--- imach/src/imach.c 2006/01/05 20:23:19 1.105
+++ imach/src/imach.c 2006/04/28 17:23:28 1.126
@@ -1,6 +1,109 @@
-/* $Id: imach.c,v 1.105 2006/01/05 20:23:19 lievre Exp $
+/* $Id: imach.c,v 1.126 2006/04/28 17:23:28 brouard Exp $
$State: Exp $
$Log: imach.c,v $
+ 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): 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
+ * imach.c (Module): Comments concerning covariates added
+
+ * imach.c (Module): refinements in the computation of lli if
+ status=-2 in order to have more reliable computation if stepm is
+ not 1 month. Version 0.98f
+
+ Revision 1.120 2006/03/16 15:10:38 lievre
+ (Module): refinements in the computation of lli if
+ status=-2 in order to have more reliable computation if stepm is
+ not 1 month. Version 0.98f
+
+ Revision 1.119 2006/03/15 17:42:26 brouard
+ (Module): Bug if status = -2, the loglikelihood was
+ computed as likelihood omitting the logarithm. Version O.98e
+
+ Revision 1.118 2006/03/14 18:20:07 brouard
+ (Module): varevsij Comments added explaining the second
+ table of variances if popbased=1 .
+ (Module): Covariances of eij, ekl added, graphs fixed, new html link.
+ (Module): Function pstamp added
+ (Module): Version 0.98d
+
+ Revision 1.117 2006/03/14 17:16:22 brouard
+ (Module): varevsij Comments added explaining the second
+ table of variances if popbased=1 .
+ (Module): Covariances of eij, ekl added, graphs fixed, new html link.
+ (Module): Function pstamp added
+ (Module): Version 0.98d
+
+ Revision 1.116 2006/03/06 10:29:27 brouard
+ (Module): Variance-covariance wrong links and
+ varian-covariance of ej. is needed (Saito).
+
+ Revision 1.115 2006/02/27 12:17:45 brouard
+ (Module): One freematrix added in mlikeli! 0.98c
+
+ Revision 1.114 2006/02/26 12:57:58 brouard
+ (Module): Some improvements in processing parameter
+ filename with strsep.
+
+ Revision 1.113 2006/02/24 14:20:24 brouard
+ (Module): Memory leaks checks with valgrind and:
+ datafile was not closed, some imatrix were not freed and on matrix
+ allocation too.
+
+ Revision 1.112 2006/01/30 09:55:26 brouard
+ (Module): Back to gnuplot.exe instead of wgnuplot.exe
+
+ Revision 1.111 2006/01/25 20:38:18 brouard
+ (Module): Lots of cleaning and bugs added (Gompertz)
+ (Module): Comments can be added in data file. Missing date values
+ can be a simple dot '.'.
+
+ Revision 1.110 2006/01/25 00:51:50 brouard
+ (Module): Lots of cleaning and bugs added (Gompertz)
+
+ Revision 1.109 2006/01/24 19:37:15 brouard
+ (Module): Comments (lines starting with a #) are allowed in data.
+
+ Revision 1.108 2006/01/19 18:05:42 lievre
+ Gnuplot problem appeared...
+ To be fixed
+
+ Revision 1.107 2006/01/19 16:20:37 brouard
+ Test existence of gnuplot in imach path
+
+ Revision 1.106 2006/01/19 13:24:36 brouard
+ Some cleaning and links added in html output
+
Revision 1.105 2006/01/05 20:23:19 lievre
*** empty log message ***
@@ -170,7 +273,7 @@
hPijx.
Also this programme outputs the covariance matrix of the parameters but also
- of the life expectancies. It also computes the stable prevalence.
+ of the life expectancies. It also computes the period (stable) prevalence.
Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
Institut national d'études démographiques, Paris.
@@ -199,7 +302,7 @@
begin-prev-date,...
open gnuplot file
open html file
- stable prevalence
+ period (stable) prevalence
for age prevalim()
h Pij x
variance of p varprob
@@ -211,7 +314,7 @@
varevsij()
if popbased==1 varevsij(,popbased)
total life expectancies
- Variance of stable prevalence
+ Variance of period (stable) prevalence
end
*/
@@ -221,8 +324,15 @@
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
+#include <string.h>
#include <unistd.h>
+#include <limits.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <errno.h>
+extern int errno;
+
/* #include <sys/time.h> */
#include <time.h>
#include "timeval.h"
@@ -231,11 +341,11 @@
/* #define _(String) gettext (String) */
#define MAXLINE 256
+
#define GNUPLOTPROGRAM "gnuplot"
/*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
#define FILENAMELENGTH 132
-/*#define DEBUG*/
-/*#define windows*/
+
#define GLOCK_ERROR_NOPATH -1 /* empty path */
#define GLOCK_ERROR_GETCWD -2 /* cannot get cwd */
@@ -253,17 +363,21 @@
#define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
#ifdef UNIX
#define DIRSEPARATOR '/'
+#define CHARSEPARATOR "/"
#define ODIRSEPARATOR '\\'
#else
#define DIRSEPARATOR '\\'
+#define CHARSEPARATOR "\\"
#define ODIRSEPARATOR '/'
#endif
-/* $Id: imach.c,v 1.105 2006/01/05 20:23:19 lievre Exp $ */
+/* $Id: imach.c,v 1.126 2006/04/28 17:23:28 brouard Exp $ */
/* $State: Exp $ */
-char version[]="Imach version 0.98, September 2005, INED-EUROREVES ";
-char fullversion[]="$Revision: 1.105 $ $Date: 2006/01/05 20:23:19 $";
+char version[]="Imach version 0.98h, April 2006, INED-EUROREVES-Institut de longevite ";
+char fullversion[]="$Revision: 1.126 $ $Date: 2006/04/28 17:23:28 $";
+char strstart[80];
+char optionfilext[10], optionfilefiname[FILENAMELENGTH];
int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */
int nvar;
int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
@@ -276,6 +390,7 @@ int popbased=0;
int *wav; /* Number of waves for this individuual 0 is possible */
int maxwav; /* Maxim number of waves */
int jmin, jmax; /* min, max spacing between 2 waves */
+int ijmin, ijmax; /* Individuals having jmin and jmax */
int gipmx, gsw; /* Global variables on the number of contributions
to the likelihood and the sum of weights (done by funcone)*/
int mle, weightopt;
@@ -286,7 +401,7 @@ int **bh; /* bh[mi][i] is the bias (+ or
double jmean; /* Mean space between 2 waves */
double **oldm, **newm, **savm; /* Working pointers to matrices */
double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
-FILE *fic,*ficpar, *ficparo,*ficres, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
+FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
FILE *ficlog, *ficrespow;
int globpr; /* Global variable for printing or not */
double fretone; /* Only one call to likelihood */
@@ -300,13 +415,17 @@ FILE *ficresprobmorprev;
FILE *fichtm, *fichtmcov; /* Html File */
FILE *ficreseij;
char filerese[FILENAMELENGTH];
+FILE *ficresstdeij;
+char fileresstde[FILENAMELENGTH];
+FILE *ficrescveij;
+char filerescve[FILENAMELENGTH];
FILE *ficresvij;
char fileresv[FILENAMELENGTH];
FILE *ficresvpl;
char fileresvpl[FILENAMELENGTH];
char title[MAXLINE];
char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH];
-char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
+char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH];
char command[FILENAMELENGTH];
int outcmd=0;
@@ -328,6 +447,10 @@ long time_value;
extern long time();
char strcurr[80], strfor[80];
+char *endptr;
+long lval;
+double dval;
+
#define NR_END 1
#define FREE_ARG char*
