Diff for /imach/src/imach.c between versions 1.78 and 1.98

version 1.78, 2003/05/27 17:26:53 version 1.98, 2004/05/16 15:05:56
Line 1 Line 1
 /* $Id$  /* $Id$
     $State$
     $Log$
     Revision 1.98  2004/05/16 15:05:56  brouard
     New version 0.97 . First attempt to estimate force of mortality
     directly from the data i.e. without the need of knowing the health
     state at each age, but using a Gompertz model: log u =a + b*age .
     This is the basic analysis of mortality and should be done before any
     other analysis, in order to test if the mortality estimated from the
     cross-longitudinal survey is different from the mortality estimated
     from other sources like vital statistic data.
   
     The same imach parameter file can be used but the option for mle should be -3.
   
     Agnès, who wrote this part of the code, tried to keep most of the
     former routines in order to include the new code within the former code.
   
     The output is very simple: only an estimate of the intercept and of
     the slope with 95% confident intervals.
   
     Current limitations:
     A) Even if you enter covariates, i.e. with the
     model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
     B) There is no computation of Life Expectancy nor Life Table.
   
     Revision 1.97  2004/02/20 13:25:42  lievre
     Version 0.96d. Population forecasting command line is (temporarily)
     suppressed.
   
     Revision 1.96  2003/07/15 15:38:55  brouard
     * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
     rewritten within the same printf. Workaround: many printfs.
   
     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
     (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
     (Module): Version 0.96b
   
     Revision 1.92  2003/06/25 16:30:45  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
   
     Revision 1.91  2003/06/25 15:30:29  brouard
     * imach.c (Repository): Duplicated warning errors corrected.
     (Repository): Elapsed time after each iteration is now output. It
     helps to forecast when convergence will be reached. Elapsed time
     is stamped in powell.  We created a new html file for the graphs
     concerning matrix of covariance. It has extension -cov.htm.
   
     Revision 1.90  2003/06/24 12:34:15  brouard
     (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
   
     Revision 1.89  2003/06/24 12:30:52  brouard
     (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
   
     Revision 1.88  2003/06/23 17:54:56  brouard
     * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
   
     Revision 1.87  2003/06/18 12:26:01  brouard
     Version 0.96
   
     Revision 1.86  2003/06/17 20:04:08  brouard
     (Module): Change position of html and gnuplot routines and added
     routine fileappend.
   
     Revision 1.85  2003/06/17 13:12:43  brouard
     * imach.c (Repository): Check when date of death was earlier that
     current date of interview. It may happen when the death was just
     prior to the death. In this case, dh was negative and likelihood
     was wrong (infinity). We still send an "Error" but patch by
     assuming that the date of death was just one stepm after the
     interview.
     (Repository): Because some people have very long ID (first column)
     we changed int to long in num[] and we added a new lvector for
     memory allocation. But we also truncated to 8 characters (left
     truncation)
     (Repository): No more line truncation errors.
   
     Revision 1.84  2003/06/13 21:44:43  brouard
     * imach.c (Repository): Replace "freqsummary" at a correct
     place. It differs from routine "prevalence" which may be called
     many times. Probs is memory consuming and must be used with
     parcimony.
     Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   
     Revision 1.83  2003/06/10 13:39:11  lievre
     *** empty log message ***
   
     Revision 1.82  2003/06/05 15:57:20  brouard
     Add log in  imach.c and  fullversion number is now printed.
   
   */
   /*
    Interpolated Markov Chain     Interpolated Markov Chain
   
   Short summary of the programme:    Short summary of the programme:
Line 58 Line 162
   read parameterfile    read parameterfile
   read datafile    read datafile
   concatwav    concatwav
     freqsummary
   if (mle >= 1)    if (mle >= 1)
     mlikeli      mlikeli
   print results files    print results files
Line 91 Line 196
 #include <stdlib.h>  #include <stdlib.h>
 #include <unistd.h>  #include <unistd.h>
   
   #include <sys/time.h>
   #include <time.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"*/
 #define FILENAMELENGTH 80  #define FILENAMELENGTH 132
 /*#define DEBUG*/  /*#define DEBUG*/
 #define windows  /*#define windows*/
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
Line 111 Line 223
 #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
 #ifdef windows  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
 #define DIRSEPARATOR '\\'  #ifdef unix
 #define ODIRSEPARATOR '/'  
 #else  
 #define DIRSEPARATOR '/'  #define DIRSEPARATOR '/'
 #define ODIRSEPARATOR '\\'  #define ODIRSEPARATOR '\\'
   #else
   #define DIRSEPARATOR '\\'
   #define ODIRSEPARATOR '/'
 #endif  #endif
   
 char version[80]="Imach version 0.95a, May 2003, INED-EUROREVES ";  /* $Id$ */
 int erreur; /* Error number */  /* $State$ */
   
   char version[]="Imach version 0.70, May 2004, INED-EUROREVES ";
   char fullversion[]="$Revision$ $Date$"; 
   int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 int nvar;  int nvar;
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 int npar=NPARMAX;  int npar=NPARMAX;
Line 132  int popbased=0; Line 249  int popbased=0;
 int *wav; /* Number of waves for this individuual 0 is possible */  int *wav; /* Number of waves for this individuual 0 is possible */
 int maxwav; /* Maxim number of waves */  int maxwav; /* Maxim number of waves */
 int jmin, jmax; /* min, max spacing between 2 waves */  int jmin, jmax; /* min, max spacing between 2 waves */
   int gipmx, gsw; /* Global variables on the number of contributions 
                      to the likelihood and the sum of weights (done by funcone)*/
 int mle, weightopt;  int mle, weightopt;
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 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 */
Line 142  double **oldm, **newm, **savm; /* Workin Line 261  double **oldm, **newm, **savm; /* Workin
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 FILE *ficlog, *ficrespow;  FILE *ficlog, *ficrespow;
   int globpr; /* Global variable for printing or not */
   double fretone; /* Only one call to likelihood */
   long ipmx; /* Number of contributions */
   double sw; /* Sum of weights */
   char filerespow[FILENAMELENGTH];
   char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   FILE *ficresilk;
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 FILE *ficresprobmorprev;  FILE *ficresprobmorprev;
 FILE *fichtm; /* Html File */  FILE *fichtm, *fichtmcov; /* Html File */
 FILE *ficreseij;  FILE *ficreseij;
 char filerese[FILENAMELENGTH];  char filerese[FILENAMELENGTH];
 FILE  *ficresvij;  FILE  *ficresvij;
Line 154  char fileresvpl[FILENAMELENGTH]; Line 280  char fileresvpl[FILENAMELENGTH];
 char title[MAXLINE];  char title[MAXLINE];
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   char command[FILENAMELENGTH];
   int  outcmd=0;
   
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   
 char filelog[FILENAMELENGTH]; /* Log file */  char filelog[FILENAMELENGTH]; /* Log file */
 char filerest[FILENAMELENGTH];  char filerest[FILENAMELENGTH];
 char fileregp[FILENAMELENGTH];  char fileregp[FILENAMELENGTH];
 char popfile[FILENAMELENGTH];  char popfile[FILENAMELENGTH];
   
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   
   struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   struct timezone tzp;
   extern int gettimeofday();
   struct tm tmg, tm, tmf, *gmtime(), *localtime();
   long time_value;
   extern long time();
   char strcurr[80], strfor[80];
   
 #define NR_END 1  #define NR_END 1
 #define FREE_ARG char*  #define FREE_ARG char*
Line 190  static double maxarg1,maxarg2; Line 328  static double maxarg1,maxarg2;
 static double sqrarg;  static double sqrarg;
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}   #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   int agegomp= AGEGOMP;
   
 int imx;   int imx; 
 int stepm;  int stepm=1;
 /* Stepm, step in month: minimum step interpolation*/  /* Stepm, step in month: minimum step interpolation*/
   
 int estepm;  int estepm;
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   
 int m,nb;  int m,nb;
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  long *num;
   int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 double **pmmij, ***probs;  double **pmmij, ***probs;
   double *ageexmed,*agecens;
 double dateintmean=0;  double dateintmean=0;
   
 double *weight;  double *weight;
Line 239  static int split( char *path, char *dirc Line 380  static int split( char *path, char *dirc
     dirc[l1-l2] = 0;                    /* add zero */      dirc[l1-l2] = 0;                    /* add zero */
   }    }
   l1 = strlen( dirc );                  /* length of directory */    l1 = strlen( dirc );                  /* length of directory */
 #ifdef windows    /*#ifdef windows
   if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
 #else  #else
   if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
 #endif  #endif
     */
   ss = strrchr( name, '.' );            /* find last / */    ss = strrchr( name, '.' );            /* find last / */
   ss++;    ss++;
   strcpy(ext,ss);                       /* save extension */    strcpy(ext,ss);                       /* save extension */
Line 257  static int split( char *path, char *dirc Line 399  static int split( char *path, char *dirc
   
 /******************************************/  /******************************************/
   
 void replace(char *s, char*t)  void replace_back_to_slash(char *s, char*t)
 {  {
   int i;    int i;
   int lg=20;    int lg=0;
   i=0;    i=0;
   lg=strlen(t);    lg=strlen(t);
   for(i=0; i<= lg; i++) {    for(i=0; i<= lg; i++) {
Line 327  void free_vector(double*v, int nl, int n Line 469  void free_vector(double*v, int nl, int n
 }  }
   
 /************************ivector *******************************/  /************************ivector *******************************/
 char *cvector(long nl,long nh)  int *ivector(long nl,long nh)
 {  {
   char *v;    int *v;
   v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   if (!v) nrerror("allocation failure in cvector");    if (!v) nrerror("allocation failure in ivector");
   return v-nl+NR_END;    return v-nl+NR_END;
 }  }
   
 /******************free ivector **************************/  /******************free ivector **************************/
 void free_cvector(char *v, long nl, long nh)  void free_ivector(int *v, long nl, long nh)
 {  {
   free((FREE_ARG)(v+nl-NR_END));    free((FREE_ARG)(v+nl-NR_END));
 }  }
   
