Diff for /imach/src/imach.c between versions 1.155 and 1.165

version 1.155, 2014/08/25 18:32:34 version 1.165, 2014/12/16 11:20:36
Line 1 Line 1
 /* $Id$  /* $Id$
   $State$    $State$
   $Log$    $Log$
     Revision 1.165  2014/12/16 11:20:36  brouard
     Summary: After compiling on Visual C
   
     * imach.c (Module): Merging 1.61 to 1.162
   
     Revision 1.164  2014/12/16 10:52:11  brouard
     Summary: Merging with Visual C after suppressing some warnings for unused variables. Also fixing Saito's bug 0.98Xn
   
     * imach.c (Module): Merging 1.61 to 1.162
   
     Revision 1.163  2014/12/16 10:30:11  brouard
     * imach.c (Module): Merging 1.61 to 1.162
   
     Revision 1.162  2014/09/25 11:43:39  brouard
     Summary: temporary backup 0.99!
   
     Revision 1.1  2014/09/16 11:06:58  brouard
     Summary: With some code (wrong) for nlopt
   
     Author:
   
     Revision 1.161  2014/09/15 20:41:41  brouard
     Summary: Problem with macro SQR on Intel compiler
   
     Revision 1.160  2014/09/02 09:24:05  brouard
     *** empty log message ***
   
     Revision 1.159  2014/09/01 10:34:10  brouard
     Summary: WIN32
     Author: Brouard
   
     Revision 1.158  2014/08/27 17:11:51  brouard
     *** empty log message ***
   
     Revision 1.157  2014/08/27 16:26:55  brouard
     Summary: Preparing windows Visual studio version
     Author: Brouard
   
     In order to compile on Visual studio, time.h is now correct and time_t
     and tm struct should be used. difftime should be used but sometimes I
     just make the differences in raw time format (time(&now).
     Trying to suppress #ifdef LINUX
     Add xdg-open for __linux in order to open default browser.
   
     Revision 1.156  2014/08/25 20:10:10  brouard
     *** empty log message ***
   
   Revision 1.155  2014/08/25 18:32:34  brouard    Revision 1.155  2014/08/25 18:32:34  brouard
   Summary: New compile, minor changes    Summary: New compile, minor changes
   Author: Brouard    Author: Brouard
Line 455 Line 502
  end   end
 */  */
   
   #define POWELL /* Instead of NLOPT */
   
   
    
 #include <math.h>  #include <math.h>
 #include <stdio.h>  #include <stdio.h>
 #include <stdlib.h>  #include <stdlib.h>
 #include <string.h>  #include <string.h>
   
   #ifdef _WIN32
   #include <io.h>
   #else
 #include <unistd.h>  #include <unistd.h>
   #endif
   
 #include <limits.h>  #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>
 extern int errno;  /* extern int errno; */
   
   /* #ifdef LINUX */
   /* #include <time.h> */
   /* #include "timeval.h" */
   /* #else */
   /* #include <sys/time.h> */
   /* #endif */
   
 #ifdef LINUX  
 #include <time.h>  #include <time.h>
 #include "timeval.h"  
 #else  
 #include <sys/time.h>  
 #endif  
   
 #ifdef GSL  #ifdef GSL
 #include <gsl/gsl_errno.h>  #include <gsl/gsl_errno.h>
 #include <gsl/gsl_multimin.h>  #include <gsl/gsl_multimin.h>
 #endif  #endif
   
   #ifdef NLOPT
   #include <nlopt.h>
   typedef struct {
     double (* function)(double [] );
   } myfunc_data ;
   #endif
   
 /* #include <libintl.h> */  /* #include <libintl.h> */
 /* #define _(String) gettext (String) */  /* #define _(String) gettext (String) */
   
Line 506  extern int errno; Line 566  extern int errno;
 #define YEARM 12. /**< Number of months per year */  #define YEARM 12. /**< Number of months per year */
 #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 _WIN32
 #define DIRSEPARATOR '/'  
 #define CHARSEPARATOR "/"  
 #define ODIRSEPARATOR '\\'  
 #else  
 #define DIRSEPARATOR '\\'  #define DIRSEPARATOR '\\'
 #define CHARSEPARATOR "\\"  #define CHARSEPARATOR "\\"
 #define ODIRSEPARATOR '/'  #define ODIRSEPARATOR '/'
   #else
   #define DIRSEPARATOR '/'
   #define CHARSEPARATOR "/"
   #define ODIRSEPARATOR '\\'
 #endif  #endif
   
 /* $Id$ */  /* $Id$ */
 /* $State$ */  /* $State$ */
   
 char version[]="Imach version 0.98nV, August 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";  char version[]="Imach version 0.99, September 2014,INED-EUROREVES-Institut de longevite-Japan Society for the Promotion of Science (Grant-in-Aid for Scientific Research 25293121)";
 char fullversion[]="$Revision$ $Date$";   char fullversion[]="$Revision$ $Date$"; 
 char strstart[80];  char strstart[80];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH];  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
Line 551  int **mw; /* mw[mi][i] is number of the Line 611  int **mw; /* mw[mi][i] is number of the
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
            * wave mi and wave mi+1 is not an exact multiple of stepm. */             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   int countcallfunc=0;  /* Count the number of calls to func */
 double jmean=1; /* Mean space between 2 waves */  double jmean=1; /* Mean space between 2 waves */
 double **matprod2(); /* test */  double **matprod2(); /* test */
 double **oldm, **newm, **savm; /* Working pointers to matrices */  double **oldm, **newm, **savm; /* Working pointers to matrices */
Line 594  char popfile[FILENAMELENGTH]; Line 655  char popfile[FILENAMELENGTH];
   
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   
 struct timeval start_time, end_time, curr_time, last_time, forecast_time;  /* struct timeval start_time, end_time, curr_time, last_time, forecast_time; */
 struct timezone tzp;  /* struct timezone tzp; */
 extern int gettimeofday();  /* extern int gettimeofday(); */
 struct tm tmg, tm, tmf, *gmtime(), *localtime();  struct tm tml, *gmtime(), *localtime();
 long time_value;  
 extern long time();  extern time_t time();
   
   struct tm start_time, end_time, curr_time, last_time, forecast_time;
   time_t  rstart_time, rend_time, rcurr_time, rlast_time, rforecast_time; /* raw time */
   struct tm tm;
   
 char strcurr[80], strfor[80];  char strcurr[80], strfor[80];
   
 char *endptr;  char *endptr;
Line 754  char *cutl(char *blocc, char *alocc, cha Line 820  char *cutl(char *blocc, char *alocc, cha
      gives blocc="abcdef2ghi" and alocc="j".       gives blocc="abcdef2ghi" and alocc="j".
      If occ is not found blocc is null and alocc is equal to in. Returns blocc       If occ is not found blocc is null and alocc is equal to in. Returns blocc
   */    */
   char *s, *t, *bl;    char *s, *t;
   t=in;s=in;    t=in;s=in;
   while ((*in != occ) && (*in != '\0')){    while ((*in != occ) && (*in != '\0')){
     *alocc++ = *in++;      *alocc++ = *in++;
Line 838  int nbocc(char *s, char occ) Line 904  int nbocc(char *s, char occ)
 /*   } */  /*   } */
 /* } */  /* } */
   
