version 1.98, 2004/05/16 15:05:56
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version 1.103, 2005/09/30 15:54:49
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/* $Id$ |
/* $Id$ |
$State$ |
$State$ |
$Log$ |
$Log$ |
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Revision 1.103 2005/09/30 15:54:49 lievre |
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(Module): sump fixed, loop imx fixed, and simplifications. |
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Revision 1.102 2004/09/15 17:31:30 brouard |
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Add the possibility to read data file including tab characters. |
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Revision 1.101 2004/09/15 10:38:38 brouard |
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Fix on curr_time |
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Revision 1.100 2004/07/12 18:29:06 brouard |
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Add version for Mac OS X. Just define UNIX in Makefile |
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Revision 1.99 2004/06/05 08:57:40 brouard |
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*** empty log message *** |
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Revision 1.98 2004/05/16 15:05:56 brouard |
Revision 1.98 2004/05/16 15:05:56 brouard |
New version 0.97 . First attempt to estimate force of mortality |
New version 0.97 . First attempt to estimate force of mortality |
directly from the data i.e. without the need of knowing the health |
directly from the data i.e. without the need of knowing the health |
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#include <stdlib.h> |
#include <stdlib.h> |
#include <unistd.h> |
#include <unistd.h> |
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#include <sys/time.h> |
/* #include <sys/time.h> */ |
#include <time.h> |
#include <time.h> |
#include "timeval.h" |
#include "timeval.h" |
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Line 224
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Line 239
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#define AGESUP 130 |
#define AGESUP 130 |
#define AGEBASE 40 |
#define AGEBASE 40 |
#define AGEGOMP 10. /* Minimal age for Gompertz adjustment */ |
#define AGEGOMP 10. /* Minimal age for Gompertz adjustment */ |
#ifdef unix |
#ifdef UNIX |
#define DIRSEPARATOR '/' |
#define DIRSEPARATOR '/' |
#define ODIRSEPARATOR '\\' |
#define ODIRSEPARATOR '\\' |
#else |
#else |
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Line 250
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/* $Id$ */ |
/* $Id$ */ |
/* $State$ */ |
/* $State$ */ |
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char version[]="Imach version 0.70, May 2004, INED-EUROREVES "; |
char version[]="Imach version 0.97c, September 2004, 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 356 double ftolhess; /* Tolerance for comput
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Line 371 double ftolhess; /* Tolerance for comput
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/**************** split *************************/ |
/**************** split *************************/ |
static int split( char *path, char *dirc, char *name, char *ext, char *finame ) |
static int split( char *path, char *dirc, char *name, char *ext, char *finame ) |
{ |
{ |
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/* From a file name with full path (either Unix or Windows) we extract the directory (dirc) |
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the name of the file (name), its extension only (ext) and its first part of the name (finame) |
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*/ |
char *ss; /* pointer */ |
char *ss; /* pointer */ |
int l1, l2; /* length counters */ |
int l1, l2; /* length counters */ |
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Line 387 static int split( char *path, char *dirc
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Line 405 static int split( char *path, char *dirc
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#endif |
#endif |
*/ |
*/ |
ss = strrchr( name, '.' ); /* find last / */ |
ss = strrchr( name, '.' ); /* find last / */ |
ss++; |
if (ss >0){ |
strcpy(ext,ss); /* save extension */ |
ss++; |
l1= strlen( name); |
strcpy(ext,ss); /* save extension */ |
l2= strlen(ss)+1; |
l1= strlen( name); |
strncpy( finame, name, l1-l2); |
l2= strlen(ss)+1; |
finame[l1-l2]= 0; |
strncpy( finame, name, l1-l2); |
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finame[l1-l2]= 0; |
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} |
return( 0 ); /* we're done */ |
return( 0 ); /* we're done */ |
} |
} |
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Line 425 int nbocc(char *s, char occ)
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Line 445 int nbocc(char *s, char occ)
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void cutv(char *u,char *v, char*t, char occ) |
void cutv(char *u,char *v, char*t, char occ) |
{ |
{ |
/* cuts string t into u and v where u is ended by char occ excluding it |
/* cuts string t into u and v where u ends before first occurence of char 'occ' |