 /************************ivector *******************************/  /************************lvector *******************************/
 int *ivector(long nl,long nh)  long *lvector(long nl,long nh)
 {  {
   int *v;    long *v;
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   if (!v) nrerror("allocation failure in ivector");    if (!v) nrerror("allocation failure in ivector");
   return v-nl+NR_END;    return v-nl+NR_END;
 }  }
   
 /******************free ivector **************************/  /******************free lvector **************************/
 void free_ivector(int *v, long nl, long nh)  void free_lvector(long *v, long nl, long nh)
 {  {
   free((FREE_ARG)(v+nl-NR_END));    free((FREE_ARG)(v+nl-NR_END));
 }  }
Line 410  double **matrix(long nrl, long nrh, long Line 552  double **matrix(long nrl, long nrh, long
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   return m;    return m;
   /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1])     /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
    */     */
 }  }
   
Line 465  void free_ma3x(double ***m, long nrl, lo Line 607  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 640  void linmin(double p[], double xi[], int Line 817  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,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
     return ascdiff;
   }
   
 /*************** powell ************************/  /*************** powell ************************/
 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 650  void powell(double p[], double **xi, int Line 840  void powell(double p[], double **xi, int
   double del,t,*pt,*ptt,*xit;    double del,t,*pt,*ptt,*xit;
   double fp,fptt;    double fp,fptt;
   double *xits;    double *xits;
     int niterf, itmp;
   
   pt=vector(1,n);     pt=vector(1,n); 
   ptt=vector(1,n);     ptt=vector(1,n); 
   xit=vector(1,n);     xit=vector(1,n); 
Line 660  void powell(double p[], double **xi, int Line 852  void powell(double p[], double **xi, int
     fp=(*fret);       fp=(*fret); 
     ibig=0;       ibig=0; 
     del=0.0;       del=0.0; 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      last_time=curr_time;
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      (void) gettimeofday(&curr_time,&tzp);
     fprintf(ficrespow,"%d %.12f",*iter,*fret);      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);
     for (i=1;i<=n;i++) {      /*    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);
       fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
       */
      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]);
       fprintf(ficrespow," %.12lf", p[i]);        fprintf(ficrespow," %.12lf", p[i]);
     }      }
     printf("\n");      printf("\n");
     fprintf(ficlog,"\n");      fprintf(ficlog,"\n");
     fprintf(ficrespow,"\n");      fprintf(ficrespow,"\n");fflush(ficrespow);
       if(*iter <=3){
         tm = *localtime(&curr_time.tv_sec);
         strcpy(strcurr,asctime(&tmf));
   /*       asctime_r(&tm,strcurr); */
         forecast_time=curr_time;
         itmp = strlen(strcurr);
         if(strcurr[itmp-1]=='\n')
           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);
         fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         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);
           tmf = *localtime(&forecast_time.tv_sec);
   /*      asctime_r(&tmf,strfor); */
           strcpy(strfor,asctime(&tmf));
           itmp = strlen(strfor);
           if(strfor[itmp-1]=='\n')
           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);
           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);
         }
       }
     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); 
Line 1083  double func( double *x) Line 1300  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 1134  double func( double *x) Line 1330  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;
       } /* end of wave */        } /* end of wave */
     } /* end of individual */      } /* end of individual */
   }else{  /* ml=4 no inter-extrapolation */    }else if (mle==4){  /* ml=4 no inter-extrapolation */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
           for(d=0; d<dh[mi][i]; d++){
             newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
           
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
             oldm=newm;
           } /* end mult */
         
           s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
           if( s2 > nlstate){ 
             lli=log(out[s1][s2] - savm[s1][s2]);
           }else{
             lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           }
           ipmx +=1;
           sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         } /* end of wave */
       } /* end of individual */
     }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){        for(mi=1; mi<= wav[i]-1; mi++){
Line 1185  double func( double *x) Line 1396  double func( double *x)
           oldm=newm;            oldm=newm;
         } /* end mult */          } /* end mult */
               
           s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
         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 */
         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;
           /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
       } /* end of wave */        } /* end of wave */
     } /* end of individual */      } /* end of individual */
   } /* End of if */    } /* End of if */
Line 1198  double func( double *x) Line 1412  double func( double *x)
   return -l;    return -l;
 }  }
   
   /*************** log-likelihood *************/
   double funcone( double *x)
   {
     /* Same as likeli but slower because of a lot of printf and if */
     int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX], cov[NCOVMAX];
     double **out;
     double lli; /* Individual log likelihood */
     double llt;
     int s1, s2;
     double bbh, survp;
     /*extern weight */
     /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
     */
     cov[1]=1.;
   
     for(k=1; k<=nlstate; k++) ll[k]=0.;
   
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){
         for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){
             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }
         for(d=0; d<dh[mi][i]; d++){
           newm=savm;
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for (kk=1; kk<=cptcovage;kk++) {
             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           }
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           savm=oldm;
           oldm=newm;
         } /* end mult */
         
         s1=s[mw[mi][i]][i];
         s2=s[mw[mi+1][i]][i];
         bbh=(double)bh[mi][i]/(double)stepm; 
         /* bias is positive if real duration
          * is higher than the multiple of stepm and negative otherwise.
          */
         if( s2 > nlstate && (mle <5) ){  /* Jackson */
           lli=log(out[s1][s2] - savm[s1][s2]);
         } else if (mle==1){
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         } else if(mle==2){
           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 */
         } else if(mle==3){  /* exponential inter-extrapolation */
           lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
         } else if (mle==4){  /* mle=4 no inter-extrapolation */
           lli=log(out[s1][s2]); /* Original formula */
         } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
           lli=log(out[s1][s2]); /* Original formula */
         } /* End of if */
         ipmx +=1;
         sw += weight[i];
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         if(globpr){
           fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
    %10.6f %10.6f %10.6f ", \
                   num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
                   2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
           for(k=1,llt=0.,l=0.; k<=nlstate; k++){
             llt +=ll[k]*gipmx/gsw;
             fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           }
           fprintf(ficresilk," %10.6f\n", -llt);
         }
       } /* end of wave */
     } /* end of individual */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     if(globpr==0){ /* First time we count the contributions and weights */
       gipmx=ipmx;
       gsw=sw;
     }
     return -l;
   }
   
   
   /*************** function likelione ***********/
   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 
        the selection of individuals/waves and
        to check the exact contribution to the likelihood.
        Plotting could be done.
      */
     int k;
   
     if(*globpri !=0){ /* Just counts and sums, no printings */
       strcpy(fileresilk,"ilk"); 
       strcat(fileresilk,fileres);
       if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", fileresilk);
         fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }
       fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
       fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       for(k=1; k<=nlstate; k++) 
         fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     }
   
     *fretone=(*funcone)(p);
     if(*globpri !=0){
       fclose(ficresilk);
       fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       fflush(fichtm); 
     } 
     return;
   }
   
   
 /*********** Maximum Likelihood Estimation ***************/  /*********** Maximum Likelihood Estimation ***************/
   
Line 1206  void mlikeli(FILE *ficres,double p[], in Line 1542  void mlikeli(FILE *ficres,double p[], in
   int i,j, iter;    int i,j, iter;
   double **xi;    double **xi;
   double fret;    double fret;
   char filerespow[FILENAMELENGTH];    double fretone; /* Only one call to likelihood */
     /*  char filerespow[FILENAMELENGTH];*/
   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 1223  void mlikeli(FILE *ficres,double p[], in Line 1560  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");
   
   powell(p,xi,npar,ftol,&iter,&fret,func);    powell(p,xi,npar,ftol,&iter,&fret,func);
   
   fclose(ficrespow);    fclose(ficrespow);
Line 1240  void hesscov(double **matcov, double p[] Line 1578  void hesscov(double **matcov, double p[]
   int i, j,jk;    int i, j,jk;
   int *indx;    int *indx;
   
   double hessii(double p[], double delta, int theta, double delti[]);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   double hessij(double p[], double delti[], int i, int j);    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   void lubksb(double **a, int npar, int *indx, double b[]) ;    void lubksb(double **a, int npar, int *indx, double b[]) ;
   void ludcmp(double **a, int npar, int *indx, double *d) ;    void ludcmp(double **a, int npar, int *indx, double *d) ;
     double gompertz(double p[]);
   hess=matrix(1,npar,1,npar);    hess=matrix(1,npar,1,npar);
   
   printf("\nCalculation of the hessian matrix. Wait...\n");    printf("\nCalculation of the hessian matrix. Wait...\n");
Line 1252  void hesscov(double **matcov, double p[] Line 1590  void hesscov(double **matcov, double p[]
   for (i=1;i<=npar;i++){    for (i=1;i<=npar;i++){
     printf("%d",i);fflush(stdout);      printf("%d",i);fflush(stdout);
     fprintf(ficlog,"%d",i);fflush(ficlog);      fprintf(ficlog,"%d",i);fflush(ficlog);
     hess[i][i]=hessii(p,ftolhess,i,delti);     
     /*printf(" %f ",p[i]);*/       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     /*printf(" %lf ",hess[i][i]);*/      
       /*  printf(" %f ",p[i]);
           printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   }    }
       
   for (i=1;i<=npar;i++) {    for (i=1;i<=npar;i++) {
Line 1262  void hesscov(double **matcov, double p[] Line 1602  void hesscov(double **matcov, double p[]
       if (j>i) {         if (j>i) { 
         printf(".%d%d",i,j);fflush(stdout);          printf(".%d%d",i,j);fflush(stdout);
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
         hess[i][j]=hessij(p,delti,i,j);          hess[i][j]=hessij(p,delti,i,j,func,npar);
           
         hess[j][i]=hess[i][j];              hess[j][i]=hess[i][j];    
         /*printf(" %lf ",hess[i][j]);*/          /*printf(" %lf ",hess[i][j]);*/
       }        }
Line 1333  void hesscov(double **matcov, double p[] Line 1674  void hesscov(double **matcov, double p[]
 }  }
   
