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version 1.4, 2001/05/02 17:34:41 version 1.82, 2003/06/05 15:57:20
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      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.82  2003/06/05 15:57:20  brouard
   individuals from different ages are interviewed on their health status    Add log in  imach.c and  fullversion number is now printed.
   or degree of  disability. At least a second wave of interviews  
   ("longitudinal") should  measure each new individual health status.  */
   Health expectancies are computed from the transistions observed between  /*
   waves and are computed for each degree of severity of disability (number     Interpolated Markov Chain
   of life states). More degrees you consider, more time is necessary to  
   reach the Maximum Likelihood of the parameters involved in the model.    Short summary of the programme:
   The simplest model is the multinomial logistic model where pij is    
   the probabibility to be observed in state j at the second wave conditional    This program computes Healthy Life Expectancies from
   to be observed in state i at the first wave. Therefore the model is:    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    first survey ("cross") where individuals from different ages are
   is a covariate. If you want to have a more complex model than "constant and    interviewed on their health status or degree of disability (in the
   age", you should modify the program where the markup    case of a health survey which is our main interest) -2- at least a
     *Covariates have to be included here again* invites you to do it.    second wave of interviews ("longitudinal") which measure each change
   More covariates you add, less is the speed of the convergence.    (if any) in individual health status.  Health expectancies are
     computed from the time spent in each health state according to a
   The advantage that this computer programme claims, comes from that if the    model. More health states you consider, more time is necessary to reach the
   delay between waves is not identical for each individual, or if some    Maximum Likelihood of the parameters involved in the model.  The
   individual missed an interview, the information is not rounded or lost, but    simplest model is the multinomial logistic model where pij is the
   taken into account using an interpolation or extrapolation.    probability to be observed in state j at the second wave
   hPijx is the probability to be    conditional to be observed in state i at the first wave. Therefore
   observed in state i at age x+h conditional to the observed state i at age    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   x. The delay 'h' can be split into an exact number (nh*stepm) of    'age' is age and 'sex' is a covariate. If you want to have a more
   unobserved intermediate  states. This elementary transition (by month or    complex model than "constant and age", you should modify the program
   quarter trimester, semester or year) is model as a multinomial logistic.    where the markup *Covariates have to be included here again* invites
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    you to do it.  More covariates you add, slower the
   and the contribution of each individual to the likelihood is simply hPijx.    convergence.
   
   Also this programme outputs the covariance matrix of the parameters but also    The advantage of this computer programme, compared to a simple
   of the life expectancies. It also computes the prevalence limits.    multinomial logistic model, is clear when the delay between waves is not
      identical for each individual. Also, if a individual missed an
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    intermediate interview, the information is lost, but taken into
            Institut national d'études démographiques, Paris.    account using an interpolation or extrapolation.  
   This software have been partly granted by Euro-REVES, a concerted action  
   from the European Union.    hPijx is the probability to be observed in state i at age x+h
   It is copyrighted identically to a GNU software product, ie programme and    conditional to the observed state i at age x. The delay 'h' can be
   software can be distributed freely for non commercial use. Latest version    split into an exact number (nh*stepm) of unobserved intermediate
   can be accessed at http://euroreves.ined.fr/imach .    states. This elementary transition (by month, quarter,
   **********************************************************************/    semester or year) is modelled as a multinomial logistic.  The hPx
      matrix is simply the matrix product of nh*stepm elementary matrices
 #include <math.h>    and the contribution of each individual to the likelihood is simply
 #include <stdio.h>    hPijx.
 #include <stdlib.h>  
 #include <unistd.h>    Also this programme outputs the covariance matrix of the parameters but also
     of the life expectancies. It also computes the stable prevalence. 
 #define MAXLINE 256    
 #define FILENAMELENGTH 80    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 /*#define DEBUG*/             Institut national d'études démographiques, Paris.
 #define windows    This software have been partly granted by Euro-REVES, a concerted action
     from the European Union.
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    It is copyrighted identically to a GNU software product, ie programme and
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    software can be distributed freely for non commercial use. Latest version
     can be accessed at http://euroreves.ined.fr/imach .
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 #define NCOVMAX 8 /* Maximum number of covariates */    
 #define MAXN 20000    **********************************************************************/
 #define YEARM 12. /* Number of months per year */  /*
 #define AGESUP 130    main
 #define AGEBASE 40    read parameterfile
     read datafile
     concatwav
 int nvar;    if (mle >= 1)
 static int cptcov;      mlikeli
 int cptcovn;    print results files
 int npar=NPARMAX;    if mle==1 
 int nlstate=2; /* Number of live states */       computes hessian
 int ndeath=1; /* Number of dead states */    read end of parameter file: agemin, agemax, bage, fage, estepm
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */        begin-prev-date,...
     open gnuplot file
 int *wav; /* Number of waves for this individuual 0 is possible */    open html file
 int maxwav; /* Maxim number of waves */    stable prevalence
 int mle, weightopt;     for age prevalim()
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    h Pij x
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    variance of p varprob
 double **oldm, **newm, **savm; /* Working pointers to matrices */    forecasting if prevfcast==1 prevforecast call prevalence()
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    health expectancies
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;    Variance-covariance of DFLE
 FILE *ficgp, *fichtm;    prevalence()
 FILE *ficreseij;     movingaverage()
   char filerese[FILENAMELENGTH];    varevsij() 
  FILE  *ficresvij;    if popbased==1 varevsij(,popbased)
   char fileresv[FILENAMELENGTH];    total life expectancies
  FILE  *ficresvpl;    Variance of stable prevalence
   char fileresvpl[FILENAMELENGTH];   end
   */
   
   
   
 #define NR_END 1   
 #define FREE_ARG char*  #include <math.h>
 #define FTOL 1.0e-10  #include <stdio.h>
   #include <stdlib.h>
 #define NRANSI  #include <unistd.h>
 #define ITMAX 200  
   #define MAXLINE 256
 #define TOL 2.0e-4  #define GNUPLOTPROGRAM "gnuplot"
   /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #define CGOLD 0.3819660  #define FILENAMELENGTH 80
 #define ZEPS 1.0e-10  /*#define DEBUG*/
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  #define windows
   #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #define GOLD 1.618034  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 #define GLIMIT 100.0  
 #define TINY 1.0e-20  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  #define NINTERVMAX 8
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
    #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  #define NCOVMAX 8 /* Maximum number of covariates */
 #define rint(a) floor(a+0.5)  #define MAXN 20000
   #define YEARM 12. /* Number of months per year */
 static double sqrarg;  #define AGESUP 130
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  #define AGEBASE 40
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  #ifdef windows
   #define DIRSEPARATOR '\\'
 int imx;  #define ODIRSEPARATOR '/'
 int stepm;  #else
 /* Stepm, step in month: minimum step interpolation*/  #define DIRSEPARATOR '/'
   #define ODIRSEPARATOR '\\'
 int m,nb;  #endif
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  /* $Id$ */
 double **pmmij;  /* $State$ */
   
 double *weight;  char version[]="Imach version 0.95a1, June 2003, INED-EUROREVES ";
 int **s; /* Status */  char fullversion[]="$Revision$ $Date$"; 
 double *agedc, **covar, idx;  int erreur; /* Error number */
 int **nbcode, *Tcode, *Tvar, **codtab;  int nvar;
   int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  int npar=NPARMAX;
 double ftolhess; /* Tolerance for computing hessian */  int nlstate=2; /* Number of live states */
   int ndeath=1; /* Number of dead states */
   int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 /******************************************/  int popbased=0;
   
 void replace(char *s, char*t)  int *wav; /* Number of waves for this individuual 0 is possible */
 {  int maxwav; /* Maxim number of waves */
   int i;  int jmin, jmax; /* min, max spacing between 2 waves */
   int lg=20;  int mle, weightopt;
   i=0;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   lg=strlen(t);  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   for(i=0; i<= lg; i++) {  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
     (s[i] = t[i]);             * wave mi and wave mi+1 is not an exact multiple of stepm. */
     if (t[i]== '\\') s[i]='/';  double jmean; /* Mean space between 2 waves */
   }  double **oldm, **newm, **savm; /* Working pointers to matrices */
 }  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 int nbocc(char *s, char occ)  FILE *ficlog, *ficrespow;
 {  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   int i,j=0;  FILE *ficresprobmorprev;
   int lg=20;  FILE *fichtm; /* Html File */
   i=0;  FILE *ficreseij;
   lg=strlen(s);  char filerese[FILENAMELENGTH];
   for(i=0; i<= lg; i++) {  FILE  *ficresvij;
   if  (s[i] == occ ) j++;  char fileresv[FILENAMELENGTH];
   }  FILE  *ficresvpl;
   return j;  char fileresvpl[FILENAMELENGTH];
 }  char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 void cutv(char *u,char *v, char*t, char occ)  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 {  
   int i,lg,j,p;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   i=0;  char filelog[FILENAMELENGTH]; /* Log file */
   for(j=0; j<=strlen(t)-1; j++) {  char filerest[FILENAMELENGTH];
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  char fileregp[FILENAMELENGTH];
   }  char popfile[FILENAMELENGTH];
   
   lg=strlen(t);  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
   for(j=0; j<p; j++) {  
     (u[j] = t[j]);  #define NR_END 1
     u[p]='\0';  #define FREE_ARG char*
   }  #define FTOL 1.0e-10
   
    for(j=0; j<= lg; j++) {  #define NRANSI 
     if (j>=(p+1))(v[j-p-1] = t[j]);  #define ITMAX 200 
   }  
 }  #define TOL 2.0e-4 
   
 /********************** nrerror ********************/  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
 void nrerror(char error_text[])  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 {  
   fprintf(stderr,"ERREUR ...\n");  #define GOLD 1.618034 
   fprintf(stderr,"%s\n",error_text);  #define GLIMIT 100.0 
   exit(1);  #define TINY 1.0e-20 
 }  
 /*********************** vector *******************/  static double maxarg1,maxarg2;
 double *vector(int nl, int nh)  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 {  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   double *v;    
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   if (!v) nrerror("allocation failure in vector");  #define rint(a) floor(a+0.5)
   return v-nl+NR_END;  
 }  static double sqrarg;
   #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 /************************ free vector ******************/  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 void free_vector(double*v, int nl, int nh)  
 {  int imx; 
   free((FREE_ARG)(v+nl-NR_END));  int stepm;
 }  /* Stepm, step in month: minimum step interpolation*/
   
 /************************ivector *******************************/  int estepm;
 int *ivector(long nl,long nh)  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 {  
   int *v;  int m,nb;
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
   if (!v) nrerror("allocation failure in ivector");  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   return v-nl+NR_END;  double **pmmij, ***probs;
 }  double dateintmean=0;
   
 /******************free ivector **************************/  double *weight;
 void free_ivector(int *v, long nl, long nh)  int **s; /* Status */
 {  double *agedc, **covar, idx;
   free((FREE_ARG)(v+nl-NR_END));  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 }  
   double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 /******************* imatrix *******************************/  double ftolhess; /* Tolerance for computing hessian */
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  /**************** split *************************/
 {  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  {
   int **m;    char  *ss;                            /* pointer */
      int   l1, l2;                         /* length counters */
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    l1 = strlen(path );                   /* length of path */
   if (!m) nrerror("allocation failure 1 in matrix()");    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   m += NR_END;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   m -= nrl;    if ( ss == NULL ) {                   /* no directory, so use current */
        /*if(strrchr(path, ODIRSEPARATOR )==NULL)
          printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   /* allocate rows and set pointers to them */      /* get current working directory */
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));      /*    extern  char* getcwd ( char *buf , int len);*/
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   m[nrl] += NR_END;        return( GLOCK_ERROR_GETCWD );
   m[nrl] -= ncl;      }
        strcpy( name, path );               /* we've got it */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    } else {                              /* strip direcotry from path */
        ss++;                               /* after this, the filename */
   /* return pointer to array of pointers to rows */      l2 = strlen( ss );                  /* length of filename */
   return m;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 }      strcpy( name, ss );         /* save file name */
       strncpy( dirc, path, l1 - l2 );     /* now the directory */
 /****************** free_imatrix *************************/      dirc[l1-l2] = 0;                    /* add zero */
 void free_imatrix(m,nrl,nrh,ncl,nch)    }
       int **m;    l1 = strlen( dirc );                  /* length of directory */
       long nch,ncl,nrh,nrl;  #ifdef windows
      /* free an int matrix allocated by imatrix() */    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
 {  #else
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   free((FREE_ARG) (m+nrl-NR_END));  #endif
 }    ss = strrchr( name, '.' );            /* find last / */
     ss++;
 /******************* matrix *******************************/    strcpy(ext,ss);                       /* save extension */
 double **matrix(long nrl, long nrh, long ncl, long nch)    l1= strlen( name);
 {    l2= strlen(ss)+1;
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    strncpy( finame, name, l1-l2);
   double **m;    finame[l1-l2]= 0;
     return( 0 );                          /* we're done */
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  }
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  
   m -= nrl;  /******************************************/
   
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  void replace(char *s, char*t)
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  {
   m[nrl] += NR_END;    int i;
   m[nrl] -= ncl;    int lg=20;
     i=0;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    lg=strlen(t);
   return m;    for(i=0; i<= lg; i++) {
 }      (s[i] = t[i]);
       if (t[i]== '\\') s[i]='/';
 /*************************free matrix ************************/    }
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  }
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  int nbocc(char *s, char occ)
   free((FREE_ARG)(m+nrl-NR_END));  {
 }    int i,j=0;
     int lg=20;
 /******************* ma3x *******************************/    i=0;
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    lg=strlen(s);
 {    for(i=0; i<= lg; i++) {
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    if  (s[i] == occ ) j++;
   double ***m;    }
     return j;
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  }
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  void cutv(char *u,char *v, char*t, char occ)
   m -= nrl;  {
     /* cuts string t into u and v where u is ended by char occ excluding it
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");       gives u="abcedf" and v="ghi2j" */
   m[nrl] += NR_END;    int i,lg,j,p=0;
   m[nrl] -= ncl;    i=0;
     for(j=0; j<=strlen(t)-1; j++) {
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     }
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    lg=strlen(t);
   m[nrl][ncl] += NR_END;    for(j=0; j<p; j++) {
   m[nrl][ncl] -= nll;      (u[j] = t[j]);
   for (j=ncl+1; j<=nch; j++)    }
     m[nrl][j]=m[nrl][j-1]+nlay;       u[p]='\0';
    
