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Diff for /imach/src/imach.c between versions 1.121 and 1.128

version 1.121, 2006/03/16 17:45:01	version 1.128, 2006/06/30 13:02:05
Line 1	Line 1
/* $Id$	/* $Id$
$State$	$State$
$Log$	$Log$
	Revision 1.128 2006/06/30 13:02:05 brouard
	(Module): Clarifications on computing e.j

	Revision 1.127 2006/04/28 18:11:50 brouard
	(Module): Yes the sum of survivors was wrong since
	imach-114 because nhstepm was no more computed in the age
	loop. Now we define nhstepma in the age loop.
	(Module): In order to speed up (in case of numerous covariates) we
	compute health expectancies (without variances) in a first step
	and then all the health expectancies with variances or standard
	deviation (needs data from the Hessian matrices) which slows the
	computation.
	In the future we should be able to stop the program is only health
	expectancies and graph are needed without standard deviations.

	Revision 1.126 2006/04/28 17:23:28 brouard
	(Module): Yes the sum of survivors was wrong since
	imach-114 because nhstepm was no more computed in the age
	loop. Now we define nhstepma in the age loop.
	Version 0.98h

	Revision 1.125 2006/04/04 15:20:31 lievre
	Errors in calculation of health expectancies. Age was not initialized.
	Forecasting file added.

	Revision 1.124 2006/03/22 17:13:53 lievre
	Parameters are printed with %lf instead of %f (more numbers after the comma).
	The log-likelihood is printed in the log file

	Revision 1.123 2006/03/20 10:52:43 brouard
	* imach.c (Module): <title> changed, corresponds to .htm file
	name. <head> headers where missing.

	* imach.c (Module): Weights can have a decimal point as for
	English (a comma might work with a correct LC_NUMERIC environment,
	otherwise the weight is truncated).
	Modification of warning when the covariates values are not 0 or
	1.
	Version 0.98g

	Revision 1.122 2006/03/20 09:45:41 brouard
	(Module): Weights can have a decimal point as for
	English (a comma might work with a correct LC_NUMERIC environment,
	otherwise the weight is truncated).
	Modification of warning when the covariates values are not 0 or
	1.
	Version 0.98g

Revision 1.121 2006/03/16 17:45:01 lievre	Revision 1.121 2006/03/16 17:45:01 lievre
* imach.c (Module): Comments concerning covariates added	* imach.c (Module): Comments concerning covariates added

Line 341 extern int errno;	Line 389 extern int errno;
/* $Id$ */	/* $Id$ */
/* $State$ */	/* $State$ */

char version[]="Imach version 0.98f, March 2006, INED-EUROREVES-Institut de longevite ";	char version[]="Imach version 0.98i, June 2006, INED-EUROREVES-Institut de longevite ";
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 416 char strcurr[80], strfor[80];	Line 464 char strcurr[80], strfor[80];

char *endptr;	char *endptr;
long lval;	long lval;
	double dval;

#define NR_END 1	#define NR_END 1
#define FREE_ARG char*	#define FREE_ARG char*
Line 981 void powell(double p[], double **xi, int	Line 1030 void powell(double p[], double **xi, int
last_time=curr_time;	last_time=curr_time;
(void) gettimeofday(&curr_time,&tzp);	(void) gettimeofday(&curr_time,&tzp);
printf("\nPowell iter=%d -2LL=%.12f %ld sec. %ld sec.",iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);	printf("\nPowell iter=%d -2LL=%.12f %ld sec. %ld sec.",iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
/* fprintf(ficlog,"\nPowell iter=%d -2LL=%.12f %ld sec. %ld sec.",iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);	fprintf(ficlog,"\nPowell iter=%d -2LL=%.12f %ld sec. %ld sec.",iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);
fprintf(ficrespow,"%d %.12f %ld",iter,fret,curr_time.tv_sec-start_time.tv_sec);	/* fprintf(ficrespow,"%d %.12f %ld",iter,fret,curr_time.tv_sec-start_time.tv_sec); */
*/
for (i=1;i<=n;i++) {	for (i=1;i<=n;i++) {
printf(" %d %.12f",i, p[i]);	printf(" %d %.12f",i, p[i]);
fprintf(ficlog," %d %.12lf",i, p[i]);	fprintf(ficlog," %d %.12lf",i, p[i]);
Line 1299 double *hpxij(double *po, int nhstep	Line 1347 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];
/*printf("i=%d j=%d h=%d po[i][j][h]=%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);/
} /* end h */	} /* end h */
	/* printf("\n H=%d \n",h); */
return po;	return po;
}	}