and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2) |
and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2') |
gives u="abcedf" and v="ghi2j" */ |
gives u="abcedf" and v="ghi2j" */ |
int i,lg,j,p=0; |
int i,lg,j,p=0; |
i=0; |
i=0; |
Line 868 void powell(double p[], double **xi, int
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Line 888 void powell(double p[], double **xi, int
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fprintf(ficrespow,"\n");fflush(ficrespow); |
fprintf(ficrespow,"\n");fflush(ficrespow); |
if(*iter <=3){ |
if(*iter <=3){ |
tm = *localtime(&curr_time.tv_sec); |
tm = *localtime(&curr_time.tv_sec); |
strcpy(strcurr,asctime(&tmf)); |
strcpy(strcurr,asctime(&tm)); |
/* asctime_r(&tm,strcurr); */ |
/* asctime_r(&tm,strcurr); */ |
forecast_time=curr_time; |
forecast_time=curr_time; |
itmp = strlen(strcurr); |
itmp = strlen(strcurr); |
if(strcurr[itmp-1]=='\n') |
if(strcurr[itmp-1]=='\n') /* Windows outputs with a new line */ |
strcurr[itmp-1]='\0'; |
strcurr[itmp-1]='\0'; |
printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec); |
printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec); |
fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec); |
fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec); |
Line 884 void powell(double p[], double **xi, int
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Line 904 void powell(double p[], double **xi, int
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itmp = strlen(strfor); |
itmp = strlen(strfor); |
if(strfor[itmp-1]=='\n') |
if(strfor[itmp-1]=='\n') |
strfor[itmp-1]='\0'; |
strfor[itmp-1]='\0'; |
printf(" - if your program needs %d iterations to converge, convergence will be \n reached in %s or\n on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr); |
printf(" - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr); |
fprintf(ficlog," - if your program needs %d iterations to converge, convergence will be \n reached in %s or\n on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr); |
fprintf(ficlog," - if your program needs %d iterations to converge, convergence will be \n reached in %s i.e.\n on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr); |
} |
} |
} |
} |
for (i=1;i<=n;i++) { |
for (i=1;i<=n;i++) { |
Line 1050 double **pmij(double **ps, double *cov,
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Line 1070 double **pmij(double **ps, double *cov,
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int i,j,j1, nc, ii, jj; |
int i,j,j1, nc, ii, jj; |
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for(i=1; i<= nlstate; i++){ |
for(i=1; i<= nlstate; i++){ |
for(j=1; j<i;j++){ |
for(j=1; j<i;j++){ |
for (nc=1, s2=0.;nc <=ncovmodel; nc++){ |
for (nc=1, s2=0.;nc <=ncovmodel; nc++){ |
/*s2 += param[i][j][nc]*cov[nc];*/ |
/*s2 += param[i][j][nc]*cov[nc];*/ |
s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc]; |
s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc]; |
/*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/ |
/* printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */ |
} |
} |
ps[i][j]=s2; |
ps[i][j]=s2; |
/*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/ |
/* printf("s1=%.17e, s2=%.17e\n",s1,s2); */ |
} |
} |
for(j=i+1; j<=nlstate+ndeath;j++){ |
for(j=i+1; j<=nlstate+ndeath;j++){ |
for (nc=1, s2=0.;nc <=ncovmodel; nc++){ |
for (nc=1, s2=0.;nc <=ncovmodel; nc++){ |
s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc]; |
s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc]; |
/*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/ |
/* printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */ |
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} |
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ps[i][j]=s2; |
} |
} |
ps[i][j]=s2; |
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} |
} |
} |
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/*ps[3][2]=1;*/ |
/*ps[3][2]=1;*/ |
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for(i=1; i<= nlstate; i++){ |
for(i=1; i<= nlstate; i++){ |
s1=0; |
s1=0; |
for(j=1; j<i; j++) |
for(j=1; j<i; j++) |
s1+=exp(ps[i][j]); |
s1+=exp(ps[i][j]); |
for(j=i+1; j<=nlstate+ndeath; j++) |
for(j=i+1; j<=nlstate+ndeath; j++) |
s1+=exp(ps[i][j]); |
s1+=exp(ps[i][j]); |
ps[i][i]=1./(s1+1.); |
ps[i][i]=1./(s1+1.); |
for(j=1; j<i; j++) |
for(j=1; j<i; j++) |
ps[i][j]= exp(ps[i][j])*ps[i][i]; |
ps[i][j]= exp(ps[i][j])*ps[i][i]; |
for(j=i+1; j<=nlstate+ndeath; j++) |
for(j=i+1; j<=nlstate+ndeath; j++) |
ps[i][j]= exp(ps[i][j])*ps[i][i]; |
ps[i][j]= exp(ps[i][j])*ps[i][i]; |
/* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */ |
/* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */ |
} /* end i */ |
} /* end i */ |
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for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){ |
for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){ |
for(jj=1; jj<= nlstate+ndeath; jj++){ |
for(jj=1; jj<= nlstate+ndeath; jj++){ |
ps[ii][jj]=0; |
ps[ii][jj]=0; |
ps[ii][ii]=1; |
ps[ii][ii]=1; |
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} |
} |
} |
} |
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/* for(ii=1; ii<= nlstate+ndeath; ii++){ |