   #ifdef _WIN32
   char * strsep(char **pp, const char *delim)
   {
     char *p, *q;
            
     if ((p = *pp) == NULL)
       return 0;
     if ((q = strpbrk (p, delim)) != NULL)
     {
       *pp = q + 1;
       *q = '\0';
     }
     else
       *pp = 0;
     return p;
   }
   #endif
   
 /********************** nrerror ********************/  /********************** nrerror ********************/
   
 void nrerror(char error_text[])  void nrerror(char error_text[])
Line 1037  char *subdirf3(char fileres[], char *pre Line 1121  char *subdirf3(char fileres[], char *pre
   return tmpout;    return tmpout;
 }  }
   
   char *asc_diff_time(long time_sec, char ascdiff[])
   {
     long sec_left, days, hours, minutes;
     days = (time_sec) / (60*60*24);
     sec_left = (time_sec) % (60*60*24);
     hours = (sec_left) / (60*60) ;
     sec_left = (sec_left) %(60*60);
     minutes = (sec_left) /60;
     sec_left = (sec_left) % (60);
     sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);  
     return ascdiff;
   }
   
 /***************** f1dim *************************/  /***************** f1dim *************************/
 extern int ncom;   extern int ncom; 
 extern double *pcom,*xicom;  extern double *pcom,*xicom;
Line 1060  double brent(double ax, double bx, doubl Line 1157  double brent(double ax, double bx, doubl
 {   { 
   int iter;     int iter; 
   double a,b,d,etemp;    double a,b,d,etemp;
   double fu,fv,fw,fx;    double fu=0,fv,fw,fx;
   double ftemp;    double ftemp=0.;
   double p,q,r,tol1,tol2,u,v,w,x,xm;     double p,q,r,tol1,tol2,u,v,w,x,xm; 
   double e=0.0;     double e=0.0; 
     
Line 1075  double brent(double ax, double bx, doubl Line 1172  double brent(double ax, double bx, doubl
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     printf(".");fflush(stdout);      printf(".");fflush(stdout);
     fprintf(ficlog,".");fflush(ficlog);      fprintf(ficlog,".");fflush(ficlog);
 #ifdef DEBUG  #ifdef DEBUGBRENT
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
Line 1145  void mnbrak(double *ax, double *bx, doub Line 1242  void mnbrak(double *ax, double *bx, doub
       }         } 
   *cx=(*bx)+GOLD*(*bx-*ax);     *cx=(*bx)+GOLD*(*bx-*ax); 
   *fc=(*func)(*cx);     *fc=(*func)(*cx); 
   while (*fb > *fc) {     while (*fb > *fc) { /* Declining fa, fb, fc */
     r=(*bx-*ax)*(*fb-*fc);       r=(*bx-*ax)*(*fb-*fc); 
     q=(*bx-*cx)*(*fb-*fa);       q=(*bx-*cx)*(*fb-*fa); 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/       u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));         (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); /* Minimum abscisse of a parabolic estimated from (a,fa), (b,fb) and (c,fc). */
     ulim=(*bx)+GLIMIT*(*cx-*bx);       ulim=(*bx)+GLIMIT*(*cx-*bx); /* Maximum abscisse where function can be evaluated */
     if ((*bx-u)*(u-*cx) > 0.0) {       if ((*bx-u)*(u-*cx) > 0.0) { /* if u between b and c */
       fu=(*func)(u);         fu=(*func)(u); 
     } else if ((*cx-u)*(u-ulim) > 0.0) {   #ifdef DEBUG
         /* f(x)=A(x-u)**2+f(u) */
         double A, fparabu; 
         A= (*fb - *fa)/(*bx-*ax)/(*bx+*ax-2*u);
         fparabu= *fa - A*(*ax-u)*(*ax-u);
         printf("mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
         fprintf(ficlog, "mnbrak (*ax=%.12f, *fa=%.12lf), (*bx=%.12f, *fb=%.12lf), (*cx=%.12f, *fc=%.12lf),  (*u=%.12f, fu=%.12lf, fparabu=%.12f)\n",*ax,*fa,*bx,*fb,*cx,*fc,u,fu, fparabu);
   #endif 
       } else if ((*cx-u)*(u-ulim) > 0.0) { /* u is after c but before ulim */
       fu=(*func)(u);         fu=(*func)(u); 
       if (fu < *fc) {         if (fu < *fc) { 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))           SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
           SHFT(*fb,*fc,fu,(*func)(u))             SHFT(*fb,*fc,fu,(*func)(u)) 
           }             } 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {       } else if ((u-ulim)*(ulim-*cx) >= 0.0) { /* u outside ulim (verifying that ulim is beyond c) */
       u=ulim;         u=ulim; 
       fu=(*func)(u);         fu=(*func)(u); 
     } else {       } else { 
Line 1172  void mnbrak(double *ax, double *bx, doub Line 1277  void mnbrak(double *ax, double *bx, doub
 }   } 
   
 /*************** linmin ************************/  /*************** linmin ************************/
   /* Given an n -dimensional point p[1..n] and an n -dimensional direction xi[1..n] , moves and
   resets p to where the function func(p) takes on a minimum along the direction xi from p ,
   and replaces xi by the actual vector displacement that p was moved. Also returns as fret
   the value of func at the returned location p . This is actually all accomplished by calling the
   routines mnbrak and brent .*/
 int ncom;   int ncom; 
 double *pcom,*xicom;  double *pcom,*xicom;
 double (*nrfunc)(double []);   double (*nrfunc)(double []); 
Line 1198  void linmin(double p[], double xi[], int Line 1307  void linmin(double p[], double xi[], int
   }     } 
   ax=0.0;     ax=0.0; 
   xx=1.0;     xx=1.0; 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);     mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); /* Find a bracket a,x,b in direction n=xi ie xicom */
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);     *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); /* Find a minimum P+lambda n in that direction (lambdamin), with TOL between abscisses */
 #ifdef DEBUG  #ifdef DEBUG
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
Line 1212  void linmin(double p[], double xi[], int Line 1321  void linmin(double p[], double xi[], int
   free_vector(pcom,1,n);     free_vector(pcom,1,n); 
 }   } 
   
 char *asc_diff_time(long time_sec, char ascdiff[])  
 {  
   long sec_left, days, hours, minutes;  
   days = (time_sec) / (60*60*24);  
   sec_left = (time_sec) % (60*60*24);  
   hours = (sec_left) / (60*60) ;  
   sec_left = (sec_left) %(60*60);  
   minutes = (sec_left) /60;  
   sec_left = (sec_left) % (60);  
   sprintf(ascdiff,"%ld day(s) %ld hour(s) %ld minute(s) %ld second(s)",days, hours, minutes, sec_left);    
   return ascdiff;  
 }  
   