Line 2219 void prevalence(double ***probs, double	Line 2268 void prevalence(double ***probs, double
if( i <= iagemax){	if( i <= iagemax){
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
	printf("Warning Observed prevalence probs[%d][%d][%d]=%lf because of lack of cases\n",jk,i,j1,probs[i][jk][j1]);
}	}
}/* end jk */	}/* end jk */
}/* end i */	}/* end i */
Line 2434 void tricode(int Tvar, int *nbcode, in	Line 2484 void tricode(int Tvar, int *nbcode, in

/********* Health Expectancies **************/	/********* Health Expectancies **************/

void evsij(char fileres[], double *eij, double x[], int nlstate, int stepm, int bage, int fage, double oldm, double **savm, int cij, int estepm,char strstart[] )	void evsij(double *eij, double x[], int nlstate, int stepm, int bage, int fage, double oldm, double **savm, int cij, int estepm,char strstart[] )

{	{
/* Health expectancies, no variances */	/* Health expectancies, no variances */
int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;	int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
	int nhstepma, nstepma; /* Decreasing with age */
double age, agelim, hf;	double age, agelim, hf;
double ***p3mat;	double ***p3mat;
double eip;	double eip;
Line 2485 void evsij(char fileres[], double ***eij	Line 2536 void evsij(char fileres[], double ***eij
hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */	hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */

agelim=AGESUP;	agelim=AGESUP;
/* nhstepm age range expressed in number of stepm */	/* If stepm=6 months */
nstepm=(int) rint((agelim-age)*YEARM/stepm);	/* Computed by stepm unit matrices, product of hstepm matrices, stored
	in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */

	/* nhstepm age range expressed in number of stepm */
	nstepm=(int) rint((agelim-bage)YEARM/stepm); / Biggest nstepm */
/* Typically if 20 years nstepm = 2012/6=40 stepm /	/* Typically if 20 years nstepm = 2012/6=40 stepm /
/* if (stepm >= YEARM) hstepm=1;*/	/* if (stepm >= YEARM) hstepm=1;*/
nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */	nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);	p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);

for (age=bage; age<=fage; age ++){ /* If stepm=6 months */	for (age=bage; age<=fage; age ++){
/* Computed by stepm unit matrices, product of hstepm matrices, stored	nstepma=(int) rint((agelim-bage)YEARM/stepm); / Biggest nstepm */
in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */	/* Typically if 20 years nstepm = 2012/6=40 stepm /
	/* if (stepm >= YEARM) hstepm=1;*/
	nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */

	/* If stepm=6 months */
	/* Computed by stepm unit matrices, product of hstepma matrices, stored
	in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */

hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);	hpxij(p3mat,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);

hf=hstepmstepm/YEARM; / Duration of hstepm expressed in year unit. */	hf=hstepmstepm/YEARM; / Duration of hstepm expressed in year unit. */

Line 2531 void evsij(char fileres[], double ***eij	Line 2592 void evsij(char fileres[], double ***eij

}	}

void cvevsij(char fileres[], double *eij, double x[], int nlstate, int stepm, int bage, int fage, double oldm, double savm, int cij, int estepm,double delti[],double matcov,char strstart[] )	void cvevsij(double *eij, double x[], int nlstate, int stepm, int bage, int fage, double oldm, double savm, int cij, int estepm,double delti[],double matcov,char strstart[] )

{	{
/* Covariances of health expectancies eij and of total life expectancies according	/* Covariances of health expectancies eij and of total life expectancies according
to initial status i, ei. .	to initial status i, ei. .
*/	*/
int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;	int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
	int nhstepma, nstepma; /* Decreasing with age */
double age, agelim, hf;	double age, agelim, hf;
double *p3matp, p3matm, **varhe;	double *p3matp, p3matm, **varhe;
double dnewm,doldm;	double dnewm,doldm;
Line 2611 void cvevsij(char fileres[], double ***e	Line 2673 void cvevsij(char fileres[], double ***e
/* If stepm=6 months */	/* If stepm=6 months */
/* nhstepm age range expressed in number of stepm */	/* nhstepm age range expressed in number of stepm */
agelim=AGESUP;	agelim=AGESUP;
nstepm=(int) rint((agelim-age)*YEARM/stepm);	nstepm=(int) rint((agelim-bage)*YEARM/stepm);
/* Typically if 20 years nstepm = 2012/6=40 stepm /	/* Typically if 20 years nstepm = 2012/6=40 stepm /
/* if (stepm >= YEARM) hstepm=1;*/	/* if (stepm >= YEARM) hstepm=1;*/
nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */	nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
Line 2624 void cvevsij(char fileres[], double ***e	Line 2686 void cvevsij(char fileres[], double ***e
gm=matrix(0,nhstepm,1,nlstate*nlstate);	gm=matrix(0,nhstepm,1,nlstate*nlstate);

