imach/src/imach.c - diff

Return to imach.c CVS log

Up to [Local Repository] / imach / src

Diff for /imach/src/imach.c between versions 1.280 and 1.308

version 1.280, 2018/02/21 07:58:13	version 1.308, 2021/03/31 13:11:57
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	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	Revision 1.280 2018/02/21 07:58:13 brouard
Summary: 0.99r15	Summary: 0.99r15

Line 1022 typedef struct {	Line 1126 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 20 /*< Maximum number of covariates, including generated covariates V1V2 */
#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 1049 typedef struct {	Line 1154 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[]="March 2021,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, INED 2000-2021";
char fullversion[]="$Revision$ $Date$";	char fullversion[]="$Revision$ $Date$";
char strstart[80];	char strstart[80];
char optionfilext[10], optionfilefiname[FILENAMELENGTH];	char optionfilext[10], optionfilefiname[FILENAMELENGTH];
Line 1073 int nqfveff=0; /**< nqfveff Number of Qu	Line 1178 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 1213 double pmmij, probs; / Global poin	Line 1319 double pmmij, probs; / Global poin
double *mobaverage, mobaverages; / New global variable */	double *mobaverage, mobaverages; / New global variable */
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 2332 void powell(double p[], double **xi, int	Line 2443 void powell(double p[], double **xi, int
/* 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 2556 void powell(double p[], double **xi, int	Line 2667 void powell(double p[], double **xi, int
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 2652 void powell(double p[], double **xi, int	Line 2764 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);

/* 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 2721 Earliest age to start was %d-%d=%d, ncvl	Line 2837 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 */
Line 2835 Earliest age to start was %d-%d=%d, ncvl	Line 2952 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 2920 double pmij(double ps, double *cov,	Line 3037 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 2941 double pmij(double ps, double *cov,	Line 3058 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 2949 double pmij(double ps, double *cov,	Line 3066 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;

Line 2968 double pmij(double ps, double *cov,	Line 3085 double pmij(double ps, double *cov,
/* 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 2995 double pmij(double ps, double *cov,	Line 3112 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 3016 double pmij(double ps, double *cov,	Line 3133 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 3088 double bpmij(double ps, double *cov,	Line 3205 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 3848 return -l;	Line 3965 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 3872 void likelione(FILE *ficres,double p[],	Line 3989 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 4347 void pstamp(FILE *fichier)	Line 4464 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 4362 void freqsummary(char fileres[], double	Line 4493 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 4375 void freqsummary(char fileres[], double	Line 4506 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 4483 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4616 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 4499 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4635 Title=%s <br>Datafile=%s Firstpass=%d La
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 (cptcoveff >0) { /* Filter is here: Must be looked at for model=V1+V2+V3+V4 */
/* for (z1=1; z1<= nqfveff; z1++) { */
/* 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 */	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]; \/ /
Line 4522 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4655 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 */
Line 4542 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4675 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 4560 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4693 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 */
	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 */
	}
/* 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 4575 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4713 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 feeded for any initial and valid live state as well as
Line 4612 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4755 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 %.0f 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");
	}
	printf(" fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));
	fprintf(ficlog," fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[z1]-meanq[z1]*meanq[z1]/idq[z1])/idq[z1]));
	fprintf(ficresphtmfr," fixed quantitative variable V%d on %.0f representatives of the population : %6.3g (%6.3g)<p>\n", ncovcol+z1, idq[z1],meanq[z1]/idq[z1], sqrt((stdq[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((cptcoveff==0 && nj==1)\|\| nj==2 ) /* no covariate and first pass */
fprintf(ficresp, " Age");	fprintf(ficresp, " Age");
Line 4846 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5010 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 4888 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5052 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 4999 void prevalence(double ***probs, double	Line 5166 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 5057 void prevalence(double ***probs, double	Line 5224 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 5080 void prevalence(double ***probs, double	Line 5246 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 5122 void concatwav(int wav[], int **dh, int	Line 5288 void concatwav(int wav[], int **dh, int
#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){
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;
}	}
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);	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;	mw[++mi][i]=m;
mli=m;	mli=m;
}	}
Line 5308 void concatwav(int wav[], int **dh, int	Line 5474 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 */
Line 5328 void concatwav(int wav[], int **dh, int	Line 5496 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("Information, IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
	fprintf(ficlog,"Information, currently IMaCh doesn't treat covariate with missing values (-1), individual %d will be skipped.\n",i);
	}
	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 5374 void concatwav(int wav[], int **dh, int	Line 5546 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 5395 void concatwav(int wav[], int **dh, int	Line 5573 void concatwav(int wav[], int **dh, int
break;	break;
} /* end switch */	} /* end switch */
} /* end dummy test */	} /* end dummy test */
	} /* end of loop on model-covariate k. nbcode[Tvark][1]=-1, nbcode[Tvark][1]=0 and nbcode[Tvark][2]=1 sets the value of covariate k*/
/* for (k=0; k<= cptcode; k++) { /\* k=-1 ? k=0 to 1 \//\ Could be 1 to 4 \//\ cptcode=modmaxcovj \/ /
/* /\recode from 0 \/ */
/* k is a modality. If we have model=V1+V1sex /
/* then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
/* But if some modality were not used, it is recoded from 0 to a newer modmaxcovj=cptcode \/ /
/* } */
/* /\* 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]); */
/* 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 5793 void concatwav(int wav[], int **dh, int	Line 5957 void concatwav(int wav[], int **dh, int
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 /
Line 5917 void concatwav(int wav[], int **dh, int	Line 6082 void concatwav(int wav[], int **dh, int
}	}
/**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and	/**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and
* returns into prlim .	* 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 we use crossection prevalences. Previous step is useless but prlim is created */
Line 5930 void concatwav(int wav[], int **dh, int	Line 6095 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.	/**< 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=0 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$, which are the probability	/**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}x\f$, which are the probability
* at horizon h in state j including mortality.	* at horizon h in state j including mortality.
*/	*/
for(j=1; j<= nlstate; j++){	for(j=1; j<= nlstate; j++){
Line 5955 void concatwav(int wav[], int **dh, int	Line 6120 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);