#define FTOL 1.0e-10
@@ -384,7 +507,7 @@ double ftolhess; /* Tolerance for comput
/**************** split *************************/
static int split( char *path, char *dirc, char *name, char *ext, char *finame )
{
- /* From a file name with full path (either Unix or Windows) we extract the directory (dirc)
+ /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
the name of the file (name), its extension only (ext) and its first part of the name (finame)
*/
char *ss; /* pointer */
@@ -393,7 +516,8 @@ static int split( char *path, char *dirc
l1 = strlen(path ); /* length of path */
if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
ss= strrchr( path, DIRSEPARATOR ); /* find last / */
- if ( ss == NULL ) { /* no directory, so use current */
+ if ( ss == NULL ) { /* no directory, so determine current directory */
+ strcpy( name, path ); /* we got the fullname name because no directory */
/*if(strrchr(path, ODIRSEPARATOR )==NULL)
printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
/* get current working directory */
@@ -401,7 +525,8 @@ static int split( char *path, char *dirc
if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
return( GLOCK_ERROR_GETCWD );
}
- strcpy( name, path ); /* we've got it */
+ /* got dirc from getcwd*/
+ printf(" DIRC = %s \n",dirc);
} else { /* strip direcotry from path */
ss++; /* after this, the filename */
l2 = strlen( ss ); /* length of filename */
@@ -409,14 +534,15 @@ static int split( char *path, char *dirc
strcpy( name, ss ); /* save file name */
strncpy( dirc, path, l1 - l2 ); /* now the directory */
dirc[l1-l2] = 0; /* add zero */
+ printf(" DIRC2 = %s \n",dirc);
}
+ /* We add a separator at the end of dirc if not exists */
l1 = strlen( dirc ); /* length of directory */
- /*#ifdef windows
- if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
-#else
- if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
-#endif
- */
+ if( dirc[l1-1] != DIRSEPARATOR ){
+ dirc[l1] = DIRSEPARATOR;
+ dirc[l1+1] = 0;
+ printf(" DIRC3 = %s \n",dirc);
+ }
ss = strrchr( name, '.' ); /* find last / */
if (ss >0){
ss++;
@@ -426,6 +552,7 @@ static int split( char *path, char *dirc
strncpy( finame, name, l1-l2);
finame[l1-l2]= 0;
}
+
return( 0 ); /* we're done */
}
@@ -888,9 +1015,8 @@ void powell(double p[], double **xi, int
last_time=curr_time;
(void) gettimeofday(&curr_time,&tzp);
printf("\nPowell iter=%d -2*LL=%.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 -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
- fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
- */
+ fprintf(ficlog,"\nPowell iter=%d -2*LL=%.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); */
for (i=1;i<=n;i++) {
printf(" %d %.12f",i, p[i]);
fprintf(ficlog," %d %.12lf",i, p[i]);
@@ -1012,7 +1138,7 @@ void powell(double p[], double **xi, int
}
}
-/**** Prevalence limit (stable prevalence) ****************/
+/**** Prevalence limit (stable or period prevalence) ****************/
double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
{
@@ -1305,23 +1431,23 @@ double func( double *x)
} else if (s2==-2) {
for (j=1,survp=0. ; j<=nlstate; j++)
- survp += out[s1][j];
- lli= survp;
- }
-
- else if (s2==-4) {
- for (j=3,survp=0. ; j<=nlstate; j++)
- survp += out[s1][j];
- lli= survp;
+ survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+ /*survp += out[s1][j]; */
+ lli= log(survp);
}
- else if (s2==-5) {
- for (j=1,survp=0. ; j<=2; j++)
- survp += out[s1][j];
- lli= survp;
- }
-
+ else if (s2==-4) {
+ for (j=3,survp=0. ; j<=nlstate; j++)
+ survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+ lli= log(survp);
+ }
+ else if (s2==-5) {
+ for (j=1,survp=0. ; j<=2; j++)
+ survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+ lli= log(survp);
+ }
+
else{
lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
/* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
@@ -1516,7 +1642,11 @@ double funcone( double *x)
*/
if( s2 > nlstate && (mle <5) ){ /* Jackson */
lli=log(out[s1][s2] - savm[s1][s2]);
- } else if (mle==1){
+ } else if (s2==-2) {
+ for (j=1,survp=0. ; j<=nlstate; j++)
+ survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
+ lli= log(survp);
+ }else if (mle==1){
lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
} else if(mle==2){
lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
@@ -1532,8 +1662,8 @@ double funcone( double *x)
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
/* printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
if(globpr){
- fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
- %10.6f %10.6f %10.6f ", \
+ fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
+ %11.6f %11.6f %11.6f ", \
num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
for(k=1,llt=0.,l=0.; k<=nlstate; k++){
@@ -1618,6 +1748,7 @@ void mlikeli(FILE *ficres,double p[], in
powell(p,xi,npar,ftol,&iter,&fret,func);
+ free_matrix(xi,1,npar,1,npar);
fclose(ficrespow);
printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
@@ -1885,6 +2016,11 @@ void lubksb(double **a, int n, int *indx
}
}
+void pstamp(FILE *fichier)
+{
+ fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
+}
+
/************ Frequencies ********************/
void freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
{ /* Some frequencies */
@@ -1894,7 +2030,6 @@ void freqsummary(char fileres[], int ia
double ***freq; /* Frequencies */
double *pp, **prop;
double pos,posprop, k2, dateintsum=0,k2cpt=0;
- FILE *ficresp;
char fileresp[FILENAMELENGTH];
pp=vector(1,nlstate);
@@ -1959,7 +2094,7 @@ void freqsummary(char fileres[], int ia
}
/* fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
-fprintf(ficresp, "#Local time at start: %s", strstart);
+ pstamp(ficresp);
if (cptcovn>0) {
fprintf(ficresp, "\n#********** Variable ");
for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
@@ -2172,11 +2307,11 @@ void concatwav(int wav[], int **dh, int
if(mi==0){
nbwarn++;
if(first==0){
- printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
+ printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
first=1;
}
if(first==1){
- fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
+ fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
}
} /* end mi==0 */
} /* End individuals */
@@ -2199,8 +2334,14 @@ void concatwav(int wav[], int **dh, int
fprintf(ficlog," We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
}
k=k+1;
- if (j >= jmax) jmax=j;
- if (j <= jmin) jmin=j;
+ if (j >= jmax){
+ jmax=j;
+ ijmax=i;
+ }
+ if (j <= jmin){
+ jmin=j;
+ ijmin=i;
+ }
sum=sum+j;
/*if (j<0) printf("j=%d num=%d \n",j,i);*/
/* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
@@ -2211,8 +2352,14 @@ void concatwav(int wav[], int **dh, int
/* if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
k=k+1;
- if (j >= jmax) jmax=j;
- else if (j <= jmin)jmin=j;
+ if (j >= jmax) {
+ jmax=j;
+ ijmax=i;
