Diff for /imach/src/imach.c between versions 1.2 and 1.56

version 1.2, 2001/03/13 18:10:26 version 1.56, 2002/07/24 17:28:25
Line 1 Line 1
      /* $Id$
 /*********************** Imach **************************************             Interpolated Markov Chain
   This program computes Healthy Life Expectancies from cross-longitudinal  
   data. Cross-longitudinal consist in a first survey ("cross") where    Short summary of the programme:
   individuals from different ages are interviewed on their health status    
   or degree of  disability. At least a second wave of interviews    This program computes Healthy Life Expectancies from
   ("longitudinal") should  measure each new individual health status.    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   Health expectancies are computed from the transistions observed between    first survey ("cross") where individuals from different ages are
   waves and are computed for each degree of severity of disability (number    interviewed on their health status or degree of disability (in the
   of life states). More degrees you consider, more time is necessary to    case of a health survey which is our main interest) -2- at least a
   reach the Maximum Likelihood of the parameters involved in the model.    second wave of interviews ("longitudinal") which measure each change
   The simplest model is the multinomial logistic model where pij is    (if any) in individual health status.  Health expectancies are
   the probabibility to be observed in state j at the second wave conditional    computed from the time spent in each health state according to a
   to be observed in state i at the first wave. Therefore the model is:    model. More health states you consider, more time is necessary to reach the
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    Maximum Likelihood of the parameters involved in the model.  The
   is a covariate. If you want to have a more complex model than "constant and    simplest model is the multinomial logistic model where pij is the
   age", you should modify the program where the markup    probability to be observed in state j at the second wave
     *Covariates have to be included here again* invites you to do it.    conditional to be observed in state i at the first wave. Therefore
   More covariates you add, less is the speed of the convergence.    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
     'age' is age and 'sex' is a covariate. If you want to have a more
   The advantage that this computer programme claims, comes from that if the    complex model than "constant and age", you should modify the program
   delay between waves is not identical for each individual, or if some    where the markup *Covariates have to be included here again* invites
   individual missed an interview, the information is not rounded or lost, but    you to do it.  More covariates you add, slower the
   taken into account using an interpolation or extrapolation.    convergence.
   hPijx is the probability to be  
   observed in state i at age x+h conditional to the observed state i at age    The advantage of this computer programme, compared to a simple
   x. The delay 'h' can be split into an exact number (nh*stepm) of    multinomial logistic model, is clear when the delay between waves is not
   unobserved intermediate  states. This elementary transition (by month or    identical for each individual. Also, if a individual missed an
   quarter trimester, semester or year) is model as a multinomial logistic.    intermediate interview, the information is lost, but taken into
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    account using an interpolation or extrapolation.  
   and the contribution of each individual to the likelihood is simply hPijx.  
     hPijx is the probability to be observed in state i at age x+h
   Also this programme outputs the covariance matrix of the parameters but also    conditional to the observed state i at age x. The delay 'h' can be
   of the life expectancies. It also computes the prevalence limits.    split into an exact number (nh*stepm) of unobserved intermediate
      states. This elementary transition (by month or quarter trimester,
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    semester or year) is model as a multinomial logistic.  The hPx
            Institut national d'études démographiques, Paris.    matrix is simply the matrix product of nh*stepm elementary matrices
   This software have been partly granted by Euro-REVES, a concerted action    and the contribution of each individual to the likelihood is simply
   from the European Union.    hPijx.
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Also this programme outputs the covariance matrix of the parameters but also
   can be accessed at http://euroreves.ined.fr/imach .    of the life expectancies. It also computes the stable prevalence. 
   **********************************************************************/    
      Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 #include <math.h>             Institut national d'études démographiques, Paris.
 #include <stdio.h>    This software have been partly granted by Euro-REVES, a concerted action
 #include <stdlib.h>    from the European Union.
 #include <unistd.h>    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
 #define MAXLINE 256    can be accessed at http://euroreves.ined.fr/imach .
 #define FILENAMELENGTH 80    **********************************************************************/
 /*#define DEBUG*/   
 #define windows  #include <math.h>
   #include <stdio.h>
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  #include <stdlib.h>
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  #include <unistd.h>
   