for (age=bage; age<=fage; age ++){	for (age=bage; age<=fage; age ++){
	nstepma=(int) rint((agelim-bage)YEARM/stepm); / Biggest nstepm */
/* Computed by stepm unit matrices, product of hstepm matrices, stored	/* Typically if 20 years nstepm = 2012/6=40 stepm /
in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */	/* if (stepm >= YEARM) hstepm=1;*/
	nhstepma = nstepma/hstepm;/* Expressed in hstepm, typically nhstepma=40/4=10 */

	/* If stepm=6 months */
	/* Computed by stepm unit matrices, product of hstepma matrices, stored
	in an array of nhstepma length: nhstepma=10, hstepm=4, stepm=6 months */

hf=hstepmstepm/YEARM; / Duration of hstepm expressed in year unit. */	hf=hstepmstepm/YEARM; / Duration of hstepm expressed in year unit. */

/* Computing Variances of health expectancies */	/* Computing Variances of health expectancies */
Line 2678 void cvevsij(char fileres[], double ***e	Line 2745 void cvevsij(char fileres[], double ***e
varhe[ij][ji][(int)age] += doldm[ij][ji]hfhf;	varhe[ij][ji][(int)age] += doldm[ij][ji]hfhf;
}	}
}	}

/* Computing expectancies */	/* Computing expectancies */
hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);	hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
Line 2805 void varevsij(char optionfilefiname[], d	Line 2873 void varevsij(char optionfilefiname[], d
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 ");
if(popbased==1)	if(popbased==1)
fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");	fprintf(ficresvij,"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(ficresvij,"the age specific period (stable) prevalences in each health state \n");	fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
fprintf(ficresvij,"# Age");	fprintf(ficresvij,"# Age");
Line 2833 void varevsij(char optionfilefiname[], d	Line 2901 void varevsij(char optionfilefiname[], d
/* 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 function hpijx to understand why (it is linked to memory size questions) */
and note for a fixed period like k years */
/* 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
means that if the survival funtion is printed every two years of age and if	means that if the survival funtion is printed every two years of age and if
Line 2900 void varevsij(char optionfilefiname[], d	Line 2967 void varevsij(char optionfilefiname[], d
}	}
}	}

for(j=1; j<= nlstate; j++){	for(j=1; j<= nlstate; j++){ /* Sum of wi * eij = e.j */
for(h=0; h<=nhstepm; h++){	for(h=0; h<=nhstepm; h++){
for(i=1, gm[h][j]=0.;i<=nlstate;i++)	for(i=1, gm[h][j]=0.;i<=nlstate;i++)
gm[h][j] += prlim[i][i]*p3mat[i][j][h];	gm[h][j] += prlim[i][i]*p3mat[i][j][h];
Line 3460 void printinghtml(char fileres[], char t	Line 3527 void printinghtml(char fileres[], char t
- Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",	- Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));	subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age: ei., eij . If one or more covariate 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, ei. (b) health expectancies by health status at initial age, eij . 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 href=\"%s\">%s</a> <br>\n</li>",	<a href=\"%s\">%s</a> <br>\n",
estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));	estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
	fprintf(fichtm,"\
	- Population projections by age and states: \
	<a href=\"%s\">%s</a> <br>\n</li>", subdirf2(fileres,"f"),subdirf2(fileres,"f"));

