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Diff for /imach/src/imach.c between versions 1.93 and 1.95

version 1.93, 2003/06/25 16:33:55 version 1.95, 2003/07/08 07:54:34
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.95  2003/07/08 07:54:34  brouard
     * imach.c (Repository):
     (Repository): Using imachwizard code to output a more meaningful covariance
     matrix (cov(a12,c31) instead of numbers.
   
     Revision 1.94  2003/06/27 13:00:02  brouard
     Just cleaning
   
   Revision 1.93  2003/06/25 16:33:55  brouard    Revision 1.93  2003/06/25 16:33:55  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 162 Line 170
 #include <time.h>  #include <time.h>
 #include "timeval.h"  #include "timeval.h"
   
   /* #include <libintl.h> */
   /* #define _(String) gettext (String) */
   
 #define MAXLINE 256  #define MAXLINE 256
 #define GNUPLOTPROGRAM "gnuplot"  #define GNUPLOTPROGRAM "gnuplot"
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
Line 242  char command[FILENAMELENGTH]; Line 253  char command[FILENAMELENGTH];
 int  outcmd=0;  int  outcmd=0;
   
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 char lfileres[FILENAMELENGTH];  
 char filelog[FILENAMELENGTH]; /* Log file */  char filelog[FILENAMELENGTH]; /* Log file */
 char filerest[FILENAMELENGTH];  char filerest[FILENAMELENGTH];
 char fileregp[FILENAMELENGTH];  char fileregp[FILENAMELENGTH];
Line 562  void free_ma3x(double ***m, long nrl, lo Line 573  void free_ma3x(double ***m, long nrl, lo
   free((FREE_ARG)(m+nrl-NR_END));    free((FREE_ARG)(m+nrl-NR_END));
 }  }
   
   /*************** function subdirf ***********/
   char *subdirf(char fileres[])
   {
     /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/"); /* Add to the right */
     strcat(tmpout,fileres);
     return tmpout;
   }
   
   /*************** function subdirf2 ***********/
   char *subdirf2(char fileres[], char *preop)
   {
     
     /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
     strcat(tmpout,preop);
     strcat(tmpout,fileres);
     return tmpout;
   }
   
   /*************** function subdirf3 ***********/
   char *subdirf3(char fileres[], char *preop, char *preop2)
   {
     
     /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
     strcat(tmpout,preop);
     strcat(tmpout,preop2);
     strcat(tmpout,fileres);
     return tmpout;
   }
   
 /***************** f1dim *************************/  /***************** f1dim *************************/
 extern int ncom;   extern int ncom; 
 extern double *pcom,*xicom;  extern double *pcom,*xicom;
Line 1219  double func( double *x) Line 1265  double func( double *x)
           oldm=newm;            oldm=newm;
         } /* end mult */          } /* end mult */
               
         /*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.  
          * 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   
          * 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  
          * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the  
          * 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  
          * -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 less biased than in previous versions.   
          */  
         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  
          * is higher than the multiple of stepm and negative otherwise.  
          */  
         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]));*/  
         /*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 */  
         /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/  
         /*if(lli ==000.0)*/  
         /*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); */  
         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 1270  double func( double *x) Line 1295  double func( double *x)
           oldm=newm;            oldm=newm;
         } /* end mult */          } /* end mult */
               
         /*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.  
          * 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   
          * 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  
          * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the  
          * 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  
          * -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 less biased than in previous versions.   
          */  
         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  
          * is higher than the multiple of stepm and negative otherwise.  
          */  
         /* 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])); /* 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]);*/  
         /*if(lli ==000.0)*/  
         /*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); */  
         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 1459  double funcone( double *x) Line 1464  double funcone( double *x)
   return -l;    return -l;
 }  }
   
 char *subdirf(char fileres[])  
 {  
   /* Caution optionfilefiname is hidden */  
   strcpy(tmpout,optionfilefiname);  
   strcat(tmpout,"/"); /* Add to the right */  
   strcat(tmpout,fileres);  
   return tmpout;  
 }  
   
 char *subdirf2(char fileres[], char *preop)  
 {  
     
   strcpy(tmpout,optionfilefiname);  
   strcat(tmpout,"/");  
   strcat(tmpout,preop);  
   strcat(tmpout,fileres);  
   return tmpout;  
 }  
 char *subdirf3(char fileres[], char *preop, char *preop2)  
 {  
     
   strcpy(tmpout,optionfilefiname);  
   strcat(tmpout,"/");  
   strcat(tmpout,preop);  
   strcat(tmpout,preop2);  
   strcat(tmpout,fileres);  
   return tmpout;  
 }  
   
