version 1.92, 2003/06/25 16:30:45
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version 1.94, 2003/06/27 13:00:02
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/* $Id$ |
/* $Id$ |
$State$ |
$State$ |
$Log$ |
$Log$ |
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Revision 1.94 2003/06/27 13:00:02 brouard |
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Just cleaning |
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Revision 1.93 2003/06/25 16:33:55 brouard |
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(Module): On windows (cygwin) function asctime_r doesn't |
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exist so I changed back to asctime which exists. |
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(Module): Version 0.96b |
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Revision 1.92 2003/06/25 16:30:45 brouard |
Revision 1.92 2003/06/25 16:30:45 brouard |
(Module): On windows (cygwin) function asctime_r doesn't |
(Module): On windows (cygwin) function asctime_r doesn't |
exist so I changed back to asctime which exists. |
exist so I changed back to asctime which exists. |
Line 188
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Line 196
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/* $Id$ */ |
/* $Id$ */ |
/* $State$ */ |
/* $State$ */ |
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char version[]="Imach version 0.96a, June 2003, INED-EUROREVES "; |
char version[]="Imach version 0.96b, June 2003, 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 237 char command[FILENAMELENGTH];
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Line 245 char command[FILENAMELENGTH];
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int outcmd=0; |
int outcmd=0; |
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char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH]; |
char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH]; |
char lfileres[FILENAMELENGTH]; |
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char filelog[FILENAMELENGTH]; /* Log file */ |
char filelog[FILENAMELENGTH]; /* Log file */ |
char filerest[FILENAMELENGTH]; |
char filerest[FILENAMELENGTH]; |
char fileregp[FILENAMELENGTH]; |
char fileregp[FILENAMELENGTH]; |
Line 557 void free_ma3x(double ***m, long nrl, lo
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Line 565 void free_ma3x(double ***m, long nrl, lo
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free((FREE_ARG)(m+nrl-NR_END)); |
free((FREE_ARG)(m+nrl-NR_END)); |
} |
} |
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/*************** function subdirf ***********/ |
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char *subdirf(char fileres[]) |
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{ |
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/* Caution optionfilefiname is hidden */ |
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strcpy(tmpout,optionfilefiname); |
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strcat(tmpout,"/"); /* Add to the right */ |
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strcat(tmpout,fileres); |
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return tmpout; |
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} |
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/*************** function subdirf2 ***********/ |
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char *subdirf2(char fileres[], char *preop) |
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{ |
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/* Caution optionfilefiname is hidden */ |
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strcpy(tmpout,optionfilefiname); |
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strcat(tmpout,"/"); |
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strcat(tmpout,preop); |
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strcat(tmpout,fileres); |
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return tmpout; |
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} |
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/*************** function subdirf3 ***********/ |
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char *subdirf3(char fileres[], char *preop, char *preop2) |
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{ |
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/* Caution optionfilefiname is hidden */ |
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strcpy(tmpout,optionfilefiname); |
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strcat(tmpout,"/"); |
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strcat(tmpout,preop); |
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strcat(tmpout,preop2); |
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strcat(tmpout,fileres); |
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return tmpout; |
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} |
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/***************** f1dim *************************/ |
/***************** f1dim *************************/ |
extern int ncom; |
extern int ncom; |
extern double *pcom,*xicom; |
extern double *pcom,*xicom; |
Line 1214 double func( double *x)
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Line 1257 double func( double *x)
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oldm=newm; |
oldm=newm; |
} /* end mult */ |
} /* end mult */ |
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/*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */ |
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/* But now since version 0.9 we anticipate for bias and large stepm. |
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* If stepm is larger than one month (smallest stepm) and if the exact delay |
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* (in months) between two waves is not a multiple of stepm, we rounded to |
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* the nearest (and in case of equal distance, to the lowest) interval but now |
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* we keep into memory the bias bh[mi][i] and also the previous matrix product |
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* (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the |
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* probability in order to take into account the bias as a fraction of the way |
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* from savm to out if bh is neagtive or even beyond if bh is positive. bh varies |
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* -stepm/2 to stepm/2 . |
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* For stepm=1 the results are the same as for previous versions of Imach. |
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* For stepm > 1 the results are less biased than in previous versions. |
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*/ |
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s1=s[mw[mi][i]][i]; |
s1=s[mw[mi][i]][i]; |
s2=s[mw[mi+1][i]][i]; |
s2=s[mw[mi+1][i]][i]; |
bbh=(double)bh[mi][i]/(double)stepm; |
bbh=(double)bh[mi][i]/(double)stepm; |
/* bias is positive if real duration |
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* is higher than the multiple of stepm and negative otherwise. |
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*/ |
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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 */ |
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 */ |
/* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/ |
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/*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */ |
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/*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/ |
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/*if(lli ==000.0)*/ |
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/*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */ |
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ipmx +=1; |
ipmx +=1; |
sw += weight[i]; |
sw += weight[i]; |
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; |
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; |
Line 1265 double func( double *x)
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Line 1287 double func( double *x)
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oldm=newm; |
oldm=newm; |
} /* end mult */ |
} /* end mult */ |
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/*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */ |
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/* But now since version 0.9 we anticipate for bias and large stepm. |