+ }
+ else if (j <= jmin){
+ jmin=j;
+ ijmin=i;
+ }
/* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
/*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
if(j<0){
@@ -2255,8 +2402,8 @@ void concatwav(int wav[], int **dh, int
} /* end wave */
}
jmean=sum/k;
- printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
- fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
+ printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
+ fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
}
/*********** Tricode ****************************/
@@ -2320,32 +2467,163 @@ void tricode(int *Tvar, int **nbcode, in
/*********** Health Expectancies ****************/
-void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov,char strstart[] )
+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[] )
+
+{
+ /* Health expectancies, no variances */
+ int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
+ int nhstepma, nstepma; /* Decreasing with age */
+ double age, agelim, hf;
+ double ***p3mat;
+ double eip;
+
+ pstamp(ficreseij);
+ fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
+ fprintf(ficreseij,"# Age");
+ for(i=1; i<=nlstate;i++){
+ for(j=1; j<=nlstate;j++){
+ fprintf(ficreseij," e%1d%1d ",i,j);
+ }
+ fprintf(ficreseij," e%1d. ",i);
+ }
+ fprintf(ficreseij,"\n");
+
+
+ if(estepm < stepm){
+ printf ("Problem %d lower than %d\n",estepm, stepm);
+ }
+ else hstepm=estepm;
+ /* We compute the life expectancy from trapezoids spaced every estepm months
+ * This is mainly to measure the difference between two models: for example
+ * if stepm=24 months pijx are given only every 2 years and by summing them
+ * we are calculating an estimate of the Life Expectancy assuming a linear
+ * progression in between and thus overestimating or underestimating according
+ * to the curvature of the survival function. If, for the same date, we
+ * estimate the model with stepm=1 month, we can keep estepm to 24 months
+ * to compare the new estimate of Life expectancy with the same linear
+ * hypothesis. A more precise result, taking into account a more precise
+ * curvature will be obtained if estepm is as small as stepm. */
+
+ /* For example we decided to compute the life expectancy with the smallest unit */
+ /* 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
+ nstepm is the number of stepm from age to agelin.
+ Look at hpijx to understand the reason of that which relies in memory size
+ and note for a fixed period like estepm months */
+ /* 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
+ means that if the survival funtion is printed only each two years of age and if
+ you sum them up and add 1 year (area under the trapezoids) you won't get the same
+ results. So we changed our mind and took the option of the best precision.
+ */
+ hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+
+ agelim=AGESUP;
+ /* If stepm=6 months */
+ /* 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 = 20*12/6=40 stepm */
+ /* if (stepm >= YEARM) hstepm=1;*/
+ nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+ p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+
+ for (age=bage; age<=fage; age ++){
+ nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
+ /* Typically if 20 years nstepm = 20*12/6=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,nhstepma,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
+
+ hf=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
+
+ printf("%d|",(int)age);fflush(stdout);
+ fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
+
+ /* Computing expectancies */
+ for(i=1; i<=nlstate;i++)
+ for(j=1; j<=nlstate;j++)
+ for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
+ eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
+
+ /* 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]);*/
+
+ }
+
+ fprintf(ficreseij,"%3.0f",age );
+ for(i=1; i<=nlstate;i++){
+ eip=0;
+ for(j=1; j<=nlstate;j++){
+ eip +=eij[i][j][(int)age];
+ fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
+ }
+ fprintf(ficreseij,"%9.4f", eip );
+ }
+ fprintf(ficreseij,"\n");
+
+ }
+ free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ printf("\n");
+ fprintf(ficlog,"\n");
+
+}
+
+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[] )
{
- /* Health expectancies */
- int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
+ /* Covariances of health expectancies eij and of total life expectancies according
+ to initial status i, ei. .
+ */
+ 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 ***p3mat,***varhe;
+ double ***p3matp, ***p3matm, ***varhe;
double **dnewm,**doldm;
- double *xp;
+ double *xp, *xm;
double **gp, **gm;
double ***gradg, ***trgradg;
int theta;
+ double eip, vip;
+
varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
xp=vector(1,npar);
+ xm=vector(1,npar);
dnewm=matrix(1,nlstate*nlstate,1,npar);
doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
- fprintf(ficreseij,"# Local time at start: %s", strstart);
- fprintf(ficreseij,"# Health expectancies\n");
- fprintf(ficreseij,"# Age");
- for(i=1; i<=nlstate;i++)
+ pstamp(ficresstdeij);
+ fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
+ fprintf(ficresstdeij,"# Age");
+ for(i=1; i<=nlstate;i++){
for(j=1; j<=nlstate;j++)
- fprintf(ficreseij," %1d-%1d (SE)",i,j);
- fprintf(ficreseij,"\n");
+ fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
+ fprintf(ficresstdeij," e%1d. ",i);
+ }
+ fprintf(ficresstdeij,"\n");
+ pstamp(ficrescveij);
+ fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
+ fprintf(ficrescveij,"# Age");
+ for(i=1; i<=nlstate;i++)
+ for(j=1; j<=nlstate;j++){
+ cptj= (j-1)*nlstate+i;
+ for(i2=1; i2<=nlstate;i2++)
+ for(j2=1; j2<=nlstate;j2++){
+ cptj2= (j2-1)*nlstate+i2;
+ if(cptj2 <= cptj)
+ fprintf(ficrescveij," %1d%1d,%1d%1d",i,j,i2,j2);
+ }
+ }
+ fprintf(ficrescveij,"\n");
+
if(estepm < stepm){
printf ("Problem %d lower than %d\n",estepm, stepm);
}
@@ -2375,77 +2653,69 @@ void evsij(char fileres[], double ***eij
*/
hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */
+ /* If stepm=6 months */
+ /* nhstepm age range expressed in number of stepm */
agelim=AGESUP;
- for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
- /* nhstepm age range expressed in number of stepm */
- nstepm=(int) rint((agelim-age)*YEARM/stepm);
+ nstepm=(int) rint((agelim-bage)*YEARM/stepm);
+ /* Typically if 20 years nstepm = 20*12/6=40 stepm */
+ /* if (stepm >= YEARM) hstepm=1;*/
+ nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
+
+ p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
+ trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
+ gp=matrix(0,nhstepm,1,nlstate*nlstate);
+ gm=matrix(0,nhstepm,1,nlstate*nlstate);
+
+ for (age=bage; age<=fage; age ++){
+ nstepma=(int) rint((agelim-bage)*YEARM/stepm); /* Biggest nstepm */
/* Typically if 20 years nstepm = 20*12/6=40 stepm */