   for (i=nrl+1; i<=nrh; i++) {     for(j=0; j<= lg; j++) {
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;      if (j>=(p+1))(v[j-p-1] = t[j]);
     for (j=ncl+1; j<=nch; j++)    }
       m[i][j]=m[i][j-1]+nlay;  }
   }  
   return m;  /********************** nrerror ********************/
 }  
   void nrerror(char error_text[])
 /*************************free ma3x ************************/  {
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    fprintf(stderr,"ERREUR ...\n");
 {    fprintf(stderr,"%s\n",error_text);
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    exit(EXIT_FAILURE);
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  }
   free((FREE_ARG)(m+nrl-NR_END));  /*********************** vector *******************/
 }  double *vector(int nl, int nh)
   {
 /***************** f1dim *************************/    double *v;
 extern int ncom;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 extern double *pcom,*xicom;    if (!v) nrerror("allocation failure in vector");
 extern double (*nrfunc)(double []);    return v-nl+NR_END;
    }
 double f1dim(double x)  
 {  /************************ free vector ******************/
   int j;  void free_vector(double*v, int nl, int nh)
   double f;  {
   double *xt;    free((FREE_ARG)(v+nl-NR_END));
    }
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  /************************ivector *******************************/
   f=(*nrfunc)(xt);  char *cvector(long nl,long nh)
   free_vector(xt,1,ncom);  {
   return f;    char *v;
 }    v=(char *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(char)));
     if (!v) nrerror("allocation failure in cvector");
 /*****************brent *************************/    return v-nl+NR_END;
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  }
 {  
   int iter;  /******************free ivector **************************/
   double a,b,d,etemp;  void free_cvector(char *v, long nl, long nh)
   double fu,fv,fw,fx;  {
   double ftemp;    free((FREE_ARG)(v+nl-NR_END));
   double p,q,r,tol1,tol2,u,v,w,x,xm;  }
   double e=0.0;  
    /************************ivector *******************************/
   a=(ax < cx ? ax : cx);  int *ivector(long nl,long nh)
   b=(ax > cx ? ax : cx);  {
   x=w=v=bx;    int *v;
   fw=fv=fx=(*f)(x);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   for (iter=1;iter<=ITMAX;iter++) {    if (!v) nrerror("allocation failure in ivector");
     xm=0.5*(a+b);    return v-nl+NR_END;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  }
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);  /******************free ivector **************************/
 #ifdef DEBUG  void free_ivector(int *v, long nl, long nh)
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  {
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    free((FREE_ARG)(v+nl-NR_END));
 #endif  }
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  
       *xmin=x;  /******************* imatrix *******************************/
       return fx;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     }       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     ftemp=fu;  { 
     if (fabs(e) > tol1) {    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       r=(x-w)*(fx-fv);    int **m; 
       q=(x-v)*(fx-fw);    
       p=(x-v)*q-(x-w)*r;    /* allocate pointers to rows */ 
       q=2.0*(q-r);    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       if (q > 0.0) p = -p;    if (!m) nrerror("allocation failure 1 in matrix()"); 
       q=fabs(q);    m += NR_END; 
       etemp=e;    m -= nrl; 
       e=d;    
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    /* allocate rows and set pointers to them */ 
       else {    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
         d=p/q;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
         u=x+d;    m[nrl] += NR_END; 
         if (u-a < tol2 || b-u < tol2)    m[nrl] -= ncl; 
           d=SIGN(tol1,xm-x);    
       }    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     } else {    
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    /* return pointer to array of pointers to rows */ 
     }    return m; 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  } 
     fu=(*f)(u);  
     if (fu <= fx) {  /****************** free_imatrix *************************/
       if (u >= x) a=x; else b=x;  void free_imatrix(m,nrl,nrh,ncl,nch)
       SHFT(v,w,x,u)        int **m;
         SHFT(fv,fw,fx,fu)        long nch,ncl,nrh,nrl; 
         } else {       /* free an int matrix allocated by imatrix() */ 
           if (u < x) a=u; else b=u;  { 
           if (fu <= fw || w == x) {    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
             v=w;    free((FREE_ARG) (m+nrl-NR_END)); 
             w=u;  } 
             fv=fw;  
             fw=fu;  /******************* matrix *******************************/
           } else if (fu <= fv || v == x || v == w) {  double **matrix(long nrl, long nrh, long ncl, long nch)
             v=u;  {
             fv=fu;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
           }    double **m;
         }  
   }    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   nrerror("Too many iterations in brent");    if (!m) nrerror("allocation failure 1 in matrix()");
   *xmin=x;    m += NR_END;
   return fx;    m -= nrl;
 }  
     m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 /****************** mnbrak ***********************/    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    m[nrl] -= ncl;
             double (*func)(double))  
 {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   double ulim,u,r,q, dum;    return m;
   double fu;    /* print *(*(m+1)+70) ou print m[1][70]; print m+1 or print &(m[1]) 
       */
   *fa=(*func)(*ax);  }
   *fb=(*func)(*bx);  
   if (*fb > *fa) {  /*************************free matrix ************************/
     SHFT(dum,*ax,*bx,dum)  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       SHFT(dum,*fb,*fa,dum)  {
       }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   *cx=(*bx)+GOLD*(*bx-*ax);    free((FREE_ARG)(m+nrl-NR_END));
   *fc=(*func)(*cx);  }
   while (*fb > *fc) {  
     r=(*bx-*ax)*(*fb-*fc);  /******************* ma3x *******************************/
     q=(*bx-*cx)*(*fb-*fa);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  {
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     ulim=(*bx)+GLIMIT*(*cx-*bx);    double ***m;
     if ((*bx-u)*(u-*cx) > 0.0) {  
       fu=(*func)(u);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     } else if ((*cx-u)*(u-ulim) > 0.0) {    if (!m) nrerror("allocation failure 1 in matrix()");
       fu=(*func)(u);    m += NR_END;
       if (fu < *fc) {    m -= nrl;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
           }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    m[nrl] += NR_END;
       u=ulim;    m[nrl] -= ncl;
       fu=(*func)(u);  
     } else {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       u=(*cx)+GOLD*(*cx-*bx);  
       fu=(*func)(u);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     }    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     SHFT(*ax,*bx,*cx,u)    m[nrl][ncl] += NR_END;
       SHFT(*fa,*fb,*fc,fu)    m[nrl][ncl] -= nll;
       }    for (j=ncl+1; j<=nch; j++) 
 }      m[nrl][j]=m[nrl][j-1]+nlay;
     
 /*************** linmin ************************/    for (i=nrl+1; i<=nrh; i++) {
       m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
 int ncom;      for (j=ncl+1; j<=nch; j++) 
 double *pcom,*xicom;        m[i][j]=m[i][j-1]+nlay;
 double (*nrfunc)(double []);    }
      return m; 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
 {             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   double brent(double ax, double bx, double cx,    */
                double (*f)(double), double tol, double *xmin);  }
   double f1dim(double x);  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  /*************************free ma3x ************************/
               double *fc, double (*func)(double));  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   int j;  {
   double xx,xmin,bx,ax;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   double fx,fb,fa;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
      free((FREE_ARG)(m+nrl-NR_END));
   ncom=n;  }
   pcom=vector(1,n);  
   xicom=vector(1,n);  /***************** f1dim *************************/
   nrfunc=func;  extern int ncom; 
   for (j=1;j<=n;j++) {  extern double *pcom,*xicom;
     pcom[j]=p[j];  extern double (*nrfunc)(double []); 
     xicom[j]=xi[j];   
   }  double f1dim(double x) 
   ax=0.0;  { 
   xx=1.0;    int j; 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    double f;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    double *xt; 
 #ifdef DEBUG   
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    xt=vector(1,ncom); 
 #endif    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   for (j=1;j<=n;j++) {    f=(*nrfunc)(xt); 
     xi[j] *= xmin;    free_vector(xt,1,ncom); 
     p[j] += xi[j];    return f; 
   }  } 
   free_vector(xicom,1,n);  
   free_vector(pcom,1,n);  /*****************brent *************************/
 }  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   { 
 /*************** powell ************************/    int iter; 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    double a,b,d,etemp;
             double (*func)(double []))    double fu,fv,fw,fx;
 {    double ftemp;
   void linmin(double p[], double xi[], int n, double *fret,    double p,q,r,tol1,tol2,u,v,w,x,xm; 
               double (*func)(double []));    double e=0.0; 
   int i,ibig,j;   
   double del,t,*pt,*ptt,*xit;    a=(ax < cx ? ax : cx); 
   double fp,fptt;    b=(ax > cx ? ax : cx); 
   double *xits;    x=w=v=bx; 
   pt=vector(1,n);    fw=fv=fx=(*f)(x); 
   ptt=vector(1,n);    for (iter=1;iter<=ITMAX;iter++) { 
   xit=vector(1,n);      xm=0.5*(a+b); 
   xits=vector(1,n);      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   *fret=(*func)(p);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   for (j=1;j<=n;j++) pt[j]=p[j];      printf(".");fflush(stdout);
   for (*iter=1;;++(*iter)) {      fprintf(ficlog,".");fflush(ficlog);
     fp=(*fret);  #ifdef DEBUG
     ibig=0;      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     del=0.0;      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     for (i=1;i<=n;i++)  #endif
       printf(" %d %.12f",i, p[i]);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     printf("\n");        *xmin=x; 
     for (i=1;i<=n;i++) {        return fx; 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];      } 
       fptt=(*fret);      ftemp=fu;
 #ifdef DEBUG      if (fabs(e) > tol1) { 
       printf("fret=%lf \n",*fret);        r=(x-w)*(fx-fv); 
 #endif        q=(x-v)*(fx-fw); 
       printf("%d",i);fflush(stdout);        p=(x-v)*q-(x-w)*r; 
       linmin(p,xit,n,fret,func);        q=2.0*(q-r); 
       if (fabs(fptt-(*fret)) > del) {        if (q > 0.0) p = -p; 
         del=fabs(fptt-(*fret));        q=fabs(q); 
         ibig=i;        etemp=e; 
       }        e=d; 
 #ifdef DEBUG        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
       printf("%d %.12e",i,(*fret));          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       for (j=1;j<=n;j++) {        else { 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);          d=p/q; 
         printf(" x(%d)=%.12e",j,xit[j]);          u=x+d; 
       }          if (u-a < tol2 || b-u < tol2) 
       for(j=1;j<=n;j++)            d=SIGN(tol1,xm-x); 
         printf(" p=%.12e",p[j]);        } 
       printf("\n");      } else { 
 #endif        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     }      } 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
 #ifdef DEBUG      fu=(*f)(u); 
       int k[2],l;      if (fu <= fx) { 
       k[0]=1;        if (u >= x) a=x; else b=x; 
       k[1]=-1;        SHFT(v,w,x,u) 
       printf("Max: %.12e",(*func)(p));          SHFT(fv,fw,fx,fu) 
       for (j=1;j<=n;j++)          } else { 
         printf(" %.12e",p[j]);            if (u < x) a=u; else b=u; 
       printf("\n");            if (fu <= fw || w == x) { 
       for(l=0;l<=1;l++) {              v=w; 
         for (j=1;j<=n;j++) {              w=u; 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];              fv=fw; 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);              fw=fu; 
         }            } else if (fu <= fv || v == x || v == w) { 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));              v=u; 
       }              fv=fu; 
 #endif            } 
           } 
     } 
       free_vector(xit,1,n);    nrerror("Too many iterations in brent"); 
       free_vector(xits,1,n);    *xmin=x; 
       free_vector(ptt,1,n);    return fx; 
       free_vector(pt,1,n);  } 
       return;  
     }  /****************** mnbrak ***********************/
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  
     for (j=1;j<=n;j++) {  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       ptt[j]=2.0*p[j]-pt[j];              double (*func)(double)) 
       xit[j]=p[j]-pt[j];  { 
       pt[j]=p[j];    double ulim,u,r,q, dum;
     }    double fu; 
     fptt=(*func)(ptt);   
     if (fptt < fp) {    *fa=(*func)(*ax); 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    *fb=(*func)(*bx); 
       if (t < 0.0) {    if (*fb > *fa) { 
         linmin(p,xit,n,fret,func);      SHFT(dum,*ax,*bx,dum) 
         for (j=1;j<=n;j++) {        SHFT(dum,*fb,*fa,dum) 
           xi[j][ibig]=xi[j][n];        } 
           xi[j][n]=xit[j];    *cx=(*bx)+GOLD*(*bx-*ax); 
         }    *fc=(*func)(*cx); 
 #ifdef DEBUG    while (*fb > *fc) { 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      r=(*bx-*ax)*(*fb-*fc); 
         for(j=1;j<=n;j++)      q=(*bx-*cx)*(*fb-*fa); 
           printf(" %.12e",xit[j]);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         printf("\n");        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 #endif      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       }      if ((*bx-u)*(u-*cx) > 0.0) { 
     }        fu=(*func)(u); 
   }      } else if ((*cx-u)*(u-ulim) > 0.0) { 
 }        fu=(*func)(u); 
         if (fu < *fc) { 
 /**** Prevalence limit ****************/          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
             SHFT(*fb,*fc,fu,(*func)(u)) 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)            } 
 {      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit        u=ulim; 
      matrix by transitions matrix until convergence is reached */        fu=(*func)(u); 
       } else { 
   int i, ii,j,k;        u=(*cx)+GOLD*(*cx-*bx); 
   double min, max, maxmin, maxmax,sumnew=0.;        fu=(*func)(u); 
   double **matprod2();      } 
   double **out, cov[NCOVMAX], **pmij();      SHFT(*ax,*bx,*cx,u) 
   double **newm;        SHFT(*fa,*fb,*fc,fu) 
   double agefin, delaymax=50 ; /* Max number of years to converge */        } 
   } 
   for (ii=1;ii<=nlstate+ndeath;ii++)  
     for (j=1;j<=nlstate+ndeath;j++){  /*************** linmin ************************/
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  
     }  int ncom; 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  double *pcom,*xicom;
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  double (*nrfunc)(double []); 
     newm=savm;   
     /* Covariates have to be included here again */  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     cov[1]=1.;  { 
     cov[2]=agefin;    double brent(double ax, double bx, double cx, 
     if (cptcovn>0){                 double (*f)(double), double tol, double *xmin); 
       for (k=1; k<=cptcovn;k++) {cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];/*printf("Tcode[ij]=%d nbcode=%d\n",Tcode[ij],nbcode[k][Tcode[ij]]);*/}    double f1dim(double x); 
     }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);                double *fc, double (*func)(double)); 
     int j; 
     savm=oldm;    double xx,xmin,bx,ax; 
     oldm=newm;    double fx,fb,fa;
     maxmax=0.;   
     for(j=1;j<=nlstate;j++){    ncom=n; 
       min=1.;    pcom=vector(1,n); 
       max=0.;    xicom=vector(1,n); 
       for(i=1; i<=nlstate; i++) {    nrfunc=func; 
         sumnew=0;    for (j=1;j<=n;j++) { 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];      pcom[j]=p[j]; 
         prlim[i][j]= newm[i][j]/(1-sumnew);      xicom[j]=xi[j]; 
         max=FMAX(max,prlim[i][j]);    } 
         min=FMIN(min,prlim[i][j]);    ax=0.0; 
       }    xx=1.0; 
       maxmin=max-min;    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       maxmax=FMAX(maxmax,maxmin);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     }  #ifdef DEBUG
     if(maxmax < ftolpl){    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       return prlim;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     }  #endif
   }    for (j=1;j<=n;j++) { 
 }      xi[j] *= xmin; 
       p[j] += xi[j]; 
 /*************** transition probabilities **********/    } 
     free_vector(xicom,1,n); 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    free_vector(pcom,1,n); 
 {  } 
   double s1, s2;  
   /*double t34;*/  /*************** powell ************************/
   int i,j,j1, nc, ii, jj;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
               double (*func)(double [])) 
     for(i=1; i<= nlstate; i++){  { 
     for(j=1; j<i;j++){    void linmin(double p[], double xi[], int n, double *fret, 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){                double (*func)(double [])); 
         /*s2 += param[i][j][nc]*cov[nc];*/    int i,ibig,j; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    double del,t,*pt,*ptt,*xit;
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    double fp,fptt;
       }    double *xits;
       ps[i][j]=s2;    pt=vector(1,n); 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    ptt=vector(1,n); 
     }    xit=vector(1,n); 
     for(j=i+1; j<=nlstate+ndeath;j++){    xits=vector(1,n); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    *fret=(*func)(p); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    for (j=1;j<=n;j++) pt[j]=p[j]; 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    for (*iter=1;;++(*iter)) { 
       }      fp=(*fret); 
       ps[i][j]=s2;      ibig=0; 
     }      del=0.0; 
   }      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
   for(i=1; i<= nlstate; i++){      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
      s1=0;      fprintf(ficrespow,"%d %.12f",*iter,*fret);
     for(j=1; j<i; j++)      for (i=1;i<=n;i++) {
       s1+=exp(ps[i][j]);        printf(" %d %.12f",i, p[i]);
     for(j=i+1; j<=nlstate+ndeath; j++)        fprintf(ficlog," %d %.12lf",i, p[i]);
       s1+=exp(ps[i][j]);        fprintf(ficrespow," %.12lf", p[i]);
     ps[i][i]=1./(s1+1.);      }
     for(j=1; j<i; j++)      printf("\n");
       ps[i][j]= exp(ps[i][j])*ps[i][i];      fprintf(ficlog,"\n");
     for(j=i+1; j<=nlstate+ndeath; j++)      fprintf(ficrespow,"\n");
       ps[i][j]= exp(ps[i][j])*ps[i][i];      for (i=1;i<=n;i++) { 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   } /* end i */        fptt=(*fret); 
   #ifdef DEBUG
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){        printf("fret=%lf \n",*fret);
     for(jj=1; jj<= nlstate+ndeath; jj++){        fprintf(ficlog,"fret=%lf \n",*fret);
       ps[ii][jj]=0;  #endif
       ps[ii][ii]=1;        printf("%d",i);fflush(stdout);
     }        fprintf(ficlog,"%d",i);fflush(ficlog);
   }        linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){          del=fabs(fptt-(*fret)); 
     for(jj=1; jj<= nlstate+ndeath; jj++){          ibig=i; 
      printf("%lf ",ps[ii][jj]);        } 
    }  #ifdef DEBUG
     printf("\n ");        printf("%d %.12e",i,(*fret));
     }        fprintf(ficlog,"%d %.12e",i,(*fret));
     printf("\n ");printf("%lf ",cov[2]);*/        for (j=1;j<=n;j++) {
 /*          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   for(i=1; i<= npar; i++) printf("%f ",x[i]);          printf(" x(%d)=%.12e",j,xit[j]);
   goto end;*/          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     return ps;        }
 }        for(j=1;j<=n;j++) {
           printf(" p=%.12e",p[j]);
 /**************** Product of 2 matrices ******************/          fprintf(ficlog," p=%.12e",p[j]);
         }
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        printf("\n");
 {        fprintf(ficlog,"\n");
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  #endif
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */      } 
   /* in, b, out are matrice of pointers which should have been initialized      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
      before: only the contents of out is modified. The function returns  #ifdef DEBUG
      a pointer to pointers identical to out */        int k[2],l;
   long i, j, k;        k[0]=1;
   for(i=nrl; i<= nrh; i++)        k[1]=-1;
     for(k=ncolol; k<=ncoloh; k++)        printf("Max: %.12e",(*func)(p));
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        fprintf(ficlog,"Max: %.12e",(*func)(p));
         out[i][k] +=in[i][j]*b[j][k];        for (j=1;j<=n;j++) {
           printf(" %.12e",p[j]);
   return out;          fprintf(ficlog," %.12e",p[j]);
 }        }
         printf("\n");
         fprintf(ficlog,"\n");
 /************* Higher Matrix Product ***************/        for(l=0;l<=1;l++) {
           for (j=1;j<=n;j++) {
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
 {            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
      duration (i.e. until          }
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
      (typically every 2 years instead of every month which is too big).        }
      Model is determined by parameters x and covariates have to be  #endif
      included manually here.  
   
