarVind[ncovv]=k;
	}
	}else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){ /* Vn is time varying quanti */
	if(Tvard[k1][2] <=ncovcol){
	Fixed[k]= 1;
	Dummy[k]= 1;
	modell[k].maintype= VTYPE;
	modell[k].subtype= VPDQ; /* Product time varying quantitative * fixed dummy */
	ncovv++; /* Varying variables without age */
	TvarV[ncovv]=Tvar[k];
	TvarVind[ncovv]=k;
	}else if(Tvard[k1][2] <=ncovcol+nqv){
	Fixed[k]= 1;
	Dummy[k]= 1;
	modell[k].maintype= VTYPE;
	modell[k].subtype= VPQQ; /* Product time varying quantitative * fixed quantitative */
	ncovv++; /* Varying variables without age */
	TvarV[ncovv]=Tvar[k];
	TvarVind[ncovv]=k;
	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
	Fixed[k]= 1;
	Dummy[k]= 1;
	modell[k].maintype= VTYPE;
	modell[k].subtype= VPDQ; /* Product time varying quantitative * time varying dummy */
	ncovv++; /* Varying variables without age */
	TvarV[ncovv]=Tvar[k];
	TvarVind[ncovv]=k;
	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
	Fixed[k]= 1;
	Dummy[k]= 1;
	modell[k].maintype= VTYPE;
	modell[k].subtype= VPQQ; /* Product time varying quantitative * time varying quantitative */
	ncovv++; /* Varying variables without age */
	TvarV[ncovv]=Tvar[k];
	TvarVind[ncovv]=k;
	}
	}else{
	printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
	fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
	} /end k1/
	}
	}else if(Typevar[k] == 3){ /* product Vn * Vm with age, V1+V3+ageV1+ageV3+V1V3 looking at V1V3, Typevar={0, 0, 1, 1, 2}, k=5, V1 is fixed, V3 is timevary, V5 is a product */
	/# ID V1 V2 weight birth death 1st s1 V3 V4 V5 2nd s2 /
	/* model V1+V3+ageV1+ageV3+V1V3 + V1V3age/
	/* Tvar={1, 3, 1, 3, 6, 6}, the 6 comes from the fact that there are already V1, V2, V3, V4, V5 native covariates */
	k1=Tposprod[k]; /* Position in the products of product k, Tposprod={0, 0, 0, 0, 1, 1} k1=1 first product but second time varying because of V3 */
	ncova++;
	TvarA[ncova]=Tvard[k1][1]; /* TvarVV[2]=V1 (because TvarVV[1] was V3, first time varying covariates */
	TvarAind[ncova]=k; /* TvarVVind[2]=5 (because TvarVVind[2] was V1V3 at position 5 /
	ncova++;
	TvarA[ncova]=Tvard[k1][2]; /* TvarVV[3]=V3 */
	TvarAind[ncova]=k; /* TvarVVind[2]=5 (because TvarVVind[2] was V1V3 at position 5 /