 /*************** hessian matrix ****************/  /*************** hessian matrix ****************/
 double hessii( double x[], double delta, int theta, double delti[])  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
 {  {
   int i;    int i;
   int l=1, lmax=20;    int l=1, lmax=20;
   double k1,k2;    double k1,k2;
   double p2[NPARMAX+1];    double p2[NPARMAX+1];
   double res;    double res;
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   double fx;    double fx;
   int k=0,kmax=10;    int k=0,kmax=10;
   double l1;    double l1;
Line 1380  double hessii( double x[], double delta, Line 1721  double hessii( double x[], double delta,
       
 }  }
   
 double hessij( double x[], double delti[], int thetai,int thetaj)  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, l1, lmax=20;
Line 1490  void lubksb(double **a, int n, int *indx Line 1831  void lubksb(double **a, int n, int *indx
 }   } 
   
 /************ Frequencies ********************/  /************ Frequencies ********************/
 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, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)  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)
 {  /* Some frequencies */  {  /* Some frequencies */
       
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
Line 1544  void  freqsummary(char fileres[], int ia Line 1885  void  freqsummary(char fileres[], int ia
         if (bool==1){          if (bool==1){
           for(m=firstpass; m<=lastpass; m++){            for(m=firstpass; m<=lastpass; m++){
             k2=anint[m][i]+(mint[m][i]/12.);              k2=anint[m][i]+(mint[m][i]/12.);
             if ((k2>=dateprev1) && (k2<=dateprev2)) {              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
               if(agev[m][i]==0) agev[m][i]=iagemax+1;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
               if(agev[m][i]==1) agev[m][i]=iagemax+2;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
               if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
Line 1557  void  freqsummary(char fileres[], int ia Line 1898  void  freqsummary(char fileres[], int ia
                 dateintsum=dateintsum+k2;                  dateintsum=dateintsum+k2;
                 k2cpt++;                  k2cpt++;
               }                }
             }                /*}*/
           }            }
         }          }
       }        }
                 
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   
       if  (cptcovn>0) {        if  (cptcovn>0) {
         fprintf(ficresp, "\n#********** Variable ");           fprintf(ficresp, "\n#********** Variable "); 
Line 1623  void  freqsummary(char fileres[], int ia Line 1964  void  freqsummary(char fileres[], int ia
           if( i <= iagemax){            if( i <= iagemax){
             if(pos>=1.e-5){              if(pos>=1.e-5){
               fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
               probs[i][jk][j1]= pp[jk]/pos;                /*probs[i][jk][j1]= pp[jk]/pos;*/
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
             }              }
             else              else
Line 1656  void  freqsummary(char fileres[], int ia Line 1997  void  freqsummary(char fileres[], int ia
 }  }
   
 /************ Prevalence ********************/  /************ Prevalence ********************/
 void prevalence(double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
 {    {  
   /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
      in each health status at the date of interview (if between dateprev1 and dateprev2).       in each health status at the date of interview (if between dateprev1 and dateprev2).
Line 1774  void  concatwav(int wav[], int **dh, int Line 2115  void  concatwav(int wav[], int **dh, int
   
     wav[i]=mi;      wav[i]=mi;
     if(mi==0){      if(mi==0){
         nbwarn++;
       if(first==0){        if(first==0){
         printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
         first=1;          first=1;
       }        }
       if(first==1){        if(first==1){
         fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
       }        }
     } /* end mi==0 */      } /* end mi==0 */
   } /* End individuals */    } /* End individuals */
Line 1791  void  concatwav(int wav[], int **dh, int Line 2133  void  concatwav(int wav[], int **dh, int
       else{        else{
         if (s[mw[mi+1][i]][i] > nlstate) { /* A death */          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
           if (agedc[i] < 2*AGESUP) {            if (agedc[i] < 2*AGESUP) {
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);               j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
           if(j==0) j=1;  /* Survives at least one month after exam */              if(j==0) j=1;  /* Survives at least one month after exam */
           k=k+1;              else if(j<0){
           if (j >= jmax) jmax=j;                nberr++;
           if (j <= jmin) jmin=j;                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
           sum=sum+j;                j=1; /* Temporary Dangerous patch */
           /*if (j<0) printf("j=%d num=%d \n",j,i);*/                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
           /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
           if(j<0)printf("Error! Negative delay (%d to death) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
               }
               k=k+1;
               if (j >= jmax) jmax=j;
               if (j <= jmin) jmin=j;
               sum=sum+j;
               /*if (j<0) printf("j=%d num=%d \n",j,i);*/
               /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
           }            }
         }          }
         else{          else{
Line 1810  void  concatwav(int wav[], int **dh, int Line 2159  void  concatwav(int wav[], int **dh, int
           else if (j <= jmin)jmin=j;            else if (j <= jmin)jmin=j;
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
           /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
           if(j<0)printf("Error! Negative delay (%d) between waves %d and %d of individual %d at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);            if(j<0){
               nberr++;
               printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             }
           sum=sum+j;            sum=sum+j;
         }          }
         jk= j/stepm;          jk= j/stepm;
         jl= j -jk*stepm;          jl= j -jk*stepm;
         ju= j -(jk+1)*stepm;          ju= j -(jk+1)*stepm;
         if(mle <=1){           if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
           if(jl==0){            if(jl==0){
             dh[mi][i]=jk;              dh[mi][i]=jk;
             bh[mi][i]=0;              bh[mi][i]=0;
Line 1841  void  concatwav(int wav[], int **dh, int Line 2194  void  concatwav(int wav[], int **dh, int
             bh[mi][i]=ju; /* At least one step */              bh[mi][i]=ju; /* At least one step */
             /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
           }            }
         }          } /* end if mle */
       } /* end if mle */        }
     } /* end wave */      } /* end wave */
   }    }
   jmean=sum/k;    jmean=sum/k;
Line 1984  void evsij(char fileres[], double ***eij Line 2337  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 2143  void varevsij(char optionfilefiname[], d Line 2496  void varevsij(char optionfilefiname[], d
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   }      }  
   fprintf(ficresprobmorprev,"\n");    fprintf(ficresprobmorprev,"\n");
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    fprintf(ficgp,"\n# Routine varevsij");
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
     exit(0);  /*   } */
   }  
   else{  
     fprintf(ficgp,"\n# Routine varevsij");  
   }  
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {  
     printf("Problem with html file: %s\n", optionfilehtm);  
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);  
     exit(0);  
   }  
   else{  
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");  
     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);  
   }  
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
Line 2371  void varevsij(char optionfilefiname[], d Line 2711  void varevsij(char optionfilefiname[], d
 /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
 /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
 /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
 */  */
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
   free_vector(xp,1,npar);    free_vector(xp,1,npar);
   free_matrix(doldm,1,nlstate,1,nlstate);    free_matrix(doldm,1,nlstate,1,nlstate);
Line 2388  void varevsij(char optionfilefiname[], d Line 2729  void varevsij(char optionfilefiname[], d
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   fclose(ficresprobmorprev);    fclose(ficresprobmorprev);
   fclose(ficgp);    fflush(ficgp);
   fclose(fichtm);    fflush(fichtm); 
 }    }  /* end varevsij */
   
 /************ Variance of prevlim ******************/  /************ Variance of prevlim ******************/
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
Line 2546  void varprob(char optionfilefiname[], do Line 2887  void varprob(char optionfilefiname[], do
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
   first=1;    first=1;
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    fprintf(ficgp,"\n# Routine varprob");
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);    fprintf(fichtm,"\n");
     exit(0);  
   }    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
   else{    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     fprintf(ficgp,"\n# Routine varprob");    file %s<br>\n",optionfilehtmcov);
   }    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {  and drawn. It helps understanding how is the covariance between two incidences.\
     printf("Problem with html file: %s\n", optionfilehtm);   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
     exit(0);  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
   }  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   else{  standard deviations wide on each axis. <br>\
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
     fprintf(fichtm,"\n");   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");  
     fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");  
     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");  
   
   }  
   
   cov[1]=1;    cov[1]=1;
   tj=cptcoveff;    tj=cptcoveff;
Line 2589  void varprob(char optionfilefiname[], do Line 2925  void varprob(char optionfilefiname[], do
         fprintf(ficgp, "**********\n#\n");          fprintf(ficgp, "**********\n#\n");
                   
                   
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
                   
         fprintf(ficresprobcor, "\n#********** Variable ");              fprintf(ficresprobcor, "\n#********** Variable ");    
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
Line 2749  void varprob(char optionfilefiname[], do Line 3085  void varprob(char optionfilefiname[], do
                     fprintf(ficgp,"\nset parametric;unset label");                      fprintf(ficgp,"\nset parametric;unset label");
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
                     fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
Line 2760  void varprob(char optionfilefiname[], do Line 3100  void varprob(char optionfilefiname[], do
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                   }else{                    }else{
                     first=0;                      first=0;
                     fprintf(fichtm," %d (%.3f),",(int) age, c12);                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
Line 2769  void varprob(char optionfilefiname[], do Line 3109  void varprob(char optionfilefiname[], do
                   }/* if first */                    }/* if first */
                 } /* age mod 5 */                  } /* age mod 5 */
               } /* end loop age */                } /* end loop age */
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
               first=1;                first=1;
             } /*l12 */              } /*l12 */
           } /* k12 */            } /* k12 */
Line 2783  void varprob(char optionfilefiname[], do Line 3123  void varprob(char optionfilefiname[], do
   fclose(ficresprob);    fclose(ficresprob);
   fclose(ficresprobcov);    fclose(ficresprobcov);
   fclose(ficresprobcor);    fclose(ficresprobcor);
   fclose(ficgp);    fflush(ficgp);
   fclose(fichtm);    fflush(fichtmcov);
 }  }
   
   
Line 2796  void printinghtml(char fileres[], char t Line 3136  void printinghtml(char fileres[], char t
                   double jprev1, double mprev1,double anprev1, \                    double jprev1, double mprev1,double anprev1, \
                   double jprev2, double mprev2,double anprev2){                    double jprev2, double mprev2,double anprev2){
   int jj1, k1, i1, cpt;    int jj1, k1, i1, cpt;
   /*char optionfilehtm[FILENAMELENGTH];*/  
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {  
     printf("Problem with %s \n",optionfilehtm), exit(0);  
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);  
   }  
   