 /*************** powell ************************/  /*************** powell ************************/
   /*
   Minimization of a function func of n variables. Input consists of an initial starting point
   p[1..n] ; an initial matrix xi[1..n][1..n] , whose columns contain the initial set of di-
   rections (usually the n unit vectors); and ftol , the fractional tolerance in the function value
   such that failure to decrease by more than this amount on one iteration signals doneness. On
   output, p is set to the best point found, xi is the then-current direction set, fret is the returned
   function value at p , and iter is the number of iterations taken. The routine linmin is used.
    */
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,   void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
             double (*func)(double []))               double (*func)(double [])) 
 {   { 
Line 1243  void powell(double p[], double **xi, int Line 1348  void powell(double p[], double **xi, int
   xits=vector(1,n);     xits=vector(1,n); 
   *fret=(*func)(p);     *fret=(*func)(p); 
   for (j=1;j<=n;j++) pt[j]=p[j];     for (j=1;j<=n;j++) pt[j]=p[j]; 
       rcurr_time = time(NULL);  
   for (*iter=1;;++(*iter)) {     for (*iter=1;;++(*iter)) { 
     fp=(*fret);       fp=(*fret); 
     ibig=0;       ibig=0; 
     del=0.0;       del=0.0; 
     last_time=curr_time;      rlast_time=rcurr_time;
     (void) gettimeofday(&curr_time,&tzp);      /* (void) gettimeofday(&curr_time,&tzp); */
     printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);      rcurr_time = time(NULL);  
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec); fflush(ficlog);      curr_time = *localtime(&rcurr_time);
 /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, rcurr_time-rlast_time, rcurr_time-rstart_time);fflush(stdout);
       fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret,rcurr_time-rlast_time, rcurr_time-rstart_time); fflush(ficlog);
   /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tm_sec-start_time.tm_sec); */
    for (i=1;i<=n;i++) {     for (i=1;i<=n;i++) {
       printf(" %d %.12f",i, p[i]);        printf(" %d %.12f",i, p[i]);
       fprintf(ficlog," %d %.12lf",i, p[i]);        fprintf(ficlog," %d %.12lf",i, p[i]);
Line 1261  void powell(double p[], double **xi, int Line 1369  void powell(double p[], double **xi, int
     fprintf(ficlog,"\n");      fprintf(ficlog,"\n");
     fprintf(ficrespow,"\n");fflush(ficrespow);      fprintf(ficrespow,"\n");fflush(ficrespow);
     if(*iter <=3){      if(*iter <=3){
       tm = *localtime(&curr_time.tv_sec);        tml = *localtime(&rcurr_time);
       strcpy(strcurr,asctime(&tm));        strcpy(strcurr,asctime(&tml));
 /*       asctime_r(&tm,strcurr); */        rforecast_time=rcurr_time; 
       forecast_time=curr_time;   
       itmp = strlen(strcurr);        itmp = strlen(strcurr);
       if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */        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 the last iteration #%d: %ld seconds,\n",*iter,rcurr_time-rlast_time);
       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,rcurr_time-rlast_time);
       for(niterf=10;niterf<=30;niterf+=10){        for(niterf=10;niterf<=30;niterf+=10){
         forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);          rforecast_time=rcurr_time+(niterf-*iter)*(rcurr_time-rlast_time);
         tmf = *localtime(&forecast_time.tv_sec);          forecast_time = *localtime(&rforecast_time);
 /*      asctime_r(&tmf,strfor); */          strcpy(strfor,asctime(&forecast_time));
         strcpy(strfor,asctime(&tmf));  
         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 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);          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(rforecast_time-rcurr_time,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);          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(rforecast_time-rcurr_time,tmpout),strfor,strcurr);
       }        }
     }      }
     for (i=1;i<=n;i++) {       for (i=1;i<=n;i++) { 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];         for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       fptt=(*fret);         fptt=(*fret); 
 #ifdef DEBUG  #ifdef DEBUG
       printf("fret=%lf \n",*fret);            printf("fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
       fprintf(ficlog,"fret=%lf \n",*fret);            fprintf(ficlog, "fret=%lf, %lf, %lf \n", *fret, *fret, *fret);
 #endif  #endif
       printf("%d",i);fflush(stdout);        printf("%d",i);fflush(stdout);
       fprintf(ficlog,"%d",i);fflush(ficlog);        fprintf(ficlog,"%d",i);fflush(ficlog);
Line 1305  void powell(double p[], double **xi, int Line 1411  void powell(double p[], double **xi, int
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       }        }
       for(j=1;j<=n;j++) {        for(j=1;j<=n;j++) {
         printf(" p=%.12e",p[j]);          printf(" p(%d)=%.12e",j,p[j]);
         fprintf(ficlog," p=%.12e",p[j]);          fprintf(ficlog," p(%d)=%.12e",j,p[j]);
       }        }
       printf("\n");        printf("\n");
       fprintf(ficlog,"\n");        fprintf(ficlog,"\n");
 #endif  #endif
     }       } /* end i */
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
 #ifdef DEBUG  #ifdef DEBUG
       int k[2],l;        int k[2],l;
Line 1344  void powell(double p[], double **xi, int Line 1450  void powell(double p[], double **xi, int
       return;         return; 
     }       } 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");       if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     for (j=1;j<=n;j++) {       for (j=1;j<=n;j++) { /* Computes an extrapolated point */
       ptt[j]=2.0*p[j]-pt[j];         ptt[j]=2.0*p[j]-pt[j]; 
       xit[j]=p[j]-pt[j];         xit[j]=p[j]-pt[j]; 
       pt[j]=p[j];         pt[j]=p[j]; 
     }       } 
     fptt=(*func)(ptt);       fptt=(*func)(ptt); 
     if (fptt < fp) {       if (fptt < fp) { /* If extrapolated point is better, decide if we keep that new direction or not */
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);         /* (x1 f1=fp), (x2 f2=*fret), (x3 f3=fptt), (xm fm) */
       if (t < 0.0) {         /* From x1 (P0) distance of x2 is at h and x3 is 2h */
         linmin(p,xit,n,fret,func);         /* Let f"(x2) be the 2nd derivative equal everywhere.  */
         /* Then the parabolic through (x1,f1), (x2,f2) and (x3,f3) */
         /* will reach at f3 = fm + h^2/2 f"m  ; f" = (f1 -2f2 +f3 ) / h**2 */
         /* f1-f3 = delta(2h) = 2 h**2 f'' = 2(f1- 2f2 +f3) */
         /* Thus we compare delta(2h) with observed f1-f3 */
         /* or best gain on one ancient line 'del' with total  */
         /* gain f1-f2 = f1 - f2 - 'del' with del  */
         /* t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); */
   
