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Diff for /imach/src/imach.c between versions 1.277 and 1.333

version 1.277, 2017/07/17 08:53:49	version 1.333, 2022/08/21 09:10:30
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	Revision 1.333 2022/08/21 09:10:30 brouard
	* src/imach.c (Module): Version 0.99r33 A lot of changes in
	reassigning covariates: my first idea was that people will always
	use the first covariate V1 into the model but in fact they are
	producing data with many covariates and can use an equation model
	with some of the covariate; it means that in a model V2+V3 instead
	of codtabm(k,Tvaraff[j]) which calculates for combination k, for
	three covariates (V1, V2, V3) the value of Tvaraff[j], but in fact
	the equation model is restricted to two variables only (V2, V3)
	and the combination for V2 should be codtabm(k,1) instead of
	(codtabm(k,2), and the code should be
	codtabm(k,TnsdVar[Tvaraff[j]]. Many many changes have been
	made. All of these should be simplified once a day like we did in
	hpxij() for example by using precov[nres] which is computed in
	decoderesult for each nres of each resultline. Loop should be done
	on the equation model globally by distinguishing only product with
	age (which are changing with age) and no more on type of
	covariates, single dummies, single covariates.

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

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

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

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

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

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

	Revision 1.328 2022/07/27 17:40:48 brouard
	Summary: valgrind bug fixed by initializing to zero DummyV as well as Tage

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

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

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

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

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

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

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

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

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

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

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

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

	Revision 1.317 2022/05/15 15:06:23 brouard
	* imach.c (Module): Some minor improvements

	Revision 1.316 2022/05/11 15:11:31 brouard
	Summary: r27

	Revision 1.315 2022/05/11 15:06:32 brouard
	* empty log message *

	Revision 1.314 2022/04/13 17:43:09 brouard
	* imach.c (Module): Adding link to text data files

	Revision 1.313 2022/04/11 15:57:42 brouard
	* imach.c (Module): Error in rewriting the 'r' file with yearsfproj or yearsbproj fixed

	Revision 1.312 2022/04/05 21:24:39 brouard
	* empty log message *

	Revision 1.311 2022/04/05 21:03:51 brouard
	Summary: Fixed quantitative covariates

	Fixed covariates (dummy or quantitative)
	with missing values have never been allowed but are ERRORS and
	program quits. Standard deviations of fixed covariates were
	wrongly computed. Mean and standard deviations of time varying
	covariates are still not computed.

	Revision 1.310 2022/03/17 08:45:53 brouard
	Summary: 99r25

	Improving detection of errors: result lines should be compatible with
	the model.

	Revision 1.309 2021/05/20 12:39:14 brouard
	Summary: Version 0.99r24

	Revision 1.308 2021/03/31 13:11:57 brouard
	Summary: Version 0.99r23


	* imach.c (Module): Still bugs in the result loop. Thank to Holly Benett

	Revision 1.307 2021/03/08 18:11:32 brouard
	Summary: 0.99r22 fixed bug on result:

	Revision 1.306 2021/02/20 15:44:02 brouard
	Summary: Version 0.99r21

	* imach.c (Module): Fix bug on quitting after result lines!
	(Module): Version 0.99r21

	Revision 1.305 2021/02/20 15:28:30 brouard
	* imach.c (Module): Fix bug on quitting after result lines!

	Revision 1.304 2021/02/12 11:34:20 brouard
	* imach.c (Module): The use of a Windows BOM (huge) file is now an error

	Revision 1.303 2021/02/11 19:50:15 brouard
	* (Module): imach.c Someone entered 'results:' instead of 'result:'. Now it is an error which is printed.

	Revision 1.302 2020/02/22 21:00:05 brouard
	* (Module): imach.c Update mle=-3 (for computing Life expectancy
	and life table from the data without any state)

	Revision 1.301 2019/06/04 13:51:20 brouard
	Summary: Error in 'r'parameter file backcast yearsbproj instead of yearsfproj

	Revision 1.300 2019/05/22 19:09:45 brouard
	Summary: version 0.99r19 of May 2019

	Revision 1.299 2019/05/22 18:37:08 brouard
	Summary: Cleaned 0.99r19

	Revision 1.298 2019/05/22 18:19:56 brouard
	* empty log message *

	Revision 1.297 2019/05/22 17:56:10 brouard
	Summary: Fix bug by moving date2dmy and nhstepm which gaefin=-1

	Revision 1.296 2019/05/20 13:03:18 brouard
	Summary: Projection syntax simplified


	We can now start projections, forward or backward, from the mean date
	of inteviews up to or down to a number of years of projection:
	prevforecast=1 yearsfproj=15.3 mobil_average=0
	or
	prevforecast=1 starting-proj-date=1/1/2007 final-proj-date=12/31/2017 mobil_average=0
	or
	prevbackcast=1 yearsbproj=12.3 mobil_average=1
	or
	prevbackcast=1 starting-back-date=1/10/1999 final-back-date=1/1/1985 mobil_average=1

	Revision 1.295 2019/05/18 09:52:50 brouard
	Summary: doxygen tex bug

	Revision 1.294 2019/05/16 14:54:33 brouard
	Summary: There was some wrong lines added

	Revision 1.293 2019/05/09 15:17:34 brouard
	* empty log message *

	Revision 1.292 2019/05/09 14:17:20 brouard
	Summary: Some updates

	Revision 1.291 2019/05/09 13:44:18 brouard
	Summary: Before ncovmax

	Revision 1.290 2019/05/09 13:39:37 brouard
	Summary: 0.99r18 unlimited number of individuals

	The number n which was limited to 20,000 cases is now unlimited, from firstobs to lastobs. If the number is too for the virtual memory, probably an error will occur.

	Revision 1.289 2018/12/13 09:16:26 brouard
	Summary: Bug for young ages (<-30) will be in r17

	Revision 1.288 2018/05/02 20:58:27 brouard
	Summary: Some bugs fixed

	Revision 1.287 2018/05/01 17:57:25 brouard
	Summary: Bug fixed by providing frequencies only for non missing covariates

	Revision 1.286 2018/04/27 14:27:04 brouard
	Summary: some minor bugs

	Revision 1.285 2018/04/21 21:02:16 brouard
	Summary: Some bugs fixed, valgrind tested

	Revision 1.284 2018/04/20 05:22:13 brouard
	Summary: Computing mean and stdeviation of fixed quantitative variables

	Revision 1.283 2018/04/19 14:49:16 brouard
	Summary: Some minor bugs fixed

	Revision 1.282 2018/02/27 22:50:02 brouard
	* empty log message *

	Revision 1.281 2018/02/27 19:25:23 brouard
	Summary: Adding second argument for quitting

	Revision 1.280 2018/02/21 07:58:13 brouard
	Summary: 0.99r15

	New Makefile with recent VirtualBox 5.26. Bug in sqrt negatve in imach.c

	Revision 1.279 2017/07/20 13:35:01 brouard
	Summary: temporary working

	Revision 1.278 2017/07/19 14:09:02 brouard
	Summary: Bug for mobil_average=0 and prevforecast fixed(?)

Revision 1.277 2017/07/17 08:53:49 brouard	Revision 1.277 2017/07/17 08:53:49 brouard
Summary: BOM files can be read now	Summary: BOM files can be read now

Line 696	Line 938

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

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

The output is very simple: only an estimate of the intercept and of	The output is very simple: only an estimate of the intercept and of
Line 875 Important routines	Line 1117 Important routines
- Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)	- Tricode which tests the modality of dummy variables (in order to warn with wrong or empty modalities)
and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.	and returns the number of efficient covariates cptcoveff and modalities nbcode[Tvar[k]][1]= 0 and nbcode[Tvar[k]][2]= 1 usually.
- printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables	- printinghtml which outputs results like life expectancy in and from a state for a combination of modalities of dummy variables
o There are 2*cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if	o There are 2**cptcoveff combinations of (0,1) for cptcoveff variables. Outputting only combinations with people, éliminating 1 1 if
race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.	race White (0 0), Black vs White (1 0), Hispanic (0 1) and 1 1 being meaningless.



Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).	Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
Institut national d'études démographiques, Paris.	Institut national d'études démographiques, Paris.
This software have been partly granted by Euro-REVES, a concerted action	This software have been partly granted by Euro-REVES, a concerted action
from the European Union.	from the European Union.
It is copyrighted identically to a GNU software product, ie programme and	It is copyrighted identically to a GNU software product, ie programme and
Line 945 Important routines	Line 1187 Important routines
#define POWELLNOF3INFF1TEST /* Skip test */	#define POWELLNOF3INFF1TEST /* Skip test */
/* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test \/ /	/* #define POWELLORIGINAL /\* Don't use Directest to decide new direction but original Powell test \/ /
/* #define MNBRAKORIGINAL /\* Don't use mnbrak fix \/ /	/* #define MNBRAKORIGINAL /\* Don't use mnbrak fix \/ /
	/* #define FLATSUP // Suppresses directions where likelihood is flat */

#include <math.h>	#include <math.h>
#include <stdio.h>	#include <stdio.h>
Line 1000 typedef struct {	Line 1243 typedef struct {

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

#define GLOCK_ERROR_NOPATH -1 /* empty path */	#define GLOCK_ERROR_NOPATH -1 /* empty path */
#define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */	#define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
Line 1011 typedef struct {	Line 1254 typedef struct {
#define NINTERVMAX 8	#define NINTERVMAX 8
#define NLSTATEMAX 8 /*< Maximum number of live states (for func) /	#define NLSTATEMAX 8 /*< Maximum number of live states (for func) /
#define NDEATHMAX 8 /*< Maximum number of dead states (for func) /	#define NDEATHMAX 8 /*< Maximum number of dead states (for func) /
#define NCOVMAX 20 /*< Maximum number of covariates, including generated covariates V1V2 */	#define NCOVMAX 30 /*< Maximum number of covariates used in the model, including generated covariates V1V2 or V1age /
#define codtabm(h,k) (1 & (h-1) >> (k-1))+1	#define codtabm(h,k) (1 & (h-1) >> (k-1))+1
/#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)/	/#define decodtabm(h,k,cptcoveff)= (h <= (1<<cptcoveff)?(((h-1) >> (k-1)) & 1) +1 : -1)/
#define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1	#define decodtabm(h,k,cptcoveff) (((h-1) >> (k-1)) & 1) +1
#define MAXN 20000	/#define MAXN 20000 / /* Should by replaced by nobs, real number of observations and unlimited */
#define YEARM 12. /*< Number of months per year /	#define YEARM 12. /*< Number of months per year /
/* #define AGESUP 130 */	/* #define AGESUP 130 */
#define AGESUP 150	/* #define AGESUP 150 */
	#define AGESUP 200
#define AGEINF 0	#define AGEINF 0
#define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */	#define AGEMARGE 25 /* Marge for agemin and agemax for(iage=agemin-AGEMARGE; iage <= agemax+3+AGEMARGE; iage++) */
#define AGEBASE 40	#define AGEBASE 40
Line 1038 typedef struct {	Line 1282 typedef struct {
/* $State$ */	/* $State$ */
#include "version.h"	#include "version.h"
char version[]=__IMACH_VERSION__;	char version[]=__IMACH_VERSION__;
char copyright[]="February 2016,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018";	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 fullversion[]="$Revision$ $Date$";	char fullversion[]="$Revision$ $Date$";
char strstart[80];	char strstart[80];
char optionfilext[10], optionfilefiname[FILENAMELENGTH];	char optionfilext[10], optionfilefiname[FILENAMELENGTH];
int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */	int erreur=0, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
int nagesqr=0, nforce=0; /* nagesqr=1 if model is including ageage, number of forces /	int nagesqr=0, nforce=0; /* nagesqr=1 if model is including ageage, number of forces /
/* Number of covariates model=V2+V1+ V3age+V2V4 */	/* Number of covariates model (1)=V2+V1+ V3age+V2V4 */
int cptcovn=0; /*< cptcovn number of covariates added in the model (excepting constant and age and ageproduct) */	/* Model(2) V1 + V2 + V3 + V8 + V7V8 + V5V6 + V8age + V3age + ageage /
int cptcovt=0; /*< cptcovt number of covariates added in the model (excepting constant and age) /	int cptcovn=0; /*< cptcovn decodemodel: number of covariates k of the models excluding ageproducts =6 and ageage /
int cptcovs=0; /*< cptcovs number of simple covariates in the model V2+V1 =2 /	int cptcovt=0; /*< cptcovt: total number of covariates of the model (2) nbocc(+)+1 = 8 excepting constant and age and ageage */
	int 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 cptcovprodnoage=0; /*< Number of covariate products without age /	int cptcovprodnoage=0; /*< Number of covariate products without age /
int cptcoveff=0; /* Total number of covariates to vary for printing results */	int cptcoveff=0; /* Total number of covariates to vary for printing results (2*cptcoveff combinations of dummies)(computed in tricode as cptcov) /
int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */	int ncovf=0; /* Total number of effective fixed covariates (dummy or quantitative) in the model */
int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */	int ncovv=0; /* Total number of effective (wave) varying covariates (dummy or quantitative) in the model */
int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */	int ncova=0; /* Total number of effective (wave and stepm) varying with age covariates (dummy of quantitative) in the model */
Line 1062 int nqfveff=0; /**< nqfveff Number of Qu	Line 1307 int nqfveff=0; /**< nqfveff Number of Qu
int ntveff=0; /*< ntveff number of effective time varying variables /	int ntveff=0; /*< ntveff number of effective time varying variables /
int nqtveff=0; /*< ntqveff number of effective time varying quantitative variables /	int nqtveff=0; /*< ntqveff number of effective time varying quantitative variables /
int cptcov=0; /* Working variable */	int cptcov=0; /* Working variable */
	int nobs=10; /* Number of observations in the data lastobs-firstobs */
int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */	int ncovcombmax=NCOVMAX; /* Maximum calculated number of covariate combination = pow(2, cptcoveff) */
int npar=NPARMAX;	int npar=NPARMAX; /* Number of parameters (nlstate+ndeath-1)nlstatencovmodel; */
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 */
Line 1200 int ncodemaxwundef; / ncodemax[j]= Nu	Line 1446 int ncodemaxwundef; / ncodemax[j]= Nu
double *agev,moisnais, annais, moisdc, andc,mint, *anint;	double *agev,moisnais, annais, moisdc, andc,mint, *anint;
double pmmij, probs; / Global pointer */	double pmmij, probs; / Global pointer */
double *mobaverage, mobaverages; / New global variable */	double *mobaverage, mobaverages; / New global variable */
	double *precov; / New global variable to store for each resultline, values of model covariates given by the resultlines (in order to speed up) */
double ageexmed,agecens;	double ageexmed,agecens;
double dateintmean=0;	double dateintmean=0;
	double anprojd, mprojd, jprojd; /* For eventual projections */
	double anprojf, mprojf, jprojf;

	double anbackd, mbackd, jbackd; /* For eventual backprojections */
	double anbackf, mbackf, jbackf;
	double jintmean,mintmean,aintmean;
double *weight;	double *weight;
int *s; / Status */	int *s; / Status */
double *agedc;	double *agedc;
Line 1214 double **cotvar; / Time varying covari	Line 1466 double **cotvar; / Time varying covari
double **cotqvar; / Time varying quantitative covariate itqv */	double **cotqvar; / Time varying quantitative covariate itqv */
double idx;	double idx;
int *nbcode, Tvar; /*< model=V2 => Tvar[1]= 2 /	int *nbcode, Tvar; /*< model=V2 => Tvar[1]= 2 /
/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */	/* Some documentation */
/k 1 2 3 4 5 6 7 8 9 /	/* Design original data
/Tvar[k]= 5 4 3 6 5 2 7 1 1 /	* V1 V2 V3 V4 V5 V6 V7 V8 Weight ddb ddth d1st s1 V9 V10 V11 V12 s2 V9 V10 V11 V12
/* Tndvar[k] 1 2 3 4 5 */	* < ncovcol=6 > nqv=2 (V7 V8) dv dv dv qtv dv dv dvv qtv
/TDvar 4 3 6 7 1 / /* For outputs only; combination of dummies fixed or varying */	* ntv=3 nqtv=1
/* Tns[k] 1 2 2 4 5 / / Number of single cova */	* cptcovn number of covariates (not including constant and age or age*age) = number of plus sign + 1 = 10+1=11
/* TvarsD[k] 1 2 3 / / Number of single dummy cova */	* For time varying covariate, quanti or dummies
/* TvarsDind 2 3 9 / / position K of single dummy cova */	* cotqvar[wav][iv(1 to nqtv)][i]= [1][12][i]=(V12) quanti
/* TvarsQ[k] 1 2 / / Number of single quantitative cova */	* cotvar[wav][ntv+iv][i]= [3+(1 to nqtv)][i]=(V12) quanti
/* TvarsQind 1 6 / / position K of single quantitative cova */	* cotvar[wav][iv(1 to ntv)][i]= [1][1][i]=(V9) dummies at wav 1
/* Tprod[i]=k 4 7 */	* cotvar[wav][iv(1 to ntv)][i]= [1][2][i]=(V10) dummies at wav 1
/* Tage[i]=k 5 8 */	* covar[Vk,i], value of the Vkth fixed covariate dummy or quanti for individual i:
/* */	* covar[1][i]= (V1), covar[4][i]=(V4), covar[8][i]=(V8)
	* Model V2 + V1 + V3age + V3 + V5V6 + V7V8 + V8age + V8 + V9 + V9*age + V10
	* k= 1 2 3 4 5 6 7 8 9 10 11
	*/
	/* According to the model, more columns can be added to covar by the product of covariates */
	/* ncovcol=1(Males=0 Females=1) nqv=1(raedyrs) ntv=2(withoutiadl=0 withiadl=1, witoutadl=0 withoutadl=1) nqtv=1(bmi) nlstate=3 ndeath=1
	# 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
	*/
	/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
	/* k 1 2 3 4 5 6 7 8 9 */
	/Typevar[k]= 0 0 0 2 1 0 2 1 0 //0 for simple covariate (dummy, quantitative,/
	/* fixed or varying), 1 for age product, 2 for*/
	/* product */
	/Dummy[k]= 1 0 0 1 3 1 1 2 0 //Dummy[k] 0=dummy (0 1), 1 quantitative /
	/(single or product without age), 2 dummy/
	/* with age product, 3 quant with age product*/
	/Tvar[k]= 5 4 3 6 5 2 7 1 1 /
	/* nsd 1 2 3 / / Counting single dummies covar fixed or tv */
	/TnsdVar[Tvar] 1 2 3 /
	/TvarsD[nsd] 4 3 1 / /* ID of single dummy cova fixed or timevary*/
	/TvarsDind[k] 2 3 9 / /* position K of single dummy cova */
	/* nsq 1 2 / / Counting single quantit tv */
	/* TvarsQ[k] 5 2 / / Number of single quantitative cova */
	/* TvarsQind 1 6 / / position K of single quantitative cova */
	/* Tprod[i]=k 1 2 / / Position in model of the ith prod without age */
	/* cptcovage 1 2 / / Counting covage in the model equation /
	/* Tage[cptcovage]=k 5 8 / / Position in the model of ith covage /
	/* Tvard[1][1]@4={4,3,1,2} V4V3 V1V2 / / Position in model of the ith prod without age */
	/* 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 /
	/* TvarFind; TvarFind[1]=6, TvarFind[2]=7, TvarFind[3]=9 // Inverse V2(6) is first fixed (single or prod) */
/* Type */	/* Type */
/* V 1 2 3 4 5 */	/* V 1 2 3 4 5 */
/* F F V V V */	/* F F V V V */
/* D Q D D Q */	/* D Q D D Q */
/* */	/* */
int *TvarsD;	int *TvarsD;
	int *TnsdVar;
int *TvarsDind;	int *TvarsDind;
int *TvarsQ;	int *TvarsQ;
int *TvarsQind;	int *TvarsQind;

#define MAXRESULTLINES 10	#define MAXRESULTLINESPONE 10+1
int nresult=0;	int nresult=0;
int parameterline=0; /* # of the parameter (type) line */	int parameterline=0; /* # of the parameter (type) line */
int TKresult[MAXRESULTLINES];	int TKresult[MAXRESULTLINESPONE];
int Tresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */	int resultmodel[MAXRESULTLINESPONE][NCOVMAX];/* resultmodel[k1]=k3: k1th position in the model correspond to the k3 position in the resultline */
int Tinvresult[MAXRESULTLINES][NCOVMAX];/* For dummy variable , value (output) */	int Tresult[MAXRESULTLINESPONE][NCOVMAX];/* For dummy variable , value (output) */
int Tvresult[MAXRESULTLINES][NCOVMAX]; /* For dummy variable , variable # (output) */	int Tinvresult[MAXRESULTLINESPONE][NCOVMAX];/* Tinvresult[nres][Name of a dummy variable]= value of the variable in the result line */
double Tqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */	double TinvDoQresult[MAXRESULTLINESPONE][NCOVMAX];/* TinvDoQresult[nres][Name of a Dummy or Q variable]= value of the variable in the result line */
double Tqinvresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , value (output) */	int Tvresult[MAXRESULTLINESPONE][NCOVMAX]; /* For dummy variable , variable # (output) */
int Tvqresult[MAXRESULTLINES][NCOVMAX]; /* For quantitative variable , variable # (output) */	double Tqresult[MAXRESULTLINESPONE][NCOVMAX]; /* Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline */
	double Tqinvresult[MAXRESULTLINESPONE][NCOVMAX]; /* For quantitative variable , value (output) */
	int Tvqresult[MAXRESULTLINESPONE][NCOVMAX]; /* Tvqresult[nres][result_position]= id of the variable at the result_position in the nres resultline */

	/* ncovcol=1(Males=0 Females=1) nqv=1(raedyrs) ntv=2(withoutiadl=0 withiadl=1, witoutadl=0 withoutadl=1) nqtv=1(bmi) nlstate=3 ndeath=1
	# 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
	*/
/* int TDvar; /\< TDvar[1]=4, TDvarF[2]=3, TDvar[3]=6 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 \/ */	/* int TDvar; /\< TDvar[1]=4, TDvarF[2]=3, TDvar[3]=6 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 \/ */
int TvarF; /< TvarF[1]=Tvar[6]=2, TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 /	int TvarF; /< TvarF[1]=Tvar[6]=2, TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 /
int TvarFind; /< TvarFind[1]=6, TvarFind[2]=7, Tvarind[3]=9 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 /	int TvarFind; /< TvarFind[1]=6, TvarFind[2]=7, Tvarind[3]=9 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 /
Line 1279 int TmodelInvQind; /* Tmodelqind[1]=1	Line 1569 int TmodelInvQind; /* Tmodelqind[1]=1
int Ndum; /* Freq of modality (tricode */	int Ndum; /* Freq of modality (tricode */
/* int *codtab;/ /*< codtab=imatrix(1,100,1,10); /	/* int *codtab;/ /*< codtab=imatrix(1,100,1,10); /
int **Tvard;	int **Tvard;
	int **Tvardk;
int Tprod;/< Gives the k position of the k1 product /	int Tprod;/< Gives the k position of the k1 product /
/* Tprod[k1=1]=3(=V1V4) for V2+V1+V1V4+ageV3 /	/* Tprod[k1=1]=3(=V1V4) for V2+V1+V1V4+ageV3 /
int Tposprod; /< Gives the k1 product from the k position /	int Tposprod; /< Gives the k1 product from the k position /
Line 1449 char cutl(char blocc, char *alocc, cha	Line 1740 char cutl(char blocc, char *alocc, cha
{	{
/* 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 cutv(blocc,alocc,"abcdef2ghi2j",'2')
gives blocc="abcdef" and alocc="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
*/	*/
char s, t;	char s, t;
Line 1731 char *subdirf(char fileres[])	Line 2022 char *subdirf(char fileres[])
/************* function subdirf2 *********/	/************* function subdirf2 *********/
char subdirf2(char fileres[], char preop)	char subdirf2(char fileres[], char preop)
{	{
	/* Example subdirf2(optionfilefiname,"FB_") with optionfilefiname="texte", result="texte/FB_texte"
	Errors in subdirf, 2, 3 while printing tmpout is
	rewritten within the same printf. Workaround: many printfs */
/* Caution optionfilefiname is hidden */	/* Caution optionfilefiname is hidden */
strcpy(tmpout,optionfilefiname);	strcpy(tmpout,optionfilefiname);
strcat(tmpout,"/");	strcat(tmpout,"/");
Line 2102 void linmin(double p[], double xi[], int	Line 2395 void linmin(double p[], double xi[], int
#endif	#endif
#ifdef LINMINORIGINAL	#ifdef LINMINORIGINAL
#else	#else
if(fb == fx){ /* Flat function in the direction */	if(fb == fx){ /* Flat function in the direction */
xmin=xx;	xmin=xx;
*flat=1;	*flat=1;
}else{	}else{
*flat=0;	*flat=0;
#endif	#endif
/Flat mnbrak2 shift (ax=0.000000000000, fa=51626.272983130431), (bx=-1.618034000000, fb=51590.149499362531), (cx=-4.236068025156, fc=51590.149499362531) /	/Flat mnbrak2 shift (ax=0.000000000000, fa=51626.272983130431), (bx=-1.618034000000, fb=51590.149499362531), (cx=-4.236068025156, fc=51590.149499362531) /
Line 2163 void linmin(double p[], double xi[], int	Line 2456 void linmin(double p[], double xi[], int

/************* powell **********************/	/************* powell **********************/
/*	/*
Minimization of a function func of n variables. Input consists of an initial starting point	Minimization of a function func of n variables. Input consists in an initial starting point
p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-	p[1..n] ; an initial matrix xi[1..n][1..n] whose columns contain the initial set of di-
rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value	rections (usually the n unit vectors); and ftol, the fractional tolerance in the function value
such that failure to decrease by more than this amount on one iteration signals doneness. On	such that failure to decrease by more than this amount in one iteration signals doneness. On
output, p is set to the best point found, xi is the then-current direction set, fret is the returned	output, p is set to the best point found, xi is the then-current direction set, fret is the returned
function value at p , and iter is the number of iterations taken. The routine linmin is used.	function value at p , and iter is the number of iterations taken. The routine linmin is used.
*/	*/
Line 2191 void powell(double p[], double **xi, int	Line 2484 void powell(double p[], double **xi, int
double fp,fptt;	double fp,fptt;
double *xits;	double *xits;
int niterf, itmp;	int niterf, itmp;
#ifdef LINMINORIGINAL
#else

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

pt=vector(1,n);	pt=vector(1,n);
ptt=vector(1,n);	ptt=vector(1,n);
Line 2206 void powell(double p[], double **xi, int	Line 2493 void powell(double p[], double **xi, int
for (j=1;j<=n;j++) pt[j]=p[j];	for (j=1;j<=n;j++) pt[j]=p[j];
rcurr_time = time(NULL);	rcurr_time = time(NULL);
for (iter=1;;++(iter)) {	for (iter=1;;++(iter)) {
fp=(fret); / From former iteration or initial value */
ibig=0;	ibig=0;
del=0.0;	del=0.0;
rlast_time=rcurr_time;	rlast_time=rcurr_time;
/* (void) gettimeofday(&curr_time,&tzp); */	/* (void) gettimeofday(&curr_time,&tzp); */
rcurr_time = time(NULL);	rcurr_time = time(NULL);
curr_time = *localtime(&rcurr_time);	curr_time = *localtime(&rcurr_time);
printf("\nPowell iter=%d -2LL=%.12f %ld sec. %ld sec.",iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);	printf("\nPowell iter=%d -2LL=%.12f gain=%.12f=%.3g %ld sec. %ld sec.",iter,fret, fp-fret,fp-*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
fprintf(ficlog,"\nPowell iter=%d -2LL=%.12f %ld sec. %ld sec.",iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);	fprintf(ficlog,"\nPowell iter=%d -2LL=%.12f gain=%.12f=%.3g %ld sec. %ld sec.",iter,fret, fp-fret,fp-*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
/* fprintf(ficrespow,"%d %.12f %ld",iter,fret,curr_time.tm_sec-start_time.tm_sec); */	/* fprintf(ficrespow,"%d %.12f %ld",iter,fret,curr_time.tm_sec-start_time.tm_sec); */
	fp=(fret); / From former iteration or initial value */
for (i=1;i<=n;i++) {	for (i=1;i<=n;i++) {
fprintf(ficrespow," %.12lf", p[i]);	fprintf(ficrespow," %.12lf", p[i]);
}	}
Line 2320 void powell(double p[], double **xi, int	Line 2607 void powell(double p[], double **xi, int
/* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */	/* Convergence test will use last linmin estimation (fret) and compare former iteration (fp) */
/* But p and xit have been updated at the end of linmin, fret corresponds to new p, xit /	/* But p and xit have been updated at the end of linmin, fret corresponds to new p, xit /
/* New value of last point Pn is not computed, P(n-1) */	/* New value of last point Pn is not computed, P(n-1) */
for(j=1;j<=n;j++) {	for(j=1;j<=n;j++) {
if(flatdir[j] >0){	if(flatdir[j] >0){
printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);	printf(" p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);	fprintf(ficlog," p(%d)=%lf flat=%d ",j,p[j],flatdir[j]);
}	}
/* printf("\n"); */	/* printf("\n"); */
/* fprintf(ficlog,"\n"); */	/* fprintf(ficlog,"\n"); */
}	}
/* if (2.0fabs(fp-(fret)) <= ftol(fabs(fp)+fabs(fret))) { /\* Did we reach enough precision? \/ /	/* if (2.0fabs(fp-(fret)) <= ftol(fabs(fp)+fabs(fret))) { /\* Did we reach enough precision? \/ /
if (2.0fabs(fp-(fret)) <= ftol) { /* Did we reach enough precision? */	if (2.0fabs(fp-(fret)) <= ftol) { /* Did we reach enough precision? */
/* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */	/* We could compare with a chi^2. chisquare(0.95,ddl=1)=3.84 */
Line 2365 void powell(double p[], double **xi, int	Line 2652 void powell(double p[], double **xi, int
}	}
#endif	#endif

#ifdef LINMINORIGINAL
#else
free_ivector(flatdir,1,n);
#endif
free_vector(xit,1,n);	free_vector(xit,1,n);
free_vector(xits,1,n);	free_vector(xits,1,n);
free_vector(ptt,1,n);	free_vector(ptt,1,n);
Line 2482 void powell(double p[], double **xi, int	Line 2765 void powell(double p[], double **xi, int
}	}
printf("\n");	printf("\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
	#ifdef FLATSUP
	free_vector(xit,1,n);
	free_vector(xits,1,n);
	free_vector(ptt,1,n);
	free_vector(pt,1,n);
	return;
	#endif
}	}
#endif	#endif
printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);	printf("Gaining to use new average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
Line 2513 void powell(double p[], double **xi, int	Line 2803 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
(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
/* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */	* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I
/* Wx is row vector: population in state 1, population in state 2, population dead */	* Wx is row vector: population in state 1, population in state 2, population dead
/* or prevalence in state 1, prevalence in state 2, 0 */	* or prevalence in state 1, prevalence in state 2, 0
/* newm is the matrix after multiplications, its rows are identical at a factor */	* newm is the matrix after multiplications, its rows are identical at a factor.
/* Initial matrix pimij */	* Inputs are the parameter, age, a tolerance for the prevalence limit ftolpl.
	* Output is prlim.
	* Initial matrix pimij
	*/
/* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */	/* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
/* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */	/* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
/* 0, 0 , 1} */	/* 0, 0 , 1} */
Line 2535 void powell(double p[], double **xi, int	Line 2828 void powell(double p[], double **xi, int
/* 0.51326036147820708, 0.48673963852179264} */	/* 0.51326036147820708, 0.48673963852179264} */
/* If we start from prlim again, prlim tends to a constant matrix */	/* If we start from prlim again, prlim tends to a constant matrix */

int i, ii,j,k;	int i, ii,j,k, k1;
double min, max, *meandiff, maxmax,sumnew=0.;	double min, max, *meandiff, maxmax,sumnew=0.;
/* double *matprod2(); / /* test */	/* double *matprod2(); / /* test */
double out, cov[NCOVMAX+1], pmij(); /* *pmmij is a global variable feeded with oldms etc /	double out, cov[NCOVMAX+1], pmij(); /* *pmmij is a global variable feeded with oldms etc /
double **newm;	double **newm;
double agefin, delaymax=200. ; /* 100 Max number of years to converge */	double agefin, delaymax=200. ; /* 100 Max number of years to converge */
int ncvloop=0;	int ncvloop=0;
	int first=0;

min=vector(1,nlstate);	min=vector(1,nlstate);
max=vector(1,nlstate);	max=vector(1,nlstate);
Line 2562 void powell(double p[], double **xi, int	Line 2856 void powell(double p[], double **xi, int
newm=savm;	newm=savm;
/* Covariates have to be included here again */	/* Covariates have to be included here again */
cov[2]=agefin;	cov[2]=agefin;
if(nagesqr==1)	if(nagesqr==1){
cov[3]= agefin*agefin;;	cov[3]= agefin*agefin;
for (k=1; k<=nsd;k++) { /* For single dummy covariates only */	}
/* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */	/* Model(2) V1 + V2 + V3 + V8 + V7V8 + V5V6 + V8age + V3age + ageage /
cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];	/* total number of covariates of the model nbocc(+)+1 = 8 excepting constant and age and ageage /
/* printf("prevalim Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */	for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */
}	if(Typevar[k1]==1){ /* A product with age */
for (k=1; k<=nsq;k++) { /* For single varying covariates only */	cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
/* Here comes the value of quantitative after renumbering k with single quantitative covariates */	}else{
cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];	cov[2+nagesqr+k1]=precov[nres][k1];
/* printf("prevalim Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */	}
}	}/* End of loop on model equation */
for (k=1; k<=cptcovage;k++){ /* For product with age */
if(Dummy[Tvar[Tage[k]]]){	/* Start of old code (replaced by a loop on position in the model equation */
cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];	/* for (k=1; k<=nsd;k++) { /\* For single dummy covariates only of the model \/ /
} else{	/* /\* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates \/ /
cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];	/* /\* cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,TvarsD[k])]; \/ /
}	/* cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,TnsdVar[TvarsD[k]])]; */
/* printf("prevalim Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */	/* /\* model = 1 +age + V1V3 + ageV1 + V2 + V1 + ageV2 + V3 + V3age + V1V2 /
}	/* * k 1 2 3 4 5 6 7 8 */
for (k=1; k<=cptcovprod;k++){ /* For product without age */	/* cov[] 1 2 3 4 5 6 7 8 9 10 /
/* printf("prevalim Prod ij=%d k=%d Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */	/* TypeVar[k] 2 1 0 0 1 0 1 2 /
if(Dummy[Tvard[k][1]==0]){	/* Dummy[k] 0 2 0 0 2 0 2 0 /
if(Dummy[Tvard[k][2]==0]){	/* Tvar[k] 4 1 2 1 2 3 3 5 /
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];	/* nsd=3 (1) (2) (3) /
}else{	/* TvarsD[nsd] [1]=2 1 3 /
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];	/* TnsdVar [2]=2 [1]=1 [3]=3 /
}	/* TvarsDind[nsd](=k) [1]=3 [2]=4 [3]=6 /
}else{	/* Tage[] [1]=1 [2]=2 [3]=3 /
if(Dummy[Tvard[k][2]==0]){	/* Tvard[] [1][1]=1 [2][1]=1 /
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];	/* * [1][2]=3 [2][2]=2 */
}else{	/* Tprod[](=k) [1]=1 [2]=8 /
cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];	/* TvarsDp(=Tvar) [1]=1 [2]=2 [3]=3 [4]=5 /
}	/* TvarD (=k) [1]=1 [2]=3 [3]=4 [3]=6 [4]=6 /
}	/* TvarsDpType /
}	/* si model= 1 + age + V3 + V2age + V2 + V3age /
	/* * nsd=1 (1) (2) */
	/* TvarsD[nsd] 3 2 /
	/* TnsdVar (3)=1 (2)=2 /
	/* TvarsDind[nsd](=k) [1]=1 [2]=3 /
	/* Tage[] [1]=2 [2]= 3 /
	/* \/ /
	/* /\* cov[++k1]=nbcode[TvarsD[k]][codtabm(ij,k)]; \/ /
	/* /\* printf("prevalim Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); \/ /
	/* } */
	/* for (k=1; k<=nsq;k++) { /\* For single quantitative varying covariates only of the model \/ /
	/* /\* Here comes the value of quantitative after renumbering k with single quantitative covariates \/ /
	/* /\* Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline \/ /
	/* /\* cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; \/ /
	/* cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][resultmodel[nres][k1]] */
	/* /\* cov[++k1]=Tqresult[nres][k]; \/ /
	/* /\* printf("prevalim Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); \/ /
	/* } */
	/* for (k=1; k<=cptcovage;k++){ /\* For product with age \/ /
	/* if(Dummy[Tage[k]]==2){ /\* dummy with age \/ /
	/* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]cov[2]; /
	/* /\* cov[++k1]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]cov[2]; \/ */
	/* } else if(Dummy[Tage[k]]==3){ /\* quantitative with age \/ /
	/* cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; */
	/* /\* cov[++k1]=Tqresult[nres][k]; \/ /
	/* } */
	/* /\* printf("prevalim Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); \/ /
	/* } */
	/* for (k=1; k<=cptcovprod;k++){ /\* For product without age \/ /
	/* /\* printf("prevalim Prod ij=%d k=%d Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); \/ /
	/* if(Dummy[Tvard[k][1]]==0){ */
	/* if(Dummy[Tvard[k][2]]==0){ */
	/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; */
	/* /\* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; \/ /
	/* }else{ */
	/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * Tqresult[nres][k]; */
	/* /\* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k]; \/ /
	/* } */
	/* }else{ */
	/* if(Dummy[Tvard[k][2]]==0){ */
	/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])] * Tqinvresult[nres][Tvard[k][1]]; */
	/* /\* cov[++k1]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]]; \/ /
	/* }else{ */
	/* cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]]; */
	/* /\* cov[++k1]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]]; \/ /
	/* } */
	/* } */
	/* } /\* End product without age \/ /
	/* ENd of old code */
/printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);/	/printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);/
/printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);/	/printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);/
/printf("ij=%d cov[3]=%lf \n",ij, cov[3]);/	/printf("ij=%d cov[3]=%lf \n",ij, cov[3]);/
/* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */	/* savm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
/* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind \/ /	/* out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /\* Bug Valgrind \/ /
/* age and covariate values of ij are in 'cov' */	/* age and covariate values of ij are in 'cov' */
out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */	out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); /* Bug Valgrind */

savm=oldm;	savm=oldm;
Line 2638 void powell(double p[], double **xi, int	Line 2980 void powell(double p[], double **xi, int
free_vector(meandiff,1,nlstate);	free_vector(meandiff,1,nlstate);
return prlim;	return prlim;
}	}
} /* age loop */	} /* agefin loop */
/* After some age loop it doesn't converge */	/* After some age loop it doesn't converge */
printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. \n\	if(!first){
Earliest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);	first=1;
	printf("Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d). Others in log file only...\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM), (int)(age-stepm/YEARM), (int)delaymax);
	fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM), (int)(age-stepm/YEARM), (int)delaymax);
	}else if (first >=1 && first <10){
	fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM), (int)(age-stepm/YEARM), (int)delaymax);
	first++;
	}else if (first ==10){
	fprintf(ficlog, "Warning: the stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.d years and %d loops. Try to lower 'ftolpl'. Youngest age to start was %d=(%d-%d).\n", (int)age, maxmax, ftolpl, *ncvyear, ncvloop, (int)(agefin+stepm/YEARM), (int)(age-stepm/YEARM), (int)delaymax);
	printf("Warning: the stable prevalence dit not converge. This warning came too often, IMaCh will stop notifying, even in its log file. Look at the graphs to appreciate the non convergence.\n");
	fprintf(ficlog,"Warning: the stable prevalence no convergence; too many cases, giving up noticing, even in log file\n");
	first++;
	}

/* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */	/* Try to lower 'ftol', for example from 1.e-8 to 6.e-9.\n", ftolpl, (int)age, (int)delaymax, (int)agefin, ncvloop, (int)age-(int)agefin); */
free_vector(min,1,nlstate);	free_vector(min,1,nlstate);
free_vector(max,1,nlstate);	free_vector(max,1,nlstate);
Line 2677 Earliest age to start was %d-%d=%d, ncvl	Line 3031 Earliest age to start was %d-%d=%d, ncvl
/* 0.51326036147820708, 0.48673963852179264} */	/* 0.51326036147820708, 0.48673963852179264} */
/* If we start from prlim again, prlim tends to a constant matrix */	/* If we start from prlim again, prlim tends to a constant matrix */

int i, ii,j,k;	int i, ii,j,k, k1;
int first=0;	int first=0;
double min, max, *meandiff, maxmax,sumnew=0.;	double min, max, *meandiff, maxmax,sumnew=0.;
/* double *matprod2(); / /* test */	/* double *matprod2(); / /* test */
Line 2707 Earliest age to start was %d-%d=%d, ncvl	Line 3061 Earliest age to start was %d-%d=%d, ncvl
/* Even if hstepm = 1, at least one multiplication by the unit matrix */	/* Even if hstepm = 1, at least one multiplication by the unit matrix */
/* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */	/* Start at agefin= age, computes the matrix of passage and loops decreasing agefin until convergence is reached */
/* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age \/ /	/* for(agefin=age+stepm/YEARM; agefin<=age+delaymax; agefin=agefin+stepm/YEARM){ /\* A changer en age \/ /
for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /* A changer en age */	/* for(agefin=age; agefin<AGESUP; agefin=agefin+stepm/YEARM){ /\* A changer en age \/ /
	for(agefin=age; agefin<FMIN(AGESUP,age+delaymax); agefin=agefin+stepm/YEARM){ /* A changer en age */
ncvloop++;	ncvloop++;
newm=savm; /* oldm should be kept from previous iteration or unity at start */	newm=savm; /* oldm should be kept from previous iteration or unity at start */
/* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */	/* newm points to the allocated table savm passed by the function it can be written, savm could be reallocated */
/* Covariates have to be included here again */	/* Covariates have to be included here again */
cov[2]=agefin;	cov[2]=agefin;
if(nagesqr==1)	if(nagesqr==1){
cov[3]= agefin*agefin;;	cov[3]= agefin*agefin;;
for (k=1; k<=nsd;k++) { /* For single dummy covariates only */	}
/* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */	for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */
cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];	if(Typevar[k1]==1){ /* A product with age */
/* printf("bprevalim Dummy agefin=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agefin,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */	cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
}
/* for (k=1; k<=cptcovn;k++) { */
/* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; \/ /
/* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
/* /\* printf("prevalim ij=%d k=%d Tvar[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, Tvar[k],nbcode[Tvar[k]][codtabm(ij,Tvar[k])],cov[2+k], ij, k, codtabm(ij,Tvar[k])]); \/ /
/* } */
for (k=1; k<=nsq;k++) { /* For single varying covariates only */
/* Here comes the value of quantitative after renumbering k with single quantitative covariates */
cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
/* printf("prevalim Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
}
/* for (k=1; k<=cptcovage;k++) cov[2+nagesqr+Tage[k]]=nbcode[Tvar[k]][codtabm(ij,k)]cov[2]; /
/* for (k=1; k<=cptcovprod;k++) /\* Useless \/ /
/* /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; \/ /
/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
for (k=1; k<=cptcovage;k++){ /* For product with age */
if(Dummy[Tvar[Tage[k]]]){
cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
} else{
cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
}
/* printf("prevalim Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
}
for (k=1; k<=cptcovprod;k++){ /* For product without age */
/* printf("prevalim Prod ij=%d k=%d Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
if(Dummy[Tvard[k][1]==0]){
if(Dummy[Tvard[k][2]==0]){
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
}else{
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k];
}
}else{	}else{
if(Dummy[Tvard[k][2]==0]){	cov[2+nagesqr+k1]=precov[nres][k1];
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]];
}else{
cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]];
}
}	}
}	}/* End of loop on model equation */

	/* Old code */

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

/printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);/	/printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);/
/printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);/	/printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);/
Line 2808 Earliest age to start was %d-%d=%d, ncvl	Line 3175 Earliest age to start was %d-%d=%d, ncvl

maxmax=0.;	maxmax=0.;
for(i=1; i<=nlstate; i++){	for(i=1; i<=nlstate; i++){
meandiff[i]=(max[i]-min[i])/(max[i]+min[i])2.; / mean difference for each column */	meandiff[i]=(max[i]-min[i])/(max[i]+min[i])2.; / mean difference for each column, could be nan! */
maxmax=FMAX(maxmax,meandiff[i]);	maxmax=FMAX(maxmax,meandiff[i]);
/* printf("Back age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, i, meandiff[i],(int)agefin, i, max[i], i, min[i],maxmax); */	/* printf("Back age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, i, meandiff[i],(int)agefin, i, max[i], i, min[i],maxmax); */
} /* i loop */	} /* i loop */
Line 2821 Earliest age to start was %d-%d=%d, ncvl	Line 3188 Earliest age to start was %d-%d=%d, ncvl
free_vector(meandiff,1,nlstate);	free_vector(meandiff,1,nlstate);
return bprlim;	return bprlim;
}	}
} /* age loop */	} /* agefin loop */
/* After some age loop it doesn't converge */	/* After some age loop it doesn't converge */
if(first){	if(!first){
first=1;	first=1;
printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. Others in log file only...\n\	printf("Warning: the back stable prevalence at age %d did not converge with the required precision (%g > ftolpl=%g) within %.0f years. Try to lower 'ftolpl'. Others in log file only...\n\
Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);	Oldest age to start was %d-%d=%d, ncvloop=%d, ncvyear=%d\n", (int)age, maxmax, ftolpl, delaymax, (int)age, (int)delaymax, (int)agefin, ncvloop, *ncvyear);
Line 2868 double pmij(double ps, double *cov,	Line 3235 double pmij(double ps, double *cov,
/* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */	/* printf("Int j<i s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */
}	}
ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */	ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
/* printf("s1=%.17e, lnpijopii=%.17e\n",s1,lnpijopii); */	/* printf("Debug pmij() i=%d j=%d nc=%d s1=%.17f, lnpijopii=%.17f\n",i,j,nc, s1,lnpijopii); */
}	}
for(j=i+1; j<=nlstate+ndeath;j++){	for(j=i+1; j<=nlstate+ndeath;j++){
for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){	for (nc=1, lnpijopii=0.;nc <=ncovmodel; nc++){
Line 2877 double pmij(double ps, double *cov,	Line 3244 double pmij(double ps, double *cov,
/* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */	/* printf("Int j>i s1=%.17e, lnpijopii=%.17e %lx %lx\n",s1,lnpijopii,s1,lnpijopii); */
}	}
ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */	ps[i][j]=lnpijopii; /* In fact ln(pij/pii) */
	/* printf("Debug pmij() i=%d j=%d nc=%d s1=%.17f, lnpijopii=%.17f\n",i,j,nc, s1,lnpijopii); */
}	}
}	}

Line 2884 double pmij(double ps, double *cov,	Line 3252 double pmij(double ps, double *cov,
s1=0;	s1=0;
for(j=1; j<i; j++){	for(j=1; j<i; j++){
s1+=exp(ps[i][j]); /* In fact sums pij/pii */	s1+=exp(ps[i][j]); /* In fact sums pij/pii */
/printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); /	/* printf("debug1 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
}	}
for(j=i+1; j<=nlstate+ndeath; j++){	for(j=i+1; j<=nlstate+ndeath; j++){
s1+=exp(ps[i][j]); /* In fact sums pij/pii */	s1+=exp(ps[i][j]); /* In fact sums pij/pii */
/printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); /	/* printf("debug2 %d %d ps=%lf exp(ps)=%lf s1+=%lf\n",i,j,ps[i][j],exp(ps[i][j]),s1); */
}	}
/* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */	/* s1= sum_{j<>i} pij/pii=(1-pii)/pii and thus pii is known from s1 */
ps[i][i]=1./(s1+1.);	ps[i][i]=1./(s1+1.);
/* Computing other pijs */	/* Computing other pijs */
for(j=1; j<i; j++)	for(j=1; j<i; j++)
ps[i][j]= exp(ps[i][j])*ps[i][i];	ps[i][j]= exp(ps[i][j])ps[i][i];/ Bug valgrind */
for(j=i+1; j<=nlstate+ndeath; j++)	for(j=i+1; j<=nlstate+ndeath; j++)
ps[i][j]= exp(ps[i][j])*ps[i][i];	ps[i][j]= exp(ps[i][j])*ps[i][i];
/* ps[i][nlstate+1]=1.-s1- ps[i][i];/ / Sum should be 1 */	/* ps[i][nlstate+1]=1.-s1- ps[i][i];/ / Sum should be 1 */
Line 2906 double pmij(double ps, double *cov,	Line 3274 double pmij(double ps, double *cov,
ps[ii][ii]=1;	ps[ii][ii]=1;
}	}
}	}


/* for(ii=1; ii<= nlstate+ndeath; ii++){ */	/* for(ii=1; ii<= nlstate+ndeath; ii++){ */
/* for(jj=1; jj<= nlstate+ndeath; jj++){ */	/* for(jj=1; jj<= nlstate+ndeath; jj++){ */
/* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */	/* printf(" pmij ps[%d][%d]=%lf ",ii,jj,ps[ii][jj]); */
Line 2927 double pmij(double ps, double *cov,	Line 3295 double pmij(double ps, double *cov,
/* double bmij(double ps, double cov, int ncovmodel, double x, int nlstate, double *prevacurrent, double dnewm, double doldm, double dsavm, int ij ) /	/* double bmij(double ps, double cov, int ncovmodel, double x, int nlstate, double *prevacurrent, double dnewm, double doldm, double dsavm, int ij ) /
double bmij(double ps, double cov, int ncovmodel, double x, int nlstate, double ***prevacurrent, int ij )	double bmij(double ps, double cov, int ncovmodel, double x, int nlstate, double ***prevacurrent, int ij )
{	{
/* Computes the backward probability at age agefin and covariate combination ij. In fact cov is already filled and x too.	/* Computes the backward probability at age agefin, cov[2], and covariate combination 'ij'. In fact cov is already filled and x too.
* Call to pmij(cov and x), call to cross prevalence, sums and inverses, left multiply, and returns in ps as well as bmij.	* Call to pmij(cov and x), call to cross prevalence, sums and inverses, left multiply, and returns in ps as well as bmij.
*/	*/
int i, ii, j,k;	int i, ii, j,k;
Line 2935 double pmij(double ps, double *cov,	Line 3303 double pmij(double ps, double *cov,
double out, pmij();	double out, pmij();
double sumnew=0.;	double sumnew=0.;
double agefin;	double agefin;
double k3=0.; /* constant of the w_x diagonal matrixe (in order for B to sum to 1 even for death state) */	double k3=0.; /* constant of the w_x diagonal matrix (in order for B to sum to 1 even for death state) */
double dnewm, dsavm, **doldm;	double dnewm, dsavm, **doldm;
double **bbmij;	double **bbmij;

doldm=ddoldms; /* global pointers */	doldm=ddoldms; /* global pointers */
dnewm=ddnewms;	dnewm=ddnewms;
dsavm=ddsavms;	dsavm=ddsavms;

	/* Debug */
	/* printf("Bmij ij=%d, cov[2}=%f\n", ij, cov[2]); */
agefin=cov[2];	agefin=cov[2];
/* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */	/* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */
/* bmij // age is cov[2], ij is included in cov, but we need for	/* bmij // age is cov[2], ij is included in cov, but we need for
Line 2950 double pmij(double ps, double *cov,	Line 3320 double pmij(double ps, double *cov,
/* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */	/* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */

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

/* Diag(w_x) */	/* Diag(w_x) */
/* Problem with prevacurrent which can be zero */	/* Rescaling the cross-sectional prevalence: Problem with prevacurrent which can be zero */
sumnew=0.;	sumnew=0.;
/for (ii=1;ii<=nlstate+ndeath;ii++){/	/for (ii=1;ii<=nlstate+ndeath;ii++){/
for (ii=1;ii<=nlstate;ii++){ /* Only on live states */	for (ii=1;ii<=nlstate;ii++){ /* Only on live states */
/* printf(" agefin=%d, ii=%d, ij=%d, prev=%f\n",(int)agefin,ii, ij, prevacurrent[(int)agefin][ii][ij]); */	/* printf(" agefin=%d, ii=%d, ij=%d, prev=%f\n",(int)agefin,ii, ij, prevacurrent[(int)agefin][ii][ij]); */
sumnew+=prevacurrent[(int)agefin][ii][ij];	sumnew+=prevacurrent[(int)agefin][ii][ij];
}	}
if(sumnew >0.01){ /* At least some value in the prevalence */	if(sumnew >0.01){ /* At least some value in the prevalence */
Line 2981 double pmij(double ps, double *cov,	Line 3351 double pmij(double ps, double *cov,
}	}
/* End doldm, At the end doldm is diag[(w_i)] */	/* End doldm, At the end doldm is diag[(w_i)] */

/* left Product of this diag matrix by pmmij=Px (dnewm=dsavmdoldm) /	/* Left product of this diag matrix by pmmij=Px (dnewm=dsavmdoldm): diag[(w_i)Px */
bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* Bug Valgrind */	bbmij=matprod2(dnewm, doldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, pmmij); /* was a Bug Valgrind */

/* Diag(Sum_i w^i_x p^ij_x */	/* Diag(Sum_i w^i_x p^ij_x, should be the prevalence at age x+stepm */
/* w1 p11 + w2 p21 only on live states N1./N..N11/N1. + N2./N..N21/N2.=(N11+N21)/N..=N.1/N.. */	/* w1 p11 + w2 p21 only on live states N1./N..N11/N1. + N2./N..N21/N2.=(N11+N21)/N..=N.1/N.. */
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
sumnew=0.;	sumnew=0.;
Line 3002 double pmij(double ps, double *cov,	Line 3372 double pmij(double ps, double *cov,
} /End ii /	} /End ii /
} /* End j, At the end dsavm is diag[1/(w_1p1i+w_2 p2i)] for ALL states even if the sum is only for live states */	} /* End j, At the end dsavm is diag[1/(w_1p1i+w_2 p2i)] for ALL states even if the sum is only for live states */

ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* Bug Valgrind */	ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* was a Bug Valgrind */
/* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */	/* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
/* end bmij */	/* end bmij */
return ps; /pointer is unchanged /	return ps; /pointer is unchanged /
Line 3074 double bpmij(double ps, double *cov,	Line 3444 double bpmij(double ps, double *cov,
ps[ii][ii]=1;	ps[ii][ii]=1;
}	}
}	}
/* Added for backcast / / Transposed matrix too */	/* Added for prevbcast / / Transposed matrix too */
for(jj=1; jj<= nlstate+ndeath; jj++){	for(jj=1; jj<= nlstate+ndeath; jj++){
s1=0.;	s1=0.;
for(ii=1; ii<= nlstate+ndeath; ii++){	for(ii=1; ii<= nlstate+ndeath; ii++){
Line 3130 double matprod2(double out, double *	Line 3500 double matprod2(double out, double *

double *hpxij(double po, int nhstepm, double age, int hstepm, double x, int nlstate, int stepm, double oldm, double savm, int ij, int nres )	double *hpxij(double po, int nhstepm, double age, int hstepm, double x, int nlstate, int stepm, double oldm, double savm, int ij, int nres )
{	{
/* Computes the transition matrix starting at age 'age' and combination of covariate values corresponding to ij over	/* 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 3142 double *hpxij(double *po, int nhstep	Line 3512 double *hpxij(double *po, int nhstep

*/	*/

int i, j, d, h, k;	int i, j, d, h, k, k1;
double **out, cov[NCOVMAX+1];	double **out, cov[NCOVMAX+1];
double **newm;	double **newm;
double agexact;	double agexact;
Line 3162 double *hpxij(double *po, int nhstep	Line 3532 double *hpxij(double *po, int nhstep
cov[1]=1.;	cov[1]=1.;
agexact=age+((h-1)hstepm + (d-1))stepm/YEARM; /* age just before transition */	agexact=age+((h-1)hstepm + (d-1))stepm/YEARM; /* age just before transition */
cov[2]=agexact;	cov[2]=agexact;
if(nagesqr==1)	if(nagesqr==1){
cov[3]= agexact*agexact;	cov[3]= agexact*agexact;
for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
/* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates */
cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
/* printf("hpxij Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,Tvar[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
}
for (k=1; k<=nsq;k++) { /* For single varying covariates only */
/* Here comes the value of quantitative after renumbering k with single quantitative covariates */
cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
/* printf("hPxij Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
}
for (k=1; k<=cptcovage;k++){
if(Dummy[Tvar[Tage[k]]]){
cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
} else{
cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
}
/* printf("hPxij Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
}
for (k=1; k<=cptcovprod;k++){ /* */
/* printf("hPxij Prod ij=%d k=%d Tprod[%d]=%d Tvard[%d][1]=V%d, Tvard[%d][2]=V%d\n",ij,k,k,Tprod[k], k,Tvard[k][1], k,Tvard[k][2]); */
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)];
}	}
	/* 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 /
	for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */
	if(Typevar[k1]==1){ /* A product with age */
	cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
	}else{
	cov[2+nagesqr+k1]=precov[nres][k1];
	}
	}/* End of loop on model equation */
	/* Old code */
	/* if( Dummy[k1]==0 && Typevar[k1]==0 ){ /\* Single dummy \/ /
	/* /\* V(Tvarsel)=Tvalsel=Tresult[nres][pos](value); V(Tvresult[nres][pos] (variable): V(variable)=value) \/ /
	/* /\* for (k=1; k<=nsd;k++) { /\\* For single dummy covariates only \\/ \/ */
	/* /\* /\\* Here comes the value of the covariate 'ij' after renumbering k with single dummy covariates \\/ \/ */
	/* /\* codtabm(ij,k) (1 & (ij-1) >> (k-1))+1 \/ /
	/* /\* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 \/ /
	/* /\* k 1 2 3 4 5 6 7 8 9 \/ /
	/* /\Tvar[k]= 5 4 3 6 5 2 7 1 1 \/ */
	/* /\* nsd 1 2 3 \/ /\ Counting single dummies covar fixed or tv \/ /
	/* /\TvarsD[nsd] 4 3 1 \/ /\* ID of single dummy cova fixed or timevary\/ /
	/* /\TvarsDind[k] 2 3 9 \/ /\* position K of single dummy cova \/ /
	/* /\* cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];or [codtabm(ij,TnsdVar[TvarsD[k]] \/ /
	/* cov[2+nagesqr+k1]=Tresult[nres][resultmodel[nres][k1]]; */
	/* /\* printf("hpxij Dummy combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov=%lf codtabm(%d,TnsdVar[TvarsD[%d])=%d \n",ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,TnsdVar[TvarsD[k]])],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,TnsdVar[TvarsD[k]])); \/ /
	/* printf("hpxij Dummy combi=%d k1=%d Tvar[%d]=V%d cov[2+%d+%d]=%lf resultmodel[nres][%d]=%d nres/nresult=%d/%d \n",ij,k1,k1, Tvar[k1],nagesqr,k1,cov[2+nagesqr+k1],k1,resultmodel[nres][k1],nres,nresult); */
	/* printf("hpxij new Dummy precov[nres=%d][k1=%d]=%.4f\n", nres, k1, precov[nres][k1]); */
	/* }else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /\* Single quantitative variables \/ /
	/* /\* resultmodel[nres][k1]=k3: k1th position in the model correspond to the k3 position in the resultline \/ /
	/* cov[2+nagesqr+k1]=Tqresult[nres][resultmodel[nres][k1]]; */
	/* /\* for (k=1; k<=nsq;k++) { /\\* For single varying covariates only \\/ \/ */
	/* /\* /\\* Here comes the value of quantitative after renumbering k with single quantitative covariates \\/ \/ */
	/* /\* cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; \/ /
	/* printf("hPxij Quantitative k1=%d resultmodel[nres][%d]=%d,Tqresult[%d][%d]=%f\n",k1,k1,resultmodel[nres][k1],nres,resultmodel[nres][k1],Tqresult[nres][resultmodel[nres][k1]]); */
	/* printf("hpxij new Quanti precov[nres=%d][k1=%d]=%.4f\n", nres, k1, precov[nres][k1]); */
	/* }else if( Dummy[k1]==2 ){ /\* For dummy with age product \/ /
	/* /\* Tvar[k1] Variable in the age product ageV1 is 1 \/ */
	/* /\* [Tinvresult[nres][V1] is its value in the resultline nres \/ /
	/* cov[2+nagesqr+k1]=TinvDoQresult[nres][Tvar[k1]]cov[2]; /
	/* printf("DhPxij Dummy with age k1=%d Tvar[%d]=%d TinvDoQresult[nres=%d][%d]=%.f age=%.2f,cov[2+%d+%d]=%.3f\n",k1,k1,Tvar[k1],nres,TinvDoQresult[nres][Tvar[k1]],cov[2],nagesqr,k1,cov[2+nagesqr+k1]); */
	/* printf("hpxij new Dummy with age product precov[nres=%d][k1=%d]=%.4f * age=%.2f\n", nres, k1, precov[nres][k1], cov[2]); */

	/* /\* cov[2+nagesqr+k1]=Tresult[nres][resultmodel[nres][k1]]; \/ /
	/* /\* for (k=1; k<=cptcovage;k++){ /\\* For product with age V1+V1age +V4 +ageV3 \\/ \/ */
	/* /\* 1+2 Tage[1]=2 TVar[2]=1 Dummy[2]=2, Tage[2]=4 TVar[4]=3 Dummy[4]=3 quant\/ /
	/* /\* \/ /
	/* /\* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 \/ /
	/* /\* k 1 2 3 4 5 6 7 8 9 \/ /
	/* /\Tvar[k]= 5 4 3 6 5 2 7 1 1 \/ */
	/* /\cptcovage=2 1 2 \/ */
	/* /\Tage[k]= 5 8 \/ */
	/* }else if( Dummy[k1]==3 ){ /\* For quant with age product \/ /
	/* cov[2+nagesqr+k1]=Tresult[nres][resultmodel[nres][k1]]; */
	/* printf("QhPxij Quant with age k1=%d resultmodel[nres][%d]=%d,Tqresult[%d][%d]=%f\n",k1,k1,resultmodel[nres][k1],nres,resultmodel[nres][k1],Tqresult[nres][resultmodel[nres][k1]]); */
	/* printf("hpxij new Quanti with age product precov[nres=%d][k1=%d] * age=%.2f\n", nres, k1, precov[nres][k1], cov[2]); */
	/* /\* if(Dummy[Tage[k]]== 2){ /\\* dummy with age \\/ \/ */
	/* /\* /\\* if(Dummy[Tvar[Tage[k]]]== 2){ /\\\* dummy with age \\\/ \\/ \/ /
	/* /\* /\\* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]cov[2]; \\/ \/ /
	/* /\* /\\* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,TnsdVar[TvarsD[Tvar[Tage[k]]]])]cov[2]; \\/ \/ /
	/* /\* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,TnsdVar[TvarsD[Tvar[Tage[k]]]])]cov[2]; \/ */
	/* /\* printf("hPxij Age combi=%d k=%d cptcovage=%d Tage[%d]=%d Tvar[Tage[%d]]=V%d nbcode[Tvar[Tage[k]]][codtabm(ij,TnsdVar[Tvar[Tage[k]]]])]=%d nres=%d\n",ij,k,cptcovage,k,Tage[k],k,Tvar[Tage[k]], nbcode[Tvar[Tage[k]]][codtabm(ij,TnsdVar[Tvar[Tage[k]]])],nres); \/ /
	/* /\* } else if(Dummy[Tage[k]]== 3){ /\\* quantitative with age \\/ \/ */
	/* /\* cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; \/ /
	/* /\* } \/ /
	/* /\* printf("hPxij Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); \/ /
	/* }else if(Typevar[k1]==2 ){ /\* For product (not with age) \/ /
	/* /\* for (k=1; k<=cptcovprod;k++){ /\\* For product without age \\/ \/ */
	/* /\* /\\* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 \\/ \/ */
	/* /\* /\\* k 1 2 3 4 5 6 7 8 9 \\/ \/ */
	/* /\* /\\Tvar[k]= 5 4 3 6 5 2 7 1 1 \\/ \/ /
	/* /\* /\\cptcovprod=1 1 2 \\/ \/ /
	/* /\* /\\Tprod[]= 4 7 \\/ \/ /
	/* /\* /\\Tvard[][1] 4 1 \\/ \/ /
	/* /\* /\\Tvard[][2] 3 2 \\/ \/ /

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

	/* /\* if(Dummy[Tvardk[k1][1]]==0){ \/ /
	/* /\* if(Dummy[Tvardk[k1][2]]==0){ /\\* Product of dummies \\/ \/ */
	/* /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; \/ /
	/* /\* cov[2+nagesqr+k1]=Tinvresult[nres][Tvardk[k1][1]] * Tinvresult[nres][Tvardk[k1][2]]; \/ /
	/* /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,TnsdVar[Tvard[k][1]])] * nbcode[Tvard[k][2]][codtabm(ij,TnsdVar[Tvard[k][2]])]; \/ /
	/* /\* }else{ /\\* Product of dummy by quantitative \\/ \/ */
	/* /\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,TnsdVar[Tvard[k][1]])] * Tqresult[nres][k]; \/ /
	/* /\* cov[2+nagesqr+k1]=Tresult[nres][Tinvresult[nres][Tvardk[k1][1]]] * Tqresult[nres][Tinvresult[nres][Tvardk[k1][2]]]; \/ /
	/* /\* } \/ /
	/* /\* }else{ /\\* Product of quantitative by...\\/ \/ */
	/* /\* if(Dummy[Tvard[k][2]]==0){ /\\* quant by dummy \\/ \/ */
	/* /\* /\\* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,TnsdVar[Tvard[k][2]])] * Tqinvresult[nres][Tvard[k][1]]; \\/ \/ */
	/* /\* cov[2+nagesqr+k1]=Tqresult[nres][Tinvresult[nres][Tvardk[k1][1]]] * Tresult[nres][Tinvresult[nres][Tvardk[k1][2]]] ; \/ /
	/* /\* }else{ /\\* Product of two quant \\/ \/ */
	/* /\* /\\* cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]]; \\/ \/ */
	/* /\* cov[2+nagesqr+k1]=Tqresult[nres][Tinvresult[nres][Tvardk[k1][1]]] * Tqresult[nres][Tinvresult[nres][Tvardk[k1][2]]] ; \/ /
	/* /\* } \/ /
	/* /\* }/\\end of products quantitative \\/ \/ /
	/* }/\end of products \/ */
	/* } /\* End of loop on model equation \/ /
/* for (k=1; k<=cptcovn;k++) */	/* for (k=1; k<=cptcovn;k++) */
/* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */	/* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
/* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 \/ /	/* for (k=1; k<=cptcovage;k++) /\* Should start at cptcovn+1 \/ /
Line 3196 double *hpxij(double *po, int nhstep	Line 3645 double *hpxij(double *po, int nhstep

/printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);/	/printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);/
/printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);/	/printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);/
/* right multiplication of oldm by the current matrix */	/* right multiplication of oldm by the current matrix */
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,
pmij(pmmij,cov,ncovmodel,x,nlstate));	pmij(pmmij,cov,ncovmodel,x,nlstate));
/* if((int)age == 70){ */	/* if((int)age == 70){ */
Line 3231 double *hpxij(double *po, int nhstep	Line 3680 double *hpxij(double *po, int nhstep
/* double *hbxij(double po, int nhstepm, double age, int hstepm, double x, double *prevacurrent, int nlstate, int stepm, double oldm, double savm, double dnewm, double doldm, double dsavm, int ij ) */	/* double *hbxij(double po, int nhstepm, double age, int hstepm, double x, double *prevacurrent, int nlstate, int stepm, double oldm, double savm, double dnewm, double doldm, double dsavm, int ij ) */
double *hbxij(double po, int nhstepm, double age, int hstepm, double x, double ***prevacurrent, int nlstate, int stepm, int ij, int nres )	double *hbxij(double po, int nhstepm, double age, int hstepm, double x, double ***prevacurrent, int nlstate, int stepm, int ij, int nres )
{	{
/* For a combination of dummy covariate ij, computes the transition matrix starting at age 'age' over	/* For dummy covariates given in each resultline (for historical, computes the corresponding combination ij),
	computes the transition matrix starting at age 'age' over
'nhstepmhstepmstepm' months (i.e. until	'nhstepmhstepmstepm' months (i.e. until
age (in years) age+nhstepmhstepmstepm/12) by multiplying	age (in years) age+nhstepmhstepmstepm/12) by multiplying
nhstepm*hstepm matrices.	nhstepm*hstepm matrices.
Line 3243 double *hbxij(double *po, int nhstep	Line 3693 double *hbxij(double *po, int nhstep
The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output	The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output
*/	*/

int i, j, d, h, k;	int i, j, d, h, k, k1;
double out, cov[NCOVMAX+1], bmij();	double out, cov[NCOVMAX+1], bmij();
double newm, *newmm;	double newm, *newmm;
double agexact;	double agexact;
Line 3266 double *hbxij(double *po, int nhstep	Line 3716 double *hbxij(double *po, int nhstep
cov[1]=1.;	cov[1]=1.;
agexact=age-( (h-1)hstepm + (d) )stepm/YEARM; /* age just before transition, d or d-1? */	agexact=age-( (h-1)hstepm + (d) )stepm/YEARM; /* age just before transition, d or d-1? */
/* agexact=age+((h-1)hstepm + (d-1))stepm/YEARM; /\* age just before transition \/ /	/* agexact=age+((h-1)hstepm + (d-1))stepm/YEARM; /\* age just before transition \/ /
	/* Debug */
	/* printf("hBxij age=%lf, agexact=%lf\n", age, agexact); */
cov[2]=agexact;	cov[2]=agexact;
if(nagesqr==1)	if(nagesqr==1){
cov[3]= agexact*agexact;	cov[3]= agexact*agexact;
for (k=1; k<=cptcovn;k++){	}
/* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */	/** New code */
/* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; \/ /	for(k1=1;k1<=cptcovt;k1++){ /* loop on model equation (including products) */
cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];	if(Typevar[k1]==1){ /* A product with age */
/* printf("hbxij Dummy agexact=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agexact,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */	cov[2+nagesqr+k1]=precov[nres][k1]*cov[2];
}	}else{
for (k=1; k<=nsq;k++) { /* For single varying covariates only */	cov[2+nagesqr+k1]=precov[nres][k1];
/* Here comes the value of quantitative after renumbering k with single quantitative covariates */	}
cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];	}/* End of loop on model equation */
/* printf("hPxij Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */	/** End of new code */
}	/** This was old code */
for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 */	/* for (k=1; k<=nsd;k++){ /\* For single dummy covariates only \//\ cptcovn error \/ /
if(Dummy[Tvar[Tage[k]]]){	/* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; \/ /
cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];	/* /\* /\\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; \\/ \/ */
} else{	/* cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,TvarsD[k])];/\* Bug valgrind \/ /
cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];	/* /\* printf("hbxij Dummy agexact=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agexact,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); \/ /
}	/* } */
/* printf("hBxij Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */	/* for (k=1; k<=nsq;k++) { /\* For single varying covariates only \/ /
}	/* /\* Here comes the value of quantitative after renumbering k with single quantitative covariates \/ /
for (k=1; k<=cptcovprod;k++){ /* Useless because included in cptcovn */	/* cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k]; */
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];	/* /\* printf("hPxij Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); \/ /
}	/* } */
/printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);/	/* for (k=1; k<=cptcovage;k++){ /\* Should start at cptcovn+1 \//\ For product with age \/ /
/printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);/	/* /\* if(Dummy[Tvar[Tage[k]]]== 2){ /\\* dummy with age error!!!\\/ \/ */
	/* if(Dummy[Tage[k]]== 2){ /\* dummy with age \/ /
	/* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]cov[2]; /
	/* } else if(Dummy[Tage[k]]== 3){ /\* quantitative with age \/ /
	/* cov[2+nagesqr+Tage[k]]=Tqresult[nres][k]; */
	/* } */
	/* /\* printf("hBxij Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); \/ /
	/* } */
	/* for (k=1; k<=cptcovprod;k++){ /\* Useless because included in cptcovn \/ /
	/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; /
	/* if(Dummy[Tvard[k][1]]==0){ */
	/* if(Dummy[Tvard[k][2]]==0){ */
	/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][1])]; */
	/* }else{ */
	/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])] * Tqresult[nres][k]; */
	/* } */
	/* }else{ */
	/* if(Dummy[Tvard[k][2]]==0){ */
	/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])] * Tqinvresult[nres][Tvard[k][1]]; */
	/* }else{ */
	/* cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]]; */
	/* } */
	/* } */
	/* } */
	/* /\printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);\/ */
	/* /\printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);\/ */
	/** End of old code */

/* Careful transposed matrix */	/* Careful transposed matrix */
/* age is in cov[2], prevacurrent at beginning of transition. */	/* age is in cov[2], prevacurrent at beginning of transition. */
/* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */	/* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
/* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */	/* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\	out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);	1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);/* Bug valgrind */
/* if((int)age == 70){ */	/* if((int)age == 70){ */
/* printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */	/* printf(" Backward hbxij age=%d agexact=%f d=%d nhstepm=%d hstepm=%d\n", (int) age, agexact, d, nhstepm, hstepm); */
/* for(i=1; i<=nlstate+ndeath; i++) { */	/* for(i=1; i<=nlstate+ndeath; i++) { */
Line 3385 double func( double *x)	Line 3863 double func( double *x)
*/	*/
ioffset=2+nagesqr ;	ioffset=2+nagesqr ;
/* Fixed */	/* Fixed */
for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */	for (k=1; k<=ncovf;k++){ /* For each fixed covariate dummu or quant or prod */
cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, only V1 is fixed (k=6)*/	/* # V1=sex, V2=raedyrs Quant Fixed, State=livarnb4..livarnb11, V3=iadl4..iald11, V4=adlw4..adlw11, V5=r4bmi..r11bmi */
	/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
	/* TvarF[1]=Tvar[6]=2, TvarF[2]=Tvar[7]=7, TvarF[3]=Tvar[9]=1 ID of fixed covariates or product V2, V1V2, V1 /
	/* TvarFind; TvarFind[1]=6, TvarFind[2]=7, TvarFind[3]=9 // Inverse V2(6) is first fixed (single or prod) */
	cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, only V1 is fixed (TvarFind[1]=6)*/
	/* V1V2 (7) TvarFind[2]=7, TvarFind[3]=9 /
}	}
/* In model V2+V1V4+ageV3+V3V2 Tvar[1] is V2, Tvar[2=V1V4]	/* In model V2+V1V4+ageV3+V3V2 Tvar[1] is V2, Tvar[2=V1V4]
is 6, Tvar[3=ageV3] should not be computed because of age Tvar[4=V3V2]	is 5, Tvar[3=ageV3] should not be computed because of age Tvar[4=V3V2]=6
has been calculated etc */	has been calculated etc */
/* For an individual i, wav[i] gives the number of effective waves */	/* For an individual i, wav[i] gives the number of effective waves */
/* We compute the contribution to Likelihood of each effective transition	/* We compute the contribution to Likelihood of each effective transition
Line 3401 double func( double *x)	Line 3884 double func( double *x)
meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]	meaning that decodemodel should be used cotvar[mw[mi+1][i]][TTvar[iv]][i]
*/	*/
for(mi=1; mi<= wav[i]-1; mi++){	for(mi=1; mi<= wav[i]-1; mi++){
for(k=1; k <= ncovv ; k++){ /* Varying covariates (single and product but no age )*/	for(k=1; k <= ncovv ; k++){ /* Varying covariates in the model (single and product but no age )"V5+V4+V3+V4V3+V5age+V1age+V1" +TvarVind 1,2,3,4(V4V3) Tvar[1]@7{5, 4, 3, 6, 5, 1, 1 ; 6 because the created covar is after V5 and is 6, minus 1+1, 3,2,1,4 positions in cotvar*/
/* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; */	/* cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]][i]; but where is the crossproduct? */
cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];	cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
}	}
for (ii=1;ii<=nlstate+ndeath;ii++)	for (ii=1;ii<=nlstate+ndeath;ii++)
Line 3417 double func( double *x)	Line 3900 double func( double *x)
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]]-ncovcol-nqv][i]*agexact;
}	}
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 3528 double func( double *x)	Line 4011 double func( double *x)
} /* end of individual */	} /* end of individual */
} else if(mle==2){	} else if(mle==2){
for (i=1,ipmx=0, sw=0.; i<=imx; i++){	for (i=1,ipmx=0, sw=0.; i<=imx; i++){
for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i];	ioffset=2+nagesqr ;
	for (k=1; k<=ncovf;k++)
	cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];
for(mi=1; mi<= wav[i]-1; mi++){	for(mi=1; mi<= wav[i]-1; mi++){
	for(k=1; k <= ncovv ; k++){
	cov[ioffset+TvarVind[k]]=cotvar[mw[mi][i]][Tvar[TvarVind[k]]-ncovcol-nqv][i];
	}
for (ii=1;ii<=nlstate+ndeath;ii++)	for (ii=1;ii<=nlstate+ndeath;ii++)
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
oldm[ii][j]=(ii==j ? 1.0 : 0.0);	oldm[ii][j]=(ii==j ? 1.0 : 0.0);
Line 3707 double funcone( double *x)	Line 4195 double funcone( double *x)
/* Fixed */	/* Fixed */
/* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */	/* for (k=1; k<=cptcovn;k++) cov[2+nagesqr+k]=covar[Tvar[k]][i]; */
/* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products \/ /	/* for (k=1; k<=ncoveff;k++){ /\* Simple and product fixed Dummy covariates without age* products \/ /
for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products */	for (k=1; k<=ncovf;k++){ /* Simple and product fixed covariates without age* products // Missing values are set to -1 but should be dropped */
cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][i];/* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, only V1 is fixed (k=6)*/	cov[ioffset+TvarFind[k]]=covar[Tvar[TvarFind[k]]][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 3834 return -l;	Line 4322 return -l;