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 6141 void concatwav(int wav[], int **dh, int	Line 6306 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 6170 void concatwav(int wav[], int **dh, int	Line 6335 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 6232 void concatwav(int wav[], int **dh, int	Line 6397 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 6450 void varprob(char optionfilefiname[], do	Line 6618 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 6720 To be simple, these graphs help to under	Line 6888 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;

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 \
Line 6743 void printinghtml(char fileresu[], char	Line 6911 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 6852 divided by h: <sub>h</sub>P<sub>ij</sub>	Line 7020 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> \
<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);	<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);
}	}
/* 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> <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);
}	}
/* 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> \
<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);	<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);
}	}
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><br> \
<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);	<img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, dateprojd, dateprojf, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,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), \
Line 6929 See page 'Matrix of variance-covariance	Line 7097 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 6993 true period expectancies (those weighted	Line 7161 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 7071 void printinggnuplot(char fileresu[], ch	Line 7239 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 */
Line 7109 void printinggnuplot(char fileresu[], ch	Line 7277 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 7147 void printinggnuplot(char fileresu[], ch	Line 7315 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 7174 void printinggnuplot(char fileresu[], ch	Line 7342 void printinggnuplot(char fileresu[], ch
}	}
} /* 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 7193 void printinggnuplot(char fileresu[], ch	Line 7361 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 7438 set ter svg size 640, 480\nunset log y\n	Line 7606 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 */
/* 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 */
Line 7481 set ter svg size 640, 480\nunset log y\n	Line 7649 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 */
/* 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 */
Line 7533 set ter svg size 640, 480\nunset log y\n	Line 7701 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 7545 set ter svg size 640, 480\nunset log y\n	Line 7713 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 */
/* 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 */
Line 7649 set ter svg size 640, 480\nunset log y\n	Line 7817 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 7762 set ter svg size 640, 480\nunset log y\n	Line 7930 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 7979 set ter svg size 640, 480\nunset log y\n	Line 8147 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 8076 set ter svg size 640, 480\nunset log y\n	Line 8245 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 8108 set ter svg size 640, 480\nunset log y\n	Line 8278 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 8200 set ter svg size 640, 480\nunset log y\n	Line 8378 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 8246 set ter svg size 640, 480\nunset log y\n	Line 8429 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");