/* for(ii=1; ii<= nlstate+ndeath; ii++){ */ |
for(jj=1; jj<= nlstate+ndeath; jj++){ |
/* for(jj=1; jj<= nlstate+ndeath; jj++){ */ |
printf("%lf ",ps[ii][jj]); |
/* printf("ddd %lf ",ps[ii][jj]); */ |
} |
/* } */ |
printf("\n "); |
/* printf("\n "); */ |
} |
/* } */ |
printf("\n ");printf("%lf ",cov[2]);*/ |
/* printf("\n ");printf("%lf ",cov[2]); */ |
/* |
/* |
for(i=1; i<= npar; i++) printf("%f ",x[i]); |
for(i=1; i<= npar; i++) printf("%f ",x[i]); |
goto end;*/ |
goto end;*/ |
return ps; |
return ps; |
} |
} |
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Line 1224 double func( double *x)
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Line 1244 double func( double *x)
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} /* end mult */ |
} /* end mult */ |
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/*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */ |
/*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */ |
/* But now since version 0.9 we anticipate for bias and large stepm. |
/* But now since version 0.9 we anticipate for bias at large stepm. |
* If stepm is larger than one month (smallest stepm) and if the exact delay |
* If stepm is larger than one month (smallest stepm) and if the exact delay |
* (in months) between two waves is not a multiple of stepm, we rounded to |
* (in months) between two waves is not a multiple of stepm, we rounded to |
* the nearest (and in case of equal distance, to the lowest) interval but now |
* the nearest (and in case of equal distance, to the lowest) interval but now |
* we keep into memory the bias bh[mi][i] and also the previous matrix product |
* we keep into memory the bias bh[mi][i] and also the previous matrix product |
* (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the |
* (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the |
* probability in order to take into account the bias as a fraction of the way |
* probability in order to take into account the bias as a fraction of the way |
* from savm to out if bh is neagtive or even beyond if bh is positive. bh varies |
* from savm to out if bh is negative or even beyond if bh is positive. bh varies |
* -stepm/2 to stepm/2 . |
* -stepm/2 to stepm/2 . |
* For stepm=1 the results are the same as for previous versions of Imach. |
* For stepm=1 the results are the same as for previous versions of Imach. |
* For stepm > 1 the results are less biased than in previous versions. |
* For stepm > 1 the results are less biased than in previous versions. |
Line 1239 double func( double *x)
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Line 1259 double func( double *x)
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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 |
/* bias bh is positive if real duration |
* is higher than the multiple of stepm and negative otherwise. |
* is higher than the multiple of stepm and negative otherwise. |
*/ |
*/ |
/* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/ |
/* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/ |
if( s2 > nlstate){ |
if( s2 > nlstate){ |
/* i.e. if s2 is a death state and if the date of death is known then the contribution |
/* i.e. if s2 is a death state and if the date of death is known then the contribution |
to the likelihood is the probability to die between last step unit time and current |
to the likelihood is the probability to die between last step unit time and current |
step unit time, which is also the differences between probability to die before dh |
step unit time, which is also equal to probability to die before dh |
and probability to die before dh-stepm . |
minus probability to die before dh-stepm . |
In version up to 0.92 likelihood was computed |
In version up to 0.92 likelihood was computed |
as if date of death was unknown. Death was treated as any other |
as if date of death was unknown. Death was treated as any other |
health state: the date of the interview describes the actual state |
health state: the date of the interview describes the actual state |
Line 3904 double gompertz(double x[])
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Line 3924 double gompertz(double x[])
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int i,n=0; /* n is the size of the sample */ |
int i,n=0; /* n is the size of the sample */ |
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;*/ |
num=num+1; |
num=num+1; |
} |
} |
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/* for (i=1; i<=imx; i++) |
/* for (i=0; i<=imx; i++) |
if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/ |
if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/ |
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for (i=0;i<=imx-1 ; 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])* |
A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp))); |
(exp(x[2]/YEARM*(agecens[i]*12-agegomp*12))-exp(x[2]/YEARM*(ageexmed[i]*12-agegomp*12))); |
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if (cens[i]==0 & wav[i]>1) |
if (cens[i]==0 & wav[i]>1) |
A=-x[1]/(x[2])* |
A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp))) |
(exp(x[2]/YEARM*(agedc[i]*12-agegomp*12))-exp(x[2]/YEARM*(ageexmed[i]*12-agegomp*12))) |