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del);
         t= t- del*SQR(fp-fptt);
         printf("t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
         fprintf(ficlog,"t1= %.12lf, t2= %.12lf, t=%.12lf\n", 2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del),del*SQR(fp-fptt),t);
   #ifdef DEBUG
         printf("t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
                (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
         fprintf(ficlog,"t3= %.12lf, t4= %.12lf, t3*= %.12lf, t4*= %.12lf\n",SQR(fp-(*fret)-del),SQR(fp-fptt),
                (fp-(*fret)-del)*(fp-(*fret)-del),(fp-fptt)*(fp-fptt));
         printf("tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
         fprintf(ficlog, "tt= %.12lf, t=%.12lf\n",2.0*(fp-2.0*(*fret)+fptt)*(fp-(*fret)-del)*(fp-(*fret)-del)-del*(fp-fptt)*(fp-fptt),t);
   #endif
         if (t < 0.0) { /* Then we use it for last direction */
           linmin(p,xit,n,fret,func); /* computes mean on the extrapolated direction.*/
         for (j=1;j<=n;j++) {           for (j=1;j<=n;j++) { 
           xi[j][ibig]=xi[j][n];             xi[j][ibig]=xi[j][n]; /* Replace the direction with biggest decrease by n */
           xi[j][n]=xit[j];             xi[j][n]=xit[j];      /* and nth direction by the extrapolated */
         }          }
           printf("Gaining to use average direction of P0 P%d instead of biggest increase direction %d :\n",n,ibig);
           fprintf(ficlog,"Gaining to use average direction of P0 P%d instead of biggest increase direction :\n",n,ibig);
   
 #ifdef DEBUG  #ifdef DEBUG
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
Line 1368  void powell(double p[], double **xi, int Line 1499  void powell(double p[], double **xi, int
         printf("\n");          printf("\n");
         fprintf(ficlog,"\n");          fprintf(ficlog,"\n");
 #endif  #endif
       }        } /* end of t negative */
     }       } /* end if (fptt < fp)  */
   }     } 
 }   } 
   
Line 1457  double **pmij(double **ps, double *cov, Line 1588  double **pmij(double **ps, double *cov,
   */    */
   double s1, lnpijopii;    double s1, lnpijopii;
   /*double t34;*/    /*double t34;*/
   int i,j,j1, nc, ii, jj;    int i,j, nc, ii, jj;
   
     for(i=1; i<= nlstate; i++){      for(i=1; i<= nlstate; i++){
       for(j=1; j<i;j++){        for(j=1; j<i;j++){
Line 1599  double ***hpxij(double ***po, int nhstep Line 1730  double ***hpxij(double ***po, int nhstep
   return po;    return po;
 }  }
   
   #ifdef NLOPT
     double  myfunc(unsigned n, const double *p1, double *grad, void *pd){
     double fret;
     double *xt;
     int j;
     myfunc_data *d2 = (myfunc_data *) pd;
   /* xt = (p1-1); */
     xt=vector(1,n); 
     for (j=1;j<=n;j++)   xt[j]=p1[j-1]; /* xt[1]=p1[0] */
   
     fret=(d2->function)(xt); /*  p xt[1]@8 is fine */
     /* fret=(*func)(xt); /\*  p xt[1]@8 is fine *\/ */
     printf("Function = %.12lf ",fret);
     for (j=1;j<=n;j++) printf(" %d %.8lf", j, xt[j]); 
     printf("\n");
    free_vector(xt,1,n);
     return fret;
   }
   #endif
   
 /*************** log-likelihood *************/  /*************** log-likelihood *************/
 double func( double *x)  double func( double *x)
Line 1617  double func( double *x) Line 1767  double func( double *x)
   /*for(i=1;i<imx;i++)     /*for(i=1;i<imx;i++) 
     printf(" %d\n",s[4][i]);      printf(" %d\n",s[4][i]);
   */    */
   
     ++countcallfunc;
   
   cov[1]=1.;    cov[1]=1.;
   
   for(k=1; k<=nlstate; k++) ll[k]=0.;    for(k=1; k<=nlstate; k++) ll[k]=0.;
Line 1998  void likelione(FILE *ficres,double p[], Line 2151  void likelione(FILE *ficres,double p[],
   
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
 {  {
   int i,j, iter;    int i,j, iter=0;
   double **xi;    double **xi;
   double fret;    double fret;
   double fretone; /* Only one call to likelihood */    double fretone; /* Only one call to likelihood */
   /*  char filerespow[FILENAMELENGTH];*/    /*  char filerespow[FILENAMELENGTH];*/
   
   #ifdef NLOPT
     int creturn;
     nlopt_opt opt;
     /* double lb[9] = { -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL, -HUGE_VAL }; /\* lower bounds *\/ */
     double *lb;
     double minf; /* the minimum objective value, upon return */
     double * p1; /* Shifted parameters from 0 instead of 1 */
     myfunc_data dinst, *d = &dinst;
   #endif
   
   
   xi=matrix(1,npar,1,npar);    xi=matrix(1,npar,1,npar);
   for (i=1;i<=npar;i++)    for (i=1;i<=npar;i++)
     for (j=1;j<=npar;j++)      for (j=1;j<=npar;j++)
Line 2019  void mlikeli(FILE *ficres,double p[], in Line 2184  void mlikeli(FILE *ficres,double p[], in
     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");
   #ifdef POWELL
   powell(p,xi,npar,ftol,&iter,&fret,func);    powell(p,xi,npar,ftol,&iter,&fret,func);
   #endif
   