      */        free_vector(xit,1,n); 
         free_vector(xits,1,n); 
   int i, j, d, h, k;        free_vector(ptt,1,n); 
   double **out, cov[NCOVMAX];        free_vector(pt,1,n); 
   double **newm;        return; 
       } 
   /* Hstepm could be zero and should return the unit matrix */      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   for (i=1;i<=nlstate+ndeath;i++)      for (j=1;j<=n;j++) { 
     for (j=1;j<=nlstate+ndeath;j++){        ptt[j]=2.0*p[j]-pt[j]; 
       oldm[i][j]=(i==j ? 1.0 : 0.0);        xit[j]=p[j]-pt[j]; 
       po[i][j][0]=(i==j ? 1.0 : 0.0);        pt[j]=p[j]; 
     }      } 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      fptt=(*func)(ptt); 
   for(h=1; h <=nhstepm; h++){      if (fptt < fp) { 
     for(d=1; d <=hstepm; d++){        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       newm=savm;        if (t < 0.0) { 
       /* Covariates have to be included here again */          linmin(p,xit,n,fret,func); 
       cov[1]=1.;          for (j=1;j<=n;j++) { 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;            xi[j][ibig]=xi[j][n]; 
       if (cptcovn>0){            xi[j][n]=xit[j]; 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];          }
     }  #ifdef DEBUG
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,          for(j=1;j<=n;j++){
                    pmij(pmmij,cov,ncovmodel,x,nlstate));            printf(" %.12e",xit[j]);
       savm=oldm;            fprintf(ficlog," %.12e",xit[j]);
       oldm=newm;          }
     }          printf("\n");
     for(i=1; i<=nlstate+ndeath; i++)          fprintf(ficlog,"\n");
       for(j=1;j<=nlstate+ndeath;j++) {  #endif
         po[i][j][h]=newm[i][j];        }
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      } 
          */    } 
       }  } 
   } /* end h */  
   return po;  /**** Prevalence limit (stable prevalence)  ****************/
 }  
   double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   {
 /*************** log-likelihood *************/    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
 double func( double *x)       matrix by transitions matrix until convergence is reached */
 {  
   int i, ii, j, k, mi, d;    int i, ii,j,k;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    double min, max, maxmin, maxmax,sumnew=0.;
   double **out;    double **matprod2();
   double sw; /* Sum of weights */    double **out, cov[NCOVMAX], **pmij();
   double lli; /* Individual log likelihood */    double **newm;
   long ipmx;    double agefin, delaymax=50 ; /* Max number of years to converge */
   /*extern weight */  
   /* We are differentiating ll according to initial status */    for (ii=1;ii<=nlstate+ndeath;ii++)
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      for (j=1;j<=nlstate+ndeath;j++){
   /*for(i=1;i<imx;i++)        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 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++){   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
        for(mi=1; mi<= wav[i]-1; mi++){    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       for (ii=1;ii<=nlstate+ndeath;ii++)      newm=savm;
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      /* Covariates have to be included here again */
             for(d=0; d<dh[mi][i]; d++){       cov[2]=agefin;
         newm=savm;    
           cov[1]=1.;        for (k=1; k<=cptcovn;k++) {
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
           if (cptcovn>0){          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
             for (k=1; k<=cptcovn;k++) cov[2+k]=covar[1+k-1][i];        }
             }        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        for (k=1; k<=cptcovprod;k++)
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           savm=oldm;  
           oldm=newm;        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
         /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       } /* end mult */      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
      
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);      savm=oldm;
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/      oldm=newm;
       ipmx +=1;      maxmax=0.;
       sw += weight[i];      for(j=1;j<=nlstate;j++){
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        min=1.;
     } /* end of wave */        max=0.;
   } /* end of individual */        for(i=1; i<=nlstate; i++) {
           sumnew=0;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */          prlim[i][j]= newm[i][j]/(1-sumnew);
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */          max=FMAX(max,prlim[i][j]);
   return -l;          min=FMIN(min,prlim[i][j]);
 }        }
         maxmin=max-min;
         maxmax=FMAX(maxmax,maxmin);
 /*********** Maximum Likelihood Estimation ***************/      }
       if(maxmax < ftolpl){
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        return prlim;
 {      }
   int i,j, iter;    }
   double **xi,*delti;  }
   double fret;  
   xi=matrix(1,npar,1,npar);  /*************** transition probabilities ***************/ 
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++)  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       xi[i][j]=(i==j ? 1.0 : 0.0);  {
   printf("Powell\n");    double s1, s2;
   powell(p,xi,npar,ftol,&iter,&fret,func);    /*double t34;*/
     int i,j,j1, nc, ii, jj;
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));      for(i=1; i<= nlstate; i++){
       for(j=1; j<i;j++){
 }        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
           /*s2 += param[i][j][nc]*cov[nc];*/
 /**** Computes Hessian and covariance matrix ***/          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
 {        }
   double  **a,**y,*x,pd;        ps[i][j]=s2;
   double **hess;        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
   int i, j,jk;      }
   int *indx;      for(j=i+1; j<=nlstate+ndeath;j++){
         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   double hessii(double p[], double delta, int theta, double delti[]);          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   double hessij(double p[], double delti[], int i, int j);          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
   void lubksb(double **a, int npar, int *indx, double b[]) ;        }
   void ludcmp(double **a, int npar, int *indx, double *d) ;        ps[i][j]=s2;
       }
     }
   hess=matrix(1,npar,1,npar);      /*ps[3][2]=1;*/
   
   printf("\nCalculation of the hessian matrix. Wait...\n");    for(i=1; i<= nlstate; i++){
   for (i=1;i<=npar;i++){       s1=0;
     printf("%d",i);fflush(stdout);      for(j=1; j<i; j++)
     hess[i][i]=hessii(p,ftolhess,i,delti);        s1+=exp(ps[i][j]);
     /*printf(" %f ",p[i]);*/      for(j=i+1; j<=nlstate+ndeath; j++)
   }        s1+=exp(ps[i][j]);
       ps[i][i]=1./(s1+1.);
   for (i=1;i<=npar;i++) {      for(j=1; j<i; j++)
     for (j=1;j<=npar;j++)  {        ps[i][j]= exp(ps[i][j])*ps[i][i];
       if (j>i) {      for(j=i+1; j<=nlstate+ndeath; j++)
         printf(".%d%d",i,j);fflush(stdout);        ps[i][j]= exp(ps[i][j])*ps[i][i];
         hess[i][j]=hessij(p,delti,i,j);      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
         hess[j][i]=hess[i][j];    } /* end i */
       }  
     }    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   }      for(jj=1; jj<= nlstate+ndeath; jj++){
   printf("\n");        ps[ii][jj]=0;
         ps[ii][ii]=1;
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");      }
      }
   a=matrix(1,npar,1,npar);  
   y=matrix(1,npar,1,npar);  
   x=vector(1,npar);    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   indx=ivector(1,npar);      for(jj=1; jj<= nlstate+ndeath; jj++){
   for (i=1;i<=npar;i++)       printf("%lf ",ps[ii][jj]);
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];     }
   ludcmp(a,npar,indx,&pd);      printf("\n ");
       }
   for (j=1;j<=npar;j++) {      printf("\n ");printf("%lf ",cov[2]);*/
     for (i=1;i<=npar;i++) x[i]=0;  /*
     x[j]=1;    for(i=1; i<= npar; i++) printf("%f ",x[i]);
     lubksb(a,npar,indx,x);    goto end;*/
     for (i=1;i<=npar;i++){      return ps;
       matcov[i][j]=x[i];  }
     }  
   }  /**************** Product of 2 matrices ******************/
   
   printf("\n#Hessian matrix#\n");  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   for (i=1;i<=npar;i++) {  {
     for (j=1;j<=npar;j++) {    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       printf("%.3e ",hess[i][j]);       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     }    /* in, b, out are matrice of pointers which should have been initialized 
     printf("\n");       before: only the contents of out is modified. The function returns
   }       a pointer to pointers identical to out */
     long i, j, k;
   /* Recompute Inverse */    for(i=nrl; i<= nrh; i++)
   for (i=1;i<=npar;i++)      for(k=ncolol; k<=ncoloh; k++)
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        for(j=ncl,out[i][k]=0.; j<=nch; j++)
   ludcmp(a,npar,indx,&pd);          out[i][k] +=in[i][j]*b[j][k];
   
   /*  printf("\n#Hessian matrix recomputed#\n");    return out;
   }
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;  /************* Higher Matrix Product ***************/
     lubksb(a,npar,indx,x);  
     for (i=1;i<=npar;i++){  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
       y[i][j]=x[i];  {
       printf("%.3e ",y[i][j]);    /* Computes the transition matrix starting at age 'age' over 
     }       'nhstepm*hstepm*stepm' months (i.e. until
     printf("\n");       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   }       nhstepm*hstepm matrices. 
   */       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
        (typically every 2 years instead of every month which is too big 
   free_matrix(a,1,npar,1,npar);       for the memory).
   free_matrix(y,1,npar,1,npar);       Model is determined by parameters x and covariates have to be 
   free_vector(x,1,npar);       included manually here. 
   free_ivector(indx,1,npar);  
   free_matrix(hess,1,npar,1,npar);       */
   
     int i, j, d, h, k;
 }    double **out, cov[NCOVMAX];
     double **newm;
 /*************** hessian matrix ****************/  
 double hessii( double x[], double delta, int theta, double delti[])    /* Hstepm could be zero and should return the unit matrix */
 {    for (i=1;i<=nlstate+ndeath;i++)
   int i;      for (j=1;j<=nlstate+ndeath;j++){
   int l=1, lmax=20;        oldm[i][j]=(i==j ? 1.0 : 0.0);
   double k1,k2;        po[i][j][0]=(i==j ? 1.0 : 0.0);
   double p2[NPARMAX+1];      }
   double res;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    for(h=1; h <=nhstepm; h++){
   double fx;      for(d=1; d <=hstepm; d++){
   int k=0,kmax=10;        newm=savm;
   double l1;        /* Covariates have to be included here again */
         cov[1]=1.;
   fx=func(x);        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   for (i=1;i<=npar;i++) p2[i]=x[i];        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   for(l=0 ; l <=lmax; l++){        for (k=1; k<=cptcovage;k++)
     l1=pow(10,l);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     delts=delt;        for (k=1; k<=cptcovprod;k++)
     for(k=1 ; k <kmax; k=k+1){          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       delt = delta*(l1*k);  
       p2[theta]=x[theta] +delt;  
       k1=func(p2)-fx;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       p2[theta]=x[theta]-delt;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
       k2=func(p2)-fx;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
       /*res= (k1-2.0*fx+k2)/delt/delt; */                     pmij(pmmij,cov,ncovmodel,x,nlstate));
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        savm=oldm;
              oldm=newm;
 #ifdef DEBUG      }
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);      for(i=1; i<=nlstate+ndeath; i++)
 #endif        for(j=1;j<=nlstate+ndeath;j++) {
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          po[i][j][h]=newm[i][j];
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
         k=kmax;           */
       }        }
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    } /* end h */
         k=kmax; l=lmax*10.;    return po;
       }  }
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  
         delts=delt;  
       }  /*************** log-likelihood *************/
     }  double func( double *x)
   }  {
   delti[theta]=delts;    int i, ii, j, k, mi, d, kk;
   return res;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
      double **out;
 }    double sw; /* Sum of weights */
     double lli; /* Individual log likelihood */
 double hessij( double x[], double delti[], int thetai,int thetaj)    int s1, s2;
 {    double bbh, survp;
   int i;    long ipmx;
   int l=1, l1, lmax=20;    /*extern weight */
   double k1,k2,k3,k4,res,fx;    /* We are differentiating ll according to initial status */
   double p2[NPARMAX+1];    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   int k;    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
   fx=func(x);    */
   for (k=1; k<=2; k++) {    cov[1]=1.;
     for (i=1;i<=npar;i++) p2[i]=x[i];  
     p2[thetai]=x[thetai]+delti[thetai]/k;    for(k=1; k<=nlstate; k++) ll[k]=0.;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k1=func(p2)-fx;    if(mle==1){
        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     p2[thetai]=x[thetai]+delti[thetai]/k;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        for(mi=1; mi<= wav[i]-1; mi++){
     k2=func(p2)-fx;          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
     p2[thetai]=x[thetai]-delti[thetai]/k;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     k3=func(p2)-fx;            }
            for(d=0; d<dh[mi][i]; d++){
     p2[thetai]=x[thetai]-delti[thetai]/k;            newm=savm;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     k4=func(p2)-fx;            for (kk=1; kk<=cptcovage;kk++) {
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 #ifdef DEBUG            }
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 #endif                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   }            savm=oldm;
   return res;            oldm=newm;
 }          } /* end mult */
         