/************* function likelione *********/	/************* function likelione *********/
void likelione(FILE ficres,double p[], int npar, int nlstate, int globpri, long ipmx, double sw, double fretone, double (funcone)(double []))	void likelione(FILE ficres,double p[], int npar, int nlstate, int globpri, long ipmx, double sw, double fretone, double (func)(double []))
{	{
/* This routine should help understanding what is done with	/* This routine should help understanding what is done with
the selection of individuals/waves and	the selection of individuals/waves and
Line 3858 void likelione(FILE *ficres,double p[],	Line 4346 void likelione(FILE *ficres,double p[],
fprintf(ficresilk," -2gipw/gswweight*ll(total)\n");	fprintf(ficresilk," -2gipw/gswweight*ll(total)\n");
}	}

fretone=(funcone)(p);	fretone=(func)(p);
if(*globpri !=0){	if(*globpri !=0){
fclose(ficresilk);	fclose(ficresilk);
if (mle ==0)	if (mle ==0)
Line 3886 void likelione(FILE *ficres,double p[],	Line 4374 void likelione(FILE *ficres,double p[],

void mlikeli(FILE ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (func)(double []))	void mlikeli(FILE ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (func)(double []))
{	{
int i,j, iter=0;	int i,j,k, jk, jkk=0, iter=0;
double **xi;	double **xi;
double fret;	double fret;
double fretone; /* Only one call to likelihood */	double fretone; /* Only one call to likelihood */
Line 3920 void mlikeli(FILE *ficres,double p[], in	Line 4408 void mlikeli(FILE *ficres,double p[], in
if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);	if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
fprintf(ficrespow,"\n");	fprintf(ficrespow,"\n");
#ifdef POWELL	#ifdef POWELL
	#ifdef LINMINORIGINAL
	#else /* LINMINORIGINAL */

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

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

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

#ifdef NLOPT	#ifdef NLOPT
#ifdef NEWUOA	#ifdef NEWUOA
Line 3949 void mlikeli(FILE *ficres,double p[], in	Line 4494 void mlikeli(FILE *ficres,double p[], in
}	}
nlopt_destroy(opt);	nlopt_destroy(opt);
#endif	#endif
	#ifdef FLATSUP
	/* npared = npar -flatd/ncovmodel; */
	/* xired= matrix(1,npared,1,npared); */
	/* paramred= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */
	/* powell(pred,xired,npared,ftol,&iter,&fret,flatdir,func); */
	/* free_matrix(xire,1,npared,1,npared); */
	#else /* FLATSUP */
	#endif /* FLATSUP */
free_matrix(xi,1,npar,1,npar);	free_matrix(xi,1,npar,1,npar);
fclose(ficrespow);	fclose(ficrespow);
printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));	printf("\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
Line 4333 void pstamp(FILE *fichier)	Line 4886 void pstamp(FILE *fichier)
fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);	fprintf(fichier,"# %s.%s\n#IMaCh version %s, %s\n#%s\n# %s", optionfilefiname,optionfilext,version,copyright, fullversion, strstart);
}	}

	void date2dmy(double date,double day, double month, double *year){
	double yp=0., yp1=0., yp2=0.;

	yp1=modf(date,&yp);/* extracts integral of date in yp and
	fractional in yp1 */
	*year=yp;
	yp2=modf((yp1*12),&yp);
	*month=yp;
	yp1=modf((yp2*30.5),&yp);
	*day=yp;
	if(day==0) day=1;
	if(month==0) month=1;
	}



/********** Frequencies ******************/	/********** Frequencies ******************/
Line 4340 void freqsummary(char fileres[], double	Line 4907 void freqsummary(char fileres[], double
int Tvaraff, int invalidvarcomb, int *nbcode, int ncodemax,double mint,double anint, char strstart[], \	int Tvaraff, int invalidvarcomb, int *nbcode, int ncodemax,double mint,double anint, char strstart[], \
int firstpass, int lastpass, int stepm, int weightopt, char model[])	int firstpass, int lastpass, int stepm, int weightopt, char model[])
{ /* Some frequencies as well as proposing some starting values */	{ /* Some frequencies as well as proposing some starting values */
	/* Frequencies of any combination of dummy covariate used in the model equation */
int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1;	int i, m, jk, j1, bool, z1,j, nj, nl, k, iv, jj=0, s1=1, s2=1;
int iind=0, iage=0;	int iind=0, iage=0;
int mi; /* Effective wave */	int mi; /* Effective wave */
Line 4348 void freqsummary(char fileres[], double	Line 4915 void freqsummary(char fileres[], double
double **freq; / Frequencies */	double **freq; / Frequencies */
double x, y, a=0.,b=0.,r=1., sa=0., sb=0.; /* for regression, y=b+mx and r is the correlation coefficient /	double x, y, a=0.,b=0.,r=1., sa=0., sb=0.; /* for regression, y=b+mx and r is the correlation coefficient /
int no=0, linreg(int ifi, int ila, int no, const double x[], const double y[], double a, double* b, double* r, double* sa, double * sb);	int no=0, linreg(int ifi, int ila, int no, const double x[], const double y[], double a, double* b, double* r, double* sa, double * sb);
double *meanq;	double meanq, stdq, *idq;
double **meanqt;	double **meanqt;
double pp, prop, posprop, *pospropt;	double pp, prop, posprop, *pospropt;
double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;	double pos=0., posproptt=0., pospropta=0., k2, dateintsum=0,k2cpt=0;
Line 4361 void freqsummary(char fileres[], double	Line 4928 void freqsummary(char fileres[], double
pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */	pospropt=vector(1,nlstate); /* Counting the number of transition starting from a live state */
/* prop=matrix(1,nlstate,iagemin,iagemax+3); */	/* prop=matrix(1,nlstate,iagemin,iagemax+3); */
meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */	meanq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
	stdq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
	idq=vector(1,nqfveff); /* Number of Quantitative Fixed Variables Effective */
meanqt=matrix(1,lastpass,1,nqtveff);	meanqt=matrix(1,lastpass,1,nqtveff);
strcpy(fileresp,"P_");	strcpy(fileresp,"P_");
strcat(fileresp,fileresu);	strcat(fileresp,fileresu);
Line 4384 void freqsummary(char fileres[], double	Line 4953 void freqsummary(char fileres[], double
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\	Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);	fileresphtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
}	}
fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies and prevalence by age at begin of transition and dummy covariate value at beginning of transition</h4>\n",fileresphtm, fileresphtm);	fprintf(ficresphtm,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies (weight=%d) and prevalence by age at begin of transition and dummy covariate value at beginning of transition</h4>\n",fileresphtm, fileresphtm, weightopt);

strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));	strcpy(fileresphtmfr,subdirfext(optionfilefiname,"PHTMFR_",".htm"));
if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {	if((ficresphtmfr=fopen(fileresphtmfr,"w"))==NULL) {
Line 4394 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4963 Title=%s <br>Datafile=%s Firstpass=%d La
exit(70);	exit(70);
} else{	} else{
fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \	fprintf(ficresphtmfr,"<html><head>\n<title>IMaCh PHTM_Frequency table %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
<hr size=\"2\" color=\"#EC5E5E\"> \n \	,<hr size=\"2\" color=\"#EC5E5E\"> \n \
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\	Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=1+age+%s<br>\n",\
fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);	fileresphtmfr,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
}	}
fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Frequencies of all effective transitions of the model, by age at begin of transition, and covariate value at the begin of transition (if the covariate is a varying covariate) </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr);	fprintf(ficresphtmfr,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>(weight=%d) frequencies of all effective transitions of the model, by age at begin of transition, and covariate value at the begin of transition (if the covariate is a varying covariate) </h4>Unknown status is -1<br/>\n",fileresphtmfr, fileresphtmfr,weightopt);

y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);	y= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);	x= vector(iagemin-AGEMARGE,iagemax+4+AGEMARGE);
Line 4407 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4976 Title=%s <br>Datafile=%s Firstpass=%d La

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


Line 4414 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4984 Title=%s <br>Datafile=%s Firstpass=%d La
reference=low_education V1=0,V2=0	reference=low_education V1=0,V2=0
med_educ V1=1 V2=0,	med_educ V1=1 V2=0,
high_educ V1=0 V2=1	high_educ V1=0 V2=1
Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcoveff	Then V1=1 and V2=1 is a noisy combination that we want to exclude for the list 2**cptcovn
*/	*/
dateintsum=0;	dateintsum=0;
k2cpt=0;	k2cpt=0;
Line 4426 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4996 Title=%s <br>Datafile=%s Firstpass=%d La

/* if a constant only model, one pass to compute frequency tables and to write it on ficresp */	/* if a constant only model, one pass to compute frequency tables and to write it on ficresp */
/* Loop on nj=1 or 2 if dummy covariates j!=0	/* Loop on nj=1 or 2 if dummy covariates j!=0
* Loop on j1(1 to 2**cptcoveff) covariate combination	* Loop on j1(1 to 2**cptcovn) covariate combination
* freq[s1][s2][iage] =0.	* freq[s1][s2][iage] =0.
* Loop on iind	* Loop on iind
* ++freq[s1][s2][iage] weighted	* ++freq[s1][s2][iage] weighted
Line 4451 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5021 Title=%s <br>Datafile=%s Firstpass=%d La
if(nj==1)	if(nj==1)
j=0; /* First pass for the constant */	j=0; /* First pass for the constant */
else{	else{
j=cptcoveff; /* Other passes for the covariate values */	j=cptcovs; /* Other passes for the covariate values */
}	}
first=1;	first=1;
for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on all covariates combination of the model, excluding quantitatives, V4=0, V3=0 for example, fixed or varying covariates */	for (j1 = 1; j1 <= (int) pow(2,j); j1++){ /* Loop on all dummy covariates combination of the model, ie excluding quantitatives, V4=0, V3=0 for example, fixed or varying covariates */
posproptt=0.;	posproptt=0.;
/*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);	/*printf("cptcovn=%d Tvaraff=%d", cptcovn,Tvaraff[1]);
scanf("%d", i);*/	scanf("%d", i);*/
for (i=-5; i<=nlstate+ndeath; i++)	for (i=-5; i<=nlstate+ndeath; i++)
for (s2=-5; s2<=nlstate+ndeath; s2++)	for (s2=-5; s2<=nlstate+ndeath; s2++)
Line 4469 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5039 Title=%s <br>Datafile=%s Firstpass=%d La
posprop[i]=0;	posprop[i]=0;
pospropt[i]=0;	pospropt[i]=0;
}	}
/* for (z1=1; z1<= nqfveff; z1++) { */	for (z1=1; z1<= nqfveff; z1++) { /* zeroing for each combination j1 as well as for the total */
/* meanq[z1]+=0.; */	idq[z1]=0.;
	meanq[z1]=0.;
	stdq[z1]=0.;
	}
	/* for (z1=1; z1<= nqtveff; z1++) { */
/* for(m=1;m<=lastpass;m++){ */	/* for(m=1;m<=lastpass;m++){ */
/* meanqt[m][z1]=0.; */	/* meanqt[m][z1]=0.; */
/* } */	/* } */
/* } */	/* } */

/* dateintsum=0; */	/* dateintsum=0; */
/* k2cpt=0; */	/* k2cpt=0; */

Line 4484 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5057 Title=%s <br>Datafile=%s Firstpass=%d La
bool=1;	bool=1;
if(j !=0){	if(j !=0){
if(anyvaryingduminmodel==0){ /* If All fixed covariates */	if(anyvaryingduminmodel==0){ /* If All fixed covariates */
if (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */	if (cptcovn >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
/* for (z1=1; z1<= nqfveff; z1++) { */	for (z1=1; z1<=cptcovn; z1++) { /* loops on covariates in the model */
/* meanq[z1]+=coqvar[Tvar[z1]][iind]; /\* Computes mean of quantitative with selected filter \/ /
/* } */
for (z1=1; z1<=cptcoveff; z1++) { /* loops on covariates in the model */
/* if(Tvaraff[z1] ==-20){ */	/* if(Tvaraff[z1] ==-20){ */
/* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; \/ /	/* /\* sumnew+=cotvar[mw[mi][iind]][z1][iind]; \/ /
/* }else if(Tvaraff[z1] ==-10){ */	/* }else if(Tvaraff[z1] ==-10){ */
/* /\* sumnew+=coqvar[z1][iind]; \/ /	/* /\* sumnew+=coqvar[z1][iind]; \/ /
/* }else */	/* }else / / TODO TODO codtabm(j1,z1) or codtabm(j1,Tvaraff[z1]]z1)*/
if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]){ /* for combination j1 of covariates */	if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]){ /* for combination j1 of covariates */
/* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */	/* Tests if the value of the covariate z1 for this individual iind responded to combination j1 (V4=1 V3=0) */
bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */	bool=0; /* bool should be equal to 1 to be selected, one covariate value failed */
/* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n",	/* printf("bool=%d i=%d, z1=%d, Tvaraff[%d]=%d, covar[Tvarff][%d]=%2f, codtabm(%d,%d)=%d, nbcode[Tvaraff][codtabm(%d,%d)=%d, j1=%d\n", */
bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),	/* bool,i,z1, z1, Tvaraff[z1],i,covar[Tvaraff[z1]][i],j1,z1,codtabm(j1,z1),*/
j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/	/* j1,z1,nbcode[Tvaraff[z1]][codtabm(j1,z1)],j1);*/
/* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/	/* For j1=7 in V1+V2+V3+V4 = 0 1 1 0 and codtabm(7,3)=1 and nbcde[3][?]=1*/
} /* Onlyf fixed */	} /* Onlyf fixed */
} /* end z1 */	} /* end z1 */
Line 4508 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5078 Title=%s <br>Datafile=%s Firstpass=%d La
}/* end j==0 */	}/* end j==0 */
if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */	if (bool==1){ /* We selected an individual iind satisfying combination j1 (V4=1 V3=0) or all fixed covariates */
/* for(m=firstpass; m<=lastpass; m++){ */	/* for(m=firstpass; m<=lastpass; m++){ */
for(mi=1; mi<wav[iind];mi++){ /* For that wave */	for(mi=1; mi<wav[iind];mi++){ /* For each wave */
m=mw[mi][iind];	m=mw[mi][iind];
if(j!=0){	if(j!=0){
if(anyvaryingduminmodel==1){ /* Some are varying covariates */	if(anyvaryingduminmodel==1){ /* Some are varying covariates */
for (z1=1; z1<=cptcoveff; z1++) {	for (z1=1; z1<=cptcovn; z1++) {
if( Fixed[Tmodelind[z1]]==1){	if( Fixed[Tmodelind[z1]]==1){
iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;	iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality. If covariate's	if (cotvar[m][iv][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) /* iv=1 to ntv, right modality. If covariate's
value is -1, we don't select. It differs from the	value is -1, we don't select. It differs from the
constant and age model which counts them. */	constant and age model which counts them. */
bool=0; /* not selected */	bool=0; /* not selected */
}else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */	}else if( Fixed[Tmodelind[z1]]== 0) { /* fixed */
if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {	if (covar[Tvaraff[z1]][iind]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) {
bool=0;	bool=0;
}	}
}	}
Line 4528 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5098 Title=%s <br>Datafile=%s Firstpass=%d La
}/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */	}/* Some are varying covariates, we tried to speed up if all fixed covariates in the model, avoiding waves loop */
} /* end j==0 */	} /* end j==0 */
/* bool =0 we keep that guy which corresponds to the combination of dummy values */	/* bool =0 we keep that guy which corresponds to the combination of dummy values */
if(bool==1){	if(bool==1){ /Selected /
/* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]	/* dh[m][iind] or dh[mw[mi][iind]][iind] is the delay between two effective (mi) waves m=mw[mi][iind]
and mw[mi+1][iind]. dh depends on stepm. */	and mw[mi+1][iind]. dh depends on stepm. */
agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/	agebegin=agev[m][iind]; /* Age at beginning of wave before transition*/
Line 4546 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5116 Title=%s <br>Datafile=%s Firstpass=%d La
if(s[m][iind]==-1)	if(s[m][iind]==-1)
printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));	printf(" num=%ld m=%d, iind=%d s1=%d s2=%d agev at m=%d agebegin=%.2f ageend=%.2f, agemed=%d\n", num[iind], m, iind,s[m][iind],s[m+1][iind], (int)agev[m][iind],agebegin, ageend, (int)((agebegin+ageend)/2.));
freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */	freq[s[m][iind]][s[m+1][iind]][(int)agev[m][iind]] += weight[iind]; /* At age of beginning of transition, where status is known */
	for (z1=1; z1<= nqfveff; z1++) { /* Quantitative variables, calculating mean on known values only */
	if(!isnan(covar[ncovcol+z1][iind])){
	idq[z1]=idq[z1]+weight[iind];
	meanq[z1]+=covar[ncovcol+z1][iind]weight[iind]; / Computes mean of quantitative with selected filter */
	/* stdq[z1]+=covar[ncovcol+z1][iind]covar[ncovcol+z1][iind]weight[iind]weight[iind]; //error/
	stdq[z1]+=covar[ncovcol+z1][iind]covar[ncovcol+z1][iind]weight[iind]; /* weight[iind];/ /* Computes mean of quantitative with selected filter */
	}
	}
/* if((int)agev[m][iind] == 55) */	/* if((int)agev[m][iind] == 55) */
/* printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */	/* printf("j=%d, j1=%d Age %d, iind=%d, num=%09ld m=%d\n",j,j1,(int)agev[m][iind],iind, num[iind],m); */
/* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */	/* freq[s[m][iind]][s[m+1][iind]][(int)((agebegin+ageend)/2.)] += weight[iind]; */
Line 4561 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5139 Title=%s <br>Datafile=%s Firstpass=%d La
bool=1;	bool=1;
}/* end bool 2 */	}/* end bool 2 */
} /* end m */	} /* end m */
	/* for (z1=1; z1<= nqfveff; z1++) { /\* Quantitative variables, calculating mean \/ /
	/* idq[z1]=idq[z1]+weight[iind]; */
	/* meanq[z1]+=covar[ncovcol+z1][iind]weight[iind]; /\ Computes mean of quantitative with selected filter \/ /
	/* stdq[z1]+=covar[ncovcol+z1][iind]covar[ncovcol+z1][iind]weight[iind]weight[iind]; /\ weight[iind];\/ /\* Computes mean of quantitative with selected filter \/ /
	/* } */
} /* end bool */	} /* end bool */
} /* end iind = 1 to imx */	} /* end iind = 1 to imx */
/* prop[s][age] is feeded for any initial and valid live state as well as	/* prop[s][age] is fed for any initial and valid live state as well as
freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */	freq[s1][s2][age] at single age of beginning the transition, for a combination j1 */


/* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/	/* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
if(cptcoveff==0 && nj==1) /* no covariate and first pass */	if(cptcovn==0 && nj==1) /* no covariate and first pass */
pstamp(ficresp);	pstamp(ficresp);
if (cptcoveff>0 && j!=0){	if (cptcovn>0 && j!=0){
pstamp(ficresp);	pstamp(ficresp);
printf( "\n#********** Variable ");	printf( "\n#********** Variable ");
fprintf(ficresp, "\n#********** Variable ");	fprintf(ficresp, "\n#********** Variable ");
fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");	fprintf(ficresphtm, "\n<br/><br/><h3>********** Variable ");
fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");	fprintf(ficresphtmfr, "\n<br/><br/><h3>********** Variable ");
fprintf(ficlog, "\n#********** Variable ");	fprintf(ficlog, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++){	for (z1=1; z1<=cptcovs; z1++){
if(!FixedV[Tvaraff[z1]]){	if(!FixedV[Tvaraff[z1]]){
printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	printf( "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	fprintf(ficresp, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	fprintf(ficresphtm, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	fprintf(ficresphtmfr, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	fprintf(ficlog, "V%d(fixed)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
}else{	}else{
printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	printf( "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	fprintf(ficresp, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	fprintf(ficresphtm, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	fprintf(ficresphtmfr, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	fprintf(ficlog, "V%d(varying)=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
}	}
}	}
printf( "**********\n#");	printf( "**********\n#");
Line 4598 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5181 Title=%s <br>Datafile=%s Firstpass=%d La
fprintf(ficresphtmfr, "**********</h3>\n");	fprintf(ficresphtmfr, "**********</h3>\n");
fprintf(ficlog, "**********\n");	fprintf(ficlog, "**********\n");
}	}
	/*
	Printing means of quantitative variables if any
	*/
	for (z1=1; z1<= nqfveff; z1++) {
	fprintf(ficlog,"Mean of fixed quantitative variable V%d on %.3g (weighted) individuals sum=%f", ncovcol+z1, idq[z1], meanq[z1]);
	fprintf(ficlog,", mean=%.3g\n",meanq[z1]/idq[z1]);
	if(weightopt==1){
	printf(" Weighted mean and standard deviation of");
	fprintf(ficlog," Weighted mean and standard deviation of");
	fprintf(ficresphtmfr," Weighted mean and standard deviation of");
	}
	/* mu = \frac{w x}{\sum w}
	var = \frac{\sum w (x-mu)^2}{\sum w} = \frac{w x^2}{\sum w} - mu^2
	*/
	printf(" fixed quantitative variable V%d on %.3g (weighted) representatives of the population : %8.5g (%8.5g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1]));
	fprintf(ficlog," fixed quantitative variable V%d on %.3g (weighted) representatives of the population : %8.5g (%8.5g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1]));
	fprintf(ficresphtmfr," fixed quantitative variable V%d on %.3g (weighted) representatives of the population : %8.5g (%8.5g)<p>\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt(stdq[z1]/idq[z1]-meanq[z1]*meanq[z1]/idq[z1]/idq[z1]));
	}
	/* for (z1=1; z1<= nqtveff; z1++) { */
	/* for(m=1;m<=lastpass;m++){ */
	/* fprintf(ficresphtmfr,"V quantitative id %d, pass id=%d, mean=%f<p>\n", z1, m, meanqt[m][z1]); */
	/* } */
	/* } */

fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");	fprintf(ficresphtm,"<table style=\"text-align:center; border: 1px solid\">");
if((cptcoveff==0 && nj==1)\|\| nj==2 ) /* no covariate and first pass */	if((cptcovn==0 && nj==1)\|\| nj==2 ) /* no covariate and first pass */
fprintf(ficresp, " Age");	fprintf(ficresp, " Age");
if(nj==2) for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " V%d=%d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	if(nj==2) for (z1=1; z1<=cptcovn; z1++) fprintf(ficresp, " V%d=%d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
for(i=1; i<=nlstate;i++) {	for(i=1; i<=nlstate;i++) {
if((cptcoveff==0 && nj==1)\|\| nj==2 ) fprintf(ficresp," Prev(%d) N(%d) N ",i,i);	if((cptcovn==0 && nj==1)\|\| nj==2 ) fprintf(ficresp," Prev(%d) N(%d) N ",i,i);
fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);	fprintf(ficresphtm, "<th>Age</th><th>Prev(%d)</th><th>N(%d)</th><th>N</th>",i,i);
}	}
if((cptcoveff==0 && nj==1)\|\| nj==2 ) fprintf(ficresp, "\n");	if((cptcovn==0 && nj==1)\|\| nj==2 ) fprintf(ficresp, "\n");
fprintf(ficresphtm, "\n");	fprintf(ficresphtm, "\n");

/* Header of frequency table by age */	/* Header of frequency table by age */
Line 4674 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5281 Title=%s <br>Datafile=%s Firstpass=%d La
}	}

/* Writing ficresp */	/* Writing ficresp */
if(cptcoveff==0 && nj==1){ /* no covariate and first pass */	if(cptcovn==0 && nj==1){ /* no covariate and first pass */
if( iage <= iagemax){	if( iage <= iagemax){
fprintf(ficresp," %d",iage);	fprintf(ficresp," %d",iage);
}	}
}else if( nj==2){	}else if( nj==2){
if( iage <= iagemax){	if( iage <= iagemax){
fprintf(ficresp," %d",iage);	fprintf(ficresp," %d",iage);
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	for (z1=1; z1<=cptcovn; z1++) fprintf(ficresp, " %d %d",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
}	}
}	}
for(s1=1; s1 <=nlstate ; s1++){	for(s1=1; s1 <=nlstate ; s1++){
Line 4696 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5303 Title=%s <br>Datafile=%s Firstpass=%d La
}	}
if( iage <= iagemax){	if( iage <= iagemax){
if(pos>=1.e-5){	if(pos>=1.e-5){
if(cptcoveff==0 && nj==1){ /* no covariate and first pass */	if(cptcovn==0 && nj==1){ /* no covariate and first pass */
fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);	fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
}else if( nj==2){	}else if( nj==2){
fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);	fprintf(ficresp," %.5f %.0f %.0f",prop[s1][iage]/pospropta, prop[s1][iage],pospropta);
Line 4705 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5312 Title=%s <br>Datafile=%s Firstpass=%d La
/probs[iage][s1][j1]= pp[s1]/pos;/	/probs[iage][s1][j1]= pp[s1]/pos;/
/printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);/	/printf("\niage=%d s1=%d j1=%d %.5f %.0f %.0f %f",iage,s1,j1,pp[s1]/pos, pp[s1],pos,probs[iage][s1][j1]);/
} else{	} else{
if((cptcoveff==0 && nj==1)\|\| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta);	if((cptcovn==0 && nj==1)\|\| nj==2 ) fprintf(ficresp," NaNq %.0f %.0f",prop[s1][iage],pospropta);
fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[s1][iage],pospropta);	fprintf(ficresphtm,"<th>%d</th><td>NaNq</td><td>%.0f</td><td>%.0f</td>",iage, prop[s1][iage],pospropta);
}	}
}	}
Line 4731 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5338 Title=%s <br>Datafile=%s Firstpass=%d La
}	}
fprintf(ficresphtmfr,"</tr>\n ");	fprintf(ficresphtmfr,"</tr>\n ");
fprintf(ficresphtm,"</tr>\n");	fprintf(ficresphtm,"</tr>\n");
if((cptcoveff==0 && nj==1)\|\| nj==2 ) {	if((cptcovn==0 && nj==1)\|\| nj==2 ) {
if(iage <= iagemax)	if(iage <= iagemax)
fprintf(ficresp,"\n");	fprintf(ficresp,"\n");
}	}
Line 4832 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5439 Title=%s <br>Datafile=%s Firstpass=%d La
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
}	}
}	}
}	} /* end of state i */
printf("#Freqsummary\n");	printf("#Freqsummary\n");
fprintf(ficlog,"\n");	fprintf(ficlog,"\n");
for(s1=-1; s1 <=nlstate+ndeath; s1++){	for(s1=-1; s1 <=nlstate+ndeath; s1++){
Line 4874 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5481 Title=%s <br>Datafile=%s Firstpass=%d La
}	}
} /* end mle=-2 */	} /* end mle=-2 */
dateintmean=dateintsum/k2cpt;	dateintmean=dateintsum/k2cpt;
	date2dmy(dateintmean,&jintmean,&mintmean,&aintmean);

fclose(ficresp);	fclose(ficresp);
fclose(ficresphtm);	fclose(ficresphtm);
fclose(ficresphtmfr);	fclose(ficresphtmfr);
	free_vector(idq,1,nqfveff);
free_vector(meanq,1,nqfveff);	free_vector(meanq,1,nqfveff);
	free_vector(stdq,1,nqfveff);
free_matrix(meanqt,1,lastpass,1,nqtveff);	free_matrix(meanqt,1,lastpass,1,nqtveff);
free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);	free_vector(x, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);	free_vector(y, iagemin-AGEMARGE, iagemax+4+AGEMARGE);
Line 4985 void prevalence(double ***probs, double	Line 5595 void prevalence(double ***probs, double
/j=cptcoveff;/	/j=cptcoveff;/
if (cptcovn<1) {j=1;ncodemax[1]=1;}	if (cptcovn<1) {j=1;ncodemax[1]=1;}

first=1;	first=0;
for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */	for(j1=1; j1<= (int) pow(2,cptcoveff);j1++){ /* For each combination of covariate */
for (i=1; i<=nlstate; i++)	for (i=1; i<=nlstate; i++)
for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)	for(iage=iagemin-AGEMARGE; iage <= iagemax+4+AGEMARGE; iage++)
Line 5004 void prevalence(double ***probs, double	Line 5614 void prevalence(double ***probs, double
for (z1=1; z1<=cptcoveff; z1++){	for (z1=1; z1<=cptcoveff; z1++){
if( Fixed[Tmodelind[z1]]==1){	if( Fixed[Tmodelind[z1]]==1){
iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;	iv= Tvar[Tmodelind[z1]]-ncovcol-nqv;
if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) /* iv=1 to ntv, right modality */	if (cotvar[m][iv][i]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) /* iv=1 to ntv, right modality */
bool=0;	bool=0;
}else if( Fixed[Tmodelind[z1]]== 0) /* fixed */	}else if( Fixed[Tmodelind[z1]]== 0) /* fixed */
if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,z1)]) {	if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]) {
bool=0;	bool=0;
}	}
}	}
Line 5043 void prevalence(double ***probs, double	Line 5653 void prevalence(double ***probs, double
if(posprop>=1.e-5){	if(posprop>=1.e-5){
probs[i][jk][j1]= prop[jk][i]/posprop;	probs[i][jk][j1]= prop[jk][i]/posprop;
} else{	} else{
if(first==1){	if(!first){
first=0;	first=1;
printf("Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);	printf("Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);
fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);
}else{	}else{
fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,jk, j1,probs[i][jk][j1]);	fprintf(ficlog,"Warning Observed prevalence doesn't sum to 1 for state %d: probs[%d][%d][%d]=%lf because of lack of cases.\n",jk,i,jk, j1,probs[i][jk][j1]);
}	}
}	}
}	}
Line 5066 void prevalence(double ***probs, double	Line 5675 void prevalence(double ***probs, double

void concatwav(int wav[], int dh, int bh, int mw, int s, double agedc, double *agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)	void concatwav(int wav[], int dh, int bh, int mw, int s, double agedc, double *agev, int firstpass, int lastpass, int imx, int nlstate, int stepm)
{	{
/* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.	/* Concatenates waves: wav[i] is the number of effective (useful waves in the sense that a non interview is useless) of individual i.
Death is a valid wave (if date is known).	Death is a valid wave (if date is known).
mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i	mw[mi][i] is the mi (mi=1 to wav[i]) effective wave of individual i
dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]	dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
and mw[mi+1][i]. dh depends on stepm.	and mw[mi+1][i]. dh depends on stepm. s[m][i] exists for any wave from firstpass to lastpass
*/	*/

int i=0, mi=0, m=0, mli=0;	int i=0, mi=0, m=0, mli=0;
Line 5091 void concatwav(int wav[], int **dh, int	Line 5700 void concatwav(int wav[], int **dh, int
for(i=1; i<=imx; i++){ /* For simple cases and if state is death */	for(i=1; i<=imx; i++){ /* For simple cases and if state is death */
mi=0; /* First valid wave */	mi=0; /* First valid wave */
mli=0; /* Last valid wave */	mli=0; /* Last valid wave */
m=firstpass;	m=firstpass; /* Loop on waves */
while(s[m][i] <= nlstate){ /* a live state */	while(s[m][i] <= nlstate){ /* a live state or unknown state */
if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */	if(m >firstpass && s[m][i]==s[m-1][i] && mint[m][i]==mint[m-1][i] && anint[m][i]==anint[m-1][i]){/* Two succesive identical information on wave m */
mli=m-1;/* mw[++mi][i]=m-1; */	mli=m-1;/* mw[++mi][i]=m-1; */
}else if(s[m][i]>=1 \|\| s[m][i]==-4 \|\| s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */	}else if(s[m][i]>=1 \|\| s[m][i]==-4 \|\| s[m][i]==-5){ /* Since 0.98r4 if status=-2 vital status is really unknown, wave should be skipped */
mw[++mi][i]=m;	mw[++mi][i]=m; /* Valid wave: incrementing mi and updating mi; mw[mi] is the wave number of mi_th valid transition */
mli=m;	mli=m;
} /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */	} /* else might be a useless wave -1 and mi is not incremented and mw[mi] not updated */
if(m < lastpass){ /* m < lastpass, standard case */	if(m < lastpass){ /* m < lastpass, standard case */
m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */	m++; /* mi gives the "effective" current wave, m the current wave, go to next wave by incrementing m */
}	}
else{ /* m >= lastpass, eventual special issue with warning */	else{ /* m = lastpass, eventual special issue with warning */
#ifdef UNKNOWNSTATUSNOTCONTRIBUTING	#ifdef UNKNOWNSTATUSNOTCONTRIBUTING
break;	break;
#else	#else
if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){	if(s[m][i]==-1 && (int) andc[i] == 9999 && (int)anint[m][i] != 9999){ /* no death date and known date of interview, case -2 (vital status unknown is warned later */
if(firsthree == 0){	if(firsthree == 0){
printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p%d%d .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);	printf("Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p_{%d%d} .\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);
firsthree=1;	firsthree=1;
	}else if(firsthree >=1 && firsthree < 10){
	fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p_{%d%d} .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);
	firsthree++;
	}else if(firsthree == 10){
	printf("Information, too many Information flags: no more reported to log either\n");
	fprintf(ficlog,"Information, too many Information flags: no more reported to log either\n");
	firsthree++;
	}else{
	firsthree++;
}	}
fprintf(ficlog,"Information! Unknown status for individual %ld line=%d occurred at last wave %d at known date %d/%d. Please, check if your unknown date of death %d/%d means a live state %d at wave %d. This case(%d)/wave(%d) contributes to the likelihood as 1-p%d%d .\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], (int) moisdc[i], (int) andc[i], s[m][i], m, i, m, s[m][i], nlstate+ndeath);	mw[++mi][i]=m; /* Valid transition with unknown status */
mw[++mi][i]=m;
mli=m;	mli=m;
}	}
if(s[m][i]==-2){ /* Vital status is really unknown */	if(s[m][i]==-2){ /* Vital status is really unknown */
nbwarn++;	nbwarn++;
if((int)anint[m][i] == 9999){ /* Has the vital status really been verified? */	if((int)anint[m][i] == 9999){ /* Has the vital status really been verified?not a transition */
printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);	printf("Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);	fprintf(ficlog,"Warning! Vital status for individual %ld (line=%d) at last wave %d interviewed at date %d/%d is unknown %d. Please, check if the vital status and the date of death %d/%d are really unknown. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], (int) moisdc[i], (int) andc[i], i, m);
}	}
Line 5142 void concatwav(int wav[], int **dh, int	Line 5759 void concatwav(int wav[], int **dh, int
#ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE	#ifndef DISPATCHINGKNOWNDEATHAFTERLASTWAVE
else if ((int) andc[i] != 9999) { /* Date of death is known */	else if ((int) andc[i] != 9999) { /* Date of death is known */
if ((int)anint[m][i]!= 9999) { /* date of last interview is known */	if ((int)anint[m][i]!= 9999) { /* date of last interview is known */
if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* death occured before last wave and status should have been death instead of -1 */	if((andc[i]+moisdc[i]/12.) <=(anint[m][i]+mint[m][i]/12.)){ /* month of death occured before last wave month and status should have been death instead of -1 */
nbwarn++;	nbwarn++;
if(firstfiv==0){	if(firstfiv==0){
printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );	printf("Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d, interviewed on %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
firstfiv=1;	firstfiv=1;
}else{	}else{
fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d interviewed at %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );	fprintf(ficlog,"Warning! Death for individual %ld line=%d occurred at %d/%d before last wave %d, interviewed on %d/%d and should have been coded as death instead of '%d'. This case (%d)/wave (%d) is contributing to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
}	}
}else{ /* Death occured afer last wave potential bias */	s[m][i]=nlstate+1; /* Fixing the status as death. Be careful if multiple death states */
	}else{ /* Month of Death occured afer last wave month, potential bias */
nberr++;	nberr++;
if(firstwo==0){	if(firstwo==0){
printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );	printf("Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d with status %d. Potential bias if other individuals are still alive on this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictitious wave at the date of last vital status scan, with a dead status. See documentation\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
firstwo=1;	firstwo=1;
}	}
fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictive wave at the date of last vital status scan, with a dead status or alive but unknown state status (-1). See documentation\n\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );	fprintf(ficlog,"Error! Death for individual %ld line=%d occurred at %d/%d after last wave %d interviewed at %d/%d with status %d. Potential bias if other individuals are still alive on this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood. Please add a new fictitious wave at the date of last vital status scan, with a dead status. See documentation\n\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
}	}
}else{ /* if date of interview is unknown */	}else{ /* if date of interview is unknown */
/* death is known but not confirmed by death status at any wave */	/* death is known but not confirmed by death status at any wave */
if(firstfour==0){	if(firstfour==0){
printf("Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );	printf("Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d with status %d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\nOthers in log file only\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
firstfour=1;	firstfour=1;
}	}
fprintf(ficlog,"Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], i,m );	fprintf(ficlog,"Error! Death for individual %ld line=%d occurred %d/%d but not confirmed by any death status for any wave, including last wave %d at unknown date %d/%d with status %d. Potential bias if other individuals are still alive at this date but ignored. This case (%d)/wave (%d) is skipped, no contribution to likelihood.\n",num[i],i,(int) moisdc[i], (int) andc[i], lastpass,(int)mint[m][i],(int)anint[m][i], s[m][i], i,m );
}	}
} /* end if date of death is known */	} /* end if date of death is known */
#endif	#endif
wav[i]=mi; /* mi should be the last effective wave (or mli) */	wav[i]=mi; /* mi should be the last effective wave (or mli), */
/* wav[i]=mw[mi][i]; */	/* wav[i]=mw[mi][i]; */
if(mi==0){	if(mi==0){
nbwarn++;	nbwarn++;
if(first==0){	if(first==0){
Line 5183 void concatwav(int wav[], int **dh, int	Line 5801 void concatwav(int wav[], int **dh, int
} /* End individuals */	} /* End individuals */
/* wav and mw are no more changed */	/* wav and mw are no more changed */

	printf("Information, you have to check %d informations which haven't been logged!\n",firsthree);
	fprintf(ficlog,"Information, you have to check %d informations which haven't been logged!\n",firsthree);


for(i=1; i<=imx; i++){	for(i=1; i<=imx; i++){
for(mi=1; mi<wav[i];mi++){	for(mi=1; mi<wav[i];mi++){
if (stepm <=0)	if (stepm <=0)
Line 5294 void concatwav(int wav[], int **dh, int	Line 5915 void concatwav(int wav[], int **dh, int
/* cptcov=0; /	/* cptcov=0; /

for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */	for (k=1; k <= maxncov; k++) ncodemax[k]=0; /* Horrible constant again replaced by NCOVMAX */
	for (k=1; k <= maxncov; k++)
	for(j=1; j<=2; j++)
	nbcode[k][j]=0; /* Valgrind */