   #ifdef NLOPT
   #ifdef NEWUOA
     opt = nlopt_create(NLOPT_LN_NEWUOA,npar);
   #else
     opt = nlopt_create(NLOPT_LN_BOBYQA,npar);
   #endif
     lb=vector(0,npar-1);
     for (i=0;i<npar;i++) lb[i]= -HUGE_VAL;
     nlopt_set_lower_bounds(opt, lb);
     nlopt_set_initial_step1(opt, 0.1);
     
     p1= (p+1); /*  p *(p+1)@8 and p *(p1)@8 are equal p1[0]=p[1] */
     d->function = func;
     printf(" Func %.12lf \n",myfunc(npar,p1,NULL,d));
     nlopt_set_min_objective(opt, myfunc, d);
     nlopt_set_xtol_rel(opt, ftol);
     if ((creturn=nlopt_optimize(opt, p1, &minf)) < 0) {
       printf("nlopt failed! %d\n",creturn); 
     }
     else {
       printf("found minimum after %d evaluations (NLOPT=%d)\n", countcallfunc ,NLOPT);
       printf("found minimum at f(%g,%g) = %0.10g\n", p[0], p[1], minf);
       iter=1; /* not equal */
     }
     nlopt_destroy(opt);
   #endif
   free_matrix(xi,1,npar,1,npar);    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 & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    fprintf(ficlog,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    fprintf(ficres,"\n#Number of iterations & function calls = %d & %d, -2 Log likelihood = %.12f\n",iter, countcallfunc,func(p));
   
 }  }
   
Line 2035  void hesscov(double **matcov, double p[] Line 2227  void hesscov(double **matcov, double p[]
 {  {
   double  **a,**y,*x,pd;    double  **a,**y,*x,pd;
   double **hess;    double **hess;
   int i, j,jk;    int i, j;
   int *indx;    int *indx;
   
   double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
Line 2169  double hessii(double x[], double delta, Line 2361  double hessii(double x[], double delta,
         k=kmax;          k=kmax;
       }        }
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
         k=kmax; l=lmax*10.;          k=kmax; l=lmax*10;
       }        }
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){         else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
         delts=delt;          delts=delt;
Line 2184  double hessii(double x[], double delta, Line 2376  double hessii(double x[], double delta,
 double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
 {  {
   int i;    int i;
   int l=1, l1, lmax=20;    int l=1, lmax=20;
   double k1,k2,k3,k4,res,fx;    double k1,k2,k3,k4,res,fx;
   double p2[MAXPARM+1];    double p2[MAXPARM+1];
   int k;    int k;
Line 2299  void pstamp(FILE *fichier) Line 2491  void pstamp(FILE *fichier)
 void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
 {  /* Some frequencies */  {  /* Some frequencies */
       
   int i, m, jk, k1,i1, j1, bool, z1,j;    int i, m, jk, j1, bool, z1,j;
   int first;    int first;
   double ***freq; /* Frequencies */    double ***freq; /* Frequencies */
   double *pp, **prop;    double *pp, **prop;
Line 2480  void prevalence(double ***probs, double Line 2672  void prevalence(double ***probs, double
      We still use firstpass and lastpass as another selection.       We still use firstpass and lastpass as another selection.
   */    */
     
   int i, m, jk, k1, i1, j1, bool, z1,j;    int i, m, jk, j1, bool, z1,j;
   double ***freq; /* Frequencies */  
   double *pp, **prop;    double **prop;
   double pos,posprop;     double posprop; 
   double  y2; /* in fractional years */    double  y2; /* in fractional years */
   int iagemin, iagemax;    int iagemin, iagemax;
   int first; /** to stop verbosity which is redirected to log file */    int first; /** to stop verbosity which is redirected to log file */
Line 2574  void  concatwav(int wav[], int **dh, int Line 2766  void  concatwav(int wav[], int **dh, int
   int j, k=0,jk, ju, jl;    int j, k=0,jk, ju, jl;
   double sum=0.;    double sum=0.;
   first=0;    first=0;
   jmin=1e+5;    jmin=100000;
   jmax=-1;    jmax=-1;
   jmean=0.;    jmean=0.;
   for(i=1; i<=imx; i++){    for(i=1; i<=imx; i++){
Line 2814  void evsij(double ***eij, double x[], in Line 3006  void evsij(double ***eij, double x[], in
   
 {  {
   /* Health expectancies, no variances */    /* Health expectancies, no variances */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;    int i, j, nhstepm, hstepm, h, nstepm;
   int nhstepma, nstepma; /* Decreasing with age */    int nhstepma, nstepma; /* Decreasing with age */
   double age, agelim, hf;    double age, agelim, hf;
   double ***p3mat;    double ***p3mat;
Line 3136  void varevsij(char optionfilefiname[], d Line 3328  void varevsij(char optionfilefiname[], d
   double **dnewm,**doldm;    double **dnewm,**doldm;
   double **dnewmp,**doldmp;    double **dnewmp,**doldmp;
   int i, j, nhstepm, hstepm, h, nstepm ;    int i, j, nhstepm, hstepm, h, nstepm ;
   int k, cptcode;    int k;
   double *xp;    double *xp;
   double **gp, **gm;  /* for var eij */    double **gp, **gm;  /* for var eij */
   double ***gradg, ***trgradg; /*for var eij */    double ***gradg, ***trgradg; /*for var eij */
Line 3436  void varprevlim(char fileres[], double * Line 3628  void varprevlim(char fileres[], double *
 {  {
   /* Variance of prevalence limit */    /* Variance of prevalence limit */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   double **newm;  
   double **dnewm,**doldm;    double **dnewm,**doldm;
   int i, j, nhstepm, hstepm;    int i, j, nhstepm, hstepm;
   int k, cptcode;  
   double *xp;    double *xp;
   double *gp, *gm;    double *gp, *gm;
   double **gradg, **trgradg;    double **gradg, **trgradg;
Line 3518  void varprevlim(char fileres[], double * Line 3709  void varprevlim(char fileres[], double *
 /************ Variance of one-step probabilities  ******************/  /************ Variance of one-step probabilities  ******************/
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
 {  {
   int i, j=0,  i1, k1, l1, t, tj;    int i, j=0,  k1, l1, tj;
   int k2, l2, j1,  z1;    int k2, l2, j1,  z1;
   int k=0,l, cptcode;    int k=0, l;
   int first=1, first1, first2;    int first=1, first1, first2;
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   double **dnewm,**doldm;    double **dnewm,**doldm;
Line 3528  void varprob(char optionfilefiname[], do Line 3719  void varprob(char optionfilefiname[], do
   double *gp, *gm;    double *gp, *gm;
   double **gradg, **trgradg;    double **gradg, **trgradg;
   double **mu;    double **mu;
   double age,agelim, cov[NCOVMAX+1];    double age, cov[NCOVMAX+1];
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   int theta;    int theta;
   char fileresprob[FILENAMELENGTH];    char fileresprob[FILENAMELENGTH];
Line 3900  fprintf(fichtm," \n<ul><li><b>Graphs</b> Line 4091  fprintf(fichtm," \n<ul><li><b>Graphs</b>
 <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);   <img src=\"%s%d_2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
        /* Period (stable) prevalence in each health state */         /* Period (stable) prevalence in each health state */
        for(cpt=1; cpt<=nlstate;cpt++){         for(cpt=1; cpt<=nlstate;cpt++){
          fprintf(fichtm,"<br>- Convergence from each state (1 to %d) to period (stable) prevalence in state %d <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \           fprintf(fichtm,"<br>- Convergence from cross-sectional prevalence in each state (1 to %d) to period (stable) prevalence in specific state %d <a href=\"%s%d_%d.png\">%s%d_%d.png</a><br> \
 <img src=\"%s%d_%d.png\">",nlstate, cpt, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);  <img src=\"%s%d_%d.png\">",nlstate, cpt, subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
        }         }
      for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
Line 3986  true period expectancies (those weighted Line 4177  true period expectancies (those weighted
 void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
   char dirfileres[132],optfileres[132];    char dirfileres[132],optfileres[132];
   int m0,cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;    int cpt=0,k1=0,i=0,k=0,j=0,jk=0,k2=0,k3=0,ij=0,l=0;
   int ng=0;    int ng=0;
 /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
 /*     printf("Problem with file %s",optionfilegnuplot); */  /*     printf("Problem with file %s",optionfilegnuplot); */
Line 4172  plot [%.f:%.f]  ", ageminpar, agemaxpar) Line 4363  plot [%.f:%.f]  ", ageminpar, agemaxpar)
        } /* end k2 */         } /* end k2 */
      } /* end jk */       } /* end jk */
    } /* end ng */     } /* end ng */
  avoid:   /* avoid: */
    fflush(ficgp);      fflush(ficgp); 
 }  /* end gnuplot */  }  /* end gnuplot */
   