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

Line 3523 fprintf(fichtm," \n<ul><li><b>Graphs</b>	Line 3592 fprintf(fichtm," \n<ul><li><b>Graphs</b>
<a href=\"%s\">%s</a> <br>\n</li>",	<a href=\"%s\">%s</a> <br>\n</li>",
estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));	estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij 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 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(fileres,"v"),subdirf2(fileres,"v"));	estepm, subdirf2(fileres,"v"),subdirf2(fileres,"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: <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",
subdirf2(fileres,"t"),subdirf2(fileres,"t"));	estepm, subdirf2(fileres,"t"),subdirf2(fileres,"t"));
fprintf(fichtm,"\	fprintf(fichtm,"\
- Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\	- Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));	subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
Line 3560 prevalence (with 95%% confidence interva	Line 3629 prevalence (with 95%% confidence interva
<img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);	<img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);
}	}
fprintf(fichtm,"\n<br>- Total life expectancy by age and \	fprintf(fichtm,"\n<br>- Total life expectancy by age and \
health expectancies in states (1) and (2): %s%d.png<br>\	health expectancies in states (1) and (2). If popbased=1 the smooth (due to the model) \
	true period expectancies (those weighted with period prevalences are also\
	drawn in addition to the population based expectancies computed using\
	observed and cahotic prevalences: %s%d.png<br>\
<img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);	<img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
} /* end i1 */	} /* end i1 */
}/* End k1 */	}/* End k1 */
Line 4323 int main(int argc, char *argv[])	Line 4395 int main(int argc, char *argv[])
int numlinepar=0; /* Current linenumber of parameter file */	int numlinepar=0; /* Current linenumber of parameter file */
int itimes;	int itimes;
int NDIM=2;	int NDIM=2;
	int vpopbased=0;

char ca[32], cb[32], cc[32];	char ca[32], cb[32], cc[32];
char dummy[]=" ";	char dummy[]=" ";
Line 4559 int main(int argc, char *argv[])	Line 4632 int main(int argc, char *argv[])
free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);	free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
fclose (ficparo);	fclose (ficparo);
fclose (ficlog);	fclose (ficlog);
	goto end;
exit(0);	exit(0);
}	}
else if(mle==-3) {	else if(mle==-3) {
Line 4589 int main(int argc, char *argv[])	Line 4663 int main(int argc, char *argv[])
j++;	j++;
fscanf(ficpar,"%1d%1d",&i1,&j1);	fscanf(ficpar,"%1d%1d",&i1,&j1);
if ((i1 != i) && (j1 != j)){	if ((i1 != i) && (j1 != j)){
printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);	printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n \
	It might be a problem of design; if ncovcol and the model are correct\n \
	run imach with mle=-1 to get a correct template of the parameter file.\n",numlinepar, i,j, i1, j1);
exit(1);	exit(1);
}	}
fprintf(ficparo,"%1d%1d",i1,j1);	fprintf(ficparo,"%1d%1d",i1,j1);
Line 4813 int main(int argc, char *argv[])	Line 4889 int main(int argc, char *argv[])

cutv(stra, strb,line,' ');	cutv(stra, strb,line,' ');
errno=0;	errno=0;
lval=strtol(strb,&endptr,10);	dval=strtod(strb,&endptr);
if( strb[0]=='\0' \|\| (*endptr != '\0')){	if( strb[0]=='\0' \|\| (*endptr != '\0')){
printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight. Exiting.\n",lval, i,line,linei);	printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight. Exiting.\n",dval, i,line,linei);
exit(1);	exit(1);
}	}
weight[i]=(double)(lval);	weight[i]=dval;
strcpy(line,stra);	strcpy(line,stra);

for (j=ncovcol;j>=1;j--){	for (j=ncovcol;j>=1;j--){
Line 4830 int main(int argc, char *argv[])	Line 4906 int main(int argc, char *argv[])
exit(1);	exit(1);
}	}
if(lval <-1 \|\| lval >1){	if(lval <-1 \|\| lval >1){
printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self). Exiting.\n",lval,linei, i,line,j);	printf("Error reading data around '%d' at line number %ld for individual %d, '%s'\n \
	Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
	for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
	For example, for multinomial values like 1, 2 and 3,\n \
	build V1=0 V2=0 for the reference value (1),\n \
	V1=1 V2=0 for (2) \n \
	and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
	output of IMaCh is often meaningless.\n \
	Exiting.\n",lval,linei, i,line,j);
exit(1);	exit(1);
}	}
covar[j][i]=(double)(lval);	covar[j][i]=(double)(lval);
Line 5126 int main(int argc, char *argv[])	Line 5210 int main(int argc, char *argv[])
printf("Problem with %s \n",optionfilehtmcov), exit(0);	printf("Problem with %s \n",optionfilehtmcov), exit(0);
}	}
else{	else{
fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \	fprintf(fichtmcov,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
<hr size=\"2\" color=\"#EC5E5E\"> \n\	<hr size=\"2\" color=\"#EC5E5E\"> \n\
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\	Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);	optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
}	}

fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \	fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><font size=\"2\">%s <br> %s</font> \
<hr size=\"2\" color=\"#EC5E5E\"> \n\	<hr size=\"2\" color=\"#EC5E5E\"> \n\
Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\	Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
\n\	\n\
Line 5143 Title=%s <br>Datafile=%s Firstpass=%d La	Line 5227 Title=%s <br>Datafile=%s Firstpass=%d La
- Log file of the run: <a href=\"%s\">%s</a><br>\n\	- Log file of the run: <a href=\"%s\">%s</a><br>\n\
- Gnuplot file name: <a href=\"%s\">%s</a><br>\n\	- Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
- Date and time at start: %s</ul>\n",\	- Date and time at start: %s</ul>\n",\
fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\	optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
optionfilefiname,optionfilext,optionfilefiname,optionfilext,\	optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
fileres,fileres,\	fileres,fileres,\
filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);	filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
Line 5326 Interval (in months) between two waves:	Line 5410 Interval (in months) between two waves:
fprintf(ficlog,"%d%d ",i,k);	fprintf(ficlog,"%d%d ",i,k);
fprintf(ficres,"%1d%1d ",i,k);	fprintf(ficres,"%1d%1d ",i,k);
for(j=1; j <=ncovmodel; j++){	for(j=1; j <=ncovmodel; j++){
printf("%f ",p[jk]);	printf("%lf ",p[jk]);
fprintf(ficlog,"%f ",p[jk]);	fprintf(ficlog,"%lf ",p[jk]);
fprintf(ficres,"%f ",p[jk]);	fprintf(ficres,"%lf ",p[jk]);
jk++;	jk++;
}	}
printf("\n");	printf("\n");
Line 5675 Interval (in months) between two waves:	Line 5759 Interval (in months) between two waves:
}	}


/---------- Health expectancies and variances ------------/	/* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */

strcpy(filerest,"t");	prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
strcat(filerest,fileres);	/* printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d, mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
if((ficrest=fopen(filerest,"w"))==NULL) {	ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
printf("Problem with total LE resultfile: %s\n", filerest);goto end;	*/
fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
	if (mobilav!=0) {
	mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
	if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
	fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
	printf(" Error in movingaverage mobilav=%d\n",mobilav);
	}
}	}
printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);


	/---------- Health expectancies, no variances ------------/

strcpy(filerese,"e");	strcpy(filerese,"e");
strcat(filerese,fileres);	strcat(filerese,fileres);
if((ficreseij=fopen(filerese,"w"))==NULL) {	if((ficreseij=fopen(filerese,"w"))==NULL) {
Line 5695 Interval (in months) between two waves:	Line 5785 Interval (in months) between two waves:
}	}
printf("Computing Health Expectancies: result on file '%s' \n", filerese);	printf("Computing Health Expectancies: result on file '%s' \n", filerese);
fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);	fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
	for(cptcov=1,k=0;cptcov<=i1;cptcov++){
	for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
	k=k+1;
	fprintf(ficreseij,"\n#****** ");
	for(j=1;j<=cptcoveff;j++) {
	fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
	}
	fprintf(ficreseij,"******\n");

	eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
	oldm=oldms;savm=savms;
	evsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);

	free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
	}
	}
	fclose(ficreseij);


	/---------- Health expectancies and variances ------------/


	strcpy(filerest,"t");
	strcat(filerest,fileres);
	if((ficrest=fopen(filerest,"w"))==NULL) {
	printf("Problem with total LE resultfile: %s\n", filerest);goto end;
	fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
	}
	printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);
	fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest);


strcpy(fileresstde,"stde");	strcpy(fileresstde,"stde");
strcat(fileresstde,fileres);	strcat(fileresstde,fileres);
Line 5723 Interval (in months) between two waves:	Line 5844 Interval (in months) between two waves:
printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);	printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);	fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);

/* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
/* printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d, mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
*/