/* Loop on covariates without age and products and no quantitative variable */	/* Loop on covariates without age and products and no quantitative variable */
/* for (j=1; j<=(cptcovs); j++) { /\* From model V1 + V2age+ V3 + V3V4 keeps V1 + V3 = 2 only \/ /
for (k=1; k<=cptcovt; k++) { /* From model V1 + V2age + V3 + V3V4 keeps V1 + V3 = 2 only */	for (k=1; k<=cptcovt; k++) { /* From model V1 + V2age + V3 + V3V4 keeps V1 + V3 = 2 only */
for (j=-1; (j < maxncov); j++) Ndum[j]=0;	for (j=-1; (j < maxncov); j++) Ndum[j]=0;
if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */	if(Dummy[k]==0 && Typevar[k] !=1){ /* Dummy covariate and not age product */
switch(Fixed[k]) {	switch(Fixed[k]) {
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;
	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*/
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
Line 5314 void concatwav(int wav[], int **dh, int	Line 5939 void concatwav(int wav[], int **dh, int
modmaxcovj=ij;	modmaxcovj=ij;
else if (ij < modmincovj)	else if (ij < modmincovj)
modmincovj=ij;	modmincovj=ij;
if ((ij < -1) && (ij > NCOVMAX)){	if (ij <0 \|\| ij >1 ){
	printf("ERROR, IMaCh doesn't treat covariate with missing values V%d=-1, individual %d will be skipped.\n",Tvar[k],i);
	fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=-1, individual %d will be skipped.\n",Tvar[k],i);
	fflush(ficlog);
	exit(1);
	}
	if ((ij < -1) \|\| (ij > NCOVMAX)){
printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );	printf( "Error: minimal is less than -1 or maximal is bigger than %d. Exiting. \n", NCOVMAX );
exit(1);	exit(1);
}else	}else
Line 5360 void concatwav(int wav[], int **dh, int	Line 5991 void concatwav(int wav[], int **dh, int
/* nbcode[Tvar[j]][3]=2; */	/* nbcode[Tvar[j]][3]=2; */
/* To be continued (not working yet). */	/* To be continued (not working yet). */
ij=0; /* ij is similar to i but can jump over null modalities */	ij=0; /* ij is similar to i but can jump over null modalities */
for (i=modmincovj; i<=modmaxcovj; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
	/* for (i=modmincovj; i<=modmaxcovj; i++) { / / i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
	/* Skipping the case of missing values by reducing nbcode to 0 and 1 and not -1, 0, 1 */
	/* model=V1+V2+V3, if V2=-1, 0 or 1, then nbcode[2][1]=0 and nbcode[2][2]=1 instead of
	* nbcode[2][1]=-1, nbcode[2][2]=0 and nbcode[2][3]=1 */
	/, could be restored in the future /
	for (i=0; i<=1; i++) { /* i= 1 to 2 for dichotomous, or from 1 to 3 or from -1 or 0 to 1 currently*/
if (Ndum[i] == 0) { /* If nobody responded to this modality k */	if (Ndum[i] == 0) { /* If nobody responded to this modality k */
break;	break;
}	}
ij++;	ij++;
nbcode[Tvar[k]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1*/	nbcode[Tvar[k]][ij]=i; /* stores the original value of modality i in an array nbcode, ij modality from 1 to last non-nul modality. nbcode[1][1]=0 nbcode[1][2]=1 . Could be -1*/
cptcode = ij; /* New max modality for covar j */	cptcode = ij; /* New max modality for covar j */
} /* end of loop on modality i=-1 to 1 or more */	} /* end of loop on modality i=-1 to 1 or more */
break;	break;
Line 5381 void concatwav(int wav[], int **dh, int	Line 6018 void concatwav(int wav[], int **dh, int
break;	break;
} /* end switch */	} /* end switch */
} /* end dummy test */	} /* end dummy test */
	if(Dummy[k]==1 && Typevar[k] !=1){ /* Dummy covariate and not age product */
/* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 \//\ Could be 1 to 4 \//\ cptcode=modmaxcovj \/ /	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*/
/* /\recode from 0 \/ */	if(isnan(covar[Tvar[k]][i])){
/* k is a modality. If we have model=V1+V1sex /	printf("ERROR, IMaCh doesn't treat fixed quantitative covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);
/* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */	fprintf(ficlog,"ERROR, currently IMaCh doesn't treat covariate with missing values V%d=., individual %d will be skipped.\n",Tvar[k],i);
/* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode \/ /	fflush(ficlog);
/* } */	exit(1);
/* /\* cptcode = ij; \/ /\ New max modality for covar j \/ /	}
/* if (ij > ncodemax[j]) { */	}
/* printf( " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */	}
/* fprintf(ficlog, " Error ij=%d > ncodemax[%d]=%d\n", ij, j, ncodemax[j]); */	} /* end of loop on model-covariate k. nbcode[Tvark][1]=-1, nbcode[Tvark][1]=0 and nbcode[Tvark][2]=1 sets the value of covariate k*/
/* break; */
/* } */
/* } /\* end of loop on modality k \/ /
} /* end of loop on model-covariate j. nbcode[Tvarj][1]=0 and nbcode[Tvarj][2]=1 sets the value of covariate j*/

for (k=-1; k< maxncov; k++) Ndum[k]=0;	for (k=-1; k< maxncov; k++) Ndum[k]=0;
/* Look at fixed dummy (single or product) covariates to check empty modalities */	/* Look at fixed dummy (single or product) covariates to check empty modalities */
Line 5430 void concatwav(int wav[], int **dh, int	Line 6063 void concatwav(int wav[], int **dh, int
} /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */	} /* Tvaraff[1]@5 {3, 4, -20, 0, 0} Very strange */
/* ij--; */	/* ij--; */
/* cptcoveff=ij; /\Number of total covariates\/ */	/* cptcoveff=ij; /\Number of total covariates\/ */
cptcov=ij; /Number of total real effective covariates: effective	cptcov=ij; / cptcov= Number of total real effective covariates: effective (used as cptcoveff in other functions)
* because they can be excluded from the model and real	* because they can be excluded from the model and real
* if in the model but excluded because missing values, but how to get k from ij?*/	* if in the model but excluded because missing values, but how to get k from ij?*/
for(j=ij+1; j<= cptcovt; j++){	for(j=ij+1; j<= cptcovt; j++){
Line 5451 void concatwav(int wav[], int **dh, int	Line 6084 void concatwav(int wav[], int **dh, int

{	{
/* Health expectancies, no variances */	/* Health expectancies, no variances */
	/* cij is the combination in the list of combination of dummy covariates */
	/* strstart is a string of time at start of computing */
int i, j, nhstepm, hstepm, h, nstepm;	int i, j, nhstepm, hstepm, h, nstepm;
int nhstepma, nstepma; /* Decreasing with age */	int nhstepma, nstepma; /* Decreasing with age */
double age, agelim, hf;	double age, agelim, hf;
Line 5519 void concatwav(int wav[], int **dh, int	Line 6154 void concatwav(int wav[], int **dh, int
/* If stepm=6 months */	/* If stepm=6 months */
/* Computed by stepm unit matrices, product of hstepma matrices, stored	/* Computed by stepm unit matrices, product of hstepma matrices, stored
in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */	in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */
	/* printf("HELLO evsij Entering hpxij age=%d cij=%d hstepm=%d x[1]=%f nres=%d\n",(int) age, cij, hstepm, x[1], nres); */
hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);	hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij, nres);

hf=hstepmstepm/YEARM; / Duration of hstepm expressed in year unit. */	hf=hstepmstepm/YEARM; / Duration of hstepm expressed in year unit. */
Line 5708 void concatwav(int wav[], int **dh, int	Line 6343 void concatwav(int wav[], int **dh, int
varhe[ij][ji][(int)age] += doldm[ij][ji]hfhf;	varhe[ij][ji][(int)age] += doldm[ij][ji]hfhf;
}	}
}	}
	/* if((int)age ==50){ */
	/* printf(" age=%d cij=%d nres=%d varhe[%d][%d]=%f ",(int)age, cij, nres, 1,2,varhe[1][2]); */
	/* } */
/* Computing expectancies */	/* Computing expectancies */
hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);	hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij,nres);
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
Line 5769 void concatwav(int wav[], int **dh, int	Line 6406 void concatwav(int wav[], int **dh, int
/********** Variance ****************/	/********** Variance ****************/
void varevsij(char optionfilefiname[], double *vareij, double matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double oldm, double savm, double *prlim, double ftolpl, int ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[], int nres)	void varevsij(char optionfilefiname[], double *vareij, double matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double oldm, double savm, double *prlim, double ftolpl, int ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[], int nres)
{	{
/* Variance of health expectancies */	/** Variance of health expectancies
/* double prevalim(double prlim, int nlstate, double xp, double age, double oldm, double * savm,double ftolpl);*/	* double prevalim(double prlim, int nlstate, double xp, double age, double oldm, double * savm,double ftolpl);
/* double *newm;/	* double **newm;
/* int movingaverage(double *probs, double bage,double fage, double mobaverage, int mobilav)/	* int movingaverage(double *probs, double bage,double fage, double *mobaverage, int mobilav)
	*/

/* int movingaverage(); */	/* int movingaverage(); */
double dnewm,doldm;	double dnewm,doldm;
double dnewmp,doldmp;	double dnewmp,doldmp;
int i, j, nhstepm, hstepm, h, nstepm ;	int i, j, nhstepm, hstepm, h, nstepm ;
	int first=0;
int k;	int k;
double *xp;	double *xp;
double gp, gm; /* for var eij */	double gp, gm; /*< for var eij /
double *gradg, trgradg; /for var eij */	double *gradg, trgradg; /< for var eij /
double gradgp, trgradgp; /* for var p point j */	double gradgp, trgradgp; /*< for var p point j /
double gpp, gmp; /* for var p point j */	double gpp, gmp; /*< for var p point j /
double *varppt; / for var p point j nlstate to nlstate+ndeath */	double varppt; /< for var p point j nlstate to nlstate+ndeath */
double ***p3mat;	double ***p3mat;
double age,agelim, hf;	double age,agelim, hf;
/* double **mobaverage; /	/* double **mobaverage; /
Line 5826 void concatwav(int wav[], int **dh, int	Line 6465 void concatwav(int wav[], int **dh, int
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 */	for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	fprintf(ficresprobmorprev," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
}	}
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,j)]);	fprintf(ficresprobmorprev,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(ij,TnsdVar[Tvaraff[j]])]);
fprintf(ficresprobmorprev,"\n");	fprintf(ficresprobmorprev,"\n");

fprintf(ficresprobmorprev,"# Age cov=%-d",ij);	fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
Line 5845 void concatwav(int wav[], int **dh, int	Line 6484 void concatwav(int wav[], int **dh, int
/* fprintf(fichtm, "#Local time at start: %s", strstart);*/	/* fprintf(fichtm, "#Local time at start: %s", strstart);*/
fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");	fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
fprintf(fichtm,"\n<br>%s <br>\n",digitp);	fprintf(fichtm,"\n<br>%s <br>\n",digitp);
/* } */
varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);	varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
pstamp(ficresvij);	pstamp(ficresvij);
fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");	fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
Line 5900 void concatwav(int wav[], int **dh, int	Line 6539 void concatwav(int wav[], int **dh, int
for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/	for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
xp[i] = x[i] + (i==theta ?delti[theta]:0);	xp[i] = x[i] + (i==theta ?delti[theta]:0);
}	}
	/**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and
	* returns into prlim .
	*/
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);	prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);

	/* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */
if (popbased==1) {	if (popbased==1) {
if(mobilav ==0){	if(mobilav ==0){
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
Line 5912 void concatwav(int wav[], int **dh, int	Line 6554 void concatwav(int wav[], int **dh, int
prlim[i][i]=mobaverage[(int)age][i][ij];	prlim[i][i]=mobaverage[(int)age][i][ij];
}	}
}	}
	/**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}x\f$ at horizon h.
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres); /* Returns p3mat[i][j][h] for h=1 to nhstepm */	*/
	hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres); /* Returns p3mat[i][j][h] for h=0 to nhstepm */
	/**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}x\f$, which are the probability
	* at horizon h in state j including mortality.
	*/
for(j=1; j<= nlstate; j++){	for(j=1; j<= nlstate; j++){
for(h=0; h<=nhstepm; h++){	for(h=0; h<=nhstepm; h++){
for(i=1, gp[h][j]=0.;i<=nlstate;i++)	for(i=1, gp[h][j]=0.;i<=nlstate;i++)
gp[h][j] += prlim[i][i]*p3mat[i][j][h];	gp[h][j] += prlim[i][i]*p3mat[i][j][h];
}	}
}	}
/* Next for computing probability of death (h=1 means	/* Next for computing shifted+ probability of death (h=1 means
computed over hstepm matrices product = hstepm*stepm months)	computed over hstepm matrices product = hstepm*stepm months)
as a weighted average of prlim.	as a weighted average of prlim(i) * p(i,j) p.3=w1p13 + w2p23 .
*/	*/
for(j=nlstate+1;j<=nlstate+ndeath;j++){	for(j=nlstate+1;j<=nlstate+ndeath;j++){
for(i=1,gpp[j]=0.; i<= nlstate; i++)	for(i=1,gpp[j]=0.; i<= nlstate; i++)
gpp[j] += prlim[i][i]*p3mat[i][j][1];	gpp[j] += prlim[i][i]*p3mat[i][j][1];
}	}
/* end probability of death */
	/* Again with minus shift */

for(i=1; i<=npar; i++) /* Computes gradient x - delta */	for(i=1; i<=npar; i++) /* Computes gradient x - delta */
xp[i] = x[i] - (i==theta ?delti[theta]:0);	xp[i] = x[i] - (i==theta ?delti[theta]:0);

prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);	prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp, ij, nres);

if (popbased==1) {	if (popbased==1) {
Line 5961 void concatwav(int wav[], int **dh, int	Line 6608 void concatwav(int wav[], int **dh, int
for(i=1,gmp[j]=0.; i<= nlstate; i++)	for(i=1,gmp[j]=0.; i<= nlstate; i++)
gmp[j] += prlim[i][i]*p3mat[i][j][1];	gmp[j] += prlim[i][i]*p3mat[i][j][1];
}	}
/* end probability of death */	/* end shifting computations */

	/**< Computing gradient matrix at horizon h
	*/
for(j=1; j<= nlstate; j++) /* vareij */	for(j=1; j<= nlstate; j++) /* vareij */
for(h=0; h<=nhstepm; h++){	for(h=0; h<=nhstepm; h++){
gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];	gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
}	}
	/**< Gradient of overall mortality p.3 (or p.j)
for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */	*/
	for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu mortality from j */
gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];	gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
}	}

} /* End theta */	} /* End theta */

	/* We got the gradient matrix for each theta and state j */
trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */	trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */

for(h=0; h<=nhstepm; h++) /* veij */	for(h=0; h<=nhstepm; h++) /* veij */
Line 5984 void concatwav(int wav[], int **dh, int	Line 6635 void concatwav(int wav[], int **dh, int
for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */	for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
for(theta=1; theta <=npar; theta++)	for(theta=1; theta <=npar; theta++)
trgradgp[j][theta]=gradgp[theta][j];	trgradgp[j][theta]=gradgp[theta][j];
	/**< as well as its transposed matrix
	*/

hf=hstepmstepm/YEARM; / Duration of hstepm expressed in year unit. */	hf=hstepmstepm/YEARM; / Duration of hstepm expressed in year unit. */
for(i=1;i<=nlstate;i++)	for(i=1;i<=nlstate;i++)
for(j=1;j<=nlstate;j++)	for(j=1;j<=nlstate;j++)
vareij[i][j][(int)age] =0.;	vareij[i][j][(int)age] =0.;

	/* Computing trgradg by matcov by gradg at age and summing over h
	* and k (nhstepm) formula 15 of article
	* Lievre-Brouard-Heathcote
	*/

for(h=0;h<=nhstepm;h++){	for(h=0;h<=nhstepm;h++){
for(k=0;k<=nhstepm;k++){	for(k=0;k<=nhstepm;k++){
matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);	matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
Line 6001 void concatwav(int wav[], int **dh, int	Line 6658 void concatwav(int wav[], int **dh, int
}	}
}	}

/* pptj */	/* pptj is p.3 or p.j = trgradgp by cov by gradgp, variance of
	* p.j overall mortality formula 49 but computed directly because
	* we compute the grad (wix pijx) instead of grad (pijx),even if
	* wix is independent of theta.
	*/
matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);	matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);	matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
for(j=nlstate+1;j<=nlstate+ndeath;j++)	for(j=nlstate+1;j<=nlstate+ndeath;j++)
Line 6104 void concatwav(int wav[], int **dh, int	Line 6765 void concatwav(int wav[], int **dh, int
int theta;	int theta;

pstamp(ficresvpl);	pstamp(ficresvpl);
fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");	fprintf(ficresvpl,"# Standard deviation of period (forward stable) prevalences \n");
fprintf(ficresvpl,"# Age ");	fprintf(ficresvpl,"# Age ");
if(nresult >=1)	if(nresult >=1)
fprintf(ficresvpl," Result# ");	fprintf(ficresvpl," Result# ");
Line 6133 void concatwav(int wav[], int **dh, int	Line 6794 void concatwav(int wav[], int **dh, int
for(i=1; i<=npar; i++){ /* Computes gradient */	for(i=1; i<=npar; i++){ /* Computes gradient */
xp[i] = x[i] + (i==theta ?delti[theta]:0);	xp[i] = x[i] + (i==theta ?delti[theta]:0);
}	}
if((int)age==79 \|\|(int)age== 80 \|\|(int)age== 81 )	/* if((int)age==79 \|\|(int)age== 80 \|\|(int)age== 81 ) */
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);	/* prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
else	/* else */
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);	prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
for(i=1;i<=nlstate;i++){	for(i=1;i<=nlstate;i++){
gp[i] = prlim[i][i];	gp[i] = prlim[i][i];
mgp[theta][i] = prlim[i][i];	mgp[theta][i] = prlim[i][i];
}	}
for(i=1; i<=npar; i++) /* Computes gradient */	for(i=1; i<=npar; i++) /* Computes gradient */
xp[i] = x[i] - (i==theta ?delti[theta]:0);	xp[i] = x[i] - (i==theta ?delti[theta]:0);
if((int)age==79 \|\|(int)age== 80 \|\|(int)age== 81 )	/* if((int)age==79 \|\|(int)age== 80 \|\|(int)age== 81 ) */
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);	/* prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres); */
else	/* else */
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);	prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij,nres);
for(i=1;i<=nlstate;i++){	for(i=1;i<=nlstate;i++){
gm[i] = prlim[i][i];	gm[i] = prlim[i][i];
mgm[theta][i] = prlim[i][i];	mgm[theta][i] = prlim[i][i];
Line 6195 void concatwav(int wav[], int **dh, int	Line 6856 void concatwav(int wav[], int **dh, int
fprintf(ficresvpl,"%.0f ",age );	fprintf(ficresvpl,"%.0f ",age );
if(nresult >=1)	if(nresult >=1)
fprintf(ficresvpl,"%d ",nres );	fprintf(ficresvpl,"%d ",nres );
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++){
fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));	fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
	/* for(j=1;j<=nlstate;j++) */
	/* fprintf(ficresvpl," %d %.5f ",j,prlim[j][i]); */
	}
fprintf(ficresvpl,"\n");	fprintf(ficresvpl,"\n");
free_vector(gp,1,nlstate);	free_vector(gp,1,nlstate);
free_vector(gm,1,nlstate);	free_vector(gm,1,nlstate);
Line 6344 void varprob(char optionfilefiname[], do	Line 7008 void varprob(char optionfilefiname[], do
int k2, l2, j1, z1;	int k2, l2, j1, z1;
int k=0, l;	int k=0, l;
int first=1, first1, first2;	int first=1, first1, first2;
	int nres=0; /* New */
double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;	double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
double dnewm,doldm;	double dnewm,doldm;
double *xp;	double *xp;
Line 6413 void varprob(char optionfilefiname[], do	Line 7078 void varprob(char optionfilefiname[], do
fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");	fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
fprintf(fichtm,"\n");	fprintf(fichtm,"\n");

fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back. %s</li>\n",optionfilehtmcov,optionfilehtmcov);	fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of one-step probabilities (drawings)</a></h4> this page is important in order to visualize confidence intervals and especially correlation between disability and recovery, or more generally, way in and way back. File %s</li>\n",optionfilehtmcov,optionfilehtmcov);
fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);	fprintf(fichtmcov,"Current page is file <a href=\"%s\">%s</a><br>\n\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n",optionfilehtmcov, optionfilehtmcov);
fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \	fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated \
and drawn. It helps understanding how is the covariance between two incidences.\	and drawn. It helps understanding how is the covariance between two incidences.\
Line 6431 To be simple, these graphs help to under	Line 7096 To be simple, these graphs help to under
tj = (int) pow(2,cptcoveff);	tj = (int) pow(2,cptcoveff);
if (cptcovn<1) {tj=1;ncodemax[1]=1;}	if (cptcovn<1) {tj=1;ncodemax[1]=1;}
j1=0;	j1=0;
for(j1=1; j1<=tj;j1++){ /* For each valid combination of covariates or only once*/
	for(nres=1;nres <=nresult; nres++){ /* For each resultline */
	for(j1=1; j1<=tj;j1++){ /* For any combination of dummy covariates, fixed and varying */
	printf("Varprob TKresult[nres]=%d j1=%d, nres=%d, cptcovn=%d, cptcoveff=%d tj=%d \n", TKresult[nres], j1, nres, cptcovn, cptcoveff, tj);
	if(tj != 1 && TKresult[nres]!= j1)
	continue;

	/* for(j1=1; j1<=tj;j1++){ /\* For each valid combination of covariates or only once\/ /
	/* for(nres=1;nres <=1; nres++){ /\* For each resultline \/ /
	/* /\* for(nres=1;nres <=nresult; nres++){ /\\* For each resultline \\/ \/ */
if (cptcovn>0) {	if (cptcovn>0) {
fprintf(ficresprob, "\n#********** Variable ");	fprintf(ficresprob, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
fprintf(ficresprob, "**********\n#\n");	fprintf(ficresprob, "**********\n#\n");
fprintf(ficresprobcov, "\n#********** Variable ");	fprintf(ficresprobcov, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
fprintf(ficresprobcov, "**********\n#\n");	fprintf(ficresprobcov, "**********\n#\n");

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


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

fprintf(ficresprobcor, "\n#********** Variable ");	fprintf(ficresprobcor, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,z1)]);	for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtabm(j1,TnsdVar[Tvaraff[z1]])]);
fprintf(ficresprobcor, "**********\n#");	fprintf(ficresprobcor, "**********\n#");
if(invalidvarcomb[j1]){	if(invalidvarcomb[j1]){
fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);	fprintf(ficgp,"\n#Combination (%d) ignored because no cases \n",j1);
Line 6466 To be simple, these graphs help to under	Line 7141 To be simple, these graphs help to under
cov[2]=age;	cov[2]=age;
if(nagesqr==1)	if(nagesqr==1)
cov[3]= age*age;	cov[3]= age*age;
for (k=1; k<=cptcovn;k++) {	/* for (k=1; k<=cptcovn;k++) { */
cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)];	/* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,k)]; */
	for (k=1; k<=nsd;k++) { /* For single dummy covariates only */
	/* Here comes the value of the covariate 'j1' after renumbering k with single dummy covariates */
	cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(j1,TnsdVar[TvarsD[k]])];
/cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];//* j1 1 2 3 4	/cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(j1,Tvar[k])];//* j1 1 2 3 4
* 1 1 1 1 1	* 1 1 1 1 1
* 2 2 1 1 1	* 2 2 1 1 1
Line 6475 To be simple, these graphs help to under	Line 7153 To be simple, these graphs help to under
*/	*/
/* nbcode[1][1]=0 nbcode[1][2]=1;*/	/* nbcode[1][1]=0 nbcode[1][2]=1;*/
}	}
/* for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; /	/* V2+V1+V4+V3age Tvar[4]=3 ; V1+V2age Tvar[2]=2; V1+V1age Tvar[2]=1, Tage[1]=2 /
for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];	/* ) p nbcode[Tvar[Tage[k]]][(1 & (ij-1) >> (k-1))+1] */
for (k=1; k<=cptcovprod;k++)	/for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; */
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];	for (k=1; k<=cptcovage;k++){ /* For product with age */
	if(Dummy[Tage[k]]==2){ /* dummy with age */
	cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(j1,TnsdVar[Tvar[Tage[k]]])]*cov[2];
	/* cov[++k1]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]cov[2]; /
	} else if(Dummy[Tage[k]]==3){ /* quantitative with age */
	printf("Internal IMaCh error, don't know which value for quantitative covariate with age, Tage[k]%d, k=%d, Tvar[Tage[k]]=V%d, age=%d\n",Tage[k],k ,Tvar[Tage[k]], (int)cov[2]);
	/* cov[2+nagesqr+Tage[k]]=meanq[k]/idq[k]cov[2];/\ Using the mean of quantitative variable Tvar[Tage[k]] /\* Tqresult[nres][k]; \/ /
	/* exit(1); */
	/* cov[++k1]=Tqresult[nres][k]; */
	}
	/* cov[2+Tage[k]+nagesqr]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]cov[2]; /
	}
	for (k=1; k<=cptcovprod;k++){/* For product without age */
	if(Dummy[Tvard[k][1]]==0){
	if(Dummy[Tvard[k][2]]==0){
	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(j1,TnsdVar[Tvard[k][1]])] * nbcode[Tvard[k][2]][codtabm(j1,TnsdVar[Tvard[k][2]])];
	/* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * nbcode[Tvard[k][2]][codtabm(ij,k)]; */
	}else{ /* Should we use the mean of the quantitative variables? */
	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(j1,TnsdVar[Tvard[k][1]])] * Tqresult[nres][resultmodel[nres][k]];
	/* cov[++k1]=nbcode[Tvard[k][1]][codtabm(ij,k)] * Tqresult[nres][k]; */
	}
	}else{
	if(Dummy[Tvard[k][2]]==0){
	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][2]][codtabm(j1,TnsdVar[Tvard[k][2]])] * Tqinvresult[nres][TnsdVar[Tvard[k][1]]];
	/* cov[++k1]=nbcode[Tvard[k][2]][codtabm(ij,k)] * Tqinvresult[nres][Tvard[k][1]]; */
	}else{
	cov[2+nagesqr+Tprod[k]]=Tqinvresult[nres][TnsdVar[Tvard[k][1]]]* Tqinvresult[nres][TnsdVar[Tvard[k][2]]];
	/* cov[++k1]=Tqinvresult[nres][Tvard[k][1]]* Tqinvresult[nres][Tvard[k][2]]; */
	}
	}
	/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]nbcode[Tvard[k][2]][codtabm(ij,k)]; /
	}
	/* For each age and combination of dummy covariates we slightly move the parameters of delti in order to get the gradient*/
for(theta=1; theta <=npar; theta++){	for(theta=1; theta <=npar; theta++){
for(i=1; i<=npar; i++)	for(i=1; i<=npar; i++)
xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);	xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
Line 6610 To be simple, these graphs help to under	Line 7318 To be simple, these graphs help to under
}	}

/* Eigen vectors */	/* Eigen vectors */
v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));	if(1+(v1-lc1)*(v1-lc1)/cv12/cv12 <1.e-5){
	printf(" Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
	fprintf(ficlog," Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
	v11=(1./sqrt(fabs(1+(v1-lc1)*(v1-lc1)/cv12/cv12)));
	}else
	v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
/v21=sqrt(1.-v11v11); // error */	/v21=sqrt(1.-v11v11); // error */
v21=(lc1-v1)/cv12*v11;	v21=(lc1-v1)/cv12*v11;
v12=-v21;	v12=-v21;
Line 6641 To be simple, these graphs help to under	Line 7354 To be simple, these graphs help to under
fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);	fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);	fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)), %11.3e +%.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)) not", \	fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)), %11.3e +%.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)) not", \
mu1,std,v11,sqrt(lc1),v12,sqrt(fabs(lc2)), \	mu1,std,v11,sqrt(fabs(lc1)),v12,sqrt(fabs(lc2)), \
mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(lc2))); /* For gnuplot only */	mu2,std,v21,sqrt(fabs(lc1)),v22,sqrt(fabs(lc2))); /* For gnuplot only */
}else{	}else{
first=0;	first=0;
fprintf(fichtmcov," %d (%.3f),",(int) age, c12);	fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
Line 6661 To be simple, these graphs help to under	Line 7374 To be simple, these graphs help to under
} /l1 /	} /l1 /
}/* k1 */	}/* k1 */
} /* loop on combination of covariates j1 */	} /* loop on combination of covariates j1 */
	} /* loop on nres */
free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);	free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);	free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
free_matrix(doldm,1,(nlstate)(nlstate+ndeath),1,(nlstate)(nlstate+ndeath));	free_matrix(doldm,1,(nlstate)(nlstate+ndeath),1,(nlstate)(nlstate+ndeath));
Line 6678 To be simple, these graphs help to under	Line 7392 To be simple, these graphs help to under
void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \	void printinghtml(char fileresu[], char title[], char datafile[], int firstpass, \
int lastpass, int stepm, int weightopt, char model[],\	int lastpass, int stepm, int weightopt, char model[],\
int imx,int jmin, int jmax, double jmeanint,char rfileres[],\	int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
int popforecast, int mobilav, int prevfcast, int mobilavproj, int backcast, int estepm , \	int popforecast, int mobilav, int prevfcast, int mobilavproj, int prevbcast, int estepm , \
double jprev1, double mprev1,double anprev1, double dateprev1, double dateproj1, double dateback1, \	double jprev1, double mprev1,double anprev1, double dateprev1, double dateprojd, double dateback1, \
double jprev2, double mprev2,double anprev2, double dateprev2, double dateproj2, double dateback2){	double jprev2, double mprev2,double anprev2, double dateprev2, double dateprojf, double dateback2){
int jj1, k1, i1, cpt, k4, nres;	int jj1, k1, i1, cpt, k4, nres;
	/* In fact some results are already printed in fichtm which is open */
fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \	fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
<li><a href='#secondorder'>Result files (second order (variance)</a>\n \	<li><a href='#secondorder'>Result files (second order (variance)</a>\n \
</ul>");	</ul>");
fprintf(fichtm,"<ul><li> model=1+age+%s\n \	/* fprintf(fichtm,"<ul><li> model=1+age+%s\n \ */
</ul>", model);	/* </ul>", model); */
fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");	fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n");
fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",	fprintf(fichtm,"<li>- Observed frequency between two states (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file)<br/>\n",
jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));	jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTMFR_",".htm"),subdirfext3(optionfilefiname,"PHTMFR_",".htm"));
fprintf(fichtm,"<li> - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file) ",	fprintf(fichtm,"<li> - Observed prevalence (cross-sectional prevalence) in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> (html file) ",
jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));	jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirfext3(optionfilefiname,"PHTM_",".htm"),subdirfext3(optionfilefiname,"PHTM_",".htm"));
fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));	fprintf(fichtm,", <a href=\"%s\">%s</a> (text file) <br>\n",subdirf2(fileresu,"P_"),subdirf2(fileresu,"P_"));
fprintf(fichtm,"\	fprintf(fichtm,"\
Line 6701 void printinghtml(char fileresu[], char	Line 7415 void printinghtml(char fileresu[], char
- Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",	- Estimated back transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));	stepm,subdirf2(fileresu,"PIJB_"),subdirf2(fileresu,"PIJB_"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",	- Period (forward) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));	subdirf2(fileresu,"PL_"),subdirf2(fileresu,"PL_"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Period (stable) back prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",	- Backward prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));	subdirf2(fileresu,"PLB_"),subdirf2(fileresu,"PLB_"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- (a) Life expectancies by health status at initial age, e<sub>i.</sub> (b) health expectancies by health status at initial age, e<sub>ij</sub> . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \	- (a) Life expectancies by health status at initial age, e<sub>i.</sub> (b) health expectancies by health status at initial age, e<sub>ij</sub> . If one or more covariates are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
Line 6720 void printinghtml(char fileresu[], char	Line 7434 void printinghtml(char fileresu[], char
m=pow(2,cptcoveff);	m=pow(2,cptcoveff);
if (cptcovn < 1) {m=1;ncodemax[1]=1;}	if (cptcovn < 1) {m=1;ncodemax[1]=1;}

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

jj1=0;	jj1=0;

Line 6755 void printinghtml(char fileresu[], char	Line 7469 void printinghtml(char fileresu[], char
fprintf(fichtm,"</a></li>");	fprintf(fichtm,"</a></li>");
} /* cptcovn >0 */	} /* cptcovn >0 */
}	}
fprintf(fichtm," \n</ul>");	fprintf(fichtm," \n</ul>");

jj1=0;	jj1=0;

Line 6789 void printinghtml(char fileresu[], char	Line 7503 void printinghtml(char fileresu[], char
}	}

/* if(nqfveff+nqtveff 0) / / Test to be done */	/* if(nqfveff+nqtveff 0) / / Test to be done */
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");	fprintf(fichtm," (model=%s) ************\n<hr size=\"2\" color=\"#EC5E5E\">",model);
if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);	fprintf(fichtm,"\n<h3>Combination (%d) ignored because no cases </h3>\n",k1);
printf("\nCombination (%d) ignored because no cases \n",k1);	printf("\nCombination (%d) ignored because no cases \n",k1);
Line 6810 divided by h: <sub>h</sub>P<sub>ij</sub>	Line 7524 divided by h: <sub>h</sub>P<sub>ij</sub>
<img src=\"%s_%d-3-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);	<img src=\"%s_%d-3-%d.svg\">",stepm,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres,subdirf2(optionfilefiname,"PE_"),k1,nres);
/* Survival functions (period) in state j */	/* Survival functions (period) in state j */
for(cpt=1; cpt<=nlstate;cpt++){	for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"<br>\n- Survival functions in state %d. Or probability to survive in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \	fprintf(fichtm,"<br>\n- Survival functions in state %d. And probability to be observed in state %d being in state (1 to %d) at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br>", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
<img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);	fprintf(fichtm," (data from text file <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"PIJ_"),subdirf2(optionfilefiname,"PIJ_"));
	fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",subdirf2(optionfilefiname,"LIJ_"),cpt,k1,nres);
}	}
/* State specific survival functions (period) */	/* State specific survival functions (period) */
for(cpt=1; cpt<=nlstate;cpt++){	for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"<br>\n- Survival functions from state %d in each live state and total.\	fprintf(fichtm,"<br>\n- Survival functions in state %d and in any other live state (total).\
Or probability to survive in various states (1 to %d) being in state %d at different ages. \	And probability to be observed in various states (up to %d) being in state %d at different ages. \
<a href=\"%s_%d-%d-%d.svg\">%s_%d%d-%d.svg</a><br> <img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);	<a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> ", cpt, nlstate, cpt, subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres,subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
	fprintf(fichtm," (data from text file <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"PIJ_"),subdirf2(optionfilefiname,"PIJ_"));
	fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",subdirf2(optionfilefiname,"LIJT_"),cpt,k1,nres);
}	}
/* Period (stable) prevalence in each health state */	/* Period (forward stable) prevalence in each health state */
for(cpt=1; cpt<=nlstate;cpt++){	for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability for a person being in state (1 to %d) at different ages, to be in state %d some years after. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \	fprintf(fichtm,"<br>\n- Convergence to period (stable) prevalence in state %d. Or probability for a person being in state (1 to %d) at different ages, to be in state %d some years after. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br>", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
<img src=\"%s_%d-%d-%d.svg\">", cpt, nlstate, cpt, subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);	fprintf(fichtm," (data from text file <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"P_"),subdirf2(optionfilefiname,"P_"));
	fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">" ,subdirf2(optionfilefiname,"P_"),cpt,k1,nres);
}	}
if(backcast==1){	if(prevbcast==1){
/* Period (stable) back 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> \
<img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);	<img src=\"%s_%d-%d-%d.svg\">", cpt, cpt, nlstate, subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
}	}
}	}
if(prevfcast==1){	if(prevfcast==1){
/* Projection of prevalence up to period (stable) prevalence in each health state */	/* Projection of prevalence up to period (forward stable) prevalence in each health state */
for(cpt=1; cpt<=nlstate;cpt++){	for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), from year %.1f up to year %.1f tending to period (stable) prevalence in state %d. Or probability to be in state %d being in an observed weighted state (from 1 to %d). <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \	fprintf(fichtm,"<br>\n- Projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), from year %.1f up to year %.1f tending to period (stable) forward prevalence in state %d. Or probability to be in state %d being in an observed weighted state (from 1 to %d). <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a>", dateprev1, dateprev2, mobilavproj, dateprojd, dateprojf, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
<img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, dateproj1, dateproj2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);	fprintf(fichtm," (data from text file <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"F_"),subdirf2(optionfilefiname,"F_"));
	fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",
	subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
}	}
}	}
if(backcast==1){	if(prevbcast==1){
/* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */	/* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */
for(cpt=1; cpt<=nlstate;cpt++){	for(cpt=1; cpt<=nlstate;cpt++){
fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \	fprintf(fichtm,"<br>\n- Back projection of cross-sectional prevalence (estimated with cases observed from %.1f to %.1f and mobil_average=%d), \
from year %.1f up to year %.1f (probably close to stable [mixed] back prevalence in state %d (randomness in cross-sectional prevalence is not taken into \	from year %.1f up to year %.1f (probably close to stable [mixed] back prevalence in state %d (randomness in cross-sectional prevalence is not taken into \
account but can visually be appreciated). Or probability to have been in an state %d, knowing that the person was in either state (1 or %d) \	account but can visually be appreciated). Or probability to have been in an state %d, knowing that the person was in either state (1 or %d) \
with weights corresponding to observed prevalence at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \	with weights corresponding to observed prevalence at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a>", dateprev1, dateprev2, mobilavproj, dateback1, dateback2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
<img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, dateback1, dateback2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);	fprintf(fichtm," (data from text file <a href=\"%s.txt\">%s.txt</a>)\n<br>",subdirf2(optionfilefiname,"FB_"),subdirf2(optionfilefiname,"FB_"));
	fprintf(fichtm," <img src=\"%s_%d-%d-%d.svg\">", subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
}	}
}	}

for(cpt=1; cpt<=nlstate;cpt++) {	for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a> <br> \	fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies in each alive state (1 to %d) (or area under each survival functions): <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a>",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);
<img src=\"%s_%d-%d-%d.svg\">",cpt,nlstate,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres,subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres);	fprintf(fichtm," (data from text file <a href=\"%s.txt\"> %s.txt</a>)\n<br>",subdirf2(optionfilefiname,"E_"),subdirf2(optionfilefiname,"E_"));
	fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">", subdirf2(optionfilefiname,"EXP_"),cpt,k1,nres );
}	}
/* } /\* end i1 \/ /	/* } /\* end i1 \/ /
}/* End k1 */	}/* End k1 */
Line 6887 See page 'Matrix of variance-covariance	Line 7609 See page 'Matrix of variance-covariance
<a href=\"%s\">%s</a> <br>\n</li>",	<a href=\"%s\">%s</a> <br>\n</li>",
estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));	estepm,subdirf2(fileresu,"STDE_"),subdirf2(fileresu,"STDE_"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",	- Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), e<sup>ij</sup> are weighted by the forward (period) prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));	estepm, subdirf2(fileresu,"V_"),subdirf2(fileresu,"V_"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",	- Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors (if popbased=1, an additional computation is done using the cross-sectional prevalences, i.e population based) (estepm=%d months): <a href=\"%s\">%s</a> <br>\n",
estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));	estepm, subdirf2(fileresu,"T_"),subdirf2(fileresu,"T_"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\	- Standard deviation of forward (period) prevalences: <a href=\"%s\">%s</a> <br>\n",\
subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));	subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));