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n     fprintf(fichtm,"\
  - Life expectancies by age and initial health status (estepm=%2d months):    - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
    <a href=\"e%s\">e%s</a> <br>\n</li>", \             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);     fprintf(fichtm,"\
    - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - Life expectancies by age and initial health status (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
Line 2826  fprintf(fichtm," \n<ul><li><b>Graphs</b> Line 3167  fprintf(fichtm," \n<ul><li><b>Graphs</b>
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      }       }
      /* Pij */       /* Pij */
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: pe%s%d1.png<br>       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);       <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
      /* Quasi-incidences */       /* Quasi-incidences */
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
        /* Stable prevalence in each health state */         /* Stable prevalence in each health state */
        for(cpt=1; cpt<nlstate;cpt++){         for(cpt=1; cpt<nlstate;cpt++){
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
        }         }
      for(cpt=1; cpt<=nlstate;cpt++) {       for(cpt=1; cpt<=nlstate;cpt++) {
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
      }       }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and  
 health expectancies in states (1) and (2): e%s%d.png<br>  
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);  
    } /* end i1 */     } /* end i1 */
  }/* End k1 */   }/* End k1 */
  fprintf(fichtm,"</ul>");   fprintf(fichtm,"</ul>");
   
   
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n   fprintf(fichtm,"\
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n  \n<br><li><h4> Result files (second order: variances)</h4>\n\
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n  
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n   fprintf(fichtm,"\
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
    fprintf(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
 /*  if(popforecast==1) fprintf(fichtm,"\n */  /*  if(popforecast==1) fprintf(fichtm,"\n */
 /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
Line 2863  health expectancies in states (1) and (2 Line 3216  health expectancies in states (1) and (2
 /*      <br>",fileres,fileres,fileres,fileres); */  /*      <br>",fileres,fileres,fileres,fileres); */
 /*  else  */  /*  else  */
 /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
 fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");   fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
  m=cptcoveff;   m=cptcoveff;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
Line 2879  fprintf(fichtm," <ul><li><b>Graphs</b></ Line 3233  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): v%s%d%d.png <br>  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
      }       }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2): %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
    } /* end i1 */     } /* end i1 */
  }/* End k1 */   }/* End k1 */
  fprintf(fichtm,"</ul>");   fprintf(fichtm,"</ul>");
 fclose(fichtm);   fflush(fichtm);
 }  }
   
 /******************* Gnuplot file **************/  /******************* Gnuplot file **************/
 void printinggnuplot(char fileres[], 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];
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
   int ng;    int ng;
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
     printf("Problem with file %s",optionfilegnuplot);  /*     printf("Problem with file %s",optionfilegnuplot); */
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   }  /*   } */
   
   /*#ifdef windows */    /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);    fprintf(ficgp,"cd \"%s\" \n",pathc);
     /*#endif */      /*#endif */
 m=pow(2,cptcoveff);    m=pow(2,cptcoveff);
     
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
  /* 1eme*/   /* 1eme*/
   for (cpt=1; cpt<= nlstate ; cpt ++) {    for (cpt=1; cpt<= nlstate ; cpt ++) {
    for (k1=1; k1<= m ; k1 ++) {     for (k1=1; k1<= m ; k1 ++) {
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
      for (i=1; i<= nlstate ; i ++) {       for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
        else fprintf(ficgp," \%%*lf (\%%*lf)");         else fprintf(ficgp," \%%*lf (\%%*lf)");
      }       }
      fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
      for (i=1; i<= nlstate ; i ++) {       for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
        else fprintf(ficgp," \%%*lf (\%%*lf)");         else fprintf(ficgp," \%%*lf (\%%*lf)");
      }        } 
      fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1);        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
      for (i=1; i<= nlstate ; i ++) {       for (i=1; i<= nlstate ; i ++) {
        if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
        else fprintf(ficgp," \%%*lf (\%%*lf)");         else fprintf(ficgp," \%%*lf (\%%*lf)");
      }         }  
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
    }     }
   }    }
   /*2 eme*/    /*2 eme*/
       
   for (k1=1; k1<= m ; k1 ++) {     for (k1=1; k1<= m ; k1 ++) { 
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
           
     for (i=1; i<= nlstate+1 ; i ++) {      for (i=1; i<= nlstate+1 ; i ++) {
       k=2*i;        k=2*i;
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       for (j=1; j<= nlstate+1 ; j ++) {        for (j=1; j<= nlstate+1 ; j ++) {
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
         else fprintf(ficgp," \%%*lf (\%%*lf)");          else fprintf(ficgp," \%%*lf (\%%*lf)");
       }           }   
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       for (j=1; j<= nlstate+1 ; j ++) {        for (j=1; j<= nlstate+1 ; j ++) {
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
         else fprintf(ficgp," \%%*lf (\%%*lf)");          else fprintf(ficgp," \%%*lf (\%%*lf)");
       }           }   
       fprintf(ficgp,"\" t\"\" w l 0,");        fprintf(ficgp,"\" t\"\" w l 0,");
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       for (j=1; j<= nlstate+1 ; j ++) {        for (j=1; j<= nlstate+1 ; j ++) {
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
         else fprintf(ficgp," \%%*lf (\%%*lf)");          else fprintf(ficgp," \%%*lf (\%%*lf)");
Line 2963  m=pow(2,cptcoveff); Line 3328  m=pow(2,cptcoveff);
   for (k1=1; k1<= m ; k1 ++) {     for (k1=1; k1<= m ; k1 ++) { 
     for (cpt=1; cpt<= nlstate ; cpt ++) {      for (cpt=1; cpt<= nlstate ; cpt ++) {
       k=2+nlstate*(2*cpt-2);        k=2+nlstate*(2*cpt-2);
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);        fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
         for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
         fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
Line 2974  m=pow(2,cptcoveff); Line 3341  m=pow(2,cptcoveff);
                   
       */        */
       for (i=1; i< nlstate ; i ++) {        for (i=1; i< nlstate ; i ++) {
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);          fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
                   
       }         } 
     }      }
Line 2984  m=pow(2,cptcoveff); Line 3351  m=pow(2,cptcoveff);
   for (k1=1; k1<= m ; k1 ++) {     for (k1=1; k1<= m ; k1 ++) { 
     for (cpt=1; cpt<=nlstate ; cpt ++) {      for (cpt=1; cpt<=nlstate ; cpt ++) {
       k=3;        k=3;
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
               
       for (i=1; i<= nlstate ; i ++)        for (i=1; i< nlstate ; i ++)
         fprintf(ficgp,"+$%d",k+i+1);          fprintf(ficgp,"+$%d",k+i+1);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
               
       l=3+(nlstate+ndeath)*cpt;        l=3+(nlstate+ndeath)*cpt;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
       for (i=1; i< nlstate ; i ++) {        for (i=1; i< nlstate ; i ++) {
         l=3+(nlstate+ndeath)*cpt;          l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,"+$%d",l+i+1);          fprintf(ficgp,"+$%d",l+i+1);
Line 3016  m=pow(2,cptcoveff); Line 3386  m=pow(2,cptcoveff);
   
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
      for(jk=1; jk <=m; jk++) {       for(jk=1; jk <=m; jk++) {
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
        if (ng==2)         if (ng==2)
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
        else         else
Line 3063  m=pow(2,cptcoveff); Line 3433  m=pow(2,cptcoveff);
        } /* end k2 */         } /* end k2 */
      } /* end jk */       } /* end jk */
    } /* end ng */     } /* end ng */
    fclose(ficgp);      fflush(ficgp); 
 }  /* end gnuplot */  }  /* end gnuplot */
   
   
Line 3126  prevforecast(char fileres[], double anpr Line 3496  prevforecast(char fileres[], double anpr
   char fileresf[FILENAMELENGTH];    char fileresf[FILENAMELENGTH];
   
   agelim=AGESUP;    agelim=AGESUP;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
   strcpy(fileresf,"f");     strcpy(fileresf,"f"); 
   strcat(fileresf,fileres);    strcat(fileresf,fileres);
Line 3249  populforecast(char fileres[], double anp Line 3619  populforecast(char fileres[], double anp
   agelim=AGESUP;    agelim=AGESUP;
   calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
       
   prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       
       
   strcpy(filerespop,"pop");     strcpy(filerespop,"pop"); 
Line 3391  populforecast(char fileres[], double anp Line 3761  populforecast(char fileres[], double anp
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   fclose(ficrespop);    fclose(ficrespop);
 }  } /* End of popforecast */
   
 /***********************************************/  
 /**************** Main Program *****************/  
 /***********************************************/  
   
 int main(int argc, char *argv[])  int fileappend(FILE *fichier, char *optionfich)
 {  {
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);    if((fichier=fopen(optionfich,"a"))==NULL) {
   int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;      printf("Problem with file: %s\n", optionfich);
   double agedeb, agefin,hf;      fprintf(ficlog,"Problem with file: %s\n", optionfich);
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;      return (0);
     }
   double fret;    fflush(fichier);
   double **xi,tmp,delta;    return (1);
   }
   
   double dum; /* Dummy variable */  
   double ***p3mat;  
   double ***mobaverage;  
   int *indx;  
   char line[MAXLINE], linepar[MAXLINE];  
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];  
   int firstobs=1, lastobs=10;  
   int sdeb, sfin; /* Status at beginning and end */  
   int c,  h , cpt,l;  
   int ju,jl, mi;  
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;  
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab;   
   int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */  
   int mobilav=0,popforecast=0;  
   int hstepm, nhstepm;  
   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 bage, fage, age, agelim, agebase;  /**************** function prwizard **********************/
   double ftolpl=FTOL;  void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   double **prlim;  {
   double *severity;  
   double ***param; /* Matrix of parameters */  
   double  *p;  
   double **matcov; /* Matrix of covariance */  
   double ***delti3; /* Scale */  
   double *delti; /* Scale */  
   double ***eij, ***vareij;  
   double **varpl; /* Variances of prevalence limits by age */  
   double *epj, vepp;  
   double kk1, kk2;  
   double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;  
   
   char *alph[]={"a","a","b","c","d","e"}, str[4];    /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
   char z[1]="c", occ;    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
 #include <sys/time.h>    fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
 #include <time.h>    for(i=1; i <=nlstate; i++){
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      jj=0;
        for(j=1; j <=nlstate+ndeath; j++){
   /* long total_usecs;        if(j==i) continue;
      struct timeval start_time, end_time;        jj++;
           /*ca[0]= k+'a'-1;ca[1]='\0';*/
      gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */        printf("%1d%1d",i,j);
   getcwd(pathcd, size);        fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 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\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# 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(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             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){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       sump=sump+1;
       num=num+1;
     }
    