/* if (stepm >= YEARM) hstepm=1;*/
- nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
- p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
- gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
- gp=matrix(0,nhstepm,1,nlstate*nlstate);
- gm=matrix(0,nhstepm,1,nlstate*nlstate);
-
- /* Computed by stepm unit matrices, product of hstepm matrices, stored
- in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
- hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);
-
+ 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=hstepm*stepm/YEARM; /* Duration of hstepm expressed in year unit. */
/* Computing Variances of health expectancies */
-
- for(theta=1; theta <=npar; theta++){
+ /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
+ decrease memory allocation */
+ for(theta=1; theta <=npar; theta++){
for(i=1; i<=npar; i++){
xp[i] = x[i] + (i==theta ?delti[theta]:0);
+ xm[i] = x[i] - (i==theta ?delti[theta]:0);
}
- hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
+ hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);
+ hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);
- cptj=0;
for(j=1; j<= nlstate; j++){
for(i=1; i<=nlstate; i++){
- cptj=cptj+1;
- for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
- gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
+ for(h=0; h<=nhstepm-1; h++){
+ gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
+ gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
}
}
}
-
- for(i=1; i<=npar; i++)
- xp[i] = x[i] - (i==theta ?delti[theta]:0);
- hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);
-
- cptj=0;
- for(j=1; j<= nlstate; j++){
- for(i=1;i<=nlstate;i++){
- cptj=cptj+1;
- for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
-
- gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
- }
- }
- }
- for(j=1; j<= nlstate*nlstate; j++)
+ for(ij=1; ij<= nlstate*nlstate; ij++)
for(h=0; h<=nhstepm-1; h++){
- gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
+ gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
}
- }
-
-/* End theta */
-
- trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
-
- for(h=0; h<=nhstepm-1; h++)
+ }/* End theta */
+
+
+ for(h=0; h<=nhstepm-1; h++)
for(j=1; j<=nlstate*nlstate;j++)
for(theta=1; theta <=npar; theta++)
trgradg[h][j][theta]=gradg[h][theta][j];
-
+
- for(i=1;i<=nlstate*nlstate;i++)
- for(j=1;j<=nlstate*nlstate;j++)
- varhe[i][j][(int)age] =0.;
+ for(ij=1;ij<=nlstate*nlstate;ij++)
+ for(ji=1;ji<=nlstate*nlstate;ji++)
+ varhe[ij][ji][(int)age] =0.;
printf("%d|",(int)age);fflush(stdout);
fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
@@ -2453,39 +2723,61 @@ void evsij(char fileres[], double ***eij
for(k=0;k<=nhstepm-1;k++){
matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
- for(i=1;i<=nlstate*nlstate;i++)
- for(j=1;j<=nlstate*nlstate;j++)
- varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
+ for(ij=1;ij<=nlstate*nlstate;ij++)
+ for(ji=1;ji<=nlstate*nlstate;ji++)
+ varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
}
}
+
/* Computing expectancies */
+ hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);
for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++)
for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
- eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
+ eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
-/* 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]);*/
}
- fprintf(ficreseij,"%3.0f",age );
- cptj=0;
+ fprintf(ficresstdeij,"%3.0f",age );
+ for(i=1; i<=nlstate;i++){
+ eip=0.;
+ vip=0.;
+ for(j=1; j<=nlstate;j++){
+ eip += eij[i][j][(int)age];
+ for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
+ vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
+ fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
+ }
+ fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
+ }
+ fprintf(ficresstdeij,"\n");
+
+ fprintf(ficrescveij,"%3.0f",age );
for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++){
- cptj++;
- fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
+ cptj= (j-1)*nlstate+i;
+ for(i2=1; i2<=nlstate;i2++)
+ for(j2=1; j2<=nlstate;j2++){
+ cptj2= (j2-1)*nlstate+i2;
+ if(cptj2 <= cptj)
+ fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
+ }
}
- fprintf(ficreseij,"\n");
+ fprintf(ficrescveij,"\n");
- free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
- free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
- free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
- free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
- free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
}
+ free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
+ free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
+ free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
+ free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
+ free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
+ free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
printf("\n");
fprintf(ficlog,"\n");
+ free_vector(xm,1,npar);
free_vector(xp,1,npar);
free_matrix(dnewm,1,nlstate*nlstate,1,npar);
free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
@@ -2546,7 +2838,7 @@ void varevsij(char optionfilefiname[], d
printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
- fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
+ pstamp(ficresprobmorprev);
fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
for(j=nlstate+1; j<=(nlstate+ndeath);j++){
@@ -2556,17 +2848,21 @@ void varevsij(char optionfilefiname[], d
}
fprintf(ficresprobmorprev,"\n");
fprintf(ficgp,"\n# Routine varevsij");
- 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<br>%s <br>\n",digitp);
/* } */
varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
- fprintf(ficresvij, "#Local time at start: %s", strstart);
- fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are the stable prevalence in health states i\n");
+ pstamp(ficresvij);
+ fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n# (weighted average of eij where weights are ");
+ if(popbased==1)
+ fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
+ else
+ fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
fprintf(ficresvij,"# Age");
for(i=1; i<=nlstate;i++)
for(j=1; j<=nlstate;j++)
- fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
+ fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
fprintf(ficresvij,"\n");
xp=vector(1,npar);
@@ -2807,8 +3103,9 @@ void varprevlim(char fileres[], double *
double **gradg, **trgradg;
double age,agelim;
int theta;
- fprintf(ficresvpl, "#Local time at start: %s", strstart);
- fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
+
+ pstamp(ficresvpl);
+ fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
fprintf(ficresvpl,"# Age");
for(i=1; i<=nlstate;i++)
fprintf(ficresvpl," %1d-%1d",i,i);