	/** Fixed[k] 0=fixed, 1 varying, 2 fixed with age product, 3 varying with age 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( FixedV[Tvardk[k][1]] == 0 && FixedV[Tvardk[k][2]] == 0){
	ncovta++;
	TvarAVVA[ncovta]=Tvard[k1][1]; /* ageV6V3 +ageV7V3 + ageV6V4 +ageV7V4 */
	TvarAVVAind[ncovta]=k;
	ncovta++;
	TvarAVVA[ncovta]=Tvard[k1][2]; /* ageV6V3 +ageV7V3 + ageV6V4 +ageV7V4 */
	TvarAVVAind[ncovta]=k;
	}else{
	ncovva++; /* HERY reached */
	TvarVVA[ncovva]=Tvard[k1][1]; /* ageV6V3 +ageV7V3 + ageV6V4 +ageV7V4 */
	TvarVVAind[ncovva]=k;
	ncovva++;
	TvarVVA[ncovva]=Tvard[k1][2]; /* */
	TvarVVAind[ncovva]=k;
	ncovta++;
	TvarAVVA[ncovta]=Tvard[k1][1]; /* ageV6V3 +ageV7V3 + ageV6V4 +ageV7V4 */
	TvarAVVAind[ncovta]=k;
	ncovta++;
	TvarAVVA[ncovta]=Tvard[k1][2]; /* ageV6V3 +ageV7V3 + ageV6V4 +ageV7V4 */
	TvarAVVAind[ncovta]=k;
	}
	if(Tvard[k1][1] <=ncovcol){ /* Vn is dummy fixed, (Tvard[1][1]=V1), (Tvard[1][1]=V3 time varying) */
	if(Tvard[k1][2] <=ncovcol){ /* Vm is dummy fixed */
	Fixed[k]= 2;
	Dummy[k]= 2;
modell[k].maintype= FTYPE;	modell[k].maintype= FTYPE;
modell[k].subtype= FPDD; /* Product fixed dummy * fixed dummy */	modell[k].subtype= FPDD; /* Product fixed dummy * fixed dummy */
ncovf++; /* Fixed variables without age */	/* TvarF[ncova]=Tvar[k]; /\* Problem to solve \/ /
TvarF[ncovf]=Tvar[k];	/* TvarFind[ncova]=k; */
TvarFind[ncovf]=k;	}else if(Tvard[k1][2] <=ncovcol+nqv){ /* Vm is quanti fixed */
}else if(Tvard[k1][2] <=ncovcol+nqv){	Fixed[k]= 2; /* Fixed product */
Fixed[k]= 0; /* or 2 ?*/	Dummy[k]= 3;
Dummy[k]= 1;
modell[k].maintype= FTYPE;	modell[k].maintype= FTYPE;
modell[k].subtype= FPDQ; /* Product fixed dummy * fixed quantitative */	modell[k].subtype= FPDQ; /* Product fixed dummy * fixed quantitative */
ncovf++; /* Varying variables without age */	/* TvarF[ncova]=Tvar[k]; */
TvarF[ncovf]=Tvar[k];	/* TvarFind[ncova]=k; */
TvarFind[ncovf]=k;	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ /* Vm is a time varying dummy covariate */
}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){	Fixed[k]= 3;
Fixed[k]= 1;	Dummy[k]= 2;
Dummy[k]= 0;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPDD; /* Product fixed dummy * varying dummy */	modell[k].subtype= VPDD; /* Product fixed dummy * varying dummy */
ncovv++; /* Varying variables without age */	TvarV[ncova]=Tvar[k]; /* TvarV[1]=Tvar[5]=5 because there is a V4 */
TvarV[ncovv]=Tvar[k];	TvarVind[ncova]=k;/* TvarVind[1]=5 */
TvarVind[ncovv]=k;	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ /* Vm is a time varying quantitative covariate */
}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){	Fixed[k]= 3;
Fixed[k]= 1;	Dummy[k]= 3;
Dummy[k]= 1;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPDQ; /* Product fixed dummy * varying quantitative */	modell[k].subtype= VPDQ; /* Product fixed dummy * varying quantitative */
ncovv++; /* Varying variables without age */	/* ncovv++; /\* Varying variables without age \/ /
TvarV[ncovv]=Tvar[k];	/* TvarV[ncovv]=Tvar[k]; */
TvarVind[ncovv]=k;	/* TvarVind[ncovv]=k; */
}	}
}else if(Tvard[k1][1] <=ncovcol+nqv){	}else if(Tvard[k1][1] <=ncovcol+nqv){ /* Vn is fixed quanti */
if(Tvard[k1][2] <=ncovcol){	if(Tvard[k1][2] <=ncovcol){ /* Vm is fixed dummy */
Fixed[k]= 0; /* or 2 ?*/	Fixed[k]= 2; /* Fixed product */
Dummy[k]= 1;	Dummy[k]= 2;
modell[k].maintype= FTYPE;	modell[k].maintype= FTYPE;
modell[k].subtype= FPDQ; /* Product fixed quantitative * fixed dummy */	modell[k].subtype= FPDQ; /* Product fixed quantitative * fixed dummy */
ncovf++; /* Fixed variables without age */	/* ncova++; /\* Fixed variables with age \/ /
TvarF[ncovf]=Tvar[k];	/* TvarF[ncovf]=Tvar[k]; */
TvarFind[ncovf]=k;	/* TvarFind[ncovf]=k; */
}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){ /* Vm is time varying */
Fixed[k]= 1;	Fixed[k]= 2;
Dummy[k]= 1;	Dummy[k]= 3;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPDQ; /* Product fixed quantitative * varying dummy */	modell[k].subtype= VPDQ; /* Product fixed quantitative * varying dummy */
ncovv++; /* Varying variables without age */	/* ncova++; /\* Varying variables with age \/ /
TvarV[ncovv]=Tvar[k];	/* TvarV[ncova]=Tvar[k]; */
TvarVind[ncovv]=k;	/* TvarVind[ncova]=k; */
}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){ /* Vm is time varying quanti */
Fixed[k]= 1;	Fixed[k]= 3;
Dummy[k]= 1;	Dummy[k]= 2;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPQQ; /* Product fixed quantitative * varying quantitative */	modell[k].subtype= VPQQ; /* Product fixed quantitative * varying quantitative */
ncovv++; /* Varying variables without age */	ncova++; /* Varying variables without age */
TvarV[ncovv]=Tvar[k];	TvarV[ncova]=Tvar[k];
TvarVind[ncovv]=k;	TvarVind[ncova]=k;
ncovv++; /* Varying variables without age */	/* ncova++; /\* Varying variables without age \/ /
TvarV[ncovv]=Tvar[k];	/* TvarV[ncova]=Tvar[k]; */
TvarVind[ncovv]=k;	/* TvarVind[ncova]=k; */
}	}
}else if(Tvard[k1][1] <=ncovcol+nqv+ntv){	}else if(Tvard[k1][1] <=ncovcol+nqv+ntv){ /* Vn is time varying dummy */
if(Tvard[k1][2] <=ncovcol){	if(Tvard[k1][2] <=ncovcol){
Fixed[k]= 1;	Fixed[k]= 2;
Dummy[k]= 1;	Dummy[k]= 2;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPDD; /* Product time varying dummy * fixed dummy */	modell[k].subtype= VPDD; /* Product time varying dummy * fixed dummy */
ncovv++; /* Varying variables without age */	/* ncova++; /\* Varying variables with age \/ /
TvarV[ncovv]=Tvar[k];	/* TvarV[ncova]=Tvar[k]; */
TvarVind[ncovv]=k;	/* TvarVind[ncova]=k; */
}else if(Tvard[k1][2] <=ncovcol+nqv){	}else if(Tvard[k1][2] <=ncovcol+nqv){
Fixed[k]= 1;	Fixed[k]= 2;
Dummy[k]= 1;	Dummy[k]= 3;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPDQ; /* Product time varying dummy * fixed quantitative */	modell[k].subtype= VPDQ; /* Product time varying dummy * fixed quantitative */
ncovv++; /* Varying variables without age */	/* ncova++; /\* Varying variables with age \/ /
TvarV[ncovv]=Tvar[k];	/* TvarV[ncova]=Tvar[k]; */
TvarVind[ncovv]=k;	/* TvarVind[ncova]=k; */
}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
Fixed[k]= 1;	Fixed[k]= 3;
Dummy[k]= 0;	Dummy[k]= 2;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPDD; /* Product time varying dummy * time varying dummy */	modell[k].subtype= VPDD; /* Product time varying dummy * time varying dummy */
ncovv++; /* Varying variables without age */	/* ncova++; /\* Varying variables with age \/ /
TvarV[ncovv]=Tvar[k];	/* TvarV[ncova]=Tvar[k]; */
TvarVind[ncovv]=k;	/* TvarVind[ncova]=k; */
}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
Fixed[k]= 1;	Fixed[k]= 3;
Dummy[k]= 1;	Dummy[k]= 3;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPDQ; /* Product time varying dummy * time varying quantitative */	modell[k].subtype= VPDQ; /* Product time varying dummy * time varying quantitative */
ncovv++; /* Varying variables without age */	/* ncova++; /\* Varying variables with age \/ /
TvarV[ncovv]=Tvar[k];	/* TvarV[ncova]=Tvar[k]; */
TvarVind[ncovv]=k;	/* TvarVind[ncova]=k; */
}	}
}else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){	}else if(Tvard[k1][1] <=ncovcol+nqv+ntv+nqtv){ /* Vn is time varying quanti */
if(Tvard[k1][2] <=ncovcol){	if(Tvard[k1][2] <=ncovcol){
Fixed[k]= 1;	Fixed[k]= 2;
Dummy[k]= 1;	Dummy[k]= 2;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPDQ; /* Product time varying quantitative * fixed dummy */	modell[k].subtype= VPDQ; /* Product time varying quantitative * fixed dummy */
ncovv++; /* Varying variables without age */	/* ncova++; /\* Varying variables with age \/ /
TvarV[ncovv]=Tvar[k];	/* TvarV[ncova]=Tvar[k]; */
TvarVind[ncovv]=k;	/* TvarVind[ncova]=k; */
}else if(Tvard[k1][2] <=ncovcol+nqv){	}else if(Tvard[k1][2] <=ncovcol+nqv){
Fixed[k]= 1;	Fixed[k]= 2;
Dummy[k]= 1;	Dummy[k]= 3;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPQQ; /* Product time varying quantitative * fixed quantitative */	modell[k].subtype= VPQQ; /* Product time varying quantitative * fixed quantitative */
ncovv++; /* Varying variables without age */	/* ncova++; /\* Varying variables with age \/ /
TvarV[ncovv]=Tvar[k];	/* TvarV[ncova]=Tvar[k]; */
TvarVind[ncovv]=k;	/* TvarVind[ncova]=k; */
}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv){
Fixed[k]= 1;	Fixed[k]= 3;
Dummy[k]= 1;	Dummy[k]= 2;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPDQ; /* Product time varying quantitative * time varying dummy */	modell[k].subtype= VPDQ; /* Product time varying quantitative * time varying dummy */
ncovv++; /* Varying variables without age */	/* ncova++; /\* Varying variables with age \/ /
TvarV[ncovv]=Tvar[k];	/* TvarV[ncova]=Tvar[k]; */
TvarVind[ncovv]=k;	/* TvarVind[ncova]=k; */
}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){	}else if(Tvard[k1][2] <=ncovcol+nqv+ntv+nqtv){
Fixed[k]= 1;	Fixed[k]= 3;
Dummy[k]= 1;	Dummy[k]= 3;
modell[k].maintype= VTYPE;	modell[k].maintype= VTYPE;
modell[k].subtype= VPQQ; /* Product time varying quantitative * time varying quantitative */	modell[k].subtype= VPQQ; /* Product time varying quantitative * time varying quantitative */
ncovv++; /* Varying variables without age */	/* ncova++; /\* Varying variables with age \/ /
TvarV[ncovv]=Tvar[k];	/* TvarV[ncova]=Tvar[k]; */
TvarVind[ncovv]=k;	/* TvarVind[ncova]=k; */
}	}
}else{	}else{
printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);	printf("Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);	fprintf(ficlog,"Error unknown type of covariate: Tvard[%d][1]=%d,Tvard[%d][2]=%d\n",k1,Tvard[k1][1],k1,Tvard[k1][2]);
} /end k1/	} /end k1/
}else{	} else{
printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);	printf("Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
fprintf(ficlog,"Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);	fprintf(ficlog,"Error, current version can't treat for performance reasons, Tvar[%d]=%d, Typevar[%d]=%d\n", k, Tvar[k], k, Typevar[k]);
}	}
printf("Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);	/* printf("Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]); */
printf(" modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype);	/* printf(" modell[%d].maintype=%d, modell[%d].subtype=%d\n",k,modell[k].maintype,k,modell[k].subtype); */
fprintf(ficlog,"Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);	fprintf(ficlog,"Decodemodel, k=%d, Tvar[%d]=V%d,Typevar=%d, Fixed=%d, Dummy=%d\n",k, k,Tvar[k],Typevar[k],Fixed[k],Dummy[k]);
}	}
	ncovvta=ncovva;
/* Searching for doublons in the model */	/* Searching for doublons in the model */
for(k1=1; k1<= cptcovt;k1++){	for(k1=1; k1<= cptcovt;k1++){
for(k2=1; k2 <k1;k2++){	for(k2=1; k2 <k1;k2++){
Line 11071 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 12285 Dummy[k] 0=dummy (0 1), 1 quantitative (
if((Typevar[k1]==Typevar[k2]) && (Fixed[k1]==Fixed[k2]) && (Dummy[k1]==Dummy[k2] )){	if((Typevar[k1]==Typevar[k2]) && (Fixed[k1]==Fixed[k2]) && (Dummy[k1]==Dummy[k2] )){
if((Typevar[k1] == 0 \|\| Typevar[k1] == 1)){ /* Simple or age product */	if((Typevar[k1] == 0 \|\| Typevar[k1] == 1)){ /* Simple or age product */
if(Tvar[k1]==Tvar[k2]){	if(Tvar[k1]==Tvar[k2]){
printf("Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[k1],Dummy[k1]);	printf("Error duplication in the model=1+age+%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[k1],Dummy[k1]);
fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[k1],Dummy[k1]); fflush(ficlog);	fprintf(ficlog,"Error duplication in the model=1+age+%s at positions (+) %d and %d, Tvar[%d]=V%d, Tvar[%d]=V%d, Typevar=%d, Fixed=%d, Dummy=%d\n", model, k1,k2, k1, Tvar[k1], k2, Tvar[k2],Typevar[k1],Fixed[k1],Dummy[k1]); fflush(ficlog);
return(1);	return(1);
}	}
}else if (Typevar[k1] ==2){	}else if (Typevar[k1] ==2){
k3=Tposprod[k1];	k3=Tposprod[k1];
k4=Tposprod[k2];	k4=Tposprod[k2];
if( ((Tvard[k3][1]== Tvard[k4][1])&&(Tvard[k3][2]== Tvard[k4][2])) \|\| ((Tvard[k3][1]== Tvard[k4][2])&&(Tvard[k3][2]== Tvard[k4][1])) ){	if( ((Tvard[k3][1]== Tvard[k4][1])&&(Tvard[k3][2]== Tvard[k4][2])) \|\| ((Tvard[k3][1]== Tvard[k4][2])&&(Tvard[k3][2]== Tvard[k4][1])) ){
printf("Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);	printf("Error duplication in the model=1+age+%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]);
fprintf(ficlog,"Error duplication in the model=%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);	fprintf(ficlog,"Error duplication in the model=1+age+%s at positions (+) %d and %d, V%d*V%d, Typevar=%d, Fixed=%d, Dummy=%d\n",model, k1,k2, Tvard[k3][1], Tvard[k3][2],Typevar[k1],Fixed[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);
return(1);	return(1);
}	}
}	}
Line 11091 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 12305 Dummy[k] 0=dummy (0 1), 1 quantitative (
fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);	fprintf(ficlog,"ncoveff=%d, nqfveff=%d, ntveff=%d, nqtveff=%d, cptcovn=%d\n",ncoveff,nqfveff,ntveff,nqtveff,cptcovn);
printf("ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);	printf("ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd,nsq);
fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd, nsq);	fprintf(ficlog,"ncovf=%d, ncovv=%d, ncova=%d, nsd=%d, nsq=%d\n",ncovf,ncovv,ncova,nsd, nsq);