 /************** Inverse of matrix **************/          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
 void ludcmp(double **a, int n, int *indx, double *d)          /* 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 
   int i,imax,j,k;           * (in months) between two waves is not a multiple of stepm, we rounded to 
   double big,dum,sum,temp;           * the nearest (and in case of equal distance, to the lowest) interval but now
   double *vv;           * 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
   vv=vector(1,n);           * probability in order to take into account the bias as a fraction of the way
   *d=1.0;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   for (i=1;i<=n;i++) {           * -stepm/2 to stepm/2 .
     big=0.0;           * For stepm=1 the results are the same as for previous versions of Imach.
     for (j=1;j<=n;j++)           * For stepm > 1 the results are less biased than in previous versions. 
       if ((temp=fabs(a[i][j])) > big) big=temp;           */
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          s1=s[mw[mi][i]][i];
     vv[i]=1.0/big;          s2=s[mw[mi+1][i]][i];
   }          bbh=(double)bh[mi][i]/(double)stepm; 
   for (j=1;j<=n;j++) {          /* bias is positive if real duration
     for (i=1;i<j;i++) {           * is higher than the multiple of stepm and negative otherwise.
       sum=a[i][j];           */
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
       a[i][j]=sum;          if( s2 > nlstate){ 
     }            /* i.e. if s2 is a death state and if the date of death is known then the contribution
     big=0.0;               to the likelihood is the probability to die between last step unit time and current 
     for (i=j;i<=n;i++) {               step unit time, which is also the differences between probability to die before dh 
       sum=a[i][j];               and probability to die before dh-stepm . 
       for (k=1;k<j;k++)               In version up to 0.92 likelihood was computed
         sum -= a[i][k]*a[k][j];          as if date of death was unknown. Death was treated as any other
       a[i][j]=sum;          health state: the date of the interview describes the actual state
       if ( (dum=vv[i]*fabs(sum)) >= big) {          and not the date of a change in health state. The former idea was
         big=dum;          to consider that at each interview the state was recorded
         imax=i;          (healthy, disable or death) and IMaCh was corrected; but when we
       }          introduced the exact date of death then we should have modified
     }          the contribution of an exact death to the likelihood. This new
     if (j != imax) {          contribution is smaller and very dependent of the step unit
       for (k=1;k<=n;k++) {          stepm. It is no more the probability to die between last interview
         dum=a[imax][k];          and month of death but the probability to survive from last
         a[imax][k]=a[j][k];          interview up to one month before death multiplied by the
         a[j][k]=dum;          probability to die within a month. Thanks to Chris
       }          Jackson for correcting this bug.  Former versions increased
       *d = -(*d);          mortality artificially. The bad side is that we add another loop
       vv[imax]=vv[j];          which slows down the processing. The difference can be up to 10%
     }          lower mortality.
     indx[j]=imax;            */
     if (a[j][j] == 0.0) a[j][j]=TINY;            lli=log(out[s1][s2] - savm[s1][s2]);
     if (j != n) {          }else{
       dum=1.0/(a[j][j]);            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       for (i=j+1;i<=n;i++) a[i][j] *= dum;            /*  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=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   free_vector(vv,1,n);  /* Doesn't work */          /*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;
           sw += weight[i];
 void lubksb(double **a, int n, int *indx, double b[])          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 {        } /* end of wave */
   int i,ii=0,ip,j;      } /* end of individual */
   double sum;    }  else if(mle==2){
        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   for (i=1;i<=n;i++) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     ip=indx[i];        for(mi=1; mi<= wav[i]-1; mi++){
     sum=b[ip];          for (ii=1;ii<=nlstate+ndeath;ii++)
     b[ip]=b[i];            for (j=1;j<=nlstate+ndeath;j++){
     if (ii)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     else if (sum) ii=i;            }
     b[i]=sum;          for(d=0; d<=dh[mi][i]; d++){
   }            newm=savm;
   for (i=n;i>=1;i--) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     sum=b[i];            for (kk=1; kk<=cptcovage;kk++) {
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     b[i]=sum/a[i][i];            }
   }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
 /************ Frequencies ********************/            oldm=newm;
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)          } /* end mult */
 {  /* Some frequencies */        
            /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          /* But now since version 0.9 we anticipate for bias and large stepm.
   double ***freq; /* Frequencies */           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   double *pp;           * (in months) between two waves is not a multiple of stepm, we rounded to 
   double pos;           * the nearest (and in case of equal distance, to the lowest) interval but now
   FILE *ficresp;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   char fileresp[FILENAMELENGTH];           * (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
   pp=vector(1,nlstate);           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
            * -stepm/2 to stepm/2 .
   strcpy(fileresp,"p");           * For stepm=1 the results are the same as for previous versions of Imach.
   strcat(fileresp,fileres);           * For stepm > 1 the results are less biased than in previous versions. 
   if((ficresp=fopen(fileresp,"w"))==NULL) {           */
     printf("Problem with prevalence resultfile: %s\n", fileresp);          s1=s[mw[mi][i]][i];
     exit(0);          s2=s[mw[mi+1][i]][i];
   }          bbh=(double)bh[mi][i]/(double)stepm; 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          /* bias is positive if real duration
   j1=0;           * is higher than the multiple of stepm and negative otherwise.
            */
   j=cptcovn;          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 */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          /* 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 */
   for(k1=1; k1<=j;k1++){          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
    for(i1=1; i1<=ncodemax[k1];i1++){          /*if(lli ==000.0)*/
        j1++;          /*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;
         for (i=-1; i<=nlstate+ndeath; i++)            sw += weight[i];
          for (jk=-1; jk<=nlstate+ndeath; jk++)            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
            for(m=agemin; m <= agemax+3; m++)        } /* end of wave */
              freq[i][jk][m]=0;      } /* end of individual */
            }  else if(mle==3){  /* exponential inter-extrapolation */
        for (i=1; i<=imx; i++) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          bool=1;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          if  (cptcovn>0) {        for(mi=1; mi<= wav[i]-1; mi++){
            for (z1=1; z1<=cptcovn; z1++)          for (ii=1;ii<=nlstate+ndeath;ii++)
              if (covar[Tvar[z1]][i]!= nbcode[Tvar[z1]][codtab[j1][z1]]) bool=0;            for (j=1;j<=nlstate+ndeath;j++){
          }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           if (bool==1) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
            for(m=firstpass; m<=lastpass-1; m++){            }
              if(agev[m][i]==0) agev[m][i]=agemax+1;          for(d=0; d<dh[mi][i]; d++){
              if(agev[m][i]==1) agev[m][i]=agemax+2;            newm=savm;
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];            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,
         if  (cptcovn>0) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
          fprintf(ficresp, "\n#Variable");            savm=oldm;
          for (z1=1; z1<=cptcovn; z1++) fprintf(ficresp, " V%d=%d",Tvar[z1],nbcode[Tvar[z1]][codtab[j1][z1]]);            oldm=newm;
        }          } /* end mult */
        fprintf(ficresp, "\n#");        
        for(i=1; i<=nlstate;i++)          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);          /* But now since version 0.9 we anticipate for bias and large stepm.
        fprintf(ficresp, "\n");           * 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 
   for(i=(int)agemin; i <= (int)agemax+3; i++){           * the nearest (and in case of equal distance, to the lowest) interval but now
     if(i==(int)agemax+3)           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       printf("Total");           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     else           * probability in order to take into account the bias as a fraction of the way
       printf("Age %d", i);           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     for(jk=1; jk <=nlstate ; jk++){           * -stepm/2 to stepm/2 .
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)           * For stepm=1 the results are the same as for previous versions of Imach.
         pp[jk] += freq[jk][m][i];           * For stepm > 1 the results are less biased than in previous versions. 
     }           */
     for(jk=1; jk <=nlstate ; jk++){          s1=s[mw[mi][i]][i];
       for(m=-1, pos=0; m <=0 ; m++)          s2=s[mw[mi+1][i]][i];
         pos += freq[jk][m][i];          bbh=(double)bh[mi][i]/(double)stepm; 
       if(pp[jk]>=1.e-10)          /* bias is positive if real duration
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);           * is higher than the multiple of stepm and negative otherwise.
       else           */
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          /* 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 */
     for(jk=1; jk <=nlstate ; jk++){          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)          /*if(lli ==000.0)*/
         pp[jk] += freq[jk][m][i];          /*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;
     for(jk=1,pos=0; jk <=nlstate ; jk++)          sw += weight[i];
       pos += pp[jk];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(jk=1; jk <=nlstate ; jk++){        } /* end of wave */
       if(pos>=1.e-5)      } /* end of individual */
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    }else{  /* ml=4 no inter-extrapolation */
       else      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       if( i <= (int) agemax){        for(mi=1; mi<= wav[i]-1; mi++){
         if(pos>=1.e-5)          for (ii=1;ii<=nlstate+ndeath;ii++)
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);            for (j=1;j<=nlstate+ndeath;j++){
       else              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       }            }
     }          for(d=0; d<dh[mi][i]; d++){
     for(jk=-1; jk <=nlstate+ndeath; jk++)            newm=savm;
       for(m=-1; m <=nlstate+ndeath; m++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);            for (kk=1; kk<=cptcovage;kk++) {
     if(i <= (int) agemax)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       fprintf(ficresp,"\n");            }
     printf("\n");          
     }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
  }            savm=oldm;
              oldm=newm;
   fclose(ficresp);          } /* end mult */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        
   free_vector(pp,1,nlstate);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           ipmx +=1;
 }  /* End of Freq */          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 /************* Waves Concatenation ***************/        } /* end of wave */
       } /* end of individual */
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    } /* End of if */
 {    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
      Death is a valid wave (if date is known).    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    return -l;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  }
      and mw[mi+1][i]. dh depends on stepm.  
      */  
   /*********** Maximum Likelihood Estimation ***************/
   int i, mi, m;  
   int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
 float sum=0.;  {
     int i,j, iter;
   for(i=1; i<=imx; i++){    double **xi;
     mi=0;    double fret;
     m=firstpass;    char filerespow[FILENAMELENGTH];
     while(s[m][i] <= nlstate){    xi=matrix(1,npar,1,npar);
       if(s[m][i]>=1)    for (i=1;i<=npar;i++)
         mw[++mi][i]=m;      for (j=1;j<=npar;j++)
       if(m >=lastpass)        xi[i][j]=(i==j ? 1.0 : 0.0);
         break;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
       else    strcpy(filerespow,"pow"); 
         m++;    strcat(filerespow,fileres);
     }/* end while */    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     if (s[m][i] > nlstate){      printf("Problem with resultfile: %s\n", filerespow);
       mi++;     /* Death is another wave */      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       /* if(mi==0)  never been interviewed correctly before death */    }
          /* Only death is a correct wave */    fprintf(ficrespow,"# Powell\n# iter -2*LL");
       mw[mi][i]=m;    for (i=1;i<=nlstate;i++)
     }      for(j=1;j<=nlstate+ndeath;j++)
         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     wav[i]=mi;    fprintf(ficrespow,"\n");
     if(mi==0)    powell(p,xi,npar,ftol,&iter,&fret,func);
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  
   }    fclose(ficrespow);
     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   for(i=1; i<=imx; i++){    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     for(mi=1; mi<wav[i];mi++){    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       if (stepm <=0)  
         dh[mi][i]=1;  }
       else{  
         if (s[mw[mi+1][i]][i] > nlstate) {  /**** Computes Hessian and covariance matrix ***/
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
           if(j=0) j=1;  /* Survives at least one month after exam */  {
         }    double  **a,**y,*x,pd;
         else{    double **hess;
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    int i, j,jk;
           k=k+1;    int *indx;
           if (j >= jmax) jmax=j;  
           else if (j <= jmin)jmin=j;    double hessii(double p[], double delta, int theta, double delti[]);
           sum=sum+j;    double hessij(double p[], double delti[], int i, int j);
         }    void lubksb(double **a, int npar, int *indx, double b[]) ;
         jk= j/stepm;    void ludcmp(double **a, int npar, int *indx, double *d) ;
         jl= j -jk*stepm;  
         ju= j -(jk+1)*stepm;    hess=matrix(1,npar,1,npar);
         if(jl <= -ju)  
           dh[mi][i]=jk;    printf("\nCalculation of the hessian matrix. Wait...\n");
         else    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
           dh[mi][i]=jk+1;    for (i=1;i<=npar;i++){
         if(dh[mi][i]==0)      printf("%d",i);fflush(stdout);
           dh[mi][i]=1; /* At least one step */      fprintf(ficlog,"%d",i);fflush(ficlog);
       }      hess[i][i]=hessii(p,ftolhess,i,delti);
     }      /*printf(" %f ",p[i]);*/
   }      /*printf(" %lf ",hess[i][i]);*/
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);    }
 }    
 /*********** Tricode ****************************/    for (i=1;i<=npar;i++) {
 void tricode(int *Tvar, int **nbcode, int imx)      for (j=1;j<=npar;j++)  {
 {        if (j>i) { 
   int Ndum[80],ij, k, j, i;          printf(".%d%d",i,j);fflush(stdout);
   int cptcode=0;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   for (k=0; k<79; k++) Ndum[k]=0;          hess[i][j]=hessij(p,delti,i,j);
   for (k=1; k<=7; k++) ncodemax[k]=0;          hess[j][i]=hess[i][j];    
            /*printf(" %lf ",hess[i][j]);*/
   for (j=1; j<=cptcovn; j++) {        }
     for (i=1; i<=imx; i++) {      }
       ij=(int)(covar[Tvar[j]][i]);    }
       Ndum[ij]++;    printf("\n");
       if (ij > cptcode) cptcode=ij;    fprintf(ficlog,"\n");
     }  
     /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     for (i=0; i<=cptcode; i++) {    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       if(Ndum[i]!=0) ncodemax[j]++;    
     }    a=matrix(1,npar,1,npar);
      y=matrix(1,npar,1,npar);
     ij=1;    x=vector(1,npar);
     for (i=1; i<=ncodemax[j]; i++) {    indx=ivector(1,npar);
       for (k=0; k<=79; k++) {    for (i=1;i<=npar;i++)
         if (Ndum[k] != 0) {      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
           nbcode[Tvar[j]][ij]=k;    ludcmp(a,npar,indx,&pd);
           ij++;  
         }    for (j=1;j<=npar;j++) {
         if (ij > ncodemax[j]) break;      for (i=1;i<=npar;i++) x[i]=0;
       }        x[j]=1;
     }      lubksb(a,npar,indx,x);
   }        for (i=1;i<=npar;i++){ 
         matcov[i][j]=x[i];
   }      }
     }
 /*********** Health Expectancies ****************/  
     printf("\n#Hessian matrix#\n");
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)    fprintf(ficlog,"\n#Hessian matrix#\n");
 {    for (i=1;i<=npar;i++) { 
   /* Health expectancies */      for (j=1;j<=npar;j++) { 
   int i, j, nhstepm, hstepm, h;        printf("%.3e ",hess[i][j]);
   double age, agelim,hf;        fprintf(ficlog,"%.3e ",hess[i][j]);
   double ***p3mat;      }
        printf("\n");
   fprintf(ficreseij,"# Health expectancies\n");      fprintf(ficlog,"\n");
   fprintf(ficreseij,"# Age");    }
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=nlstate;j++)    /* Recompute Inverse */
       fprintf(ficreseij," %1d-%1d",i,j);    for (i=1;i<=npar;i++)
   fprintf(ficreseij,"\n");      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     ludcmp(a,npar,indx,&pd);
   hstepm=1*YEARM; /*  Every j years of age (in month) */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    /*  printf("\n#Hessian matrix recomputed#\n");
   
