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 1.265 and 1.292

version 1.265, 2017/04/26 16:22:11	version 1.292, 2019/05/09 14:17:20
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	Revision 1.292 2019/05/09 14:17:20 brouard
	Summary: Some updates

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

	Revision 1.276 2017/06/30 15:48:31 brouard
	Summary: Graphs improvements

	Revision 1.275 2017/06/30 13:39:33 brouard
	Summary: Saito's color

	Revision 1.274 2017/06/29 09:47:08 brouard
	Summary: Version 0.99r14

	Revision 1.273 2017/06/27 11:06:02 brouard
	Summary: More documentation on projections

	Revision 1.272 2017/06/27 10:22:40 brouard
	Summary: Color of backprojection changed from 6 to 5(yellow)

	Revision 1.271 2017/06/27 10:17:50 brouard
	Summary: Some bug with rint

	Revision 1.270 2017/05/24 05:45:29 brouard
	* empty log message *

	Revision 1.269 2017/05/23 08:39:25 brouard
	Summary: Code into subroutine, cleanings

	Revision 1.268 2017/05/18 20:09:32 brouard
	Summary: backprojection and confidence intervals of backprevalence

	Revision 1.267 2017/05/13 10:25:05 brouard
	Summary: temporary save for backprojection

	Revision 1.266 2017/05/13 07:26:12 brouard
	Summary: Version 0.99r13 (improvements and bugs fixed)

Revision 1.265 2017/04/26 16:22:11 brouard	Revision 1.265 2017/04/26 16:22:11 brouard
Summary: imach 0.99r13 Some bugs fixed	Summary: imach 0.99r13 Some bugs fixed

Line 815 Back prevalence and projections:	Line 900 Back prevalence and projections:
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
oldm=oldms;savm=savms;	oldm=oldms;savm=savms;

- hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);	- hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k, nres);
Computes the transition matrix starting at age 'age' over	Computes the transition matrix starting at age 'age' over
'nhstepmhstepmstepm' months (i.e. until	'nhstepmhstepmstepm' months (i.e. until
age (in years) age+nhstepmhstepmstepm/12) by multiplying	age (in years) age+nhstepmhstepmstepm/12) by multiplying
Line 975 typedef struct {	Line 1060 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 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
#define AGEOVERFLOW 1.e20	#define AGEOVERFLOW 1.e20
Line 1001 typedef struct {	Line 1088 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[]="April 2018,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121), Intel Software 2015-2018";
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 1025 int nqfveff=0; /**< nqfveff Number of Qu	Line 1112 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;
int nlstate=2; /* Number of live states */	int nlstate=2; /* Number of live states */
Line 1074 FILE *ficrescveij;	Line 1162 FILE *ficrescveij;
char filerescve[FILENAMELENGTH];	char filerescve[FILENAMELENGTH];
FILE *ficresvij;	FILE *ficresvij;
char fileresv[FILENAMELENGTH];	char fileresv[FILENAMELENGTH];
FILE *ficresvpl;
char fileresvpl[FILENAMELENGTH];
char title[MAXLINE];	char title[MAXLINE];
char model[MAXLINE]; /*< The model line /	char model[MAXLINE]; /*< The model line /
char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH];	char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH], fileresplb[FILENAMELENGTH];
Line 1173 double *agedc;	Line 1260 double *agedc;
double covar; /< covar[j,i], value of jth covariate for individual i,	double covar; /< covar[j,i], value of jth covariate for individual i,
* covar=matrix(0,NCOVMAX,1,n);	* covar=matrix(0,NCOVMAX,1,n);
* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]age; /	* cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]age; /
double *coqvar; / Fixed quantitative covariate iqv */	double *coqvar; / Fixed quantitative covariate nqv */
double **cotvar; / Time varying covariate itv */	double **cotvar; / Time varying covariate ntv */
double **cotqvar; / Time varying quantitative covariate itqv */	double **cotqvar; / Time varying quantitative covariate itqv */
double idx;	double idx;
int *nbcode, Tvar; /*< model=V2 => Tvar[1]= 2 /	int *nbcode, Tvar; /*< model=V2 => Tvar[1]= 2 /
Line 2477 void powell(double p[], double **xi, int	Line 2564 void powell(double p[], double **xi, int

double prevalim(double prlim, int nlstate, double x[], double age, double oldm, double savm, double ftolpl, int *ncvyear, int ij, int nres)	double prevalim(double prlim, int nlstate, double x[], double age, double oldm, double savm, double ftolpl, int *ncvyear, int ij, int nres)
{	{
/* Computes the prevalence limit in each live state at age x and for covariate combination ij	/**< Computes the prevalence limit in each live state at age x and for covariate combination ij
(and selected quantitative values in nres)	* (and selected quantitative values in nres)
by left multiplying the unit	* by left multiplying the unit
matrix by transitions matrix until convergence is reached with precision ftolpl */	* matrix by transitions matrix until convergence is reached with precision ftolpl
/* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I */	* Wx= Wx-1 Px-1= Wx-2 Px-2 Px-1 = Wx-n Px-n ... Px-2 Px-1 I
/* Wx is row vector: population in state 1, population in state 2, population dead */	* Wx is row vector: population in state 1, population in state 2, population dead
/* or prevalence in state 1, prevalence in state 2, 0 */	* or prevalence in state 1, prevalence in state 2, 0
/* newm is the matrix after multiplications, its rows are identical at a factor */	* newm is the matrix after multiplications, its rows are identical at a factor.
/* Initial matrix pimij */	* Inputs are the parameter, age, a tolerance for the prevalence limit ftolpl.
	* Output is prlim.
	* Initial matrix pimij
	*/
/* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */	/* {0.85204250825084937, 0.13044499163996345, 0.017512500109187184, */
/* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */	/* 0.090851990222114765, 0.88271245433047185, 0.026435555447413338, */
/* 0, 0 , 1} */	/* 0, 0 , 1} */
Line 2506 void powell(double p[], double **xi, int	Line 2596 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 2602 void powell(double p[], double **xi, int	Line 2693 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 2657 Earliest age to start was %d-%d=%d, ncvl	Line 2752 Earliest age to start was %d-%d=%d, ncvl
max=vector(1,nlstate);	max=vector(1,nlstate);
meandiff=vector(1,nlstate);	meandiff=vector(1,nlstate);

dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;	dnewm=ddnewms; doldm=ddoldms; dsavm=ddsavms;
oldm=oldms; savm=savms;	oldm=oldms; savm=savms;

/* Starting with matrix unity */	/* Starting with matrix unity */
for (ii=1;ii<=nlstate+ndeath;ii++)	for (ii=1;ii<=nlstate+ndeath;ii++)
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
oldm[ii][j]=(ii==j ? 1.0 : 0.0);	oldm[ii][j]=(ii==j ? 1.0 : 0.0);
}	}

Line 2671 Earliest age to start was %d-%d=%d, ncvl	Line 2766 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 2736 Earliest age to start was %d-%d=%d, ncvl	Line 2832 Earliest age to start was %d-%d=%d, ncvl
/* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, ageminpar, agemaxpar, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind \/ /	/* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, ageminpar, agemaxpar, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind \/ /
/* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind \/ /	/* out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij)); /\* Bug Valgrind \/ /
out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij)); /* Bug Valgrind */	out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij)); /* Bug Valgrind */
	/* if((int)age == 86 \|\| (int)age == 87){ */
	/* printf(" Backward prevalim age=%d agefin=%d \n", (int) age, (int) agefin); */
	/* for(i=1; i<=nlstate+ndeath; i++) { */
	/* printf("%d newm= ",i); */
	/* for(j=1;j<=nlstate+ndeath;j++) { */
	/* printf("%f ",newm[i][j]); */
	/* } */
	/* printf("oldm * "); */
	/* for(j=1;j<=nlstate+ndeath;j++) { */
	/* printf("%f ",oldm[i][j]); */
	/* } */
	/* printf(" bmmij "); */
	/* for(j=1;j<=nlstate+ndeath;j++) { */
	/* printf("%f ",pmmij[i][j]); */
	/* } */
	/* printf("\n"); */
	/* } */
	/* } */
savm=oldm;	savm=oldm;
oldm=newm;	oldm=newm;

for(j=1; j<=nlstate; j++){	for(j=1; j<=nlstate; j++){
max[j]=0.;	max[j]=0.;
min[j]=1.;	min[j]=1.;
Line 2756 Earliest age to start was %d-%d=%d, ncvl	Line 2871 Earliest age to start was %d-%d=%d, ncvl
meandiff[i]=(max[i]-min[i])/(max[i]+min[i])2.; / mean difference for each column */	meandiff[i]=(max[i]-min[i])/(max[i]+min[i])2.; / mean difference for each column */
maxmax=FMAX(maxmax,meandiff[i]);	maxmax=FMAX(maxmax,meandiff[i]);
/* printf("Back age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, i, meandiff[i],(int)agefin, i, max[i], i, min[i],maxmax); */	/* printf("Back age= %d meandiff[%d]=%f, agefin=%d max[%d]=%f min[%d]=%f maxmax=%f\n", (int)age, i, meandiff[i],(int)agefin, i, max[i], i, min[i],maxmax); */
} /* j loop */	} /* i loop */
*ncvyear= -( (int)age- (int)agefin);	*ncvyear= -( (int)age- (int)agefin);
/* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, ncvyear);/	/* printf("Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, ncvyear); /
if(maxmax < ftolpl){	if(maxmax < ftolpl){
/* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, ncvyear); /	/* printf("OK Back maxmax=%lf ncvloop=%d, age=%d, agefin=%d ncvyear=%d \n", maxmax, ncvloop, (int)age, (int)agefin, ncvyear); /
free_vector(min,1,nlstate);	free_vector(min,1,nlstate);
Line 2766 Earliest age to start was %d-%d=%d, ncvl	Line 2881 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 2788 Oldest age to start was %d-%d=%d, ncvloo	Line 2903 Oldest age to start was %d-%d=%d, ncvloo
double pmij(double ps, double cov, int ncovmodel, double x, int nlstate )	double pmij(double ps, double cov, int ncovmodel, double x, int nlstate )
{	{
/* According to parameters values stored in x and the covariate's values stored in cov,	/* According to parameters values stored in x and the covariate's values stored in cov,
computes the probability to be observed in state j being in state i by appying the	computes the probability to be observed in state j (after stepm years) being in state i by appying the
model to the ncovmodel covariates (including constant and age).	model to the ncovmodel covariates (including constant and age).
lnpijopii=ln(pij/pii)= aij+bijage+cijv1+dijv2+... = sum_nc=1^ncovmodel xij(nc)cov[nc]	lnpijopii=ln(pij/pii)= aij+bijage+cijv1+dijv2+... = sum_nc=1^ncovmodel xij(nc)cov[nc]
and, according on how parameters are entered, the position of the coefficient xij(nc) of the	and, according on how parameters are entered, the position of the coefficient xij(nc) of the
Line 2797 double pmij(double ps, double *cov,	Line 2912 double pmij(double ps, double *cov,
j>=i nc + ((i-1)(nlstate+ndeath-1)+(j-2))ncovmodel	j>=i nc + ((i-1)(nlstate+ndeath-1)+(j-2))ncovmodel
Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,	Computes ln(pij/pii) (lnpijopii), deduces pij/pii by exponentiation,
sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.	sums on j different of i to get 1-pii/pii, deduces pii, and then all pij.
Outputs ps[i][j] the probability to be observed in j being in j according to	Outputs ps[i][j] or probability to be observed in j being in i according to
the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]	the values of the covariates cov[nc] and corresponding parameter values x[nc+shiftij]
	Sum on j ps[i][j] should equal to 1.
*/	*/
double s1, lnpijopii;	double s1, lnpijopii;
/double t34;/	/double t34;/
Line 2862 double pmij(double ps, double *cov,	Line 2978 double pmij(double ps, double *cov,
/*	/*
for(i=1; i<= npar; i++) printf("%f ",x[i]);	for(i=1; i<= npar; i++) printf("%f ",x[i]);
goto end;*/	goto end;*/
return ps;	return ps; /* Pointer is unchanged since its call */
}	}

/************* backward transition probabilities *************/	/************* backward transition probabilities *************/
Line 2871 double pmij(double ps, double *cov,	Line 2987 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 ij	/* Computes the backward probability at age agefin and covariate combination ij. In fact cov is already filled and x too.
* 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;

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 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 2888 double pmij(double ps, double *cov,	Line 3004 double pmij(double ps, double *cov,
dsavm=ddsavms;	dsavm=ddsavms;

agefin=cov[2];	agefin=cov[2];
	/* Bx = Diag(w_x) P_x Diag(Sum_i w^i_x p^ij_x */
/* bmij // age is cov[2], ij is included in cov, but we need for	/* bmij // age is cov[2], ij is included in cov, but we need for
the observed prevalence (with this covariate ij) */	the observed prevalence (with this covariate ij) at beginning of transition */
dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate);	/* dsavm=pmij(pmmij,cov,ncovmodel,x,nlstate); */
/* We do have the matrix Px in savm and we need pij */
	/* P_x */
	pmmij=pmij(pmmij,cov,ncovmodel,x,nlstate); /This is forward probability from agefin to agefin + stepm /
	/* outputs pmmij which is a stochastic matrix in row */

	/* Diag(w_x) */
	/* Rescaling the cross-sectional prevalence: Problem with prevacurrent which can be zero */
	sumnew=0.;
	/for (ii=1;ii<=nlstate+ndeath;ii++){/
	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]); */
	sumnew+=prevacurrent[(int)agefin][ii][ij];
	}
	if(sumnew >0.01){ /* At least some value in the prevalence */
	for (ii=1;ii<=nlstate+ndeath;ii++){
	for (j=1;j<=nlstate+ndeath;j++)
	doldm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij]/sumnew : 0.0);
	}
	}else{
	for (ii=1;ii<=nlstate+ndeath;ii++){
	for (j=1;j<=nlstate+ndeath;j++)
	doldm[ii][j]=(ii==j ? 1./nlstate : 0.0);
	}
	/* if(sumnew <0.9){ */
	/* printf("Problem internal bmij B: sum on i wi <0.9: j=%d, sum_i wi=%lf,agefin=%d\n",j,sumnew, (int)agefin); */
	/* } */
	}
	k3=0.0; /* We put the last diagonal to 0 */
	for (ii=nlstate+1;ii<=nlstate+ndeath;ii++){
	doldm[ii][ii]= k3;
	}
	/* End doldm, At the end doldm is diag[(w_i)] */

	/* 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); /* was a Bug Valgrind */

	/* 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.. */
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
sumnew=0.; /* w1 p11 + w2 p21 only on live states */	sumnew=0.;
for (ii=1;ii<=nlstate;ii++){	for (ii=1;ii<=nlstate;ii++){
sumnew+=dsavm[ii][j]*prevacurrent[(int)agefin][ii][ij];	/* sumnew+=dsavm[ii][j]prevacurrent[(int)agefin][ii][ij]; /
	sumnew+=pmmij[ii][j]doldm[ii][ii]; / Yes prevalence at beginning of transition */
} /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */	} /* sumnew is (N11+N21)/N..= N.1/N.. = sum on i of w_i pij */
for (ii=1;ii<=nlstate+ndeath;ii++){	for (ii=1;ii<=nlstate+ndeath;ii++){
if(sumnew >= 1.e-10){
/* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */	/* if(agefin >= agemaxpar && agefin <= agemaxpar+stepm/YEARM){ */
/* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */	/* dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
/* }else if(agefin >= agemaxpar+stepm/YEARM){ */	/* }else if(agefin >= agemaxpar+stepm/YEARM){ */
/* doldm[ii][j]=(ii==j ? 1./sumnew : 0.0); */	/* dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0); */
/* }else */	/* }else */
doldm[ii][j]=(ii==j ? 1./sumnew : 0.0);	dsavm[ii][j]=(ii==j ? 1./sumnew : 0.0);
}else{
;
/* printf("ii=%d, i=%d, doldm=%lf dsavm=%lf, probs=%lf, sumnew=%lf,agefin=%d\n",ii,j,doldm[ii][j],dsavm[ii][j],prevacurrent[(int)agefin][ii][ij],sumnew, (int)agefin); */
}
} /End ii /	} /End ii /
} /* End j, At the end doldm is diag[1/(w_1p1i+w_2 p2i)] */	} /* 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 */
/* left Product of this diag matrix by dsavm=Px (newm=dsavmdoldm) /
bbmij=matprod2(dnewm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, doldm); /* Bug Valgrind */	ps=matprod2(ps, dnewm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dsavm); /* was a Bug Valgrind */
/* dsavm=doldm; /\* dsavm is now diag [1/(w_1p1i+w_2 p2i)] but can be overwritten\/ /	/* ps is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
/* doldm=dnewm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] \/ /
/* dnewm=dsavm; /\* doldm is now Px * diag [1/(w_1p1i+w_2 p2i)] \/ /
/* left Product of this matrix by diag matrix of prevalences (savm) */
for (j=1;j<=nlstate+ndeath;j++){
for (ii=1;ii<=nlstate+ndeath;ii++){
dsavm[ii][j]=(ii==j ? prevacurrent[(int)agefin][ii][ij] : 0.0);
}
} /* End j, At the end oldm is diag[1/(w_1p1i+w_2 p2i)] */
ps=matprod2(doldm, dsavm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, dnewm); /* Bug Valgrind */
/* newm or out is now diag[w_i] * Px * diag [1/(w_1p1i+w_2 p2i)] */
/* end bmij */	/* end bmij */
return ps;	return ps; /pointer is unchanged /
}	}
/************* transition probabilities *************/	/************* transition probabilities *************/

Line 3138 double *hpxij(double *po, int nhstep	Line 3278 double *hpxij(double *po, int nhstep
}	}
for(i=1; i<=nlstate+ndeath; i++)	for(i=1; i<=nlstate+ndeath; i++)
for(j=1;j<=nlstate+ndeath;j++) {	for(j=1;j<=nlstate+ndeath;j++) {
po[i][j][h]=newm[i][j];	po[i][j][h]=newm[i][j];
/if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);/	/if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);/
}	}
/printf("h=%d ",h);/	/printf("h=%d ",h);/
} /* end h */	} /* end h */
/* printf("\n H=%d \n",h); */	/* printf("\n H=%d \n",h); */
return po;	return po;
}	}