	free_imatrix(existcomb,1,NCOVMAX,1,NCOVMAX);
return (0); /* with covar[new additional covariate if product] and Tage if age */	return (0); /* with covar[new additional covariate if product] and Tage if age */
/endread:/	/endread:/
printf("Exiting decodemodel: ");	printf("Exiting decodemodel: ");
Line 11436 int prevalence_limit(double p, double	Line 12652 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(TKresult[nres]==0) k=1; /* To be checked for noresult */
	/* 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++){ */
Line 11450 int prevalence_limit(double p, double	Line 12668 int prevalence_limit(double p, double
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,Tvaraff[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\/ /
fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); /* Here problem for varying dummy*/	/* printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[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,TnsdVar[Tvaraff[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]]);
}	printf(" V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	fprintf(ficlog," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	}
fprintf(ficrespl," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	/* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value \/ /
fprintf(ficlog," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	/* 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 11472 int prevalence_limit(double p, double	Line 12692 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,TnsdVar[Tvaraff[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,TnsdVar[Tvaraff[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 11492 int prevalence_limit(double p, double	Line 12718 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 11535 int back_prevalence_limit(double *p, dou	Line 12761 int back_prevalence_limit(double *p, dou
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++){ /* 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)	k=TKresult[nres];
continue;	if(TKresult[nres]==0) k=1; /* To be checked for noresult */
/printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));/	/* if(i1 != 1 && TKresult[nres]!= k) */
	/* continue; */
	/* /\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<=cptcovs ;j++) {/*< cptcovs number of SIMPLE covariates in the model or resultline V2+V1 =2 (dummy or quantit or time varying) /
fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);	printf(" V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);	fprintf(ficresplb," 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]])]);	fprintf(ficlog," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
}	}
for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */	/* for(j=1;j<=cptcoveff ;j++) {/\* all covariates \/ /
printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);	/* fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[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][resultmodel[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=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[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][resultmodel[nres][j]]); */
	/* } */
fprintf(ficresplb,"******\n");	fprintf(ficresplb,"******\n");
printf("******\n");	printf("******\n");
fprintf(ficlog,"******\n");	fprintf(ficlog,"******\n");
Line 11563 int back_prevalence_limit(double *p, dou	Line 12796 int back_prevalence_limit(double *p, dou
}	}