Line 8287 set ter svg size 640, 480\nunset log y\n	Line 8475 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 8307 set ter svg size 640, 480\nunset log y\n	Line 8495 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,j)]);
fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+hhstepm/YEARMstepm);	fprintf(ficresf,"%.f %.f ",anprojd+yearp,agec+hhstepm/YEARMstepm);

for(j=1; j<=nlstate+ndeath;j++) {	for(j=1; j<=nlstate+ndeath;j++) {
ppij=0.;	ppij=0.;
Line 8335 set ter svg size 640, 480\nunset log y\n	Line 8523 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 8344 set ter svg size 640, 480\nunset log y\n	Line 8533 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 8387 set ter svg size 640, 480\nunset log y\n	Line 8576 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 8426 set ter svg size 640, 480\nunset log y\n	Line 8615 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 8452 set ter svg size 640, 480\nunset log y\n	Line 8641 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,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 8487 set ter svg size 640, 480\nunset log y\n	Line 8676 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 8498 set ter svg size 640, 480\nunset log y\n	Line 8687 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 8539 set ter svg size 640, 480\nunset log y\n	Line 8728 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 8900 void prwizard(int ncovmodel, int nlstate	Line 9089 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 8908 double gompertz(double x[])	Line 9097 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 8938 double gompertz(double x[])	Line 9133 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 9031 int readdata(char datafile[], int firsto	Line 9226 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;
Line 9064 int readdata(char datafile[], int firsto	Line 9260 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 9186 int readdata(char datafile[], int firsto	Line 9427 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 9225 int readdata(char datafile[], int firsto	Line 9470 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 9348 int decoderesult ( char resultline[], in	Line 9600 int decoderesult ( char resultline[], in
char stra[80], strb[80], strc[80], strd[80],stre[80];	char stra[80], strb[80], strc[80], strd[80],stre[80];

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

if (strstr(resultline,"v") !=0){	if (strstr(resultline,"v") !=0){
printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);	printf("Error. 'v' must be in upper case 'V' result: %s ",resultline);
Line 9363 int decoderesult ( char resultline[], in	Line 9614 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 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 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 variable in the resultline, %d, differs from the number of variable used in the model line, %d.\n",j, cptcovs);
Line 9683 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 9933 Dummy[k] 0=dummy (0 1), 1 quantitative (
Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\	Typevar: 0 for simple covariate (dummy, quantitative, fixed or varying), 1 for age product, 2 for product \n\
Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\	Fixed[k] 0=fixed (product or simple), 1 varying, 2 fixed with age product, 3 varying with age product \n\
Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);	Dummy[k] 0=dummy (0 1), 1 quantitative (single or product without age), 2 dummy with age product, 3 quant with age product\n",model);
for(k=1;k<=cptcovt; k++){ Fixed[k]=0; Dummy[k]=0;}	for(k=-1;k<=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 9933 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 10183 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 10109 BOOL IsWow64()	Line 10360 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 10145 void syscompilerinfo(int logged)	Line 10398 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 10161 void syscompilerinfo(int logged)	Line 10416 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 10248 void syscompilerinfo(int logged)	Line 10501 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 10269 void syscompilerinfo(int logged)	Line 10522 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) --------------/
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 10278 int prevalence_limit(double p, double	Line 10531 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 10359 int prevalence_limit(double p, double	Line 10612 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 10374 int back_prevalence_limit(double *p, dou	Line 10627 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 10569 int hPijx(double *p, int bage, int fage)	Line 10822 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 10599 int hPijx(double *p, int bage, int fage)	Line 10852 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 10648 int main(int argc, char *argv[])	Line 10901 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 10683 int main(int argc, char *argv[])	Line 10937 int main(int argc, char *argv[])

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 10691 int main(int argc, char *argv[])	Line 10945 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 10716 int main(int argc, char *argv[])	Line 10977 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 10795 int main(int argc, char *argv[])	Line 11057 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 10874 int main(int argc, char *argv[])	Line 11141 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 10909 int main(int argc, char *argv[])	Line 11174 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 10939 int main(int argc, char *argv[])	Line 11205 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,ficres);	fprintf(ficparo,"%s",line);
fputs(line,ficlog);	fprintf(ficlog,"%s",line);
continue;	continue;
}else	}else
break;	break;
Line 10961 int main(int argc, char *argv[])	Line 11232 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 10971 int main(int argc, char *argv[])	Line 11253 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,ficres);	fprintf(ficparo,"%s",line);
fputs(line,ficlog);	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 != 1){	if (num_filled != 1){
printf("ERROR %d: Model should be at minimum 'model=1+age' %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' %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';	model[0]='\0';
goto end;	goto end;
}	}
Line 10995 int main(int argc, char *argv[])	Line 11277 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]=='#'){
Line 11028 int main(int argc, char *argv[])	Line 11313 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 11094 int main(int argc, char *argv[])	Line 11379 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 11234 Please run with mle=-1 to get a correct	Line 11528 Please run with mle=-1 to get a correct