/*********** Higher Back Matrix Product *************/	/*********** Higher Back Matrix Product *************/
/* double *hbxij(double po, int nhstepm, double age, int hstepm, double x, double *prevacurrent, int nlstate, int stepm, double oldm, double savm, double dnewm, double doldm, double dsavm, int ij ) */	/* double *hbxij(double po, int nhstepm, double age, int hstepm, double x, double *prevacurrent, int nlstate, int stepm, double oldm, double savm, double dnewm, double doldm, double dsavm, int ij ) */
double *hbxij(double po, int nhstepm, double age, int hstepm, double x, double ***prevacurrent, int nlstate, int stepm, int ij )	double *hbxij(double po, int nhstepm, double age, int hstepm, double x, double ***prevacurrent, int nlstate, int stepm, int ij, int nres )
{	{
/* Computes the transition matrix starting at age 'age' over	/* For a combination of dummy covariate ij, computes the transition matrix starting at age 'age' over
'nhstepmhstepmstepm' months (i.e. until	'nhstepmhstepmstepm' months (i.e. until
age (in years) age+nhstepmhstepmstepm/12) by multiplying	age (in years) age+nhstepmhstepmstepm/12) by multiplying
nhstepm*hstepm matrices.	nhstepm*hstepm matrices.
Line 3159 double *hbxij(double *po, int nhstep	Line 3299 double *hbxij(double *po, int nhstep
(typically every 2 years instead of every month which is too big	(typically every 2 years instead of every month which is too big
for the memory).	for the memory).
Model is determined by parameters x and covariates have to be	Model is determined by parameters x and covariates have to be
included manually here.	included manually here. Then we use a call to bmij(x and cov)
	The addresss of po (p3mat allocated to the dimension of nhstepm) should be stored for output
*/	*/

int i, j, d, h, k;	int i, j, d, h, k;
double **out, cov[NCOVMAX+1];	double out, cov[NCOVMAX+1], bmij();
double **newm;	double newm, *newmm;
double agexact;	double agexact;
double agebegin, ageend;	double agebegin, ageend;
double oldm, savm;	double oldm, savm;

oldm=oldms;savm=savms;	newmm=po; /* To be saved */
	oldm=oldms;savm=savms; /* Global pointers */
/* Hstepm could be zero and should return the unit matrix */	/* Hstepm could be zero and should return the unit matrix */
for (i=1;i<=nlstate+ndeath;i++)	for (i=1;i<=nlstate+ndeath;i++)
for (j=1;j<=nlstate+ndeath;j++){	for (j=1;j<=nlstate+ndeath;j++){
Line 3183 double *hbxij(double *po, int nhstep	Line 3324 double *hbxij(double *po, int nhstep
newm=savm;	newm=savm;
/* Covariates have to be included here again */	/* Covariates have to be included here again */
cov[1]=1.;	cov[1]=1.;
agexact=age-((h-1)hstepm + (d-1))stepm/YEARM; /* age just before transition */	agexact=age-( (h-1)hstepm + (d) )stepm/YEARM; /* age just before transition, d or d-1? */
/* agexact=age+((h-1)hstepm + (d-1))stepm/YEARM; /\* age just before transition \/ /	/* agexact=age+((h-1)hstepm + (d-1))stepm/YEARM; /\* age just before transition \/ /
cov[2]=agexact;	cov[2]=agexact;
if(nagesqr==1)	if(nagesqr==1)
cov[3]= agexact*agexact;	cov[3]= agexact*agexact;
for (k=1; k<=cptcovn;k++)	for (k=1; k<=cptcovn;k++){
cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)];	/* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,k)]; */
/* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; */	/* /\* cov[2+nagesqr+k]=nbcode[Tvar[k]][codtabm(ij,Tvar[k])]; \/ /
for (k=1; k<=cptcovage;k++) /* Should start at cptcovn+1 */	cov[2+nagesqr+TvarsDind[k]]=nbcode[TvarsD[k]][codtabm(ij,k)];
/* cov[2+Tage[k]]=cov[2+Tage[k]]cov[2]; /	/* printf("hbxij Dummy agexact=%.0f combi=%d k=%d TvarsD[%d]=V%d TvarsDind[%d]=%d nbcode=%d cov[%d]=%lf codtabm(%d,Tvar[%d])=%d \n",agexact,ij,k, k, TvarsD[k],k,TvarsDind[k],nbcode[TvarsD[k]][codtabm(ij,k)],2+nagesqr+TvarsDind[k],cov[2+nagesqr+TvarsDind[k]], ij, k, codtabm(ij,k)); */
cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];	}
/* cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,Tvar[Tage[k]])]cov[2]; /	for (k=1; k<=nsq;k++) { /* For single varying covariates only */
for (k=1; k<=cptcovprod;k++) /* Useless because included in cptcovn */	/* Here comes the value of quantitative after renumbering k with single quantitative covariates */
	cov[2+nagesqr+TvarsQind[k]]=Tqresult[nres][k];
	/* printf("hPxij Quantitative k=%d TvarsQind[%d]=%d, TvarsQ[%d]=V%d,Tqresult[%d][%d]=%f\n",k,k,TvarsQind[k],k,TvarsQ[k],nres,k,Tqresult[nres][k]); */
	}
	for (k=1; k<=cptcovage;k++){ /* Should start at cptcovn+1 */
	if(Dummy[Tvar[Tage[k]]]){
	cov[2+nagesqr+Tage[k]]=nbcode[Tvar[Tage[k]]][codtabm(ij,k)]*cov[2];
	} else{
	cov[2+nagesqr+Tage[k]]=Tqresult[nres][k];
	}
	/* printf("hBxij Age combi=%d k=%d Tage[%d]=V%d Tqresult[%d][%d]=%f\n",ij,k,k,Tage[k],nres,k,Tqresult[nres][k]); */
	}
	for (k=1; k<=cptcovprod;k++){ /* Useless because included in cptcovn */
cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];	cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,k)]*nbcode[Tvard[k][2]][codtabm(ij,k)];
/* cov[2+nagesqr+Tprod[k]]=nbcode[Tvard[k][1]][codtabm(ij,Tvard[k][1])]nbcode[Tvard[k][2]][codtabm(ij,Tvard[k][2])]; /	}


/printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);/	/printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);/
/printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);/	/printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);/

/* Careful transposed matrix */	/* Careful transposed matrix */
/* age is in cov[2] */	/* age is in cov[2], prevacurrent at beginning of transition. */
/* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */	/* out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent, dnewm, doldm, dsavm,ij),\ */
/* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */	/* 1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm); */
out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\	out=matprod2(newm, bmij(pmmij,cov,ncovmodel,x,nlstate,prevacurrent,ij),\
Line 3228 double *hbxij(double *po, int nhstep	Line 3380 double *hbxij(double *po, int nhstep
for(i=1; i<=nlstate+ndeath; i++)	for(i=1; i<=nlstate+ndeath; i++)
for(j=1;j<=nlstate+ndeath;j++) {	for(j=1;j<=nlstate+ndeath;j++) {
po[i][j][h]=newm[i][j];	po[i][j][h]=newm[i][j];
/if(h==nhstepm) printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]);/	/* if(h==nhstepm) */
	/* printf("po[%d][%d][%d]=%f ",i,j,h,po[i][j][h]); */
}	}
/printf("h=%d ",h);/	/* printf("h=%d %.1f ",h, agexact); */
} /* end h */	} /* end h */
/* printf("\n H=%d \n",h); */	/* printf("\n H=%d nhs=%d \n",h, nhstepm); */
return po;	return po;
}	}

Line 3687 double funcone( double *x)	Line 3840 double funcone( double *x)
s1=s[mw[mi][i]][i];	s1=s[mw[mi][i]][i];
s2=s[mw[mi+1][i]][i];	s2=s[mw[mi+1][i]][i];
/* if(s2==-1){ */	/* if(s2==-1){ */
/* printf(" s1=%d, s2=%d i=%d \n", s1, s2, i); */	/* printf(" ERROR s1=%d, s2=%d i=%d \n", s1, s2, i); */
/* /\* exit(1); \/ /	/* /\* exit(1); \/ /
/* } */	/* } */
bbh=(double)bh[mi][i]/(double)stepm;	bbh=(double)bh[mi][i]/(double)stepm;
Line 3720 double funcone( double *x)	Line 3873 double funcone( double *x)
fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\	fprintf(ficresilk,"%09ld %6.1f %6.1f %6d %2d %2d %2d %2d %3d %15.6f %8.4f %8.3f\
%11.6f %11.6f %11.6f ", \	%11.6f %11.6f %11.6f ", \
num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,	num[i], agebegin, ageend, i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],weight[i]*gipmx/gsw,
2weight[i]lli,out[s1][s2],savm[s1][s2]);	2weight[i]lli,(s2==-1? -1: out[s1][s2]),(s2==-1? -1: savm[s1][s2]));
for(k=1,llt=0.,l=0.; k<=nlstate; k++){	for(k=1,llt=0.,l=0.; k<=nlstate; k++){
llt +=ll[k]*gipmx/gsw;	llt +=ll[k]*gipmx/gsw;
fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);	fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
Line 3741 return -l;	Line 3894 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 3765 void likelione(FILE *ficres,double p[],	Line 3918 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 3773 void likelione(FILE *ficres,double p[],	Line 3926 void likelione(FILE *ficres,double p[],
else if(mle >=1)	else if(mle >=1)
fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);	fprintf(fichtm,"\n<br>File of contributions to the likelihood computed with optimized parameters mle = %d.",mle);
fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));	fprintf(fichtm," You should at least run with mle >= 1 to get starting values corresponding to the optimized parameters in order to visualize the real contribution of each individual/wave: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
	fprintf(fichtm,"\n<br>Equation of the model: <b>model=1+age+%s</b><br>\n",model);

for (k=1; k<= nlstate ; k++) {	for (k=1; k<= nlstate ; k++) {
fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Dot's sizes are related to corresponding weight: <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \	fprintf(fichtm,"<br>- Probability p<sub>%dj</sub> by origin %d and destination j. Dot's sizes are related to corresponding weight: <a href=\"%s-p%dj.png\">%s-p%dj.png</a><br> \
Line 4240 void pstamp(FILE *fichier)	Line 4393 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);
}	}

int linreg(int ifi, int ila, int no, const double x[], const double y[], double a, double* b, double* r, double* sa, double * sb) {

/* y=a+bx regression */
double sumx = 0.0; /* sum of x */
double sumx2 = 0.0; /* sum of x*2 /
double sumxy = 0.0; /* sum of x * y */
double sumy = 0.0; /* sum of y */
double sumy2 = 0.0; /* sum of y*2 /
double sume2; /* sum of square or residuals */
double yhat;

double denom=0;
int i;
int ne=*no;

for ( i=ifi, ne=0;i<=ila;i++) {
if(!isfinite(x[i]) \|\| !isfinite(y[i])){
/* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
continue;
}
ne=ne+1;
sumx += x[i];
sumx2 += x[i]*x[i];
sumxy += x[i] * y[i];
sumy += y[i];
sumy2 += y[i]*y[i];
denom = (ne * sumx2 - sumx*sumx);
/* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
}

denom = (ne * sumx2 - sumx*sumx);
if (denom == 0) {
// vertical, slope m is infinity
*b = INFINITY;
*a = 0;
if (r) *r = 0;
return 1;
}

b = (ne sumxy - sumx * sumy) / denom;
a = (sumy sumx2 - sumx * sumxy) / denom;
if (r!=NULL) {
r = (sumxy - sumx sumy / ne) / /* compute correlation coeff */
sqrt((sumx2 - sumxsumx/ne)
(sumy2 - sumy*sumy/ne));
}
*no=ne;
for ( i=ifi, ne=0;i<=ila;i++) {
if(!isfinite(x[i]) \|\| !isfinite(y[i])){
/* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
continue;
}
ne=ne+1;
yhat = y[i] - a -b* x[i];
sume2 += yhat * yhat ;

denom = (ne * sumx2 - sumx*sumx);
/* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
}
sb = sqrt(sume2/(ne-2)/(sumx2 - sumx sumx /ne));
sa= sb * sqrt(sumx2/ne);

return 0;
}

/********** Frequencies ******************/	/********** Frequencies ******************/
void freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int s, double agev, int nlstate, int imx, \	void freqsummary(char fileres[], double p[], double pstart[], int iagemin, int iagemax, int s, double agev, int nlstate, int imx, \
Line 4316 void freqsummary(char fileres[], double	Line 4406 void freqsummary(char fileres[], double
int mi; /* Effective wave */	int mi; /* Effective wave */
int first;	int first;
double **freq; / Frequencies */	double **freq; / Frequencies */
double x, y, a,b,r, sa, sb; /* 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;	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 4331 void freqsummary(char fileres[], double	Line 4421 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 4439 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4531 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 4455 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4550 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 4478 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4570 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 4498 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4590 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 4516 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4608 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 4531 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4628 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 4568 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4670 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 4755 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4878 Title=%s <br>Datafile=%s Firstpass=%d La
y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);	y[iage]= log(freq[i][k][iage]/freq[i][i][iage]);
/* printf("i=%d, k=%d, s1=%d, j1=%d, jj=%d, y[%d]=%f\n",i,k,s1,j1,jj, iage, y[iage]); */	/* printf("i=%d, k=%d, s1=%d, j1=%d, jj=%d, y[%d]=%f\n",i,k,s1,j1,jj, iage, y[iage]); */
}	}
	/* Some are not finite, but linreg will ignore these ages */
	no=0;
linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+bx with standard errors /	linreg(iagemin,iagemax,&no,x,y,&a,&b,&r, &sa, &sb ); /* y= a+bx with standard errors /
pstart[s1]=b;	pstart[s1]=b;
pstart[s1-1]=a;	pstart[s1-1]=a;
Line 4800 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4925 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 4846 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4971 Title=%s <br>Datafile=%s Firstpass=%d La
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 4858 Title=%s <br>Datafile=%s Firstpass=%d La	Line 4985 Title=%s <br>Datafile=%s Firstpass=%d La
/* End of freqsummary */	/* End of freqsummary */
}	}

	/* Simple linear regression */
	int linreg(int ifi, int ila, int no, const double x[], const double y[], double a, double* b, double* r, double* sa, double * sb) {

	/* y=a+bx regression */
	double sumx = 0.0; /* sum of x */
	double sumx2 = 0.0; /* sum of x*2 /
	double sumxy = 0.0; /* sum of x * y */
	double sumy = 0.0; /* sum of y */
	double sumy2 = 0.0; /* sum of y*2 /
	double sume2 = 0.0; /* sum of square or residuals */
	double yhat;

	double denom=0;
	int i;
	int ne=*no;

	for ( i=ifi, ne=0;i<=ila;i++) {
	if(!isfinite(x[i]) \|\| !isfinite(y[i])){
	/* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
	continue;
	}
	ne=ne+1;
	sumx += x[i];
	sumx2 += x[i]*x[i];
	sumxy += x[i] * y[i];
	sumy += y[i];
	sumy2 += y[i]*y[i];
	denom = (ne * sumx2 - sumx*sumx);
	/* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
	}

	denom = (ne * sumx2 - sumx*sumx);
	if (denom == 0) {
	// vertical, slope m is infinity
	*b = INFINITY;
	*a = 0;
	if (r) *r = 0;
	return 1;
	}

	b = (ne sumxy - sumx * sumy) / denom;
	a = (sumy sumx2 - sumx * sumxy) / denom;
	if (r!=NULL) {
	r = (sumxy - sumx sumy / ne) / /* compute correlation coeff */
	sqrt((sumx2 - sumxsumx/ne)
	(sumy2 - sumy*sumy/ne));
	}
	*no=ne;
	for ( i=ifi, ne=0;i<=ila;i++) {
	if(!isfinite(x[i]) \|\| !isfinite(y[i])){
	/* printf(" x[%d]=%f, y[%d]=%f\n",i,x[i],i,y[i]); */
	continue;
	}
	ne=ne+1;
	yhat = y[i] - a -b* x[i];
	sume2 += yhat * yhat ;

	denom = (ne * sumx2 - sumx*sumx);
	/* printf("ne=%d, i=%d,x[%d]=%f, y[%d]=%f sumx=%f, sumx2=%f, sumxy=%f, sumy=%f, sumy2=%f, denom=%f\n",ne,i,i,x[i],i,y[i], sumx, sumx2,sumxy, sumy, sumy2,denom); */
	}
	sb = sqrt(sume2/(double)(ne-2)/(sumx2 - sumx sumx /(double)ne));
	sa= sb * sqrt(sumx2/ne);

	return 0;
	}

/********** Prevalence ******************/	/********** Prevalence ******************/
void prevalence(double *probs, double agemin, double agemax, int s, double *agev, int nlstate, int imx, int Tvar, int *nbcode, int ncodemax,double mint,double anint, double dateprev1,double dateprev2, int firstpass, int lastpass)	void prevalence(double *probs, double agemin, double agemax, int s, double *agev, int nlstate, int imx, int Tvar, int *nbcode, int ncodemax,double mint,double anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
{	{
Line 4887 void prevalence(double ***probs, double	Line 5080 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 4945 void prevalence(double ***probs, double	Line 5138 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 probs[%d][%d][%d]=%lf because of lack of cases\nSee others in log file...\n",jk,i,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]);
	}else{
	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 5193 void concatwav(int wav[], int **dh, int	Line 5388 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 5213 void concatwav(int wav[], int **dh, int	Line 5410 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 5259 void concatwav(int wav[], int **dh, int	Line 5460 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 5280 void concatwav(int wav[], int **dh, int	Line 5487 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 5387 void concatwav(int wav[], int **dh, int	Line 5580 void concatwav(int wav[], int **dh, int
/* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.	/* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.
nhstepm is the number of hstepm from age to agelim	nhstepm is the number of hstepm from age to agelim
nstepm is the number of stepm from age to agelin.	nstepm is the number of stepm from age to agelin.
Look at hpijx to understand the reason of that which relies in memory size	Look at hpijx to understand the reason which relies in memory size consideration
and note for a fixed period like estepm months */	and note for a fixed period like estepm months */
/* We decided (b) to get a life expectancy respecting the most precise curvature of the	/* We decided (b) to get a life expectancy respecting the most precise curvature of the
survival function given by stepm (the optimization length). Unfortunately it	survival function given by stepm (the optimization length). Unfortunately it
Line 5618 void concatwav(int wav[], int **dh, int	Line 5811 void concatwav(int wav[], int **dh, int
/* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/	/* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/