@@ -2922,15 +3219,15 @@ void varprob(char optionfilefiname[], do
fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
- fprintf(ficresprob, "#Local time at start: %s", strstart);
+ pstamp(ficresprob);
fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
fprintf(ficresprob,"# Age");
- fprintf(ficresprobcov, "#Local time at start: %s", strstart);
+ pstamp(ficresprobcov);
fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
fprintf(ficresprobcov,"# Age");
- fprintf(ficresprobcor, "#Local time at start: %s", strstart);
+ pstamp(ficresprobcor);
fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
- fprintf(ficresprobcov,"# Age");
+ fprintf(ficresprobcor,"# Age");
for(i=1; i<=nlstate;i++)
@@ -3181,6 +3478,8 @@ To be simple, these graphs help to under
}
free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
+ free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
+ free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
free_vector(xp,1,npar);
fclose(ficresprob);
fclose(ficresprobcov);
@@ -3199,19 +3498,25 @@ void printinghtml(char fileres[], char t
double jprev2, double mprev2,double anprev2){
int jj1, k1, i1, cpt;
- fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
+ fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
+ <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
+</ul>");
+ fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
- Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
fprintf(fichtm,"\
- Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
fprintf(fichtm,"\
- - 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"));
fprintf(fichtm,"\
- - Life expectancies by age and initial health status (estepm=%2d months): \
- <a href=\"%s\">%s</a> <br>\n</li>",
+ - (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 href=\"%s\">%s</a> <br>\n",
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>");
@@ -3229,20 +3534,20 @@ fprintf(fichtm," \n<ul><li><b>Graphs</b>
fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
}
/* Pij */
- fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
-<img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+ fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
+<img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
/* Quasi-incidences */
fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
- before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
-<img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
- /* Stable prevalence in each health state */
+ before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
+<img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);
+ /* Period (stable) prevalence in each health state */
for(cpt=1; cpt<nlstate;cpt++){
- fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
-<img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
+ fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
+<img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
}
for(cpt=1; cpt<=nlstate;cpt++) {
- fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
-<img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
+ fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
+<img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
}
} /* end i1 */
}/* End k1 */
@@ -3250,7 +3555,7 @@ fprintf(fichtm," \n<ul><li><b>Graphs</b>
fprintf(fichtm,"\
-\n<br><li><h4> Result files (second order: variances)</h4>\n\
+\n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
- Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
@@ -3263,13 +3568,21 @@ fprintf(fichtm," \n<ul><li><b>Graphs</b>
- Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
fprintf(fichtm,"\
- - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
+ - Variances and covariances of health expectancies by age and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
+ <a href=\"%s\">%s</a> <br>\n</li>",
+ estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
+ fprintf(fichtm,"\
+ - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
+ <a href=\"%s\">%s</a> <br>\n</li>",
+ estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
+ 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",
estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
fprintf(fichtm,"\
- - Health expectancies with their variances (no covariance): <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: <a href=\"%s\">%s</a> <br>\n",
subdirf2(fileres,"t"),subdirf2(fileres,"t"));
fprintf(fichtm,"\
- - Standard deviation of 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"));
/* if(popforecast==1) fprintf(fichtm,"\n */
@@ -3341,7 +3654,7 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
else fprintf(ficgp," \%%*lf (\%%*lf)");
}
- fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
+ fprintf(ficgp,"\" t\"Period (stable) prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
for (i=1; i<= nlstate ; i ++) {
if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
else fprintf(ficgp," \%%*lf (\%%*lf)");
@@ -3389,7 +3702,8 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u
for (k1=1; k1<= m ; k1 ++) {
for (cpt=1; cpt<= nlstate ; cpt ++) {
- k=2+nlstate*(2*cpt-2);
+ /* k=2+nlstate*(2*cpt-2); */
+ k=2+(nlstate+1)*(cpt-1);
fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
fprintf(ficgp,"set ter png small\n\
set size 0.65,0.65\n\
@@ -3403,9 +3717,11 @@ plot [%.f:%.f] \"%s\" every :::%d::%d u
*/
for (i=1; i< nlstate ; i ++) {
- fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
+ fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
+ /* fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
}
+ fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
}
}
@@ -3964,6 +4280,7 @@ double gompertz(double x[])
{
double A,B,L=0.0,sump=0.,num=0.;
int i,n=0; /* n is the size of the sample */
+
for (i=0;i<=imx-1 ; i++) {
sump=sump+weight[i];
/* sump=sump+1;*/
@@ -3976,14 +4293,15 @@ double gompertz(double x[])
for (i=1;i<=imx ; i++)
{
- if (cens[i]==1 & wav[i]>1)
+ if (cens[i] == 1 && wav[i]>1)
A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
- if (cens[i]==0 & wav[i]>1)
+ if (cens[i] == 0 && wav[i]>1)
A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
+log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);
- if (wav[i]>1 & agecens[i]>15) {
+ /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
+ if (wav[i] > 1 ) { /* ??? */
L=L+A*weight[i];
/* printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
}
@@ -4009,7 +4327,7 @@ void printinghtmlmort(char fileres[], ch
fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
- fprintf(fichtm,"\nAge lx qx dx Lx Tx e(x)<br>");
+ fprintf(fichtm,"\nAge l<inf>x</inf> q<inf>x</inf> d(x,x+1) L<inf>x</inf> T<inf>x</inf> e<infx</inf><br>");
for (k=agegomp;k<(agemortsup-2);k++)
fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
@@ -4044,6 +4362,7 @@ void printinggnuplotmort(char fileres[],
+
/***********************************************/