    
     /* for (i=1; 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]);*/
   
   printf("\n%s",version);    for (i=0;i<=imx-1 ; i++)
       {
         if (cens[i]==1 & wav[i]>1)
           A=-x[1]/(x[2])*
             (exp(x[2]/YEARM*(agecens[i]*12-agegomp*12))-exp(x[2]/YEARM*(ageexmed[i]*12-agegomp*12)));
         
         if (cens[i]==0 & wav[i]>1)
           A=-x[1]/(x[2])*
                (exp(x[2]/YEARM*(agedc[i]*12-agegomp*12))-exp(x[2]/YEARM*(ageexmed[i]*12-agegomp*12)))
             +log(x[1]/YEARM)+x[2]/YEARM*(agedc[i]*12-agegomp*12)+log(YEARM);      
         
         if (wav[i]>1 & agecens[i]>15) {
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov){
     int i;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     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 jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE]; 
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     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 bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char strstart[80], *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     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 */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
   if(argc <=1){    if(argc <=1){
     printf("\nEnter the parameter file name: ");      printf("\nEnter the parameter file name: ");
     scanf("%s",pathtot);      scanf("%s",pathtot);
Line 3462  int main(int argc, char *argv[]) Line 4084  int main(int argc, char *argv[])
   else{    else{
     strcpy(pathtot,argv[1]);      strcpy(pathtot,argv[1]);
   }    }
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
   /*cygwin_split_path(pathtot,path,optionfile);    /*cygwin_split_path(pathtot,path,optionfile);
     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,'\\');*/
   
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
   printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   chdir(path);    chdir(path);
   replace(pathc,path);    strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
   /*-------- arguments in the command line --------*/    /*-------- arguments in the command line --------*/
   
Line 3482  int main(int argc, char *argv[]) Line 4114  int main(int argc, char *argv[])
     goto end;      goto end;
   }    }
   fprintf(ficlog,"Log filename:%s\n",filelog);    fprintf(ficlog,"Log filename:%s\n",filelog);
   fprintf(ficlog,"\n%s",version);    fprintf(ficlog,"\n%s\n%s",version,fullversion);
   fprintf(ficlog,"\nEnter the parameter file name: ");    fprintf(ficlog,"\nEnter the parameter file name: ");
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    fprintf(ficlog,"pathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
   fflush(ficlog);    fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
   /* */    /* */
   strcpy(fileres,"r");    strcpy(fileres,"r");
Line 3497  int main(int argc, char *argv[]) Line 4138  int main(int argc, char *argv[])
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    if((ficpar=fopen(optionfile,"r"))==NULL)    {
     printf("Problem with optionfile %s\n",optionfile);      printf("Problem with optionfile %s\n",optionfile);
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);      fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
     goto end;      goto end;
   }    }
   
   
   
   strcpy(filereso,"o");    strcpy(filereso,"o");
   strcat(filereso,fileres);    strcat(filereso,fileres);
   if((ficparo=fopen(filereso,"w"))==NULL) {    if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
     printf("Problem with Output resultfile: %s\n", filereso);      printf("Problem with Output resultfile: %s\n", filereso);
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);      fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
     goto end;      goto end;
   }    }
   
   /* Reads comments: lines beginning with '#' */    /* Reads comments: lines beginning with '#' */
     numlinepar=0;
   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);
       numlinepar++;
     puts(line);      puts(line);
     fputs(line,ficparo);      fputs(line,ficparo);
       fputs(line,ficlog);
   }    }
   ungetc(c,ficpar);    ungetc(c,ficpar);
   
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);    printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);    fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
   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);
       numlinepar++;
     puts(line);      puts(line);
     fputs(line,ficparo);      fputs(line,ficparo);
       fputs(line,ficlog);
   }    }
   ungetc(c,ficpar);    ungetc(c,ficpar);
     
         
   covar=matrix(0,NCOVMAX,1,n);     covar=matrix(0,NCOVMAX,1,n); 
   cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
Line 3535  int main(int argc, char *argv[]) Line 4188  int main(int argc, char *argv[])
   
   ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */    ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
       npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   /* Read guess parameters */  
   /* Reads comments: lines beginning with '#' */    delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
   while((c=getc(ficpar))=='#' && c!= EOF){    delti=delti3[1][1];
     ungetc(c,ficpar);    /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     fgets(line, MAXLINE, ficpar);    if(mle==-1){ /* Print a wizard for help writing covariance matrix */
     puts(line);      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
     fputs(line,ficparo);      printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
   }    }
   ungetc(c,ficpar);    else if(mle==-3) {
         prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
   for(i=1; i <=nlstate; i++)      fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
     for(j=1; j <=nlstate+ndeath-1; j++){      param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       fscanf(ficpar,"%1d%1d",&i1,&j1);      matcov=matrix(1,npar,1,npar);
       fprintf(ficparo,"%1d%1d",i1,j1);    }
       if(mle==1)    else{
         printf("%1d%1d",i,j);      /* Read guess parameters */
       fprintf(ficlog,"%1d%1d",i,j);      /* Reads comments: lines beginning with '#' */
       for(k=1; k<=ncovmodel;k++){      while((c=getc(ficpar))=='#' && c!= EOF){
         fscanf(ficpar," %lf",&param[i][j][k]);        ungetc(c,ficpar);
         if(mle==1){        fgets(line, MAXLINE, ficpar);
           printf(" %lf",param[i][j][k]);        numlinepar++;
           fprintf(ficlog," %lf",param[i][j][k]);        puts(line);
         }        fputs(line,ficparo);
         else        fputs(line,ficlog);
           fprintf(ficlog," %lf",param[i][j][k]);  
         fprintf(ficparo," %lf",param[i][j][k]);  
       }  
       fscanf(ficpar,"\n");  
       if(mle==1)  
         printf("\n");  
       fprintf(ficlog,"\n");  
       fprintf(ficparo,"\n");  
     }      }
         ungetc(c,ficpar);
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/      
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
   p=param[1][1];  
         p=param[1][1];
   /* Reads comments: lines beginning with '#' */      
   while((c=getc(ficpar))=='#' && c!= EOF){      /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
     ungetc(c,ficpar);      ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);  
     puts(line);  
     fputs(line,ficparo);  
   }  
   ungetc(c,ficpar);  
   
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      for(i=1; i <=nlstate; i++){
   /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */        for(j=1; j <=nlstate+ndeath-1; j++){
   for(i=1; i <=nlstate; i++){          fscanf(ficpar,"%1d%1d",&i1,&j1);
     for(j=1; j <=nlstate+ndeath-1; j++){          if ((i1-i)*(j1-j)!=0){
       fscanf(ficpar,"%1d%1d",&i1,&j1);            printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
       printf("%1d%1d",i,j);            exit(1);
       fprintf(ficparo,"%1d%1d",i1,j1);          }
       for(k=1; k<=ncovmodel;k++){          printf("%1d%1d",i,j);
         fscanf(ficpar,"%le",&delti3[i][j][k]);          fprintf(ficparo,"%1d%1d",i1,j1);
         printf(" %le",delti3[i][j][k]);          fprintf(ficlog,"%1d%1d",i1,j1);
         fprintf(ficparo," %le",delti3[i][j][k]);          for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
       }        }
       fscanf(ficpar,"\n");  
       printf("\n");  
       fprintf(ficparo,"\n");  
     }      }
   }      fflush(ficlog);
   delti=delti3[1][1];  
       delti=delti3[1][1];
   
   
   /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */      /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
       
   /* Reads comments: lines beginning with '#' */      /* Reads comments: lines beginning with '#' */
   while((c=getc(ficpar))=='#' && c!= EOF){      while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
     ungetc(c,ficpar);      ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);  
     puts(line);  
     fputs(line,ficparo);  
   }  
   ungetc(c,ficpar);  
       
   matcov=matrix(1,npar,1,npar);      matcov=matrix(1,npar,1,npar);
   for(i=1; i <=npar; i++){      for(i=1; i <=npar; i++){
     fscanf(ficpar,"%s",&str);        fscanf(ficpar,"%s",&str);
     if(mle==1)        if(mle==1)
       printf("%s",str);          printf("%s",str);
     fprintf(ficlog,"%s",str);        fprintf(ficlog,"%s",str);
     fprintf(ficparo,"%s",str);        fprintf(ficparo,"%s",str);
     for(j=1; j <=i; j++){        for(j=1; j <=i; j++){
       fscanf(ficpar," %le",&matcov[i][j]);          fscanf(ficpar," %le",&matcov[i][j]);
       if(mle==1){          if(mle==1){
         printf(" %.5le",matcov[i][j]);            printf(" %.5le",matcov[i][j]);
           }
         fprintf(ficlog," %.5le",matcov[i][j]);          fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
       }        }
       else        fscanf(ficpar,"\n");
         fprintf(ficlog," %.5le",matcov[i][j]);        numlinepar++;
       fprintf(ficparo," %.5le",matcov[i][j]);        if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
     }      }
     fscanf(ficpar,"\n");      for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
     if(mle==1)      if(mle==1)
       printf("\n");        printf("\n");
     fprintf(ficlog,"\n");      fprintf(ficlog,"\n");
     fprintf(ficparo,"\n");  
   }  
   for(i=1; i <=npar; i++)  
     for(j=i+1;j<=npar;j++)  
       matcov[i][j]=matcov[j][i];  
      
   if(mle==1)  
     printf("\n");  
   fprintf(ficlog,"\n");  
   