Line 4226  prevforecast(char fileres[], double anpr Line 4417  prevforecast(char fileres[], double anpr
      dateprev1 dateprev2 range of dates during which prevalence is computed       dateprev1 dateprev2 range of dates during which prevalence is computed
      anproj2 year of en of projection (same day and month as proj1).       anproj2 year of en of projection (same day and month as proj1).
   */    */
   int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;    int yearp, stepsize, hstepm, nhstepm, j, k, cptcod, i, h, i1;
   int *popage;  
   double agec; /* generic age */    double agec; /* generic age */
   double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
   double *popeffectif,*popcount;    double *popeffectif,*popcount;
Line 4521  void prwizard(int ncovmodel, int nlstate Line 4711  void prwizard(int ncovmodel, int nlstate
   
   /* Wizard to print covariance matrix template */    /* Wizard to print covariance matrix template */
   
   char ca[32], cb[32], cc[32];    char ca[32], cb[32];
   int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;    int i,j, k, li, lj, lk, ll, jj, npar, itimes;
   int numlinepar;    int numlinepar;
   
   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
Line 4743  fprintf(fichtm,"<ul><li><h4>Life table</ Line 4933  fprintf(fichtm,"<ul><li><h4>Life table</
 void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
   char dirfileres[132],optfileres[132];    char dirfileres[132],optfileres[132];
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;  
   int ng;    int ng;
   
   
Line 4768  int readdata(char datafile[], int firsto Line 4958  int readdata(char datafile[], int firsto
   /*-------- data file ----------*/    /*-------- data file ----------*/
   FILE *fic;    FILE *fic;
   char dummy[]="                         ";    char dummy[]="                         ";
   int i, j, n;    int i=0, j=0, n=0;
   int linei, month, year,iout;    int linei, month, year,iout;
   char line[MAXLINE], linetmp[MAXLINE];    char line[MAXLINE], linetmp[MAXLINE];
   char stra[80], strb[80];    char stra[MAXLINE], strb[MAXLINE];
   char *stratrunc;    char *stratrunc;
   int lstra;    int lstra;
   
Line 4799  int readdata(char datafile[], int firsto Line 4989  int readdata(char datafile[], int firsto
       continue;        continue;
     }      }
     trimbb(linetmp,line); /* Trims multiple blanks in line */      trimbb(linetmp,line); /* Trims multiple blanks in line */
     for (j=0; line[j]!='\0';j++){      strcpy(line, linetmp);
       line[j]=linetmp[j];  
     }  
       
   
     for (j=maxwav;j>=1;j--){      for (j=maxwav;j>=1;j--){
Line 4940  int readdata(char datafile[], int firsto Line 5128  int readdata(char datafile[], int firsto
   fclose(fic);    fclose(fic);
     
   return (0);    return (0);
   endread:    /* endread: */
     printf("Exiting readdata: ");      printf("Exiting readdata: ");
     fclose(fic);      fclose(fic);
     return (1);      return (1);
Line 4971  int decodemodel ( char model[], int last Line 5159  int decodemodel ( char model[], int last
  */   */
 {  {
   int i, j, k, ks;    int i, j, k, ks;
   int i1, j1, k1, k2;    int  j1, k1, k2;
   char modelsav[80];    char modelsav[80];
   char stra[80], strb[80], strc[80], strd[80],stre[80];    char stra[80], strb[80], strc[80], strd[80],stre[80];
   
Line 5120  int decodemodel ( char model[], int last Line 5308  int decodemodel ( char model[], int last
   
   
   return (0); /* with covar[new additional covariate if product] and Tage if age */     return (0); /* with covar[new additional covariate if product] and Tage if age */ 
   endread:    /*endread:*/
     printf("Exiting decodemodel: ");      printf("Exiting decodemodel: ");
     return (1);      return (1);
 }  }
Line 5179  calandcheckages(int imx, int maxwav, dou Line 5367  calandcheckages(int imx, int maxwav, dou
           }            }
           else if(agev[m][i] >*agemax){            else if(agev[m][i] >*agemax){
             *agemax=agev[m][i];              *agemax=agev[m][i];
             printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);              /* printf(" Max anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.2f\n",m,i,anint[m][i], i,annais[i], *agemax);*/
           }            }
           /*agev[m][i]=anint[m][i]-annais[i];*/            /*agev[m][i]=anint[m][i]-annais[i];*/
           /*     agev[m][i] = age[i]+2*m;*/            /*     agev[m][i] = age[i]+2*m;*/
Line 5217  calandcheckages(int imx, int maxwav, dou Line 5405  calandcheckages(int imx, int maxwav, dou
   fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax);     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, *agemin, *agemax); 
   
   return (0);    return (0);
   endread:   /* endread:*/
     printf("Exiting calandcheckages: ");      printf("Exiting calandcheckages: ");
     return (1);      return (1);
 }  }
Line 5237  int main(int argc, char *argv[]) Line 5425  int main(int argc, char *argv[])
   double ssval;    double ssval;
 #endif  #endif
   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=0,m,size=100, cptcod;
   int linei, month, year,iout;  
   int jj, ll, li, lj, lk, imk;    int jj, ll, li, lj, lk;
   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;
   int vpopbased=0;    int vpopbased=0;
   