}	}

	/* Standard deviation of expectancies ij */
fprintf(ficresstdeij,"%3.0f",age );	fprintf(ficresstdeij,"%3.0f",age );
for(i=1; i<=nlstate;i++){	for(i=1; i<=nlstate;i++){
eip=0.;	eip=0.;
Line 5633 void concatwav(int wav[], int **dh, int	Line 5827 void concatwav(int wav[], int **dh, int
}	}
fprintf(ficresstdeij,"\n");	fprintf(ficresstdeij,"\n");

	/* Variance of expectancies ij */
fprintf(ficrescveij,"%3.0f",age );	fprintf(ficrescveij,"%3.0f",age );
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++){	for(j=1; j<=nlstate;j++){
Line 5666 void concatwav(int wav[], int **dh, int	Line 5861 void concatwav(int wav[], int **dh, int
/********** Variance ****************/	/********** Variance ****************/
void varevsij(char optionfilefiname[], double *vareij, double matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double oldm, double savm, double *prlim, double ftolpl, int ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[], int nres)	void varevsij(char optionfilefiname[], double *vareij, double matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double oldm, double savm, double *prlim, double ftolpl, int ncvyearp, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[], int nres)
{	{
/* Variance of health expectancies */	/** Variance of health expectancies
/* double prevalim(double prlim, int nlstate, double xp, double age, double oldm, double * savm,double ftolpl);*/	* double prevalim(double prlim, int nlstate, double xp, double age, double oldm, double * savm,double ftolpl);
/* double *newm;/	* double **newm;
/* int movingaverage(double *probs, double bage,double fage, double mobaverage, int mobilav)/	* int movingaverage(double *probs, double bage,double fage, double *mobaverage, int mobilav)
	*/

/* int movingaverage(); */	/* int movingaverage(); */
double dnewm,doldm;	double dnewm,doldm;
double dnewmp,doldmp;	double dnewmp,doldmp;
int i, j, nhstepm, hstepm, h, nstepm ;	int i, j, nhstepm, hstepm, h, nstepm ;
	int first=0;
int k;	int k;
double *xp;	double *xp;
double gp, gm; /* for var eij */	double gp, gm; /*< for var eij /
double *gradg, trgradg; /for var eij */	double *gradg, trgradg; /< for var eij /
double gradgp, trgradgp; /* for var p point j */	double gradgp, trgradgp; /*< for var p point j /
double gpp, gmp; /* for var p point j */	double gpp, gmp; /*< for var p point j /
double *varppt; / for var p point j nlstate to nlstate+ndeath */	double varppt; /< for var p point j nlstate to nlstate+ndeath */
double ***p3mat;	double ***p3mat;
double age,agelim, hf;	double age,agelim, hf;
/* double **mobaverage; /	/* double **mobaverage; /
Line 5742 void concatwav(int wav[], int **dh, int	Line 5939 void concatwav(int wav[], int **dh, int
/* fprintf(fichtm, "#Local time at start: %s", strstart);*/	/* fprintf(fichtm, "#Local time at start: %s", strstart);*/
fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");	fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
fprintf(fichtm,"\n<br>%s <br>\n",digitp);	fprintf(fichtm,"\n<br>%s <br>\n",digitp);
/* } */
varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);	varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
pstamp(ficresvij);	pstamp(ficresvij);
fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");	fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
Line 5797 void concatwav(int wav[], int **dh, int	Line 5994 void concatwav(int wav[], int **dh, int
for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/	for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
xp[i] = x[i] + (i==theta ?delti[theta]:0);	xp[i] = x[i] + (i==theta ?delti[theta]:0);
}	}
	/**< Computes the prevalence limit with parameter theta shifted of delta up to ftolpl precision and
	* returns into prlim .
	*/
prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);	prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ncvyearp,ij, nres);

	/* If popbased = 1 we use crossection prevalences. Previous step is useless but prlim is created */
if (popbased==1) {	if (popbased==1) {
if(mobilav ==0){	if(mobilav ==0){
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
Line 5809 void concatwav(int wav[], int **dh, int	Line 6009 void concatwav(int wav[], int **dh, int
prlim[i][i]=mobaverage[(int)age][i][ij];	prlim[i][i]=mobaverage[(int)age][i][ij];
}	}
}	}
	/**< Computes the shifted transition matrix \f$ {}{h}_p^{ij}_x\f$ at horizon h.
hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres); /* Returns p3mat[i][j][h] for h=1 to nhstepm */	*/
	hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij,nres); /* Returns p3mat[i][j][h] for h=0 to nhstepm */
	/**< And for each alive state j, sums over i \f$ w^i_x {}{h}_p^{ij}x\f$, which are the probability
	* at horizon h in state j including mortality.
	*/
for(j=1; j<= nlstate; j++){	for(j=1; j<= nlstate; j++){
for(h=0; h<=nhstepm; h++){	for(h=0; h<=nhstepm; h++){
for(i=1, gp[h][j]=0.;i<=nlstate;i++)	for(i=1, gp[h][j]=0.;i<=nlstate;i++)
gp[h][j] += prlim[i][i]*p3mat[i][j][h];	gp[h][j] += prlim[i][i]*p3mat[i][j][h];
}	}
}	}
/* Next for computing probability of death (h=1 means	/* Next for computing shifted+ probability of death (h=1 means
computed over hstepm matrices product = hstepm*stepm months)	computed over hstepm matrices product = hstepm*stepm months)
as a weighted average of prlim.	as a weighted average of prlim(i) * p(i,j) p.3=w1p13 + w2p23 .
*/	*/
for(j=nlstate+1;j<=nlstate+ndeath;j++){	for(j=nlstate+1;j<=nlstate+ndeath;j++){
for(i=1,gpp[j]=0.; i<= nlstate; i++)	for(i=1,gpp[j]=0.; i<= nlstate; i++)
gpp[j] += prlim[i][i]*p3mat[i][j][1];	gpp[j] += prlim[i][i]*p3mat[i][j][1];
}	}
/* end probability of death */
	/* Again with minus shift */

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

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

if (popbased==1) {	if (popbased==1) {
Line 5858 void concatwav(int wav[], int **dh, int	Line 6063 void concatwav(int wav[], int **dh, int
for(i=1,gmp[j]=0.; i<= nlstate; i++)	for(i=1,gmp[j]=0.; i<= nlstate; i++)
gmp[j] += prlim[i][i]*p3mat[i][j][1];	gmp[j] += prlim[i][i]*p3mat[i][j][1];
}	}
/* end probability of death */	/* end shifting computations */

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

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

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

for(h=0; h<=nhstepm; h++) /* veij */	for(h=0; h<=nhstepm; h++) /* veij */
Line 5881 void concatwav(int wav[], int **dh, int	Line 6090 void concatwav(int wav[], int **dh, int
for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */	for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
for(theta=1; theta <=npar; theta++)	for(theta=1; theta <=npar; theta++)
trgradgp[j][theta]=gradgp[theta][j];	trgradgp[j][theta]=gradgp[theta][j];
	/**< as well as its transposed matrix
	*/

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

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

for(h=0;h<=nhstepm;h++){	for(h=0;h<=nhstepm;h++){
for(k=0;k<=nhstepm;k++){	for(k=0;k<=nhstepm;k++){
matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);	matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
Line 5898 void concatwav(int wav[], int **dh, int	Line 6113 void concatwav(int wav[], int **dh, int
}	}
}	}

/* pptj */	/* pptj is p.3 or p.j = trgradgp by cov by gradgp, variance of
	* p.j overall mortality formula 49 but computed directly because
	* we compute the grad (wix pijx) instead of grad (pijx),even if
	* wix is independent of theta.
	*/
matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);	matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);	matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
for(j=nlstate+1;j<=nlstate+ndeath;j++)	for(j=nlstate+1;j<=nlstate+ndeath;j++)
Line 5986 void concatwav(int wav[], int **dh, int	Line 6205 void concatwav(int wav[], int **dh, int
} /* end varevsij */	} /* end varevsij */

/********** Variance of prevlim ****************/	/********** Variance of prevlim ****************/
void varprevlim(char fileres[], double varpl, double matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double oldm, double savm, double *prlim, double ftolpl, int ncvyearp, int ij, char strstart[], int nres)	void varprevlim(char fileresvpl[], FILE ficresvpl, double varpl, double matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double oldm, double savm, double prlim, double ftolpl, int ncvyearp, int ij, char strstart[], int nres)
{	{
/* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/	/* Variance of prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
/* double prevalim(double prlim, int nlstate, double xp, double age, double oldm, double savm,double ftolpl);/	/* double prevalim(double prlim, int nlstate, double xp, double age, double oldm, double savm,double ftolpl);/

double dnewm,doldm;	double dnewmpar,doldm;
int i, j, nhstepm, hstepm;	int i, j, nhstepm, hstepm;
double *xp;	double *xp;
double gp, gm;	double gp, gm;
Line 6001 void concatwav(int wav[], int **dh, int	Line 6220 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 6010 void concatwav(int wav[], int **dh, int	Line 6229 void concatwav(int wav[], int **dh, int
fprintf(ficresvpl,"\n");	fprintf(ficresvpl,"\n");

xp=vector(1,npar);	xp=vector(1,npar);
dnewm=matrix(1,nlstate,1,npar);	dnewmpar=matrix(1,nlstate,1,npar);
doldm=matrix(1,nlstate,1,nlstate);	doldm=matrix(1,nlstate,1,nlstate);

hstepm=1YEARM; / Every year of age */	hstepm=1YEARM; / Every year of age */
Line 6030 void concatwav(int wav[], int **dh, int	Line 6249 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 6080 void concatwav(int wav[], int **dh, int	Line 6299 void concatwav(int wav[], int **dh, int
for(i=1;i<=nlstate;i++)	for(i=1;i<=nlstate;i++)
varpl[i][(int)age] =0.;	varpl[i][(int)age] =0.;
if((int)age==79 \|\|(int)age== 80 \|\|(int)age== 81){	if((int)age==79 \|\|(int)age== 80 \|\|(int)age== 81){
matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);	matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);	matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
}else{	}else{
matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);	matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);	matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
}	}
for(i=1;i<=nlstate;i++)	for(i=1;i<=nlstate;i++)
varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */	varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
Line 6092 void concatwav(int wav[], int **dh, int	Line 6311 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 6105 void concatwav(int wav[], int **dh, int	Line 6327 void concatwav(int wav[], int **dh, int

free_vector(xp,1,npar);	free_vector(xp,1,npar);
free_matrix(doldm,1,nlstate,1,npar);	free_matrix(doldm,1,nlstate,1,npar);
free_matrix(dnewm,1,nlstate,1,nlstate);	free_matrix(dnewmpar,1,nlstate,1,nlstate);

	}


	/********** Variance of backprevalence limit ****************/
	void varbrevlim(char fileresvbl[], FILE ficresvbl, double varbpl, double matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double oldm, double savm, double bprlim, double ftolpl, int mobilavproj, int ncvyearp, int ij, char strstart[], int nres)
	{
	/* Variance of backward prevalence limit for each state ij using current parameters x[] and estimates of neighbourhood give by delti*/
	/* double prevalim(double prlim, int nlstate, double xp, double age, double oldm, double savm,double ftolpl);/

	double dnewmpar,doldm;
	int i, j, nhstepm, hstepm;
	double *xp;
	double gp, gm;
	double gradg, trgradg;
	double mgm, mgp;
	double age,agelim;
	int theta;

	pstamp(ficresvbl);
	fprintf(ficresvbl,"# Standard deviation of back (stable) prevalences \n");
	fprintf(ficresvbl,"# Age ");
	if(nresult >=1)
	fprintf(ficresvbl," Result# ");
	for(i=1; i<=nlstate;i++)
	fprintf(ficresvbl," %1d-%1d",i,i);
	fprintf(ficresvbl,"\n");

	xp=vector(1,npar);
	dnewmpar=matrix(1,nlstate,1,npar);
	doldm=matrix(1,nlstate,1,nlstate);

	hstepm=1YEARM; / Every year of age */
	hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */
	agelim = AGEINF;
	for (age=fage; age>=bage; age --){ /* If stepm=6 months */
	nhstepm=(int) rint((age-agelim)YEARM/stepm); / Typically 20 years = 2012/6=40 /
	if (stepm >= YEARM) hstepm=1;
	nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
	gradg=matrix(1,npar,1,nlstate);
	mgp=matrix(1,npar,1,nlstate);
	mgm=matrix(1,npar,1,nlstate);
	gp=vector(1,nlstate);
	gm=vector(1,nlstate);

	for(theta=1; theta <=npar; theta++){
	for(i=1; i<=npar; i++){ /* Computes gradient */
	xp[i] = x[i] + (i==theta ?delti[theta]:0);
	}
	if(mobilavproj > 0 )
	bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
	else
	bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
	for(i=1;i<=nlstate;i++){
	gp[i] = bprlim[i][i];
	mgp[theta][i] = bprlim[i][i];
	}
	for(i=1; i<=npar; i++) /* Computes gradient */
	xp[i] = x[i] - (i==theta ?delti[theta]:0);
	if(mobilavproj > 0 )
	bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
	else
	bprevalim(bprlim, mobaverage,nlstate,xp,age,ftolpl,ncvyearp,ij,nres);
	for(i=1;i<=nlstate;i++){
	gm[i] = bprlim[i][i];
	mgm[theta][i] = bprlim[i][i];
	}
	for(i=1;i<=nlstate;i++)
	gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
	/* gradg[theta][2]= -gradg[theta][1]; / / For testing if nlstate=2 */
	} /* End theta */

	trgradg =matrix(1,nlstate,1,npar);

	for(j=1; j<=nlstate;j++)
	for(theta=1; theta <=npar; theta++)
	trgradg[j][theta]=gradg[theta][j];
	/* if((int)age==79 \|\|(int)age== 80 \|\|(int)age== 81 ){ */
	/* printf("\nmgm mgp %d ",(int)age); */
	/* for(j=1; j<=nlstate;j++){ */
	/* printf(" %d ",j); */
	/* for(theta=1; theta <=npar; theta++) */
	/* printf(" %d %lf %lf",theta,mgm[theta][j],mgp[theta][j]); */
	/* printf("\n "); */
	/* } */
	/* } */
	/* if((int)age==79 \|\|(int)age== 80 \|\|(int)age== 81 ){ */
	/* printf("\n gradg %d ",(int)age); */
	/* for(j=1; j<=nlstate;j++){ */
	/* printf("%d ",j); */
	/* for(theta=1; theta <=npar; theta++) */
	/* printf("%d %lf ",theta,gradg[theta][j]); */
	/* printf("\n "); */
	/* } */
	/* } */

	for(i=1;i<=nlstate;i++)
	varbpl[i][(int)age] =0.;
	if((int)age==79 \|\|(int)age== 80 \|\|(int)age== 81){
	matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
	matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
	}else{
	matprod2(dnewmpar,trgradg,1,nlstate,1,npar,1,npar,matcov);
	matprod2(doldm,dnewmpar,1,nlstate,1,npar,1,nlstate,gradg);
	}
	for(i=1;i<=nlstate;i++)
	varbpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */

	fprintf(ficresvbl,"%.0f ",age );
	if(nresult >=1)
	fprintf(ficresvbl,"%d ",nres );
	for(i=1; i<=nlstate;i++)
	fprintf(ficresvbl," %.5f (%.5f)",bprlim[i][i],sqrt(varbpl[i][(int)age]));
	fprintf(ficresvbl,"\n");
	free_vector(gp,1,nlstate);
	free_vector(gm,1,nlstate);
	free_matrix(mgm,1,npar,1,nlstate);
	free_matrix(mgp,1,npar,1,nlstate);
	free_matrix(gradg,1,npar,1,nlstate);
	free_matrix(trgradg,1,nlstate,1,npar);
	} /* End age */

	free_vector(xp,1,npar);
	free_matrix(doldm,1,nlstate,1,npar);
	free_matrix(dnewmpar,1,nlstate,1,nlstate);

}	}

Line 6185 void varprob(char optionfilefiname[], do	Line 6532 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.</li>\n",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 6382 To be simple, these graphs help to under	Line 6729 To be simple, these graphs help to under
}	}

/* Eigen vectors */	/* Eigen vectors */
v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));	if(1+(v1-lc1)*(v1-lc1)/cv12/cv12 <1.e-5){
	printf(" Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
	fprintf(ficlog," Error sqrt of a negative number: %lf\n",1+(v1-lc1)*(v1-lc1)/cv12/cv12);
	v11=(1./sqrt(fabs(1+(v1-lc1)*(v1-lc1)/cv12/cv12)));
	}else
	v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
/v21=sqrt(1.-v11v11); // error */	/v21=sqrt(1.-v11v11); // error */
v21=(lc1-v1)/cv12*v11;	v21=(lc1-v1)/cv12*v11;
v12=-v21;	v12=-v21;
Line 6402 To be simple, these graphs help to under	Line 6754 To be simple, these graphs help to under
fprintf(ficgp,"\nset parametric;unset label");	fprintf(ficgp,"\nset parametric;unset label");
fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);	fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
fprintf(ficgp,"\nset ter svg size 640, 480");	fprintf(ficgp,"\nset ter svg size 640, 480");
fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\	fprintf(fichtmcov,"\n<p><br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
:<a href=\"%s_%d%1d%1d-%1d%1d.svg\"> \	:<a href=\"%s_%d%1d%1d-%1d%1d.svg\"> \
%s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\	%s_%d%1d%1d-%1d%1d.svg</A>, ",k1,l1,k2,l2,\
subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \	subdirf2(optionfilefiname,"VARPIJGR_"), j1,k1,l1,k2,l2, \
Line 6413 To be simple, these graphs help to under	Line 6765 To be simple, these graphs help to under
fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);	fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);	fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)), %11.3e +%.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)) not", \	fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)), %11.3e +%.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)) not", \
mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \	mu1,std,v11,sqrt(fabs(lc1)),v12,sqrt(fabs(lc2)), \
mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));	mu2,std,v21,sqrt(fabs(lc1)),v22,sqrt(fabs(lc2))); /* For gnuplot only */
}else{	}else{
first=0;	first=0;
fprintf(fichtmcov," %d (%.3f),",(int) age, c12);	fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);	fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);	fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
fprintf(ficgp,"\nreplot %11.3e+ %.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)), %11.3e +%.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)) not", \	fprintf(ficgp,"\nreplot %11.3e+ %.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)), %11.3e +%.3f(%11.3e%11.3ecos(t)+%11.3e%11.3esin(t)) not", \
mu1,std,v11,sqrt(lc1),v12,sqrt(lc2), \	mu1,std,v11,sqrt(lc1),v12,sqrt(fabs(lc2)), \
mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));	mu2,std,v21,sqrt(lc1),v22,sqrt(fabs(lc2)));
}/* if first */	}/* if first */
} /* age mod 5 */	} /* age mod 5 */
} /* end loop age */	} /* end loop age */
Line 6451 void printinghtml(char fileresu[], char	Line 6803 void printinghtml(char fileresu[], char
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 backcast, int estepm , \
double jprev1, double mprev1,double anprev1, double dateprev1, \	double jprev1, double mprev1,double anprev1, double dateprev1, double dateproj1, double dateback1, \
double jprev2, double mprev2,double anprev2, double dateprev2){	double jprev2, double mprev2,double anprev2, double dateprev2, double dateproj2, 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 6473 void printinghtml(char fileresu[], char	Line 6825 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 6582 divided by h: <sub>h</sub>P<sub>ij</sub>	Line 6934 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(backcast==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) up to period (stable) prevalence in state %d. Or probability to be 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- 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, 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, dateproj1, dateproj2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJ_"),cpt,k1,nres);
	}
	}
	if(backcast==1){
	/* Back projection of prevalence up to stable (mixed) back-prevalence in each health state */
	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), \
	from year %.1f up to year %.1f (probably close to stable [mixed] back prevalence in state %d (randomness in cross-sectional prevalence is not taken into \
	account but can visually be appreciated). Or probability to have been in an state %d, knowing that the person was in either state (1 or %d) \
	with weights corresponding to observed prevalence at different ages. <a href=\"%s_%d-%d-%d.svg\">%s_%d-%d-%d.svg</a><br> \
	<img src=\"%s_%d-%d-%d.svg\">", dateprev1, dateprev2, mobilavproj, dateback1, dateback2, cpt, cpt, nlstate, subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres,subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
}	}
}	}