 #define NINTERVMAX 8  #define MAXLINE 256
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  #define GNUPLOTPROGRAM "gnuplot"
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #define NCOVMAX 8 /* Maximum number of covariates */  #define FILENAMELENGTH 80
 #define MAXN 80000  /*#define DEBUG*/
 #define YEARM 12. /* Number of months per year */  #define windows
 #define AGESUP 130  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #define AGEBASE 40  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
   #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 int nvar;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 static int cptcov;  
 int cptcovn;  #define NINTERVMAX 8
 int npar=NPARMAX;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 int nlstate=2; /* Number of live states */  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 int ndeath=1; /* Number of dead states */  #define NCOVMAX 8 /* Maximum number of covariates */
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  #define MAXN 20000
   #define YEARM 12. /* Number of months per year */
 int *wav; /* Number of waves for this individuual 0 is possible */  #define AGESUP 130
 int maxwav; /* Maxim number of waves */  #define AGEBASE 40
 int mle, weightopt;  #ifdef windows
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  #define DIRSEPARATOR '\\'
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  #define ODIRSEPARATOR '/'
 double **oldm, **newm, **savm; /* Working pointers to matrices */  #else
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  #define DIRSEPARATOR '/'
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;  #define ODIRSEPARATOR '\\'
 FILE *ficgp, *fichtm;  #endif
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];  char version[80]="Imach version 0.8k, July 2002, INED-EUROREVES ";
  FILE  *ficresvij;  int erreur; /* Error number */
   char fileresv[FILENAMELENGTH];  int nvar;
  FILE  *ficresvpl;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   char fileresvpl[FILENAMELENGTH];  int npar=NPARMAX;
   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;
 #define NR_END 1  
 #define FREE_ARG char*  int *wav; /* Number of waves for this individuual 0 is possible */
 #define FTOL 1.0e-10  int maxwav; /* Maxim number of waves */
   int jmin, jmax; /* min, max spacing between 2 waves */
 #define NRANSI  int mle, weightopt;
 #define ITMAX 200  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 #define TOL 2.0e-4  double jmean; /* Mean space between 2 waves */
   double **oldm, **newm, **savm; /* Working pointers to matrices */
 #define CGOLD 0.3819660  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 #define ZEPS 1.0e-10  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  FILE *ficlog;
   FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 #define GOLD 1.618034  FILE *ficresprobmorprev;
 #define GLIMIT 100.0  FILE *fichtm; /* Html File */
 #define TINY 1.0e-20  FILE *ficreseij;
   char filerese[FILENAMELENGTH];
 static double maxarg1,maxarg2;  FILE  *ficresvij;
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  char fileresv[FILENAMELENGTH];
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  FILE  *ficresvpl;
    char fileresvpl[FILENAMELENGTH];
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  char title[MAXLINE];
 #define rint(a) floor(a+0.5)  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  char filelog[FILENAMELENGTH]; /* Log file */
   char filerest[FILENAMELENGTH];
 int imx;  char fileregp[FILENAMELENGTH];
 int stepm;  char popfile[FILENAMELENGTH];
 /* Stepm, step in month: minimum step interpolation*/  
   char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax;  #define NR_END 1
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  #define FREE_ARG char*
 double **pmmij;  #define FTOL 1.0e-10
   