fprintf(ficresplb,"#Age ");	fprintf(ficresplb,"#Age ");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcovs;j++) {
fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);	fprintf(ficresplb,"V%d %lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][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 11587 int back_prevalence_limit(double *p, dou	Line 12820 int back_prevalence_limit(double *p, dou
/* exit(1); */	/* exit(1); */
}	}
fprintf(ficresplb,"%.0f ",age );	fprintf(ficresplb,"%.0f ",age );
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcovs;j++)
fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);	fprintf(ficresplb,"%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 += bprlim[i][i];	tot += bprlim[i][i];
Line 11598 int back_prevalence_limit(double *p, dou	Line 12831 int back_prevalence_limit(double *p, dou
} /* Age */	} /* Age */
/* was end of cptcod */	/* was end of cptcod */
/fprintf(ficresplb,"\n");/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */	/fprintf(ficresplb,"\n");/ /* Seems to be necessary for gnuplot only if two result lines and no covariate. */
} /* end of any combination */	/* } /\* end of any combination \/ /
} /* end of nres */	} /* end of nres */
/* hBijx(p, bage, fage); */	/* hBijx(p, bage, fage); */
/* fclose(ficrespijb); */	/* fclose(ficrespijb); */
Line 11608 int back_prevalence_limit(double *p, dou	Line 12841 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 11618 int hPijx(double *p, int bage, int fage)	Line 12851 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)	if(TKresult[nres]==0) k=1; /* To be checked for noresult */
continue;	/* for(k=1; k<=i1;k++){ */
fprintf(ficrespij,"\n#****** ");	/* if(i1 != 1 && TKresult[nres]!= k) */
for(j=1;j<=cptcoveff;j++)	/* continue; */
fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);	fprintf(ficrespij,"\n#****** ");
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for(j=1;j<=cptcovs;j++){
printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficrespij," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	/* fprintf(ficrespij,"@wV%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
}	/* for (k4=1; k4<= nsq; k4++){ /\* For each selected (single) quantitative value \/ /
fprintf(ficrespij,"******\n");	/* printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
	/* fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]); */
for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */	}
nhstepm=(int) rint((agelim-agedeb)YEARM/stepm); / Typically 20 years = 2012/6=40 /	fprintf(ficrespij,"******\n");
nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
	for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
/* nhstepm=nhstepmYEARM; aff par mois/	nhstepm=(int) rint((agelim-agedeb)YEARM/stepm); / Typically 20 years = 2012/6=40 /
	nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
oldm=oldms;savm=savms;	/* nhstepm=nhstepmYEARM; aff par mois/
hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");	p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
	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 11720 int hPijx(double *p, int bage, int fage)	Line 12956 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)	if(TKresult[nres]==0) k=1; /* To be checked for noresult */
continue;	/* for(k=1; k<=i1;k++){ /\* For any combination of dummy covariates, fixed and varying \/ /
fprintf(ficrespijb,"\n#****** ");	/* if(i1 != 1 && TKresult[nres]!= k) */
for(j=1;j<=cptcoveff;j++)	/* continue; */
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 */	for(j=1;j<=cptcovs;j++){
fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);	fprintf(ficrespijb," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
}	/* for(j=1;j<=cptcoveff;j++) */
fprintf(ficrespijb,"******\n");	/* fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
if(invalidvarcomb[k]){ /* Is it necessary here? */	/* for (j=1; j<= nsq; j++){ /\* For each selected (single) quantitative value \/ /
fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);	/* fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); */
continue;	}
}	fprintf(ficrespijb,"******\n");
	if(invalidvarcomb[k]){ /* Is it necessary here? */
/* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months \/ /	fprintf(ficrespijb,"\n#Combination (%d) ignored because no cases \n",k);
for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */	continue;
/* 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 */
nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 or 28*/	/* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months \/ /
	for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
/* nhstepm=nhstepmYEARM; aff par mois/	/* 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 */
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */	nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 or 28*/
/* and memory limitations if stepm is small */
	/* nhstepm=nhstepmYEARM; aff par mois/
/* oldm=oldms;savm=savms; */
/* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */	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,prevacurrent,nlstate,stepm, k, nres);/* Bug valgrind */	/* and memory limitations if stepm is small */
/* 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=");	/* oldm=oldms;savm=savms; */
	/* 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]);/* Bug valgrind */
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 11816 int main(int argc, char *argv[])	Line 13056 int main(int argc, char *argv[])
/* double **mobaverage; /	/* double **mobaverage; /
double wald;	double wald;