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* If stepm is larger than one month (smallest stepm) and if the exact delay |
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* (in months) between two waves is not a multiple of stepm, we rounded to |
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* the nearest (and in case of equal distance, to the lowest) interval but now |
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* we keep into memory the bias bh[mi][i] and also the previous matrix product |
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* (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the |
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* probability in order to take into account the bias as a fraction of the way |
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* from savm to out if bh is neagtive or even beyond if bh is positive. bh varies |
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* -stepm/2 to stepm/2 . |
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* For stepm=1 the results are the same as for previous versions of Imach. |
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* For stepm > 1 the results are less biased than in previous versions. |
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*/ |
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s1=s[mw[mi][i]][i]; |
s1=s[mw[mi][i]][i]; |
s2=s[mw[mi+1][i]][i]; |
s2=s[mw[mi+1][i]][i]; |
bbh=(double)bh[mi][i]/(double)stepm; |
bbh=(double)bh[mi][i]/(double)stepm; |
/* bias is positive if real duration |
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* is higher than the multiple of stepm and negative otherwise. |
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*/ |
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/* 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 */ |
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lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */ |
lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */ |
/*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/ |
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/*if(lli ==000.0)*/ |
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/*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */ |
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ipmx +=1; |
ipmx +=1; |
sw += weight[i]; |
sw += weight[i]; |
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; |
ll[s[mw[mi][i]][i]] += 2*weight[i]*lli; |
Line 1454 double funcone( double *x)
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Line 1456 double funcone( double *x)
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return -l; |
return -l; |
} |
} |
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char *subdirf(char fileres[]) |
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{ |
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/* Caution optionfilefiname is hidden */ |
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strcpy(tmpout,optionfilefiname); |
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strcat(tmpout,"/"); /* Add to the right */ |
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strcat(tmpout,fileres); |
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return tmpout; |
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} |
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char *subdirf2(char fileres[], char *preop) |
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{ |
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strcpy(tmpout,optionfilefiname); |
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strcat(tmpout,"/"); |
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strcat(tmpout,preop); |
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strcat(tmpout,fileres); |
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return tmpout; |
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} |
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char *subdirf3(char fileres[], char *preop, char *preop2) |
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{ |
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strcpy(tmpout,optionfilefiname); |
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strcat(tmpout,"/"); |
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strcat(tmpout,preop); |
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strcat(tmpout,preop2); |
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strcat(tmpout,fileres); |
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return tmpout; |
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} |
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/*************** function likelione ***********/ |
void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double [])) |
void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double [])) |
{ |
{ |
/* This routine should help understanding what is done with |
/* This routine should help understanding what is done with |
Line 3746 int fileappend(FILE *fichier, char *opti
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Line 3721 int fileappend(FILE *fichier, char *opti
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fflush(fichier); |
fflush(fichier); |
return (1); |
return (1); |
} |
} |
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/**************** function prwizard **********************/ |
void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo) |
void prwizard(int ncovmodel, int nlstate, int ndeath, char model[], FILE *ficparo) |
{ |
{ |
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/* Wizard to print covariance matrix template */ |
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char ca[32], cb[32], cc[32]; |
char ca[32], cb[32], cc[32]; |
int i,j, k, l, li, lj, lk, ll, jj, npar, itimes; |
int i,j, k, l, li, lj, lk, ll, jj, npar, itimes; |
int numlinepar; |
int numlinepar; |
Line 4004 int main(int argc, char *argv[])
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Line 3984 int main(int argc, char *argv[])
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optionfilext=%s\n\ |
optionfilext=%s\n\ |
optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname); |
optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname); |
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printf("Localtime (at start):%s",strstart); |
printf("Local time (at start):%s",strstart); |
fprintf(ficlog,"Localtime (at start): %s",strstart); |
fprintf(ficlog,"Local time (at start): %s",strstart); |
fflush(ficlog); |
fflush(ficlog); |
/* (void) gettimeofday(&curr_time,&tzp); */ |
/* (void) gettimeofday(&curr_time,&tzp); */ |
/* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */ |
/* printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */ |
Line 4581 Title=%s <br>Datafile=%s Firstpass=%d La
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Line 4561 Title=%s <br>Datafile=%s Firstpass=%d La
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strcpy(pathr,path); |
strcpy(pathr,path); |
strcat(pathr,optionfilefiname); |
strcat(pathr,optionfilefiname); |
chdir(optionfilefiname); /* Move to directory named optionfile */ |
chdir(optionfilefiname); /* Move to directory named optionfile */ |
strcpy(lfileres,fileres); |
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strcat(lfileres,"/"); |
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strcat(lfileres,optionfilefiname); |
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/* Calculates basic frequencies. Computes observed prevalence at single age |
/* Calculates basic frequencies. Computes observed prevalence at single age |
and prints on file fileres'p'. */ |
and prints on file fileres'p'. */ |
Line 5124 ageminpar, agemax, s[lastpass][imx], age
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Line 5101 ageminpar, agemax, s[lastpass][imx], age
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tm = *localtime(&end_time.tv_sec); |
tm = *localtime(&end_time.tv_sec); |
tmg = *gmtime(&end_time.tv_sec); |
tmg = *gmtime(&end_time.tv_sec); |
strcpy(strtend,asctime(&tm)); |
strcpy(strtend,asctime(&tm)); |
printf("Localtime at start %s\nLocaltime at end %s",strstart, strtend); |
printf("Local time at start %s\nLocaltime at end %s",strstart, strtend); |
fprintf(ficlog,"Localtime at start %s\nLocal time at end %s\n",strstart, strtend); |
fprintf(ficlog,"Local time at start %s\nLocal time at end %s\n",strstart, strtend); |
printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout)); |
printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout)); |
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printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec); |
printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec); |