   /*************** 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 2321  void evsij(char fileres[], double ***eij Line 2299  void evsij(char fileres[], double ***eij
   
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
     /* Computing Variances of health expectancies */      /* Computing  Variances of health expectancies */
   
      for(theta=1; theta <=npar; theta++){       for(theta=1; theta <=npar; theta++){
       for(i=1; i<=npar; i++){         for(i=1; i<=npar; i++){ 
Line 2875  void varprob(char optionfilefiname[], do Line 2853  void varprob(char optionfilefiname[], do
   fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
   fprintf(fichtm,"\n");    fprintf(fichtm,"\n");
   
   fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Computing matrix of variance-covariance of step probabilities</a></h4></li>\n",optionfilehtmcov);    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
   fprintf(fichtmcov,"\n<h4>Computing matrix of variance-covariance of step probabilities</h4>\n\    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
   file %s<br>\n",optionfilehtmcov);    file %s<br>\n",optionfilehtmcov);
   fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
 and drawn. It helps understanding how is the covariance between two incidences.\  and drawn. It helps understanding how is the covariance between two incidences.\
Line 3214  fprintf(fichtm," <ul><li><b>Graphs</b></ Line 3192  fprintf(fichtm," <ul><li><b>Graphs</b></
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      }       }
      for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
        fprintf(fichtm,"<br>- Observed and period prevalence (with confident\         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
 interval) in state (%d): %s%d%d.png <br>\  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
 <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);    <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
      }       }
    } /* end i1 */     } /* end i1 */
Line 3751  int fileappend(FILE *fichier, char *opti Line 3729  int fileappend(FILE *fichier, char *opti
   fflush(fichier);    fflush(fichier);
   return (1);    return (1);
 }  }
   
   
   /**************** 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)
 {  {
   
     /* Wizard to print covariance matrix template */
   
   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 3867  void prwizard(int ncovmodel, int nlstate Line 3850  void prwizard(int ncovmodel, int nlstate
         } /* end k*/          } /* end k*/
       } /*end j */        } /*end j */
     } /* end i */      } /* end i */
   }    } /* end itimes */
   
 } /* end of prwizard */  } /* end of prwizard */
   
Line 3880  int main(int argc, char *argv[]) Line 3863  int main(int argc, char *argv[])
 {  {
   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;
   int jj, 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;
   
     char ca[32], cb[32], cc[32];
   /*  FILE *fichtm; *//* Html File */    /*  FILE *fichtm; *//* Html File */
   /* FILE *ficgp;*/ /*Gnuplot File */    /* FILE *ficgp;*/ /*Gnuplot File */
   double agedeb, agefin,hf;    double agedeb, agefin,hf;
Line 3936  int main(int argc, char *argv[]) Line 3922  int main(int argc, char *argv[])
   
   long total_usecs;    long total_usecs;
     
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
   /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
   (void) gettimeofday(&start_time,&tzp);    (void) gettimeofday(&start_time,&tzp);
   curr_time=start_time;    curr_time=start_time;
Line 4009  int main(int argc, char *argv[]) Line 4001  int main(int argc, char *argv[])
  optionfilext=%s\n\   optionfilext=%s\n\
  optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);   optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   
   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 4586  Title=%s <br>Datafile=%s Firstpass=%d La Line 4578  Title=%s <br>Datafile=%s Firstpass=%d La
   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);  
   strcat(lfileres,"/");  
   strcat(lfileres,optionfilefiname);  
       