   agelim=AGESUP;    for (j=1;j<=npar;j++) {
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      for (i=1;i<=npar;i++) x[i]=0;
     /* nhstepm age range expressed in number of stepm */      x[j]=1;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);      lubksb(a,npar,indx,x);
     /* Typically if 20 years = 20*12/6=40 stepm */      for (i=1;i<=npar;i++){ 
     if (stepm >= YEARM) hstepm=1;        y[i][j]=x[i];
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */        printf("%.3e ",y[i][j]);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        fprintf(ficlog,"%.3e ",y[i][j]);
     /* Computed by stepm unit matrices, product of hstepm matrices, stored      }
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */      printf("\n");
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);        fprintf(ficlog,"\n");
     }
     */
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++)    free_matrix(a,1,npar,1,npar);
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){    free_matrix(y,1,npar,1,npar);
           eij[i][j][(int)age] +=p3mat[i][j][h];    free_vector(x,1,npar);
         }    free_ivector(indx,1,npar);
        free_matrix(hess,1,npar,1,npar);
     hf=1;  
     if (stepm >= YEARM) hf=stepm/YEARM;  
     fprintf(ficreseij,"%.0f",age );  }
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){  /*************** hessian matrix ****************/
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);  double hessii( double x[], double delta, int theta, double delti[])
       }  {
     fprintf(ficreseij,"\n");    int i;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int l=1, lmax=20;
   }    double k1,k2;
 }    double p2[NPARMAX+1];
     double res;
 /************ Variance ******************/    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)    double fx;
 {    int k=0,kmax=10;
   /* Variance of health expectancies */    double l1;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  
   double **newm;    fx=func(x);
   double **dnewm,**doldm;    for (i=1;i<=npar;i++) p2[i]=x[i];
   int i, j, nhstepm, hstepm, h;    for(l=0 ; l <=lmax; l++){
   int k, cptcode;      l1=pow(10,l);
    double *xp;      delts=delt;
   double **gp, **gm;      for(k=1 ; k <kmax; k=k+1){
   double ***gradg, ***trgradg;        delt = delta*(l1*k);
   double ***p3mat;        p2[theta]=x[theta] +delt;
   double age,agelim;        k1=func(p2)-fx;
   int theta;        p2[theta]=x[theta]-delt;
         k2=func(p2)-fx;
    fprintf(ficresvij,"# Covariances of life expectancies\n");        /*res= (k1-2.0*fx+k2)/delt/delt; */
   fprintf(ficresvij,"# Age");        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   for(i=1; i<=nlstate;i++)        
     for(j=1; j<=nlstate;j++)  #ifdef DEBUG
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   fprintf(ficresvij,"\n");        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   #endif
   xp=vector(1,npar);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   dnewm=matrix(1,nlstate,1,npar);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   doldm=matrix(1,nlstate,1,nlstate);          k=kmax;
          }
   hstepm=1*YEARM; /* Every year of age */        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          k=kmax; l=lmax*10.;
   agelim = AGESUP;        }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          delts=delt;
     if (stepm >= YEARM) hstepm=1;        }
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    }
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    delti[theta]=delts;
     gp=matrix(0,nhstepm,1,nlstate);    return res; 
     gm=matrix(0,nhstepm,1,nlstate);    
   }
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient */  double hessij( double x[], double delti[], int thetai,int thetaj)
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  {
       }    int i;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      int l=1, l1, lmax=20;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double k1,k2,k3,k4,res,fx;
       for(j=1; j<= nlstate; j++){    double p2[NPARMAX+1];
         for(h=0; h<=nhstepm; h++){    int k;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    fx=func(x);
         }    for (k=1; k<=2; k++) {
       }      for (i=1;i<=npar;i++) p2[i]=x[i];
          p2[thetai]=x[thetai]+delti[thetai]/k;
       for(i=1; i<=npar; i++) /* Computes gradient */      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      k1=func(p2)-fx;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      p2[thetai]=x[thetai]+delti[thetai]/k;
       for(j=1; j<= nlstate; j++){      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         for(h=0; h<=nhstepm; h++){      k2=func(p2)-fx;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];      p2[thetai]=x[thetai]-delti[thetai]/k;
         }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       }      k3=func(p2)-fx;
       for(j=1; j<= nlstate; j++)    
         for(h=0; h<=nhstepm; h++){      p2[thetai]=x[thetai]-delti[thetai]/k;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         }      k4=func(p2)-fx;
     } /* End theta */      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   #ifdef DEBUG
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     for(h=0; h<=nhstepm; h++)  #endif
       for(j=1; j<=nlstate;j++)    }
         for(theta=1; theta <=npar; theta++)    return res;
           trgradg[h][j][theta]=gradg[h][theta][j];  }
   
     for(i=1;i<=nlstate;i++)  /************** Inverse of matrix **************/
       for(j=1;j<=nlstate;j++)  void ludcmp(double **a, int n, int *indx, double *d) 
         vareij[i][j][(int)age] =0.;  { 
     for(h=0;h<=nhstepm;h++){    int i,imax,j,k; 
       for(k=0;k<=nhstepm;k++){    double big,dum,sum,temp; 
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    double *vv; 
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);   
         for(i=1;i<=nlstate;i++)    vv=vector(1,n); 
           for(j=1;j<=nlstate;j++)    *d=1.0; 
             vareij[i][j][(int)age] += doldm[i][j];    for (i=1;i<=n;i++) { 
       }      big=0.0; 
     }      for (j=1;j<=n;j++) 
     h=1;        if ((temp=fabs(a[i][j])) > big) big=temp; 
     if (stepm >= YEARM) h=stepm/YEARM;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     fprintf(ficresvij,"%.0f ",age );      vv[i]=1.0/big; 
     for(i=1; i<=nlstate;i++)    } 
       for(j=1; j<=nlstate;j++){    for (j=1;j<=n;j++) { 
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);      for (i=1;i<j;i++) { 
       }        sum=a[i][j]; 
     fprintf(ficresvij,"\n");        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     free_matrix(gp,0,nhstepm,1,nlstate);        a[i][j]=sum; 
     free_matrix(gm,0,nhstepm,1,nlstate);      } 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);      big=0.0; 
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      for (i=j;i<=n;i++) { 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        sum=a[i][j]; 
   } /* End age */        for (k=1;k<j;k++) 
            sum -= a[i][k]*a[k][j]; 
   free_vector(xp,1,npar);        a[i][j]=sum; 
   free_matrix(doldm,1,nlstate,1,npar);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   free_matrix(dnewm,1,nlstate,1,nlstate);          big=dum; 
           imax=i; 
 }        } 
       } 
 /************ Variance of prevlim ******************/      if (j != imax) { 
 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)        for (k=1;k<=n;k++) { 
 {          dum=a[imax][k]; 
   /* Variance of prevalence limit */          a[imax][k]=a[j][k]; 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          a[j][k]=dum; 
   double **newm;        } 
   double **dnewm,**doldm;        *d = -(*d); 
   int i, j, nhstepm, hstepm;        vv[imax]=vv[j]; 
   int k, cptcode;      } 
   double *xp;      indx[j]=imax; 
   double *gp, *gm;      if (a[j][j] == 0.0) a[j][j]=TINY; 
   double **gradg, **trgradg;      if (j != n) { 
   double age,agelim;        dum=1.0/(a[j][j]); 
   int theta;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
          } 
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    } 
   fprintf(ficresvpl,"# Age");    free_vector(vv,1,n);  /* Doesn't work */
   for(i=1; i<=nlstate;i++)  ;
       fprintf(ficresvpl," %1d-%1d",i,i);  } 
   fprintf(ficresvpl,"\n");  
   void lubksb(double **a, int n, int *indx, double b[]) 
   xp=vector(1,npar);  { 
   dnewm=matrix(1,nlstate,1,npar);    int i,ii=0,ip,j; 
   doldm=matrix(1,nlstate,1,nlstate);    double sum; 
     
   hstepm=1*YEARM; /* Every year of age */    for (i=1;i<=n;i++) { 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      ip=indx[i]; 
   agelim = AGESUP;      sum=b[ip]; 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      b[ip]=b[i]; 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      if (ii) 
     if (stepm >= YEARM) hstepm=1;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      else if (sum) ii=i; 
     gradg=matrix(1,npar,1,nlstate);      b[i]=sum; 
     gp=vector(1,nlstate);    } 
     gm=vector(1,nlstate);    for (i=n;i>=1;i--) { 
       sum=b[i]; 
     for(theta=1; theta <=npar; theta++){      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       for(i=1; i<=npar; i++){ /* Computes gradient */      b[i]=sum/a[i][i]; 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    } 
       }  } 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)  /************ Frequencies ********************/
         gp[i] = prlim[i][i];  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)
      {  /* Some frequencies */
       for(i=1; i<=npar; i++) /* Computes gradient */    
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    int first;
       for(i=1;i<=nlstate;i++)    double ***freq; /* Frequencies */
         gm[i] = prlim[i][i];    double *pp, **prop;
     double pos,posprop, k2, dateintsum=0,k2cpt=0;
       for(i=1;i<=nlstate;i++)    FILE *ficresp;
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    char fileresp[FILENAMELENGTH];
     } /* End theta */    
     pp=vector(1,nlstate);
     trgradg =matrix(1,nlstate,1,npar);    prop=matrix(1,nlstate,iagemin,iagemax+3);
     strcpy(fileresp,"p");
     for(j=1; j<=nlstate;j++)    strcat(fileresp,fileres);
       for(theta=1; theta <=npar; theta++)    if((ficresp=fopen(fileresp,"w"))==NULL) {
         trgradg[j][theta]=gradg[theta][j];      printf("Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     for(i=1;i<=nlstate;i++)      exit(0);
       varpl[i][(int)age] =0.;    }
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    j1=0;
     for(i=1;i<=nlstate;i++)    
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    j=cptcoveff;
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
     fprintf(ficresvpl,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)    first=1;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));  
     fprintf(ficresvpl,"\n");    for(k1=1; k1<=j;k1++){
     free_vector(gp,1,nlstate);      for(i1=1; i1<=ncodemax[k1];i1++){
     free_vector(gm,1,nlstate);        j1++;
     free_matrix(gradg,1,npar,1,nlstate);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     free_matrix(trgradg,1,nlstate,1,npar);          scanf("%d", i);*/
   } /* End age */        for (i=-1; i<=nlstate+ndeath; i++)  
           for (jk=-1; jk<=nlstate+ndeath; jk++)  
   free_vector(xp,1,npar);            for(m=iagemin; m <= iagemax+3; m++)
   free_matrix(doldm,1,nlstate,1,npar);              freq[i][jk][m]=0;
   free_matrix(dnewm,1,nlstate,1,nlstate);  
       for (i=1; i<=nlstate; i++)  
 }        for(m=iagemin; m <= iagemax+3; m++)
           prop[i][m]=0;
         
         dateintsum=0;
 /***********************************************/        k2cpt=0;
 /**************** Main Program *****************/        for (i=1; i<=imx; i++) {
 /***********************************************/          bool=1;
           if  (cptcovn>0) {
 /*int main(int argc, char *argv[])*/            for (z1=1; z1<=cptcoveff; z1++) 
 int main()              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
 {                bool=0;
           }
   int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;          if (bool==1){
   double agedeb, agefin,hf;            for(m=firstpass; m<=lastpass; m++){
   double agemin=1.e20, agemax=-1.e20;              k2=anint[m][i]+(mint[m][i]/12.);
               if ((k2>=dateprev1) && (k2<=dateprev2)) {
   double fret;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   double **xi,tmp,delta;                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];
   double dum; /* Dummy variable */                if (m<lastpass) {
   double ***p3mat;                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   int *indx;                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
   char line[MAXLINE], linepar[MAXLINE];                }
   char title[MAXLINE];                
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];                  dateintsum=dateintsum+k2;
   char filerest[FILENAMELENGTH];                  k2cpt++;
   char fileregp[FILENAMELENGTH];                }
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];              }
   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,jk,aa,bb, stepsize;        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;  
          if  (cptcovn>0) {
   int hstepm, nhstepm;          fprintf(ficresp, "\n#********** Variable "); 
   double bage, fage, age, agelim, agebase;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   double ftolpl=FTOL;          fprintf(ficresp, "**********\n#");
   double **prlim;        }
   double *severity;        for(i=1; i<=nlstate;i++) 
   double ***param; /* Matrix of parameters */          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   double  *p;        fprintf(ficresp, "\n");
   double **matcov; /* Matrix of covariance */        
   double ***delti3; /* Scale */        for(i=iagemin; i <= iagemax+3; i++){
   double *delti; /* Scale */          if(i==iagemax+3){
   double ***eij, ***vareij;            fprintf(ficlog,"Total");
   double **varpl; /* Variances of prevalence limits by age */          }else{
   double *epj, vepp;            if(first==1){
   char version[80]="Imach version 0.64, May 2000, INED-EUROREVES ";              first=0;
   char *alph[]={"a","a","b","c","d","e"}, str[4];              printf("See log file for details...\n");
   char z[1]="c", occ;            }
 #include <sys/time.h>            fprintf(ficlog,"Age %d", i);
 #include <time.h>          }
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];          for(jk=1; jk <=nlstate ; jk++){
   /* long total_usecs;            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   struct timeval start_time, end_time;              pp[jk] += freq[jk][m][i]; 
            }
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pos=0; m <=0 ; m++)
               pos += freq[jk][m][i];
   printf("\nIMACH, Version 0.64a");            if(pp[jk]>=1.e-10){
   printf("\nEnter the parameter file name: ");              if(first==1){
               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 #ifdef windows              }
   scanf("%s",pathtot);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   cygwin_split_path(pathtot,path,optionfile);            }else{
      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);              if(first==1)
      chdir(path);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   /*size=30;            }
   getcwd(pathcd, size);            }
   printf("pathcd=%s, path=%s, optionfile=%s\n",pathcd,path,optionfile);  
   cutv(path,optionfile,pathtot,'\\');          for(jk=1; jk <=nlstate ; jk++){
   chdir(path);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   replace(pathc,path);              pp[jk] += freq[jk][m][i];
   printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);          }       
   */          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
 #endif            pos += pp[jk];
 #ifdef unix            posprop += prop[jk][i];
   scanf("%s",optionfile);          }
 #endif          for(jk=1; jk <=nlstate ; jk++){
             if(pos>=1.e-5){
 /*-------- arguments in the command line --------*/              if(first==1)
                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   strcpy(fileres,"r");              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   strcat(fileres, optionfile);            }else{
               if(first==1)
   /*---------arguments file --------*/                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {            }
     printf("Problem with optionfile %s\n",optionfile);            if( i <= iagemax){
     goto end;              if(pos>=1.e-5){
   }                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                 probs[i][jk][j1]= pp[jk]/pos;
   strcpy(filereso,"o");                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   strcat(filereso,fileres);              }
   if((ficparo=fopen(filereso,"w"))==NULL) {              else
     printf("Problem with Output resultfile: %s\n", filereso);goto end;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   }            }
           }
   /* Reads comments: lines beginning with '#' */          
   while((c=getc(ficpar))=='#' && c!= EOF){          for(jk=-1; jk <=nlstate+ndeath; jk++)
     ungetc(c,ficpar);            for(m=-1; m <=nlstate+ndeath; m++)
     fgets(line, MAXLINE, ficpar);              if(freq[jk][m][i] !=0 ) {
     puts(line);              if(first==1)
     fputs(line,ficparo);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   }                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   ungetc(c,ficpar);              }
           if(i <= iagemax)
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);            fprintf(ficresp,"\n");
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);          if(first==1)
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);            printf("Others in log...\n");
           fprintf(ficlog,"\n");
   covar=matrix(1,NCOVMAX,1,n);            }
   if (strlen(model)<=1) cptcovn=0;      }
   else {    }
     j=0;    dateintmean=dateintsum/k2cpt; 
     j=nbocc(model,'+');   
     cptcovn=j+1;    fclose(ficresp);
   }    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
     free_vector(pp,1,nlstate);
   ncovmodel=2+cptcovn;    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    /* End of Freq */
    }
   /* Read guess parameters */  
   /* Reads comments: lines beginning with '#' */  /************ Prevalence ********************/
   while((c=getc(ficpar))=='#' && c!= EOF){  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)
     ungetc(c,ficpar);  {  
     fgets(line, MAXLINE, ficpar);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     puts(line);       in each health status at the date of interview (if between dateprev1 and dateprev2).
     fputs(line,ficparo);       We still use firstpass and lastpass as another selection.
   }    */
   ungetc(c,ficpar);   
      int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    double ***freq; /* Frequencies */
     for(i=1; i <=nlstate; i++)    double *pp, **prop;
     for(j=1; j <=nlstate+ndeath-1; j++){    double pos,posprop; 
       fscanf(ficpar,"%1d%1d",&i1,&j1);    double  y2; /* in fractional years */
       fprintf(ficparo,"%1d%1d",i1,j1);    int iagemin, iagemax;
       printf("%1d%1d",i,j);  
       for(k=1; k<=ncovmodel;k++){    iagemin= (int) agemin;
         fscanf(ficpar," %lf",&param[i][j][k]);    iagemax= (int) agemax;
         printf(" %lf",param[i][j][k]);    /*pp=vector(1,nlstate);*/
         fprintf(ficparo," %lf",param[i][j][k]);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
       }    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
       fscanf(ficpar,"\n");    j1=0;
       printf("\n");    
       fprintf(ficparo,"\n");    j=cptcoveff;
     }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
      