Line 6649 See page 'Matrix of variance-covariance	Line 7011 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 6713 true period expectancies (those weighted	Line 7075 true period expectancies (those weighted
}	}

/***************** Gnuplot file ************/	/***************** Gnuplot file ************/
void printinggnuplot(char fileresu[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , int prevfcast, int backcast, char pathc[], double p[]){	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){

char dirfileres[132],optfileres[132];	char dirfileres[132],optfileres[132];
char gplotcondition[132], gplotlabel[132];	char gplotcondition[132], gplotlabel[132];
Line 6722 void printinggnuplot(char fileresu[], ch	Line 7084 void printinggnuplot(char fileresu[], ch
int ng=0;	int ng=0;
int vpopbased;	int vpopbased;
int ioffset; /* variable offset for columns */	int ioffset; /* variable offset for columns */
	int iyearc=1; /* variable column for year of projection */
	int iagec=1; /* variable column for age of projection */
int nres=0; /* Index of resultline */	int nres=0; /* Index of resultline */
	int istart=1; /* For starting graphs in projections */

/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */	/* if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
/* printf("Problem with file %s",optionfilegnuplot); */	/* printf("Problem with file %s",optionfilegnuplot); */
Line 6734 void printinggnuplot(char fileresu[], ch	Line 7099 void printinggnuplot(char fileresu[], ch
/#endif /	/#endif /
m=pow(2,cptcoveff);	m=pow(2,cptcoveff);

	/* diagram of the model */
	fprintf(ficgp,"\n#Diagram of the model \n");
	fprintf(ficgp,"\ndelta=0.03;delta2=0.07;unset arrow;\n");
	fprintf(ficgp,"yoff=(%d > 2? 0:1);\n",nlstate);
	fprintf(ficgp,"\n#Peripheral arrows\nset for [i=1:%d] for [j=1:%d] arrow i10+j from cos(pi((1-(%d/2)2./%d)/2+(i-1)2./%d))-(i!=j?(i-j)/abs(i-j)delta:0), yoff +sin(pi((1-(%d/2)2./%d)/2+(i-1)2./%d)) + (i!=j?(i-j)/abs(i-j)delta:0) rto -0.95(cos(pi((1-(%d/2)2./%d)/2+(i-1)2./%d))+(i!=j?(i-j)/abs(i-j)delta:0) - cos(pi((1-(%d/2)2./%d)/2+(j-1)2./%d)) + (i!=j?(i-j)/abs(i-j)delta2:0)), -0.95(sin(pi((1-(%d/2)2./%d)/2+(i-1)2./%d)) + (i!=j?(i-j)/abs(i-j)delta:0) - sin(pi((1-(%d/2)2./%d)/2+(j-1)2./%d))+( i!=j?(i-j)/abs(i-j)*delta2:0)) ls (i < j? 1:2)\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);

	fprintf(ficgp,"\n#Centripete arrows (turning in other direction (1-i) instead of (i-1)) \nset for [i=1:%d] arrow (%d+1)10+i from cos(pi((1-(%d/2)2./%d)/2+(1-i)2./%d))-(i!=j?(i-j)/abs(i-j)delta:0), yoff +sin(pi((1-(%d/2)2./%d)/2+(1-i)2./%d)) + (i!=j?(i-j)/abs(i-j)delta:0) rto -0.80(cos(pi((1-(%d/2)2./%d)/2+(1-i)2./%d))+(i!=j?(i-j)/abs(i-j)delta:0) ), -0.80(sin(pi((1-(%d/2)2./%d)/2+(1-i)2./%d)) + (i!=j?(i-j)/abs(i-j)*delta:0) + yoff ) ls 4\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
	fprintf(ficgp,"\n#show arrow\nunset label\n");
	fprintf(ficgp,"\n#States labels, starting from 2 (2-i) instead of (1-i), was (i-1)\nset for [i=1:%d] label i sprintf(\"State %%d\",i) center at cos(pi((1-(%d/2)2./%d)/2+(2-i)2./%d)), yoff+sin(pi((1-(%d/2)2./%d)/2+(2-i)2./%d)) font \"helvetica, 16\" tc rgbcolor \"blue\"\n",nlstate,nlstate,nlstate,nlstate,nlstate,nlstate,nlstate);
	fprintf(ficgp,"\nset label %d+1 sprintf(\"State %%d\",%d+1) center at 0.,0. font \"helvetica, 16\" tc rgbcolor \"red\"\n",nlstate,nlstate);
	fprintf(ficgp,"\n#show label\nunset border;unset xtics; unset ytics;\n");
	fprintf(ficgp,"\n\nset ter svg size 640, 480;set out \"%s_.svg\" \n",subdirf2(optionfilefiname,"D_"));
	fprintf(ficgp,"unset log y; plot [-1.2:1.2][yoff-1.2:1.2] 1/0 not; set out;reset;\n");

/* Contribution to likelihood */	/* Contribution to likelihood */
/* Plot the probability implied in the likelihood */	/* Plot the probability implied in the likelihood */
fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");	fprintf(ficgp,"\n# Contributions to the Likelihood, mle >=1. For mle=4 no interpolation, pure matrix products.\n#\n");
Line 6774 void printinggnuplot(char fileresu[], ch	Line 7153 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 6803 void printinggnuplot(char fileresu[], ch	Line 7182 void printinggnuplot(char fileresu[], ch

fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"V_"),cpt,k1,nres);
fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);	fprintf(ficgp,"\n#set out \"V_%s_%d-%d-%d.svg\" \n",optionfilefiname,cpt,k1,nres);
fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);	/* fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel); */
	fprintf(ficgp,"set title \"Alive state %d %s\" font \"Helvetica,12\"\n",cpt,gplotlabel);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),nres-1,nres-1,nres);
/* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */	/* fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter svg size 640, 480\nplot [%.f:%.f] \"%s\" every :::%d::%d u 1:($2==%d ? $3:1/0) \"%%lf %%lf",ageminpar,fage,subdirf2(fileresu,"VPL_"),k1-1,k1-1,nres); */
/* k1-1 error should be nres-1*/	/* k1-1 error should be nres-1*/
Line 6811 void printinggnuplot(char fileresu[], ch	Line 7191 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 6825 void printinggnuplot(char fileresu[], ch	Line 7205 void printinggnuplot(char fileresu[], ch

fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" u 1:((",subdirf2(fileresu,"P_"));	fprintf(ficgp,"\" t\"\" w l lt 1,\"%s\" u 1:((",subdirf2(fileresu,"P_"));
if(cptcoveff ==0){	if(cptcoveff ==0){
fprintf(ficgp,"$%d)) t 'Observed prevalence in state %d' with line lt 3", 2+(cpt-1), cpt );	fprintf(ficgp,"$%d)) t 'Observed prevalence in state %d' with line lt 3", 2+3*(cpt-1), cpt );
}else{	}else{
kl=0;	kl=0;
for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */	for (k=1; k<=cptcoveff; k++){ /* For each combination of covariate */
Line 6876 void printinggnuplot(char fileresu[], ch	Line 7256 void printinggnuplot(char fileresu[], ch
}	}
} /* end covariate */	} /* end covariate */
} /* end if no covariate */	} /* end if no covariate */
	if(backcast == 1){
	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*/
	for (i=1; i<= nlstate ; i ++) {
	if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
	else fprintf(ficgp," %%lf (%%lf)");
	}
	fprintf(ficgp,"\" t\"Backward (stable) prevalence\" w l lt 6 dt 3,\"%s\" every :::%d::%d u 1:($2==%d ? $3+1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
	for (i=1; i<= nlstate ; i ++) {
	if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
	else fprintf(ficgp," %%lf (%%lf)");
	}
	fprintf(ficgp,"\" t\"95%% CI\" w l lt 4,\"%s\" every :::%d::%d u 1:($2==%d ? $3-1.96*$4 : 1/0) \"%%lf %%lf",subdirf2(fileresu,"VBL_"),nres-1,nres-1,nres);
	for (i=1; i<= nlstate ; i ++) {
	if (i==cpt) fprintf(ficgp," %%lf (%%lf)");
	else fprintf(ficgp," %%lf (%%lf)");
	}
	fprintf(ficgp,"\" t\"\" w l lt 4");
	} /* end if backprojcast */
} /* end if backcast */	} /* end if backcast */
fprintf(ficgp,"\nset out ;unset label;\n");	/* fprintf(ficgp,"\nset out ;unset label;\n"); */
	fprintf(ficgp,"\nset out ;unset title;\n");
} /* nres */	} /* nres */
} /* k1 */	} /* k1 */
} /* cpt */	} /* cpt */
Line 7120 set ter svg size 640, 480\nunset log y\n	Line 7520 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 7164 set ter svg size 640, 480\nunset log y\n	Line 7564 set ter svg size 640, 480\nunset log y\n

/* 7eme */	/* 7eme */
if(backcast == 1){	if(backcast == 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 ending 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 7193 set ter svg size 640, 480\nunset log y\n	Line 7593 set ter svg size 640, 480\nunset log y\n
}	}

fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PB_"),cpt,k1,nres);
fprintf(ficgp,"set label \"Ending alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);	fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);	set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
k=3; /* Offset */	k=3; /* Offset */
for (i=1; i<= nlstate ; i ++){ /* State of origin */	for (i=1; i<= nlstate ; i ++){ /* State of arrival */
if(i==1)	if(i==1)
fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));	fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"PIJB_"));
else	else
Line 7210 set ter svg size 640, 480\nunset log y\n	Line 7610 set ter svg size 640, 480\nunset log y\n
/* for (j=2; j<= nlstate ; j ++) */	/* for (j=2; j<= nlstate ; j ++) */
/* fprintf(ficgp,"+$%d",k+l+j-1); */	/* fprintf(ficgp,"+$%d",k+l+j-1); */
/* /\* fprintf(ficgp,"+$%d",k+l+j-1); \/ /	/* /\* fprintf(ficgp,"+$%d",k+l+j-1); \/ /
fprintf(ficgp,") t \"bprev(%d,%d)\" w l",i,cpt);	fprintf(ficgp,") t \"bprev(%d,%d)\" w l",cpt,i);
} /* nlstate */	} /* nlstate */
fprintf(ficgp,"\nset out; unset label;\n");	fprintf(ficgp,"\nset out; unset label;\n");
} /* end cpt state*/	} /* end cpt state*/
Line 7219 set ter svg size 640, 480\nunset log y\n	Line 7619 set ter svg size 640, 480\nunset log y\n

/* 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 7227 set ter svg size 640, 480\nunset log y\n	Line 7627 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 7253 set ter svg size 640, 480\nunset log y\n	Line 7653 set ter svg size 640, 480\nunset log y\n
fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);	fprintf(ficgp,"set label \"Alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);	set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);
for (i=1; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
	/* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 \/ /
	istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
	/istart=1;/ /* Could be one if by state, but nlstate+1 is w.i projection only */
	for (i=istart; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
/# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3/	/# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3/
/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 /	/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 /
/# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3/	/# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3/
/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 /	/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 /
if(i==1){	if(i==istart){
fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));	fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"F_"));
}else{	}else{
fprintf(ficgp,",\\\n '' ");	fprintf(ficgp,",\\\n '' ");
Line 7270 set ter svg size 640, 480\nunset log y\n	Line 7674 set ter svg size 640, 480\nunset log y\n
/# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4/	/# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4/
/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 /	/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 /
fprintf(ficgp," u %d:(", ioffset);	fprintf(ficgp," u %d:(", ioffset);
if(i==nlstate+1)	if(i==nlstate+1){
fprintf(ficgp," $%d/(1.-$%d)) t 'pw.%d' with line ", \	fprintf(ficgp," $%d/(1.-$%d)):1 t 'pw.%d' with line lc variable ", \
ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)nlstate,cpt );	ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)nlstate,cpt );
else	fprintf(ficgp,",\\\n '' ");
	fprintf(ficgp," u %d:(",ioffset);
	fprintf(ficgp," (($1-$2) == %d ) ? $%d/(1.-$%d) : 1/0):1 with labels center not ", \
	offyear, \
	ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)nlstate );
	}else
fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \	fprintf(ficgp," $%d/(1.-$%d)) t 'p%d%d' with line ", \
ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)nlstate,i,cpt );	ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)nlstate,i,cpt );
}else{ /* more than 2 covariates */	}else{ /* more than 2 covariates */
if(cptcoveff ==1){	ioffset=2cptcoveff+2; / Age is in 4 or 6 or etc.*/
ioffset=4; /* Age is in 4 */	/# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3/
}else{	/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 /
ioffset=6; /* Age is in 6 */	iyearc=ioffset-1;
/# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3/	iagec=ioffset;
/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 /
}
fprintf(ficgp," u %d:(",ioffset);	fprintf(ficgp," u %d:(",ioffset);
kl=0;	kl=0;
strcpy(gplotcondition,"(");	strcpy(gplotcondition,"(");
Line 7305 set ter svg size 640, 480\nunset log y\n	Line 7712 set ter svg size 640, 480\nunset log y\n
/6+1+(i-1)+(nlstate+1)nlstate; 6+1+(1-1) +(2+1)2=13 /	/6+1+(i-1)+(nlstate+1)nlstate; 6+1+(1-1) +(2+1)2=13 /
/* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/	/* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
if(i==nlstate+1){	if(i==nlstate+1){
fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p.%d' with line ", gplotcondition, \	fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0):%d t 'p.%d' with line lc variable", gplotcondition, \
ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)nlstate,cpt );	ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)nlstate,iyearc, cpt );
	fprintf(ficgp,",\\\n '' ");
	fprintf(ficgp," u %d:(",iagec);
	fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d/(1.-$%d) : 1/0):%d with labels center not ", gplotcondition, \
	iyearc, iagec, offyear, \
	ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)nlstate, iyearc );
	/* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
}else{	}else{
fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \	fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \
ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)nlstate,i,cpt );	ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset +1+(i-1)+(nlstate+1)nlstate,i,cpt );
Line 7318 set ter svg size 640, 480\nunset log y\n	Line 7731 set ter svg size 640, 480\nunset log y\n
} /* end covariate */	} /* end covariate */
} /* End if prevfcast */	} /* End if prevfcast */

	if(backcast==1){
	/* Back projection from cross-sectional to stable (mixed) for each covariate */

	for (k1=1; k1<= m ; k1 ++) /* For each covariate combination if any */
	for(nres=1; nres <= nresult; nres++){ /* For each resultline */
	if(m != 1 && TKresult[nres]!= k1)
	continue;
	for (cpt=1; cpt<=nlstate ; cpt ++) { /* For each life state */
	strcpy(gplotlabel,"(");
	fprintf(ficgp,"\n#\n#\n#Back projection of prevalence to stable (mixed) back prevalence: 'BPROJ_' files, covariatecombination#=%d originstate=%d",k1, cpt);
	for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */
	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(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
	vlv= nbcode[Tvaraff[k]][lv];
	fprintf(ficgp," V%d=%d ",Tvaraff[k],vlv);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%d ",Tvaraff[k],vlv);
	}
	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
	fprintf(ficgp," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	sprintf(gplotlabel+strlen(gplotlabel)," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	}
	strcpy(gplotlabel+strlen(gplotlabel),")");
	fprintf(ficgp,"\n#\n");
	if(invalidvarcomb[k1]){
	fprintf(ficgp,"#Combination (%d) ignored because no cases \n",k1);
	continue;
	}

	fprintf(ficgp,"# hbijx=backprobability over h years, hb.jx is weighted by observed prev at destination state\n ");
	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" \n",subdirf2(optionfilefiname,"PROJB_"),cpt,k1,nres);
	fprintf(ficgp,"set label \"Origin alive state %d %s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",cpt,gplotlabel);
	fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Prevalence\" \n\
	set ter svg size 640, 480\nunset log y\nplot [%.f:%.f] ", ageminpar, agemaxpar);