char line[MAXLINE];	char line[MAXLINE], linetmp[MAXLINE];
char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];	char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE];

char modeltemp[MAXLINE];	char modeltemp[MAXLINE];
Line 12149 int main(int argc, char *argv[])	Line 13389 int main(int argc, char *argv[])
}else	}else
break;	break;
}	}
if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){	if((num_filled=sscanf(line,"model=%[^.\n]", model)) !=EOF){ /* Every character after model but dot and return */
	if (num_filled != 1){
	printf("ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
	fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
	model[0]='\0';
	goto end;
	}else{
	trimbtab(linetmp,line); /* Trims multiple blanks in line */
	strcpy(line, linetmp);
	}
	}
	if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){ /* Every character after 1+age but dot and return */
if (num_filled != 1){	if (num_filled != 1){
printf("ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);	printf("ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);	fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age+' instead of '%s'\n",num_filled, line);
Line 12163 int main(int argc, char *argv[])	Line 13414 int main(int argc, char *argv[])
strcpy(model,modeltemp);	strcpy(model,modeltemp);
}	}
}	}
/* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */	/* printf(" model=1+age%s modeltemp= %s, model=1+age+%s\n",model, modeltemp, model);fflush(stdout); */
printf("model=1+age+%s\n",model);fflush(stdout);	printf("model=1+age+%s\n",model);fflush(stdout);
fprintf(ficparo,"model=1+age+%s\n",model);fflush(stdout);	fprintf(ficparo,"model=1+age+%s\n",model);fflush(stdout);
fprintf(ficres,"model=1+age+%s\n",model);fflush(stdout);	fprintf(ficres,"model=1+age+%s\n",model);fflush(stdout);
Line 12191 int main(int argc, char *argv[])	Line 13442 int main(int argc, char *argv[])
numlinepar++;	numlinepar++;
if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */	if(line[1]=='q'){ /* This #q will quit imach (the answer is q) */
z[0]=line[1];	z[0]=line[1];
	}else if(line[1]=='d'){ /* For debugging individual values of covariates in ficresilk */
	debugILK=1;printf("DebugILK\n");
}	}
/* printf("***line [1] = %c \n",line[1]); /	/* printf("***line [1] = %c \n",line[1]); /
fputs(line, stdout);	fputs(line, stdout);
Line 12204 int main(int argc, char *argv[])	Line 13457 int main(int argc, char *argv[])
covar=matrix(0,NCOVMAX,firstobs,lastobs); /*< used in readdata /	covar=matrix(0,NCOVMAX,firstobs,lastobs); /*< used in readdata /
if(nqv>=1)coqvar=matrix(1,nqv,firstobs,lastobs); /*< Fixed quantitative covariate /	if(nqv>=1)coqvar=matrix(1,nqv,firstobs,lastobs); /*< Fixed quantitative covariate /
if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,firstobs,lastobs); /*< Time varying quantitative covariate /	if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,firstobs,lastobs); /*< Time varying quantitative covariate /
if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,firstobs,lastobs); /*< Time varying covariate (dummy and quantitative)/	/* if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,1,ntv+nqtv,firstobs,lastobs); /\*< Time varying covariate (dummy and quantitative)\/ */
	if(ntv+nqtv>=1)cotvar=ma3x(1,maxwav,ncovcol+nqv+1,ncovcol+nqv+ntv+nqtv,firstobs,lastobs); /*< Might be better /
cptcovn=0; /Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn/	cptcovn=0; /Number of covariates, i.e. number of '+' in model statement plus one, indepently of n in Vn/
/* v1+v2+v3+v2v4+v5age makes cptcovn = 5	/* v1+v2+v3+v2v4+v5age makes cptcovn = 5
v1+v2age+v2v3 makes cptcovn = 3	v1+v2age+v2v3 makes cptcovn = 3
Line 12447 Please run with mle=-1 to get a correct	Line 13701 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));	/* 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 12485 Please run with mle=-1 to get a correct	Line 13739 Please run with mle=-1 to get a correct
TvarVDind=ivector(1,NCOVMAX); /* */	TvarVDind=ivector(1,NCOVMAX); /* */
TvarVQ=ivector(1,NCOVMAX); /* */	TvarVQ=ivector(1,NCOVMAX); /* */
TvarVQind=ivector(1,NCOVMAX); /* */	TvarVQind=ivector(1,NCOVMAX); /* */
	TvarVV=ivector(1,NCOVMAX); /* */
	TvarVVind=ivector(1,NCOVMAX); /* */
	TvarVVA=ivector(1,NCOVMAX); /* */
	TvarVVAind=ivector(1,NCOVMAX); /* */
	TvarAVVA=ivector(1,NCOVMAX); /* */
	TvarAVVAind=ivector(1,NCOVMAX); /* */