/* if(popforecast==1) fprintf(fichtm,"\n */	/* if(popforecast==1) fprintf(fichtm,"\n */
Line 6903 See page 'Matrix of variance-covariance	Line 7625 See page 'Matrix of variance-covariance
/* 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=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
fflush(fichtm);	fflush(fichtm);
fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");

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

	fprintf(fichtm," <ul><li><b>Graphs (second order)</b></li><p>");

	jj1=0;

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

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

jj1=0;	jj1=0;

for(nres=1; nres <= nresult; nres++){ /* For each resultline */	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
Line 6917 See page 'Matrix of variance-covariance	Line 7675 See page 'Matrix of variance-covariance
/* 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");
	for (cpt=1; cpt<=cptcoveff;cpt++){
	fprintf(fichtm,"_V%d=%d_",Tvresult[nres][cpt],(int)Tresult[nres][cpt]);
	}
	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
	fprintf(fichtm,"_V%d=%f_",Tvqresult[nres][k4],Tqresult[nres][k4]);
	}
	fprintf(fichtm,"\"</a>");

fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");	fprintf(fichtm,"<hr size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
for (cpt=1; cpt<=cptcoveff;cpt++) /*< cptcoveff number of variables /	for (cpt=1; cpt<=cptcoveff;cpt++){ /*< cptcoveff number of variables /
fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);	fprintf(fichtm," V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);
	printf(" V%d=%d ",Tvresult[nres][cpt],Tresult[nres][cpt]);fflush(stdout);
/* 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 */	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," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}

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

if(invalidvarcomb[k1]){	if(invalidvarcomb[k1]){
fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);	fprintf(fichtm,"\n<h4>Combination (%d) ignored because no cases </h4>\n",k1);
Line 6934 See page 'Matrix of variance-covariance	Line 7703 See page 'Matrix of variance-covariance
}	}
for(cpt=1; cpt<=nlstate;cpt++) {	for(cpt=1; cpt<=nlstate;cpt++) {
fprintf(fichtm,"\n<br>- Observed (cross-sectional 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>\n <br>\	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);
<img src=\"%s_%d-%d-%d.svg\">",mobilav,cpt,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres,subdirf2(optionfilefiname,"V_"),cpt,k1,nres);	fprintf(fichtm," (data from text file <a href=\"%s\">%s</a>)\n <br>",subdirf2(fileresu,"VPL_"),subdirf2(fileresu,"VPL_"));
	fprintf(fichtm,"<img src=\"%s_%d-%d-%d.svg\">",subdirf2(optionfilefiname,"V_"), cpt,k1,nres);
}	}
fprintf(fichtm,"\n<br>- Total life expectancy by age and \	fprintf(fichtm,"\n<br>- Total life expectancy by age and \
health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \	health expectancies in each live states (1 to %d). If popbased=1 the smooth (due to the model) \
true period expectancies (those weighted with period prevalences are also\	true period expectancies (those weighted with period prevalences are also\
drawn in addition to the population based expectancies computed using\	drawn in addition to the population based expectancies computed using\
observed and cahotic prevalences: <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>\n<br>\	observed and cahotic prevalences: <a href=\"%s_%d-%d.svg\">%s_%d-%d.svg</a>",nlstate, subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);
<img src=\"%s_%d-%d.svg\">",subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres,subdirf2(optionfilefiname,"E_"),k1,nres);	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);
/* } /\* end i1 \/ /	/* } /\* end i1 \/ /
}/* End k1 */	}/* End k1 */
}/* End nres */	}/* End nres */
Line 6951 true period expectancies (those weighted	Line 7722 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 backcast, 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[132],optfileres[132];
char gplotcondition[132], gplotlabel[132];	char gplotcondition[132], gplotlabel[132];
Line 7029 void printinggnuplot(char fileresu[], ch	Line 7800 void printinggnuplot(char fileresu[], ch
continue;	continue;
/* We are interested in selected combination by the resultline */	/* We are interested in selected combination by the resultline */
/* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */	/* printf("\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt); */
fprintf(ficgp,"\n# 1st: Period (stable) prevalence with CI: 'VPL_' files and live state =%d ", cpt);	fprintf(ficgp,"\n# 1st: 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<=cptcoveff; k++){ /* For each covariate k get corresponding value lv for combination k1 */
lv= decodtabm(k1,k,cptcoveff); /* Should be the value of the covariate corresponding to k1 combination */	/* lv= decodtabm(k1,k,cptcoveff); /\* Should be the value of the covariate corresponding to k1 combination \/ /
	lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
Line 7059 void printinggnuplot(char fileresu[], ch	Line 7831 void printinggnuplot(char fileresu[], ch
fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);	fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
/* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */	/* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
fprintf(ficgp,"set title \"Alive state %d %s\" font \"Helvetica,12\"\n",cpt,gplotlabel);	fprintf(ficgp,"set title \"Alive state %d %s model=%s\" font \"Helvetica,12\"\n",cpt,gplotlabel,model);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
/* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */	/* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */
/* k1-1 error should be nres-1*/	/* k1-1 error should be nres-1*/
Line 7067 void printinggnuplot(char fileresu[], ch	Line 7839 void printinggnuplot(char fileresu[], ch
if (i==cpt) fprintf(ficgp," %%lf (%%lf)");	if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%lf (%%lf)");	else fprintf(ficgp," %%lf (%%lf)");
}	}
fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);	fprintf(ficgp,"\" t\"Forward prevalence\" w l lt 0,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," %%lf (%%lf)");	if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
else fprintf(ficgp," %%lf (%%lf)");	else fprintf(ficgp," %%lf (%%lf)");
Line 7085 void printinggnuplot(char fileresu[], ch	Line 7857 void printinggnuplot(char fileresu[], ch
}else{	}else{
kl=0;	kl=0;
for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */	for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */	/* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to k1 combination and kth covariate \/ /
	lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
Line 7105 void printinggnuplot(char fileresu[], ch	Line 7878 void printinggnuplot(char fileresu[], ch
} /* end covariate */	} /* end covariate */
} /* end if no covariate */	} /* end if no covariate */

if(backcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */	if(prevbcast==1){ /* We need to get the corresponding values of the covariates involved in this combination k1 */
/* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */	/* fprintf(ficgp,",\"%s\" every :::%d::%d u 1:($%d) t\"Backward stable prevalence\" w l lt 3",subdirf2(fileresu,"PLB_"),k1-1,k1-1,1+cpt); */
fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */	fprintf(ficgp,",\"%s\" u 1:((",subdirf2(fileresu,"PLB_")); /* Age is in 1, nres in 2 to be fixed */
if(cptcoveff ==0){	if(cptcoveff ==0){
Line 7113 void printinggnuplot(char fileresu[], ch	Line 7886 void printinggnuplot(char fileresu[], ch
}else{	}else{
kl=0;	kl=0;
for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */	for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */	/* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to k1 combination and kth covariate \/ /
	lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];	/* vlv= nbcode[Tvaraff[k]][lv]; */
	vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];
kl++;	kl++;
/* kl=6+(cpt-1)(nlstate+1)+1+(i-1); /\ 6+(1-1)(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 \/ */	/* kl=6+(cpt-1)(nlstate+1)+1+(i-1); /\ 6+(1-1)(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 \/ */
/6+(cpt-1)(nlstate+1)+1+(i-1)+(nlstate+1)nlstate; 6+(1-1)(2+1)+1+(1-1) +(2+1)2=13 /	/6+(cpt-1)(nlstate+1)+1+(i-1)+(nlstate+1)nlstate; 6+(1-1)(2+1)+1+(1-1) +(2+1)2=13 /
Line 7127 void printinggnuplot(char fileresu[], ch	Line 7902 void printinggnuplot(char fileresu[], ch
fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \	fprintf(ficgp,"$%d==%d && $%d==%d)? $%d : 1/0) t 'Backward prevalence in state %d' w l lt 3",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv], \
2+cptcoveff2+(cpt-1), cpt ); / 4 or 6 ?*/	2+cptcoveff2+(cpt-1), cpt ); / 4 or 6 ?*/
}else{	}else{
fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][lv]);	fprintf(ficgp,"$%d==%d && $%d==%d && ",kl+1, Tvaraff[k],kl+1+1,nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])]);
kl++;	kl++;
}	}
} /* end covariate */	} /* end covariate */
} /* end if no covariate */	} /* end if no covariate */
if(backcast == 1){	if(prevbcast == 1){
fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);	fprintf(ficgp,", \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
/* k1-1 error should be nres-1*/	/* k1-1 error should be nres-1*/
for (i=1; i<= nlstate ; i ++) {	for (i=1; i<= nlstate ; i ++) {
Line 7151 void printinggnuplot(char fileresu[], ch	Line 7926 void printinggnuplot(char fileresu[], ch
}	}
fprintf(ficgp,"\" t\"\" w l lt 4");	fprintf(ficgp,"\" t\"\" w l lt 4");
} /* end if backprojcast */	} /* end if backprojcast */
} /* end if backcast */	} /* end if prevbcast */
/* 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 */
Line 7167 void printinggnuplot(char fileresu[], ch	Line 7942 void printinggnuplot(char fileresu[], ch
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<=cptcoveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	/* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate number corresponding to k1 combination \/ /
	lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];	/* vlv= nbcode[Tvaraff[k]][lv]; */
	vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
Line 7230 void printinggnuplot(char fileresu[], ch	Line 8007 void printinggnuplot(char fileresu[], ch
if(m != 1 && TKresult[nres]!= k1)	if(m != 1 && TKresult[nres]!= k1)
continue;	continue;

for (cpt=1; cpt<= nlstate ; cpt ++) {	for (cpt=1; cpt<= nlstate ; cpt ++) { /* Fragile no verification of covariate values */
fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files: combination=%d state=%d",k1, cpt);	fprintf(ficgp,"\n\n# 3d: Life expectancy with EXP_ files: combination=%d state=%d",k1, cpt);
strcpy(gplotlabel,"(");	strcpy(gplotlabel,"(");
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	/* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate number corresponding to k1 combination \/ /
	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(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];	/* vlv= nbcode[Tvaraff[k]][lv]; */
	vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][resultmodel[nres][k4]]);
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[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");
Line 7288 plot [%.f:%.f] \"%s\" every :::%d::%d u	Line 8067 plot [%.f:%.f] \"%s\" every :::%d::%d u
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 j : 'LIJ_' files, cov=%d state=%d",k1, cpt);
for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */	for (k=1; k<=cptcoveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
	/* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate number corresponding to k1 combination \/ /
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];	/* vlv= nbcode[Tvaraff[k]][lv]; */
	vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[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 7339 set ter svg size 640, 480\nunset log y\n	Line 8120 set ter svg size 640, 480\nunset log y\n
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<=cptcoveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
	/* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate number corresponding to k1 combination \/ /
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];	/* vlv= nbcode[Tvaraff[k]][lv]; */
	vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[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 7396 set ter svg size 640, 480\nunset log y\n	Line 8179 set ter svg size 640, 480\nunset log y\n
continue;	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 (period): '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<=cptcoveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	/* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate number corresponding to k1 combination \/ /
	lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];	/* vlv= nbcode[Tvaraff[k]][lv]; */
	vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[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 7439 set ter svg size 640, 480\nunset log y\n	Line 8224 set ter svg size 640, 480\nunset log y\n


/* 7eme */	/* 7eme */
if(backcast == 1){	if(prevbcast == 1){
/* CV back preval stable (period) 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)	if(m != 1 && TKresult[nres]!= k1)
continue;	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 Back preval stable (period): '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<=cptcoveff; k++){ /* For each covariate and each value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate number corresponding to k1 combination */	/* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate number corresponding to k1 combination \/ /
	lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];	/* vlv= nbcode[Tvaraff[k]][lv]; */
	vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[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 7480 set ter svg size 640, 480\nunset log y\n	Line 8267 set ter svg size 640, 480\nunset log y\n
fprintf(ficgp,", '' ");	fprintf(ficgp,", '' ");
/* l=(nlstate+ndeath)(i-1)+1; /	/* l=(nlstate+ndeath)(i-1)+1; /
l=(nlstate+ndeath)(cpt-1)+1; / fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2(nlstate+ndeath) /	l=(nlstate+ndeath)(cpt-1)+1; / fixed for i; cpt=1 1, cpt=2 1+ nlstate+ndeath, 1+2(nlstate+ndeath) /
/* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier \/ /	/* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l); /\* a vérifier \/ /
/* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier \/ /	/* fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d/($%d",k1,k+l+(cpt-1),k+l+(cpt-1)+i-1); /\* a vérifier \/ /
fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */	fprintf(ficgp," u ($1==%d ? ($3):1/0):($%d",k1,k+l+i-1); /* To be verified */
/* for (j=2; j<= nlstate ; j ++) */	/* for (j=2; j<= nlstate ; j ++) */
/* fprintf(ficgp,"+$%d",k+l+j-1); */	/* fprintf(ficgp,"+$%d",k+l+j-1); */
Line 7491 set ter svg size 640, 480\nunset log y\n	Line 8278 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 if backcast */	} /* End if prevbcast */

/* 8eme */	/* 8eme */
if(prevfcast==1){	if(prevfcast==1){
/* Projection from cross-sectional to stable (period) 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 */
Line 7503 set ter svg size 640, 480\nunset log y\n	Line 8290 set ter svg size 640, 480\nunset log y\n
continue;	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 stable (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<=cptcoveff; k++){ /* For each correspondig covariate value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */	/* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to k1 combination and kth covariate \/ /
	lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];	/* vlv= nbcode[Tvaraff[k]][lv]; */
	vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[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 7571 set ter svg size 640, 480\nunset log y\n	Line 8360 set ter svg size 640, 480\nunset log y\n
kl=0;	kl=0;
strcpy(gplotcondition,"(");	strcpy(gplotcondition,"(");
for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */	for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */	/* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to combination k1 and covariate k \/ /
	lv=codtabm(k1,TnsdVar[Tvaraff[k]]);
/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */	/* vlv= nbcode[Tvaraff[k]][lv]; /\* Value of the modality of Tvaraff[k] \/ /
	vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];
kl++;	kl++;
sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);	sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
kl++;	kl++;
Line 7607 set ter svg size 640, 480\nunset log y\n	Line 8398 set ter svg size 640, 480\nunset log y\n
} /* end covariate */	} /* end covariate */
} /* End if prevfcast */	} /* End if prevfcast */

if(backcast==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 */
Line 7618 set ter svg size 640, 480\nunset log y\n	Line 8409 set ter svg size 640, 480\nunset log y\n
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<=cptcoveff; k++){ /* For each correspondig covariate value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */	/* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to k1 combination and kth covariate \/ /
	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(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];	/* vlv= nbcode[Tvaraff[k]][lv]; */
	vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[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 7684 set ter svg size 640, 480\nunset log y\n	Line 8477 set ter svg size 640, 480\nunset log y\n
kl=0;	kl=0;
strcpy(gplotcondition,"(");	strcpy(gplotcondition,"(");
for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */	for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */	/* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to combination k1 and covariate k \/ /
	lv= codtabm(k1,TnsdVar[Tvaraff[k]]); /* 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(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */	/* vlv= nbcode[Tvaraff[k]][lv]; /\* Value of the modality of Tvaraff[k] \/ /
	vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];
kl++;	kl++;
sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);	sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
kl++;	kl++;
Line 7720 set ter svg size 640, 480\nunset log y\n	Line 8515 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 if backcast */	} /* End if prevbcast */


/* 9eme writing MLE parameters */	/* 9eme writing MLE parameters */
Line 7769 set ter svg size 640, 480\nunset log y\n	Line 8564 set ter svg size 640, 480\nunset log y\n
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<=cptcoveff; k++){ /* For each correspondig covariate value */
lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to k1 combination and kth covariate */	/* lv= decodtabm(k1,k,cptcoveff); /\* Should be the covariate value corresponding to k1 combination and kth covariate \/ /
	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(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
vlv= nbcode[Tvaraff[k]][lv];	/* vlv= nbcode[Tvaraff[k]][lv]; */
	vlv= nbcode[Tvaraff[k]][codtabm(k1,TnsdVar[Tvaraff[k]])];
fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficgp," V%d=%f ",Tvqresult[nres][resultmodel[nres][k4]],Tqresult[nres][resultmodel[nres][k4]]);
sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[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 7830 set ter svg size 640, 480\nunset log y\n	Line 8627 set ter svg size 640, 480\nunset log y\n
/* for(j=3; j <=ncovmodel-nagesqr; j++) { */	/* for(j=3; j <=ncovmodel-nagesqr; j++) { */
for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */	for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
/* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */	/* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
if(cptcovage >0){ /* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, 2 V5 and V1 */	switch(Typevar[j]){
if(j==Tage[ij]) { /* Product by age To be looked at!!*/	case 1:
if(ij <=cptcovage) { /* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, 2 V5 and V1 */	if(cptcovage >0){ /* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, 2 V5 and V1 */
if(DummyV[j]==0){	if(j==Tage[ij]) { /* Product by age To be looked at!!// Bug valgrind */
fprintf(ficgp,"+p%d%dx",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;	if(ij <=cptcovage) { /* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, 2 V5 and V1 */
}else{ /* quantitative */	if(DummyV[j]==0){/* Bug valgrind */
fprintf(ficgp,"+p%d%fx",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */	fprintf(ficgp,"+p%d%dx",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
/* fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */	}else{ /* quantitative */
	fprintf(ficgp,"+p%d%fx",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
	/* fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
	}
	ij++;
}	}
ij++;
}	}
}	}
}else if(cptcovprod >0){	break;
if(j==Tprod[ijp]) { /* */	case 2:
/* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */	if(cptcovprod >0){
if(ijp <=cptcovprod) { /* Product */	if(j==Tprod[ijp]) { /* */
if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */	/* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */	if(ijp <=cptcovprod) { /* Product */
/* fprintf(ficgp,"+p%d%d%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */	if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
fprintf(ficgp,"+p%d%d%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);	if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
}else{ /* Vn is dummy and Vm is quanti */	/* fprintf(ficgp,"+p%d%d%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */
/* fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */	fprintf(ficgp,"+p%d%d%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);	}else{ /* Vn is dummy and Vm is quanti */
}	/* fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
}else{ /* VnVm Vn is quanti /	fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
if(DummyV[Tvard[ijp][2]]==0){	}
fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);	}else{ /* VnVm Vn is quanti /
}else{ /* Both quanti */	if(DummyV[Tvard[ijp][2]]==0){
fprintf(ficgp,"+p%d%f%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);	fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
	}else{ /* Both quanti */
	fprintf(ficgp,"+p%d%f%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
	}
}	}
	ijp++;
}	}
ijp++;	} /* end Tprod */
}	}
} /* end Tprod */	break;
} else{ /* simple covariate */	case 0:
	/* simple covariate */
/* fprintf(ficgp,"+p%d%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\ Valgrind bug nbcode \/ /	/* fprintf(ficgp,"+p%d%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\ Valgrind bug nbcode \/ /
if(Dummy[j]==0){	if(Dummy[j]==0){
fprintf(ficgp,"+p%d%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); / */	fprintf(ficgp,"+p%d%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); / */
Line 7872 set ter svg size 640, 480\nunset log y\n	Line 8677 set ter svg size 640, 480\nunset log y\n
fprintf(ficgp,"+p%d%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); / */	fprintf(ficgp,"+p%d%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); / */
/* fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */	/* fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
}	}
} /* end simple */	/* end simple */
	break;
	default:
	break;
	} /* end switch */
} /* end j */	} /* end j */
}else{	}else{ /* k=k2 */
i=i-ncovmodel;	if(ng !=1 ){ /* For logit formula of log p11 is more difficult to get */
if(ng !=1 ) /* For logit formula of log p11 is more difficult to get */	fprintf(ficgp," (1.");i=i-ncovmodel;
fprintf(ficgp," (1.");	}else
	i=i-ncovmodel;
}	}

if(ng != 1){	if(ng != 1){
Line 7890 set ter svg size 640, 480\nunset log y\n	Line 8700 set ter svg size 640, 480\nunset log y\n
fprintf(ficgp,"+exp(p%d+p%dx+p%dxx",k3+(cpt-1)ncovmodel,k3+(cpt-1)ncovmodel+1,k3+(cpt-1)ncovmodel+1+nagesqr);	fprintf(ficgp,"+exp(p%d+p%dx+p%dxx",k3+(cpt-1)ncovmodel,k3+(cpt-1)ncovmodel+1,k3+(cpt-1)ncovmodel+1+nagesqr);

ij=1;	ij=1;
for(j=3; j <=ncovmodel-nagesqr; j++){	ijp=1;
if(cptcovage >0){	/* for(j=3; j <=ncovmodel-nagesqr; j++){ */
if((j-2)==Tage[ij]) { /* Bug valgrind */	for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
if(ij <=cptcovage) { /* Bug valgrind */	switch(Typevar[j]){
fprintf(ficgp,"+p%d%dx",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);	case 1:
/* fprintf(ficgp,"+p%d%dx",k3+(cpt-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); /	if(cptcovage >0){
ij++;	if(j==Tage[ij]) { /* Bug valgrind */
}	if(ij <=cptcovage) { /* Bug valgrind */
}	if(DummyV[j]==0){/* Bug valgrind */
}else	/* fprintf(ficgp,"+p%d%dx",k3+(cpt-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]); /
fprintf(ficgp,"+p%d%d",k3+(cpt-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);/* Valgrind bug nbcode */	/* fprintf(ficgp,"+p%d%dx",k3+(cpt-1)ncovmodel+1+j+nagesqr,nbcode[Tvar[j]][codtabm(k1,j)]); /
	fprintf(ficgp,"+p%d%dx",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvar[j]]);
	/* fprintf(ficgp,"+p%d%dx",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);; */
	/* fprintf(ficgp,"+p%d%dx",k3+(cpt-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); /
	}else{ /* quantitative */
	/* fprintf(ficgp,"+p%d%fx",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /\* Tqinvresult in decoderesult \/ /
	fprintf(ficgp,"+p%d%fx",k3+(cpt-1)ncovmodel+1+j+nagesqr,Tqinvresult[nres][Tvar[j]]); / Tqinvresult in decoderesult */
	/* fprintf(ficgp,"+p%d%fx",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /\* Tqinvresult in decoderesult \/ /
	/* fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
	}
	ij++;
	}
	}
	}
	break;
	case 2:
	if(cptcovprod >0){
	if(j==Tprod[ijp]) { /* */
	/* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
	if(ijp <=cptcovprod) { /* Product */
	if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
	if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
	/* fprintf(ficgp,"+p%d%d%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */
	fprintf(ficgp,"+p%d%d%d",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
	/* fprintf(ficgp,"+p%d%d%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]); */
	}else{ /* Vn is dummy and Vm is quanti */
	/* fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
	fprintf(ficgp,"+p%d%d%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
	/* fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); */
	}
	}else{ /* VnVm Vn is quanti /
	if(DummyV[Tvard[ijp][2]]==0){
	fprintf(ficgp,"+p%d%d%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
	/* fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]); */
	}else{ /* Both quanti */
	fprintf(ficgp,"+p%d%f%f",k3+(cpt-1)*ncovmodel+1+j+nagesqr,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
	/* fprintf(ficgp,"+p%d%f%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]); */
	}
	}
	ijp++;
	}
	} /* end Tprod */
	} /* end if */
	break;
	case 0:
	/* simple covariate */
	/* fprintf(ficgp,"+p%d%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\ Valgrind bug nbcode \/ /
	if(Dummy[j]==0){
	/* fprintf(ficgp,"+p%d%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /\ \/ /
	fprintf(ficgp,"+p%d%d",k3+(cpt-1)ncovmodel+1+j+nagesqr,Tinvresult[nres][Tvar[j]]); /* */
	/* fprintf(ficgp,"+p%d%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]); /\ \/ /
	}else{ /* quantitative */
	fprintf(ficgp,"+p%d%f",k3+(cpt-1)ncovmodel+1+j+nagesqr,Tqinvresult[nres][Tvar[j]]); /* */
	/* fprintf(ficgp,"+p%d%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /\ \/ /
	/* fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
	}
	/* end simple */
	/* fprintf(ficgp,"+p%d%d",k3+(cpt-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);/\* Valgrind bug nbcode \/ /
	break;
	default:
	break;
	} /* end switch */
}	}
fprintf(ficgp,")");	fprintf(ficgp,")");
}	}
Line 7909 set ter svg size 640, 480\nunset log y\n	Line 8780 set ter svg size 640, 480\nunset log y\n
fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"p%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);	fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"p%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
else /* ng= 3 */	else /* ng= 3 */
fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"i%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);	fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"i%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
}else{ /* end ng <> 1 */	}else{ /* end ng <> 1 */
if( k !=k2) /* logit p11 is hard to draw */	if( k !=k2) /* logit p11 is hard to draw */
fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"logit(p%d%d)\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);	fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"logit(p%d%d)\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
}	}
Line 7937 set ter svg size 640, 480\nunset log y\n	Line 8808 set ter svg size 640, 480\nunset log y\n
int modcovmax =1;	int modcovmax =1;
int mobilavrange, mob;	int mobilavrange, mob;
int iage=0;	int iage=0;
	int firstA1=0, firstA2=0;

double sum=0., sumr=0.;	double sum=0., sumr=0.;
double age;	double age;
Line 7945 set ter svg size 640, 480\nunset log y\n	Line 8817 set ter svg size 640, 480\nunset log y\n
double agemingoodr, agemaxgoodr;	double agemingoodr, agemaxgoodr;


/* modcovmax=2cptcoveff;/\ Max number of modalities. We suppose */	/* modcovmax=2cptcoveff; Max number of modalities. We suppose /
/* a covariate has 2 modalities, should be equal to ncovcombmax \/ /	/* a covariate has 2 modalities, should be equal to ncovcombmax */

sumnewp = vector(1,ncovcombmax);	sumnewp = vector(1,ncovcombmax);
sumnewm = vector(1,ncovcombmax);	sumnewm = vector(1,ncovcombmax);
Line 8034 set ter svg size 640, 480\nunset log y\n	Line 8906 set ter svg size 640, 480\nunset log y\n
} /* age */	} /* age */
/* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */	/* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */
/* but they will change */	/* but they will change */
	firstA1=0;firstA2=0;
for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */	for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, filling up to the youngest */
sumnewm[cptcod]=0.;	sumnewm[cptcod]=0.;
sumnewmr[cptcod]=0.;	sumnewmr[cptcod]=0.;
Line 8066 set ter svg size 640, 480\nunset log y\n	Line 8939 set ter svg size 640, 480\nunset log y\n
sumr+=probs[(int)age][i][cptcod];	sumr+=probs[(int)age][i][cptcod];
}	}
if(fabs(sum - 1.) > 1.e-3) { /* bad */	if(fabs(sum - 1.) > 1.e-3) { /* bad */
printf("Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);	if(!firstA1){
	firstA1=1;
	printf("Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d. Others in log file...\n",cptcod,sumr, (int)age, (int)bage);
	}
	fprintf(ficlog,"Moving average A1: For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one (%f) at any descending age! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);
} /* end bad */	} /* end bad */
/* else{ /\* We found some ages summing to one, we will smooth the oldest \/ /	/* else{ /\* We found some ages summing to one, we will smooth the oldest \/ /
if(fabs(sumr - 1.) > 1.e-3) { /* bad */	if(fabs(sumr - 1.) > 1.e-3) { /* bad */
printf("Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);	if(!firstA2){
	firstA2=1;
	printf("Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d. Others in log file...\n",cptcod,sumr, (int)age, (int)bage);
	}
	fprintf(ficlog,"Moving average A2: For this combination of covariate cptcod=%d, the raw prevalence doesn't sums to one (%f) even with smoothed values at young ages! age=%d, could you increase bage=%d\n",cptcod,sumr, (int)age, (int)bage);
} /* end bad */	} /* end bad */
}/* age */	}/* age */

Line 8158 set ter svg size 640, 480\nunset log y\n	Line 9039 set ter svg size 640, 480\nunset log y\n
}/* End movingaverage */	}/* End movingaverage */



/************ Forecasting ****************/	/************ Forecasting ****************/
void prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double ***prev, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){	/* void prevforecast(char fileres[], double dateintmean, double anprojd, double mprojd, double jprojd, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double **prev, double bage, double fage, int firstpass, int lastpass, double anprojf, double p[], int cptcoveff)/
/* proj1, year, month, day of starting projection	void prevforecast(char fileres[], double dateintmean, double dateprojd, double dateprojf, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double ***prev, double bage, double fage, int firstpass, int lastpass, double p[], int cptcoveff){
	/* dateintemean, mean date of interviews
	dateprojd, year, month, day of starting projection
	dateprojf date of end of projection;year of end of projection (same day and month as proj1).
agemin, agemax range of age	agemin, agemax range of age
dateprev1 dateprev2 range of dates during which prevalence is computed	dateprev1 dateprev2 range of dates during which prevalence is computed
anproj2 year of en of projection (same day and month as proj1).
*/	*/
	/* double anprojd, mprojd, jprojd; */
	/* double anprojf, mprojf, jprojf; */
int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;	int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
double agec; /* generic age */	double agec; /* generic age */
double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;	double agelim, ppij, yp,yp1,yp2;
double popeffectif,popcount;	double popeffectif,popcount;
double ***p3mat;	double ***p3mat;
/* double **mobaverage; /	/* double **mobaverage; /
Line 8204 set ter svg size 640, 480\nunset log y\n	Line 9090 set ter svg size 640, 480\nunset log y\n
if(estepm > stepm){ /* Yes every two year */	if(estepm > stepm){ /* Yes every two year */
stepsize=2;	stepsize=2;
}	}
	hstepm=hstepm/stepm;


	/* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
	/* fractional in yp1 \/ /
	/* aintmean=yp; */
	/* yp2=modf((yp112),&yp); /
	/* mintmean=yp; */
	/* yp1=modf((yp230.5),&yp); /
	/* jintmean=yp; */
	/* if(jintmean==0) jintmean=1; */
	/* if(mintmean==0) mintmean=1; */

hstepm=hstepm/stepm;
yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and
fractional in yp1 */
anprojmean=yp;
yp2=modf((yp1*12),&yp);
mprojmean=yp;
yp1=modf((yp2*30.5),&yp);
jprojmean=yp;
if(jprojmean==0) jprojmean=1;
if(mprojmean==0) jprojmean=1;

	/* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); */
	/* date2dmy(dateprojd,&jprojd, &mprojd, &anprojd); */
	/* 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",jprojmean,mprojmean,anprojmean,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++){	for(k=1; k<=i1;k++){ /* We want to find the combination k corresponding to the values of the dummies given in this resut line (to be cleaned one day) */
if(i1 != 1 && TKresult[nres]!= k)	if(i1 != 1 && TKresult[nres]!= k)
continue;	continue;
if(invalidvarcomb[k]){	if(invalidvarcomb[k]){
Line 8234 set ter svg size 640, 480\nunset log y\n	Line 9125 set ter svg size 640, 480\nunset log y\n
}	}
fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");	fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcoveff;j++) {
fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	/* fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); */
	fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
Line 8245 set ter svg size 640, 480\nunset log y\n	Line 9137 set ter svg size 640, 480\nunset log y\n
fprintf(ficresf," p%d%d",i,j);	fprintf(ficresf," p%d%d",i,j);
fprintf(ficresf," wp.%d",j);	fprintf(ficresf," wp.%d",j);
}	}
for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {	for (yearp=0; yearp<=(anprojf-anprojd);yearp +=stepsize) {
fprintf(ficresf,"\n");	fprintf(ficresf,"\n");
fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);	fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jprojd,mprojd,anprojd+yearp);
/* for (agec=fage; agec>=(ageminpar-1); agec--){ */	/* for (agec=fage; agec>=(ageminpar-1); agec--){ */
for (agec=fage; agec>=(bage); agec--){	for (agec=fage; agec>=(bage); agec--){
nhstepm=(int) rint((agelim-agec)*YEARM/stepm);	nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
Line 8264 set ter svg size 640, 480\nunset log y\n	Line 9156 set ter svg size 640, 480\nunset log y\n
}	}
fprintf(ficresf,"\n");	fprintf(ficresf,"\n");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	/* fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); /\* Tvaraff not correct \/ /
fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+hhstepm/YEARMstepm);	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);

for(j=1; j<=nlstate+ndeath;j++) {	for(j=1; j<=nlstate+ndeath;j++) {
ppij=0.;	ppij=0.;
for(i=1; i<=nlstate;i++) {	for(i=1; i<=nlstate;i++) {
/* if (mobilav>=1) */	if (mobilav>=1)
ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];	ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
/* else { / / even if mobilav==-1 we use mobaverage */	else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */
/* ppij=ppij+p3mat[i][j][h]probs[(int)(agec)][i][k]; /	ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
/* } */	}
fprintf(ficresf," %.3f", p3mat[i][j][h]);	fprintf(ficresf," %.3f", p3mat[i][j][h]);
} /* end i */	} /* end i */
fprintf(ficresf," %.3f", ppij);	fprintf(ficresf," %.3f", ppij);
Line 8293 set ter svg size 640, 480\nunset log y\n	Line 9186 set ter svg size 640, 480\nunset log y\n
}	}

/************ Back Forecasting ****************/	/************ Back Forecasting ****************/
void prevbackforecast(char fileres[], double ***prevacurrent, double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){	/* void prevbackforecast(char fileres[], double **prevacurrent, double anback1, double mback1, double jback1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anback2, double p[], int cptcoveff){ /
/* back1, year, month, day of starting backection	void prevbackforecast(char fileres[], double ***prevacurrent, double dateintmean, double dateprojd, double dateprojf, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double p[], int cptcoveff){
	/* back1, year, month, day of starting backprojection
agemin, agemax range of age	agemin, agemax range of age
dateprev1 dateprev2 range of dates during which prevalence is computed	dateprev1 dateprev2 range of dates during which prevalence is computed
anback2 year of end of backprojection (same day and month as back1).	anback2 year of end of backprojection (same day and month as back1).
Line 8302 set ter svg size 640, 480\nunset log y\n	Line 9196 set ter svg size 640, 480\nunset log y\n
*/	*/
int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;	int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
double agec; /* generic age */	double agec; /* generic age */
double agelim, ppij, ppi, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;	double agelim, ppij, ppi, yp,yp1,yp2; /* ,jintmean,mintmean,aintmean;*/
double popeffectif,popcount;	double popeffectif,popcount;
double ***p3mat;	double ***p3mat;
/* double **mobaverage; /	/* double **mobaverage; /
Line 8345 set ter svg size 640, 480\nunset log y\n	Line 9239 set ter svg size 640, 480\nunset log y\n
}	}

hstepm=hstepm/stepm;	hstepm=hstepm/stepm;
yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp and	/* yp1=modf(dateintmean,&yp);/\* extracts integral of datemean in yp and */
fractional in yp1 */	/* fractional in yp1 \/ /
anprojmean=yp;	/* aintmean=yp; */
yp2=modf((yp1*12),&yp);	/* yp2=modf((yp112),&yp); /
mprojmean=yp;	/* mintmean=yp; */
yp1=modf((yp2*30.5),&yp);	/* yp1=modf((yp230.5),&yp); /
jprojmean=yp;	/* jintmean=yp; */
if(jprojmean==0) jprojmean=1;	/* if(jintmean==0) jintmean=1; */
if(mprojmean==0) jprojmean=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",jprojmean,mprojmean,anprojmean,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",jprojmean,mprojmean,anprojmean,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");

Line 8373 set ter svg size 640, 480\nunset log y\n	Line 9267 set ter svg size 640, 480\nunset log y\n
}	}
fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");	fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcoveff;j++) {
fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
Line 8384 set ter svg size 640, 480\nunset log y\n	Line 9278 set ter svg size 640, 480\nunset log y\n
fprintf(ficresfb," b%d%d",i,j);	fprintf(ficresfb," b%d%d",i,j);
fprintf(ficresfb," b.%d",j);	fprintf(ficresfb," b.%d",j);
}	}
for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {	for (yearp=0; yearp>=(anbackf-anbackd);yearp -=stepsize) {
/* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { */	/* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { */
fprintf(ficresfb,"\n");	fprintf(ficresfb,"\n");
fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);	fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jbackd,mbackd,anbackd+yearp);
/* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */	/* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
/* for (agec=bage; agec<=agemax-1; agec++){ /\* testing \/ /	/* for (agec=bage; agec<=agemax-1; agec++){ /\* testing \/ /
for (agec=bage; agec<=fage; agec++){ /* testing */	for (agec=bage; agec<=fage; agec++){ /* testing */
Line 8409 set ter svg size 640, 480\nunset log y\n	Line 9303 set ter svg size 640, 480\nunset log y\n
}	}
fprintf(ficresfb,"\n");	fprintf(ficresfb,"\n");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
fprintf(ficresfb,"%.f %.f ",anback1+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.;
for(j=1; j<=nlstate;j++) {	for(j=1; j<=nlstate;j++) {
Line 8445 set ter svg size 640, 480\nunset log y\n	Line 9339 set ter svg size 640, 480\nunset log y\n