/* 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 11253 Please run with mle=-1 to get a correct	Line 11556 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 */
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 11357 Please run with mle=-1 to get a correct	Line 11660 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 11384 Please run with mle=-1 to get a correct	Line 11687 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 11567 Title=%s <br>Datafile=%s Firstpass=%d La	Line 11870 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 11575 Title=%s <br>Datafile=%s Firstpass=%d La	Line 11878 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 11610 Interval (in months) between two waves:	Line 11913 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 11647 Interval (in months) between two waves:	Line 11950 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 11774 Interval (in months) between two waves:	Line 12077 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 11823 Please run with mle=-1 to get a correct	Line 12126 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 11863 Please run with mle=-1 to get a correct	Line 12167 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");
Line 12025 Please run with mle=-1 to get a correct	Line 12329 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 12070 Please run with mle=-1 to get a correct	Line 12375 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 12095 Please run with mle=-1 to get a correct	Line 12401 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 12117 Please run with mle=-1 to get a correct	Line 12424 Please run with mle=-1 to get a correct
}	}

/* Results */	/* Results */
	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=%lf.2 mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
	fprintf(ficlog,"prevforecast=%d yearsfproj=%lf.2 mobil_average=%d\n",prevfcast,yrfproj,mobilavproj);
	fprintf(ficres,"prevforecast=%d yearsfproj=%lf.2 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=%lf.2 mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
	fprintf(ficlog,"prevbackcast=%d yearsbproj=%lf.2 mobil_average=%d\n",prevbcast,yrbproj,mobilavproj);
	fprintf(ficres,"prevbackcast=%d yearsbproj=%lf.2 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",resultline);
if (num_filled == 0){	nresult++; /* Sum of resultlines */
resultline[0]='\0';	printf("Result %d: result:%s\n",nresult, resultline);
printf("Warning %d: no result line! It should be at minimum 'result: V2=0 V1=1 or result:.\n%s\n", num_filled, line);	if(nresult > MAXRESULTLINES){
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);	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. ",MAXRESULTLINES,nresult,rfileres);
break;	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. ",MAXRESULTLINES,nresult,rfileres);
} else if (num_filled != 1){	goto end;
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 %d: result line! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",num_filled, line);	decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */
}	fprintf(ficparo,"result: %s\n",resultline);
nresult++; /* Sum of resultlines */	fprintf(ficres,"result: %s\n",resultline);
printf("Result %d: result=%s\n",nresult, resultline);	fprintf(ficlog,"result: %s\n",resultline);
if(nresult > MAXRESULTLINES){	break;
printf("ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);	case 14:
fprintf(ficlog,"ERROR: Current version of IMaCh limits the number of resultlines to %d, you used %d\n",MAXRESULTLINES,nresult);	printf("Error: Unknown command '%s'\n",line);
goto end;	fprintf(ficlog,"Error: Unknown command '%s'\n",line);
}	if(ncovmodel >=2 && nresult==0 ){
decoderesult(resultline, nresult); /* Fills TKresult[nresult] combination and Tresult[nresult][k4+1] combination values */	printf("ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
fprintf(ficparo,"result: %s\n",resultline);	fprintf(ficlog,"ERROR: no result lines! It should be at minimum 'result: V2=0 V1=1 or result:.' %s\n",line);
fprintf(ficres,"result: %s\n",resultline);
fprintf(ficlog,"result: %s\n",resultline);
break;
case 14:
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);
goto end;
}
break;
default:
nresult=1;
decoderesult(".",nresult ); /* No covariate */
}	}
	/* 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 12222 This is probably because your parameter	Line 12542 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 12235 Please run with mle=-1 to get a correct	Line 12588 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 12299 Please run with mle=-1 to get a correct	Line 12652 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 12320 Please run with mle=-1 to get a correct	Line 12683 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 12329 Please run with mle=-1 to get a correct	Line 12698 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 12493 Please run with mle=-1 to get a correct	Line 12862 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 12546 Please run with mle=-1 to get a correct	Line 12915 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(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 12575 Please run with mle=-1 to get a correct	Line 12944 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 12661 Please run with mle=-1 to get a correct	Line 13030 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 12696 Please run with mle=-1 to get a correct	Line 13067 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 12729 end:	Line 13103 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);
}	}

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

Removed from v.1.280
changed lines
	Added in v.1.308