	/* for (i=1; i<= nlstate+1 ; i ++){ /\* nlstate +1 p11 p21 p.1 \/ /
	istart=nlstate+1; /* Could be one if by state, but nlstate+1 is w.i projection only */
	/istart=1;/ /* Could be one if by state, but nlstate+1 is w.i projection only */
	for (i=istart; i<= nlstate+1 ; i ++){ /* nlstate +1 p11 p21 p.1 */
	/# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3/
	/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 /
	/# yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3/
	/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 /
	if(i==istart){
	fprintf(ficgp,"\"%s\"",subdirf2(fileresu,"FB_"));
	}else{
	fprintf(ficgp,",\\\n '' ");
	}
	if(cptcoveff ==0){ /* No covariate */
	ioffset=2; /* Age is in 2 */
	/# yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4/
	/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 /
	/# V1 = 1 yearproj age p11 p21 p31 p.1 p12 p22 p32 p.2 p13 p23 p33 p.3 p14 p24 p34 p.4/
	/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 /
	fprintf(ficgp," u %d:(", ioffset);
	if(i==nlstate+1){
	fprintf(ficgp," $%d/(1.-$%d)):1 t 'bw%d' with line lc variable ", \
	ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)nlstate,cpt );
	fprintf(ficgp,",\\\n '' ");
	fprintf(ficgp," u %d:(",ioffset);
	fprintf(ficgp," (($1-$2) == %d ) ? $%d : 1/0):1 with labels center not ", \
	offbyear, \
	ioffset+(cpt-1)*(nlstate+1)+1+(i-1) );
	}else
	fprintf(ficgp," $%d/(1.-$%d)) t 'b%d%d' with line ", \
	ioffset+(cpt-1)(nlstate+1)+1+(i-1), ioffset+1+(i-1)+(nlstate+1)nlstate,cpt,i );
	}else{ /* more than 2 covariates */
	ioffset=2cptcoveff+2; / Age is in 4 or 6 or etc.*/
	/# V1 = 1 V2 = 0 yearproj age p11 p21 p.1 p12 p22 p.2 p13 p23 p.3/
	/# 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 /
	iyearc=ioffset-1;
	iagec=ioffset;
	fprintf(ficgp," u %d:(",ioffset);
	kl=0;
	strcpy(gplotcondition,"(");
	for (k=1; k<=cptcoveff; k++){ /* For each covariate writing the chain of conditions */
	lv= decodtabm(k1,k,cptcoveff); /* Should be the covariate value corresponding to combination k1 and covariate k */
	/* decodtabm(1,1,4) = 1 because h=1 k= (1) 1 1 1 */
	/* decodtabm(1,2,4) = 1 because h=1 k= 1 (1) 1 1 */
	/* decodtabm(13,3,4)= 2 because h=13 k= 1 1 (2) 2 */
	vlv= nbcode[Tvaraff[k]][lv]; /* Value of the modality of Tvaraff[k] */
	kl++;
	sprintf(gplotcondition+strlen(gplotcondition),"$%d==%d && $%d==%d " ,kl,Tvaraff[k], kl+1, nbcode[Tvaraff[k]][lv]);
	kl++;
	if(k <cptcoveff && cptcoveff>1)
	sprintf(gplotcondition+strlen(gplotcondition)," && ");
	}
	strcpy(gplotcondition+strlen(gplotcondition),")");
	/* kl=6+(cpt-1)(nlstate+1)+1+(i-1); /\ 6+(1-1)(2+1)+1+(1-1)=7, 6+(2-1)(2+1)+1+(1-1)=10 \/ */
	/6+(cpt-1)(nlstate+1)+1+(i-1)+(nlstate+1)nlstate; 6+(1-1)(2+1)+1+(1-1) +(2+1)2=13 /
	/6+1+(i-1)+(nlstate+1)nlstate; 6+1+(1-1) +(2+1)2=13 /
	/* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0)? $9/(1.-$15) : 1/0):($5==2000? 3:2) t 'p.1' with line lc variable*/
	if(i==nlstate+1){
	fprintf(ficgp,"%s ? $%d : 1/0):%d t 'bw%d' with line lc variable", gplotcondition, \
	ioffset+(cpt-1)*(nlstate+1)+1+(i-1),iyearc,cpt );
	fprintf(ficgp,",\\\n '' ");
	fprintf(ficgp," u %d:(",iagec);
	/* fprintf(ficgp,"%s && (($5-$6) == %d ) ? $%d/(1.-$%d) : 1/0):5 with labels center not ", gplotcondition, \ */
	fprintf(ficgp,"%s && (($%d-$%d) == %d ) ? $%d : 1/0):%d with labels center not ", gplotcondition, \
	iyearc,iagec,offbyear, \
	ioffset+(cpt-1)*(nlstate+1)+1+(i-1), iyearc );
	/* '' u 6:(($1==1 && $2==0 && $3==2 && $4==0) && (($5-$6) == 1947) ? $10/(1.-$22) : 1/0):5 with labels center boxed not*/
	}else{
	/* fprintf(ficgp,"%s ? $%d/(1.-$%d) : 1/0) t 'p%d%d' with line ", gplotcondition, \ */
	fprintf(ficgp,"%s ? $%d : 1/0) t 'b%d%d' with line ", gplotcondition, \
	ioffset+(cpt-1)*(nlstate+1)+1+(i-1), cpt,i );
	}
	} /* end if covariate */
	} /* nlstate */
	fprintf(ficgp,"\nset out; unset label;\n");
	} /* end cpt state*/
	} /* end covariate */
	} /* End if backcast */


/* 9eme writing MLE parameters */	/* 9eme writing MLE parameters */
fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");	fprintf(ficgp,"\n##############\n#9eme MLE estimated parameters\n#############\n");
Line 7363 set ter svg size 640, 480\nunset log y\n	Line 7891 set ter svg size 640, 480\nunset log y\n
continue;	continue;
fprintf(ficgp,"\n\n# Combination of dummy k1=%d which is ",k1);	fprintf(ficgp,"\n\n# Combination of dummy k1=%d which is ",k1);
strcpy(gplotlabel,"(");	strcpy(gplotlabel,"(");
sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);	/sprintf(gplotlabel+strlen(gplotlabel)," Dummy combination %d ",k1);/
for (k=1; k<=cptcoveff; k++){ /* For each correspondig covariate value */	for (k=1; k<=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 7380 set ter svg size 640, 480\nunset log y\n	Line 7908 set ter svg size 640, 480\nunset log y\n
strcpy(gplotlabel+strlen(gplotlabel),")");	strcpy(gplotlabel+strlen(gplotlabel),")");
fprintf(ficgp,"\n#\n");	fprintf(ficgp,"\n#\n");
fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);	fprintf(ficgp,"\nset out \"%s_%d-%d-%d.svg\" ",subdirf2(optionfilefiname,"PE_"),k1,ng,nres);
fprintf(ficgp,"\nset label \"%s\" at graph 0.98,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel);	fprintf(ficgp,"\nset key outside ");
	/* fprintf(ficgp,"\nset label \"%s\" at graph 1.2,0.5 center rotate font \"Helvetica,12\"\n",gplotlabel); */
	fprintf(ficgp,"\nset title \"%s\" font \"Helvetica,12\"\n",gplotlabel);
fprintf(ficgp,"\nset ter svg size 640, 480 ");	fprintf(ficgp,"\nset ter svg size 640, 480 ");
if (ng==1){	if (ng==1){
fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12x) could be nice /	fprintf(ficgp,"\nset ylabel \"Value of the logit of the model\"\n"); /* exp(a12+b12x) could be nice /
Line 7424 set ter svg size 640, 480\nunset log y\n	Line 7954 set ter svg size 640, 480\nunset log y\n
/* for(j=3; j <=ncovmodel-nagesqr; j++) { */	/* for(j=3; j <=ncovmodel-nagesqr; j++) { */
for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */	for(j=1; j <=cptcovt; j++) { /* For each covariate of the simplified model */
/* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */	/* printf("Tage[%d]=%d, j=%d\n", ij, Tage[ij], j); */
if(j==Tage[ij]) { /* Product by age */	if(cptcovage >0){ /* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, 2 V5 and V1 */
if(ij <=cptcovage) { /* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, 2 V5 and V1 */	if(j==Tage[ij]) { /* Product by age To be looked at!!*/
if(DummyV[j]==0){	if(ij <=cptcovage) { /* V5+V4+V3+V4V3+V5age+V2+V1V2+V1age+V1, 2 V5 and V1 */
fprintf(ficgp,"+p%d%dx",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;	if(DummyV[j]==0){
}else{ /* quantitative */	fprintf(ficgp,"+p%d%dx",i+j+2+nagesqr-1,Tinvresult[nres][Tvar[j]]);;
fprintf(ficgp,"+p%d%fx",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */	}else{ /* quantitative */
/* fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */	fprintf(ficgp,"+p%d%fx",i+j+2+nagesqr-1,Tqinvresult[nres][Tvar[j]]); /* Tqinvresult in decoderesult */
}	/* fprintf(ficgp,"+p%d%dx",i+j+nagesqr-1,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); */
ij++;
}
}else if(j==Tprod[ijp]) { /* */
/* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
if(ijp <=cptcovprod) { /* Product */
if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
/* fprintf(ficgp,"+p%d%d%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */
fprintf(ficgp,"+p%d%d%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
}else{ /* Vn is dummy and Vm is quanti */
/* fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
}	}
}else{ /* VnVm Vn is quanti /	ij++;
if(DummyV[Tvard[ijp][2]]==0){	}
fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);	}
}else{ /* Both quanti */	}else if(cptcovprod >0){
fprintf(ficgp,"+p%d%f%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);	if(j==Tprod[ijp]) { /* */
	/* printf("Tprod[%d]=%d, j=%d\n", ij, Tprod[ijp], j); */
	if(ijp <=cptcovprod) { /* Product */
	if(DummyV[Tvard[ijp][1]]==0){/* Vn is dummy */
	if(DummyV[Tvard[ijp][2]]==0){/* Vn and Vm are dummy */
	/* fprintf(ficgp,"+p%d%d%d",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],nbcode[Tvard[ijp][2]][codtabm(k1,j)]); */
	fprintf(ficgp,"+p%d%d%d",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tinvresult[nres][Tvard[ijp][2]]);
	}else{ /* Vn is dummy and Vm is quanti */
	/* fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,nbcode[Tvard[ijp][1]][codtabm(k1,j)],Tqinvresult[nres][Tvard[ijp][2]]); */
	fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
	}
	}else{ /* VnVm Vn is quanti /
	if(DummyV[Tvard[ijp][2]]==0){
	fprintf(ficgp,"+p%d%d%f",i+j+2+nagesqr-1,Tinvresult[nres][Tvard[ijp][2]],Tqinvresult[nres][Tvard[ijp][1]]);
	}else{ /* Both quanti */
	fprintf(ficgp,"+p%d%f%f",i+j+2+nagesqr-1,Tqinvresult[nres][Tvard[ijp][1]],Tqinvresult[nres][Tvard[ijp][2]]);
	}
}	}
	ijp++;
}	}
ijp++;	} /* end Tprod */
}
} else{ /* simple covariate */	} else{ /* simple covariate */
/* fprintf(ficgp,"+p%d%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\ Valgrind bug nbcode \/ /	/* fprintf(ficgp,"+p%d%d",i+j+2+nagesqr-1,nbcode[Tvar[j]][codtabm(k1,j)]); /\ Valgrind bug nbcode \/ /
if(Dummy[j]==0){	if(Dummy[j]==0){
Line 7481 set ter svg size 640, 480\nunset log y\n	Line 8015 set ter svg size 640, 480\nunset log y\n

ij=1;	ij=1;
for(j=3; j <=ncovmodel-nagesqr; j++){	for(j=3; j <=ncovmodel-nagesqr; j++){
if((j-2)==Tage[ij]) { /* Bug valgrind */	if(cptcovage >0){
if(ij <=cptcovage) { /* Bug valgrind */	if((j-2)==Tage[ij]) { /* Bug valgrind */
fprintf(ficgp,"+p%d%dx",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);	if(ij <=cptcovage) { /* Bug valgrind */
/* fprintf(ficgp,"+p%d%dx",k3+(cpt-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); /	fprintf(ficgp,"+p%d%dx",k3+(cpt-1)*ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);
ij++;	/* fprintf(ficgp,"+p%d%dx",k3+(cpt-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,Tvar[j-2])]); /
}	ij++;
}	}
else	}
fprintf(ficgp,"+p%d%d",k3+(cpt-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);/* Valgrind bug nbcode */	}else
	fprintf(ficgp,"+p%d%d",k3+(cpt-1)ncovmodel+1+j-2+nagesqr,nbcode[Tvar[j-2]][codtabm(k1,j-2)]);/* Valgrind bug nbcode */
}	}
fprintf(ficgp,")");	fprintf(ficgp,")");
}	}
fprintf(ficgp,")");	fprintf(ficgp,")");
if(ng ==2)	if(ng ==2)
fprintf(ficgp," t \"p%d%d\" ", k2,k);	fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"p%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
else /* ng= 3 */	else /* ng= 3 */
fprintf(ficgp," t \"i%d%d\" ", k2,k);	fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"i%d%d\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
}else{ /* end ng <> 1 */	}else{ /* end ng <> 1 */
if( k !=k2) /* logit p11 is hard to draw */	if( k !=k2) /* logit p11 is hard to draw */
fprintf(ficgp," t \"logit(p%d%d)\" ", k2,k);	fprintf(ficgp," w l lw 2 lt (%d*%d+%d)%%%d+1 dt %d t \"logit(p%d%d)\" ", nlstate+ndeath, k2, k, nlstate+ndeath, k2, k2,k);
}	}
if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)	if ((k+k2)!= (nlstate*2+ndeath) && ng != 1)
fprintf(ficgp,",");	fprintf(ficgp,",");
Line 7509 set ter svg size 640, 480\nunset log y\n	Line 8044 set ter svg size 640, 480\nunset log y\n
i=i+ncovmodel;	i=i+ncovmodel;
} /* end k */	} /* end k */
} /* end k2 */	} /* end k2 */
fprintf(ficgp,"\n set out; unset label;\n");	/* fprintf(ficgp,"\n set out; unset label;set key default;\n"); */
	fprintf(ficgp,"\n set out; unset title;set key default;\n");
} /* end k1 */	} /* end k1 */
} /* end ng */	} /* end ng */
/* avoid: */	/* avoid: */
Line 7525 set ter svg size 640, 480\nunset log y\n	Line 8061 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.;	double sum=0., sumr=0.;
double age;	double age;
double sumnewp, sumnewm;	double sumnewp, sumnewm, *sumnewmr;
double agemingood, agemaxgood; /* Currently identical for all covariates */	double agemingood, agemaxgood;
	double agemingoodr, agemaxgoodr;


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

sumnewp = vector(1,ncovcombmax);	sumnewp = vector(1,ncovcombmax);
sumnewm = vector(1,ncovcombmax);	sumnewm = vector(1,ncovcombmax);
	sumnewmr = vector(1,ncovcombmax);
agemingood = vector(1,ncovcombmax);	agemingood = vector(1,ncovcombmax);
	agemingoodr = vector(1,ncovcombmax);
agemaxgood = vector(1,ncovcombmax);	agemaxgood = vector(1,ncovcombmax);
	agemaxgoodr = vector(1,ncovcombmax);

for (cptcod=1;cptcod<=ncovcombmax;cptcod++){	for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
sumnewm[cptcod]=0.;	sumnewm[cptcod]=0.; sumnewmr[cptcod]=0.;
sumnewp[cptcod]=0.;	sumnewp[cptcod]=0.;
agemingood[cptcod]=0;	agemingood[cptcod]=0, agemingoodr[cptcod]=0;
agemaxgood[cptcod]=0;	agemaxgood[cptcod]=0, agemaxgoodr[cptcod]=0;
}	}
if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */	if (cptcovn<1) ncovcombmax=1; /* At least 1 pass */

if(mobilav==1\|\|mobilav ==3 \|\|mobilav==5 \|\|mobilav== 7){	if(mobilav==-1 \|\| mobilav==1\|\|mobilav ==3 \|\|mobilav==5 \|\|mobilav== 7){
if(mobilav==1) mobilavrange=5; /* default */	if(mobilav==1 \|\| mobilav==-1) mobilavrange=5; /* default */
else mobilavrange=mobilav;	else mobilavrange=mobilav;
for (age=bage; age<=fage; age++)	for (age=bage; age<=fage; age++)
for (i=1; i<=nlstate;i++)	for (i=1; i<=nlstate;i++)
Line 7561 set ter svg size 640, 480\nunset log y\n	Line 8102 set ter svg size 640, 480\nunset log y\n
*/	*/
for (mob=3;mob <=mobilavrange;mob=mob+2){	for (mob=3;mob <=mobilavrange;mob=mob+2){
for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){	for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
for (i=1; i<=nlstate;i++){	for (cptcod=1;cptcod<=ncovcombmax;cptcod++){
for (cptcod=1;cptcod<=ncovcombmax;cptcod++){	sumnewm[cptcod]=0.;
	for (i=1; i<=nlstate;i++){
mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];	mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
for (cpt=1;cpt<=(mob-1)/2;cpt++){	for (cpt=1;cpt<=(mob-1)/2;cpt++){
mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];	mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];	mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
}	}
mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;	mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
}	sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
}	} /* end i */
	if(sumnewm[cptcod] >1.e-3) mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/sumnewm[cptcod]; /* Rescaling to sum one */
	} /* end cptcod */
}/* end age */	}/* end age */
}/* end mob */	}/* end mob */
}else	}else{
	printf("Error internal in movingaverage, mobilav=%d.\n",mobilav);
return -1;	return -1;
for (cptcod=1;cptcod<=ncovcombmax;cptcod++){	}

	for (cptcod=1;cptcod<=ncovcombmax;cptcod++){ /* for each combination */
/* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */	/* for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ */
if(invalidvarcomb[cptcod]){	if(invalidvarcomb[cptcod]){
printf("\nCombination (%d) ignored because no cases \n",cptcod);	printf("\nCombination (%d) ignored because no cases \n",cptcod);
continue;	continue;
}	}