Tvalsel=vector(1,NCOVMAX); /* */	Tvalsel=vector(1,NCOVMAX); /* */
Tvarsel=ivector(1,NCOVMAX); /* */	Tvarsel=ivector(1,NCOVMAX); /* */
Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */	Typevar=ivector(-1,NCOVMAX); /* -1 to 2 */
Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */	Fixed=ivector(-1,NCOVMAX); /* -1 to 3 */
Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */	Dummy=ivector(-1,NCOVMAX); /* -1 to 3 */
	DummyV=ivector(-1,NCOVMAX); /* 1 to 3 */
	FixedV=ivector(-1,NCOVMAX); /* 1 to 3 */

/* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).	/* V2+V1+V4+age*V3 is a model with 4 covariates (3 plus signs).
For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,	For each model-covariate stores the data-covariate id. Tvar[1]=2, Tvar[2]=1, Tvar[3]=4,
Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.	Tvar[4=age*V3] is 3 and 'age' is recorded in Tage.
Line 12510 Please run with mle=-1 to get a correct	Line 13773 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);	Tvardk=imatrix(0,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
Line 12530 Please run with mle=-1 to get a correct	Line 13793 Please run with mle=-1 to get a correct
* Tmodelqind[1]=1,Tvaraff[1]@9={4,	* Tmodelqind[1]=1,Tvaraff[1]@9={4,
* 3, 1, 0, 0, 0, 0, 0, 0},	* 3, 1, 0, 0, 0, 0, 0, 0},
* model=V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1*/	* model=V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1*/

	/* Probably useless zeroes */
	for(i=1;i<NCOVMAX;i++){
	DummyV[i]=0;
	FixedV[i]=0;
	}

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



/* Main decodemodel */	/* Main decodemodel */


Line 12594 Please run with mle=-1 to get a correct	Line 13887 Please run with mle=-1 to get a correct
}	}

ncovcombmax=pow(2,cptcoveff);	ncovcombmax=pow(2,cptcoveff);
invalidvarcomb=ivector(1, ncovcombmax);	invalidvarcomb=ivector(0, ncovcombmax);
for(i=1;i<ncovcombmax;i++)	for(i=0;i<ncovcombmax;i++)
invalidvarcomb[i]=0;	invalidvarcomb[i]=0;

/* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in	/* Nbcode gives the value of the lth modality (currently 1 to 2) of jth covariate, in
Line 12740 Title=%s <br>Datafile=%s Firstpass=%d La	Line 14033 Title=%s <br>Datafile=%s Firstpass=%d La
fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\"> \n\	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\
This file: <a href=\"%s\">%s</a>Title=%s <br>Datafile=<a href=\"%s\">%s</a> 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 13106 Please run with mle=-1 to get a correct	Line 14399 Please run with mle=-1 to get a correct
fprintf(ficres," + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);	fprintf(ficres," + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
fprintf(ficlog," + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);	fprintf(ficlog," + V%d*V%d ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
fprintf(fichtm, "<th>+ V%d*V%d</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);	fprintf(fichtm, "<th>+ V%d*V%d</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
	}else if(Typevar[j]==3) { /* TO VERIFY */
	printf(" + V%dV%dage ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
	fprintf(ficres," + V%dV%dage ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
	fprintf(ficlog," + V%dV%dage ",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
	fprintf(fichtm, "<th>+ V%dV%dage</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
}	}
}	}
printf("\n");	printf("\n");
Line 13165 Please run with mle=-1 to get a correct	Line 14463 Please run with mle=-1 to get a correct
fprintf(fichtm, "<th>+ V%d*age</th>",Tvar[j]);	fprintf(fichtm, "<th>+ V%d*age</th>",Tvar[j]);
}else if(Typevar[j]==2) {	}else if(Typevar[j]==2) {
fprintf(fichtm, "<th>+ V%d*V%d</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);	fprintf(fichtm, "<th>+ V%d*V%d</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
	}else if(Typevar[j]==3) { /* TO VERIFY */
	fprintf(fichtm, "<th>+ V%dV%dage</th>",Tvard[Tposprod[j]][1],Tvard[Tposprod[j]][2]);
}	}
}	}
fprintf(fichtm, "</tr>\n");	fprintf(fichtm, "</tr>\n");
Line 13222 Please run with mle=-1 to get a correct	Line 14522 Please run with mle=-1 to get a correct
}	}

fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");	fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
if(mle >= 1) /* To big for the screen */	if(mle >= 1) /* Too big for the screen */
printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");	printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");	fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n# ...\n# 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n");
/* # 121 Var(a12)\n\ */	/* # 121 Var(a12)\n\ */
Line 13486 Please run with mle=-1 to get a correct	Line 14786 Please run with mle=-1 to get a correct
case 13:	case 13:
num_filled=sscanf(line,"result:%[^\n]\n",resultlineori);	num_filled=sscanf(line,"result:%[^\n]\n",resultlineori);
nresult++; /* Sum of resultlines */	nresult++; /* Sum of resultlines */
printf("Result %d: result:%s\n",nresult, resultlineori);	/* printf("Result %d: result:%s\n",nresult, resultlineori); */
/* removefirstspace(&resultlineori); */	/* removefirstspace(&resultlineori); */

