version 1.108, 2006/01/19 18:05:42
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version 1.115, 2006/02/27 12:17:45
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Line 1
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/* $Id$ |
/* $Id$ |
$State$ |
$State$ |
$Log$ |
$Log$ |
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Revision 1.115 2006/02/27 12:17:45 brouard |
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(Module): One freematrix added in mlikeli! 0.98c |
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Revision 1.114 2006/02/26 12:57:58 brouard |
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(Module): Some improvements in processing parameter |
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filename with strsep. |
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Revision 1.113 2006/02/24 14:20:24 brouard |
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(Module): Memory leaks checks with valgrind and: |
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datafile was not closed, some imatrix were not freed and on matrix |
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allocation too. |
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Revision 1.112 2006/01/30 09:55:26 brouard |
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(Module): Back to gnuplot.exe instead of wgnuplot.exe |
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Revision 1.111 2006/01/25 20:38:18 brouard |
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(Module): Lots of cleaning and bugs added (Gompertz) |
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(Module): Comments can be added in data file. Missing date values |
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can be a simple dot '.'. |
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Revision 1.110 2006/01/25 00:51:50 brouard |
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(Module): Lots of cleaning and bugs added (Gompertz) |
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Revision 1.109 2006/01/24 19:37:15 brouard |
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(Module): Comments (lines starting with a #) are allowed in data. |
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Revision 1.108 2006/01/19 18:05:42 lievre |
Revision 1.108 2006/01/19 18:05:42 lievre |
Gnuplot problem appeared... |
Gnuplot problem appeared... |
To be fixed |
To be fixed |
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Line 260
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#include <string.h> |
#include <string.h> |
#include <unistd.h> |
#include <unistd.h> |
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#include <limits.h> |
#include <sys/types.h> |
#include <sys/types.h> |
#include <sys/stat.h> |
#include <sys/stat.h> |
#include <errno.h> |
#include <errno.h> |
Line 280 extern int errno;
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Line 307 extern int errno;
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/* $Id$ */ |
/* $Id$ */ |
/* $State$ */ |
/* $State$ */ |
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char version[]="Imach version 0.98a, January 2006, INED-EUROREVES "; |
char version[]="Imach version 0.98c, February 2006, INED-EUROREVES "; |
char fullversion[]="$Revision$ $Date$"; |
char fullversion[]="$Revision$ $Date$"; |
int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */ |
int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings */ |
int nvar; |
int nvar; |
Line 294 int popbased=0;
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Line 321 int popbased=0;
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int *wav; /* Number of waves for this individuual 0 is possible */ |
int *wav; /* Number of waves for this individuual 0 is possible */ |
int maxwav; /* Maxim number of waves */ |
int maxwav; /* Maxim number of waves */ |
int jmin, jmax; /* min, max spacing between 2 waves */ |
int jmin, jmax; /* min, max spacing between 2 waves */ |
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int ijmin, ijmax; /* Individuals having jmin and jmax */ |
int gipmx, gsw; /* Global variables on the number of contributions |
int gipmx, gsw; /* Global variables on the number of contributions |
to the likelihood and the sum of weights (done by funcone)*/ |
to the likelihood and the sum of weights (done by funcone)*/ |
int mle, weightopt; |
int mle, weightopt; |
Line 324 FILE *ficresvpl;
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Line 352 FILE *ficresvpl;
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char fileresvpl[FILENAMELENGTH]; |
char fileresvpl[FILENAMELENGTH]; |
char title[MAXLINE]; |
char title[MAXLINE]; |
char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH]; |
char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH], filerespl[FILENAMELENGTH]; |
char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH]; |
char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH]; |
char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH]; |
char tmpout[FILENAMELENGTH], tmpout2[FILENAMELENGTH]; |
char command[FILENAMELENGTH]; |
char command[FILENAMELENGTH]; |
int outcmd=0; |
int outcmd=0; |
Line 346 long time_value;
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Line 374 long time_value;