   /* 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 4630  Interval (in months) between two waves: Line 4619  Interval (in months) between two waves:
   fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);    fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
   
   jk=1;  
   fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
   fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
   for(i=1,jk=1; i <=nlstate; i++){    for(i=1,jk=1; i <=nlstate; i++){
     for(k=1; k <=(nlstate+ndeath); k++){      for(k=1; k <=(nlstate+ndeath); k++){
       if (k != i)         if (k != i) {
         {          printf("%d%d ",i,k);
           printf("%d%d ",i,k);          fprintf(ficlog,"%d%d ",i,k);
           fprintf(ficlog,"%d%d ",i,k);          fprintf(ficres,"%1d%1d ",i,k);
           fprintf(ficres,"%1d%1d ",i,k);          for(j=1; j <=ncovmodel; j++){
           for(j=1; j <=ncovmodel; j++){            printf("%f ",p[jk]);
             printf("%f ",p[jk]);            fprintf(ficlog,"%f ",p[jk]);
             fprintf(ficlog,"%f ",p[jk]);            fprintf(ficres,"%f ",p[jk]);
             fprintf(ficres,"%f ",p[jk]);            jk++; 
             jk++;   
           }  
           printf("\n");  
           fprintf(ficlog,"\n");  
           fprintf(ficres,"\n");  
         }          }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
     }      }
   }    }
   if(mle!=0){    if(mle!=0){
Line 4681  Interval (in months) between two waves: Line 4668  Interval (in months) between two waves:
   }    }
         
   fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");    fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
   if(mle==1)    if(mle>=1)
     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");      printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
   fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");    fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
   for(i=1,k=1;i<=npar;i++){  /* # 121 Var(a12)\n\ */
     /*  if (k>nlstate) k=1;  /* # 122 Cov(b12,a12) Var(b12)\n\ */
         i1=(i-1)/(ncovmodel*nlstate)+1;   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
         fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);  /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
         printf("%s%d%d",alph[k],i1,tab[i]);  /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
     */  /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
     fprintf(ficres,"%3d",i);  /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
     if(mle==1)  /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       printf("%3d",i);  
     fprintf(ficlog,"%3d",i);  
     for(j=1; j<=i;j++){  /* Just to have a covariance matrix which will be more understandable
       fprintf(ficres," %.5e",matcov[i][j]);     even is we still don't want to manage dictionary of variables
       if(mle==1)  */
         printf(" %.5e",matcov[i][j]);    for(itimes=1;itimes<=2;itimes++){
       fprintf(ficlog," %.5e",matcov[i][j]);      jj=0;
     }      for(i=1; i <=nlstate; i++){
     fprintf(ficres,"\n");        for(j=1; j <=nlstate+ndeath; j++){
     if(mle==1)          if(j==i) continue;
       printf("\n");          for(k=1; k<=ncovmodel;k++){
     fprintf(ficlog,"\n");            jj++;
     k++;            ca[0]= k+'a'-1;ca[1]='\0';
   }            if(itimes==1){
                  if(mle>=1)
                 printf("#%1d%1d%d",i,j,k);
               fprintf(ficlog,"#%1d%1d%d",i,j,k);
               fprintf(ficres,"#%1d%1d%d",i,j,k);
             }else{
               if(mle>=1)
                 printf("%1d%1d%d",i,j,k);
               fprintf(ficlog,"%1d%1d%d",i,j,k);
               fprintf(ficres,"%1d%1d%d",i,j,k);
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         if(mle>=1)
                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         if(mle>=1)
                           printf(" %.5e",matcov[jj][ll]); 
                         fprintf(ficlog," %.5e",matcov[jj][ll]); 
                         fprintf(ficres," %.5e",matcov[jj][ll]); 
                       }
                     }else{
                       if(itimes==1){
                         if(mle>=1)
                           printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         if(mle>=1)
                           printf(" %.5e",matcov[jj][ll]); 
                         fprintf(ficlog," %.5e",matcov[jj][ll]); 
                         fprintf(ficres," %.5e",matcov[jj][ll]); 
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             if(mle>=1)
               printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
     fflush(ficlog);
     fflush(ficres);
   
   while((c=getc(ficpar))=='#' && c!= EOF){    while((c=getc(ficpar))=='#' && c!= EOF){
     ungetc(c,ficpar);      ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);      fgets(line, MAXLINE, ficpar);
Line 5117  ageminpar, agemax, s[lastpass][imx], age Line 5163  ageminpar, agemax, s[lastpass][imx], age
       
   
   if((nberr >0) || (nbwarn>0)){    if((nberr >0) || (nbwarn>0)){
     printf("End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);      printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
     fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);      fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
   }else{    }else{
     printf("End of Imach\n");      printf("End of Imach\n");
Line 5129  ageminpar, agemax, s[lastpass][imx], age Line 5175  ageminpar, agemax, s[lastpass][imx], age
   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));
   
   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);
Removed from v.1.93  
changed lines
  Added in v.1.95

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