/**************** Main Program *****************/
/***********************************************/
@@ -4052,14 +4371,17 @@ int main(int argc, char *argv[])
{
int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
+ int linei, month, year,iout;
int jj, ll, li, lj, lk, imk;
int numlinepar=0; /* Current linenumber of parameter file */
int itimes;
int NDIM=2;
char ca[32], cb[32], cc[32];
+ char dummy[]=" ";
/* FILE *fichtm; *//* Html File */
/* FILE *ficgp;*/ /*Gnuplot File */
+ struct stat info;
double agedeb, agefin,hf;
double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
@@ -4073,6 +4395,7 @@ int main(int argc, char *argv[])
char line[MAXLINE], linepar[MAXLINE];
char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
char pathr[MAXLINE], pathimach[MAXLINE];
+ char **bp, *tok, *val; /* pathtot */
int firstobs=1, lastobs=10;
int sdeb, sfin; /* Status at beginning and end */
int c, h , cpt,l;
@@ -4108,7 +4431,7 @@ int main(int argc, char *argv[])
char z[1]="c", occ;
char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
- char strstart[80], *strt, strtend[80];
+ char *strt, strtend[80];
char *stratrunc;
int lstra;
@@ -4150,7 +4473,17 @@ int main(int argc, char *argv[])
printf("\n%s\n%s",version,fullversion);
if(argc <=1){
printf("\nEnter the parameter file name: ");
- scanf("%s",pathtot);
+ fgets(pathr,FILENAMELENGTH,stdin);
+ i=strlen(pathr);
+ if(pathr[i-1]=='\n')
+ pathr[i-1]='\0';
+ for (tok = pathr; tok != NULL; ){
+ printf("Pathr |%s|\n",pathr);
+ while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
+ printf("val= |%s| pathr=%s\n",val,pathr);
+ strcpy (pathtot, val);
+ if(pathr[0] == '\0') break; /* Dirty */
+ }
}
else{
strcpy(pathtot,argv[1]);
@@ -4160,11 +4493,17 @@ int main(int argc, char *argv[])
printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
/* cutv(path,optionfile,pathtot,'\\');*/
+ /* Split argv[0], imach program to get pathimach */
+ printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
+ printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
/* strcpy(pathimach,argv[0]); */
+ /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
split(pathtot,path,optionfile,optionfilext,optionfilefiname);
- printf("pathimach=%s, pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
- chdir(path);
+ printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
+ chdir(path); /* Can be a relative path */
+ if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
+ printf("Current directory %s!\n",pathcd);
strcpy(command,"mkdir ");
strcat(command,optionfilefiname);
if((outcmd=system(command)) != 0){
@@ -4273,6 +4612,7 @@ int main(int argc, char *argv[])
free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
fclose (ficparo);
fclose (ficlog);
+ goto end;
exit(0);
}
else if(mle==-3) {
@@ -4303,7 +4643,9 @@ int main(int argc, char *argv[])
j++;
fscanf(ficpar,"%1d%1d",&i1,&j1);
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);
}
fprintf(ficparo,"%1d%1d",i1,j1);
@@ -4330,7 +4672,6 @@ int main(int argc, char *argv[])
}
fflush(ficlog);
-
p=param[1][1];
/* Reads comments: lines beginning with '#' */
@@ -4431,8 +4772,8 @@ int main(int argc, char *argv[])
/*-------- data file ----------*/
if((fic=fopen(datafile,"r"))==NULL) {
- printf("Problem with datafile: %s\n", datafile);goto end;
- fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
+ printf("Problem while opening datafile: %s\n", datafile);goto end;
+ fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
}
n= lastobs;
@@ -4454,43 +4795,125 @@ int main(int argc, char *argv[])
ncodemax=ivector(1,8);
i=1;
- while (fgets(line, MAXLINE, fic) != NULL) {
- if ((i >= firstobs) && (i <=lastobs)) {
- for(j=0; line[j] != '\n';j++){ /* Untabifies line */
- if(line[j] == '\t')
- line[j] = ' ';
- }
- for (j=maxwav;j>=1;j--){
- cutv(stra, strb,line,' '); s[j][i]=atoi(strb);
- strcpy(line,stra);
- cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
- cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
+ linei=0;
+ while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
+ linei=linei+1;
+ for(j=strlen(line); j>=0;j--){ /* Untabifies line */
+ if(line[j] == '\t')
+ line[j] = ' ';
+ }
+ for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
+ ;
+ };
+ line[j+1]=0; /* Trims blanks at end of line */
+ if(line[0]=='#'){
+ fprintf(ficlog,"Comment line\n%s\n",line);
+ printf("Comment line\n%s\n",line);
+ continue;
+ }
+
+ for (j=maxwav;j>=1;j--){
+ cutv(stra, strb,line,' ');
+ errno=0;
+ lval=strtol(strb,&endptr,10);
+ /* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
+ if( strb[0]=='\0' || (*endptr != '\0')){
+ printf("Error reading data around '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong. Exiting.\n", strb, linei,i,line,j,maxwav);
+ exit(1);
}
-
- cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
- cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
-
- cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
- cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
-
- cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
- for (j=ncovcol;j>=1;j--){
- cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
- }
- lstra=strlen(stra);
- if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
- stratrunc = &(stra[lstra-9]);
- num[i]=atol(stratrunc);
+ s[j][i]=lval;
+
+ strcpy(line,stra);
+ cutv(stra, strb,line,' ');
+ if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+ }
+ else if(iout=sscanf(strb,"%s.") != 0){
+ month=99;
+ year=9999;
+ }else{
+ printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d. Exiting.\n",strb, linei,i, line,j);
+ exit(1);
+ }
+ anint[j][i]= (double) year;
+ mint[j][i]= (double)month;
+ strcpy(line,stra);
+ } /* ENd Waves */
+
+ cutv(stra, strb,line,' ');
+ if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+ }
+ else if(iout=sscanf(strb,"%s.",dummy) != 0){
+ month=99;
+ year=9999;
+ }else{
+ printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .). Exiting.\n",strb, linei,i,line);
+ exit(1);
+ }
+ andc[i]=(double) year;
+ moisdc[i]=(double) month;
+ strcpy(line,stra);
+
+ cutv(stra, strb,line,' ');
+ if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
+ }
+ else if(iout=sscanf(strb,"%s.") != 0){
+ month=99;
+ year=9999;
+ }else{
+ printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .). Exiting.\n",strb, linei,i,line,j);
+ exit(1);
+ }
+ annais[i]=(double)(year);
+ moisnais[i]=(double)(month);
+ strcpy(line,stra);
+
+ cutv(stra, strb,line,' ');
+ errno=0;
+ dval=strtod(strb,&endptr);
+ if( strb[0]=='\0' || (*endptr != '\0')){
+ 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);
+ }
+ weight[i]=dval;
+ strcpy(line,stra);
+
+ for (j=ncovcol;j>=1;j--){
+ cutv(stra, strb,line,' ');
+ errno=0;
+ lval=strtol(strb,&endptr,10);
+ if( strb[0]=='\0' || (*endptr != '\0')){
+ printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1). Exiting.\n",lval, linei,i, line);