+log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM); |
+log(x[1]/YEARM)+x[2]/YEARM*(agedc[i]*12-agegomp*12)+log(YEARM); |
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if (wav[i]>1 & agecens[i]>15) { |
if (wav[i]>1 & agecens[i]>15) { |
L=L+A*weight[i]; |
L=L+A*weight[i]; |
Line 4003 int main(int argc, char *argv[])
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Line 4021 int main(int argc, char *argv[])
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int *indx; |
int *indx; |
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]; |
char pathr[MAXLINE], pathimach[MAXLINE]; |
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 4089 int main(int argc, char *argv[])
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Line 4107 int main(int argc, char *argv[])
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printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/ |
printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/ |
/* cutv(path,optionfile,pathtot,'\\');*/ |
/* cutv(path,optionfile,pathtot,'\\');*/ |
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split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname); |
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/* strcpy(pathimach,argv[0]); */ |
split(pathtot,path,optionfile,optionfilext,optionfilefiname); |
split(pathtot,path,optionfile,optionfilext,optionfilefiname); |
printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",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); |
chdir(path); |
strcpy(command,"mkdir "); |
strcpy(command,"mkdir "); |
strcat(command,optionfilefiname); |
strcat(command,optionfilefiname); |
Line 4115 int main(int argc, char *argv[])
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Line 4135 int main(int argc, char *argv[])
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} |
} |
fprintf(ficlog,"Log filename:%s\n",filelog); |
fprintf(ficlog,"Log filename:%s\n",filelog); |
fprintf(ficlog,"\n%s\n%s",version,fullversion); |
fprintf(ficlog,"\n%s\n%s",version,fullversion); |
fprintf(ficlog,"\nEnter the parameter file name: "); |
fprintf(ficlog,"\nEnter the parameter file name: \n"); |
fprintf(ficlog,"pathtot=%s\n\ |
fprintf(ficlog,"pathimach=%s\npathtot=%s\n\ |
path=%s \n\ |
path=%s \n\ |
optionfile=%s\n\ |
optionfile=%s\n\ |
optionfilext=%s\n\ |
optionfilext=%s\n\ |
optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname); |
optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname); |
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printf("Local time (at start):%s",strstart); |
printf("Local time (at start):%s",strstart); |
fprintf(ficlog,"Local time (at start): %s",strstart); |
fprintf(ficlog,"Local time (at start): %s",strstart); |
Line 4383 int main(int argc, char *argv[])
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Line 4403 int main(int argc, char *argv[])
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i=1; |
i=1; |
while (fgets(line, MAXLINE, fic) != NULL) { |
while (fgets(line, MAXLINE, fic) != NULL) { |
if ((i >= firstobs) && (i <=lastobs)) { |
if ((i >= firstobs) && (i <=lastobs)) { |
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for(j=0; line[j] != '\n';j++){ /* Untabifies line */ |
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if(line[j] == '\t') |
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line[j] = ' '; |
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} |
for (j=maxwav;j>=1;j--){ |
for (j=maxwav;j>=1;j--){ |
cutv(stra, strb,line,' '); s[j][i]=atoi(strb); |
cutv(stra, strb,line,' '); s[j][i]=atoi(strb); |
strcpy(line,stra); |
strcpy(line,stra); |
Line 5411 Interval (in months) between two waves:
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Line 5434 Interval (in months) between two waves:
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/*------ End -----------*/ |
/*------ End -----------*/ |
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chdir(path); |
chdir(path); |
strcpy(plotcmd,GNUPLOTPROGRAM); |
strcpy(plotcmd,"\""); |
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strcat(plotcmd,pathimach); |
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strcat(plotcmd,GNUPLOTPROGRAM); |
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strcat(plotcmd,"\""); |
strcat(plotcmd," "); |
strcat(plotcmd," "); |
strcat(plotcmd,optionfilegnuplot); |
strcat(plotcmd,optionfilegnuplot); |
printf("Starting graphs with: %s",plotcmd);fflush(stdout); |
printf("Starting graphs with: %s",plotcmd);fflush(stdout); |
Line 5424 Interval (in months) between two waves:
|
Line 5450 Interval (in months) between two waves:
|
printf("\nType e to edit output files, g to graph again and q for exiting: "); |
printf("\nType e to edit output files, g to graph again and q for exiting: "); |
scanf("%s",z); |
scanf("%s",z); |
/* if (z[0] == 'c') system("./imach"); */ |
/* if (z[0] == 'c') system("./imach"); */ |
if (z[0] == 'e') system(optionfilehtm); |
if (z[0] == 'e') { |
|
printf("Starting browser with: %s",optionfilehtm);fflush(stdout); |
|
system(optionfilehtm); |
|
} |
else if (z[0] == 'g') system(plotcmd); |
else if (z[0] == 'g') system(plotcmd); |
else if (z[0] == 'q') exit(0); |
else if (z[0] == 'q') exit(0); |
} |
} |