agemingood[cptcod]=fage-(mob-1)/2;	for (age=fage-(mob-1)/2; age>=bage+(mob-1)/2; age--){ /looking for the youngest and oldest good age /
for (age=fage-(mob-1)/2; age>=bage; age--){/* From oldest to youngest, finding the youngest wrong */
sumnewm[cptcod]=0.;	sumnewm[cptcod]=0.;
	sumnewmr[cptcod]=0.;
for (i=1; i<=nlstate;i++){	for (i=1; i<=nlstate;i++){
sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];	sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
	sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
	}
	if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
	agemingoodr[cptcod]=age;
}	}
if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */	if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
agemingood[cptcod]=age;	agemingood[cptcod]=age;
}else{ /* bad */	}
for (i=1; i<=nlstate;i++){	} /* age */
mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];	for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){ /looking for the youngest and oldest good age /
} /* i */
} /* end bad */
}/* age */
sum=0.;
for (i=1; i<=nlstate;i++){
sum+=mobaverage[(int)agemingood[cptcod]][i][cptcod];
}
if(fabs(sum - 1.) > 1.e-3) { /* bad */
printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any descending age!\n",cptcod);
/* for (i=1; i<=nlstate;i++){ */
/* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
/* } /\* i \/ /
} /* end bad */
/* else{ /\* We found some ages summing to one, we will smooth the oldest \/ /
/* From youngest, finding the oldest wrong */
agemaxgood[cptcod]=bage+(mob-1)/2;
for (age=bage+(mob-1)/2; age<=fage; age++){
sumnewm[cptcod]=0.;	sumnewm[cptcod]=0.;
	sumnewmr[cptcod]=0.;
for (i=1; i<=nlstate;i++){	for (i=1; i<=nlstate;i++){
sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];	sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
	sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
	}
	if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
	agemaxgoodr[cptcod]=age;
}	}
if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */	if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
agemaxgood[cptcod]=age;	agemaxgood[cptcod]=age;
}else{ /* bad */	}
for (i=1; i<=nlstate;i++){	} /* age */
mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];	/* Thus we have agemingood and agemaxgood as well as goodr for raw (preobs) */
} /* i */	/* 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 */
	sumnewm[cptcod]=0.;
	sumnewmr[cptcod]=0.;
	for (i=1; i<=nlstate;i++){
	sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
	sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
	}
	if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
	if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good without smoothing */
	agemaxgoodr[cptcod]=age; /* age min */
	for (i=1; i<=nlstate;i++)
	mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
	}else{ /* bad we change the value with the values of good ages */
	for (i=1; i<=nlstate;i++){
	mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgoodr[cptcod]][i][cptcod];
	} /* i */
	} /* end bad */
	}else{
	if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
	agemaxgood[cptcod]=age;
	}else{ /* bad we change the value with the values of good ages */
	for (i=1; i<=nlstate;i++){
	mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];
	} /* i */
	} /* end bad */
	}/* end else */
	sum=0.;sumr=0.;
	for (i=1; i<=nlstate;i++){
	sum+=mobaverage[(int)age][i][cptcod];
	sumr+=probs[(int)age][i][cptcod];
	}
	if(fabs(sum - 1.) > 1.e-3) { /* bad */
	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 */
	/* else{ /\* We found some ages summing to one, we will smooth the oldest \/ /
	if(fabs(sumr - 1.) > 1.e-3) { /* bad */
	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 */
sum=0.;
for (i=1; i<=nlstate;i++){	for (age=bage+(mob-1)/2; age<=fage; age++){/* From youngest, finding the oldest wrong */
sum+=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];	sumnewm[cptcod]=0.;
}	sumnewmr[cptcod]=0.;
if(fabs(sum - 1.) > 1.e-3) { /* bad */	for (i=1; i<=nlstate;i++){
printf("For this combination of covariate cptcod=%d, we can't get a smoothed prevalence which sums to one at any ascending age!\n",cptcod);	sumnewm[cptcod]+=mobaverage[(int)age][i][cptcod];
/* for (i=1; i<=nlstate;i++){ */	sumnewmr[cptcod]+=probs[(int)age][i][cptcod];
/* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */	}
/* } /\* i \/ /	if(mobilav==-1){ /* Forcing raw ages if good else agemingood */
} /* end bad */	if(fabs(sumnewmr[cptcod] - 1.) <= 1.e-3) { /* good */
	agemingoodr[cptcod]=age;
	for (i=1; i<=nlstate;i++)
	mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
	}else{ /* bad we change the value with the values of good ages */
	for (i=1; i<=nlstate;i++){
	mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingoodr[cptcod]][i][cptcod];
	} /* i */
	} /* end bad */
	}else{
	if(fabs(sumnewm[cptcod] - 1.) <= 1.e-3) { /* good */
	agemingood[cptcod]=age;
	}else{ /* bad */
	for (i=1; i<=nlstate;i++){
	mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];
	} /* i */
	} /* end bad */
	}/* end else */
	sum=0.;sumr=0.;
	for (i=1; i<=nlstate;i++){
	sum+=mobaverage[(int)age][i][cptcod];
	sumr+=mobaverage[(int)age][i][cptcod];
	}
	if(fabs(sum - 1.) > 1.e-3) { /* bad */
	printf("Moving average B1: 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 decrease fage=%d?\n",cptcod, sum, (int) age, (int)fage);
	} /* end bad */
	/* else{ /\* We found some ages summing to one, we will smooth the oldest \/ /
	if(fabs(sumr - 1.) > 1.e-3) { /* bad */
	printf("Moving average B2: 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 fage=%d\n",cptcod,sumr, (int)age, (int)fage);
	} /* end bad */
	}/* age */


for (age=bage; age<=fage; age++){	for (age=bage; age<=fage; age++){
/* printf("%d %d ", cptcod, (int)age); */	/* printf("%d %d ", cptcod, (int)age); */
Line 7646 set ter svg size 640, 480\nunset log y\n	Line 8262 set ter svg size 640, 480\nunset log y\n
}	}
/* printf("\n"); */	/* printf("\n"); */
/* } */	/* } */

/* brutal averaging */	/* brutal averaging */
for (i=1; i<=nlstate;i++){	/* for (i=1; i<=nlstate;i++){ */
for (age=1; age<=bage; age++){	/* for (age=1; age<=bage; age++){ */
mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod];	/* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemingood[cptcod]][i][cptcod]; */
/* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */	/* /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); \/ /
}	/* } */
for (age=fage; age<=AGESUP; age++){	/* for (age=fage; age<=AGESUP; age++){ */
mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod];	/* mobaverage[(int)age][i][cptcod]=mobaverage[(int)agemaxgood[cptcod]][i][cptcod]; */
/* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); */	/* /\* printf("age=%d i=%d cptcod=%d mobaverage=%.4f \n",(int)age,i, cptcod, mobaverage[(int)age][i][cptcod]); \/ /
}	/* } */
} /* end i status */	/* } /\* end i status \/ /
for (i=nlstate+1; i<=nlstate+ndeath;i++){	/* for (i=nlstate+1; i<=nlstate+ndeath;i++){ */
for (age=1; age<=AGESUP; age++){	/* for (age=1; age<=AGESUP; age++){ */
/printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);/	/* /\printf("i=%d, age=%d, cptcod=%d\n",i, (int)age, cptcod);\/ */
mobaverage[(int)age][i][cptcod]=0.;	/* mobaverage[(int)age][i][cptcod]=0.; */
}	/* } */
}	/* } */
}/* end cptcod */	}/* end cptcod */
free_vector(sumnewm,1, ncovcombmax);	free_vector(agemaxgoodr,1, ncovcombmax);
free_vector(sumnewp,1, ncovcombmax);
free_vector(agemaxgood,1, ncovcombmax);	free_vector(agemaxgood,1, ncovcombmax);
free_vector(agemingood,1, ncovcombmax);	free_vector(agemingood,1, ncovcombmax);
	free_vector(agemingoodr,1, ncovcombmax);
	free_vector(sumnewmr,1, ncovcombmax);
	free_vector(sumnewm,1, ncovcombmax);
	free_vector(sumnewp,1, ncovcombmax);
return 0;	return 0;
}/* 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 bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){	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){
/* proj1, year, month, day of starting projection	/* proj1, year, month, day of starting projection
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).	anproj2 year of en of projection (same day and month as proj1).
*/	*/
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,jprojmean,mprojmean,anprojmean;
double popeffectif,popcount;	double popeffectif,popcount;
Line 7705 set ter svg size 640, 480\nunset log y\n	Line 8325 set ter svg size 640, 480\nunset log y\n
fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);	fprintf(ficlog,"\nComputing forecasting: result on file '%s', please wait... \n", fileresf);

if (cptcoveff==0) ncodemax[cptcoveff]=1;	if (cptcoveff==0) ncodemax[cptcoveff]=1;


	stepsize=(int) (stepm+YEARM-1)/YEARM;
	if (stepm<=12) stepsize=1;
	if(estepm < stepm){
	printf ("Problem %d lower than %d\n",estepm, stepm);
	}
	else{
	hstepm=estepm;
	}
	if(estepm > stepm){ /* Yes every two year */
	stepsize=2;
	}

	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;

	i1=pow(2,cptcoveff);
	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,"#**** Routine prevforecast \n");

	/* if (h==(int)(YEARMyearp)){ /
	for(nres=1; nres <= nresult; nres++) /* For each resultline */
	for(k=1; k<=i1;k++){
	if(i1 != 1 && TKresult[nres]!= k)
	continue;
	if(invalidvarcomb[k]){
	printf("\nCombination (%d) projection ignored because no cases \n",k);
	continue;
	}
	fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");
	for(j=1;j<=cptcoveff;j++) {
	fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
	}
	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
	fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
	}
	fprintf(ficresf," yearproj age");
	for(j=1; j<=nlstate+ndeath;j++){
	for(i=1; i<=nlstate;i++)
	fprintf(ficresf," p%d%d",i,j);
	fprintf(ficresf," wp.%d",j);
	}
	for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {
	fprintf(ficresf,"\n");
	fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);
	/* for (agec=fage; agec>=(ageminpar-1); agec--){ */
	for (agec=fage; agec>=(bage); agec--){
	nhstepm=(int) rint((agelim-agec)*YEARM/stepm);
	nhstepm = nhstepm/hstepm;
	p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
	oldm=oldms;savm=savms;
	/* We compute pii at age agec over nhstepm);*/
	hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);
	/* Then we print p3mat for h corresponding to the right agec+hstepms=yearp /
	for (h=0; h<=nhstepm; h++){
	if (hhstepm/YEARMstepm ==yearp) {
	break;
	}
	}
	fprintf(ficresf,"\n");
	for(j=1;j<=cptcoveff;j++)
	fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
	fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+hhstepm/YEARMstepm);

	for(j=1; j<=nlstate+ndeath;j++) {
	ppij=0.;
	for(i=1; i<=nlstate;i++) {
	if (mobilav>=1)
	ppij=ppij+p3mat[i][j][h]*prev[(int)agec][i][k];
	else { /* even if mobilav==-1 we use mobaverage, probs may not sums to 1 */
	ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];
	}
	fprintf(ficresf," %.3f", p3mat[i][j][h]);
	} /* end i */
	fprintf(ficresf," %.3f", ppij);
	}/* end j */
	free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
	} /* end agec */
	/* diffyear=(int) anproj1+yearp-ageminpar-1; */
	/printf("Prevforecast %d+%d-%d=diffyear=%d\n",(int) anproj1, (int)yearp,(int)ageminpar,(int) anproj1-(int)ageminpar);/
	} /* end yearp */
	} /* end k */

	fclose(ficresf);
	printf("End of Computing forecasting \n");
	fprintf(ficlog,"End of Computing forecasting\n");

	}

	/************ 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){
	/* back1, year, month, day of starting backection
	agemin, agemax range of age
	dateprev1 dateprev2 range of dates during which prevalence is computed
	anback2 year of end of backprojection (same day and month as back1).
	prevacurrent and prev are prevalences.
	*/
	int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1, k4, nres=0;
	double agec; /* generic age */
	double agelim, ppij, ppi, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
	double popeffectif,popcount;
	double ***p3mat;
	/* double **mobaverage; /
	char fileresfb[FILENAMELENGTH];

	agelim=AGEINF;
	/* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
	in each health status at the date of interview (if between dateprev1 and dateprev2).
	We still use firstpass and lastpass as another selection.
	*/
	/* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ */
	/* firstpass, lastpass, stepm, weightopt, model); */

	/Do we need to compute prevalence again?/

	/* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */

	strcpy(fileresfb,"FB_");
	strcat(fileresfb,fileresu);
	if((ficresfb=fopen(fileresfb,"w"))==NULL) {
	printf("Problem with back forecast resultfile: %s\n", fileresfb);
	fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb);
	}
	printf("\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);
	fprintf(ficlog,"\nComputing back forecasting: result on file '%s', please wait... \n", fileresfb);

	if (cptcoveff==0) ncodemax[cptcoveff]=1;


stepsize=(int) (stepm+YEARM-1)/YEARM;	stepsize=(int) (stepm+YEARM-1)/YEARM;
if (stepm<=12) stepsize=1;	if (stepm<=12) stepsize=1;
if(estepm < stepm){	if(estepm < stepm){
printf ("Problem %d lower than %d\n",estepm, stepm);	printf ("Problem %d lower than %d\n",estepm, stepm);
}	}
else hstepm=estepm;	else{
	hstepm=estepm;
hstepm=hstepm/stepm;	}
	if(estepm >= stepm){ /* Yes every two year */
	stepsize=2;
	}

	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;	anprojmean=yp;
Line 7724 set ter svg size 640, 480\nunset log y\n	Line 8488 set ter svg size 640, 480\nunset log y\n
jprojmean=yp;	jprojmean=yp;
if(jprojmean==0) jprojmean=1;	if(jprojmean==0) jprojmean=1;
if(mprojmean==0) jprojmean=1;	if(mprojmean==0) jprojmean=1;

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(ficresfb,"# 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",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2);

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

/* if (h==(int)(YEARMyearp)){ /
for(nres=1; nres <= nresult; nres++) /* For each resultline */	for(nres=1; nres <= nresult; nres++) /* For each resultline */
for(k=1; k<=i1;k++){	for(k=1; k<=i1;k++){
if(i1 != 1 && TKresult[nres]!= k)	if(i1 != 1 && TKresult[nres]!= k)
Line 7741 set ter svg size 640, 480\nunset log y\n	Line 8505 set ter svg size 640, 480\nunset log y\n
printf("\nCombination (%d) projection ignored because no cases \n",k);	printf("\nCombination (%d) projection ignored because no cases \n",k);
continue;	continue;
}	}
fprintf(ficresf,"\n#****** hpijx=probability over h years, hp.jx is weighted by observed prev \n#");	fprintf(ficresfb,"\n#****** hbijx=probability over h years, hb.jx is weighted by observed prev \n#");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcoveff;j++) {
fprintf(ficresf," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
}	}
for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */	for (k4=1; k4<= nsq; k4++){ /* For each selected (single) quantitative value */
fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);	fprintf(ficresf," V%d=%f ",Tvqresult[nres][k4],Tqresult[nres][k4]);
}	}
fprintf(ficresf," yearproj age");	fprintf(ficresfb," yearbproj age");
for(j=1; j<=nlstate+ndeath;j++){	for(j=1; j<=nlstate+ndeath;j++){
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
fprintf(ficresf," p%d%d",i,j);	fprintf(ficresfb," b%d%d",i,j);
fprintf(ficresf," wp.%d",j);	fprintf(ficresfb," b.%d",j);
}	}
for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) {	for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) {
fprintf(ficresf,"\n");	/* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { */
fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);	fprintf(ficresfb,"\n");
for (agec=fage; agec>=(ageminpar-1); agec--){	fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp);
nhstepm=(int) rint((agelim-agec)*YEARM/stepm);	/* printf("\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
nhstepm = nhstepm/hstepm;	/* for (agec=bage; agec<=agemax-1; agec++){ /\* testing \/ /
	for (agec=bage; agec<=fage; agec++){ /* testing */
	/* We compute bij at age agec over nhstepm, nhstepm decreases when agec increases because of agemax;*/
	nhstepm=(int) (agec-agelim) YEARM/stepm;/ nhstepm=(int) rint((agec-agelim)YEARM/stepm);/
	nhstepm = nhstepm/hstepm;
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
oldm=oldms;savm=savms;	oldm=oldms;savm=savms;
hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k,nres);	/* computes hbxij at age agec over 1 to nhstepm */
	/* printf("####prevbackforecast debug agec=%.2f nhstepm=%d\n",agec, nhstepm);fflush(stdout); */
	hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
	/* hpxij(p3mat,nhstepm,agec,hstepm,p, nlstate,stepm,oldm,savm, k,nres); */
	/* Then we print p3mat for h corresponding to the right agec+hstepms=yearp /
	/* printf(" agec=%.2f\n",agec);fflush(stdout); */
for (h=0; h<=nhstepm; h++){	for (h=0; h<=nhstepm; h++){
if (hhstepm/YEARMstepm ==yearp) {	if (hhstepm/YEARMstepm ==-yearp) {
fprintf(ficresf,"\n");	break;
for(j=1;j<=cptcoveff;j++)	}
fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);	}
fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+hhstepm/YEARMstepm);	fprintf(ficresfb,"\n");
}	for(j=1;j<=cptcoveff;j++)
for(j=1; j<=nlstate+ndeath;j++) {	fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
ppij=0.;	fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec-hhstepm/YEARMstepm);
for(i=1; i<=nlstate;i++) {	for(i=1; i<=nlstate+ndeath;i++) {
if (mobilav==1)	ppij=0.;ppi=0.;
ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][k];	for(j=1; j<=nlstate;j++) {
else {	/* if (mobilav==1) */
ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][k];	ppij=ppij+p3mat[i][j][h]*prevacurrent[(int)agec][j][k];
}	ppi=ppi+prevacurrent[(int)agec][j][k];
if (hhstepm/YEARMstepm== yearp) {	/* ppij=ppij+p3mat[i][j][h]mobaverage[(int)agec][j][k]; /
fprintf(ficresf," %.3f", p3mat[i][j][h]);	/* ppi=ppi+mobaverage[(int)agec][j][k]; */
}	/* else { */
} /* end i */	/* ppij=ppij+p3mat[i][j][h]probs[(int)(agec)][i][k]; /
if (hhstepm/YEARMstepm==yearp) {	/* } */
fprintf(ficresf," %.3f", ppij);	fprintf(ficresfb," %.3f", p3mat[i][j][h]);
}	} /* end j */
}/* end j */	if(ppi <0.99){
} /* end h */	printf("Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
	fprintf(ficlog,"Error in prevbackforecast, prevalence doesn't sum to 1 for state %d: %3f\n",i, ppi);
	}
	fprintf(ficresfb," %.3f", ppij);
	}/* end j */
free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
} /* end agec */	} /* end agec */
} /* end yearp */	} /* end yearp */
} /* end k */	} /* end k */

fclose(ficresf);
printf("End of Computing forecasting \n");
fprintf(ficlog,"End of Computing forecasting\n");