/* Variance of prevalence limit: varprlim */	/* Variance of prevalence limit: varprlim */
void varprlim(char fileresu[], int nresult, double *prevacurrent, int mobilavproj, double bage, double fage, double prlim, int ncvyearp, double ftolpl, double p[], double matcov, double delti, int stepm, int cptcoveff){	void varprlim(char fileresu[], int nresult, double *prevacurrent, int mobilavproj, double bage, double fage, double prlim, int ncvyearp, double ftolpl, double p[], double matcov, double delti, int stepm, int cptcoveff){
/------- Variance of period (stable) prevalence------/	/------- Variance of forward period (stable) prevalence------/

char fileresvpl[FILENAMELENGTH];	char fileresvpl[FILENAMELENGTH];
FILE *ficresvpl;	FILE *ficresvpl;
Line 8456 set ter svg size 640, 480\nunset log y\n	Line 9350 set ter svg size 640, 480\nunset log y\n
strcpy(fileresvpl,"VPL_");	strcpy(fileresvpl,"VPL_");
strcat(fileresvpl,fileresu);	strcat(fileresvpl,fileresu);
if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {	if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);	printf("Problem with variance of forward period (stable) prevalence resultfile: %s\n", fileresvpl);
exit(0);	exit(0);
}	}
printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);	printf("Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);	fprintf(ficlog, "Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);

/*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++){*/
Line 8469 set ter svg size 640, 480\nunset log y\n	Line 9363 set ter svg size 640, 480\nunset log y\n
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(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<=cptcoveff;j++) {
fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
}	}
for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */	for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[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][j]);	fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
}	}
fprintf(ficresvpl,"******\n");	fprintf(ficresvpl,"******\n");
printf("******\n");	printf("******\n");
Line 8497 set ter svg size 640, 480\nunset log y\n	Line 9391 set ter svg size 640, 480\nunset log y\n
}	}

fclose(ficresvpl);	fclose(ficresvpl);
printf("done variance-covariance of period prevalence\n");fflush(stdout);	printf("done variance-covariance of forward period prevalence\n");fflush(stdout);
fprintf(ficlog,"done variance-covariance of period prevalence\n");fflush(ficlog);	fprintf(ficlog,"done variance-covariance of forward period prevalence\n");fflush(ficlog);

}	}
/* Variance of back prevalence: varbprlim */	/* Variance of back prevalence: varbprlim */
Line 8533 set ter svg size 640, 480\nunset log y\n	Line 9427 set ter svg size 640, 480\nunset log y\n
printf("\n#****** ");	printf("\n#****** ");
fprintf(ficlog,"\n#****** ");	fprintf(ficlog,"\n#****** ");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcoveff;j++) {
fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
}	}
for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */	for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[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][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 8858 void prwizard(int ncovmodel, int nlstate	Line 9752 void prwizard(int ncovmodel, int nlstate
/***************** Gompertz Likelihood ****************************/	/***************** Gompertz Likelihood ****************************/
double gompertz(double x[])	double gompertz(double x[])
{	{
double A,B,L=0.0,sump=0.,num=0.;	double A=0.0,B=0.,L=0.0,sump=0.,num=0.;
int i,n=0; /* n is the size of the sample */	int i,n=0; /* n is the size of the sample */

for (i=1;i<=imx ; i++) {	for (i=1;i<=imx ; i++) {
Line 8866 double gompertz(double x[])	Line 9760 double gompertz(double x[])
/* sump=sump+1;*/	/* sump=sump+1;*/
num=num+1;	num=num+1;
}	}
	L=0.0;
	/* agegomp=AGEGOMP; */
/* for (i=0; i<=imx; i++)	/* for (i=0; i<=imx; i++)
if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/	if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/

for (i=1;i<=imx ; i++)	for (i=1;i<=imx ; i++) {
{	/* mu(a)=mu(agecomp)exp(teta(age-agegomp))
if (cens[i] == 1 && wav[i]>1)	mu(a)=x[1]exp(x[2](age-agegomp)); x[1] and x[2] are per year.
A=-x[1]/(x[2])(exp(x[2](agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));	* L= Product mu(agedeces)exp(-\int_ageexam^agedc mu(u) du ) for a death between agedc (in month)
	* and agedc +1 month, cens[i]=0: log(x[1]/YEARM)
if (cens[i] == 0 && wav[i]>1)	* +
	* exp(-\int_ageexam^agecens mu(u) du ) when censored, cens[i]=1
	*/
	if (wav[i] > 1 \|\| agedc[i] < AGESUP) {
	if (cens[i] == 1){
	A=-x[1]/(x[2])(exp(x[2](agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
	} else if (cens[i] == 0){
A=-x[1]/(x[2])(exp(x[2](agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))	A=-x[1]/(x[2])(exp(x[2](agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);	+log(x[1]/YEARM) +x[2]*(agedc[i]-agegomp)+log(YEARM);
	} else
	printf("Gompertz cens[%d] neither 1 nor 0\n",i);
/if (wav[i] > 1 && agecens[i] > 15) {/ /* ??? */	/if (wav[i] > 1 && agecens[i] > 15) {/ /* ??? */
if (wav[i] > 1 ) { /* ??? */	L=L+A*weight[i];
L=L+A*weight[i];
/* printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]12,agecens[i]12,cens[i],agedc[i]12,weight[i]);/	/* printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]12,agecens[i]12,cens[i],agedc[i]12,weight[i]);/
}	}
}	}

/printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);/	/printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);/

return -2Lnum/sump;	return -2Lnum/sump;
}	}
Line 8896 double gompertz(double x[])	Line 9796 double gompertz(double x[])
/***************** Gompertz_f Likelihood ****************************/	/***************** Gompertz_f Likelihood ****************************/
double gompertz_f(const gsl_vector v, void params)	double gompertz_f(const gsl_vector v, void params)
{	{
double A,B,LL=0.0,sump=0.,num=0.;	double A=0.,B=0.,LL=0.0,sump=0.,num=0.;
double x= (double ) v->data;	double x= (double ) v->data;
int i,n=0; /* n is the size of the sample */	int i,n=0; /* n is the size of the sample */

Line 8989 int readdata(char datafile[], int firsto	Line 9889 int readdata(char datafile[], int firsto
int i=0, j=0, n=0, iv=0, v;	int i=0, j=0, n=0, iv=0, v;
int lstra;	int lstra;
int linei, month, year,iout;	int linei, month, year,iout;
	int noffset=0; /* This is the offset if BOM data file */
char line[MAXLINE], linetmp[MAXLINE];	char line[MAXLINE], linetmp[MAXLINE];
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;
	FixedV[v]=0;
	}

for(v=1; v <=ncovcol;v++){	for(v=1; v <=ncovcol;v++){
DummyV[v]=0;	DummyV[v]=0;
Line 9022 int readdata(char datafile[], int firsto	Line 9927 int readdata(char datafile[], int firsto
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;
}	}

i=1;	/* Is it a BOM UTF-8 Windows file? */
	/* First data line */
linei=0;	linei=0;
	while(fgets(line, MAXLINE, fic)) {
	noffset=0;
	if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
	{
	noffset=noffset+3;
	printf("# Data file '%s' is an UTF8 BOM file, please convert to UTF8 or ascii file and rerun.\n",datafile);fflush(stdout);
	fprintf(ficlog,"# Data file '%s' is an UTF8 BOM file, please convert to UTF8 or ascii file and rerun.\n",datafile);
	fflush(ficlog); return 1;
	}
	/* else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/
	else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
	{
	noffset=noffset+2;
	printf("# Error Data file '%s' is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);fflush(stdout);
	fprintf(ficlog,"# Error Data file '%s' is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);
	fflush(ficlog); return 1;
	}
	else if( line[0] == 0 && line[1] == 0)
	{
	if( line[2] == (char)0xFE && line[3] == (char)0xFF){
	noffset=noffset+4;
	printf("# Error Data file '%s' is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);fflush(stdout);
	fprintf(ficlog,"# Error Data file '%s' is a huge UTF16BE BOM file, please convert to UTF8 or ascii file (for example with dos2unix) and rerun.\n",datafile);
	fflush(ficlog); return 1;
	}
	} else{
	;/printf(" Not a BOM file\n");/
	}
	/* If line starts with a # it is a comment */
	if (line[noffset] == '#') {
	linei=linei+1;
	break;
	}else{
	break;
	}
	}
	fclose(fic);
	if((fic=fopen(datafile,"r"))==NULL) {
	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;
	}
	/* Not a Bom file */

	i=1;
while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {	while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
linei=linei+1;	linei=linei+1;
for(j=strlen(line); j>=0;j--){ /* Untabifies line */	for(j=strlen(line); j>=0;j--){ /* Untabifies line */
Line 9090 int readdata(char datafile[], int firsto	Line 10040 int readdata(char datafile[], int firsto
}	}
if(lval <-1 \|\| lval >1){	if(lval <-1 \|\| lval >1){
printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \	printf("Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \	Should be a value of %d(nth) covariate of wave %d (0 should be the value for the reference and 1\n \
for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \	for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
For example, for multinomial values like 1, 2 and 3,\n \	For example, for multinomial values like 1, 2 and 3,\n \
build V1=0 V2=0 for the reference value (1),\n \	build V1=0 V2=0 for the reference value (1),\n \
V1=1 V2=0 for (2) \n \	V1=1 V2=0 for (2) \n \
and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \	and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
output of IMaCh is often meaningless.\n \	output of IMaCh is often meaningless.\n \
Exiting.\n",lval,linei, i,line,j);	Exiting.\n",lval,linei, i,line,iv,j);
fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \	fprintf(ficlog,"Error reading data around '%ld' at line number %d for individual %d, '%s'\n \
Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \	Should be a value of %d(nth) covariate of wave %d (0 should be the value for the reference and 1\n \
for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \	for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
For example, for multinomial values like 1, 2 and 3,\n \	For example, for multinomial values like 1, 2 and 3,\n \
build V1=0 V2=0 for the reference value (1),\n \	build V1=0 V2=0 for the reference value (1),\n \
V1=1 V2=0 for (2) \n \	V1=1 V2=0 for (2) \n \
and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \	and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
output of IMaCh is often meaningless.\n \	output of IMaCh is often meaningless.\n \
Exiting.\n",lval,linei, i,line,j);fflush(ficlog);	Exiting.\n",lval,linei, i,line,iv,j);fflush(ficlog);
return 1;	return 1;
}	}
cotvar[j][iv][i]=(double)(lval);	cotvar[j][iv][i]=(double)(lval);
Line 9144 int readdata(char datafile[], int firsto	Line 10094 int readdata(char datafile[], int firsto
return 1;	return 1;
}	}
anint[j][i]= (double) year;	anint[j][i]= (double) year;
mint[j][i]= (double)month;	mint[j][i]= (double)month;
	/* if( (int)anint[j][i]+ (int)(mint[j][i])/12. < (int) (moisnais[i]/12.+annais[i])){ */
	/* printf("Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, mint[j][i],anint[j][i], moisnais[i],annais[i]); */
	/* fprintf(ficlog,"Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, mint[j][i],anint[j][i], moisnais[i],annais[i]); */
	/* } */
strcpy(line,stra);	strcpy(line,stra);
} /* End loop on waves */	} /* End loop on waves */

Line 9183 int readdata(char datafile[], int firsto	Line 10137 int readdata(char datafile[], int firsto

}	}
annais[i]=(double)(year);	annais[i]=(double)(year);
moisnais[i]=(double)(month);	moisnais[i]=(double)(month);
	for (j=1;j<=maxwav;j++){
	if( (int)anint[j][i]+ (int)(mint[j][i])/12. < (int) (moisnais[i]/12.+annais[i])){
	printf("Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, (int)mint[j][i],(int)anint[j][i], j,(int)moisnais[i],(int)annais[i]);
	fprintf(ficlog,"Warning reading data around '%s' at line number %d for individual %d, '%s'\nThe date of interview (%2d/%4d) at wave %d occurred before the date of birth (%2d/%4d).\n",strb, linei,i, line, (int)mint[j][i],(int)anint[j][i], j, (int)moisnais[i],(int)annais[i]);
	}
	}

strcpy(line,stra);	strcpy(line,stra);

/* Sample weight */	/* Sample weight */
Line 9203 int readdata(char datafile[], int firsto	Line 10164 int readdata(char datafile[], int firsto
cutv(stra, strb, line, ' ');	cutv(stra, strb, line, ' ');
if(strb[0]=='.') { /* Missing value */	if(strb[0]=='.') { /* Missing value */
lval=-1;	lval=-1;
	coqvar[iv][i]=NAN;
	covar[ncovcol+iv][i]=NAN; /* including qvar in standard covar for performance reasons */
}else{	}else{
errno=0;	errno=0;
/* what_kind_of_number(strb); */	/* what_kind_of_number(strb); */
Line 9296 void removefirstspace(char *stri){/, c	Line 10259 void removefirstspace(char *stri){/, c
*stri=p2;	*stri=p2;
}	}

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

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

if (strstr(resultline,"v") !=0){	strcpy(resultsav,resultline);
printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);	printf("Decoderesult resultsav=\"%s\" resultline=\"%s\"\n", resultsav, resultline);
fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultline);fflush(ficlog);
return 1;
}
trimbb(resultsav, resultline);
if (strlen(resultsav) >1){	if (strlen(resultsav) >1){
j=nbocc(resultsav,'='); /*< j=Number of covariate values'=' /	j=nbocc(resultsav,'='); /*< j=Number of covariate values'=' /
}	}
Line 9321 int decoderesult ( char resultline[], in	Line 10280 int decoderesult ( char resultline[], in
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 variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);	printf("ERROR: the number of variables in the resultline which is %d, differs from the number %d of variables used in the model line, %s.\n",j, cptcovs, model);
fprintf(ficlog,"ERROR: the number of variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);	fprintf(ficlog,"ERROR: the number of variables in the resultline which is %d, differs from the number %d of variables used in the model line, %s.\n",j, cptcovs, model);
	/* return 1;*/
}	}
for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */	for(k=1; k<=j;k++){ /* Loop on any covariate of the result line */
if(nbocc(resultsav,'=') >1){	if(nbocc(resultsav,'=') >1){
cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' '	cutl(stra,strb,resultsav,' '); /* keeps in strb after the first ' ' (stra is the rest of the resultline to be analyzed in the next loop // resultsav= "V4=1 V5=25.1 V3=0" stra= "V5=25.1 V3=0" strb= "V4=1" */
resultsav= V4=1 V5=25.1 V3=0 strb=V3=0 stra= V4=1 V5=25.1 */	/* If resultsav= "V4= 1 V5=25.1 V3=0" with a blank then strb="V4=" and stra="1 V5=25.1 V3=0" */
cutl(strc,strd,strb,'='); /* strb:V4=1 strc=1 strd=V4 */	cutl(strc,strd,strb,'='); /* strb:"V4=1" strc="1" strd="V4" */
	/* If a blank, then strc="V4=" and strd='\0' */
	if(strc[0]=='\0'){
	printf("Error in resultline, probably a blank after the \"%s\", \"result:%s\", stra=\"%s\" resultsav=\"%s\"\n",strb,resultline, stra, resultsav);
	fprintf(ficlog,"Error in resultline, probably a blank after the \"V%s=\", resultline=%s\n",strb,resultline);
	return 1;
	}
}else	}else
cutl(strc,strd,resultsav,'=');	cutl(strc,strd,resultsav,'=');
Tvalsel[k]=atof(strc); /* 1 */	Tvalsel[k]=atof(strc); /* 1 / / Tvalsel of k is the float value of the kth covariate appearing in this result line */

cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;	cutl(strc,stre,strd,'V'); /* strd='V4' strc=4 stre='V' */;
Tvarsel[k]=atoi(strc);	Tvarsel[k]=atoi(strc); /* 4 / / Tvarsel is the id of the kth covariate in the result line Tvarsel[1] in "V4=1.." is 4.*/
/* Typevarsel[k]=1; /\* 1 for age product \/ /	/* Typevarsel[k]=1; /\* 1 for age product \/ /
/* cptcovsel++; */	/* cptcovsel++; */
if (nbocc(stra,'=') >0)	if (nbocc(stra,'=') >0)
strcpy(resultsav,stra); /* and analyzes it */	strcpy(resultsav,stra); /* and analyzes it */
}	}
/* Checking for missing or useless values in comparison of current model needs */	/* Checking for missing or useless values in comparison of current model needs */
for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */	/* Feeds resultmodel[nres][k1]=k2 for k1th product covariate with age in the model equation fed by the index k2 of the resutline*/
	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 covariate in model */	if(Typevar[k1]==0){ /* Single covariate in model */
	/* 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product */
match=0;	match=0;
for(k2=1; k2 <=j;k2++){/* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */	for(k2=1; k2 <=j;k2++){/* Loop on resultline. In result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
if(Tvar[k1]==Tvarsel[k2]) {/* Tvar[1]=5 == Tvarsel[2]=5 */	if(Tvar[k1]==Tvarsel[k2]) {/* Tvar is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5 */
modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2 modelresult[3]=3 modelresult[6]=4 modelresult[9]=5 */	modelresult[k2]=k1;/* modelresult[2]=1 modelresult[1]=2 modelresult[3]=3 modelresult[6]=4 modelresult[9]=5 */
match=1;	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: %d value missing; result: %s, model=%s\n",k1, resultline, model);	printf("Error in result line (Dummy single): V%d is missing in result: %s according to model=%s. Tvar[k1=%d]=%d is different from Tvarsel[k2=%d]=%d.\n",Tvar[k1], resultline, model,k1, Tvar[k1], k2, Tvarsel[k2]);
	fprintf(ficlog,"Error in result line (Dummy single): V%d is missing in result: %s according to model=%s\n",Tvar[k1], resultline, model);
	return 1;
}	}
}	}else if(Typevar[k1]==1){ /* Product with age We want to get the position k2 in the resultline of the product k1 in the model line*/
}	/* We feed resultmodel[k1]=k2; */
	match=0;
	for(k2=1; k2 <=j;k2++){/* Loop on resultline. jth occurence of = signs in the result line. In result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
	if(Tvar[k1]==Tvarsel[k2]) {/* Tvar is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5 */
	modelresult[k2]=k1;/* we found a Vn=1 corrresponding to Vnage in the model modelresult[2]=1 modelresult[1]=2 modelresult[3]=3 modelresult[6]=4 modelresult[9]=5 /
	resultmodel[nres][k1]=k2; /* Added here */
	printf("Decoderesult first modelresult[k2=%d]=%d (k1) V%d*AGE\n",k2,k1,Tvar[k1]);
	match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
	break;
	}
	}
	if(match == 0){
	printf("Error in result line (Product with age): V%d is missing in result: %s according to model=%s (Tvarsel[k2=%d]=%d)\n",Tvar[k1], resultline, model, k2, Tvarsel[k2]);
	fprintf(ficlog,"Error in result line (Product with age): V%d is missing in result: %s according to model=%s (Tvarsel[k2=%d]=%d)\n",Tvar[k1], resultline, model, k2, Tvarsel[k2]);
	return 1;
	}
	}else if(Typevar[k1]==2){ /* Product No age We want to get the position in the resultline of the product in the model line*/
	/* resultmodel[nres][of such a Vn * Vm product k1] is not unique, so can't exist, we feed Tvard[k1][1] and [2] */
	match=0;
	printf("Decoderesult very first Product Tvardk[k1=%d][1]=%d Tvardk[k1=%d][2]=%d V%d * V%d\n",k1,Tvardk[k1][1],k1,Tvardk[k1][2],Tvardk[k1][1],Tvardk[k1][2]);
	for(k2=1; k2 <=j;k2++){/* Loop on resultline. In result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
	if(Tvardk[k1][1]==Tvarsel[k2]) {/* Tvardk is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5 */
	/* modelresult[k2]=k1; */
	printf("Decoderesult first Product modelresult[k2=%d]=%d (k1) V%d * \n",k2,k1,Tvarsel[k2]);
	match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
	}
	}
	if(match == 0){
	printf("Error in result line (Product without age first variable): V%d is missing in result: %s according to model=%s\n",Tvardk[k1][1], resultline, model);
	fprintf(ficlog,"Error in result line (Product without age first variable): V%d is missing in result: %s according to model=%s\n",Tvardk[k1][1], resultline, model);
	return 1;
	}
	match=0;
	for(k2=1; k2 <=j;k2++){/* Loop on resultline. In result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
	if(Tvardk[k1][2]==Tvarsel[k2]) {/* Tvardk is coming from the model, Tvarsel from the result. Tvar[1]=5 == Tvarsel[2]=5 */
	/* modelresult[k2]=k1;*/
	printf("Decoderesult second Product modelresult[k2=%d]=%d (k1) * V%d \n ",k2,k1,Tvarsel[k2]);
	match=1; /* modelresult of k2 variable of resultline is identical to k1 variable of the model good */
	break;
	}
	}
	if(match == 0){
	printf("Error in result line (Product without age second variable): V%d is missing in result: %s according to model=%s\n",Tvardk[k1][2], resultline, model);
	fprintf(ficlog,"Error in result line (Product without age second variable): V%d is missing in result : %s according to model=%s\n",Tvardk[k1][2], resultline, model);
	return 1;
	}
	}/* End of testing */
	}/* End loop cptcovt */
/* Checking for missing or useless values in comparison of current model needs */	/* Checking for missing or useless values in comparison of current model needs */
for(k2=1; k2 <=j;k2++){ /* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */	/* Feeds resultmodel[nres][k1]=k2 for single covariate (k1) in the model equation */
	for(k2=1; k2 <=j;k2++){ /* Loop on resultline variables: result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */
match=0;	match=0;
for(k1=1; k1<= cptcovt ;k1++){ /* model line V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */	for(k1=1; k1<= cptcovt ;k1++){ /* loop on model: model line V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
if(Typevar[k1]==0){ /* Single */	if(Typevar[k1]==0){ /* Single only */
if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4 */	if(Tvar[k1]==Tvarsel[k2]) { /* Tvar[2]=4 == Tvarsel[1]=4 */
resultmodel[k1]=k2; /* 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 */
++match;	++match;
}	}
}	}
}	}
if(match == 0){	if(match == 0){
printf("Error in result line: %d value missing; result: %s, model=%s\n",k1, resultline, model);	printf("Error in result line: variable V%d is missing in model; result: %s, model=%s\n",Tvarsel[k2], resultline, model);
	fprintf(ficlog,"Error in result line: variable V%d is missing in model; result: %s, model=%s\n",Tvarsel[k2], resultline, model);
	return 1;
}else if(match > 1){	}else if(match > 1){
printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);	printf("Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
	fprintf(ficlog,"Error in result line: %d doubled; result: %s, model=%s\n",k2, resultline, model);
	return 1;
}	}
}	}

/* We need to deduce which combination number is chosen and save quantitative values */	/* We need to deduce which combination number is chosen and save quantitative values */
/* model line V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */	/* model line V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
/* result line V4=1 V5=25.1 V3=0 V2=8 V1=1 */	/* nres=1st result line: V4=1 V5=25.1 V3=0 V2=8 V1=1 */
/* should give a combination of dummy V4=1, V3=0, V1=1 => V42(0) + V32*(1) + V12*(2) = 5 + (1offset) = 6/	/* should correspond to the combination 6 of dummy: V4=1, V3=0, V1=1 => V42(0) + V32*(1) + V12*(2) = 11 + 02 + 14 = 5 + (1offset) = 6*/
/* result line V4=1 V5=24.1 V3=1 V2=8 V1=0 */	/* nres=2nd result line: V4=1 V5=24.1 V3=1 V2=8 V1=0 */
/* should give a combination of dummy V4=1, V3=1, V1=0 => V42(0) + V32*(1) + V12*(2) = 3 + (1offset) = 4/	/* should give a combination of dummy V4=1, V3=1, V1=0 => V42(0) + V32*(1) + V12*(2) = 3 + (1offset) = 4/
/* 1 0 0 0 */	/* 1 0 0 0 */
/* 2 1 0 0 */	/* 2 1 0 0 */
/* 3 0 1 0 */	/* 3 0 1 0 */
/* 4 1 1 0 / / V4=1, V3=1, V1=0 */	/* 4 1 1 0 / / V4=1, V3=1, V1=0 (nres=2)*/
/* 5 0 0 1 */	/* 5 0 0 1 */
/* 6 1 0 1 / / V4=1, V3=0, V1=1 */	/* 6 1 0 1 / / V4=1, V3=0, V1=1 (nres=1)*/
/* 7 0 1 1 */	/* 7 0 1 1 */
/* 8 1 1 1 */	/* 8 1 1 1 */
/* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */	/* V(Tvresult)=Tresult V4=1 V3=0 V1=1 Tresult[nres=1][2]=0 */
/* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */	/* V(Tvqresult)=Tqresult V5=25.1 V2=8 Tqresult[nres=1][1]=25.1 */
/* V5age V5 known which value for nres? /	/* V5age V5 known which value for nres? /
/* Tqinvresult[2]=8 Tqinvresult[1]=25.1 */	/* Tqinvresult[2]=8 Tqinvresult[1]=25.1 */
for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* model line */	for(k1=1, k=0, k4=0, k4q=0; k1 <=cptcovt;k1++){ /* loop k1 on position in the model line (excluding product) */
if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Single dummy */	/* k counting number of combination of single dummies in the equation model */
k3= resultmodel[k1]; /* resultmodel[2(V4)] = 1=k3 */	/* k4 counting single dummies in the equation model */
k2=(int)Tvarsel[k3]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */	/* k4q counting single quantitatives in the equation model */
k+=Tvalsel[k3]pow(2,k4); / Tvalsel[1]=1 */	if( Dummy[k1]==0 && Typevar[k1]==0 ){ /* Dummy and Single */
Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres][1]=1(V4=1) Tresult[nres][2]=0(V3=0) */	/* k4+1= position in the resultline V(Tvarsel)=Tvalsel=Tresult[nres][pos](value); V(Tvresult[nres][pos] (variable): V(variable)=value) */
	/* modelresult[k3]=k1: k3th position in the result line corresponds to the k1 position in the model line (doesn't work with products)*/
	/* Value in the (current nres) resultline of the variable at the k1th position in the model equation resultmodel[nres][k1]= k3 */
	/* resultmodel[nres][k1]=k3: k1th position in the model correspond to the k3 position in the resultline */
	/* k3 is the position in the nres result line of the k1th variable of the model equation */
	/* Tvarsel[k3]: Name of the variable at the k3th position in the result line. */
	/* Tvalsel[k3]: Value of the variable at the k3th position in the result line. */
	/* Tresult[nres][result_position]= value of the dummy variable at the result_position in the nres resultline */
	/* Tvresult[nres][result_position]= id of the dummy variable at the result_position in the nres resultline */
	/* Tinvresult[nres][Name of a dummy variable]= value of the variable in the result line */
	/* TinvDoQresult[nres][Name of a Dummy or Q variable]= value of the variable in the result line */
	k3= resultmodel[nres][k1]; /* From position k1 in model get position k3 in result line */
	/* nres=1 k1=2 resultmodel[2(V4)] = 1=k3 ; k1=3 resultmodel[3(V3)] = 2=k3*/
	k2=(int)Tvarsel[k3]; /* from position k3 in resultline get name k2: nres=1 k1=2=>k3=1 Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 (V4); k1=3=>k3=2 Tvarsel[2]=3 (V3)*/
	k+=Tvalsel[k3]pow(2,k4); / nres=1 k1=2 Tvalsel[1]=1 (V4=1); k1=3 k3=2 Tvalsel[2]=0 (V3=0) */
	TinvDoQresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Stores the value into the name of the variable. */
	/* Tinvresult[nres][4]=1 */
	Tresult[nres][k4+1]=Tvalsel[k3];/* Tresult[nres=2][1]=1(V4=1) Tresult[nres=2][2]=0(V3=0) */
Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */	Tvresult[nres][k4+1]=(int)Tvarsel[k3];/* Tvresult[nres][1]=4 Tvresult[nres][3]=1 */
Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */	Tinvresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
printf("Decoderesult Dummy k=%d, V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k2, k3, (int)Tvalsel[k3], k4);	precov[nres][k1]=Tvalsel[k3];
	printf("Decoderesult Dummy k=%d, k1=%d precov[nres=%d][k1=%d]=%.f V(k2=V%d)= Tvalsel[%d]=%d, 2**(%d)\n",k, k1, nres, k1,precov[nres][k1], k2, k3, (int)Tvalsel[k3], k4);
k4++;;	k4++;;
} else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Single quantitative */	}else if( Dummy[k1]==1 && Typevar[k1]==0 ){ /* Quantitative and single */
k3q= resultmodel[k1]; /* resultmodel[2] = 1=k3 */	/* Tqresult[nres][result_position]= value of the variable at the result_position in the nres resultline */
k2q=(int)Tvarsel[k3q]; /* Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 */	/* Tvqresult[nres][result_position]= id of the variable at the result_position in the nres resultline */
	/* Tqinvresult[nres][Name of a quantitative variable]= value of the variable in the result line */
	k3q= resultmodel[nres][k1]; /* resultmodel[1(V5)] = 5 =k3q */
	k2q=(int)Tvarsel[k3q]; /* Name of variable at k3q th position in the resultline */
	/* Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */
Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */	Tqresult[nres][k4q+1]=Tvalsel[k3q]; /* Tqresult[nres][1]=25.1 */
Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */	Tvqresult[nres][k4q+1]=(int)Tvarsel[k3q]; /* Tvqresult[nres][1]=5 */
Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */	Tqinvresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
printf("Decoderesult Quantitative nres=%d, V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);	TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
	precov[nres][k1]=Tvalsel[k3q];
	printf("Decoderesult Quantitative nres=%d,precov[nres=%d][k1=%d]=%.f V(k2q=V%d)= Tvalsel[%d]=%d, Tvarsel[%d]=%f\n",nres, nres, k1,precov[nres][k1], k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
k4q++;;	k4q++;;
	}else if( Dummy[k1]==2 ){ /* For dummy with age product */
	/* Tvar[k1]; / / Age variable */
	/* Wrong we want the value of variable name Tvar[k1] */

	k3= resultmodel[nres][k1]; /* nres=1 k1=2 resultmodel[2(V4)] = 1=k3 ; k1=3 resultmodel[3(V3)] = 2=k3*/
	k2=(int)Tvarsel[k3]; /* nres=1 k1=2=>k3=1 Tvarsel[resultmodel[2]]= Tvarsel[1] = 4=k2 (V4); k1=3=>k3=2 Tvarsel[2]=3 (V3)*/
	TinvDoQresult[nres][(int)Tvarsel[k3]]=Tvalsel[k3]; /* Tinvresult[nres][4]=1 */
	precov[nres][k1]=Tvalsel[k3];
	printf("Decoderesult Dummy with age k=%d, k1=%d precov[nres=%d][k1=%d]=%.f Tvar[%d]=V%d k2=Tvarsel[%d]=%d Tvalsel[%d]=%d\n",k, k1, nres, k1,precov[nres][k1], k1, Tvar[k1], k3,(int)Tvarsel[k3], k3, (int)Tvalsel[k3]);
	}else if( Dummy[k1]==3 ){ /* For quant with age product */
	k3q= resultmodel[nres][k1]; /* resultmodel[1(V5)] = 25.1=k3q */
	k2q=(int)Tvarsel[k3q]; /* Tvarsel[resultmodel[1]]= Tvarsel[1] = 4=k2 */
	TinvDoQresult[nres][(int)Tvarsel[k3q]]=Tvalsel[k3q]; /* Tqinvresult[nres][5]=25.1 */
	precov[nres][k1]=Tvalsel[k3q];
	printf("Decoderesult Quantitative with age nres=%d, k1=%d, precov[nres=%d][k1=%d]=%.f Tvar[%d]=V%d V(k2q=%d)= Tvarsel[%d]=%d, Tvalsel[%d]=%f\n",nres, k1, nres, k1,precov[nres][k1], k1, Tvar[k1], k2q, k3q, Tvarsel[k3q], k3q, Tvalsel[k3q]);
	}else if(Typevar[k1]==2 ){ /* For product quant or dummy (not with age) */
	precov[nres][k1]=TinvDoQresult[nres][Tvardk[k1][1]] * TinvDoQresult[nres][Tvardk[k1][2]];
	printf("Decoderesult Quantitative or Dummy (not with age) nres=%d k1=%d precov[nres=%d][k1=%d]=%.f V%d(=%.f) * V%d(=%.f) \n",nres, k1, nres, k1,precov[nres][k1], Tvardk[k1][1], TinvDoQresult[nres][Tvardk[k1][1]], Tvardk[k1][2], TinvDoQresult[nres][Tvardk[k1][2]]);
	}else{
	printf("Error Decoderesult probably a product Dummy[%d]==%d && Typevar[%d]==%d\n", k1, Dummy[k1], k1, Typevar[k1]);
	fprintf(ficlog,"Error Decoderesult probably a product Dummy[%d]==%d && Typevar[%d]==%d\n", k1, Dummy[k1], k1, Typevar[k1]);
}	}
}	}