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extern long time(); |
extern long time(); |
char strcurr[80], strfor[80]; |
char strcurr[80], strfor[80]; |
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char *endptr; |
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long lval; |
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#define NR_END 1 |
#define NR_END 1 |
#define FREE_ARG char* |
#define FREE_ARG char* |
#define FTOL 1.0e-10 |
#define FTOL 1.0e-10 |
Line 1640 void mlikeli(FILE *ficres,double p[], in
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Line 1671 void mlikeli(FILE *ficres,double p[], in
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powell(p,xi,npar,ftol,&iter,&fret,func); |
powell(p,xi,npar,ftol,&iter,&fret,func); |
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free_matrix(xi,1,npar,1,npar); |
fclose(ficrespow); |
fclose(ficrespow); |
printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p)); |
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)); |
fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p)); |
Line 2194 void concatwav(int wav[], int **dh, int
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Line 2226 void concatwav(int wav[], int **dh, int
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if(mi==0){ |
if(mi==0){ |
nbwarn++; |
nbwarn++; |
if(first==0){ |
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; |
first=1; |
} |
} |
if(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 mi==0 */ |
} /* End individuals */ |
} /* End individuals */ |
Line 2221 void concatwav(int wav[], int **dh, int
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Line 2253 void concatwav(int wav[], int **dh, int
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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); |
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; |
k=k+1; |
if (j >= jmax) jmax=j; |
if (j >= jmax){ |
if (j <= jmin) jmin=j; |
jmax=j; |
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ijmax=i; |
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} |
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if (j <= jmin){ |
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jmin=j; |
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ijmin=i; |
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} |
sum=sum+j; |
sum=sum+j; |
/*if (j<0) printf("j=%d num=%d \n",j,i);*/ |
/*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);*/ |
/* printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/ |
Line 2233 void concatwav(int wav[], int **dh, int
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Line 2271 void concatwav(int wav[], int **dh, int
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/* 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]); */ |
/* 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]); */ |
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k=k+1; |
k=k+1; |
if (j >= jmax) jmax=j; |
if (j >= jmax) { |
else if (j <= jmin)jmin=j; |
jmax=j; |
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ijmax=i; |
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} |
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else if (j <= jmin){ |
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jmin=j; |
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ijmin=i; |
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} |
/* if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,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]);*/ |
/*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){ |
if(j<0){ |
Line 2277 void concatwav(int wav[], int **dh, int
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Line 2321 void concatwav(int wav[], int **dh, int
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} /* end wave */ |
} /* end wave */ |
} |
} |
jmean=sum/k; |
jmean=sum/k; |
printf("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 Max=%d Mean=%f\n\n ",jmin, jmax,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); |
} |
} |
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/*********** Tricode ****************************/ |
/*********** Tricode ****************************/ |
Line 3203 To be simple, these graphs help to under
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Line 3247 To be simple, these graphs help to under
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} |
} |
free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage); |
free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage); |
free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage); |
free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage); |
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free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath)); |
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free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar); |
free_vector(xp,1,npar); |
free_vector(xp,1,npar); |
fclose(ficresprob); |
fclose(ficresprob); |
fclose(ficresprobcov); |
fclose(ficresprobcov); |
Line 3989 double gompertz(double x[])
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Line 4035 double gompertz(double x[])
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{ |
{ |
double A,B,L=0.0,sump=0.,num=0.; |
double A,B,L=0.0,sump=0.,num=0.; |