}

/* /\************ Back Forecasting ***************\/ /
/* void prevbackforecast(char fileres[], 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 */
/* agemin, agemax range of age */
/* dateprev1 dateprev2 range of dates during which prevalence is computed */
/* anback2 year of en of backection (same day and month as back1). */
/* \/ /
/* int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1; */
/* double agec; /\* generic age \/ /
/* double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean; */
/* double popeffectif,popcount; */
/* double **p3mat; /
/* /\* double **mobaverage; \/ */
/* char fileresfb[FILENAMELENGTH]; */

/* agelim=AGESUP; */
/* /\* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people */
/* in each health status at the date of interview (if between dateprev1 and dateprev2). */
/* We still use firstpass and lastpass as another selection. */
/* \/ /
/* /\* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart,\ \/ /
/* /\* firstpass, lastpass, stepm, weightopt, model); \/ /
/* prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */

/* strcpy(fileresfb,"FB_"); */
/* strcat(fileresfb,fileresu); */
/* if((ficresfb=fopen(fileresfb,"w"))==NULL) { */
/* printf("Problem with back forecast resultfile: %s\n", fileresfb); */
/* fprintf(ficlog,"Problem with back forecast resultfile: %s\n", fileresfb); */
/* } */
/* printf("Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */
/* fprintf(ficlog,"Computing back forecasting: result on file '%s', please wait... \n", fileresfb); */

/* if (cptcoveff==0) ncodemax[cptcoveff]=1; */

/* /\* if (mobilav!=0) { \/ /
/* /\* mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX); \/ /
/* /\* if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){ \/ /
/* /\* fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav); \/ /
/* /\* printf(" Error in movingaverage mobilav=%d\n",mobilav); \/ /
/* /\* } \/ /
/* /\* } \/ /

/* stepsize=(int) (stepm+YEARM-1)/YEARM; */
/* if (stepm<=12) stepsize=1; */
/* if(estepm < stepm){ */
/* printf ("Problem %d lower than %d\n",estepm, stepm); */
/* } */
/* else hstepm=estepm; */

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

/* i1=cptcoveff; */
/* 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); */	/* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); */

/* fprintf(ficresfb,"#**** Routine prevbackforecast \n"); */	fclose(ficresfb);
	printf("End of Computing Back forecasting \n");
/* /\* if (h==(int)(YEARMyearp)){ \/ */	fprintf(ficlog,"End of Computing Back forecasting\n");
/* for(cptcov=1, k=0;cptcov<=i1;cptcov++){ */
/* for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){ */
/* k=k+1; */
/* fprintf(ficresfb,"\n#****** hbijx=probability over h years, hp.jx is weighted by observed prev \n#"); */
/* for(j=1;j<=cptcoveff;j++) { */
/* fprintf(ficresfb," V%d (=) %d",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
/* } */
/* fprintf(ficresfb," yearbproj age"); */
/* for(j=1; j<=nlstate+ndeath;j++){ */
/* for(i=1; i<=nlstate;i++) */
/* fprintf(ficresfb," p%d%d",i,j); */
/* fprintf(ficresfb," p.%d",j); */
/* } */
/* for (yearp=0; yearp>=(anback2-anback1);yearp -=stepsize) { */
/* /\* for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { \/ /
/* fprintf(ficresfb,"\n"); */
/* fprintf(ficresfb,"\n# Back Forecasting at date %.lf/%.lf/%.lf ",jback1,mback1,anback1+yearp); */
/* for (agec=fage; agec>=(ageminpar-1); agec--){ */
/* nhstepm=(int) rint((agelim-agec)YEARM/stepm); /
/* nhstepm = nhstepm/hstepm; */
/* p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
/* oldm=oldms;savm=savms; */
/* hbxij(p3mat,nhstepm,agec,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm,oldm,savm, dnewm, doldm, dsavm, k); */
/* for (h=0; h<=nhstepm; h++){ */
/* if (hhstepm/YEARMstepm ==yearp) { */
/* fprintf(ficresfb,"\n"); */
/* for(j=1;j<=cptcoveff;j++) */
/* fprintf(ficresfb,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]); */
/* fprintf(ficresfb,"%.f %.f ",anback1+yearp,agec+hhstepm/YEARMstepm); */
/* } */
/* for(j=1; j<=nlstate+ndeath;j++) { */
/* ppij=0.; */
/* for(i=1; i<=nlstate;i++) { */
/* if (mobilav==1) */
/* ppij=ppij+p3mat[i][j][h]mobaverage[(int)agec][i][cptcod]; /
/* else { */
/* ppij=ppij+p3mat[i][j][h]probs[(int)(agec)][i][cptcod]; /
/* } */
/* if (hhstepm/YEARMstepm== yearp) { */
/* fprintf(ficresfb," %.3f", p3mat[i][j][h]); */
/* } */
/* } /\* end i \/ /
/* if (hhstepm/YEARMstepm==yearp) { */
/* fprintf(ficresfb," %.3f", ppij); */
/* } */
/* }/\* end j \/ /
/* } /\* end h \/ /
/* free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); */
/* } /\* end agec \/ /
/* } /\* end yearp \/ /
/* } /\* end cptcod \/ /
/* } /\* end cptcov \/ /

/* /\* if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX); \/ /

/* fclose(ficresfb); */
/* printf("End of Computing Back forecasting \n"); */
/* fprintf(ficlog,"End of Computing Back forecasting\n"); */

/* } */	}

	/* 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){
	/------- Variance of forward period (stable) prevalence------/

	char fileresvpl[FILENAMELENGTH];
	FILE *ficresvpl;
	double oldm, savm;
	double *varpl; / Variances of prevalence limits by age */
	int i1, k, nres, j ;

	strcpy(fileresvpl,"VPL_");
	strcat(fileresvpl,fileresu);
	if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
	printf("Problem with variance of forward period (stable) prevalence resultfile: %s\n", fileresvpl);
	exit(0);
	}
	printf("Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
	fprintf(ficlog, "Computing Variance-covariance of forward period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);

	/*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
	for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/

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

	for(nres=1; nres <= nresult; nres++) /* For each resultline */
	for(k=1; k<=i1;k++){
	if(i1 != 1 && TKresult[nres]!= k)
	continue;
	fprintf(ficresvpl,"\n#****** ");
	printf("\n#****** ");
	fprintf(ficlog,"\n#****** ");
	for(j=1;j<=cptcoveff;j++) {
	fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
	fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
	printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
	}
	for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
	printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
	fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
	fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
	}
	fprintf(ficresvpl,"******\n");
	printf("******\n");
	fprintf(ficlog,"******\n");

	varpl=matrix(1,nlstate,(int) bage, (int) fage);
	oldm=oldms;savm=savms;
	varprevlim(fileresvpl, ficresvpl, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, ncvyearp, k, strstart, nres);
	free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
	/}/
	}

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

	}
	/* Variance of back prevalence: varbprlim */
	void varbprlim(char fileresu[], int nresult, double *prevacurrent, int mobilavproj, double bage, double fage, double bprlim, int ncvyearp, double ftolpl, double p[], double matcov, double delti, int stepm, int cptcoveff){
	/------- Variance of back (stable) prevalence------/

	char fileresvbl[FILENAMELENGTH];
	FILE *ficresvbl;

	double oldm, savm;
	double *varbpl; / Variances of back prevalence limits by age */
	int i1, k, nres, j ;

	strcpy(fileresvbl,"VBL_");
	strcat(fileresvbl,fileresu);
	if((ficresvbl=fopen(fileresvbl,"w"))==NULL) {
	printf("Problem with variance of back (stable) prevalence resultfile: %s\n", fileresvbl);
	exit(0);
	}
	printf("Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(stdout);
	fprintf(ficlog, "Computing Variance-covariance of back (stable) prevalence: file '%s' ...", fileresvbl);fflush(ficlog);


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

	for(nres=1; nres <= nresult; nres++) /* For each resultline */
	for(k=1; k<=i1;k++){
	if(i1 != 1 && TKresult[nres]!= k)
	continue;
	fprintf(ficresvbl,"\n#****** ");
	printf("\n#****** ");
	fprintf(ficlog,"\n#****** ");
	for(j=1;j<=cptcoveff;j++) {
	fprintf(ficresvbl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
	fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
	printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
	}
	for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
	printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
	fprintf(ficresvbl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
	fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
	}
	fprintf(ficresvbl,"******\n");
	printf("******\n");
	fprintf(ficlog,"******\n");

	varbpl=matrix(1,nlstate,(int) bage, (int) fage);
	oldm=oldms;savm=savms;

	varbrevlim(fileresvbl, ficresvbl, varbpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, bprlim, ftolpl, mobilavproj, ncvyearp, k, strstart, nres);
	free_matrix(varbpl,1,nlstate,(int) bage, (int)fage);
	/}/
	}

	fclose(ficresvbl);
	printf("done variance-covariance of back prevalence\n");fflush(stdout);
	fprintf(ficlog,"done variance-covariance of back prevalence\n");fflush(ficlog);

	} /* End of varbprlim */

/************ Forecasting *not tested NB***********/	/************ Forecasting *not tested NB***********/
/* void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2s, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ */	/* void populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2s, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){ */
Line 9010 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 9775 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 9260 Dummy[k] 0=dummy (0 1), 1 quantitative (	Line 10025 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 9436 BOOL IsWow64()	Line 10202 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 9472 void syscompilerinfo(int logged)	Line 10240 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 9488 void syscompilerinfo(int logged)	Line 10258 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 9575 void syscompilerinfo(int logged)	Line 10343 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 9596 void syscompilerinfo(int logged)	Line 10364 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 9605 int prevalence_limit(double p, double	Line 10373 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 9686 int prevalence_limit(double p, double	Line 10454 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 9701 int back_prevalence_limit(double *p, dou	Line 10469 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 9771 int back_prevalence_limit(double *p, dou	Line 10539 int back_prevalence_limit(double *p, dou
}else{	}else{
/* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */	/* bprevalim(bprlim, probs, nlstate, p, age, oldm, savm, dnewm, doldm, dsavm, ftolpl, ncvyearp, k); */
bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);	bprevalim(bprlim, probs, nlstate, p, age, ftolpl, ncvyearp, k,nres);
	/* printf("TOTOT\n"); */
	/* exit(1); */
}	}
fprintf(ficresplb,"%.0f ",age );	fprintf(ficresplb,"%.0f ",age );
for(j=1;j<=cptcoveff;j++)	for(j=1;j<=cptcoveff;j++)
Line 9894 int hPijx(double *p, int bage, int fage)	Line 10664 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 9929 int hPijx(double *p, int bage, int fage)	Line 10699 int hPijx(double *p, int bage, int fage)

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

p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm); /* We can't have it at an upper level because of nhstepm */
	/* and memory limitations if stepm is small */

/* oldm=oldms;savm=savms; */	/* oldm=oldms;savm=savms; */
/* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */	/* hbxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k); */
hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k);	hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm, k, nres);
/* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */	/* hbxij(p3mat,nhstepm,agedeb,hstepm,p,prevacurrent,nlstate,stepm,oldm,savm, dnewm, doldm, dsavm, k); */
fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");	fprintf(ficrespijb,"# Cov Agex agex-h hbijx with i,j=");
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
Line 9971 int main(int argc, char *argv[])	Line 10743 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 9981 int main(int argc, char *argv[])	Line 10754 int main(int argc, char *argv[])
int vpopbased=0;	int vpopbased=0;
int nres=0;	int nres=0;
int endishere=0;	int endishere=0;
	int noffset=0;
	int ncurrv=0; /* Temporary variable */

char ca[32], cb[32];	char ca[32], cb[32];
/* FILE fichtm; //* Html File */	/* FILE fichtm; //* Html File */
/* FILE ficgp;/ /Gnuplot File /	/* FILE ficgp;/ /Gnuplot File /
Line 10004 int main(int argc, char *argv[])	Line 10779 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 10012 int main(int argc, char *argv[])	Line 10787 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;	/* int backcast=0; / / defined as global for mlikeli and mle */
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 10033 int main(int argc, char *argv[])	Line 10808 int main(int argc, char *argv[])
double delti; / Scale */	double delti; / Scale */
double *eij, *vareij;	double *eij, *vareij;
double *varpl; / Variances of prevalence limits by age */	double *varpl; / Variances of prevalence limits by age */

double *epj, vepp;	double *epj, vepp;

double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;	double dateprev1, dateprev2;
double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000;	double jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000, dateproj1=0, dateproj2=0;
	double jback1=1,mback1=1,anback1=2000,jback2=1,mback2=1,anback2=2000, dateback1=0, dateback2=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 10114 int main(int argc, char *argv[])	Line 10891 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 10193 int main(int argc, char *argv[])	Line 10975 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 10203 int main(int argc, char *argv[])	Line 10983 int main(int argc, char *argv[])
fflush(ficlog);	fflush(ficlog);
goto end;	goto end;
}	}
	/-------- Rewriting parameter file ----------/
	strcpy(rfileres,"r"); /* "Rparameterfile */
	strcat(rfileres,optionfilefiname); /* Parameter file first name */
	strcat(rfileres,"."); /* */
	strcat(rfileres,optionfilext); /* Other files have txt extension */
	if((ficres =fopen(rfileres,"w"))==NULL) {
	printf("Problem writing new parameter file: %s\n", rfileres);goto end;
	fprintf(ficlog,"Problem writing new parameter file: %s\n", rfileres);goto end;
	fflush(ficlog);
	goto end;
	}
	fprintf(ficres,"#IMaCh %s\n",version);


/* Reads comments: lines beginning with '#' */	/* Reads comments: lines beginning with '#' */
numlinepar=0;	numlinepar=0;
	/* Is it a BOM UTF-8 Windows file? */
/* First parameter line */	/* First parameter line */
while(fgets(line, MAXLINE, ficpar)) {	while(fgets(line, MAXLINE, ficpar)) {
	noffset=0;
	if( line[0] == (char)0xEF && line[1] == (char)0xBB) /* EF BB BF */
	{
	noffset=noffset+3;
	printf("# File is an UTF8 Bom.\n"); // 0xBF
	}
	else if( line[0] == (char)0xFE && line[1] == (char)0xFF)
	{
	noffset=noffset+2;
	printf("# File is an UTF16BE BOM file\n");
	}
	else if( line[0] == 0 && line[1] == 0)
	{
	if( line[2] == (char)0xFE && line[3] == (char)0xFF){
	noffset=noffset+4;
	printf("# File is an UTF16BE BOM file\n");
	}
	} else{
	;/printf(" Not a BOM file\n");/
	}

/* If line starts with a # it is a comment */	/* If line starts with a # it is a comment */
if (line[0] == '#') {	if (line[noffset] == '#') {
numlinepar++;	numlinepar++;
fputs(line,stdout);	fputs(line,stdout);
fputs(line,ficparo);	fputs(line,ficparo);
	fputs(line,ficres);
fputs(line,ficlog);	fputs(line,ficlog);
continue;	continue;
}else	}else
Line 10223 int main(int argc, char *argv[])	Line 11038 int main(int argc, char *argv[])
title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){	title, datafile, &lastobs, &firstpass,&lastpass)) !=EOF){
if (num_filled != 5) {	if (num_filled != 5) {
printf("Should be 5 parameters\n");	printf("Should be 5 parameters\n");
	fprintf(ficlog,"Should be 5 parameters\n");
}	}
numlinepar++;	numlinepar++;
printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);	printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
	fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
	fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
	fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\n", title, datafile, lastobs, firstpass,lastpass);
}	}
/* Second parameter line */	/* Second parameter line */
while(fgets(line, MAXLINE, ficpar)) {	while(fgets(line, MAXLINE, ficpar)) {
/* If line starts with a # it is a comment */	/* while(fscanf(ficpar,"%[^\n]", line)) { */
	/* If line starts with a # it is a comment. Strangely fgets reads the EOL and fputs doesn't */
if (line[0] == '#') {	if (line[0] == '#') {
numlinepar++;	numlinepar++;
fputs(line,stdout);	printf("%s",line);
fputs(line,ficparo);	fprintf(ficres,"%s",line);
fputs(line,ficlog);	fprintf(ficparo,"%s",line);
	fprintf(ficlog,"%s",line);
continue;	continue;
}else	}else
break;	break;
Line 10244 int main(int argc, char *argv[])	Line 11065 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);
}	}
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);	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);
	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 10254 int main(int argc, char *argv[])	Line 11086 int main(int argc, char *argv[])
/* If line starts with a # it is a comment */	/* If line starts with a # it is a comment */
if (line[0] == '#') {	if (line[0] == '#') {
numlinepar++;	numlinepar++;
fputs(line,stdout);	printf("%s",line);
fputs(line,ficparo);	fprintf(ficres,"%s",line);
fputs(line,ficlog);	fprintf(ficparo,"%s",line);
	fprintf(ficlog,"%s",line);
continue;	continue;
}else	}else
break;	break;
}	}
if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){	if((num_filled=sscanf(line,"model=1+age%[^.\n]", model)) !=EOF){
if (num_filled == 0){	if (num_filled != 1){
printf("ERROR %d: Model should be at minimum 'model=1+age.' WITHOUT space:'%s'\n",num_filled, line);	printf("ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line);
fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' WITHOUT space:'%s'\n",num_filled, line);	fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age' %s\n",num_filled, line);
model[0]='\0';
goto end;
} else if (num_filled != 1){
printf("ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
fprintf(ficlog,"ERROR %d: Model should be at minimum 'model=1+age.' %s\n",num_filled, line);
model[0]='\0';	model[0]='\0';
goto end;	goto end;
}	}
Line 10282 int main(int argc, char *argv[])	Line 11110 int main(int argc, char *argv[])
}	}
/* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */	/* printf(" model=1+age%s modeltemp= %s, model=%s\n",model, modeltemp, model);fflush(stdout); */
printf("model=1+age+%s\n",model);fflush(stdout);	printf("model=1+age+%s\n",model);fflush(stdout);
	fprintf(ficparo,"model=1+age+%s\n",model);fflush(stdout);
	fprintf(ficres,"model=1+age+%s\n",model);fflush(stdout);
	fprintf(ficlog,"model=1+age+%s\n",model);fflush(stdout);
}	}
/* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */	/* fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=1+age+%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model); */
/* numlinepar=numlinepar+3; /\* In general \/ /	/* numlinepar=numlinepar+3; /\* In general \/ /
/* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */	/* printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model); */
fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);	/* fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); */
fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model);	/* fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nqv=%d ntv=%d nqtv=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=1+age+%s.\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol, nqv, ntv, nqtv, nlstate,ndeath,maxwav, mle, weightopt,model); */
fflush(ficlog);	fflush(ficlog);
/* if(model[0]=='#'\|\| model[0]== '\0'){ */	/* if(model[0]=='#'\|\| model[0]== '\0'){ */
if(model[0]=='#'){	if(model[0]=='#'){
printf("Error in 'model' line: model should start with 'model=1+age+' and end with '.' \n \	printf("Error in 'model' line: model should start with 'model=1+age+' and end without space \n \
'model=1+age+.' or 'model=1+age+V1.' or 'model=1+age+ageage+V1+V1age.' or \n \	'model=1+age+' or 'model=1+age+V1.' or 'model=1+age+ageage+V1+V1age' or \n \
'model=1+age+V1+V2.' or 'model=1+age+V1+V2+V1*V2.' etc. \n"); \	'model=1+age+V1+V2' or 'model=1+age+V1+V2+V1*V2' etc. \n"); \
if(mle != -1){	if(mle != -1){
printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter file.\n");	printf("Fix the model line and run imach with mle=-1 to get a correct template of the parameter vectors and subdiagonal covariance matrix.\n");
exit(1);	exit(1);
}	}
}	}
Line 10315 int main(int argc, char *argv[])	Line 11146 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 /
coqvar=matrix(1,nqv,1,n); /*< Fixed quantitative covariate /	if(nqv>=1)coqvar=matrix(1,nqv,firstobs,lastobs); /*< Fixed quantitative covariate /
cotvar=ma3x(1,maxwav,1,ntv+nqtv,1,n); /*< Time varying covariate (dummy and quantitative)/	if(nqtv>=1)cotqvar=ma3x(1,maxwav,1,nqtv,firstobs,lastobs); /*< Time varying quantitative covariate /
cotqvar=ma3x(1,maxwav,1,nqtv,1,n); /*< Time varying quantitative covariate /	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 10381 int main(int argc, char *argv[])	Line 11212 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 10517 Please run with mle=-1 to get a correct	Line 11357 Please run with mle=-1 to get a correct

fflush(ficlog);	fflush(ficlog);