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;    for(k1=1; k1<=j;k1++){
   p=param[1][1];      for(i1=1; i1<=ncodemax[k1];i1++){
          j1++;
   /* Reads comments: lines beginning with '#' */        
   while((c=getc(ficpar))=='#' && c!= EOF){        for (i=1; i<=nlstate; i++)  
     ungetc(c,ficpar);          for(m=iagemin; m <= iagemax+3; m++)
     fgets(line, MAXLINE, ficpar);            prop[i][m]=0.0;
     puts(line);       
     fputs(line,ficparo);        for (i=1; i<=imx; i++) { /* Each individual */
   }          bool=1;
   ungetc(c,ficpar);          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */                bool=0;
   for(i=1; i <=nlstate; i++){          } 
     for(j=1; j <=nlstate+ndeath-1; j++){          if (bool==1) { 
       fscanf(ficpar,"%1d%1d",&i1,&j1);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
       printf("%1d%1d",i,j);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
       fprintf(ficparo,"%1d%1d",i1,j1);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
       for(k=1; k<=ncovmodel;k++){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
         fscanf(ficpar,"%le",&delti3[i][j][k]);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         printf(" %le",delti3[i][j][k]);                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
         fprintf(ficparo," %le",delti3[i][j][k]);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
       }                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
       fscanf(ficpar,"\n");                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
       printf("\n");                  prop[s[m][i]][iagemax+3] += weight[i]; 
       fprintf(ficparo,"\n");                } 
     }              }
   }            } /* end selection of waves */
   delti=delti3[1][1];          }
          }
   /* Reads comments: lines beginning with '#' */        for(i=iagemin; i <= iagemax+3; i++){  
   while((c=getc(ficpar))=='#' && c!= EOF){          
     ungetc(c,ficpar);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     fgets(line, MAXLINE, ficpar);            posprop += prop[jk][i]; 
     puts(line);          } 
     fputs(line,ficparo);  
   }          for(jk=1; jk <=nlstate ; jk++){     
   ungetc(c,ficpar);            if( i <=  iagemax){ 
                if(posprop>=1.e-5){ 
   matcov=matrix(1,npar,1,npar);                probs[i][jk][j1]= prop[jk][i]/posprop;
   for(i=1; i <=npar; i++){              } 
     fscanf(ficpar,"%s",&str);            } 
     printf("%s",str);          }/* end jk */ 
     fprintf(ficparo,"%s",str);        }/* end i */ 
     for(j=1; j <=i; j++){      } /* end i1 */
       fscanf(ficpar," %le",&matcov[i][j]);    } /* end k1 */
       printf(" %.5le",matcov[i][j]);    
       fprintf(ficparo," %.5le",matcov[i][j]);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     }    /*free_vector(pp,1,nlstate);*/
     fscanf(ficpar,"\n");    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
     printf("\n");  }  /* End of prevalence */
     fprintf(ficparo,"\n");  
   }  /************* Waves Concatenation ***************/
   for(i=1; i <=npar; i++)  
     for(j=i+1;j<=npar;j++)  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
       matcov[i][j]=matcov[j][i];  {
        /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   printf("\n");       Death is a valid wave (if date is known).
        mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
        dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
    if(mle==1){       and mw[mi+1][i]. dh depends on stepm.
     /*-------- data file ----------*/       */
     if((ficres =fopen(fileres,"w"))==NULL) {  
       printf("Problem with resultfile: %s\n", fileres);goto end;    int i, mi, m;
     }    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     fprintf(ficres,"#%s\n",version);       double sum=0., jmean=0.;*/
        int first;
     if((fic=fopen(datafile,"r"))==NULL)    {    int j, k=0,jk, ju, jl;
       printf("Problem with datafile: %s\n", datafile);goto end;    double sum=0.;
     }    first=0;
     jmin=1e+5;
     n= lastobs;    jmax=-1;
     severity = vector(1,maxwav);    jmean=0.;
     outcome=imatrix(1,maxwav+1,1,n);    for(i=1; i<=imx; i++){
     num=ivector(1,n);      mi=0;
     moisnais=vector(1,n);      m=firstpass;
     annais=vector(1,n);      while(s[m][i] <= nlstate){
     moisdc=vector(1,n);        if(s[m][i]>=1)
     andc=vector(1,n);          mw[++mi][i]=m;
     agedc=vector(1,n);        if(m >=lastpass)
     cod=ivector(1,n);          break;
     weight=vector(1,n);        else
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */          m++;
     mint=matrix(1,maxwav,1,n);      }/* end while */
     anint=matrix(1,maxwav,1,n);      if (s[m][i] > nlstate){
     s=imatrix(1,maxwav+1,1,n);        mi++;     /* Death is another wave */
     adl=imatrix(1,maxwav+1,1,n);            /* if(mi==0)  never been interviewed correctly before death */
     tab=ivector(1,NCOVMAX);           /* Only death is a correct wave */
     ncodemax=ivector(1,8);        mw[mi][i]=m;
       }
     i=1;  
     while (fgets(line, MAXLINE, fic) != NULL)    {      wav[i]=mi;
       if ((i >= firstobs) && (i <=lastobs)) {      if(mi==0){
                if(first==0){
         for (j=maxwav;j>=1;j--){          printf("Warning! None valid information for:%d line=%d (skipped) and may be others, see log file\n",num[i],i);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);          first=1;
           strcpy(line,stra);        }
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        if(first==1){
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          fprintf(ficlog,"Warning! None valid information for:%d line=%d (skipped)\n",num[i],i);
         }        }
              } /* end mi==0 */
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    } /* End individuals */
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);  
     for(i=1; i<=imx; i++){
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);      for(mi=1; mi<wav[i];mi++){
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);        if (stepm <=0)
           dh[mi][i]=1;
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);        else{
         for (j=ncov;j>=1;j--){          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);            if (agedc[i] < 2*AGESUP) {
         }            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
         num[i]=atol(stra);            if(j==0) j=1;  /* Survives at least one month after exam */
             k=k+1;
         /*printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.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]),  (mint[5][i]), (anint[5][i]), (s[5][i]),  (mint[6][i]), (anint[6][i]), (s[6][i]));*/            if (j >= jmax) jmax=j;
             if (j <= jmin) jmin=j;
         i=i+1;            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);*/
             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]);
     /*scanf("%d",i);*/            }
   imx=i-1; /* Number of individuals */          }
           else{
   /* Calculation of the number of parameter from char model*/            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   Tvar=ivector(1,8);                /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
                k=k+1;
   if (strlen(model) >1){            if (j >= jmax) jmax=j;
     j=0;            else if (j <= jmin)jmin=j;
     j=nbocc(model,'+');            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     cptcovn=j+1;            /*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]);
     strcpy(modelsav,model);            sum=sum+j;
     if (j==0) {          }
       cutv(stra,strb,modelsav,'V'); Tvar[1]=atoi(strb);          jk= j/stepm;
     }          jl= j -jk*stepm;
     else {          ju= j -(jk+1)*stepm;
       for(i=j; i>=1;i--){          if(mle <=1){ 
         cutv(stra,strb,modelsav,'+');            if(jl==0){
         if (strchr(strb,'*')) {              dh[mi][i]=jk;
           cutv(strd,strc,strb,'*');              bh[mi][i]=0;
           cutv(strb,stre,strc,'V');Tvar[i+1]=ncov+1;            }else{ /* We want a negative bias in order to only have interpolation ie
           cutv(strb,strc,strd,'V');                    * at the price of an extra matrix product in likelihood */
           for (k=1; k<=lastobs;k++)              dh[mi][i]=jk+1;
             covar[ncov+1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];              bh[mi][i]=ju;
         }            }
         else {cutv(strd,strc,strb,'V');          }else{
         Tvar[i+1]=atoi(strc);            if(jl <= -ju){
         }              dh[mi][i]=jk;
         strcpy(modelsav,stra);                bh[mi][i]=jl;       /* bias is positive if real duration
       }                                   * is higher than the multiple of stepm and negative otherwise.
       cutv(strd,strc,stra,'V');                                   */
       Tvar[1]=atoi(strc);            }
     }            else{
   }              dh[mi][i]=jk+1;
   /*printf("tvar=%d ",Tvar[1]);              bh[mi][i]=ju;
   scanf("%d ",i);*/            }
     fclose(fic);            if(dh[mi][i]==0){
               dh[mi][i]=1; /* At least one step */
     if (weightopt != 1) { /* Maximisation without weights*/              bh[mi][i]=ju; /* At least one step */
       for(i=1;i<=n;i++) weight[i]=1.0;              /*  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);*/
     }            }
     /*-calculation of age at interview from date of interview and age at death -*/          }
     agev=matrix(1,maxwav,1,imx);        } /* end if mle */
          } /* end wave */
     for (i=1; i<=imx; i++)  {    }
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    jmean=sum/k;
       for(m=1; (m<= maxwav); m++){    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
         if(s[m][i] >0){    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
           if (s[m][i] == nlstate+1) {   }
             if(agedc[i]>0)  
               if(moisdc[i]!=99 && andc[i]!=9999)  /*********** Tricode ****************************/
               agev[m][i]=agedc[i];  void tricode(int *Tvar, int **nbcode, int imx)
             else{  {
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    
               agev[m][i]=-1;    int Ndum[20],ij=1, k, j, i, maxncov=19;
             }    int cptcode=0;
           }    cptcoveff=0; 
           else if(s[m][i] !=9){ /* Should no more exist */   
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    for (k=0; k<maxncov; k++) Ndum[k]=0;
             if(mint[m][i]==99 || anint[m][i]==9999)    for (k=1; k<=7; k++) ncodemax[k]=0;
               agev[m][i]=1;  
             else if(agev[m][i] <agemin){    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
               agemin=agev[m][i];      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/                                 modality*/ 
             }        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
             else if(agev[m][i] >agemax){        Ndum[ij]++; /*store the modality */
               agemax=agev[m][i];        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
             }                                         Tvar[j]. If V=sex and male is 0 and 
             /*agev[m][i]=anint[m][i]-annais[i];*/                                         female is 1, then  cptcode=1.*/
             /*   agev[m][i] = age[i]+2*m;*/      }
           }  
           else { /* =9 */      for (i=0; i<=cptcode; i++) {
             agev[m][i]=1;        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
             s[m][i]=-1;      }
           }  
         }      ij=1; 
         else /*= 0 Unknown */      for (i=1; i<=ncodemax[j]; i++) {
           agev[m][i]=1;        for (k=0; k<= maxncov; k++) {
       }          if (Ndum[k] != 0) {
                nbcode[Tvar[j]][ij]=k; 
     }            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
     for (i=1; i<=imx; i++)  {            
       for(m=1; (m<= maxwav); m++){            ij++;
         if (s[m][i] > (nlstate+ndeath)) {          }
           printf("Error: Wrong value in nlstate or ndeath\n");            if (ij > ncodemax[j]) break; 
           goto end;        }  
         }      } 
       }    }  
     }  
    for (k=0; k< maxncov; k++) Ndum[k]=0;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);  
    for (i=1; i<=ncovmodel-2; i++) { 
     free_vector(severity,1,maxwav);     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     free_imatrix(outcome,1,maxwav+1,1,n);     ij=Tvar[i];
     free_vector(moisnais,1,n);     Ndum[ij]++;
     free_vector(annais,1,n);   }
     free_matrix(mint,1,maxwav,1,n);  
     free_matrix(anint,1,maxwav,1,n);   ij=1;
     free_vector(moisdc,1,n);   for (i=1; i<= maxncov; i++) {
     free_vector(andc,1,n);     if((Ndum[i]!=0) && (i<=ncovcol)){
        Tvaraff[ij]=i; /*For printing */
           ij++;
     wav=ivector(1,imx);     }
     dh=imatrix(1,lastpass-firstpass+1,1,imx);   }
     mw=imatrix(1,lastpass-firstpass+1,1,imx);   
       cptcoveff=ij-1; /*Number of simple covariates*/
     /* Concatenates waves */  }
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  
   /*********** Health Expectancies ****************/
   