int i,n=0; /* n is the size of the sample */ |
int i,n=0; /* n is the size of the sample */ |
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for (i=0;i<=imx-1 ; i++) { |
for (i=0;i<=imx-1 ; i++) { |
sump=sump+weight[i]; |
sump=sump+weight[i]; |
/* sump=sump+1;*/ |
/* sump=sump+1;*/ |
Line 4001 double gompertz(double x[])
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Line 4048 double gompertz(double x[])
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for (i=1;i<=imx ; i++) |
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))); |
A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp))); |
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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))) |
A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp))) |
+log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM); |
+log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM); |
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if (wav[i]>1 & agecens[i]>15) { |
/*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */ |
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if (wav[i] > 1 ) { /* ??? */ |
L=L+A*weight[i]; |
L=L+A*weight[i]; |
/* printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/ |
/* printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/ |
} |
} |
Line 4077 int main(int argc, char *argv[])
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Line 4125 int main(int argc, char *argv[])
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{ |
{ |
int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav); |
int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav); |
int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod; |
int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod; |
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int linei, month, year,iout; |
int jj, ll, li, lj, lk, imk; |
int jj, ll, li, lj, lk, imk; |
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; |
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char ca[32], cb[32], cc[32]; |
char ca[32], cb[32], cc[32]; |
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char dummy[]=" "; |
/* FILE *fichtm; *//* Html File */ |
/* FILE *fichtm; *//* Html File */ |
/* FILE *ficgp;*/ /*Gnuplot File */ |
/* FILE *ficgp;*/ /*Gnuplot File */ |
struct stat info; |
struct stat info; |
Line 4099 int main(int argc, char *argv[])
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Line 4149 int main(int argc, char *argv[])
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char line[MAXLINE], linepar[MAXLINE]; |
char line[MAXLINE], linepar[MAXLINE]; |
char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE]; |
char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE]; |
char pathr[MAXLINE], pathimach[MAXLINE]; |
char pathr[MAXLINE], pathimach[MAXLINE]; |
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char **bp, *tok, *val; /* pathtot */ |
int firstobs=1, lastobs=10; |
int firstobs=1, lastobs=10; |
int sdeb, sfin; /* Status at beginning and end */ |
int sdeb, sfin; /* Status at beginning and end */ |
int c, h , cpt,l; |
int c, h , cpt,l; |
Line 4176 int main(int argc, char *argv[])
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Line 4227 int main(int argc, char *argv[])
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printf("\n%s\n%s",version,fullversion); |
printf("\n%s\n%s",version,fullversion); |
if(argc <=1){ |
if(argc <=1){ |
printf("\nEnter the parameter file name: "); |
printf("\nEnter the parameter file name: "); |
scanf("%s",pathtot); |
fgets(pathr,FILENAMELENGTH,stdin); |
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i=strlen(pathr); |
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if(pathr[i-1]=='\n') |
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pathr[i-1]='\0'; |
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for (tok = pathr; tok != NULL; ){ |
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printf("Pathr |%s|\n",pathr); |
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while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0'); |
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printf("val= |%s| pathr=%s\n",val,pathr); |
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strcpy (pathtot, val); |
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if(pathr[0] == '\0') break; /* Un peu sale */ |
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} |
} |
} |
else{ |
else{ |
strcpy(pathtot,argv[1]); |
strcpy(pathtot,argv[1]); |
Line 4360 int main(int argc, char *argv[])
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Line 4421 int main(int argc, char *argv[])
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} |
} |
fflush(ficlog); |
fflush(ficlog); |
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p=param[1][1]; |
p=param[1][1]; |
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/* Reads comments: lines beginning with '#' */ |
/* Reads comments: lines beginning with '#' */ |
Line 4484 int main(int argc, char *argv[])
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Line 4544 int main(int argc, char *argv[])
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ncodemax=ivector(1,8); |
ncodemax=ivector(1,8); |
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i=1; |