Line 9429 int decodemodel( char model[], int lasto	Line 10495 int decodemodel( char model[], int lasto
* - cptcovs number of simple covariates	* - cptcovs number of simple covariates
* - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10	* - Tvar[k] is the id of the kth covariate Tvar[1]@12 {1, 2, 3, 8, 10, 11, 8, 3, 7, 8, 5, 6}, thus Tvar[5=V7*V8]=10
* which is a new column after the 9 (ncovcol) variables.	* which is a new column after the 9 (ncovcol) variables.
* - if k is a product Vn*Vm covar[k][i] is filled with correct values for each individual	* - if k is a product Vn*Vm, covar[k][i] is filled with correct values for each individual
* - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage	* - Tprod[l] gives the kth covariates of the product Vn*Vm l=1 to cptcovprod-cptcovage
* Tprod[1]@2 {5, 6}: position of first product V7V8 is 5, and second V5V6 is 6.	* Tprod[1]@2 {5, 6}: position of first product V7V8 is 5, and second V5V6 is 6.
* - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7V8 and V5V6 .	* - Tvard[k] p Tvard[1][1]@4 {7, 8, 5, 6} for V7V8 and V5V6 .
*/	*/
	/* V2+V1+V4+V3age Tvar[4]=3 ; V1+V2age Tvar[2]=2; V1+V1age Tvar[2]=1, Tage[1]=2 /
{	{
int i, j, k, ks, v;	int i, j, k, ks, v;
int j1, k1, k2, k3, k4;	int j1, k1, k2, k3, k4;
Line 9511 int decodemodel( char model[], int lasto	Line 10578 int decodemodel( char model[], int lasto
* Model V2 + V1 + V3age + V3 + V5V6 + V7V8 + V8age + V8 d1 d1 d2 d2	* Model V2 + V1 + V3age + V3 + V5V6 + V7V8 + V8age + V8 d1 d1 d2 d2
* k= 1 2 3 4 5 6 7 8 9 10 11 12	* k= 1 2 3 4 5 6 7 8 9 10 11 12
* Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8	* Tvar[k]= 2 1 3 3 10 11 8 8 5 6 7 8
* p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}	* p Tvar[1]@12={2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
* p Tprod[1]@2={ 6, 5}	* p Tprod[1]@2={ 6, 5}
*p Tvard[1][1]@4= {7, 8, 5, 6}	*p Tvard[1][1]@4= {7, 8, 5, 6}
* covar[k][i]= V2 V1 ? V3 V5V6? V7V8? ? V8	* covar[k][i]= V2 V1 ? V3 V5V6? V7V8? ? V8
* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];	* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
*How to reorganize?	*How to reorganize? Tvars(orted)
* Model V1 + V2 + V3 + V8 + V5V6 + V7V8 + V3age + V8age	* Model V1 + V2 + V3 + V8 + V5V6 + V7V8 + V3age + V8age
* Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}	* Tvars {2, 1, 3, 3, 11, 10, 8, 8, 7, 8, 5, 6}
* {2, 1, 4, 8, 5, 6, 3, 7}	* {2, 1, 4, 8, 5, 6, 3, 7}
Line 9541 int decodemodel( char model[], int lasto	Line 10608 int decodemodel( char model[], int lasto
Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;	Tvar[k]=0; Tprod[k]=0; Tposprod[k]=0;
}	}
cptcovage=0;	cptcovage=0;
for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model */	for(k=1; k<=cptcovt;k++){ /* Loop on total covariates of the model line */
cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+'	cutl(stra,strb,modelsav,'+'); /* keeps in strb after the first '+' cutl from left to right
modelsav==V2+V1+V4+V3age strb=V3age stra=V2+V1+V4 */	modelsav==V2+V1+V5age+V4+V3age strb=V3age stra=V2+V1V5age+V4 / / <model> "V5+V4+V3+V4V3+V5age+V1age+V1" strb="V5" stra="V4+V3+V4V3+V5age+V1age+V1" */
if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */	if (nbocc(modelsav,'+')==0)
	strcpy(strb,modelsav); /* and analyzes it */
/* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/	/* printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
/scanf("%d",i);/	/scanf("%d",i);/
if (strchr(strb,'')) { /< Model includes a product V2+V1+V4+V3age strb=V3age /	if (strchr(strb,'')) { /< Model includes a product V2+V1+V5age+ V4+V3age strb=V3age */
cutl(strc,strd,strb,''); /< strdstrc VmVn: strb=V3age(input) strc=age strd=V3 ; V3V2 strc=V2, strd=V3 /	cutl(strc,strd,strb,''); /< k=1 strdstrc VmVn: strb=V3age(input) strc=age strd=V3 ; V3V2 strc=V2, strd=V3 /
if (strcmp(strc,"age")==0) { /*< Model includes age: Vnage */	if (strcmp(strc,"age")==0) { /*< Model includes age: Vnage */
/* covar is not filled and then is empty */	/* covar is not filled and then is empty */
cptcovprod--;	cptcovprod--;
cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */	cutl(stre,strb,strd,'V'); /* strd=V3(input): stre="3" */
Tvar[k]=atoi(stre); /* V2+V1+V4+V3age Tvar[4]=3 ; V1+V2age Tvar[2]=2; V1+V1age Tvar[2]=1 /	Tvar[k]=atoi(stre); /* V2+V1+V5age+V4+V3age Tvar[5]=3 ; V1+V2age Tvar[2]=2; V1+V1age Tvar[2]=1 */
Typevar[k]=1; /* 1 for age product */	Typevar[k]=1; /* 1 for age product */
cptcovage++; /* Sums the number of covariates which include age as a product */	cptcovage++; /* Counts the number of covariates which include age as a product */
Tage[cptcovage]=k; /* Tvar[4]=3, Tage[1] = 4 or V1+V1age Tvar[2]=1, Tage[1]=2 /	Tage[cptcovage]=k; /* V2+V1+V4+V3age Tvar[4]=3, Tage[1] = 4 or V1+V1age Tvar[2]=1, Tage[1]=2 */
/printf("stre=%s ", stre);/	/printf("stre=%s ", stre);/
} else if (strcmp(strd,"age")==0) { /* or ageVn /	} else if (strcmp(strd,"age")==0) { /* or ageVn /
cptcovprod--;	cptcovprod--;
Line 9573 int decodemodel( char model[], int lasto	Line 10641 int decodemodel( char model[], int lasto
Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but	Tvar[k]=ncovcol+nqv+ntv+nqtv+k1; /* For model-covariate k tells which data-covariate to use but
because this model-covariate is a construction we invent a new column	because this model-covariate is a construction we invent a new column
which is after existing variables ncovcol+nqv+ntv+nqtv + k1	which is after existing variables ncovcol+nqv+ntv+nqtv + k1
If already ncovcol=4 and model=V2+V1+V1V4+ageV3+V3*V2	If already ncovcol=4 and model=V2 + V1 +V1V4 +ageV3 +V3*V2
Tvar[3=V1V4]=4+1 Tvar[5=V3V2]=4 + 2= 6, etc */	thus after V4 we invent V5 and V6 because age*V3 will be computed in 4
	Tvar[3=V1V4]=4+1=5 Tvar[5=V3V2]=4 + 2= 6, Tvar[4=ageV3]=4 etc /
Typevar[k]=2; /* 2 for double fixed dummy covariates */	Typevar[k]=2; /* 2 for double fixed dummy covariates */
cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */	cutl(strc,strb,strd,'V'); /* strd was Vm, strc is m */
Tprod[k1]=k; /* Tprod[1]=3(=V1V4) for V2+V1+V1V4+ageV3+V3V2 */	Tprod[k1]=k; /* Tprod[1]=3(=V1V4) for V2+V1+V1V4+ageV3+V3V2 */
Tposprod[k]=k1; /* Tpsprod[3]=1, Tposprod[2]=5 */	Tposprod[k]=k1; /* Tposprod[3]=1, Tposprod[2]=5 */
Tvard[k1][1] =atoi(strc); /* m 1 for V1*/	Tvard[k1][1] =atoi(strc); /* m 1 for V1*/
	Tvardk[k][1] =atoi(strc); /* m 1 for V1*/
Tvard[k1][2] =atoi(stre); /* n 4 for V4*/	Tvard[k1][2] =atoi(stre); /* n 4 for V4*/
	Tvardk[k][2] =atoi(stre); /* n 4 for V4*/
k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in VnVm at the end of Tvar /	k2=k2+2; /* k2 is initialize to -1, We want to store the n and m in VnVm at the end of Tvar /
/* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) \/ /	/* Tvar[cptcovt+k2]=Tvard[k1][1]; /\* Tvar[(cptcovt=4+k2=1)=5]= 1 (V1) \/ /
/* Tvar[cptcovt+k2+1]=Tvard[k1][2]; /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) \/ /	/* Tvar[cptcovt+k2+1]=Tvard[k1][2]; /\* Tvar[(cptcovt=4+(k2=1)+1)=6]= 4 (V4) \/ /
Line 9593 int decodemodel( char model[], int lasto	Line 10664 int decodemodel( char model[], int lasto
}	}
} /* End age is not in the model */	} /* End age is not in the model */
} /* End if model includes a product */	} /* End if model includes a product */
else { /* no more sum */	else { /* not a product */
/printf("d=%s c=%s b=%s\n", strd,strc,strb);/	/printf("d=%s c=%s b=%s\n", strd,strc,strb);/
/* scanf("%d",i);*/	/* scanf("%d",i);*/
cutl(strd,strc,strb,'V');	cutl(strd,strc,strb,'V');
Line 9624 int decodemodel( char model[], int lasto	Line 10695 int decodemodel( char model[], int lasto
model= V5 + V4 +V3 + V4V3 + V5age + V2 + V1V2 + V1age + V5*age, V1 is not used saving its place	model= V5 + V4 +V3 + V4V3 + V5age + V2 + V1V2 + V1age + V5*age, V1 is not used saving its place
k = 1 2 3 4 5 6 7 8 9	k = 1 2 3 4 5 6 7 8 9
Tvar[k]= 5 4 3 1+1+2+1+1=6 5 2 7 1 5	Tvar[k]= 5 4 3 1+1+2+1+1=6 5 2 7 1 5
Typevar[k]= 0 0 0 2 1 0 2 1 1	Typevar[k]= 0 0 0 2 1 0 2 1 0
Fixed[k] 1 1 1 1 3 0 0 or 2 2 3	Fixed[k] 1 1 1 1 3 0 0 or 2 2 3
Dummy[k] 1 0 0 0 3 1 1 2 3	Dummy[k] 1 0 0 0 3 1 1 2 3
Tmodelind[combination of covar]=k;	Tmodelind[combination of covar]=k;
Line 9633 int decodemodel( char model[], int lasto	Line 10704 int decodemodel( char model[], int lasto
/* If Tvar[k] >ncovcol it is a product */	/* If Tvar[k] >ncovcol it is a product */
/* 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=%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 \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=%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 \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<=cptcovt; 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, ncovf=0, nsd=0, nsq=0, ncovv=0, ncova=0, ncoveff=0, nqfveff=0, ntveff=0, nqtveff=0;k<=cptcovt; k++){ /* or cptocvt */
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;
Line 9652 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 10723 Dummy[k] 0=dummy (0 1), 1 quantitative (
modell[k].maintype= FTYPE;	modell[k].maintype= FTYPE;
TvarsD[nsd]=Tvar[k];	TvarsD[nsd]=Tvar[k];
TvarsDind[nsd]=k;	TvarsDind[nsd]=k;
	TnsdVar[Tvar[k]]=nsd;
TvarF[ncovf]=Tvar[k];	TvarF[ncovf]=Tvar[k];
TvarFind[ncovf]=k;	TvarFind[ncovf]=k;
TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */	TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
Line 9663 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 10735 Dummy[k] 0=dummy (0 1), 1 quantitative (
ncovf++;	ncovf++;
modell[k].maintype= FTYPE;	modell[k].maintype= FTYPE;
TvarF[ncovf]=Tvar[k];	TvarF[ncovf]=Tvar[k];
	/* TnsdVar[Tvar[k]]=nsd; / / To be done */
TvarFind[ncovf]=k;	TvarFind[ncovf]=k;
TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */	TvarFD[ncoveff]=Tvar[k]; /* TvarFD[1]=V1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */	TvarFDind[ncoveff]=k; /* TvarFDind[1]=9 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 */
Line 9689 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 10762 Dummy[k] 0=dummy (0 1), 1 quantitative (
nsd++;	nsd++;
TvarsD[nsd]=Tvar[k];	TvarsD[nsd]=Tvar[k];
TvarsDind[nsd]=k;	TvarsDind[nsd]=k;
	TnsdVar[Tvar[k]]=nsd; /* To be verified */
ncovv++; /* Only simple time varying variables */	ncovv++; /* Only simple time varying variables */
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k; /* TvarVind[2]=2 TvarVind[3]=3 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Any time varying singele */	TvarVind[ncovv]=k; /* TvarVind[2]=2 TvarVind[3]=3 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Any time varying singele */
Line 9704 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 10778 Dummy[k] 0=dummy (0 1), 1 quantitative (
modell[k].subtype= VQ;	modell[k].subtype= VQ;
ncovv++; /* Only simple time varying variables */	ncovv++; /* Only simple time varying variables */
nsq++;	nsq++;
TvarsQ[nsq]=Tvar[k];	TvarsQ[nsq]=Tvar[k]; /* k=1 Tvar=5 nsq=1 TvarsQ[1]=5 */
TvarsQind[nsq]=k;	TvarsQind[nsq]=k; /* For single quantitative covariate gives the model position of each single quantitative covariate */
TvarV[ncovv]=Tvar[k];	TvarV[ncovv]=Tvar[k];
TvarVind[ncovv]=k; /* TvarVind[1]=1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Any time varying singele */	TvarVind[ncovv]=k; /* TvarVind[1]=1 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Any time varying singele */
TvarVQ[nqtveff]=Tvar[k]; /* TvarVQ[1]=V5 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple time varying quantitative variable */	TvarVQ[nqtveff]=Tvar[k]; /* TvarVQ[1]=V5 in V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1 / / Only simple time varying quantitative variable */
Line 9891 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 10965 Dummy[k] 0=dummy (0 1), 1 quantitative (
/* 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++){
if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[k2]] )){	/* if((Typevar[k1]==Typevar[k2]) && (Fixed[Tvar[k1]]==Fixed[Tvar[k2]]) && (Dummy[Tvar[k1]]==Dummy[Tvar[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[Tvar[k1]],Dummy[Tvar[k1]]);	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]);
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[Tvar[k1]],Dummy[Tvar[k1]]); fflush(ficlog);	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);
return(1);	return(1);
}	}
}else if (Typevar[k1] ==2){	}else if (Typevar[k1] ==2){
Line 10067 BOOL IsWow64()	Line 11142 BOOL IsWow64()
#endif	#endif

void syscompilerinfo(int logged)	void syscompilerinfo(int logged)
{	{
/* #include "syscompilerinfo.h"*/	#include <stdint.h>

	/* #include "syscompilerinfo.h"*/
/* command line Intel compiler 32bit windows, XP compatible:*/	/* command line Intel compiler 32bit windows, XP compatible:*/
/* /GS /W3 /Gy	/* /GS /W3 /Gy
/Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D	/Zc:wchar_t /Zi /O2 /Fd"Release\vc120.pdb" /D "WIN32" /D "NDEBUG" /D
Line 10103 void syscompilerinfo(int logged)	Line 11180 void syscompilerinfo(int logged)
/ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF	/ManifestFile:"Release\IMaCh.exe.intermediate.manifest" /OPT:ICF
/NOLOGO /TLBID:1	/NOLOGO /TLBID:1
*/	*/


#if defined __INTEL_COMPILER	#if defined __INTEL_COMPILER
#if defined(__GNUC__)	#if defined(__GNUC__)
struct utsname sysInfo; /* For Intel on Linux and OS/X */	struct utsname sysInfo; /* For Intel on Linux and OS/X */
Line 10119 void syscompilerinfo(int logged)	Line 11198 void syscompilerinfo(int logged)
}	}
#endif	#endif

#include <stdint.h>

printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");	printf("Compiled with:");if(logged)fprintf(ficlog,"Compiled with:");
#if defined(__clang__)	#if defined(__clang__)
printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */	printf(" Clang/LLVM");if(logged)fprintf(ficlog," Clang/LLVM"); /* Clang/LLVM. ---------------------------------------------- */
Line 10206 void syscompilerinfo(int logged)	Line 11283 void syscompilerinfo(int logged)
#endif	#endif
#endif	#endif

// void main()	// void main ()
// {	// {
#if defined(_MSC_VER)	#if defined(_MSC_VER)
if (IsWow64()){	if (IsWow64()){
Line 10227 void syscompilerinfo(int logged)	Line 11304 void syscompilerinfo(int logged)
}	}

int prevalence_limit(double p, double prlim, double ageminpar, double agemaxpar, double ftolpl, int ncvyearp){	int prevalence_limit(double p, double prlim, double ageminpar, double agemaxpar, double ftolpl, int ncvyearp){
/--------------- Prevalence limit (period or stable prevalence) --------------/	/--------------- Prevalence limit (forward period or forward stable prevalence) --------------/
	/* Computes the prevalence limit for each combination of the dummy covariates */
int i, j, k, i1, k4=0, nres=0 ;	int i, j, k, i1, k4=0, nres=0 ;
/* double ftolpl = 1.e-10; */	/* double ftolpl = 1.e-10; */
double age, agebase, agelim;	double age, agebase, agelim;
Line 10236 int prevalence_limit(double p, double	Line 11314 int prevalence_limit(double p, double
strcpy(filerespl,"PL_");	strcpy(filerespl,"PL_");
strcat(filerespl,fileresu);	strcat(filerespl,fileresu);
if((ficrespl=fopen(filerespl,"w"))==NULL) {	if((ficrespl=fopen(filerespl,"w"))==NULL) {
printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;	printf("Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);return 1;	fprintf(ficlog,"Problem with forward period (stable) prevalence resultfile: %s\n", filerespl);return 1;
}	}
printf("\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);	printf("\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
fprintf(ficlog,"\nComputing period (stable) prevalence: result on file '%s' \n", filerespl);	fprintf(ficlog,"\nComputing forward period (stable) prevalence: result on file '%s' \n", filerespl);
pstamp(ficrespl);	pstamp(ficrespl);
fprintf(ficrespl,"# Period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);	fprintf(ficrespl,"# Forward period (stable) prevalence. Precision given by ftolpl=%g \n", ftolpl);
fprintf(ficrespl,"#Age ");	fprintf(ficrespl,"#Age ");
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,"\n");	fprintf(ficrespl,"\n");
Line 10266 int prevalence_limit(double p, double	Line 11344 int prevalence_limit(double p, double
//for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){	//for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
/* k=k+1; */	/* k=k+1; */
/* to clean */	/* to clean */
//printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));	/printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));/
fprintf(ficrespl,"#******");	fprintf(ficrespl,"#******");
printf("#******");	printf("#******");
fprintf(ficlog,"#******");	fprintf(ficlog,"#******");
for(j=1;j<=cptcoveff ;j++) {/* all covariates */	for(j=1;j<=cptcoveff ;j++) {/* all covariates */
fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); /* Here problem for varying dummy*/	/* fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,Tvaraff[j])]); /\* Here problem for varying dummy\/ /
printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]); /* Here problem for varying dummy*/
fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
	fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
Line 10292 int prevalence_limit(double p, double	Line 11371 int prevalence_limit(double p, double

fprintf(ficrespl,"#Age ");	fprintf(ficrespl,"#Age ");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcoveff;j++) {
fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficrespl,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
}	}
for(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");
Line 10302 int prevalence_limit(double p, double	Line 11381 int prevalence_limit(double p, double
prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);	prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, ncvyearp, k, nres);
fprintf(ficrespl,"%.0f ",age );	fprintf(ficrespl,"%.0f ",age );
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
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 10317 int prevalence_limit(double p, double	Line 11396 int prevalence_limit(double p, double
}	}

int back_prevalence_limit(double p, double bprlim, double ageminpar, double agemaxpar, double ftolpl, int ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj){	int back_prevalence_limit(double p, double bprlim, double ageminpar, double agemaxpar, double ftolpl, int ncvyearp, double dateprev1,double dateprev2, int firstpass, int lastpass, int mobilavproj){
/--------------- Back Prevalence limit (period or stable prevalence) --------------/	/--------------- Back Prevalence limit (backward stable prevalence) --------------/

/* Computes the back prevalence limit for any combination of covariate values	/* Computes the back prevalence limit for any combination of covariate values
* at any age between ageminpar and agemaxpar	* at any age between ageminpar and agemaxpar
Line 10332 int back_prevalence_limit(double *p, dou	Line 11411 int back_prevalence_limit(double *p, dou
strcpy(fileresplb,"PLB_");	strcpy(fileresplb,"PLB_");
strcat(fileresplb,fileresu);	strcat(fileresplb,fileresu);
if((ficresplb=fopen(fileresplb,"w"))==NULL) {	if((ficresplb=fopen(fileresplb,"w"))==NULL) {
printf("Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;	printf("Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
fprintf(ficlog,"Problem with period (stable) back prevalence resultfile: %s\n", fileresplb);return 1;	fprintf(ficlog,"Problem with backward prevalence resultfile: %s\n", fileresplb);return 1;
}	}
printf("Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);	printf("Computing backward prevalence: result on file '%s' \n", fileresplb);
fprintf(ficlog,"Computing period (stable) back prevalence: result on file '%s' \n", fileresplb);	fprintf(ficlog,"Computing backward prevalence: result on file '%s' \n", fileresplb);
pstamp(ficresplb);	pstamp(ficresplb);
fprintf(ficresplb,"# Period (stable) back prevalence. Precision given by ftolpl=%g \n", ftolpl);	fprintf(ficresplb,"# Backward prevalence. Precision given by ftolpl=%g \n", ftolpl);
fprintf(ficresplb,"#Age ");	fprintf(ficresplb,"#Age ");
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,"\n");	fprintf(ficresplb,"\n");
Line 10357 int back_prevalence_limit(double *p, dou	Line 11436 int back_prevalence_limit(double *p, dou
for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */	for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
if(i1 != 1 && TKresult[nres]!= k)	if(i1 != 1 && TKresult[nres]!= k)
continue;	continue;
//printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));	/printf("cptcov=%d cptcod=%d codtab=%d\n",cptcov, cptcod,codtabm(cptcod,cptcov));/
fprintf(ficresplb,"#******");	fprintf(ficresplb,"#******");
printf("#******");	printf("#******");
fprintf(ficlog,"#******");	fprintf(ficlog,"#******");
for(j=1;j<=cptcoveff ;j++) {/* all covariates */	for(j=1;j<=cptcoveff ;j++) {/* all covariates */
fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresplb," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
}	}
for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */	for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	fprintf(ficresplb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
}	}
fprintf(ficresplb,"******\n");	fprintf(ficresplb,"******\n");
printf("******\n");	printf("******\n");
Line 10383 int back_prevalence_limit(double *p, dou	Line 11462 int back_prevalence_limit(double *p, dou

fprintf(ficresplb,"#Age ");	fprintf(ficresplb,"#Age ");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcoveff;j++) {
fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresplb,"V%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
}	}
for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);	for(i=1; i<=nlstate;i++) fprintf(ficresplb," %d-%d ",i,i);
fprintf(ficresplb,"Total Years_to_converge\n");	fprintf(ficresplb,"Total Years_to_converge\n");
Line 10407 int back_prevalence_limit(double *p, dou	Line 11486 int back_prevalence_limit(double *p, dou
}	}
fprintf(ficresplb,"%.0f ",age );	fprintf(ficresplb,"%.0f ",age );
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresplb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
tot=0.;	tot=0.;
for(i=1; i<=nlstate;i++){	for(i=1; i<=nlstate;i++){
tot += bprlim[i][i];	tot += bprlim[i][i];
Line 10465 int hPijx(double *p, int bage, int fage)	Line 11544 int hPijx(double *p, int bage, int fage)
continue;	continue;
fprintf(ficrespij,"\n#****** ");	fprintf(ficrespij,"\n#****** ");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	printf(" V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficrespij," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
Line 10527 int hPijx(double *p, int bage, int fage)	Line 11606 int hPijx(double *p, int bage, int fage)
/if (stepm<=24) stepsize=2;/	/if (stepm<=24) stepsize=2;/

/* agelim=AGESUP; */	/* agelim=AGESUP; */
ageminl=30;	ageminl=AGEINF; /* was 30 */
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 */

Line 10544 int hPijx(double *p, int bage, int fage)	Line 11623 int hPijx(double *p, int bage, int fage)
continue;	continue;
fprintf(ficrespijb,"\n#****** ");	fprintf(ficrespijb,"\n#****** ");
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficrespijb,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficrespijb,"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 */
fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	fprintf(ficrespijb," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
}	}
fprintf(ficrespijb,"******\n");	fprintf(ficrespijb,"******\n");
if(invalidvarcomb[k]){ /* Is it necessary here? */	if(invalidvarcomb[k]){ /* Is it necessary here? */
Line 10557 int hPijx(double *p, int bage, int fage)	Line 11636 int hPijx(double *p, int bage, int fage)
/* for (agedeb=fage; agedeb>=bage; agedeb--){ /\* If stepm=6 months \/ /	/* 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) */	for (agedeb=bage; agedeb<=fage; agedeb++){ /* If stepm=6 months and estepm=24 (2 years) */
/* nhstepm=(int) rint((agelim-agedeb)YEARM/stepm); /\ Typically 20 years = 2012/6=40 \/ */	/* nhstepm=(int) rint((agelim-agedeb)YEARM/stepm); /\ Typically 20 years = 2012/6=40 \/ */
nhstepm=(int) rint((agedeb-ageminl)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 */	nhstepm = nhstepm/hstepm; /* Typically 40/4=10, because estepm=24 stepm=6 => hstepm=24/6=4 or 28*/

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

Line 10567 int hPijx(double *p, int bage, int fage)	Line 11646 int hPijx(double *p, int bage, int fage)

/* oldm=oldms;savm=savms; */	/* oldm=oldms;savm=savms; */
/* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */	/* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);	hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);/* Bug valgrind */
/* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */	/* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");	fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
Line 10580 int hPijx(double *p, int bage, int fage)	Line 11659 int hPijx(double *p, int bage, int fage)
/* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + hhstepm/YEARMstepm ); */	/* fprintf(ficrespijb,"%d %3.f %3.f",k, agedeb, agedeb + hhstepm/YEARMstepm ); */
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate+ndeath;j++)	for(j=1; j<=nlstate+ndeath;j++)
fprintf(ficrespijb," %.5f", p3mat[i][j][h]);	fprintf(ficrespijb," %.5f", p3mat[i][j][h]);/* Bug valgrind */
fprintf(ficrespijb,"\n");	fprintf(ficrespijb,"\n");
}	}
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
Line 10606 int main(int argc, char *argv[])	Line 11685 int main(int argc, char *argv[])
double ssval;	double ssval;
#endif	#endif
int movingaverage(double *probs, double bage,double fage, double *mobaverage, int mobilav);	int movingaverage(double *probs, double bage,double fage, double *mobaverage, int mobilav);
int i,j, k, n=MAXN,iter=0,m,size=100, cptcod;	int i,j, k, iter=0,m,size=100, cptcod; /* Suppressing because nobs */
	/* int i,j, k, n=MAXN,iter=0,m,size=100, cptcod; */
int ncvyear=0; /* Number of years needed for the period prevalence to converge */	int ncvyear=0; /* Number of years needed for the period prevalence to converge */
int jj, ll, li, lj, lk;	int jj, ll, li, lj, lk;
int numlinepar=0; /* Current linenumber of parameter file */	int numlinepar=0; /* Current linenumber of parameter file */
Line 10632 int main(int argc, char *argv[])	Line 11712 int main(int argc, char *argv[])
double dum=0.; /* Dummy variable */	double dum=0.; /* Dummy variable */
double ***p3mat;	double ***p3mat;
/* double **mobaverage; /	/* double **mobaverage; /
	double wald;

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

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

char pathr[MAXLINE], pathimach[MAXLINE];	char pathr[MAXLINE], pathimach[MAXLINE];
char tok, val; /* pathtot */	char tok, val; /* pathtot */
int firstobs=1, lastobs=10;	int firstobs=1, lastobs=10; /* nobs = lastobs-firstobs declared globally ;*/
int c, h , cpt, c2;	int c, h , cpt, c2;
int jl=0;	int jl=0;
int i1, j1, jk, stepsize=0;	int i1, j1, jk, stepsize=0;
Line 10649 int main(int argc, char *argv[])	Line 11730 int main(int argc, char *argv[])

int *tab;	int *tab;
int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */	int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
int backcast=0;	/* double anprojd, mprojd, jprojd; /\* For eventual projections \/ /
	/* double anprojf, mprojf, jprojf; */
	/* double jintmean,mintmean,aintmean; */
	int prvforecast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
	int prvbackcast = 0; /* Might be 1 (date of beginning of projection is a choice or 2 is the dateintmean */
	double yrfproj= 10.0; /* Number of years of forward projections */
	double yrbproj= 10.0; /* Number of years of backward projections */
	int prevbcast=0; /* defined as global for mlikeli and mle, replacing backcast */
int mobilav=0,popforecast=0;	int mobilav=0,popforecast=0;
int hstepm=0, nhstepm=0;	int hstepm=0, nhstepm=0;
int agemortsup;	int agemortsup;
Line 10661 int main(int argc, char *argv[])	Line 11749 int main(int argc, char *argv[])
double ftolpl=FTOL;	double ftolpl=FTOL;
double **prlim;	double **prlim;
double **bprlim;	double **bprlim;
double **param; / Matrix of parameters */	double **param; / Matrix of parameters, param[i][j][k] param=ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel)
	state of origin, state of destination including death, for each covariate: constante, age, and V1 V2 etc. */
double **paramstart; / Matrix of starting parameter values */	double **paramstart; / Matrix of starting parameter values */
double p, pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */	double p, pstart; /* p=param[1][1] pstart is for starting values guessed by freqsummary */
double *matcov; / Matrix of covariance */	double *matcov; / Matrix of covariance */
Line 10674 int main(int argc, char *argv[])	Line 11763 int main(int argc, char *argv[])
double *epj, vepp;	double *epj, vepp;

double dateprev1, dateprev2;	double dateprev1, dateprev2;
double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0;	double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0, dateprojd=0, dateprojf=0;
double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=0;	double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=0, datebackd=0, datebackf=0;


double **ximort;	double **ximort;
char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";	char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
Line 10753 int main(int argc, char *argv[])	Line 11843 int main(int argc, char *argv[])
if(pathr[0] == '\0') break; /* Dirty */	if(pathr[0] == '\0') break; /* Dirty */
}	}
}	}
	else if (argc<=2){
	strcpy(pathtot,argv[1]);
	}
else{	else{
strcpy(pathtot,argv[1]);	strcpy(pathtot,argv[1]);
	strcpy(z,argv[2]);
	printf("\nargv[2]=%s z=%c\n",argv[2],z[0]);
}	}
/if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");/	/if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");/
/*cygwin_split_path(pathtot,path,optionfile);	/*cygwin_split_path(pathtot,path,optionfile);
Line 10832 int main(int argc, char *argv[])	Line 11927 int main(int argc, char *argv[])
exit(70);	exit(70);
}	}



strcpy(filereso,"o");	strcpy(filereso,"o");
strcat(filereso,fileresu);	strcat(filereso,fileresu);
if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */	if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
Line 10842 int main(int argc, char *argv[])	Line 11935 int main(int argc, char *argv[])
fflush(ficlog);	fflush(ficlog);
goto end;	goto end;
}	}
	/-------- Rewriting parameter file ----------/
	strcpy(rfileres,"r"); /* "Rparameterfile */
	strcat(rfileres,optionfilefiname); /* Parameter file first name */
	strcat(rfileres,"."); /* */
	strcat(rfileres,optionfilext); /* Other files have txt extension */
	if((ficres =fopen(rfileres,"w"))==NULL) {
	printf("Problem writing new parameter file: %s\n", rfileres);goto end;
	fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
	fflush(ficlog);
	goto end;
	}
	fprintf(ficres,"#IMaCh %s\n",version);


/* Reads comments: lines beginning with '#' */	/* Reads comments: lines beginning with '#' */
numlinepar=0;	numlinepar=0;
/* Is it a BOM UTF-8 Windows file? */	/* Is it a BOM UTF-8 Windows file? */
Line 10854 int main(int argc, char *argv[])	Line 11960 int main(int argc, char *argv[])
noffset=noffset+3;	noffset=noffset+3;
printf("# File is an UTF8 Bom.\n"); // 0xBF	printf("# File is an UTF8 Bom.\n"); // 0xBF
}	}
else if( line[0] == (char)0xFE && line[1] == (char)0xFF)	/* else if( line[0] == (char)0xFE && line[1] == (char)0xFF)*/
	else if( line[0] == (char)0xFF && line[1] == (char)0xFE)
{	{
noffset=noffset+2;	noffset=noffset+2;
printf("# File is an UTF16BE BOM file\n");	printf("# File is an UTF16BE BOM file\n");
Line 10874 int main(int argc, char *argv[])	Line 11981 int main(int argc, char *argv[])
numlinepar++;	numlinepar++;
fputs(line,stdout);	fputs(line,stdout);
fputs(line,ficparo);	fputs(line,ficparo);
	fputs(line,ficres);
fputs(line,ficlog);	fputs(line,ficlog);
continue;	continue;
}else	}else
Line 10883 int main(int argc, char *argv[])	Line 11991 int main(int argc, char *argv[])
title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){	title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
if (num_filled != 5) {	if (num_filled != 5) {
printf("Should be 5 parameters\n");	printf("Should be 5 parameters\n");
	fprintf(ficlog,"Should be 5 parameters\n");
}	}
numlinepar++;	numlinepar++;
printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);	printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
	fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
	fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
	fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
}	}
/* Second parameter line */	/* Second parameter line */
while(fgets(line, MAXLINE, ficpar)) {	while(fgets(line, MAXLINE, ficpar)) {
/* If line starts with a # it is a comment */	/* while(fscanf(ficpar,"%[^\n]", line)) { */
	/* If line starts with a # it is a comment. Strangely fgets reads the EOL and fputs doesn't */
if (line[0] == '#') {	if (line[0] == '#') {
numlinepar++;	numlinepar++;
fputs(line,stdout);	printf("%s",line);
fputs(line,ficparo);	fprintf(ficres,"%s",line);
fputs(line,ficlog);	fprintf(ficparo,"%s",line);
	fprintf(ficlog,"%s",line);
continue;	continue;
}else	}else
break;	break;
Line 10904 int main(int argc, char *argv[])	Line 12018 int main(int argc, char *argv[])
if (num_filled != 11) {	if (num_filled != 11) {
printf("Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");	printf("Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
printf("but line=%s\n",line);	printf("but line=%s\n",line);
	fprintf(ficlog,"Not 11 parameters, for example:ftol=1.e-8 stepm=12 ncovcol=2 nqv=1 ntv=2 nqtv=1 nlstate=2 ndeath=1 maxwav=3 mle=1 weight=1\n");
	fprintf(ficlog,"but line=%s\n",line);
	}
	if( lastpass > maxwav){
	printf("Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
	fprintf(ficlog,"Error (lastpass = %d) > (maxwav = %d)\n",lastpass, maxwav);
	fflush(ficlog);
	goto end;
}	}
printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);	printf("ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
	fprintf(ficparo,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
	fprintf(ficres,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, 0, weightopt);
	fprintf(ficlog,"ftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\n",ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, mle, weightopt);
}	}
/* ftolpl=6ftol1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit \/ /	/* ftolpl=6ftol1.e5; /\* 6.e-3 make convergences in less than 80 loops for the prevalence limit \/ /
/ftolpl=6.e-4; //* 6.e-3 make convergences in less than 80 loops for the prevalence limit */	/ftolpl=6.e-4; //* 6.e-3 make convergences in less than 80 loops for the prevalence limit */
Line 10914 int main(int argc, char *argv[])	Line 12039 int main(int argc, char *argv[])
/* If line starts with a # it is a comment */	/* If line starts with a # it is a comment */
if (line[0] == '#') {	if (line[0] == '#') {
numlinepar++;	numlinepar++;
fputs(line,stdout);	printf("%s",line);
fputs(line,ficparo);	fprintf(ficres,"%s",line);
fputs(line,ficlog);	fprintf(ficparo,"%s",line);
	fprintf(ficlog,"%s",line);
continue;	continue;
}else	}else
break;	break;
}	}
if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){	if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
if (num_filled == 0){	if (num_filled != 1){
printf("ERROR %d: Model should be at minimum 'model=1+age.' WITHOUT space:'%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.' WITHOUT space:'%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 if (num_filled != 1){
printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
model[0]='\0';	model[0]='\0';
goto end;	goto end;
}	}
Line 10942 int main(int argc, char *argv[])	Line 12063 int main(int argc, char *argv[])
}	}
/* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */	/* printf(" model=1+age%s modeltemp= %s, model=%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(ficres,"model=1+age+%s\n",model);fflush(stdout);
	fprintf(ficlog,"model=1+age+%s\n",model);fflush(stdout);
}	}
/* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */	/* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */
/* numlinepar=numlinepar+3; /\* In general \/ /	/* numlinepar=numlinepar+3; /\* In general \/ /
/* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */	/* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);	/* fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); */
fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);	/* fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); */
fflush(ficlog);	fflush(ficlog);
/* if(model[0]=='#'\|\| model[0]== '\0'){ */	/* if(model[0]=='#'\|\| model[0]== '\0'){ */
if(model[0]=='#'){	if(model[0]=='#'){
printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \	printf("Error in 'model' line: model should start with 'model=1+age+' and end without space \n \
'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+ageage+V1+V1age.' or \n \	'model=1+age+' or 'model=1+age+V1.' or 'model=1+age+ageage+V1+V1age' or \n \
'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \	'model=1+age+V1+V2' or 'model=1+age+V1+V2+V1*V2' etc. \n"); \
if(mle != -1){	if(mle != -1){
printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");	printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter vectors and subdiagonal covariance matrix.\n");
exit(1);	exit(1);
}	}
}	}
Line 10975 int main(int argc, char *argv[])	Line 12099 int main(int argc, char *argv[])
ungetc(c,ficpar);	ungetc(c,ficpar);


covar=matrix(0,NCOVMAX,1,n); /*< used in readdata /	covar=matrix(0,NCOVMAX,firstobs,lastobs); /*< used in readdata /
if(nqv>=1)coqvar=matrix(1,nqv,1,n); /*< Fixed quantitative covariate /	if(nqv>=1)coqvar=matrix(1,nqv,firstobs,lastobs); /*< Fixed quantitative covariate /
if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,1,n); /*< 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,1,n); /*< 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)/
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 11041 int main(int argc, char *argv[])	Line 12165 int main(int argc, char *argv[])
for(jj=1; jj <=nlstate+ndeath; jj++){	for(jj=1; jj <=nlstate+ndeath; jj++){
if(jj==i) continue;	if(jj==i) continue;
j++;	j++;
	while((c=getc(ficpar))=='#' && c!= EOF){
	ungetc(c,ficpar);
	fgets(line, MAXLINE, ficpar);
	numlinepar++;
	fputs(line,stdout);
	fputs(line,ficparo);
	fputs(line,ficlog);
	}
	ungetc(c,ficpar);
fscanf(ficpar,"%1d%1d",&i1,&j1);	fscanf(ficpar,"%1d%1d",&i1,&j1);
if ((i1 != i) \|\| (j1 != jj)){	if ((i1 != i) \|\| (j1 != jj)){
printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \	printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
Line 11177 Please run with mle=-1 to get a correct	Line 12310 Please run with mle=-1 to get a correct

fflush(ficlog);	fflush(ficlog);

/-------- Rewriting parameter file ----------/
strcpy(rfileres,"r"); /* "Rparameterfile */
strcat(rfileres,optionfilefiname); /* Parameter file first name*/
strcat(rfileres,"."); /* */
strcat(rfileres,optionfilext); /* Other files have txt extension */
if((ficres =fopen(rfileres,"w"))==NULL) {
printf("Problem writing new parameter file: %s\n", rfileres);goto end;
fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
}
fprintf(ficres,"#%s\n",version);
} /* End of mle != -3 */	} /* End of mle != -3 */

/* Main data	/* Main data
*/	*/
n= lastobs;	nobs=lastobs-firstobs+1; /* was = lastobs;*/
num=lvector(1,n);	/* num=lvector(1,n); */
moisnais=vector(1,n);	/* moisnais=vector(1,n); */
annais=vector(1,n);	/* annais=vector(1,n); */
moisdc=vector(1,n);	/* moisdc=vector(1,n); */
andc=vector(1,n);	/* andc=vector(1,n); */
weight=vector(1,n);	/* weight=vector(1,n); */
agedc=vector(1,n);	/* agedc=vector(1,n); */
cod=ivector(1,n);	/* cod=ivector(1,n); */
for(i=1;i<=n;i++){	/* for(i=1;i<=n;i++){ */
	num=lvector(firstobs,lastobs);
	moisnais=vector(firstobs,lastobs);
	annais=vector(firstobs,lastobs);
	moisdc=vector(firstobs,lastobs);
	andc=vector(firstobs,lastobs);
	weight=vector(firstobs,lastobs);
	agedc=vector(firstobs,lastobs);
	cod=ivector(firstobs,lastobs);
	for(i=firstobs;i<=lastobs;i++){
num[i]=0;	num[i]=0;
moisnais[i]=0;	moisnais[i]=0;
annais[i]=0;	annais[i]=0;
Line 11210 Please run with mle=-1 to get a correct	Line 12342 Please run with mle=-1 to get a correct
cod[i]=0;	cod[i]=0;
weight[i]=1.0; /* Equal weights, 1 by default */	weight[i]=1.0; /* Equal weights, 1 by default */
}	}
mint=matrix(1,maxwav,1,n);	mint=matrix(1,maxwav,firstobs,lastobs);
anint=matrix(1,maxwav,1,n);	anint=matrix(1,maxwav,firstobs,lastobs);
s=imatrix(1,maxwav+1,1,n); /* s[i][j] health state for wave i and individual j */	s=imatrix(1,maxwav+1,firstobs,lastobs); /* s[i][j] health state for wave i and individual j */
	printf("BUG ncovmodel=%d NCOVMAX=%d 2**ncovmodel=%f BUG\n",ncovmodel,NCOVMAX,pow(2,ncovmodel));
tab=ivector(1,NCOVMAX);	tab=ivector(1,NCOVMAX);
ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2*ncov; V1+V2+V3+V4=>16 /	ncodemax=ivector(1,NCOVMAX); /* Number of code per covariate; if O and 1 only, 2*ncov; V1+V2+V3+V4=>16 /
ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2*ncov; V1+V2+V3+V4=>16 /	ncodemaxwundef=ivector(1,NCOVMAX); /* Number of code per covariate; if - 1 O and 1 only, 2*ncov; V1+V2+V3+V4=>16 /
Line 11231 Please run with mle=-1 to get a correct	Line 12364 Please run with mle=-1 to get a correct

Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */	Tvar=ivector(1,NCOVMAX); /* Was 15 changed to NCOVMAX. */
TvarsDind=ivector(1,NCOVMAX); /* */	TvarsDind=ivector(1,NCOVMAX); /* */
	TnsdVar=ivector(1,NCOVMAX); /* */
TvarsD=ivector(1,NCOVMAX); /* */	TvarsD=ivector(1,NCOVMAX); /* */
TvarsQind=ivector(1,NCOVMAX); /* */	TvarsQind=ivector(1,NCOVMAX); /* */
TvarsQ=ivector(1,NCOVMAX); /* */	TvarsQ=ivector(1,NCOVMAX); /* */
Line 11273 Please run with mle=-1 to get a correct	Line 12407 Please run with mle=-1 to get a correct
Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1] and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm	Tvard=imatrix(1,NCOVMAX,1,2); /* n=Tvard[k1][1] and m=Tvard[k1][2] gives the couple n,m of the k1 th product Vn*Vm
* For V3V2 (in V2+V1+V1V4+ageV3+V3V2), V3*V2 position is 2nd.	* For V3V2 (in V2+V1+V1V4+ageV3+V3V2), V3*V2 position is 2nd.
* Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */	* Tvard[k1=2][1]=3 (V3) Tvard[k1=2][2]=2(V2) */
	Tvardk=imatrix(1,NCOVMAX,1,2);
Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + ageV4 + V3age	Tage=ivector(1,NCOVMAX); /* Gives the covariate id of covariates associated with age: V2 + V1 + ageV4 + V3age
4 covariates (3 plus signs)	4 covariates (3 plus signs)
Tage[1=V3age]= 4; Tage[2=ageV4] = 3	Tage[1=V3age]= 4; Tage[2=ageV4] = 3
*/	*/
	for(i=1;i<NCOVMAX;i++)
	Tage[i]=0;
Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an	Tmodelind=ivector(1,NCOVMAX);/** gives the k model position of an
* individual dummy, fixed or varying:	* individual dummy, fixed or varying:
* Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,	* Tmodelind[Tvaraff[3]]=9,Tvaraff[1]@9={4,
Line 11314 Please run with mle=-1 to get a correct	Line 12451 Please run with mle=-1 to get a correct


agegomp=(int)agemin;	agegomp=(int)agemin;
free_vector(moisnais,1,n);	free_vector(moisnais,firstobs,lastobs);
free_vector(annais,1,n);	free_vector(annais,firstobs,lastobs);
/* free_matrix(mint,1,maxwav,1,n);	/* free_matrix(mint,1,maxwav,1,n);
free_matrix(anint,1,maxwav,1,n);*/	free_matrix(anint,1,maxwav,1,n);*/
/* free_vector(moisdc,1,n); */	/* free_vector(moisdc,1,n); */
Line 11341 Please run with mle=-1 to get a correct	Line 12478 Please run with mle=-1 to get a correct
concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);	concatwav(wav, dh, bh, mw, s, agedc, agev, firstpass, lastpass, imx, nlstate, stepm);
/* Concatenates waves */	/* Concatenates waves */

free_vector(moisdc,1,n);	free_vector(moisdc,firstobs,lastobs);
free_vector(andc,1,n);	free_vector(andc,firstobs,lastobs);

/* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */	/* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);	nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);
Line 11380 Please run with mle=-1 to get a correct	Line 12517 Please run with mle=-1 to get a correct
* For k=4 covariates, h goes from 1 to m=2**k	* For k=4 covariates, h goes from 1 to m=2**k
* codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;	* codtabm(h,k)= (1 & (h-1) >> (k-1)) + 1;
* #define codtabm(h,k) (1 & (h-1) >> (k-1))+1	* #define codtabm(h,k) (1 & (h-1) >> (k-1))+1
* h\k 1 2 3 4	* h\k 1 2 3 4 * h-1\k-1 4 3 2 1
*______________________________	______________________________ ______________________
* 1 i=1 1 i=1 1 i=1 1 i=1 1	* 1 i=1 1 i=1 1 i=1 1 i=1 1 * 0 0 0 0 0
* 2 2 1 1 1	* 2 2 1 1 1 * 1 0 0 0 1
* 3 i=2 1 2 1 1	* 3 i=2 1 2 1 1 * 2 0 0 1 0
* 4 2 2 1 1	* 4 2 2 1 1 * 3 0 0 1 1
* 5 i=3 1 i=2 1 2 1	* 5 i=3 1 i=2 1 2 1 * 4 0 1 0 0
* 6 2 1 2 1	* 6 2 1 2 1 * 5 0 1 0 1
* 7 i=4 1 2 2 1	* 7 i=4 1 2 2 1 * 6 0 1 1 0
* 8 2 2 2 1	* 8 2 2 2 1 * 7 0 1 1 1
* 9 i=5 1 i=3 1 i=2 1 2	* 9 i=5 1 i=3 1 i=2 1 2 * 8 1 0 0 0
* 10 2 1 1 2	* 10 2 1 1 2 * 9 1 0 0 1
* 11 i=6 1 2 1 2	* 11 i=6 1 2 1 2 * 10 1 0 1 0
* 12 2 2 1 2	* 12 2 2 1 2 * 11 1 0 1 1
* 13 i=7 1 i=4 1 2 2	* 13 i=7 1 i=4 1 2 2 * 12 1 1 0 0
* 14 2 1 2 2	* 14 2 1 2 2 * 13 1 1 0 1
* 15 i=8 1 2 2 2	* 15 i=8 1 2 2 2 * 14 1 1 1 0
* 16 2 2 2 2	* 16 2 2 2 2 * 15 1 1 1 1
*/	*/
/* How to do the opposite? From combination h (=1 to 2*k) how to get the value on the covariates? /	/* How to do the opposite? From combination h (=1 to 2*k) how to get the value on the covariates? /
/* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4	/* from h=5 and m, we get then number of covariates k=log(m)/log(2)=4
* and the value of each covariate?	* and the value of each covariate?
Line 11489 Title=%s <br>Datafile=%s Firstpass=%d La	Line 12626 Title=%s <br>Datafile=%s Firstpass=%d La
optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);	optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
}	}

fprintf(fichtm,"<html><head>\n<head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n<title>IMaCh %s</title></head>\n <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n<font size=\"3\">Sponsored by Copyright (C) 2002-2015 <a href=http://www.ined.fr>INED</a>-EUROREVES-Institut de longévité-2013-2016-Japan Society for the Promotion of Sciences 日本学術振興会 (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - <a href=https://software.intel.com/en-us>Intel Software 2015-2018</a></font><br> \	fprintf(fichtm,"<html><head>\n<head>\n<meta charset=\"utf-8\"/><meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n<title>IMaCh %s</title></head>\n <body><font size=\"7\"><a href=http:/euroreves.ined.fr/imach>IMaCh for Interpolated Markov Chain</a> </font><br>\n<font size=\"3\">Sponsored by Copyright (C) 2002-2015 <a href=http://www.ined.fr>INED</a>-EUROREVES-Institut de longévité-2013-2022-Japan Society for the Promotion of Sciences 日本学術振興会 (<a href=https://www.jsps.go.jp/english/e-grants/>Grant-in-Aid for Scientific Research 25293121</a>) - <a href=https://software.intel.com/en-us>Intel Software 2015-2018</a></font><br> \
<hr size=\"2\" color=\"#EC5E5E\"> \n\	<hr size=\"2\" color=\"#EC5E5E\"> \n\
<font size=\"2\">IMaCh-%s <br> %s</font> \	<font size=\"2\">IMaCh-%s <br> %s</font> \
<hr size=\"2\" color=\"#EC5E5E\"> \n\	<hr size=\"2\" color=\"#EC5E5E\"> \n\
Line 11524 Title=%s <br>Datafile=%s Firstpass=%d La	Line 12661 Title=%s <br>Datafile=%s Firstpass=%d La
firstpass, lastpass, stepm, weightopt, model);	firstpass, lastpass, stepm, weightopt, model);

fprintf(fichtm,"\n");	fprintf(fichtm,"\n");
fprintf(fichtm,"<h4>Parameter line 2</h4><ul><li>Tolerance for the convergence of the likelihood: ftol=%f \n<li>Interval for the elementary matrix (in month): stepm=%d",\	fprintf(fichtm,"<h4>Parameter line 2</h4><ul><li>Tolerance for the convergence of the likelihood: ftol=%g \n<li>Interval for the elementary matrix (in month): stepm=%d",\
ftol, stepm);	ftol, stepm);
fprintf(fichtm,"\n<li>Number of fixed dummy covariates: ncovcol=%d ", ncovcol);	fprintf(fichtm,"\n<li>Number of fixed dummy covariates: ncovcol=%d ", ncovcol);
ncurrv=1;	ncurrv=1;
Line 11532 Title=%s <br>Datafile=%s Firstpass=%d La	Line 12669 Title=%s <br>Datafile=%s Firstpass=%d La
fprintf(fichtm,"\n<li> Number of fixed quantitative variables: nqv=%d ", nqv);	fprintf(fichtm,"\n<li> Number of fixed quantitative variables: nqv=%d ", nqv);
ncurrv=i;	ncurrv=i;
for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i);	for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i);
fprintf(fichtm,"\n<li> Number of time varying (wave varying) covariates: ntv=%d ", ntv);	fprintf(fichtm,"\n<li> Number of time varying (wave varying) dummy covariates: ntv=%d ", ntv);
ncurrv=i;	ncurrv=i;
for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i);	for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i);
fprintf(fichtm,"\n<li>Number of quantitative time varying covariates: nqtv=%d ", nqtv);	fprintf(fichtm,"\n<li>Number of time varying quantitative covariates: nqtv=%d ", nqtv);
ncurrv=i;	ncurrv=i;
for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", i);	for(i=ncurrv; i <=ncurrv-1+nqtv; i++) fprintf(fichtm,"V%d ", i);
fprintf(fichtm,"\n<li>Weights column \n<br>Number of alive states: nlstate=%d <br>Number of death states (not really implemented): ndeath=%d \n<li>Number of waves: maxwav=%d \n<li>Parameter for maximization (1), using parameter values (0), for design of parameters and variance-covariance matrix: mle=%d \n<li>Does the weight column be taken into account (1), or not (0): weight=%d</ul>\n", \	fprintf(fichtm,"\n<li>Weights column \n<br>Number of alive states: nlstate=%d <br>Number of death states (not really implemented): ndeath=%d \n<li>Number of waves: maxwav=%d \n<li>Parameter for maximization (1), using parameter values (0), for design of parameters and variance-covariance matrix: mle=%d \n<li>Does the weight column be taken into account (1), or not (0): weight=%d</ul>\n", \
Line 11545 Title=%s <br>Datafile=%s Firstpass=%d La	Line 12682 Title=%s <br>Datafile=%s Firstpass=%d La
<img src=\"%s_.svg\">", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));	<img src=\"%s_.svg\">", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));


fprintf(fichtm,"\n<h4>Some descriptive statistics </h4>\n<br>Total number of observations=%d <br>\n\	fprintf(fichtm,"\n<h4>Some descriptive statistics </h4>\n<br>Number of (used) observations=%d <br>\n\
Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\	Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\	Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
imx,agemin,agemax,jmin,jmax,jmean);	imx,agemin,agemax,jmin,jmax,jmean);
Line 11567 Interval (in months) between two waves:	Line 12704 Interval (in months) between two waves:
for(j=1;j<=NDIM;j++)	for(j=1;j<=NDIM;j++)
ximort[i][j]=0.;	ximort[i][j]=0.;
/* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */	/* ximort=gsl_matrix_alloc(1,NDIM,1,NDIM); */
cens=ivector(1,n);	cens=ivector(firstobs,lastobs);
ageexmed=vector(1,n);	ageexmed=vector(firstobs,lastobs);
agecens=vector(1,n);	agecens=vector(firstobs,lastobs);
dcwave=ivector(1,n);	dcwave=ivector(firstobs,lastobs);

for (i=1; i<=imx; i++){	for (i=1; i<=imx; i++){
dcwave[i]=-1;	dcwave[i]=-1;
Line 11604 Interval (in months) between two waves:	Line 12741 Interval (in months) between two waves:
ximort[i][j]=(i == j ? 1.0 : 0.0);	ximort[i][j]=(i == j ? 1.0 : 0.0);
}	}

/p[1]=0.0268; p[NDIM]=0.083;/	p[1]=0.0268; p[NDIM]=0.083;
/printf("%lf %lf", p[1], p[2]);/	/* printf("%lf %lf", p[1], p[2]); */


#ifdef GSL	#ifdef GSL
Line 11731 Interval (in months) between two waves:	Line 12868 Interval (in months) between two waves:
printf("%f [%f ; %f]\n",p[i],p[i]-2sqrt(matcov[i][i]),p[i]+2sqrt(matcov[i][i]));	printf("%f [%f ; %f]\n",p[i],p[i]-2sqrt(matcov[i][i]),p[i]+2sqrt(matcov[i][i]));
fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2sqrt(matcov[i][i]),p[i]+2sqrt(matcov[i][i]));	fprintf(ficlog,"%f [%f ; %f]\n",p[i],p[i]-2sqrt(matcov[i][i]),p[i]+2sqrt(matcov[i][i]));
}	}
lsurv=vector(1,AGESUP);	lsurv=vector(agegomp,AGESUP);
lpop=vector(1,AGESUP);	lpop=vector(agegomp,AGESUP);
tpop=vector(1,AGESUP);	tpop=vector(agegomp,AGESUP);
lsurv[agegomp]=100000;	lsurv[agegomp]=100000;

for (k=agegomp;k<=AGESUP;k++) {	for (k=agegomp;k<=AGESUP;k++) {
Line 11780 Please run with mle=-1 to get a correct	Line 12917 Please run with mle=-1 to get a correct
stepm, weightopt,\	stepm, weightopt,\
model,imx,p,matcov,agemortsup);	model,imx,p,matcov,agemortsup);

free_vector(lsurv,1,AGESUP);	free_vector(lsurv,agegomp,AGESUP);
free_vector(lpop,1,AGESUP);	free_vector(lpop,agegomp,AGESUP);
free_vector(tpop,1,AGESUP);	free_vector(tpop,agegomp,AGESUP);
free_matrix(ximort,1,NDIM,1,NDIM);	free_matrix(ximort,1,NDIM,1,NDIM);
free_ivector(cens,1,n);	free_ivector(dcwave,firstobs,lastobs);
free_vector(agecens,1,n);	free_vector(agecens,firstobs,lastobs);
free_ivector(dcwave,1,n);	free_vector(ageexmed,firstobs,lastobs);
	free_ivector(cens,firstobs,lastobs);
#ifdef GSL	#ifdef GSL
#endif	#endif
} /* Endof if mle==-3 mortality only */	} /* Endof if mle==-3 mortality only */
Line 11820 Please run with mle=-1 to get a correct	Line 12958 Please run with mle=-1 to get a correct
printf("\n");	printf("\n");

/--------- results files --------------/	/--------- results files --------------/
fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, weightopt,model);	/* fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nqv, ntv, nqtv, nlstate, ndeath, maxwav, weightopt,model); */


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

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

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


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

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

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

/* */	/* */
fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");	fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
Line 11982 Please run with mle=-1 to get a correct	Line 13202 Please run with mle=-1 to get a correct
fputs(line,stdout);	fputs(line,stdout);
fputs(line,ficparo);	fputs(line,ficparo);
fputs(line,ficlog);	fputs(line,ficlog);
	fputs(line,ficres);
continue;	continue;
}else	}else
break;	break;
Line 12027 Please run with mle=-1 to get a correct	Line 13248 Please run with mle=-1 to get a correct
fputs(line,stdout);	fputs(line,stdout);
fputs(line,ficparo);	fputs(line,ficparo);
fputs(line,ficlog);	fputs(line,ficlog);
	fputs(line,ficres);
continue;	continue;
}else	}else
break;	break;
Line 12052 Please run with mle=-1 to get a correct	Line 13274 Please run with mle=-1 to get a correct
fputs(line,stdout);	fputs(line,stdout);
fputs(line,ficparo);	fputs(line,ficparo);
fputs(line,ficlog);	fputs(line,ficlog);
	fputs(line,ficres);
continue;	continue;
}else	}else
break;	break;
Line 12074 Please run with mle=-1 to get a correct	Line 13297 Please run with mle=-1 to get a correct
}	}

/* Results */	/* Results */
	/* Value of covariate in each resultine will be compututed (if product) and sorted according to model rank */
	/* It is precov[] because we need the varying age in order to compute the real cov[] of the model equation */
	precov=matrix(1,MAXRESULTLINESPONE,1,NCOVMAX+1);
	endishere=0;
nresult=0;	nresult=0;
	parameterline=0;
do{	do{
if(!fgets(line, MAXLINE, ficpar)){	if(!fgets(line, MAXLINE, ficpar)){
endishere=1;	endishere=1;
parameterline=14;	parameterline=15;
}else if (line[0] == '#') {	}else if (line[0] == '#') {
/* If line starts with a # it is a comment */	/* If line starts with a # it is a comment */
numlinepar++;	numlinepar++;
fputs(line,stdout);	fputs(line,stdout);
fputs(line,ficparo);	fputs(line,ficparo);
fputs(line,ficlog);	fputs(line,ficlog);
	fputs(line,ficres);
continue;	continue;
}else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))	}else if(sscanf(line,"prevforecast=%[^\n]\n",modeltemp))
parameterline=11;	parameterline=11;
else if(sscanf(line,"backcast=%[^\n]\n",modeltemp))	else if(sscanf(line,"prevbackcast=%[^\n]\n",modeltemp))
parameterline=12;	parameterline=12;
else if(sscanf(line,"result:%[^\n]\n",modeltemp))	else if(sscanf(line,"result:%[^\n]\n",modeltemp)){
parameterline=13;	parameterline=13;
	}
else{	else{
parameterline=14;	parameterline=14;
}	}
switch (parameterline){	switch (parameterline){ /* =0 only if only comments */
case 11:	case 11:
if((num_filled=sscanf(line,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj)) !=EOF){	if((num_filled=sscanf(line,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj)) !=EOF && (num_filled == 8)){
if (num_filled != 8) {	fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
printf("Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mov_average=0\n, your line=%s . Probably you are running an older format.\n",num_filled,line);
goto end;
}
fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);	printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);	fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);	fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
/* day and month of proj2 are not used but only year anproj2.*/	/* day and month of proj2 are not used but only year anproj2.*/
dateproj1=anproj1+(mproj1-1)/12.+(jproj1-1)/365.;	dateproj1=anproj1+(mproj1-1)/12.+(jproj1-1)/365.;
dateproj2=anproj2+(mproj2-1)/12.+(jproj2-1)/365.;	dateproj2=anproj2+(mproj2-1)/12.+(jproj2-1)/365.;
	prvforecast = 1;
	}
	else if((num_filled=sscanf(line,"prevforecast=%d yearsfproj=%lf mobil_average=%d\n",&prevfcast,&yrfproj,&mobilavproj)) !=EOF){/* && (num_filled == 3))*/
	printf("prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
	fprintf(ficlog,"prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
	fprintf(ficres,"prevforecast=%d yearsfproj=%.2lf mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
	prvforecast = 2;
	}
	else {
	printf("Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevforecast=1 yearsfproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
	fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevforecast=1 starting-proj-date=1/1/1990 final-proj-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevforecast=1 yearproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
	goto end;
}	}
break;	break;
case 12:	case 12:
/fscanf(ficpar,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj);/	if((num_filled=sscanf(line,"prevbackcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&prevbcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj)) !=EOF && (num_filled == 8)){
if((num_filled=sscanf(line,"backcast=%d starting-back-date=%lf/%lf/%lf final-back-date=%lf/%lf/%lf mobil_average=%d\n",&backcast,&jback1,&mback1,&anback1,&jback2,&mback2,&anback2,&mobilavproj)) !=EOF){	fprintf(ficparo,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
if (num_filled != 8) {	printf("prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
printf("Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);	fprintf(ficlog,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:backcast=1 starting-back-date=1/1/1990 final-back-date=1/1/1970 mobil_average=1\n, your line=%s . Probably you are running an older format.\n",num_filled,line);	fprintf(ficres,"prevbackcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevbcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
goto end;	/* day and month of back2 are not used but only year anback2.*/
}
printf("backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
fprintf(ficparo,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
fprintf(ficlog,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
fprintf(ficres,"backcast=%d starting-back-date=%.lf/%.lf/%.lf final-back-date=%.lf/%.lf/%.lf mobil_average=%d\n",backcast,jback1,mback1,anback1,jback2,mback2,anback2,mobilavproj);
/* day and month of proj2 are not used but only year anproj2.*/
dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;	dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;
dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;	dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;
	prvbackcast = 1;
	}
	else if((num_filled=sscanf(line,"prevbackcast=%d yearsbproj=%lf mobil_average=%d\n",&prevbcast,&yrbproj,&mobilavproj)) ==3){/* && (num_filled == 3))*/
	printf("prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
	fprintf(ficlog,"prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
	fprintf(ficres,"prevbackcast=%d yearsbproj=%.2lf mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
	prvbackcast = 2;
	}
	else {
	printf("Error: Not 8 (data)parameters in line but %d, for example:prevbackcast=1 starting-back-date=1/1/1990 final-back-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevbackcast=1 yearsbproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
	fprintf(ficlog,"Error: Not 8 (data)parameters in line but %d, for example:prevbackcast=1 starting-back-date=1/1/1990 final-back-date=1/1/2000 mobil_average=0\nnor 3 (data)parameters, for example:prevbackcast=1 yearbproj=10 mobil_average=0. Your line=%s . You are running probably an older format.\n, ",num_filled,line);
	goto end;
}	}
break;	break;
case 13:	case 13:
if((num_filled=sscanf(line,"result:%[^\n]\n",resultline)) !=EOF){	num_filled=sscanf(line,"result:%[^\n]\n",resultlineori);
if (num_filled == 0){	nresult++; /* Sum of resultlines */
resultline[0]='\0';	printf("Result %d: result:%s\n",nresult, resultlineori);
printf("Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);	/* removefirstspace(&resultlineori); */
fprintf(ficlog,"Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);
break;	if(strstr(resultlineori,"v") !=0){
} else if (num_filled != 1){	printf("Error. 'v' must be in upper case 'V' result: %s ",resultlineori);
printf("ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);	fprintf(ficlog,"Error. 'v' must be in upper case result: %s ",resultlineori);fflush(ficlog);
fprintf(ficlog,"ERROR %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);	return 1;
}	}
nresult++; /* Sum of resultlines */	trimbb(resultline, resultlineori); /* Suppressing double blank in the resultline */
printf("Result %d: result=%s\n",nresult, resultline);	printf("Decoderesult resultline=\"%s\" resultlineori=\"%s\"\n", resultline, resultlineori);
if(nresult > MAXRESULTLINES){	if(nresult > MAXRESULTLINESPONE-1){
printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);	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\n",MAXRESULTLINES,nresult);	fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\nYou can use the 'r' parameter file '%s' which uses option mle=0 to get other results. ",MAXRESULTLINESPONE-1,nresult,rfileres);
goto end;	goto end;
}	}
decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
	if(!decoderesult(resultline, nresult)){ /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
fprintf(ficparo,"result: %s\n",resultline);	fprintf(ficparo,"result: %s\n",resultline);
fprintf(ficres,"result: %s\n",resultline);	fprintf(ficres,"result: %s\n",resultline);
fprintf(ficlog,"result: %s\n",resultline);	fprintf(ficlog,"result: %s\n",resultline);
break;	} else
case 14:	goto end;
if(ncovmodel >2 && nresult==0 ){	break;
printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);	case 14:
goto end;	printf("Error: Unknown command '%s'\n",line);
}	fprintf(ficlog,"Error: Unknown command '%s'\n",line);
break;	if(line[0] == ' ' \|\| line[0] == '\n'){
default:	printf("It should not be an empty line '%s'\n",line);
nresult=1;	fprintf(ficlog,"It should not be an empty line '%s'\n",line);
decoderesult(".",nresult ); /* No covariate */	}
	if(ncovmodel >=2 && nresult==0 ){
	printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
	fprintf(ficlog,"ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
}	}
	/* goto end; */
	break;
	case 15:
	printf("End of resultlines.\n");
	fprintf(ficlog,"End of resultlines.\n");
	break;
	default: /* parameterline =0 */
	nresult=1;
	decoderesult(".",nresult ); /* No covariate */
} /* End switch parameterline */	} /* End switch parameterline */
}while(endishere==0); /* End do */	}while(endishere==0); /* End do */

Line 12179 This is probably because your parameter	Line 13434 This is probably because your parameter
Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);	Please run with mle=-1 to get a correct covariance matrix.\n",ageminpar,agemaxpar);
}else{	}else{
/* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */	/* printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,fage, prevfcast, backcast, pathc,p, (int)anproj1-(int)agemin, (int)anback1-(int)agemax+1); */
printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, backcast, pathc,p, (int)anproj1-bage, (int)anback1-fage);	/* It seems that anprojd which is computed from the mean year at interview which is known yet because of freqsummary */
	/* date2dmy(dateintmean,&jintmean,&mintmean,&aintmean); / / Done in freqsummary */
	if(prvforecast==1){
	dateprojd=(jproj1+12mproj1+365anproj1)/365;
	jprojd=jproj1;
	mprojd=mproj1;
	anprojd=anproj1;
	dateprojf=(jproj2+12mproj2+365anproj2)/365;
	jprojf=jproj2;
	mprojf=mproj2;
	anprojf=anproj2;
	} else if(prvforecast == 2){
	dateprojd=dateintmean;
	date2dmy(dateprojd,&jprojd, &mprojd, &anprojd);
	dateprojf=dateintmean+yrfproj;
	date2dmy(dateprojf,&jprojf, &mprojf, &anprojf);
	}
	if(prvbackcast==1){
	datebackd=(jback1+12mback1+365anback1)/365;
	jbackd=jback1;
	mbackd=mback1;
	anbackd=anback1;
	datebackf=(jback2+12mback2+365anback2)/365;
	jbackf=jback2;
	mbackf=mback2;
	anbackf=anback2;
	} else if(prvbackcast == 2){
	datebackd=dateintmean;
	date2dmy(datebackd,&jbackd, &mbackd, &anbackd);
	datebackf=dateintmean-yrbproj;
	date2dmy(datebackf,&jbackf, &mbackf, &anbackf);
	}

	printinggnuplot(fileresu, optionfilefiname,ageminpar,agemaxpar,bage, fage, prevfcast, prevbcast, pathc,p, (int)anprojd-bage, (int)anbackd-fage);
}	}
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,backcast, estepm, \	model,imx,jmin,jmax,jmean,rfileres,popforecast,mobilav,prevfcast,mobilavproj,prevbcast, estepm, \
jprev1,mprev1,anprev1,dateprev1, dateproj1, dateback1,jprev2,mprev2,anprev2,dateprev2,dateproj2, dateback2);	jprev1,mprev1,anprev1,dateprev1, dateprojd, datebackd,jprev2,mprev2,anprev2,dateprev2,dateprojf, datebackf);

/------------ free_vector -------------/	/------------ free_vector -------------/
/* chdir(path); */	/* chdir(path); */
Line 12192 Please run with mle=-1 to get a correct	Line 13480 Please run with mle=-1 to get a correct
/* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */	/* free_imatrix(dh,1,lastpass-firstpass+2,1,imx); */
/* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */	/* free_imatrix(bh,1,lastpass-firstpass+2,1,imx); */
/* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */	/* free_imatrix(mw,1,lastpass-firstpass+2,1,imx); */
free_lvector(num,1,n);	free_lvector(num,firstobs,lastobs);
free_vector(agedc,1,n);	free_vector(agedc,firstobs,lastobs);
/free_matrix(covar,0,NCOVMAX,1,n);/	/free_matrix(covar,0,NCOVMAX,1,n);/
/free_matrix(covar,1,NCOVMAX,1,n);/	/free_matrix(covar,1,NCOVMAX,1,n);/
fclose(ficparo);	fclose(ficparo);
Line 12206 Please run with mle=-1 to get a correct	Line 13494 Please run with mle=-1 to get a correct
/--------------- Prevalence limit (period or stable prevalence) --------------/	/--------------- Prevalence limit (period or stable prevalence) --------------/
/#include "prevlim.h"/ /* Use ficrespl, ficlog */	/#include "prevlim.h"/ /* Use ficrespl, ficlog */
prlim=matrix(1,nlstate,1,nlstate);	prlim=matrix(1,nlstate,1,nlstate);
	/* Computes the prevalence limit for each combination k of the dummy covariates by calling prevalim(k) */
prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);	prevalence_limit(p, prlim, ageminpar, agemaxpar, ftolpl, &ncvyear);
fclose(ficrespl);	fclose(ficrespl);

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

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

Line 12256 Please run with mle=-1 to get a correct	Line 13547 Please run with mle=-1 to get a correct
}/* end if moving average */	}/* end if moving average */

/---------- Forecasting ------------------/	/---------- Forecasting ------------------/
if(prevfcast==1){	if(prevfcast==1){
/* if(stepm ==1){*/	/* /\* if(stepm ==1){\/ /
prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);	/* /\* anproj1, mproj1, jproj1 either read explicitly or yrfproj \/ /
	/This done previously after freqsummary./
	/* dateprojd=(jproj1+12mproj1+365anproj1)/365; */
	/* dateprojf=(jproj2+12mproj2+365anproj2)/365; */

	/* } else if (prvforecast==2){ */
	/* /\* if(stepm ==1){\/ /
	/* /\* anproj1, mproj1, jproj1 either read explicitly or yrfproj \/ /
	/* } */
	/prevforecast(fileresu, dateintmean, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);/
	prevforecast(fileresu,dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, p, cptcoveff);
}	}

/* Backcasting */	/* Prevbcasting */
if(backcast==1){	if(prevbcast==1){
ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);	ddnewms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);	ddoldms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);	ddsavms=matrix(1,nlstate+ndeath,1,nlstate+ndeath);
Line 12277 Please run with mle=-1 to get a correct	Line 13578 Please run with mle=-1 to get a correct
hBijx(p, bage, fage, mobaverage);	hBijx(p, bage, fage, mobaverage);
fclose(ficrespijb);	fclose(ficrespijb);

prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2,	/* /\* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, \/ /
mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff);	/* /\* mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); \/ /
	/* prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, */
	/* mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */
	prevbackforecast(fileresu, mobaverage, dateintmean, dateprojd, dateprojf, agemin, agemax, dateprev1, dateprev2,
	mobilavproj, bage, fage, firstpass, lastpass, p, cptcoveff);


varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);	varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);


Line 12286 Please run with mle=-1 to get a correct	Line 13593 Please run with mle=-1 to get a correct
free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);	free_matrix(ddnewms, 1, nlstate+ndeath, 1, nlstate+ndeath);
free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);	free_matrix(ddsavms, 1, nlstate+ndeath, 1, nlstate+ndeath);
free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);	free_matrix(ddoldms, 1, nlstate+ndeath, 1, nlstate+ndeath);
} /* end Backcasting */	} /* end Prevbcasting */


/* ------ Other prevalence ratios------------ */	/* ------ Other prevalence ratios------------ */
Line 12320 Please run with mle=-1 to get a correct	Line 13627 Please run with mle=-1 to get a correct
fprintf(ficreseij,"\n#****** ");	fprintf(ficreseij,"\n#****** ");
printf("\n#****** ");	printf("\n#****** ");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcoveff;j++) {
fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
}	}
for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */	for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	fprintf(ficreseij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
}	}
fprintf(ficreseij,"******\n");	fprintf(ficreseij,"******\n");
printf("******\n");	printf("******\n");

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

free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);	free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
Line 12385 Please run with mle=-1 to get a correct	Line 13693 Please run with mle=-1 to get a correct
for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */	for(k=1; k<=i1;k++){ /* For any combination of dummy covariates, fixed and varying */
if(i1 != 1 && TKresult[nres]!= k)	if(i1 != 1 && TKresult[nres]!= k)
continue;	continue;
printf("\n#****** Result for:");	printf("\n# model %s \n#****** Result for:", model);
fprintf(ficrest,"\n#****** Result for:");	fprintf(ficrest,"\n# model %s \n#****** Result for:", model);
fprintf(ficlog,"\n#****** Result for:");	fprintf(ficlog,"\n# model %s \n#****** Result for:", model);
for(j=1;j<=cptcoveff;j++){	for(j=1;j<=cptcoveff;j++){
printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
}	}
for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */	for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	fprintf(ficrest," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
}	}
fprintf(ficrest,"******\n");	fprintf(ficrest,"******\n");
fprintf(ficlog,"******\n");	fprintf(ficlog,"******\n");
Line 12405 Please run with mle=-1 to get a correct	Line 13713 Please run with mle=-1 to get a correct
fprintf(ficresstdeij,"\n#****** ");	fprintf(ficresstdeij,"\n#****** ");
fprintf(ficrescveij,"\n#****** ");	fprintf(ficrescveij,"\n#****** ");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcoveff;j++) {
fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[Tvaraff[j]])]);
fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,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 */	for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	fprintf(ficresstdeij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	fprintf(ficrescveij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]);
}	}
fprintf(ficresstdeij,"******\n");	fprintf(ficresstdeij,"******\n");
fprintf(ficrescveij,"******\n");	fprintf(ficrescveij,"******\n");
Line 12418 Please run with mle=-1 to get a correct	Line 13726 Please run with mle=-1 to get a correct
fprintf(ficresvij,"\n#****** ");	fprintf(ficresvij,"\n#****** ");
/* pstamp(ficresvij); */	/* pstamp(ficresvij); */
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,TnsdVar[TnsdVar[Tvaraff[j]]])]);
for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */	for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);	/* fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]); /\* To solve \/ /
	fprintf(ficresvij," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][resultmodel[nres][j]]); /* Solved */
}	}
fprintf(ficresvij,"******\n");	fprintf(ficresvij,"******\n");

Line 12450 Please run with mle=-1 to get a correct	Line 13759 Please run with mle=-1 to get a correct
if(vpopbased==1)	if(vpopbased==1)
fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);	fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
else	else
fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");	fprintf(ficrest,"the age specific forward period (stable) prevalences in each health state \n");
fprintf(ficrest,"# Age popbased mobilav e.. (std) ");	fprintf(ficrest,"# Age popbased mobilav e.. (std) ");
for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);	for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
fprintf(ficrest,"\n");	fprintf(ficrest,"\n");
/* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */	/* printf("Which p?\n"); for(i=1;i<=npar;i++)printf("p[i=%d]=%lf,",i,p[i]);printf("\n"); */
printf("Computing age specific period (stable) prevalences in each health state \n");	printf("Computing age specific forward period (stable) prevalences in each health state \n");
fprintf(ficlog,"Computing age specific period (stable) prevalences in each health state \n");	fprintf(ficlog,"Computing age specific forward period (stable) prevalences in each health state \n");
for(age=bage; age <=fage ;age++){	for(age=bage; age <=fage ;age++){
prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /ZZ Is it the correct prevalim /	prevalim(prlim, nlstate, p, age, oldm, savm, ftolpl, &ncvyear, k, nres); /ZZ Is it the correct prevalim /
if (vpopbased==1) {	if (vpopbased==1) {
Line 12503 Please run with mle=-1 to get a correct	Line 13812 Please run with mle=-1 to get a correct
printf("done State-specific expectancies\n");fflush(stdout);	printf("done State-specific expectancies\n");fflush(stdout);
fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);	fprintf(ficlog,"done State-specific expectancies\n");fflush(ficlog);

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


free_vector(weight,1,n);	free_vector(weight,firstobs,lastobs);
	free_imatrix(Tvardk,1,NCOVMAX,1,2);
free_imatrix(Tvard,1,NCOVMAX,1,2);	free_imatrix(Tvard,1,NCOVMAX,1,2);
free_imatrix(s,1,maxwav+1,1,n);	free_imatrix(s,1,maxwav+1,firstobs,lastobs);
free_matrix(anint,1,maxwav,1,n);	free_matrix(anint,1,maxwav,firstobs,lastobs);
free_matrix(mint,1,maxwav,1,n);	free_matrix(mint,1,maxwav,firstobs,lastobs);
free_ivector(cod,1,n);	free_ivector(cod,firstobs,lastobs);
free_ivector(tab,1,NCOVMAX);	free_ivector(tab,1,NCOVMAX);
fclose(ficresstdeij);	fclose(ficresstdeij);
fclose(ficrescveij);	fclose(ficrescveij);
Line 12532 Please run with mle=-1 to get a correct	Line 13842 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,1,n);	if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,firstobs,lastobs);
if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);	if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,firstobs,lastobs);
if(nqv>=1)free_matrix(coqvar,1,nqv,1,n);	if(nqv>=1)free_matrix(coqvar,1,nqv,firstobs,lastobs);
free_matrix(covar,0,NCOVMAX,1,n);	free_matrix(covar,0,NCOVMAX,firstobs,lastobs);
free_matrix(matcov,1,npar,1,npar);	free_matrix(matcov,1,npar,1,npar);
free_matrix(hess,1,npar,1,npar);	free_matrix(hess,1,npar,1,npar);
/free_vector(delti,1,npar);/	/free_vector(delti,1,npar);/
Line 12555 Please run with mle=-1 to get a correct	Line 13865 Please run with mle=-1 to get a correct
free_ivector(TvarsQ,1,NCOVMAX);	free_ivector(TvarsQ,1,NCOVMAX);
free_ivector(TvarsQind,1,NCOVMAX);	free_ivector(TvarsQind,1,NCOVMAX);
free_ivector(TvarsD,1,NCOVMAX);	free_ivector(TvarsD,1,NCOVMAX);
	free_ivector(TnsdVar,1,NCOVMAX);
free_ivector(TvarsDind,1,NCOVMAX);	free_ivector(TvarsDind,1,NCOVMAX);
free_ivector(TvarFD,1,NCOVMAX);	free_ivector(TvarFD,1,NCOVMAX);
free_ivector(TvarFDind,1,NCOVMAX);	free_ivector(TvarFDind,1,NCOVMAX);
Line 12580 Please run with mle=-1 to get a correct	Line 13891 Please run with mle=-1 to get a correct
free_ivector(Tmodelind,1,NCOVMAX);	free_ivector(Tmodelind,1,NCOVMAX);
free_ivector(TmodelInvind,1,NCOVMAX);	free_ivector(TmodelInvind,1,NCOVMAX);
free_ivector(TmodelInvQind,1,NCOVMAX);	free_ivector(TmodelInvQind,1,NCOVMAX);

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

free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);	free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
/* free_imatrix(codtab,1,100,1,10); */	/* free_imatrix(codtab,1,100,1,10); */
fflush(fichtm);	fflush(fichtm);
Line 12618 Please run with mle=-1 to get a correct	Line 13931 Please run with mle=-1 to get a correct
fclose(ficlog);	fclose(ficlog);
/------ End -----------/	/------ End -----------/


	/* Executes gnuplot */

printf("Before Current directory %s!\n",pathcd);	printf("Before Current directory %s!\n",pathcd);
#ifdef WIN32	#ifdef WIN32
Line 12653 Please run with mle=-1 to get a correct	Line 13968 Please run with mle=-1 to get a correct

sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);	sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);	printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
	strcpy(pplotcmd,plotcmd);

if((outcmd=system(plotcmd)) != 0){	if((outcmd=system(plotcmd)) != 0){
printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);	printf("Error in gnuplot, command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");	printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);	sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
if((outcmd=system(plotcmd)) != 0)	if((outcmd=system(plotcmd)) != 0){
printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);	printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
	strcpy(plotcmd,pplotcmd);
	}
}	}
printf(" Successful, please wait...");	printf(" Successful, please wait...");
while (z[0] != 'q') {	while (z[0] != 'q') {
Line 12686 end:	Line 14004 end:
printf("\nType q for exiting: "); fflush(stdout);	printf("\nType q for exiting: "); fflush(stdout);
scanf("%s",z);	scanf("%s",z);
}	}
	printf("End\n");
	exit(0);
}	}

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