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

/* Main data	/* Main data
*/	*/
n= lastobs;	nobs=lastobs-firstobs+1; /* was = lastobs;*/
num=lvector(1,n);	/* num=lvector(1,n); */
moisnais=vector(1,n);	/* moisnais=vector(1,n); */
annais=vector(1,n);	/* annais=vector(1,n); */
moisdc=vector(1,n);	/* moisdc=vector(1,n); */
andc=vector(1,n);	/* andc=vector(1,n); */
weight=vector(1,n);	/* weight=vector(1,n); */
agedc=vector(1,n);	/* agedc=vector(1,n); */
cod=ivector(1,n);	/* cod=ivector(1,n); */
for(i=1;i<=n;i++){	/* for(i=1;i<=n;i++){ */
	num=lvector(firstobs,lastobs);
	moisnais=vector(firstobs,lastobs);
	annais=vector(firstobs,lastobs);
	moisdc=vector(firstobs,lastobs);
	andc=vector(firstobs,lastobs);
	weight=vector(firstobs,lastobs);
	agedc=vector(firstobs,lastobs);
	cod=ivector(firstobs,lastobs);
	for(i=firstobs;i<=lastobs;i++){
num[i]=0;	num[i]=0;
moisnais[i]=0;	moisnais[i]=0;
annais[i]=0;	annais[i]=0;
Line 10550 Please run with mle=-1 to get a correct	Line 11389 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 10654 Please run with mle=-1 to get a correct	Line 11493 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 10681 Please run with mle=-1 to get a correct	Line 11520 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 10864 Title=%s <br>Datafile=%s Firstpass=%d La	Line 11703 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,"<br>Total number of observations=%d <br>\n\	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);
	fprintf(fichtm,"\n<li>Number of fixed dummy covariates: ncovcol=%d ", ncovcol);
	ncurrv=1;
	for(i=ncurrv; i <=ncovcol; i++) fprintf(fichtm,"V%d ", i);
	fprintf(fichtm,"\n<li> Number of fixed quantitative variables: nqv=%d ", nqv);
	ncurrv=i;
	for(i=ncurrv; i <=ncurrv-1+nqv; i++) fprintf(fichtm,"V%d ", i);
	fprintf(fichtm,"\n<li> Number of time varying (wave varying) dummy covariates: ntv=%d ", ntv);
	ncurrv=i;
	for(i=ncurrv; i <=ncurrv-1+ntv; i++) fprintf(fichtm,"V%d ", i);
	fprintf(fichtm,"\n<li>Number of time varying quantitative covariates: nqtv=%d ", nqtv);
	ncurrv=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", \
	nlstate, ndeath, maxwav, mle, weightopt);

	fprintf(fichtm,"<h4> Diagram of states <a href=\"%s_.svg\">%s_.svg</a></h4> \n\
	<img src=\"%s_.svg\">", subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"),subdirf2(optionfilefiname,"D_"));


	fprintf(fichtm,"\n<h4>Some descriptive statistics </h4>\n<br>Total number of observations=%d <br>\n\
Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\	Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\	Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
imx,agemin,agemax,jmin,jmax,jmean);	imx,agemin,agemax,jmin,jmax,jmean);
pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */	pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */	oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */	newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */	savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */	oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */

/* For Powell, parameters are in a vector p[] starting at p[1]	/* For Powell, parameters are in a vector p[] starting at p[1]
so we point p on param[1][1] so that p[1] maps on param[1][1][1] */	so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
Line 10886 Interval (in months) between two waves:	Line 11746 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 11103 Please run with mle=-1 to get a correct	Line 11963 Please run with mle=-1 to get a correct
free_vector(lpop,1,AGESUP);	free_vector(lpop,1,AGESUP);
free_vector(tpop,1,AGESUP);	free_vector(tpop,1,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 11139 Please run with mle=-1 to get a correct	Line 12000 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 11427 Please run with mle=-1 to get a correct	Line 12288 Please run with mle=-1 to get a correct
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.;
	dateproj2=anproj2+(mproj2-1)/12.+(jproj2-1)/365.;

}	}
break;	break;
case 12:	case 12:
Line 11442 Please run with mle=-1 to get a correct	Line 12306 Please run with mle=-1 to get a correct
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(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);	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.*/	/* day and month of proj2 are not used but only year anproj2.*/
	dateback1=anback1+(mback1-1)/12.+(jback1-1)/365.;
	dateback2=anback2+(mback2-1)/12.+(jback2-1)/365.;
}	}
break;	break;
case 13:	case 13:
Line 11492 Please run with mle=-1 to get a correct	Line 12358 Please run with mle=-1 to get a correct
This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\	This is probably because your parameter file doesn't \n contain the exact number of lines (or columns) corresponding to your model line.\n\
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);	/* 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);
}	}
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,backcast, estepm, \
jprev1,mprev1,anprev1,dateprev1,jprev2,mprev2,anprev2,dateprev2);	jprev1,mprev1,anprev1,dateprev1, dateproj1, dateback1,jprev2,mprev2,anprev2,dateprev2,dateproj2, dateback2);

/------------ free_vector -------------/	/------------ free_vector -------------/
/* chdir(path); */	/* chdir(path); */
Line 11505 Please run with mle=-1 to get a correct	Line 12372 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 11532 Please run with mle=-1 to get a correct	Line 12399 Please run with mle=-1 to get a correct
k=1;	k=1;
varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);	varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);

/* Prevalence for each covariates in probs[age][status][cov] */	/* Prevalence for each covariate combination in probs[age][status][cov] */
probs= ma3x(1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);	probs= ma3x(AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
for(i=1;i<=AGESUP;i++)	for(i=AGEINF;i<=AGESUP;i++)
for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */	for(j=1;j<=nlstate+ndeath;j++) /* ndeath is useless but a necessity to be compared with mobaverages */
for(k=1;k<=ncovcombmax;k++)	for(k=1;k<=ncovcombmax;k++)
probs[i][j][k]=0.;	probs[i][j][k]=0.;
prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);	prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode,
	ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
if (mobilav!=0 \|\|mobilavproj !=0 ) {	if (mobilav!=0 \|\|mobilavproj !=0 ) {
mobaverages= ma3x(1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);	mobaverages= ma3x(AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
for(i=1;i<=AGESUP;i++)	for(i=AGEINF;i<=AGESUP;i++)
for(j=1;j<=nlstate;j++)	for(j=1;j<=nlstate+ndeath;j++)
for(k=1;k<=ncovcombmax;k++)	for(k=1;k<=ncovcombmax;k++)
mobaverages[i][j][k]=0.;	mobaverages[i][j][k]=0.;
mobaverage=mobaverages;	mobaverage=mobaverages;
Line 11553 Please run with mle=-1 to get a correct	Line 12421 Please run with mle=-1 to get a correct
fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);	fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
printf(" Error in movingaverage mobilav=%d\n",mobilav);	printf(" Error in movingaverage mobilav=%d\n",mobilav);
}	}
}	} else if (mobilavproj !=0) {
/* /\* Prevalence for each covariates in probs[age][status][cov] \/ /
/* prevalence(probs, ageminpar, agemaxpar, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass); */
else if (mobilavproj !=0) {
printf("Movingaveraging projected observed prevalence\n");	printf("Movingaveraging projected observed prevalence\n");
fprintf(ficlog,"Movingaveraging projected observed prevalence\n");	fprintf(ficlog,"Movingaveraging projected observed prevalence\n");
if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){	if (movingaverage(probs, ageminpar, agemaxpar, mobaverage, mobilavproj)!=0){
fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);	fprintf(ficlog," Error in movingaverage mobilavproj=%d\n",mobilavproj);
printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);	printf(" Error in movingaverage mobilavproj=%d\n",mobilavproj);
}	}
	}else{
	printf("Internal error moving average\n");
	fflush(stdout);
	exit(1);
}	}
}/* end if moving average */	}/* end if moving average */

/---------- Forecasting ------------------/	/---------- Forecasting ------------------/
/if((stepm == 1) && (strcmp(model,".")==0)){/
if(prevfcast==1){	if(prevfcast==1){
/* if(stepm ==1){*/	/* if(stepm ==1){*/
prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);	prevforecast(fileresu, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, mobaverage, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
}	}

	/* Backcasting */
if(backcast==1){	if(backcast==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);
Line 11580 Please run with mle=-1 to get a correct	Line 12450 Please run with mle=-1 to get a correct
/--------------- Back Prevalence limit (period or stable prevalence) --------------/	/--------------- Back Prevalence limit (period or stable prevalence) --------------/

bprlim=matrix(1,nlstate,1,nlstate);	bprlim=matrix(1,nlstate,1,nlstate);

back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);	back_prevalence_limit(p, bprlim, ageminpar, agemaxpar, ftolpl, &ncvyear, dateprev1, dateprev2, firstpass, lastpass, mobilavproj);
fclose(ficresplb);	fclose(ficresplb);

hBijx(p, bage, fage, mobaverage);	hBijx(p, bage, fage, mobaverage);
fclose(ficrespijb);	fclose(ficrespijb);
free_matrix(bprlim,1,nlstate,1,nlstate); /here or after loop ? /

/* prevbackforecast(fileresu, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2, mobilavproj,	prevbackforecast(fileresu, mobaverage, anback1, mback1, jback1, agemin, agemax, dateprev1, dateprev2,
bage, fage, firstpass, lastpass, anback2, p, cptcoveff); */	mobilavproj, bage, fage, firstpass, lastpass, anback2, p, cptcoveff);
	varbprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, bprlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);


	free_matrix(bprlim,1,nlstate,1,nlstate); /here or after loop ? /
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 */


/* ------ Other prevalence ratios------------ */	/* ------ Other prevalence ratios------------ */

Line 11645 Please run with mle=-1 to get a correct	Line 12519 Please run with mle=-1 to get a correct
fclose(ficreseij);	fclose(ficreseij);
printf("done evsij\n");fflush(stdout);	printf("done evsij\n");fflush(stdout);
fprintf(ficlog,"done evsij\n");fflush(ficlog);	fprintf(ficlog,"done evsij\n");fflush(ficlog);


/---------- State-specific expectancies and variances ------------/	/---------- State-specific expectancies and variances ------------/


strcpy(filerest,"T_");	strcpy(filerest,"T_");
strcat(filerest,fileresu);	strcat(filerest,fileresu);
if((ficrest=fopen(filerest,"w"))==NULL) {	if((ficrest=fopen(filerest,"w"))==NULL) {
Line 11657 Please run with mle=-1 to get a correct	Line 12531 Please run with mle=-1 to get a correct
}	}
printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);	printf("Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(stdout);
fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);	fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' ...\n", filerest); fflush(ficlog);


strcpy(fileresstde,"STDE_");	strcpy(fileresstde,"STDE_");
strcat(fileresstde,fileresu);	strcat(fileresstde,fileresu);
if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {	if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
Line 11686 Please run with mle=-1 to get a correct	Line 12558 Please run with mle=-1 to get a correct
printf(" Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);	printf(" Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(stdout);
fprintf(ficlog," Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);	fprintf(ficlog," Computing Variance-covariance of State-specific Expectancies: file '%s' ... ", fileresv);fflush(ficlog);

/*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/

i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */	i1=pow(2,cptcoveff); /* Number of combination of dummy covariates */
if (cptcovn < 1){i1=1;}	if (cptcovn < 1){i1=1;}

Line 11750 Please run with mle=-1 to get a correct	Line 12619 Please run with mle=-1 to get a correct
vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);	vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
pstamp(ficrest);	pstamp(ficrest);

	epj=vector(1,nlstate+1);
for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/	for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
oldm=oldms;savm=savms; /* ZZ Segmentation fault */	oldm=oldms;savm=savms; /* ZZ Segmentation fault */
cptcod= 0; /* To be deleted */	cptcod= 0; /* To be deleted */
Line 11761 Please run with mle=-1 to get a correct	Line 12630 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"); */
epj=vector(1,nlstate+1);	printf("Computing age specific forward period (stable) prevalences in each health state \n");
printf("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");
fprintf(ficlog,"Computing age specific 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 11804 Please run with mle=-1 to get a correct	Line 12672 Please run with mle=-1 to get a correct
fprintf(ficrest,"\n");	fprintf(ficrest,"\n");
}	}
} /* End vpopbased */	} /* End vpopbased */
	free_vector(epj,1,nlstate+1);
free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);	free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);	free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
free_vector(epj,1,nlstate+1);
printf("done selection\n");fflush(stdout);	printf("done selection\n");fflush(stdout);
fprintf(ficlog,"done selection\n");fflush(ficlog);	fprintf(ficlog,"done selection\n");fflush(ficlog);

/}/
} /* End k selection */	} /* End k selection */

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 of period (stable) prevalence------/	/* variance-covariance of forward period prevalence*/
	varprlim(fileresu, nresult, mobaverage, mobilavproj, bage, fage, prlim, &ncvyear, ftolpl, p, matcov, delti, stepm, cptcoveff);
strcpy(fileresvpl,"VPL_");
strcat(fileresvpl,fileresu);
if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
exit(0);
}
printf("Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(stdout);
fprintf(ficlog, "Computing Variance-covariance of period (stable) prevalence: file '%s' ...", fileresvpl);fflush(ficlog);

/*for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){*/

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

for(nres=1; nres <= nresult; nres++) /* For each resultline */
for(k=1; k<=i1;k++){
if(i1 != 1 && TKresult[nres]!= k)
continue;
fprintf(ficresvpl,"\n#****** ");
printf("\n#****** ");
fprintf(ficlog,"\n#****** ");
for(j=1;j<=cptcoveff;j++) {
fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
fprintf(ficlog,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
printf("V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtabm(k,j)]);
}
for (j=1; j<= nsq; j++){ /* For each selected (single) quantitative value */
printf(" V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
fprintf(ficresvpl," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
fprintf(ficlog," V%d=%f ",Tvqresult[nres][j],Tqresult[nres][j]);
}
fprintf(ficresvpl,"******\n");
printf("******\n");
fprintf(ficlog,"******\n");

varpl=matrix(1,nlstate,(int) bage, (int) fage);
oldm=oldms;savm=savms;
varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl, &ncvyear, k, strstart, nres);
free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
/}/
}

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

free_vector(weight,1,n);
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 11881 Please run with mle=-1 to get a correct	Line 12703 Please run with mle=-1 to get a correct

/---------- End : free ----------------/	/---------- End : free ----------------/
if (mobilav!=0 \|\|mobilavproj !=0)	if (mobilav!=0 \|\|mobilavproj !=0)
free_ma3x(mobaverages,1, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */	free_ma3x(mobaverages,AGEINF, AGESUP,1,nlstate+ndeath, 1,ncovcombmax); /* We need to have a squared matrix with prevalence of the dead! */
free_ma3x(probs,1,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);	free_ma3x(probs,AGEINF,AGESUP,1,nlstate+ndeath, 1,ncovcombmax);
free_matrix(prlim,1,nlstate,1,nlstate); /here or after loop ? /	free_matrix(prlim,1,nlstate,1,nlstate); /here or after loop ? /
free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);	free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
} /* mle==-3 arrives here for freeing */	} /* mle==-3 arrives here for freeing */
Line 11890 Please run with mle=-1 to get a correct	Line 12712 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);
free_ma3x(cotqvar,1,maxwav,1,nqtv,1,n);	if(ntv+nqtv>=1)free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,firstobs,lastobs);
free_ma3x(cotvar,1,maxwav,1,ntv+nqtv,1,n);	if(nqtv>=1)free_ma3x(cotqvar,1,maxwav,1,nqtv,firstobs,lastobs);
free_matrix(coqvar,1,maxwav,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);/
free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);	free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
free_matrix(agev,1,maxwav,1,imx);	free_matrix(agev,1,maxwav,1,imx);
	free_ma3x(paramstart,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);	free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);

free_ivector(ncodemax,1,NCOVMAX);	free_ivector(ncodemax,1,NCOVMAX);
Line 11975 Please run with mle=-1 to get a correct	Line 12798 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 12010 Please run with mle=-1 to get a correct	Line 12835 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 12043 end:	Line 12871 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.1.265
changed lines
	Added in v.1.292