if(strstr(resultlineori,"v") !=0){	if(strstr(resultlineori,"v") !=0){
Line 13495 Please run with mle=-1 to get a correct	Line 14795 Please run with mle=-1 to get a correct
return 1;	return 1;
}	}
trimbb(resultline, resultlineori); /* Suppressing double blank in the resultline */	trimbb(resultline, resultlineori); /* Suppressing double blank in the resultline */
printf("Decoderesult resultline=\"%s\" resultlineori=\"%s\"\n", resultline, resultlineori);	/* printf("Decoderesult resultline=\"%s\" resultlineori=\"%s\"\n", resultline, resultlineori); */
if(nresult > MAXRESULTLINESPONE-1){	if(nresult > MAXRESULTLINESPONE-1){
printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINESPONE-1,nresult,rfileres);	printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINESPONE-1,nresult,rfileres);
fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINESPONE-1,nresult,rfileres);	fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINESPONE-1,nresult,rfileres);
Line 13578 Please run with mle=-1 to get a correct	Line 14878 Please run with mle=-1 to get a correct
date2dmy(datebackf,&jbackf, &mbackf, &anbackf);	date2dmy(datebackf,&jbackf, &mbackf, &anbackf);
}	}

printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, prevbcast, pathc,p, (int)anprojd-bage, (int)anbackd-fage);	printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, prevbcast, pathc,p, (int)anprojd-bage, (int)anbackd-fage);/* HERE valgrind Tvard*/
}	}
printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \	printinghtml(fileresu,title,datafile, firstpass, lastpass, stepm, weightopt, \
model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,prevbcast, estepm, \	model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,prevbcast, estepm, \
Line 13728 Please run with mle=-1 to get a correct	Line 15028 Please run with mle=-1 to get a correct

pstamp(ficreseij);	pstamp(ficreseij);

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 */
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; */
fprintf(ficreseij,"\n#****** ");	fprintf(ficreseij,"\n#****** ");
printf("\n#****** ");	printf("\n#****** ");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcovs;j++){
fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);	/* for(j=1;j<=cptcoveff;j++) { */
printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);	/* fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); */
	fprintf(ficreseij," V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]);
	printf(" V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][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 ",TvarsQ[j], TinvDoQresult[nres][TvarsQ[j]]); /* TvarsQ[j] gives the name of the jth quantitative (fixed or time v) */	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 ",TvarsQ[j], TinvDoQresult[nres][TvarsQ[j]]);	fprintf(ficreseij,"V%d=%lg ",TvarsQ[j], TinvDoQresult[nres][TvarsQ[j]]);
}	}
fprintf(ficreseij,"******\n");	fprintf(ficreseij,"******\n");
printf("******\n");	printf("******\n");
Line 13761 Please run with mle=-1 to get a correct	Line 15064 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 13808 Please run with mle=-1 to get a correct	Line 15111 Please run with mle=-1 to get a correct
/* */	/* */
if(i1 != 1 && TKresult[nres]!= k) /* TKresult[nres] is the combination of this nres resultline. All the i1 combinations are not output */	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); /* HERE model is empty */
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);
/* It might not be a good idea to mix dummies and quantitative */	/* It might not be a good idea to mix dummies and quantitative */
Line 13832 Please run with mle=-1 to get a correct	Line 15135 Please run with mle=-1 to get a correct
/* Tvresult[nres][j] Name of the variable at position j in this resultline */	/* Tvresult[nres][j] Name of the variable at position j in this resultline */
/* Tresult[nres][j] Value of this variable at position j could be a float if quantitative */	/* Tresult[nres][j] Value of this variable at position j could be a float if quantitative */
/* We give up with the combinations!! */	/* We give up with the combinations!! */
printf("\n j=%d In computing T_ Dummy[modelresult[%d][%d]]=%d, modelresult[%d][%d]=%d cptcovs=%d, cptcoveff=%d Fixed[modelresult[nres][j]]=%d\n", j, nres, j, Dummy[modelresult[nres][j]],nres,j,modelresult[nres][j],cptcovs, cptcoveff,Fixed[modelresult[nres][j]]); /* end if dummy or quanti */	/* if(debugILK) */
	/* printf("\n j=%d In computing T_ Dummy[modelresult[%d][%d]]=%d, modelresult[%d][%d]=%d cptcovs=%d, cptcoveff=%d Fixed[modelresult[nres][j]]=%d\n", j, nres, j, Dummy[modelresult[nres][j]],nres,j,modelresult[nres][j],cptcovs, cptcoveff,Fixed[modelresult[nres][j]]); /\* end if dummy or quanti \/ /

if(Dummy[modelresult[nres][j]]==0){/* Dummy variable of the variable in position modelresult in the model corresponding to j in resultline */	if(Dummy[modelresult[nres][j]]==0){/* Dummy variable of the variable in position modelresult in the model corresponding to j in resultline */
printf("V%d=%d ",Tvresult[nres][j],Tresult[nres][j]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline */	/* printf("V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][j]); /\* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline \/ / /* TinvDoQresult[nres][Name of the variable] */
fprintf(ficlog,"V%d=%d ",Tvresult[nres][j],Tresult[nres][j]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline */	printf("V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]); /* Output of each value for the combination TKresult[nres], ordered by the covariate values in the resultline */
fprintf(ficrest,"V%d=%d ",Tvresult[nres][j],Tresult[nres][j]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline */	fprintf(ficlog,"V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline */
	fprintf(ficrest,"V%d=%lg ",Tvresult[nres][j],TinvDoQresult[nres][Tvresult[nres][j]]); /* Output of each value for the combination TKresult[nres], ordere by the covariate values in the resultline */
if(Fixed[modelresult[nres][j]]==0){ /* Fixed */	if(Fixed[modelresult[nres][j]]==0){ /* Fixed */
printf("fixed ");fprintf(ficlog,"fixed ");fprintf(ficrest,"fixed ");	printf("fixed ");fprintf(ficlog,"fixed ");fprintf(ficrest,"fixed ");
}else{	}else{
Line 13847 Please run with mle=-1 to get a correct	Line 15152 Please run with mle=-1 to get a correct
/* fprintf(ficlog,"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 */	}else if(Dummy[modelresult[nres][j]]==1){ /* Quanti variable */
/* For each selected (single) quantitative value */	/* For each selected (single) quantitative value */
printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	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 */	if(Fixed[modelresult[nres][j]]==0){ /* Fixed */
printf("fixed ");fprintf(ficlog,"fixed ");fprintf(ficrest,"fixed ");	printf("fixed ");fprintf(ficlog,"fixed ");fprintf(ficrest,"fixed ");
}else{	}else{
Line 13870 Please run with mle=-1 to get a correct	Line 15177 Please run with mle=-1 to get a correct