i=1; |
while (fgets(line, MAXLINE, fic) != NULL) { |
linei=0; |
if ((i >= firstobs) && (i <=lastobs)) { |
while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) { |
for(j=0; line[j] != '\n';j++){ /* Untabifies line */ |
linei=linei+1; |
if(line[j] == '\t') |
for(j=strlen(line); j>=0;j--){ /* Untabifies line */ |
line[j] = ' '; |
if(line[j] == '\t') |
} |
line[j] = ' '; |
for (j=maxwav;j>=1;j--){ |
} |
cutv(stra, strb,line,' '); s[j][i]=atoi(strb); |
for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){ |
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); |
line[j+1]=0; /* Trims blanks at end of line */ |
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if(line[0]=='#'){ |
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fprintf(ficlog,"Comment line\n%s\n",line); |
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printf("Comment line\n%s\n",line); |
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continue; |
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} |
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for (j=maxwav;j>=1;j--){ |
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cutv(stra, strb,line,' '); |
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errno=0; |
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lval=strtol(strb,&endptr,10); |
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/* if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/ |
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if( strb[0]=='\0' || (*endptr != '\0')){ |
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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); |
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exit(1); |
} |
} |
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s[j][i]=lval; |
cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra); |
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cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra); |
strcpy(line,stra); |
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cutv(stra, strb,line,' '); |
cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra); |
if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){ |
cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra); |
} |
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else if(iout=sscanf(strb,"%s.") != 0){ |
cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra); |
month=99; |
for (j=ncovcol;j>=1;j--){ |
year=9999; |
cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra); |
}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); |
lstra=strlen(stra); |
exit(1); |
if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */ |
} |
stratrunc = &(stra[lstra-9]); |
anint[j][i]= (double) year; |
num[i]=atol(stratrunc); |
mint[j][i]= (double)month; |
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strcpy(line,stra); |
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} /* ENd Waves */ |
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cutv(stra, strb,line,' '); |
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if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){ |
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} |
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else if(iout=sscanf(strb,"%s.",dummy) != 0){ |
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month=99; |
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year=9999; |
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}else{ |
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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); |
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exit(1); |
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} |
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andc[i]=(double) year; |
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moisdc[i]=(double) month; |
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strcpy(line,stra); |
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cutv(stra, strb,line,' '); |
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if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){ |
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} |
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else if(iout=sscanf(strb,"%s.") != 0){ |
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month=99; |
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year=9999; |
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}else{ |
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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); |
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exit(1); |
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} |
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annais[i]=(double)(year); |
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moisnais[i]=(double)(month); |
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strcpy(line,stra); |
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cutv(stra, strb,line,' '); |
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errno=0; |
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lval=strtol(strb,&endptr,10); |
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if( strb[0]=='\0' || (*endptr != '\0')){ |