   char ca[32], cb[32], cc[32];    char ca[32], cb[32];
   /*  FILE *fichtm; *//* Html File */    /*  FILE *fichtm; *//* Html File */
   /* FILE *ficgp;*/ /*Gnuplot File */    /* FILE *ficgp;*/ /*Gnuplot File */
   struct stat info;    struct stat info;
   double agedeb, agefin,hf;    double agedeb;
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
   double fret;    double fret;
   double **xi,tmp,delta;  
   
   double dum; /* Dummy variable */    double dum; /* Dummy variable */
   double ***p3mat;    double ***p3mat;
   double ***mobaverage;    double ***mobaverage;
   int *indx;  
   char line[MAXLINE], linepar[MAXLINE];    char line[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]; 
   char **bp, *tok, *val; /* pathtot */    char *tok, *val; /* pathtot */
   int firstobs=1, lastobs=10;    int firstobs=1, lastobs=10;
   int sdeb, sfin; /* Status at beginning and end */    int c,  h , cpt;
   int c,  h , cpt,l;    int jl;
   int ju,jl, mi;    int i1, j1, jk, stepsize;
   int i1,j1, jk,aa,bb, stepsize, ij;    int *tab; 
   int jnais,jdc,jint4,jint1,jint2,jint3,*tab;   
   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
   int mobilav=0,popforecast=0;    int mobilav=0,popforecast=0;
   int hstepm, nhstepm;    int hstepm, nhstepm;
Line 5277  int main(int argc, char *argv[]) Line 5462  int main(int argc, char *argv[])
   double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;    double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
   double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;    double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
   double bage, fage, age, agelim, agebase;    double bage=0, fage=110, age, agelim, agebase;
   double ftolpl=FTOL;    double ftolpl=FTOL;
   double **prlim;    double **prlim;
   double ***param; /* Matrix of parameters */    double ***param; /* Matrix of parameters */
Line 5288  int main(int argc, char *argv[]) Line 5473  int main(int argc, char *argv[])
   double ***eij, ***vareij;    double ***eij, ***vareij;
   double **varpl; /* Variances of prevalence limits by age */    double **varpl; /* Variances of prevalence limits by age */
   double *epj, vepp;    double *epj, vepp;
   double kk1, kk2;  
   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;    double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   double **ximort;    double **ximort;
   char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";    char *alph[]={"a","a","b","c","d","e"}, str[4]="1234";
   int *dcwave;    int *dcwave;
   
   char z[1]="c", occ;    char z[1]="c";
   
   /*char  *strt;*/    /*char  *strt;*/
   char strtend[80];    char strtend[80];
   
   long total_usecs;  
    
 /*   setlocale (LC_ALL, ""); */  /*   setlocale (LC_ALL, ""); */
 /*   bindtextdomain (PACKAGE, LOCALEDIR); */  /*   bindtextdomain (PACKAGE, LOCALEDIR); */
 /*   textdomain (PACKAGE); */  /*   textdomain (PACKAGE); */
Line 5308  int main(int argc, char *argv[]) Line 5492  int main(int argc, char *argv[])
 /*   setlocale (LC_MESSAGES, ""); */  /*   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);    rstart_time = time(NULL);  
     /*  (void) gettimeofday(&start_time,&tzp);*/
     start_time = *localtime(&rstart_time);
   curr_time=start_time;    curr_time=start_time;
   tm = *localtime(&start_time.tv_sec);    /*tml = *localtime(&start_time.tm_sec);*/
   tmg = *gmtime(&start_time.tv_sec);    /* strcpy(strstart,asctime(&tml)); */
   strcpy(strstart,asctime(&tm));    strcpy(strstart,asctime(&start_time));
   
 /*  printf("Localtime (at start)=%s",strstart); */  /*  printf("Localtime (at start)=%s",strstart); */
 /*  tp.tv_sec = tp.tv_sec +86400; */  /*  tp.tm_sec = tp.tm_sec +86400; */
 /*  tm = *localtime(&start_time.tv_sec); */  /*  tm = *localtime(&start_time.tm_sec); */
 /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */  /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
 /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */  /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
 /*   tmg.tm_hour=tmg.tm_hour + 1; */  /*   tmg.tm_hour=tmg.tm_hour + 1; */
 /*   tp.tv_sec = mktime(&tmg); */  /*   tp.tm_sec = mktime(&tmg); */
 /*   strt=asctime(&tmg); */  /*   strt=asctime(&tmg); */
 /*   printf("Time(after) =%s",strstart);  */  /*   printf("Time(after) =%s",strstart);  */
 /*  (void) time (&time_value);  /*  (void) time (&time_value);
Line 5341  int main(int argc, char *argv[]) Line 5527  int main(int argc, char *argv[])
     i=strlen(pathr);      i=strlen(pathr);
     if(pathr[i-1]=='\n')      if(pathr[i-1]=='\n')
       pathr[i-1]='\0';        pathr[i-1]='\0';
       i=strlen(pathr);
       if(pathr[i-1]==' ') /* This may happen when dragging on oS/X! */
         pathr[i-1]='\0';
    for (tok = pathr; tok != NULL; ){     for (tok = pathr; tok != NULL; ){
       printf("Pathr |%s|\n",pathr);        printf("Pathr |%s|\n",pathr);
       while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');        while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
Line 5396  int main(int argc, char *argv[]) Line 5585  int main(int argc, char *argv[])
  path=%s \n\   path=%s \n\
  optionfile=%s\n\   optionfile=%s\n\
  optionfilext=%s\n\   optionfilext=%s\n\
  optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);   optionfilefiname='%s'\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
   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);
   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.tm_sec-start_time.tm_sec,tmpout)); */
   
   /* */    /* */
   strcpy(fileres,"r");    strcpy(fileres,"r");
Line 5566  run imach with mle=-1 to get a correct t Line 5755  run imach with mle=-1 to get a correct t
     for(i=1; i <=nlstate; i++){      for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){        for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);          fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1-i)*(j1-j)!=0){          if ( (i1-i) * (j1-j) != 0){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);            printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);            exit(1);
         }          }
Line 5935  Interval (in months) between two waves: Line 6124  Interval (in months) between two waves:
           