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

for(cptcov=1,k=0;cptcov<=i1;cptcov++){	for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){	for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
k=k+1;	k=k+1;
Line 5745 Interval (in months) between two waves:	Line 5852 Interval (in months) between two waves:
fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
fprintf(ficrest,"******\n");	fprintf(ficrest,"******\n");

fprintf(ficreseij,"\n#****** ");
fprintf(ficresstdeij,"\n#****** ");	fprintf(ficresstdeij,"\n#****** ");
fprintf(ficrescveij,"\n#****** ");	fprintf(ficrescveij,"\n#****** ");
for(j=1;j<=cptcoveff;j++) {	for(j=1;j<=cptcoveff;j++) {
fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);	fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
}	}
fprintf(ficreseij,"******\n");
fprintf(ficresstdeij,"******\n");	fprintf(ficresstdeij,"******\n");
fprintf(ficrescveij,"******\n");	fprintf(ficrescveij,"******\n");

Line 5764 Interval (in months) between two waves:	Line 5868 Interval (in months) between two waves:

eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);	eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
oldm=oldms;savm=savms;	oldm=oldms;savm=savms;
evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);	cvevsij(eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);

vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);	vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
oldm=oldms;savm=savms;
varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
if(popbased==1){
varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
}

pstamp(ficrest);	pstamp(ficrest);
fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");	for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);	oldm=oldms;savm=savms;
fprintf(ficrest,"\n");	varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# (weighted average of eij where weights are ");
	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);
	else
	fprintf(ficrest,"the age specific period (stable) prevalences in each health state \n");
	fprintf(ficrest,"# Age e.. (std) ");
	for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
	fprintf(ficrest,"\n");

epj=vector(1,nlstate+1);	epj=vector(1,nlstate+1);
for(age=bage; age <=fage ;age++){	for(age=bage; age <=fage ;age++){
prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);	prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
if (popbased==1) {	if (vpopbased==1) {
if(mobilav ==0){	if(mobilav ==0){
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
prlim[i][i]=probs[(int)age][i][k];	prlim[i][i]=probs[(int)age][i][k];
}else{ /* mobilav */	}else{ /* mobilav */
for(i=1; i<=nlstate;i++)	for(i=1; i<=nlstate;i++)
prlim[i][i]=mobaverage[(int)age][i][k];	prlim[i][i]=mobaverage[(int)age][i][k];
	}
}	}
}

fprintf(ficrest," %4.0f",age);	fprintf(ficrest," %4.0f",age);
for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){	for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
for(i=1, epj[j]=0.;i <=nlstate;i++) {	for(i=1, epj[j]=0.;i <=nlstate;i++) {
epj[j] += prlim[i][i]*eij[i][j][(int)age];	epj[j] += prlim[i][i]*eij[i][j][(int)age];
/* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/	/* printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
	}
	epj[nlstate+1] +=epj[j];
}	}
epj[nlstate+1] +=epj[j];
}

for(i=1, vepp=0.;i <=nlstate;i++)	for(i=1, vepp=0.;i <=nlstate;i++)
for(j=1;j <=nlstate;j++)	for(j=1;j <=nlstate;j++)
vepp += vareij[i][j][(int)age];	vepp += vareij[i][j][(int)age];
fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));	fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
for(j=1;j <=nlstate;j++){	for(j=1;j <=nlstate;j++){
fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));	fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
	}
	fprintf(ficrest,"\n");
}	}
fprintf(ficrest,"\n");
}	}
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);
Line 5822 Interval (in months) between two waves:	Line 5927 Interval (in months) between two waves:
free_matrix(mint,1,maxwav,1,n);	free_matrix(mint,1,maxwav,1,n);
free_ivector(cod,1,n);	free_ivector(cod,1,n);
free_ivector(tab,1,NCOVMAX);	free_ivector(tab,1,NCOVMAX);
fclose(ficreseij);
fclose(ficresstdeij);	fclose(ficresstdeij);
fclose(ficrescveij);	fclose(ficrescveij);
fclose(ficresvij);	fclose(ficresvij);
Line 5908 Interval (in months) between two waves:	Line 6012 Interval (in months) between two waves:
fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);	fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
/* printf("Total time was %d uSec.\n", total_usecs);*/	/* printf("Total time was %d uSec.\n", total_usecs);*/
/* if(fileappend(fichtm,optionfilehtm)){ */	/* if(fileappend(fichtm,optionfilehtm)){ */
fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>",strstart, strtend);	fprintf(fichtm,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
fclose(fichtm);	fclose(fichtm);
	fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end %s<br>\n</body></html>",strstart, strtend);
fclose(fichtmcov);	fclose(fichtmcov);
fclose(ficgp);	fclose(ficgp);
fclose(ficlog);	fclose(ficlog);

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

Removed from v.1.121
changed lines
	Added in v.1.128