 Tcode=ivector(1,100);  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
    nbcode=imatrix(1,nvar,1,8);    
    ncodemax[1]=1;  {
    if (cptcovn > 0) tricode(Tvar,nbcode,imx);    /* Health expectancies */
      int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
    codtab=imatrix(1,100,1,10);    double age, agelim, hf;
    h=0;    double ***p3mat,***varhe;
    m=pow(2,cptcovn);    double **dnewm,**doldm;
      double *xp;
    for(k=1;k<=cptcovn; k++){    double **gp, **gm;
      for(i=1; i <=(m/pow(2,k));i++){    double ***gradg, ***trgradg;
        for(j=1; j <= ncodemax[k]; j++){    int theta;
          for(cpt=1; cpt <=(m/pow(2,cptcovn+1-k)); cpt++){  
            h++;    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
            if (h>m) h=1;codtab[h][k]=j;    xp=vector(1,npar);
          }    dnewm=matrix(1,nlstate*nlstate,1,npar);
        }    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
      }    
    }    fprintf(ficreseij,"# Health expectancies\n");
     fprintf(ficreseij,"# Age");
    /*for(i=1; i <=m ;i++){    for(i=1; i<=nlstate;i++)
      for(k=1; k <=cptcovn; k++){      for(j=1; j<=nlstate;j++)
        printf("i=%d k=%d %d ",i,k,codtab[i][k]);        fprintf(ficreseij," %1d-%1d (SE)",i,j);
      }    fprintf(ficreseij,"\n");
      printf("\n");  
    }*/    if(estepm < stepm){
    /*scanf("%d",i);*/      printf ("Problem %d lower than %d\n",estepm, stepm);
        }
    /* Calculates basic frequencies. Computes observed prevalence at single age    else  hstepm=estepm;   
        and prints on file fileres'p'. */    /* We compute the life expectancy from trapezoids spaced every estepm months
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);     * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
      * we are calculating an estimate of the Life Expectancy assuming a linear 
   /*scanf("%d ",i);*/     * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */     * to compare the new estimate of Life expectancy with the same linear 
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */     * hypothesis. A more precise result, taking into account a more precise
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */     * curvature will be obtained if estepm is as small as stepm. */
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    /* For example we decided to compute the life expectancy with the smallest unit */
        /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     /* For Powell, parameters are in a vector p[] starting at p[1]       nhstepm is the number of hstepm from age to agelim 
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */       nstepm is the number of stepm from age to agelin. 
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */       Look at hpijx to understand the reason of that which relies in memory size
           and note for a fixed period like estepm months */
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
           means that if the survival funtion is printed only each two years of age and if
     /*--------- results files --------------*/       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);       results. So we changed our mind and took the option of the best precision.
        */
    jk=1;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
    fprintf(ficres,"# Parameters\n");  
    printf("# Parameters\n");    agelim=AGESUP;
    for(i=1,jk=1; i <=nlstate; i++){    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
      for(k=1; k <=(nlstate+ndeath); k++){      /* nhstepm age range expressed in number of stepm */
        if (k != i)      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
          {      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
            printf("%d%d ",i,k);      /* if (stepm >= YEARM) hstepm=1;*/
            fprintf(ficres,"%1d%1d ",i,k);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
            for(j=1; j <=ncovmodel; j++){      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
              printf("%f ",p[jk]);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
              fprintf(ficres,"%f ",p[jk]);      gp=matrix(0,nhstepm,1,nlstate*nlstate);
              jk++;      gm=matrix(0,nhstepm,1,nlstate*nlstate);
            }  
            printf("\n");      /* Computed by stepm unit matrices, product of hstepm matrices, stored
            fprintf(ficres,"\n");         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
          }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
      }   
    }  
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     /* Computing hessian and covariance matrix */  
     ftolhess=ftol; /* Usually correct */      /* Computing Variances of health expectancies */
     hesscov(matcov, p, npar, delti, ftolhess, func);  
     fprintf(ficres,"# Scales\n");       for(theta=1; theta <=npar; theta++){
     printf("# Scales\n");        for(i=1; i<=npar; i++){ 
      for(i=1,jk=1; i <=nlstate; i++){          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       for(j=1; j <=nlstate+ndeath; j++){        }
         if (j!=i) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           fprintf(ficres,"%1d%1d",i,j);    
           printf("%1d%1d",i,j);        cptj=0;
           for(k=1; k<=ncovmodel;k++){        for(j=1; j<= nlstate; j++){
             printf(" %.5e",delti[jk]);          for(i=1; i<=nlstate; i++){
             fprintf(ficres," %.5e",delti[jk]);            cptj=cptj+1;
             jk++;            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
           }              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
           printf("\n");            }
           fprintf(ficres,"\n");          }
         }        }
       }       
       }       
            for(i=1; i<=npar; i++) 
     k=1;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     fprintf(ficres,"# Covariance\n");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     printf("# Covariance\n");        
     for(i=1;i<=npar;i++){        cptj=0;
       /*  if (k>nlstate) k=1;        for(j=1; j<= nlstate; j++){
       i1=(i-1)/(ncovmodel*nlstate)+1;          for(i=1;i<=nlstate;i++){
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);            cptj=cptj+1;
       printf("%s%d%d",alph[k],i1,tab[i]);*/            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
       fprintf(ficres,"%3d",i);  
       printf("%3d",i);              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
       for(j=1; j<=i;j++){            }
         fprintf(ficres," %.5e",matcov[i][j]);          }
         printf(" %.5e",matcov[i][j]);        }
       }        for(j=1; j<= nlstate*nlstate; j++)
       fprintf(ficres,"\n");          for(h=0; h<=nhstepm-1; h++){
       printf("\n");            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
       k++;          }
     }       } 
         
     while((c=getc(ficpar))=='#' && c!= EOF){  /* End theta */
       ungetc(c,ficpar);  
       fgets(line, MAXLINE, ficpar);       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
       puts(line);  
       fputs(line,ficparo);       for(h=0; h<=nhstepm-1; h++)
     }        for(j=1; j<=nlstate*nlstate;j++)
     ungetc(c,ficpar);          for(theta=1; theta <=npar; theta++)
              trgradg[h][j][theta]=gradg[h][theta][j];
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);       
      
     if (fage <= 2) {       for(i=1;i<=nlstate*nlstate;i++)
       bage = agemin;        for(j=1;j<=nlstate*nlstate;j++)
       fage = agemax;          varhe[i][j][(int)age] =0.;
     }  
        printf("%d|",(int)age);fflush(stdout);
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);       for(h=0;h<=nhstepm-1;h++){
 /*------------ gnuplot -------------*/        for(k=0;k<=nhstepm-1;k++){
 chdir(pathcd);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
   if((ficgp=fopen("graph.plt","w"))==NULL) {          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
     printf("Problem with file graph.plt");goto end;          for(i=1;i<=nlstate*nlstate;i++)
   }            for(j=1;j<=nlstate*nlstate;j++)
 #ifdef windows              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
   fprintf(ficgp,"cd \"%s\" \n",pathc);        }
 #endif      }
 m=pow(2,cptcovn);      /* Computing expectancies */
        for(i=1; i<=nlstate;i++)
  /* 1eme*/        for(j=1; j<=nlstate;j++)
   for (cpt=1; cpt<= nlstate ; cpt ++) {          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
    for (k1=1; k1<= m ; k1 ++) {            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
             
 #ifdef windows  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);  
 #endif          }
 #ifdef unix  
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);      fprintf(ficreseij,"%3.0f",age );
 #endif      cptj=0;
       for(i=1; i<=nlstate;i++)
 for (i=1; i<= nlstate ; i ++) {        for(j=1; j<=nlstate;j++){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          cptj++;
   else fprintf(ficgp," \%%*lf (\%%*lf)");          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
 }        }
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);      fprintf(ficreseij,"\n");
     for (i=1; i<= nlstate ; i ++) {     
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
 }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
      for (i=1; i<= nlstate ; i ++) {      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    }
   else fprintf(ficgp," \%%*lf (\%%*lf)");    printf("\n");
 }      fprintf(ficlog,"\n");
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));  
 #ifdef unix    free_vector(xp,1,npar);
 fprintf(ficgp,"\nset ter gif small size 400,300");    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
 #endif    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
    }  }
   }  
   /*2 eme*/  /************ Variance ******************/
   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
   for (k1=1; k1<= m ; k1 ++) {  {
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);    /* Variance of health expectancies */
        /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     for (i=1; i<= nlstate+1 ; i ++) {    /* double **newm;*/
       k=2*i;    double **dnewm,**doldm;
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    double **dnewmp,**doldmp;
       for (j=1; j<= nlstate+1 ; j ++) {    int i, j, nhstepm, hstepm, h, nstepm ;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    int k, cptcode;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double *xp;
 }      double **gp, **gm;  /* for var eij */
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    double ***gradg, ***trgradg; /*for var eij */
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    double **gradgp, **trgradgp; /* for var p point j */
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    double *gpp, *gmp; /* for var p point j */
       for (j=1; j<= nlstate+1 ; j ++) {    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    double ***p3mat;
         else fprintf(ficgp," \%%*lf (\%%*lf)");    double age,agelim, hf;
 }      double ***mobaverage;
       fprintf(ficgp,"\" t\"\" w l 0,");    int theta;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    char digit[4];
       for (j=1; j<= nlstate+1 ; j ++) {    char digitp[25];
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");    char fileresprobmorprev[FILENAMELENGTH];
 }    
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    if(popbased==1){
       else fprintf(ficgp,"\" t\"\" w l 0,");      if(mobilav!=0)
     }        strcpy(digitp,"-populbased-mobilav-");
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);      else strcpy(digitp,"-populbased-nomobil-");
   }    }
      else 
   /*3eme*/      strcpy(digitp,"-stablbased-");
   
    for (k1=1; k1<= m ; k1 ++) {    if (mobilav!=0) {
     for (cpt=1; cpt<= nlstate ; cpt ++) {      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       k=2+nlstate*(cpt-1);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
       for (i=1; i< nlstate ; i ++) {        printf(" Error in movingaverage mobilav=%d\n",mobilav);
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);      }
       }    }
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
     }    strcpy(fileresprobmorprev,"prmorprev"); 
    }    sprintf(digit,"%-d",ij);
      /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   /* CV preval stat */    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     for (k1=1; k1<= m ; k1 ++) {    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     for (cpt=1; cpt<nlstate ; cpt ++) {    strcat(fileresprobmorprev,fileres);
       k=3;    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       for (i=1; i< nlstate ; i ++)      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
         fprintf(ficgp,"+$%d",k+i+1);    }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
          fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       l=3+(nlstate+ndeath)*cpt;    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
       for (i=1; i< nlstate ; i ++) {    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         l=3+(nlstate+ndeath)*cpt;      fprintf(ficresprobmorprev," p.%-d SE",j);
         fprintf(ficgp,"+$%d",l+i+1);      for(i=1; i<=nlstate;i++)
       }        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      }  
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    fprintf(ficresprobmorprev,"\n");
     }    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   }      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
        fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
   /* proba elementaires */      exit(0);
   for(i=1,jk=1; i <=nlstate; i++){    }
     for(k=1; k <=(nlstate+ndeath); k++){    else{
       if (k != i) {      fprintf(ficgp,"\n# Routine varevsij");
         /*  fprintf(ficgp,"%1d%1d ",i,k);*/    }
         for(j=1; j <=ncovmodel; j++){    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
           fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);      printf("Problem with html file: %s\n", optionfilehtm);
           jk++;      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
           fprintf(ficgp,"\n");      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);
   for(jk=1; jk <=m; jk++) {    }
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   for(i=1; i <=nlstate; i++) {  
     for(k=1; k <=(nlstate+ndeath); k++){    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");
       if (k != i) {    fprintf(ficresvij,"# Age");
         fprintf(ficgp," exp(a%d%d+b%d%d*x",i,k,i,k);    for(i=1; i<=nlstate;i++)
         for(j=3; j <=ncovmodel; j++)      for(j=1; j<=nlstate;j++)
           fprintf(ficgp,"+%s%d%d*%d",alph[j],i,k,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
         fprintf(ficgp,")/(1");    fprintf(ficresvij,"\n");
         for(k1=1; k1 <=(nlstate+ndeath); k1++)  
           if (k1 != i) {    xp=vector(1,npar);
             fprintf(ficgp,"+exp(a%d%d+b%d%d*x",i,k1,i,k1);    dnewm=matrix(1,nlstate,1,npar);
             for(j=3; j <=ncovmodel; j++)    doldm=matrix(1,nlstate,1,nlstate);
               fprintf(ficgp,"+%s%d%d*%d",alph[j],i,k,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
             fprintf(ficgp,")");    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           }  
         fprintf(ficgp,") t \"p%d%d\" ", i,k);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
       if ((i+k)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    gpp=vector(nlstate+1,nlstate+ndeath);
       }    gmp=vector(nlstate+1,nlstate+ndeath);
     }    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   }    
 fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);      if(estepm < stepm){
   }      printf ("Problem %d lower than %d\n",estepm, stepm);
      }
  fclose(ficgp);    else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
     chdir(path);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     free_matrix(agev,1,maxwav,1,imx);       nhstepm is the number of hstepm from age to agelim 
     free_ivector(wav,1,imx);       nstepm is the number of stepm from age to agelin. 
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);       Look at hpijx to understand the reason of that which relies in memory size
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);       and note for a fixed period like k years */
        /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     free_imatrix(s,1,maxwav+1,1,n);       survival function given by stepm (the optimization length). Unfortunately it
           means that if the survival funtion is printed every two years of age and if
           you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     free_ivector(num,1,n);       results. So we changed our mind and took the option of the best precision.
     free_vector(agedc,1,n);    */
     free_vector(weight,1,n);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     /*free_matrix(covar,1,NCOVMAX,1,n);*/    agelim = AGESUP;
     fclose(ficparo);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     fclose(ficres);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
    }      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    /*________fin mle=1_________*/      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
          gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
    