 #ifdef GSL  #ifdef GSL
     printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");      printf("GSL optimization\n");  fprintf(ficlog,"Powell\n");
 #elsedef  #else
     printf("Powell\n");  fprintf(ficlog,"Powell\n");      printf("Powell\n");  fprintf(ficlog,"Powell\n");
 #endif  #endif
     strcpy(filerespow,"pow-mort");       strcpy(filerespow,"pow-mort"); 
Line 5946  Interval (in months) between two waves: Line 6135  Interval (in months) between two waves:
     }      }
 #ifdef GSL  #ifdef GSL
     fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");      fprintf(ficrespow,"# GSL optimization\n# iter -2*LL");
 #elsedef  #else
     fprintf(ficrespow,"# Powell\n# iter -2*LL");      fprintf(ficrespow,"# Powell\n# iter -2*LL");
 #endif  #endif
     /*  for (i=1;i<=nlstate;i++)      /*  for (i=1;i<=nlstate;i++)
Line 6508  Interval (in months) between two waves: Line 6697  Interval (in months) between two waves:
   
         for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/          for(vpopbased=0; vpopbased <= popbased; vpopbased++){ /* Done for vpopbased=0 and vpopbased=1 if popbased==1*/
           oldm=oldms;savm=savms; /* Segmentation fault */            oldm=oldms;savm=savms; /* Segmentation fault */
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart);            cptcod= 0; /* To be deleted */
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,vpopbased,mobilav, strstart); /* cptcod not initialized Intel */
           fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");            fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n#  (weighted average of eij where weights are ");
           if(vpopbased==1)            if(vpopbased==1)
             fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);              fprintf(ficrest,"the age specific prevalence observed (cross-sectionally) in the population i.e cross-sectionally\n in each health state (popbased=1) (mobilav=%d)\n",mobilav);
Line 6600  Interval (in months) between two waves: Line 6790  Interval (in months) between two waves:
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     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 */
  endfree:   /* endfree:*/
     free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */      free_matrix(prlim,1,nlstate,1,nlstate); /*here or after loop ? */
     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);
Line 6634  Interval (in months) between two waves: Line 6824  Interval (in months) between two waves:
   }    }
   printf("See log file on %s\n",filelog);    printf("See log file on %s\n",filelog);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
   (void) gettimeofday(&end_time,&tzp);    /*(void) gettimeofday(&end_time,&tzp);*/
   tm = *localtime(&end_time.tv_sec);    rend_time = time(NULL);  
   tmg = *gmtime(&end_time.tv_sec);    end_time = *localtime(&rend_time);
   strcpy(strtend,asctime(&tm));    /* tml = *localtime(&end_time.tm_sec); */
     strcpy(strtend,asctime(&end_time));
   printf("Local time at start %s\nLocal time at end   %s",strstart, strtend);     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
   fprintf(ficlog,"Local time 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(rend_time -rstart_time,tmpout));
   
   printf("Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);    printf("Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
   fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));    fprintf(ficlog,"Total time used %s\n", asc_diff_time(rend_time -rstart_time,tmpout));
   fprintf(ficlog,"Total time was %ld Sec.\n", end_time.tv_sec -start_time.tv_sec);    fprintf(ficlog,"Total time was %.0lf Sec.\n", difftime(rend_time,rstart_time));
   /*  printf("Total time was %d uSec.\n", total_usecs);*/    /*  printf("Total time was %d uSec.\n", total_usecs);*/
 /*   if(fileappend(fichtm,optionfilehtm)){ */  /*   if(fileappend(fichtm,optionfilehtm)){ */
   fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);    fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
Line 6663  Interval (in months) between two waves: Line 6854  Interval (in months) between two waves:
     printf("Current directory %s!\n",pathcd);      printf("Current directory %s!\n",pathcd);
   /*strcat(plotcmd,CHARSEPARATOR);*/    /*strcat(plotcmd,CHARSEPARATOR);*/
   sprintf(plotcmd,"gnuplot");    sprintf(plotcmd,"gnuplot");
 #ifndef UNIX  #ifdef _WIN32
   sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);    sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
 #endif  #endif
   if(!stat(plotcmd,&info)){    if(!stat(plotcmd,&info)){
     printf("Error or gnuplot program not found: %s\n",plotcmd);fflush(stdout);      printf("Error or gnuplot program not found: '%s'\n",plotcmd);fflush(stdout);
     if(!stat(getenv("GNUPLOTBIN"),&info)){      if(!stat(getenv("GNUPLOTBIN"),&info)){
       printf("Error or gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);        printf("Error or gnuplot program not found: '%s' Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
     }else      }else
       strcpy(pplotcmd,plotcmd);        strcpy(pplotcmd,plotcmd);
 #ifdef UNIX  #ifdef __unix
     strcpy(plotcmd,GNUPLOTPROGRAM);      strcpy(plotcmd,GNUPLOTPROGRAM);
     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);
     }else      }else
       strcpy(pplotcmd,plotcmd);        strcpy(pplotcmd,plotcmd);
 #endif  #endif
Line 6683  Interval (in months) between two waves: Line 6874  Interval (in months) between two waves:
     strcpy(pplotcmd,plotcmd);      strcpy(pplotcmd,plotcmd);
       
   sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);    sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
   printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);    printf("Starting graphs with: '%s'\n",plotcmd);fflush(stdout);
   
   if((outcmd=system(plotcmd)) != 0){    if((outcmd=system(plotcmd)) != 0){
     printf("gnuplot command might not be in your path: %s, err=%d\n", plotcmd, outcmd);      printf("gnuplot command might not be in your path: '%s', err=%d\n", plotcmd, outcmd);
     printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");      printf("\n Trying if gnuplot resides on the same directory that IMaCh\n");
     sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);      sprintf(plotcmd,"%sgnuplot %s", pathimach, optionfilegnuplot);
     if((outcmd=system(plotcmd)) != 0)      if((outcmd=system(plotcmd)) != 0)
       printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);        printf("\n Still a problem with gnuplot command %s, err=%d\n", plotcmd, outcmd);
   }    }
   printf(" Successul, please wait...");    printf(" Successful, please wait...");
   while (z[0] != 'q') {    while (z[0] != 'q') {
     /* chdir(path); */      /* chdir(path); */
     printf("\nType e to edit results with your browser, g to graph again and q for exit: ");      printf("\nType e to edit results with your browser, g to graph again and q for exit: ");
     scanf("%s",z);      scanf("%s",z);
 /*     if (z[0] == 'c') system("./imach"); */  /*     if (z[0] == 'c') system("./imach"); */
     if (z[0] == 'e') {      if (z[0] == 'e') {
 #ifdef OSX  #ifdef __APPLE__
       sprintf(pplotcmd, "open %s", optionfilehtm);        sprintf(pplotcmd, "open %s", optionfilehtm);
   #elif __linux
         sprintf(pplotcmd, "xdg-open %s", optionfilehtm);
 #else  #else
       sprintf(pplotcmd, "%s", optionfilehtm);        sprintf(pplotcmd, "%s", optionfilehtm);
 #endif  #endif
Line 6716  Interval (in months) between two waves: Line 6909  Interval (in months) between two waves:
     scanf("%s",z);      scanf("%s",z);
   }    }
 }  }
   
   
   

Removed from v.1.155  
changed lines
  Added in v.1.165


FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>