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 ",Tvresult[nres][j],Tresult[nres][j]);	fprintf(ficresstdeij,"V%d=%d ",Tvresult[nres][j],Tresult[nres][j]);
/* fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[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]])]); */	/* 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, TvarsQind gives the position of a quantitative in model equation */	for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value, TvarsQind gives the position of a quantitative in model equation */
fprintf(ficresstdeij," V%d=%f ",Tvar[TvarsQind[j]],Tqresult[nres][resultmodel[nres][TvarsQind[j]]]);	fprintf(ficresstdeij," V%d=%lg ",Tvar[TvarsQind[j]],Tqresult[nres][resultmodel[nres][TvarsQind[j]]]);
fprintf(ficrescveij," V%d=%f ",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 13889 Please run with mle=-1 to get a correct	Line 15198 Please run with mle=-1 to get a correct
/* fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[TnsdVar[Tvaraff[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]); /\* To solve \/ /	/* fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); /\* To solve \/ /
fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); /* Solved */	fprintf(ficresvij," V%d=%lg ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); /* Solved */
}	}
fprintf(ficresvij,"******\n");	fprintf(ficresvij,"******\n");

Line 13977 Please run with mle=-1 to get a correct	Line 15286 Please run with mle=-1 to get a correct


free_vector(weight,firstobs,lastobs);	free_vector(weight,firstobs,lastobs);
free_imatrix(Tvardk,1,NCOVMAX,1,2);	free_imatrix(Tvardk,0,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 14002 Please run with mle=-1 to get a correct	Line 15311 Please run with mle=-1 to get a correct
free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);	free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);	free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);	free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,firstobs,lastobs);	/* if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,firstobs,lastobs); */
	if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,ncovcol+nqv+1,ncovcol+nqv+ntv+nqtv,firstobs,lastobs);
if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,firstobs,lastobs);	if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,firstobs,lastobs);
if(nqv>=1)free_matrix(coqvar,1,nqv,firstobs,lastobs);	if(nqv>=1)free_matrix(coqvar,1,nqv,firstobs,lastobs);
free_matrix(covar,0,NCOVMAX,firstobs,lastobs);	free_matrix(covar,0,NCOVMAX,firstobs,lastobs);
Line 14018 Please run with mle=-1 to get a correct	Line 15328 Please run with mle=-1 to get a correct
free_ivector(ncodemaxwundef,1,NCOVMAX);	free_ivector(ncodemaxwundef,1,NCOVMAX);
free_ivector(Dummy,-1,NCOVMAX);	free_ivector(Dummy,-1,NCOVMAX);
free_ivector(Fixed,-1,NCOVMAX);	free_ivector(Fixed,-1,NCOVMAX);
free_ivector(DummyV,1,NCOVMAX);	free_ivector(DummyV,-1,NCOVMAX);
free_ivector(FixedV,1,NCOVMAX);	free_ivector(FixedV,-1,NCOVMAX);
free_ivector(Typevar,-1,NCOVMAX);	free_ivector(Typevar,-1,NCOVMAX);
free_ivector(Tvar,1,NCOVMAX);	free_ivector(Tvar,1,NCOVMAX);
free_ivector(TvarsQ,1,NCOVMAX);	free_ivector(TvarsQ,1,NCOVMAX);
Line 14041 Please run with mle=-1 to get a correct	Line 15351 Please run with mle=-1 to get a correct
free_ivector(TvarVDind,1,NCOVMAX);	free_ivector(TvarVDind,1,NCOVMAX);
free_ivector(TvarVQ,1,NCOVMAX);	free_ivector(TvarVQ,1,NCOVMAX);
free_ivector(TvarVQind,1,NCOVMAX);	free_ivector(TvarVQind,1,NCOVMAX);
	free_ivector(TvarAVVA,1,NCOVMAX);
	free_ivector(TvarAVVAind,1,NCOVMAX);
	free_ivector(TvarVVA,1,NCOVMAX);
	free_ivector(TvarVVAind,1,NCOVMAX);
	free_ivector(TvarVV,1,NCOVMAX);
	free_ivector(TvarVVind,1,NCOVMAX);

free_ivector(Tvarsel,1,NCOVMAX);	free_ivector(Tvarsel,1,NCOVMAX);
free_vector(Tvalsel,1,NCOVMAX);	free_vector(Tvalsel,1,NCOVMAX);
free_ivector(Tposprod,1,NCOVMAX);	free_ivector(Tposprod,1,NCOVMAX);
free_ivector(Tprod,1,NCOVMAX);	free_ivector(Tprod,1,NCOVMAX);
free_ivector(Tvaraff,1,NCOVMAX);	free_ivector(Tvaraff,1,NCOVMAX);
free_ivector(invalidvarcomb,1,ncovcombmax);	free_ivector(invalidvarcomb,0,ncovcombmax);
free_ivector(Tage,1,NCOVMAX);	free_ivector(Tage,1,NCOVMAX);
free_ivector(Tmodelind,1,NCOVMAX);	free_ivector(Tmodelind,1,NCOVMAX);
free_ivector(TmodelInvind,1,NCOVMAX);	free_ivector(TmodelInvind,1,NCOVMAX);

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