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printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight. Exiting.\n",lval, i,line,linei); |
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exit(1); |
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} |
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weight[i]=(double)(lval); |
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strcpy(line,stra); |
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for (j=ncovcol;j>=1;j--){ |
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cutv(stra, strb,line,' '); |
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errno=0; |
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lval=strtol(strb,&endptr,10); |
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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 %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); |
|
exit(1); |
} |
} |
else |
covar[j][i]=(double)(lval); |
num[i]=atol(stra); |
strcpy(line,stra); |
|
} |
/*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){ |
lstra=strlen(stra); |
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;}*/ |
|
|
if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */ |
i=i+1; |
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); |
/* printf("ii=%d", ij); |
scanf("%d",i);*/ |
scanf("%d",i);*/ |
imx=i-1; /* Number of individuals */ |
imx=i-1; /* Number of individuals */ |
Line 4618 int main(int argc, char *argv[])
|
Line 4752 int main(int argc, char *argv[])
|
printf("cptcovprod=%d ", cptcovprod); |
printf("cptcovprod=%d ", cptcovprod); |
fprintf(ficlog,"cptcovprod=%d ", cptcovprod); |
fprintf(ficlog,"cptcovprod=%d ", cptcovprod); |
|
|
scanf("%d ",i); |
scanf("%d ",i);*/ |
fclose(fic);*/ |
|
|
|
/* if(mle==1){*/ |
/* if(mle==1){*/ |
if (weightopt != 1) { /* Maximisation without weights*/ |
if (weightopt != 1) { /* Maximisation without weights*/ |
Line 4844 Interval (in months) between two waves:
|
Line 4977 Interval (in months) between two waves:
|
p=param[1][1]; /* *(*(*(param +1)+1)+0) */ |
p=param[1][1]; /* *(*(*(param +1)+1)+0) */ |
|
|
globpr=0; /* To get the number ipmx of contributions and the sum of weights*/ |
globpr=0; /* To get the number ipmx of contributions and the sum of weights*/ |
|
|
if (mle==-3){ |
if (mle==-3){ |
ximort=matrix(1,NDIM,1,NDIM); |
ximort=matrix(1,NDIM,1,NDIM); |
cens=ivector(1,n); |
cens=ivector(1,n); |
Line 4853 Interval (in months) between two waves:
|
Line 4987 Interval (in months) between two waves:
|
|
|
for (i=1; i<=imx; i++){ |
for (i=1; i<=imx; i++){ |
dcwave[i]=-1; |
dcwave[i]=-1; |
for (j=1; j<=lastpass; j++) |
for (m=firstpass; m<=lastpass; m++) |
if (s[j][i]>nlstate) { |
if (s[m][i]>nlstate) { |
dcwave[i]=j; |
dcwave[i]=m; |
/* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/ |
/* printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/ |
break; |
break; |
} |
} |
Line 4864 Interval (in months) between two waves:
|
Line 4998 Interval (in months) between two waves:
|
for (i=1; i<=imx; i++) { |
for (i=1; i<=imx; i++) { |
if (wav[i]>0){ |
if (wav[i]>0){ |
ageexmed[i]=agev[mw[1][i]][i]; |
ageexmed[i]=agev[mw[1][i]][i]; |
j=wav[i];agecens[i]=1.; |
j=wav[i]; |
if (ageexmed[i]>1 & wav[i]>0) agecens[i]=agev[mw[j][i]][i]; |
agecens[i]=1.; |
cens[i]=1; |
|
|
if (ageexmed[i]> 1 && wav[i] > 0){ |
if (ageexmed[i]<1) cens[i]=-1; |
agecens[i]=agev[mw[j][i]][i]; |
if (agedc[i]< AGESUP & agedc[i]>1 & dcwave[i]>firstpass & dcwave[i]<=lastpass) cens[i]=0 ; |
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; |
else cens[i]=-1; |
} |
} |
Line 4878 Interval (in months) between two waves:
|
Line 5016 Interval (in months) between two waves:
|
for (j=1;j<=NDIM;j++) |
for (j=1;j<=NDIM;j++) |
ximort[i][j]=(i == j ? 1.0 : 0.0); |
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("%lf %lf", p[1], p[2]);*/ |
|
|
|
|
printf("Powell\n"); fprintf(ficlog,"Powell\n"); |
printf("Powell\n"); fprintf(ficlog,"Powell\n"); |
strcpy(filerespow,"pow-mort"); |
strcpy(filerespow,"pow-mort"); |
strcat(filerespow,fileres); |
strcat(filerespow,fileres); |
if((ficrespow=fopen(filerespow,"w"))==NULL) { |
if((ficrespow=fopen(filerespow,"w"))==NULL) { |
printf("Problem with resultfile: %s\n", filerespow); |
printf("Problem with resultfile: %s\n", filerespow); |
fprintf(ficlog,"Problem with resultfile: %s\n", filerespow); |
fprintf(ficlog,"Problem with resultfile: %s\n", filerespow); |
} |
} |
fprintf(ficrespow,"# Powell\n# iter -2*LL"); |
fprintf(ficrespow,"# Powell\n# iter -2*LL"); |
/* for (i=1;i<=nlstate;i++) |
/* for (i=1;i<=nlstate;i++) |
for(j=1;j<=nlstate+ndeath;j++) |
for(j=1;j<=nlstate+ndeath;j++) |
if(j!=i)fprintf(ficrespow," p%1d%1d",i,j); |
if(j!=i)fprintf(ficrespow," p%1d%1d",i,j); |
*/ |
*/ |
fprintf(ficrespow,"\n"); |
fprintf(ficrespow,"\n"); |
|
|
powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz); |
powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz); |
fclose(ficrespow); |
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(i=1; i <=NDIM; i++) |
for(j=i+1;j<=NDIM;j++) |
for(j=i+1;j<=NDIM;j++) |
Line 4918 Interval (in months) between two waves:
|
Line 5056 Interval (in months) between two waves:
|
for (i=1;i<=NDIM;i++) |
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])); |
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); |