+ exit(1);
+ }
+ if(lval <-1 || lval >1){
+ 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);
}
- else
- num[i]=atol(stra);
-
- /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
- printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
-
- i=i+1;
- }
- }
+ covar[j][i]=(double)(lval);
+ strcpy(line,stra);
+ }
+ lstra=strlen(stra);
+
+ if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
+ stratrunc = &(stra[lstra-9]);
+ num[i]=atol(stratrunc);
+ }
+ else
+ num[i]=atol(stra);
+ /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
+ printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
+
+ i=i+1;
+ } /* End loop reading data */
+ fclose(fic);
/* printf("ii=%d", ij);
scanf("%d",i);*/
imx=i-1; /* Number of individuals */
@@ -4504,12 +4927,12 @@ int main(int argc, char *argv[])
if (s[4][i]==9) s[4][i]=-1;
printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]), (mint[2][i]), (anint[2][i]), (s[2][i]), (mint[3][i]), (anint[3][i]), (s[3][i]), (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
- for (i=1; i<=imx; i++)
+ /* for (i=1; i<=imx; i++) */
/*if ((s[3][i]==3) || (s[4][i]==3)) weight[i]=0.08;
else weight[i]=1;*/
- /* Calculation of the number of parameter from char model*/
+ /* Calculation of the number of parameters from char model */
Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
Tprod=ivector(1,15);
Tvaraff=ivector(1,15);
@@ -4588,8 +5011,7 @@ int main(int argc, char *argv[])
printf("cptcovprod=%d ", cptcovprod);
fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
- scanf("%d ",i);
- fclose(fic);*/
+ scanf("%d ",i);*/
/* if(mle==1){*/
if (weightopt != 1) { /* Maximisation without weights*/
@@ -4638,8 +5060,7 @@ int main(int argc, char *argv[])
}
}
else if(s[m][i] !=9){ /* Standard case, age in fractional
- years but with the precision of a
- month */
+ years but with the precision of a month */
agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
agev[m][i]=1;
@@ -4769,23 +5190,25 @@ int main(int argc, char *argv[])
printf("Problem with %s \n",optionfilehtmcov), exit(0);
}
else{
- fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s\n %s
%s \
+ fprintf(fichtmcov,"\nIMaCh Cov %s\n %s
%s \
\n\
Title=%s
Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s
\n",\
- fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
+ optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
}
- fprintf(fichtm,"\nIMaCh %s\n %s
%s \
+ fprintf(fichtm,"\nIMaCh %s\n %s
%s \
\n\
Title=%s
Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s
\n\
\n\
\
Parameter files
\n\
+ - Parameter file: %s.%s
\n\
- Copy of the parameter file: o%s
\n\
- Log file of the run: %s
\n\
- Gnuplot file name: %s
\n\
- Date and time at start: %s
\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,\
fileres,fileres,\
filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
fflush(fichtm);
@@ -4815,6 +5238,7 @@ Interval (in months) between two waves:
p=param[1][1]; /* *(*(*(param +1)+1)+0) */
globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
+
if (mle==-3){
ximort=matrix(1,NDIM,1,NDIM);
cens=ivector(1,n);
@@ -4824,9 +5248,9 @@ Interval (in months) between two waves:
for (i=1; i<=imx; i++){
dcwave[i]=-1;
- for (j=1; j<=lastpass; j++)
- if (s[j][i]>nlstate) {
- dcwave[i]=j;
+ for (m=firstpass; m<=lastpass; m++)
+ if (s[m][i]>nlstate) {
+ dcwave[i]=m;
/* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
break;
}
@@ -4835,12 +5259,16 @@ Interval (in months) between two waves:
for (i=1; i<=imx; i++) {
if (wav[i]>0){
ageexmed[i]=agev[mw[1][i]][i];
- j=wav[i];agecens[i]=1.;
- if (ageexmed[i]>1 & wav[i]>0) agecens[i]=agev[mw[j][i]][i];
- cens[i]=1;
-
- if (ageexmed[i]<1) cens[i]=-1;
- if (agedc[i]< AGESUP & agedc[i]>1 & dcwave[i]>firstpass & dcwave[i]<=lastpass) cens[i]=0 ;
+ j=wav[i];
+ agecens[i]=1.;
+
+ if (ageexmed[i]> 1 && wav[i] > 0){
+ agecens[i]=agev[mw[j][i]][i];
+ cens[i]= 1;
+ }else if (ageexmed[i]< 1)
+ cens[i]= -1;
+ if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
+ cens[i]=0 ;
}
else cens[i]=-1;
}
@@ -4849,29 +5277,29 @@ Interval (in months) between two waves:
for (j=1;j<=NDIM;j++)
ximort[i][j]=(i == j ? 1.0 : 0.0);
}
-
- p[1]=0.1; p[2]=0.1;
+
+ p[1]=0.0268; p[NDIM]=0.083;
/*printf("%lf %lf", p[1], p[2]);*/
- printf("Powell\n"); fprintf(ficlog,"Powell\n");
- strcpy(filerespow,"pow-mort");
- strcat(filerespow,fileres);
- if((ficrespow=fopen(filerespow,"w"))==NULL) {
- printf("Problem with resultfile: %s\n", filerespow);
- fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
- }
- fprintf(ficrespow,"# Powell\n# iter -2*LL");
- /* for (i=1;i<=nlstate;i++)
- for(j=1;j<=nlstate+ndeath;j++)
- if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
- */
- fprintf(ficrespow,"\n");
-
+ printf("Powell\n"); fprintf(ficlog,"Powell\n");
+ strcpy(filerespow,"pow-mort");
+ strcat(filerespow,fileres);
+ if((ficrespow=fopen(filerespow,"w"))==NULL) {
+ printf("Problem with resultfile: %s\n", filerespow);
+ fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
+ }
+ fprintf(ficrespow,"# Powell\n# iter -2*LL");
+ /* for (i=1;i<=nlstate;i++)
+ for(j=1;j<=nlstate+ndeath;j++)
+ if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
+ */
+ fprintf(ficrespow,"\n");
+
powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
fclose(ficrespow);
- hesscov(matcov, p, NDIM,delti, 1e-4, gompertz);
+ hesscov(matcov, p, NDIM, delti, 1e-4, gompertz);
for(i=1; i <=NDIM; i++)
for(j=i+1;j<=NDIM;j++)
@@ -4889,48 +5317,48 @@ Interval (in months) between two waves:
for (i=1;i<=NDIM;i++)
printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
-lsurv=vector(1,AGESUP);
+ lsurv=vector(1,AGESUP);
lpop=vector(1,AGESUP);
tpop=vector(1,AGESUP);
lsurv[agegomp]=100000;
-
- for (k=agegomp;k<=AGESUP;k++) {
+
+ for (k=agegomp;k<=AGESUP;k++) {
agemortsup=k;
if (p[1]*exp(p[2]*(k-agegomp))>1) break;
}
-
- for (k=agegomp;k=1 */
likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
@@ -4962,9 +5390,9 @@ lsurv=vector(1,AGESUP);
fprintf(ficlog,"%d%d ",i,k);
fprintf(ficres,"%1d%1d ",i,k);
for(j=1; j <=ncovmodel; j++){
- printf("%f ",p[jk]);
- fprintf(ficlog,"%f ",p[jk]);
- fprintf(ficres,"%f ",p[jk]);
+ printf("%lf ",p[jk]);
+ fprintf(ficlog,"%lf ",p[jk]);
+ fprintf(ficres,"%lf ",p[jk]);
jk++;
}
printf("\n");
@@ -5156,7 +5584,7 @@ lsurv=vector(1,AGESUP);
/* freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
/*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
- replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
+ replace_back_to_slash(pathc,pathcd); /* Even gnuplot wants a / */
printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
@@ -5178,18 +5606,18 @@ lsurv=vector(1,AGESUP);
fclose(ficres);
- /*--------------- Prevalence limit (stable prevalence) --------------*/
+ /*--------------- Prevalence limit (period or stable prevalence) --------------*/
strcpy(filerespl,"pl");