     /* No more information from the sample is required now */  
   /* Reads comments: lines beginning with '#' */      for(theta=1; theta <=npar; theta++){
   while((c=getc(ficpar))=='#' && c!= EOF){        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
     ungetc(c,ficpar);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     fgets(line, MAXLINE, ficpar);        }
     puts(line);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     fputs(line,ficparo);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   }  
   ungetc(c,ficpar);        if (popbased==1) {
            if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);              prlim[i][i]=probs[(int)age][i][ij];
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);          }else{ /* mobilav */ 
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);            for(i=1; i<=nlstate;i++)
 /*--------- index.htm --------*/              prlim[i][i]=mobaverage[(int)age][i][ij];
           }
   if((fichtm=fopen("index.htm","w"))==NULL)    {        }
     printf("Problem with index.htm \n");goto end;    
   }        for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
  fprintf(fichtm,"<body><ul> Imach, Version 0.63<hr> <li>Outputs files<br><br>\n            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>          }
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>        }
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>        /* This for computing probability of death (h=1 means
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>           computed over hstepm matrices product = hstepm*stepm months) 
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>           as a weighted average of prlim.
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>        */
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>        for(j=nlstate+1;j<=nlstate+ndeath;j++){
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
  fprintf(fichtm," <li>Graphs</li>\n<p>");        }    
         /* end probability of death */
  m=cptcovn;  
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
  j1=0;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
  for(k1=1; k1<=m;k1++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    for(i1=1; i1<=ncodemax[k1];i1++){   
        j1++;        if (popbased==1) {
        if (cptcovn > 0) {          if(mobilav ==0){
          fprintf(fichtm,"<hr>************ Results for covariates");            for(i=1; i<=nlstate;i++)
          for (cpt=1; cpt<=cptcovn;cpt++)              prlim[i][i]=probs[(int)age][i][ij];
            fprintf(fichtm," V%d=%d ",Tvar[cpt],nbcode[Tvar[cpt]][codtab[j1][cpt]]);          }else{ /* mobilav */ 
          fprintf(fichtm," ************\n<hr>");            for(i=1; i<=nlstate;i++)
        }              prlim[i][i]=mobaverage[(int)age][i][ij];
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>          }
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);            }
        for(cpt=1; cpt<nlstate;cpt++){  
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>        for(j=1; j<= nlstate; j++){
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);          for(h=0; h<=nhstepm; h++){
        }            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
     for(cpt=1; cpt<=nlstate;cpt++) {              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident          }
 interval) in state (%d): v%s%d%d.gif <br>        }
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);          /* This for computing probability of death (h=1 means
      }           computed over hstepm matrices product = hstepm*stepm months) 
      for(cpt=1; cpt<=nlstate;cpt++) {           as a weighted average of prlim.
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>        */
 <img src=\"ex%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
      }          for(i=1,gmp[j]=0.; i<= nlstate; i++)
      fprintf(fichtm,"\n<br>- Total life expectancy by age and           gmp[j] += prlim[i][i]*p3mat[i][j][1];
 health expectancies in states (1) and (2): e%s%d.gif<br>        }    
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);        /* end probability of death */
 fprintf(fichtm,"\n</body>");  
    }        for(j=1; j<= nlstate; j++) /* vareij */
  }          for(h=0; h<=nhstepm; h++){
 fclose(fichtm);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   /*--------------- Prevalence limit --------------*/  
          for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   strcpy(filerespl,"pl");          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   strcat(filerespl,fileres);        }
   if((ficrespl=fopen(filerespl,"w"))==NULL) {  
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;      } /* End theta */
   }  
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   fprintf(ficrespl,"#Prevalence limit\n");  
   fprintf(ficrespl,"#Age ");      for(h=0; h<=nhstepm; h++) /* veij */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);        for(j=1; j<=nlstate;j++)
   fprintf(ficrespl,"\n");          for(theta=1; theta <=npar; theta++)
              trgradg[h][j][theta]=gradg[h][theta][j];
   prlim=matrix(1,nlstate,1,nlstate);  
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(theta=1; theta <=npar; theta++)
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          trgradgp[j][theta]=gradgp[theta][j];
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
   k=0;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   agebase=agemin;      for(i=1;i<=nlstate;i++)
   agelim=agemax;        for(j=1;j<=nlstate;j++)
   ftolpl=1.e-10;          vareij[i][j][(int)age] =0.;
   i1=cptcovn;  
   if (cptcovn < 1){i1=1;}      for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
   for(cptcov=1;cptcov<=i1;cptcov++){          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
         k=k+1;          for(i=1;i<=nlstate;i++)
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/            for(j=1;j<=nlstate;j++)
         fprintf(ficrespl,"\n#****** ");              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         for(j=1;j<=cptcovn;j++)        }
           fprintf(ficrespl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);      }
         fprintf(ficrespl,"******\n");    
              /* pptj */
         for (age=agebase; age<=agelim; age++){      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
           fprintf(ficrespl,"%.0f",age );      for(j=nlstate+1;j<=nlstate+ndeath;j++)
           for(i=1; i<=nlstate;i++)        for(i=nlstate+1;i<=nlstate+ndeath;i++)
           fprintf(ficrespl," %.5f", prlim[i][i]);          varppt[j][i]=doldmp[j][i];
           fprintf(ficrespl,"\n");      /* end ppptj */
         }      /*  x centered again */
       }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
     }      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   fclose(ficrespl);   
   /*------------- h Pij x at various ages ------------*/      if (popbased==1) {
          if(mobilav ==0){
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);          for(i=1; i<=nlstate;i++)
   if((ficrespij=fopen(filerespij,"w"))==NULL) {            prlim[i][i]=probs[(int)age][i][ij];
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;        }else{ /* mobilav */ 
   }          for(i=1; i<=nlstate;i++)
   printf("Computing pij: result on file '%s' \n", filerespij);            prlim[i][i]=mobaverage[(int)age][i][ij];
          }
   stepsize=(int) (stepm+YEARM-1)/YEARM;      }
   if (stepm<=24) stepsize=2;               
       /* This for computing probability of death (h=1 means
   agelim=AGESUP;         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
   hstepm=stepsize*YEARM; /* Every year of age */         as a weighted average of prlim.
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */      */
        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   k=0;        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   for(cptcov=1;cptcov<=i1;cptcov++){          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      }    
       k=k+1;      /* end probability of death */
         fprintf(ficrespij,"\n#****** ");  
         for(j=1;j<=cptcovn;j++)      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
           fprintf(ficrespij,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficrespij,"******\n");        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
                for(i=1; i<=nlstate;i++){
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        }
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      } 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      fprintf(ficresprobmorprev,"\n");
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        fprintf(ficresvij,"%.0f ",age );
           fprintf(ficrespij,"# Age");      for(i=1; i<=nlstate;i++)
           for(i=1; i<=nlstate;i++)        for(j=1; j<=nlstate;j++){
             for(j=1; j<=nlstate+ndeath;j++)          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
               fprintf(ficrespij," %1d-%1d",i,j);        }
           fprintf(ficrespij,"\n");      fprintf(ficresvij,"\n");
           for (h=0; h<=nhstepm; h++){      free_matrix(gp,0,nhstepm,1,nlstate);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );      free_matrix(gm,0,nhstepm,1,nlstate);
             for(i=1; i<=nlstate;i++)      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
               for(j=1; j<=nlstate+ndeath;j++)      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");    } /* End age */
           }    free_vector(gpp,nlstate+1,nlstate+ndeath);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    free_vector(gmp,nlstate+1,nlstate+ndeath);
           fprintf(ficrespij,"\n");    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
         }    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     }    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
   }    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   fclose(ficrespij);  /*   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); */
   /*---------- Health expectancies and variances ------------*/  /*   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);
   strcpy(filerest,"t");    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
   strcat(filerest,fileres);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
   if((ficrest=fopen(filerest,"w"))==NULL) {    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    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 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);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);  */
     fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
   
   strcpy(filerese,"e");    free_vector(xp,1,npar);
   strcat(filerese,fileres);    free_matrix(doldm,1,nlstate,1,nlstate);
   if((ficreseij=fopen(filerese,"w"))==NULL) {    free_matrix(dnewm,1,nlstate,1,npar);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   }    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  strcpy(fileresv,"v");    fclose(ficresprobmorprev);
   strcat(fileresv,fileres);    fclose(ficgp);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    fclose(fichtm);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  }  
   }  
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);  /************ 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)
   k=0;  {
   for(cptcov=1;cptcov<=i1;cptcov++){    /* Variance of prevalence limit */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
       k=k+1;    double **newm;
       fprintf(ficrest,"\n#****** ");    double **dnewm,**doldm;
       for(j=1;j<=cptcovn;j++)    int i, j, nhstepm, hstepm;
         fprintf(ficrest,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);    int k, cptcode;
       fprintf(ficrest,"******\n");    double *xp;
     double *gp, *gm;
       fprintf(ficreseij,"\n#****** ");    double **gradg, **trgradg;
       for(j=1;j<=cptcovn;j++)    double age,agelim;
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    int theta;
       fprintf(ficreseij,"******\n");     
     fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
       fprintf(ficresvij,"\n#****** ");    fprintf(ficresvpl,"# Age");
       for(j=1;j<=cptcovn;j++)    for(i=1; i<=nlstate;i++)
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);        fprintf(ficresvpl," %1d-%1d",i,i);
       fprintf(ficresvij,"******\n");    fprintf(ficresvpl,"\n");
   
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    xp=vector(1,npar);
       oldm=oldms;savm=savms;    dnewm=matrix(1,nlstate,1,npar);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);      doldm=matrix(1,nlstate,1,nlstate);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    
       oldm=oldms;savm=savms;    hstepm=1*YEARM; /* Every year of age */
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
          agelim = AGESUP;
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       fprintf(ficrest,"\n");      if (stepm >= YEARM) hstepm=1;
              nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       hf=1;      gradg=matrix(1,npar,1,nlstate);
       if (stepm >= YEARM) hf=stepm/YEARM;      gp=vector(1,nlstate);
       epj=vector(1,nlstate+1);      gm=vector(1,nlstate);
       for(age=bage; age <=fage ;age++){  
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      for(theta=1; theta <=npar; theta++){
         fprintf(ficrest," %.0f",age);        for(i=1; i<=npar; i++){ /* Computes gradient */
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {        }
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           }        for(i=1;i<=nlstate;i++)
           epj[nlstate+1] +=epj[j];          gp[i] = prlim[i][i];
         }      
         for(i=1, vepp=0.;i <=nlstate;i++)        for(i=1; i<=npar; i++) /* Computes gradient */
           for(j=1;j <=nlstate;j++)          xp[i] = x[i] - (i==theta ?delti[theta]:0);
             vepp += vareij[i][j][(int)age];        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));        for(i=1;i<=nlstate;i++)
         for(j=1;j <=nlstate;j++){          gm[i] = prlim[i][i];
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));  
         }        for(i=1;i<=nlstate;i++)
         fprintf(ficrest,"\n");          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       }      } /* End theta */
     }  
   }      trgradg =matrix(1,nlstate,1,npar);
          
  fclose(ficreseij);      for(j=1; j<=nlstate;j++)
  fclose(ficresvij);        for(theta=1; theta <=npar; theta++)
   fclose(ficrest);          trgradg[j][theta]=gradg[theta][j];
   fclose(ficpar);  
   free_vector(epj,1,nlstate+1);      for(i=1;i<=nlstate;i++)
   /*scanf("%d ",i); */        varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   /*------- Variance limit prevalence------*/        matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
 strcpy(fileresvpl,"vpl");        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   strcat(fileresvpl,fileres);  
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      fprintf(ficresvpl,"%.0f ",age );
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);      for(i=1; i<=nlstate;i++)
     exit(0);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   }      fprintf(ficresvpl,"\n");
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);      free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
  k=0;      free_matrix(gradg,1,npar,1,nlstate);
  for(cptcov=1;cptcov<=i1;cptcov++){      free_matrix(trgradg,1,nlstate,1,npar);
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    } /* End age */
      k=k+1;  
      fprintf(ficresvpl,"\n#****** ");    free_vector(xp,1,npar);
      for(j=1;j<=cptcovn;j++)    free_matrix(doldm,1,nlstate,1,npar);
        fprintf(ficresvpl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);    free_matrix(dnewm,1,nlstate,1,nlstate);
      fprintf(ficresvpl,"******\n");  
        }
      varpl=matrix(1,nlstate,(int) bage, (int) fage);  
      oldm=oldms;savm=savms;  /************ Variance of one-step probabilities  ******************/
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
    }  {
  }    int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
   fclose(ficresvpl);    int k=0,l, cptcode;
     int first=1, first1;
   /*---------- End : free ----------------*/    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    double **dnewm,**doldm;
      double *xp;
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    double *gp, *gm;
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    double **gradg, **trgradg;
      double **mu;
      double age,agelim, cov[NCOVMAX];
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    int theta;
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    char fileresprob[FILENAMELENGTH];
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    char fileresprobcov[FILENAMELENGTH];
      char fileresprobcor[FILENAMELENGTH];
   free_matrix(matcov,1,npar,1,npar);  
   free_vector(delti,1,npar);    double ***varpij;
    
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
   printf("End of Imach\n");    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      printf("Problem with resultfile: %s\n", fileresprob);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   /* 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);*/    }
   /*printf("Total time was %d uSec.\n", total_usecs);*/    strcpy(fileresprobcov,"probcov"); 
   /*------ End -----------*/    strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
  end:      printf("Problem with resultfile: %s\n", fileresprobcov);
 #ifdef windows      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
  chdir(pathcd);    }
 #endif    strcpy(fileresprobcor,"probcor"); 
  system("wgnuplot graph.plt");    strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
 #ifdef windows      printf("Problem with resultfile: %s\n", fileresprobcor);
   while (z[0] != 'q') {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     chdir(pathcd);    }
     printf("\nType e to edit output files, c to start again, and q for exiting: ");    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     scanf("%s",z);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     if (z[0] == 'c') system("./imach");    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     else if (z[0] == 'e') {    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
       chdir(path);    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
       system("index.htm");    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     }    
     else if (z[0] == 'q') exit(0);    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   }    fprintf(ficresprob,"# Age");
 #endif    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
 }    fprintf(ficresprobcov,"# Age");
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcov,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
    xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
       fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
       exit(0);
     }
     else{
       fprintf(ficgp,"\n# Routine varprob");
     }
     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 and drawing one step probabilities with their confidence intervals</h4></li>\n");
       fprintf(fichtm,"\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;
     tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
         j1++;
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtm, "\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]]);
           fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
   
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nset noparametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       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 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(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
                       fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
                       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,"\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",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtm," %d (%.3f),",(int) age, c12);
                       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,"\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",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fclose(ficgp);
     fclose(fichtm);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     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
    - 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
    - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n
    - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
    - Life expectancies by age and initial health status (estepm=%2d months): 
      <a href=\"e%s\">e%s</a> <br>\n</li>", \
     jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* 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>
   <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
        /* 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>
   <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
          /* Stable prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            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);
          }
        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>
   <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),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 k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n
    - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n
    - 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
    - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n 
    - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n
    - 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);
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  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," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed and period prevalence (with confident
   interval) in state (%d): v%s%d%d.png <br>
   <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   fclose(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
     if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
       fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
     }
   
     /*#ifdef windows */
       fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   m=pow(2,cptcoveff);
     
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),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);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) 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);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) 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*$3) \"\%%lf",fileres,k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
       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 ++) {
         k=2*i;
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         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);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),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,",\"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) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           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) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         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);
           
         } 
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),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);
         
         for (i=1; i<= nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fclose(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   }
   
   /***********************************************/
   /**************** 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;
     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[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;
     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;
   
     char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
     char z[1]="c", occ;
   #include <sys/time.h>
   #include <time.h>
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
    
     /* long total_usecs;
        struct timeval start_time, end_time;
     
        gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     replace(pathc,path);
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s",version);
     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);
     fflush(ficlog);
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       goto end;
     }
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) {
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     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);
     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);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     
     /* Read guess parameters */
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++)
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         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");
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       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);
     /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         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]);
         }
         fscanf(ficpar,"\n");
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     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 */
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);
       if(mle==1)
         printf("%s",str);
       fprintf(ficlog,"%s",str);
       fprintf(ficparo,"%s",str);
       for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
           printf(" %.5le",matcov[i][j]);
           fprintf(ficlog," %.5le",matcov[i][j]);
         }
         else
           fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       if(mle==1)
         printf("\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);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=ivector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         num[i]=atol(stra);
           
         /*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;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        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]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         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);
           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);
           s[m][i]=-1;
         }
         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]); 
           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]); 
           s[m][i]=-1;
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   printf("Warning negative age at death: %d line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (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);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     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("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); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
   
       pmmij= 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 */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[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) */
   
     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);
     
   
     jk=1;
     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);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
       }
     }
     if(mle==1){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# 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(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);
             jk++;
           }
           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");
     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");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
           i1=(i-1)/(ncovmodel*nlstate)+1; 
           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
           printf("%s%d%d",alph[k],i1,tab[i]);
       */
       fprintf(ficres,"%3d",i);
       if(mle==1)
         printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     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) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     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);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     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,"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);
     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);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     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,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     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);
     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_imatrix(dh,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_ivector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("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);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;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]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("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);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* 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 ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         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 = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           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(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");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
   
     /*---------- 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);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
   /*      }  */
   /*      else{ */
   /*        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); */
   /*        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 ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("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); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("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);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("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);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* 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);
     /*  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);
     */
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         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);
         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);
         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);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           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_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     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++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         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);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     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);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     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);
   
     /*  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{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     
     /* 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);*/
     /*printf("Total time was %d uSec.\n", total_usecs);*/
     /*------ End -----------*/
   
     end:
   #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);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     system(plotcmd);
     printf(" Wait...");
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   
Removed from v.1.4  
changed lines
  Added in v.1.82

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