lpop=vector(1,AGESUP); |
tpop=vector(1,AGESUP); |
tpop=vector(1,AGESUP); |
lsurv[agegomp]=100000; |
lsurv[agegomp]=100000; |
|
|
for (k=agegomp;k<=AGESUP;k++) { |
for (k=agegomp;k<=AGESUP;k++) { |
agemortsup=k; |
agemortsup=k; |
if (p[1]*exp(p[2]*(k-agegomp))>1) break; |
if (p[1]*exp(p[2]*(k-agegomp))>1) break; |
} |
} |
|
|
for (k=agegomp;k<agemortsup;k++) |
for (k=agegomp;k<agemortsup;k++) |
lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp))); |
lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp))); |
|
|
for (k=agegomp;k<agemortsup;k++){ |
for (k=agegomp;k<agemortsup;k++){ |
lpop[k]=(lsurv[k]+lsurv[k+1])/2.; |
lpop[k]=(lsurv[k]+lsurv[k+1])/2.; |
sumlpop=sumlpop+lpop[k]; |
sumlpop=sumlpop+lpop[k]; |
} |
} |
|
|
tpop[agegomp]=sumlpop; |
tpop[agegomp]=sumlpop; |
for (k=agegomp;k<(agemortsup-3);k++){ |
for (k=agegomp;k<(agemortsup-3);k++){ |
/* tpop[k+1]=2;*/ |
/* tpop[k+1]=2;*/ |
tpop[k+1]=tpop[k]-lpop[k]; |
tpop[k+1]=tpop[k]-lpop[k]; |
} |
} |
|
|
|
|
printf("\nAge lx qx dx Lx Tx e(x)\n"); |
printf("\nAge lx qx dx Lx Tx e(x)\n"); |
for (k=agegomp;k<(agemortsup-2);k++) |
for (k=agegomp;k<(agemortsup-2);k++) |
printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\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]); |
printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\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]); |
|
|
|
|
replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */ |
replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */ |
printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p); |
printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p); |
|
|
printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \ |
printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \ |
stepm, weightopt,\ |
stepm, weightopt,\ |
model,imx,p,matcov,agemortsup); |
model,imx,p,matcov,agemortsup); |
|
|
free_vector(lsurv,1,AGESUP); |
free_vector(lsurv,1,AGESUP); |
free_vector(lpop,1,AGESUP); |
free_vector(lpop,1,AGESUP); |
free_vector(tpop,1,AGESUP); |
free_vector(tpop,1,AGESUP); |
} /* Endof if mle==-3 */ |
} /* Endof if mle==-3 */ |
|
|
else{ /* For mle >=1 */ |
else{ /* For mle >=1 */ |
|
|
likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */ |
likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */ |
Line 5498 lsurv=vector(1,AGESUP);
|
Line 5636 lsurv=vector(1,AGESUP);
|
free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX); |
free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX); |
|
|
} /* mle==-3 arrives here for freeing */ |
} /* mle==-3 arrives here for freeing */ |
|
free_matrix(prlim,1,nlstate,1,nlstate); |
free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath); |
free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath); |
free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath); |
free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath); |
free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath); |
free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath); |
free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath); |
free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath); |
|
|
free_matrix(covar,0,NCOVMAX,1,n); |
free_matrix(covar,0,NCOVMAX,1,n); |
free_matrix(matcov,1,npar,1,npar); |
free_matrix(matcov,1,npar,1,npar); |
/*free_vector(delti,1,npar);*/ |
/*free_vector(delti,1,npar);*/ |
Line 5517 lsurv=vector(1,AGESUP);
|
Line 5655 lsurv=vector(1,AGESUP);
|
free_ivector(Tage,1,15); |
free_ivector(Tage,1,15); |
free_ivector(Tcode,1,100); |
free_ivector(Tcode,1,100); |
|
|
|
free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX); |
|
free_imatrix(codtab,1,100,1,10); |
fflush(fichtm); |
fflush(fichtm); |
fflush(ficgp); |
fflush(ficgp); |
|
|
Line 5552 lsurv=vector(1,AGESUP);
|
Line 5691 lsurv=vector(1,AGESUP);
|
/*------ End -----------*/ |
/*------ End -----------*/ |
|
|
chdir(path); |
chdir(path); |
#ifndef UNIX |
|
/* strcpy(plotcmd,"\""); */ |
|
#endif |
|
strcpy(plotcmd,pathimach); |
|
/*strcat(plotcmd,CHARSEPARATOR);*/ |
/*strcat(plotcmd,CHARSEPARATOR);*/ |
strcat(plotcmd,GNUPLOTPROGRAM); |
sprintf(plotcmd,"gnuplot"); |
#ifndef UNIX |
#ifndef UNIX |
strcat(plotcmd,".exe"); |
sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach); |
/* strcat(plotcmd,"\"");*/ |
|
#endif |
#endif |
if(stat(plotcmd,&info)){ |
if(!stat(plotcmd,&info)){ |
printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout); |
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); |
#ifndef UNIX |
}else |
strcpy(plotcmd,"\""); |
strcpy(pplotcmd,plotcmd); |
#endif |
#ifdef UNIX |
strcat(plotcmd,pathimach); |
strcpy(plotcmd,GNUPLOTPROGRAM); |
strcat(plotcmd,GNUPLOTPROGRAM); |
if(!stat(plotcmd,&info)){ |
#ifndef UNIX |
printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout); |
strcat(plotcmd,".exe"); |
}else |
strcat(plotcmd,"\""); |
strcpy(pplotcmd,plotcmd); |
#endif |
#endif |
strcat(plotcmd," "); |
}else |
strcat(plotcmd,optionfilegnuplot); |
strcpy(pplotcmd,plotcmd); |
printf("Starting graphs with: %s",plotcmd);fflush(stdout); |
|
|
sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot); |
|
printf("Starting graphs with: %s\n",plotcmd);fflush(stdout); |
|
|
if((outcmd=system(plotcmd)) != 0){ |
if((outcmd=system(plotcmd)) != 0){ |
printf("\n Problem with gnuplot\n"); |
printf("\n Problem with gnuplot\n"); |