strcat(filerespl,fileres);
if((ficrespl=fopen(filerespl,"w"))==NULL) {
- printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
- fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
+ printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
+ fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
}
- printf("Computing stable prevalence: result on file '%s' \n", filerespl);
- fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
- fprintf(ficrespl, "#Local time at start: %s", strstart);
- fprintf(ficrespl,"#Stable prevalence \n");
+ printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+ fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
+ pstamp(ficrespl);
+ fprintf(ficrespl,"# Period (stable) prevalence \n");
fprintf(ficrespl,"#Age ");
for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
fprintf(ficrespl,"\n");
@@ -5249,7 +5677,7 @@ lsurv=vector(1,AGESUP);
hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */
/* hstepm=1; aff par mois*/
- fprintf(ficrespij, "#Local time at start: %s", strstart);
+ pstamp(ficrespij);
fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
@@ -5319,8 +5747,8 @@ lsurv=vector(1,AGESUP);
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 LEs with variances: file '%s' \n", filerest);
- fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);
+ 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(filerese,"e");
@@ -5332,6 +5760,24 @@ lsurv=vector(1,AGESUP);
printf("Computing Health Expectancies: result on file '%s' \n", filerese);
fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
+ strcpy(fileresstde,"stde");
+ strcat(fileresstde,fileres);
+ if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
+ printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+ fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
+ }
+ printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+ fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
+
+ strcpy(filerescve,"cve");
+ strcat(filerescve,fileres);
+ if((ficrescveij=fopen(filerescve,"w"))==NULL) {
+ printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+ fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
+ }
+ printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+ fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
+
strcpy(fileresv,"v");
strcat(fileresv,fileres);
if((ficresvij=fopen(fileresv,"w"))==NULL) {
@@ -5364,9 +5810,16 @@ lsurv=vector(1,AGESUP);
fprintf(ficrest,"******\n");
fprintf(ficreseij,"\n#****** ");
- for(j=1;j<=cptcoveff;j++)
+ fprintf(ficresstdeij,"\n#****** ");
+ fprintf(ficrescveij,"\n#****** ");
+ 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(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
+ }
fprintf(ficreseij,"******\n");
+ fprintf(ficresstdeij,"******\n");
+ fprintf(ficrescveij,"******\n");
fprintf(ficresvij,"\n#****** ");
for(j=1;j<=cptcoveff;j++)
@@ -5375,7 +5828,8 @@ lsurv=vector(1,AGESUP);
eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
oldm=oldms;savm=savms;
- evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);
+ evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, 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);
oldm=oldms;savm=savms;
@@ -5384,8 +5838,8 @@ lsurv=vector(1,AGESUP);
varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
}
- fprintf(ficrest, "#Local time at start: %s", strstart);
- fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
+ 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 (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
fprintf(ficrest,"\n");
@@ -5433,19 +5887,21 @@ lsurv=vector(1,AGESUP);
free_ivector(cod,1,n);
free_ivector(tab,1,NCOVMAX);
fclose(ficreseij);
+ fclose(ficresstdeij);
+ fclose(ficrescveij);
fclose(ficresvij);
fclose(ficrest);
fclose(ficpar);
- /*------- Variance of stable prevalence------*/
+ /*------- Variance of period (stable) prevalence------*/
strcpy(fileresvpl,"vpl");
strcat(fileresvpl,fileres);
if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
- printf("Problem with variance of stable prevalence resultfile: %s\n", fileresvpl);
+ printf("Problem with variance of period (stable) prevalence resultfile: %s\n", fileresvpl);
exit(0);
}
- printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
+ printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
for(cptcov=1,k=0;cptcov<=i1;cptcov++){
for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
@@ -5469,11 +5925,11 @@ lsurv=vector(1,AGESUP);
free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
} /* mle==-3 arrives here for freeing */
+ free_matrix(prlim,1,nlstate,1,nlstate);
free_matrix(pmmij,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(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
-
free_matrix(covar,0,NCOVMAX,1,n);
free_matrix(matcov,1,npar,1,npar);
/*free_vector(delti,1,npar);*/
@@ -5488,7 +5944,8 @@ lsurv=vector(1,AGESUP);
free_ivector(Tage,1,15);
free_ivector(Tcode,1,100);
-
+ free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
+ free_imatrix(codtab,1,100,1,10);
fflush(fichtm);
fflush(ficgp);
@@ -5515,23 +5972,46 @@ lsurv=vector(1,AGESUP);
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);*/
/* if(fileappend(fichtm,optionfilehtm)){ */
- fprintf(fichtm,"
Local time at start %s
Local time at end %s
",strstart, strtend);
+ fprintf(fichtm,"
Local time at start %s
Local time at end %s
\n",strstart, strtend);
fclose(fichtm);
+ fprintf(fichtmcov,"
Local time at start %s
Local time at end %s
\n",strstart, strtend);
fclose(fichtmcov);
fclose(ficgp);
fclose(ficlog);
/*------ End -----------*/
- chdir(path);
- strcpy(plotcmd,"\"");
- strcat(plotcmd,pathimach);
- strcat(plotcmd,GNUPLOTPROGRAM);
- strcat(plotcmd,"\"");
- strcat(plotcmd," ");
- strcat(plotcmd,optionfilegnuplot);
- printf("Starting graphs with: %s",plotcmd);fflush(stdout);
+
+ printf("Before Current directory %s!\n",pathcd);
+ if(chdir(pathcd) != 0)
+ printf("Can't move to directory %s!\n",path);
+ if(getcwd(pathcd,MAXLINE) > 0)
+ printf("Current directory %s!\n",pathcd);
+ /*strcat(plotcmd,CHARSEPARATOR);*/
+ sprintf(plotcmd,"gnuplot");
+#ifndef UNIX
+ sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
+#endif
+ if(!stat(plotcmd,&info)){
+ printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+ if(!stat(getenv("GNUPLOTBIN"),&info)){
+ printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
+ }else
+ strcpy(pplotcmd,plotcmd);
+#ifdef UNIX
+ strcpy(plotcmd,GNUPLOTPROGRAM);
+ if(!stat(plotcmd,&info)){
+ printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
+ }else
+ strcpy(pplotcmd,plotcmd);
+#endif
+ }else
+ strcpy(pplotcmd,plotcmd);
+
+ sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
+ printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
+
if((outcmd=system(plotcmd)) != 0){
- printf(" Problem with gnuplot\n");
+ printf("\n Problem with gnuplot\n");
}
printf(" Wait...");
while (z[0] != 'q') {