   
   /*-------- Rewriting paramater file ----------*/  
   strcpy(rfileres,"r");    /* "Rparameterfile */  
   strcat(rfileres,optionfilefiname);    /* Parameter file first name*/  
   strcat(rfileres,".");    /* */  
   strcat(rfileres,optionfilext);    /* Other files have txt extension */  
   if((ficres =fopen(rfileres,"w"))==NULL) {  
     printf("Problem writing new parameter file: %s\n", fileres);goto end;  
     fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;  
   }  
   fprintf(ficres,"#%s\n",version);  
           
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
   /*-------- data file ----------*/    /*-------- data file ----------*/
   if((fic=fopen(datafile,"r"))==NULL)    {    if((fic=fopen(datafile,"r"))==NULL)    {
     printf("Problem with datafile: %s\n", datafile);goto end;      printf("Problem with datafile: %s\n", datafile);goto end;
Line 3667  int main(int argc, char *argv[]) Line 4365  int main(int argc, char *argv[])
   n= lastobs;    n= lastobs;
   severity = vector(1,maxwav);    severity = vector(1,maxwav);
   outcome=imatrix(1,maxwav+1,1,n);    outcome=imatrix(1,maxwav+1,1,n);
   num=ivector(1,n);    num=lvector(1,n);
   moisnais=vector(1,n);    moisnais=vector(1,n);
   annais=vector(1,n);    annais=vector(1,n);
   moisdc=vector(1,n);    moisdc=vector(1,n);
Line 3703  int main(int argc, char *argv[]) Line 4401  int main(int argc, char *argv[])
       for (j=ncovcol;j>=1;j--){        for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);          cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
       }         } 
       num[i]=atol(stra);        lstra=strlen(stra);
         if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
           stratrunc = &(stra[lstra-9]);
           num[i]=atol(stratrunc);
         }
         else
           num[i]=atol(stra);
                   
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){        /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/          printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
       i=i+1;        i=i+1;
     }      }
Line 3722  int main(int argc, char *argv[]) Line 4426  int main(int argc, char *argv[])
     }*/      }*/
    /*  for (i=1; i<=imx; i++){     /*  for (i=1; i<=imx; i++){
      if (s[4][i]==9)  s[4][i]=-1;        if (s[4][i]==9)  s[4][i]=-1; 
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/       printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
       
  for (i=1; i<=imx; i++)   for (i=1; i<=imx; i++)
     
Line 3825  int main(int argc, char *argv[]) Line 4529  int main(int argc, char *argv[])
         s[m][i]=-1;          s[m][i]=-1;
       }        }
       if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){        if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
         printf("Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);          nberr++;
         fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %d on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);          printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
         s[m][i]=-1;          s[m][i]=-1;
       }        }
       if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){        if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
         printf("Error! Month of death of individual %d on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]);           nberr++;
         fprintf(ficlog,"Error! Month of death of individual %d on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]);           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
         s[m][i]=-1;          fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
       }        }
     }      }
   }    }
Line 3848  int main(int argc, char *argv[]) Line 4554  int main(int argc, char *argv[])
           /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/            /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
             else {              else {
               if ((int)andc[i]!=9999){                if ((int)andc[i]!=9999){
                 printf("Warning negative age at death: %d line:%d\n",num[i],i);                  nbwarn++;
                 fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);                  printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                 agev[m][i]=-1;                  agev[m][i]=-1;
               }                }
             }              }
Line 3884  int main(int argc, char *argv[]) Line 4591  int main(int argc, char *argv[])
   for (i=1; i<=imx; i++)  {    for (i=1; i<=imx; i++)  {
     for(m=firstpass; (m<=lastpass); m++){      for(m=firstpass; (m<=lastpass); m++){
       if (s[m][i] > (nlstate+ndeath)) {        if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
         printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);               printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
         fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);               fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
         goto end;          goto end;
Line 3893  int main(int argc, char *argv[]) Line 4601  int main(int argc, char *argv[])
   
   /*for (i=1; i<=imx; i++){    /*for (i=1; i<=imx; i++){
   for (m=firstpass; (m<lastpass); m++){    for (m=firstpass; (m<lastpass); m++){
      printf("%d %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);       printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
 }  }
   
 }*/  }*/
   
   
   printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    printf("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);     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
   free_vector(severity,1,maxwav);    free_vector(severity,1,maxwav);
   free_imatrix(outcome,1,maxwav+1,1,n);    free_imatrix(outcome,1,maxwav+1,1,n);
   free_vector(moisnais,1,n);    free_vector(moisnais,1,n);
Line 3952  int main(int argc, char *argv[]) Line 4662  int main(int argc, char *argv[])
      }       }
      scanf("%d",i);*/       scanf("%d",i);*/
           
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
   /* 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'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
   
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
Line 3966  int main(int argc, char *argv[]) Line 4738  int main(int argc, char *argv[])
      so we point p on param[1][1] so that p[1] maps on param[1][1][1] */       so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
   p=param[1][1]; /* *(*(*(param +1)+1)+0) */    p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
   if(mle>=1){ /* Could be 1 or 2 */    globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM);
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (j=1; j<=lastpass; j++)
           if (s[j][i]>nlstate) {
             dcwave[i]=j;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];agecens[i]=1.; 
           if (ageexmed[i]>1 & wav[i]>0) agecens[i]=agev[mw[j][i]][i];
           cens[i]=1;
           
           if (ageexmed[i]<1) cens[i]=-1;
           if (agedc[i]< AGESUP & agedc[i]>1 & dcwave[i]>firstpass & dcwave[i]<=lastpass) cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
   
       p[1]=0.1; p[2]=0.1;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow-mort"); 
     strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   }    }
     fprintf(ficrespow,"# Powell\n# iter -2*LL");
     /*  for (i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate+ndeath;j++)
         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     */
     fprintf(ficrespow,"\n");
   
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       fclose(ficrespow);
           
   /*--------- results files --------------*/      hesscov(matcov, p, NDIM,delti, 1e-4, gompertz); 
   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;      for(i=1; i <=NDIM; i++)
   fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");        for(j=i+1;j<=NDIM;j++)
   printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");          matcov[i][j]=matcov[j][i];
   fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");      
   for(i=1,jk=1; i <=nlstate; i++){      printf("\nCovariance matrix\n ");
     for(k=1; k <=(nlstate+ndeath); k++){      for(i=1; i <=NDIM; i++) {
       if (k != i)         for(j=1;j<=NDIM;j++){ 
         {          printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov);
     } /* Endof if mle==-3 */
   
     else{ /* For mle >=1 */
     
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       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,"# 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");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           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);
Line 3995  int main(int argc, char *argv[]) Line 4860  int main(int argc, char *argv[])
           fprintf(ficlog,"\n");            fprintf(ficlog,"\n");
           fprintf(ficres,"\n");            fprintf(ficres,"\n");
         }          }
         }
     }      }
   }      if(mle!=0){
   if(mle==1){        /* Computing hessian and covariance matrix */
     /* Computing hessian and covariance matrix */        ftolhess=ftol; /* Usually correct */
     ftolhess=ftol; /* Usually correct */        hesscov(matcov, p, npar, delti, ftolhess, func);
     hesscov(matcov, p, npar, delti, ftolhess, func);      }
   }      fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
   fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");      printf("# Scales (for hessian or gradient estimation)\n");
   printf("# Scales (for hessian or gradient estimation)\n");      fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
   fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");      for(i=1,jk=1; i <=nlstate; i++){
   for(i=1,jk=1; i <=nlstate; i++){        for(j=1; j <=nlstate+ndeath; j++){
     for(j=1; j <=nlstate+ndeath; j++){          if (j!=i) {
       if (j!=i) {            fprintf(ficres,"%1d%1d",i,j);
         fprintf(ficres,"%1d%1d",i,j);            printf("%1d%1d",i,j);
         printf("%1d%1d",i,j);            fprintf(ficlog,"%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);            for(k=1; k<=ncovmodel;k++){
         for(k=1; k<=ncovmodel;k++){              printf(" %.5e",delti[jk]);
           printf(" %.5e",delti[jk]);              fprintf(ficlog," %.5e",delti[jk]);
           fprintf(ficlog," %.5e",delti[jk]);              fprintf(ficres," %.5e",delti[jk]);
           fprintf(ficres," %.5e",delti[jk]);              jk++;
           jk++;            }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
         }          }
         printf("\n");  
         fprintf(ficlog,"\n");  
         fprintf(ficres,"\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");
   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");      /* # 121 Var(a12)\n\ */
   for(i=1,k=1;i<=npar;i++){      /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /*  if (k>nlstate) k=1;      /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
         i1=(i-1)/(ncovmodel*nlstate)+1;       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
         fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);      /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
         printf("%s%d%d",alph[k],i1,tab[i]);      /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
     */      */
     fprintf(ficres,"%3d",i);      for(itimes=1;itimes<=2;itimes++){
     if(mle==1)        jj=0;
       printf("%3d",i);        for(i=1; i <=nlstate; i++){
     fprintf(ficlog,"%3d",i);          for(j=1; j <=nlstate+ndeath; j++){
     for(j=1; j<=i;j++){            if(j==i) continue;
       fprintf(ficres," %.5e",matcov[i][j]);            for(k=1; k<=ncovmodel;k++){
       if(mle==1)              jj++;
         printf(" %.5e",matcov[i][j]);              ca[0]= k+'a'-1;ca[1]='\0';
       fprintf(ficlog," %.5e",matcov[i][j]);              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){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
     }      }
     fprintf(ficres,"\n");  
     if(mle==1)  
       printf("\n");  
     fprintf(ficlog,"\n");  
     k++;  
   }  
      
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);      
     puts(line);      estepm=0;
     fputs(line,ficparo);      fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
   }      if (estepm==0 || estepm < stepm) estepm=stepm;
   ungetc(c,ficpar);      if (fage <= 2) {
         bage = ageminpar;
   estepm=0;        fage = agemaxpar;
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);      }
   if (estepm==0 || estepm < stepm) estepm=stepm;      
   if (fage <= 2) {      fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     bage = ageminpar;      fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fage = agemaxpar;      fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
   }      
          while((c=getc(ficpar))=='#' && c!= EOF){
   fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");        ungetc(c,ficpar);
   fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);        fgets(line, MAXLINE, ficpar);
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);        puts(line);
            fputs(line,ficparo);
   while((c=getc(ficpar))=='#' && c!= EOF){      }
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  
     puts(line);  
     fputs(line,ficparo);  
   }  
   ungetc(c,ficpar);  
     
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);  
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);  
   fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);  
   printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);  
   fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);  
      
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);      
     puts(line);      fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fputs(line,ficparo);      fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
   }      fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
   ungetc(c,ficpar);      printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
        fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
   dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;      while((c=getc(ficpar))=='#' && c!= EOF){
   dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;        ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
   fscanf(ficpar,"pop_based=%d\n",&popbased);        puts(line);
   fprintf(ficparo,"pop_based=%d\n",popbased);           fputs(line,ficparo);
   fprintf(ficres,"pop_based=%d\n",popbased);         }
     
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);      
     puts(line);      
     fputs(line,ficparo);      dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
   }      dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   ungetc(c,ficpar);      
       fscanf(ficpar,"pop_based=%d\n",&popbased);
   fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);      fprintf(ficparo,"pop_based=%d\n",popbased);   
   fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);      fprintf(ficres,"pop_based=%d\n",popbased);   
   printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);      
   fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);      while((c=getc(ficpar))=='#' && c!= EOF){
   fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);        ungetc(c,ficpar);
   /* day and month of proj2 are not used but only year anproj2.*/        fgets(line, MAXLINE, ficpar);
         puts(line);
   while((c=getc(ficpar))=='#' && c!= EOF){        fputs(line,ficparo);
       }
     ungetc(c,ficpar);      ungetc(c,ficpar);
     fgets(line, MAXLINE, ficpar);      
     puts(line);      fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fputs(line,ficparo);      fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
   }      printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
   ungetc(c,ficpar);      fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);      /* day and month of proj2 are not used but only year anproj2.*/
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);      
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);      
       
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
   /*------------ gnuplot -------------*/      replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
   strcpy(optionfilegnuplot,optionfilefiname);      printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
   strcat(optionfilegnuplot,".gp");      
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {      printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
     printf("Problem with file %s",optionfilegnuplot);                   model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
   }                   jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
   else{        
     fprintf(ficgp,"\n# %s\n", version);      /*------------ free_vector  -------------*/
     fprintf(ficgp,"# %s\n", optionfilegnuplot);      /*  chdir(path); */
     fprintf(ficgp,"set missing 'NaNq'\n");  
   }  
   fclose(ficgp);  
   printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);  
   /*--------- index.htm --------*/  
   
   strcpy(optionfilehtm,optionfile);  
   strcat(optionfilehtm,".htm");  
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {  
     printf("Problem with %s \n",optionfilehtm), exit(0);  
   }  
   
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n  
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n  
 \n  
 Total number of observations=%d <br>\n  
 Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n  
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n  
 <hr  size=\"2\" color=\"#EC5E5E\">  
  <ul><li><h4>Parameter files</h4>\n  
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n  
  - Log file of the run: <a href=\"%s\">%s</a><br>\n  
  - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,agemin,agemax,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);  
    fclose(fichtm);  
   
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);  
    
   /*------------ free_vector  -------------*/  
   chdir(path);  
     
   free_ivector(wav,1,imx);      free_ivector(wav,1,imx);
   free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
   free_imatrix(bh,1,lastpass-firstpass+1,1,imx);      free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
   free_imatrix(mw,1,lastpass-firstpass+1,1,imx);         free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
   free_ivector(num,1,n);      free_lvector(num,1,n);
   free_vector(agedc,1,n);      free_vector(agedc,1,n);
   /*free_matrix(covar,0,NCOVMAX,1,n);*/      /*free_matrix(covar,0,NCOVMAX,1,n);*/
   /*free_matrix(covar,1,NCOVMAX,1,n);*/      /*free_matrix(covar,1,NCOVMAX,1,n);*/
   fclose(ficparo);      fclose(ficparo);
   fclose(ficres);      fclose(ficres);
   
   
   /*--------------- Prevalence limit  (stable prevalence) --------------*/      /*--------------- Prevalence limit  (stable prevalence) --------------*/
       
   strcpy(filerespl,"pl");      strcpy(filerespl,"pl");
   strcat(filerespl,fileres);      strcat(filerespl,fileres);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {      if((ficrespl=fopen(filerespl,"w"))==NULL) {
     printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;        printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;        fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
   }      }
   printf("Computing stable prevalence: result on file '%s' \n", filerespl);      printf("Computing stable prevalence: result on file '%s' \n", filerespl);
   fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);      fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
   fprintf(ficrespl,"#Stable prevalence \n");      fprintf(ficrespl,"#Stable prevalence \n");
   fprintf(ficrespl,"#Age ");      fprintf(ficrespl,"#Age ");
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
   fprintf(ficrespl,"\n");      fprintf(ficrespl,"\n");
       
   prlim=matrix(1,nlstate,1,nlstate);      prlim=matrix(1,nlstate,1,nlstate);
   
   agebase=ageminpar;      agebase=ageminpar;
   agelim=agemaxpar;      agelim=agemaxpar;
   ftolpl=1.e-10;      ftolpl=1.e-10;
   i1=cptcoveff;      i1=cptcoveff;
   if (cptcovn < 1){i1=1;}      if (cptcovn < 1){i1=1;}
   
   for(cptcov=1,k=0;cptcov<=i1;cptcov++){      for(cptcov=1,k=0;cptcov<=i1;cptcov++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
       k=k+1;          k=k+1;
       /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/          /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
       fprintf(ficrespl,"\n#******");          fprintf(ficrespl,"\n#******");
       printf("\n#******");          printf("\n#******");
       fprintf(ficlog,"\n#******");          fprintf(ficlog,"\n#******");
       for(j=1;j<=cptcoveff;j++) {          for(j=1;j<=cptcoveff;j++) {
         fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       }          }
       fprintf(ficrespl,"******\n");          fprintf(ficrespl,"******\n");
       printf("******\n");          printf("******\n");
       fprintf(ficlog,"******\n");          fprintf(ficlog,"******\n");
                   
       for (age=agebase; age<=agelim; age++){          for (age=agebase; age<=agelim; age++){
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
         fprintf(ficrespl,"%.0f ",age );            fprintf(ficrespl,"%.0f ",age );
         for(j=1;j<=cptcoveff;j++)            for(j=1;j<=cptcoveff;j++)
           fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         for(i=1; i<=nlstate;i++)            for(i=1; i<=nlstate;i++)
           fprintf(ficrespl," %.5f", prlim[i][i]);              fprintf(ficrespl," %.5f", prlim[i][i]);
         fprintf(ficrespl,"\n");            fprintf(ficrespl,"\n");
           }
       }        }
     }      }
   }      fclose(ficrespl);
   fclose(ficrespl);  
   
   /*------------- h Pij x at various ages ------------*/      /*------------- h Pij x at various ages ------------*/
       
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);      strcpy(filerespij,"pij");  strcat(filerespij,fileres);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {      if((ficrespij=fopen(filerespij,"w"))==NULL) {
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;        printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;        fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
   }      }
   printf("Computing pij: result on file '%s' \n", filerespij);      printf("Computing pij: result on file '%s' \n", filerespij);
   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);      fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
       
   stepsize=(int) (stepm+YEARM-1)/YEARM;      stepsize=(int) (stepm+YEARM-1)/YEARM;
   /*if (stepm<=24) stepsize=2;*/      /*if (stepm<=24) stepsize=2;*/
   
   agelim=AGESUP;      agelim=AGESUP;
   hstepm=stepsize*YEARM; /* Every year of age */      hstepm=stepsize*YEARM; /* Every year of age */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
   /* hstepm=1;   aff par mois*/      /* hstepm=1;   aff par mois*/
   
   fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");      fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
   for(cptcov=1,k=0;cptcov<=i1;cptcov++){      for(cptcov=1,k=0;cptcov<=i1;cptcov++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
       k=k+1;          k=k+1;
       fprintf(ficrespij,"\n#****** ");          fprintf(ficrespij,"\n#****** ");
       for(j=1;j<=cptcoveff;j++)           for(j=1;j<=cptcoveff;j++) 
         fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       fprintf(ficrespij,"******\n");          fprintf(ficrespij,"******\n");
                   
       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
         /*        nhstepm=nhstepm*YEARM; aff par mois*/            /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         oldm=oldms;savm=savms;            oldm=oldms;savm=savms;
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
         fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");            fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
         for(i=1; i<=nlstate;i++)  
           for(j=1; j<=nlstate+ndeath;j++)  
             fprintf(ficrespij," %1d-%1d",i,j);  
         fprintf(ficrespij,"\n");  
         for (h=0; h<=nhstepm; h++){  
           fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  
           for(i=1; i<=nlstate;i++)            for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)              for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %.5f", p3mat[i][j][h]);                fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");            fprintf(ficrespij,"\n");
         }          }
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         fprintf(ficrespij,"\n");  
       }        }
     }      }
   }  
   
   varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);  
   
   fclose(ficrespij);      varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
       fclose(ficrespij);
   
   /*---------- Forecasting ------------------*/      probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   /*if((stepm == 1) && (strcmp(model,".")==0)){*/      for(i=1;i<=AGESUP;i++)
   if(prevfcast==1){        for(j=1;j<=NCOVMAX;j++)
     /*    if(stepm ==1){*/          for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
       prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);        prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
       /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/        /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
 /*      }  */        /*      }  */
 /*      else{ */        /*      else{ */
 /*        erreur=108; */        /*        erreur=108; */
 /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */        /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
 /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */        /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
 /*      } */        /*      } */
   }      }
       
   
   /*---------- Health expectancies and variances ------------*/      /*---------- Health expectancies and variances ------------*/
   
   strcpy(filerest,"t");      strcpy(filerest,"t");
   strcat(filerest,fileres);      strcat(filerest,fileres);
   if((ficrest=fopen(filerest,"w"))==NULL) {      if((ficrest=fopen(filerest,"w"))==NULL) {
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;        printf("Problem with total LE resultfile: %s\n", filerest);goto end;
     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;        fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
   }      }
   printf("Computing Total LEs with variances: file '%s' \n", filerest);       printf("Computing Total LEs with variances: file '%s' \n", filerest); 
   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);       fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
   strcpy(filerese,"e");      strcpy(filerese,"e");
   strcat(filerese,fileres);      strcat(filerese,fileres);
   if((ficreseij=fopen(filerese,"w"))==NULL) {      if((ficreseij=fopen(filerese,"w"))==NULL) {
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
   }      }
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      printf("Computing Health Expectancies: result on file '%s' \n", filerese);
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);      fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
   strcpy(fileresv,"v");      strcpy(fileresv,"v");
   strcat(fileresv,fileres);      strcat(fileresv,fileres);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {      if((ficresvij=fopen(fileresv,"w"))==NULL) {
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);        fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
   }      }
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);      printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);      fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
   /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */      /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
   prevalence(agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);      prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\      /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
 ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);          ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
   */      */
   
   if (mobilav!=0) {      if (mobilav!=0) {
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){        if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
       fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);          fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       printf(" Error in movingaverage mobilav=%d\n",mobilav);          printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
     }      }
   }  
   
   for(cptcov=1,k=0;cptcov<=i1;cptcov++){      for(cptcov=1,k=0;cptcov<=i1;cptcov++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
       k=k+1;           k=k+1; 
       fprintf(ficrest,"\n#****** ");          fprintf(ficrest,"\n#****** ");
       for(j=1;j<=cptcoveff;j++)           for(j=1;j<=cptcoveff;j++) 
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       fprintf(ficrest,"******\n");          fprintf(ficrest,"******\n");
   
       fprintf(ficreseij,"\n#****** ");          fprintf(ficreseij,"\n#****** ");
       for(j=1;j<=cptcoveff;j++)           for(j=1;j<=cptcoveff;j++) 
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       fprintf(ficreseij,"******\n");          fprintf(ficreseij,"******\n");
   
       fprintf(ficresvij,"\n#****** ");          fprintf(ficresvij,"\n#****** ");
       for(j=1;j<=cptcoveff;j++)           for(j=1;j<=cptcoveff;j++) 
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       fprintf(ficresvij,"******\n");          fprintf(ficresvij,"******\n");
   
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
       oldm=oldms;savm=savms;          oldm=oldms;savm=savms;
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);            evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
     
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
       oldm=oldms;savm=savms;          oldm=oldms;savm=savms;
       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);          varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
       if(popbased==1){          if(popbased==1){
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);            varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
       }          }
   
     
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");          fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);          for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
       fprintf(ficrest,"\n");          fprintf(ficrest,"\n");
   
       epj=vector(1,nlstate+1);          epj=vector(1,nlstate+1);
       for(age=bage; age <=fage ;age++){          for(age=bage; age <=fage ;age++){
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
         if (popbased==1) {            if (popbased==1) {
           if(mobilav ==0){              if(mobilav ==0){
             for(i=1; i<=nlstate;i++)                for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][k];                  prlim[i][i]=probs[(int)age][i][k];
           }else{ /* mobilav */               }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)                for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][k];                  prlim[i][i]=mobaverage[(int)age][i][k];
               }
           }            }
         }  
                   
         fprintf(ficrest," %4.0f",age);            fprintf(ficrest," %4.0f",age);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){            for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
           for(i=1, epj[j]=0.;i <=nlstate;i++) {              for(i=1, epj[j]=0.;i <=nlstate;i++) {
             epj[j] += prlim[i][i]*eij[i][j][(int)age];                epj[j] += prlim[i][i]*eij[i][j][(int)age];
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/                /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
               }
               epj[nlstate+1] +=epj[j];
           }            }
           epj[nlstate+1] +=epj[j];  
         }  
   
         for(i=1, vepp=0.;i <=nlstate;i++)            for(i=1, vepp=0.;i <=nlstate;i++)
           for(j=1;j <=nlstate;j++)              for(j=1;j <=nlstate;j++)
             vepp += vareij[i][j][(int)age];                vepp += vareij[i][j][(int)age];
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));            fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
         for(j=1;j <=nlstate;j++){            for(j=1;j <=nlstate;j++){
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));              fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
             }
             fprintf(ficrest,"\n");
         }          }
         fprintf(ficrest,"\n");          free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
       }          free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
       free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);          free_vector(epj,1,nlstate+1);
       free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);        }
       free_vector(epj,1,nlstate+1);      }
     }      free_vector(weight,1,n);
   }      free_imatrix(Tvard,1,15,1,2);
   free_vector(weight,1,n);      free_imatrix(s,1,maxwav+1,1,n);
   free_imatrix(Tvard,1,15,1,2);      free_matrix(anint,1,maxwav,1,n); 
   free_imatrix(s,1,maxwav+1,1,n);      free_matrix(mint,1,maxwav,1,n);
   free_matrix(anint,1,maxwav,1,n);       free_ivector(cod,1,n);
   free_matrix(mint,1,maxwav,1,n);      free_ivector(tab,1,NCOVMAX);
   free_ivector(cod,1,n);      fclose(ficreseij);
   free_ivector(tab,1,NCOVMAX);      fclose(ficresvij);
   fclose(ficreseij);      fclose(ficrest);
   fclose(ficresvij);      fclose(ficpar);
   fclose(ficrest);    
   fclose(ficpar);      /*------- Variance of stable prevalence------*/   
     
   /*------- Variance of stable prevalence------*/         strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
   strcpy(fileresvpl,"vpl");      if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
   strcat(fileresvpl,fileres);        printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {        exit(0);
     printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);      }
     exit(0);      printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   }  
   printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);      for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
   for(cptcov=1,k=0;cptcov<=i1;cptcov++){          k=k+1;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          fprintf(ficresvpl,"\n#****** ");
       k=k+1;          for(j=1;j<=cptcoveff;j++) 
       fprintf(ficresvpl,"\n#****** ");            fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
       for(j=1;j<=cptcoveff;j++)           fprintf(ficresvpl,"******\n");
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficresvpl,"******\n");  
               
       varpl=matrix(1,nlstate,(int) bage, (int) fage);          varpl=matrix(1,nlstate,(int) bage, (int) fage);
       oldm=oldms;savm=savms;          oldm=oldms;savm=savms;
       varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);          varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
       free_matrix(varpl,1,nlstate,(int) bage, (int)fage);          free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
     }      }
   }  
   
   fclose(ficresvpl);      fclose(ficresvpl);
   
   /*---------- End : free ----------------*/      /*---------- End : free ----------------*/
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);      free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    }  /* mle==-3 arrives here for freeing */
         free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
   free_matrix(covar,0,NCOVMAX,1,n);      free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
   free_matrix(matcov,1,npar,1,npar);      free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
   /*free_vector(delti,1,npar);*/      free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
   free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);     
   free_matrix(agev,1,maxwav,1,imx);      free_matrix(covar,0,NCOVMAX,1,n);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      free_matrix(matcov,1,npar,1,npar);
   if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      /*free_vector(delti,1,npar);*/
   free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
       free_ivector(Tcode,1,100);
   
   
     fflush(fichtm);
     fflush(ficgp);
     
   
   free_ivector(ncodemax,1,8);    if((nberr >0) || (nbwarn>0)){
   free_ivector(Tvar,1,15);      printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
   free_ivector(Tprod,1,15);      fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
   free_ivector(Tvaraff,1,15);  
   free_ivector(Tage,1,15);  
   free_ivector(Tcode,1,100);  
   
   /*  fclose(fichtm);*/  
   /*  fclose(ficgp);*/ /* ALready done */  
     
   
   if(erreur >0){  
     printf("End of Imach with error or warning %d\n",erreur);  
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);  
   }else{    }else{
    printf("End of Imach\n");      printf("End of Imach\n");
    fprintf(ficlog,"End of Imach\n");      fprintf(ficlog,"End of Imach\n");
   }    }
   printf("See log file on %s\n",filelog);    printf("See log file on %s\n",filelog);
   fclose(ficlog);  
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
       (void) gettimeofday(&end_time,&tzp);
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/    tm = *localtime(&end_time.tv_sec);
   /*printf("Total time was %d uSec.\n", total_usecs);*/    tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocaltime at end   %s",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 was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
     fclose(fichtm);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
   /*------ End -----------*/    /*------ End -----------*/
   
   end:    chdir(path);
 #ifdef windows  
   /* chdir(pathcd);*/  
 #endif   
  /*system("wgnuplot graph.plt");*/  
  /*system("../gp37mgw/wgnuplot graph.plt");*/  
  /*system("cd ../gp37mgw");*/  
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/  
   strcpy(plotcmd,GNUPLOTPROGRAM);    strcpy(plotcmd,GNUPLOTPROGRAM);
   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);
   system(plotcmd);    if((outcmd=system(plotcmd)) != 0){
       printf(" Problem with gnuplot\n");
     }
   printf(" Wait...");    printf(" Wait...");
   
  /*#ifdef windows*/  
   while (z[0] != 'q') {    while (z[0] != 'q') {
     /* chdir(path); */      /* chdir(path); */
     printf("\nType e to edit output files, g to graph again, c to start 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"); */
     else if (z[0] == 'e') system(optionfilehtm);      if (z[0] == 'e') 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);
   }    }
   /*#endif */    end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
 }  }
   
   
   

Removed from v.1.78  
changed lines
  Added in v.1.98


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