 double *weight;  #define NRANSI 
 int **s; /* Status */  #define ITMAX 200 
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab;  #define TOL 2.0e-4 
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  #define CGOLD 0.3819660 
 double ftolhess; /* Tolerance for computing hessian */  #define ZEPS 1.0e-10 
   #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   
 /******************************************/  #define GOLD 1.618034 
   #define GLIMIT 100.0 
 void replace(char *s, char*t)  #define TINY 1.0e-20 
 {  
   int i;  static double maxarg1,maxarg2;
   int lg=20;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   i=0;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   lg=strlen(t);    
   for(i=0; i<= lg; i++) {  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
     (s[i] = t[i]);  #define rint(a) floor(a+0.5)
     if (t[i]== '\\') s[i]='/';  
   }  static double sqrarg;
 }  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 int nbocc(char *s, char occ)  
 {  int imx; 
   int i,j=0;  int stepm;
   int lg=20;  /* Stepm, step in month: minimum step interpolation*/
   i=0;  
   lg=strlen(s);  int estepm;
   for(i=0; i<= lg; i++) {  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   if  (s[i] == occ ) j++;  
   }  int m,nb;
   return j;  int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 }  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double **pmmij, ***probs;
 void cutv(char *u,char *v, char*t, char occ)  double dateintmean=0;
 {  
   int i,lg,j,p;  double *weight;
   i=0;  int **s; /* Status */
   if (t[0]== occ) p=0;  double *agedc, **covar, idx;
   for(j=0; j<=strlen(t)-1; j++) {  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
     if((t[j]!= occ) && (t[j+1]==occ)) p=j+1;  
   }  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   double ftolhess; /* Tolerance for computing hessian */
   lg=strlen(t);  
   for(j=0; j<p; j++) {  /**************** split *************************/
     (u[j] = t[j]);  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     u[p]='\0';  {
   }     char *s;                             /* pointer */
      int  l1, l2;                         /* length counters */
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);     l1 = strlen( path );                 /* length of path */
   }     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 }     s= strrchr( path, DIRSEPARATOR );            /* find last / */
      if ( s == NULL ) {                   /* no directory, so use current */
        /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 /********************** nrerror ********************/         printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   #if     defined(__bsd__)                /* get current working directory */
 void nrerror(char error_text[])        extern char       *getwd( );
 {  
   fprintf(stderr,"ERREUR ...\n");        if ( getwd( dirc ) == NULL ) {
   fprintf(stderr,"%s\n",error_text);  #else
   exit(1);        extern char       *getcwd( );
 }  
 /*********************** vector *******************/        if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 double *vector(int nl, int nh)  #endif
 {           return( GLOCK_ERROR_GETCWD );
   double *v;        }
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));        strcpy( name, path );             /* we've got it */
   if (!v) nrerror("allocation failure in vector");     } else {                             /* strip direcotry from path */
   return v-nl+NR_END;        s++;                              /* after this, the filename */
 }        l2 = strlen( s );                 /* length of filename */
         if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 /************************ free vector ******************/        strcpy( name, s );                /* save file name */
 void free_vector(double*v, int nl, int nh)        strncpy( dirc, path, l1 - l2 );   /* now the directory */
 {        dirc[l1-l2] = 0;                  /* add zero */
   free((FREE_ARG)(v+nl-NR_END));     }
 }     l1 = strlen( dirc );                 /* length of directory */
   #ifdef windows
 /************************ivector *******************************/     if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
 int *ivector(long nl,long nh)  #else
 {     if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   int *v;  #endif
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));     s = strrchr( name, '.' );            /* find last / */
   if (!v) nrerror("allocation failure in ivector");     s++;
   return v-nl+NR_END;     strcpy(ext,s);                       /* save extension */
 }     l1= strlen( name);
      l2= strlen( s)+1;
 /******************free ivector **************************/     strncpy( finame, name, l1-l2);
 void free_ivector(int *v, long nl, long nh)     finame[l1-l2]= 0;
 {     return( 0 );                         /* we're done */
   free((FREE_ARG)(v+nl-NR_END));  }
 }  
   
 /******************* imatrix *******************************/  /******************************************/
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  void replace(char *s, char*t)
 {  {
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    int i;
   int **m;    int lg=20;
      i=0;
   /* allocate pointers to rows */    lg=strlen(t);
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    for(i=0; i<= lg; i++) {
   if (!m) nrerror("allocation failure 1 in matrix()");      (s[i] = t[i]);
   m += NR_END;      if (t[i]== '\\') s[i]='/';
   m -= nrl;    }
    }
    
   /* allocate rows and set pointers to them */  int nbocc(char *s, char occ)
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  {
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    int i,j=0;
   m[nrl] += NR_END;    int lg=20;
   m[nrl] -= ncl;    i=0;
      lg=strlen(s);
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    for(i=0; i<= lg; i++) {
      if  (s[i] == occ ) j++;
   /* return pointer to array of pointers to rows */    }
   return m;    return j;
 }  }
   
 /****************** free_imatrix *************************/  void cutv(char *u,char *v, char*t, char occ)
 void free_imatrix(m,nrl,nrh,ncl,nch)  {
       int **m;    /* cuts string t into u and v where u is ended by char occ excluding it
       long nch,ncl,nrh,nrl;       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
      /* free an int matrix allocated by imatrix() */       gives u="abcedf" and v="ghi2j" */
 {    int i,lg,j,p=0;
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    i=0;
   free((FREE_ARG) (m+nrl-NR_END));    for(j=0; j<=strlen(t)-1; j++) {
 }      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     }
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)    lg=strlen(t);
 {    for(j=0; j<p; j++) {
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;      (u[j] = t[j]);
   double **m;    }
        u[p]='\0';
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");     for(j=0; j<= lg; j++) {
   m += NR_END;      if (j>=(p+1))(v[j-p-1] = t[j]);
   m -= nrl;    }
   }
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  /********************** nrerror ********************/
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  void nrerror(char error_text[])
   {
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    fprintf(stderr,"ERREUR ...\n");
   return m;    fprintf(stderr,"%s\n",error_text);
 }    exit(1);
   }
 /*************************free matrix ************************/  /*********************** vector *******************/
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  double *vector(int nl, int nh)
 {  {
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    double *v;
   free((FREE_ARG)(m+nrl-NR_END));    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 }    if (!v) nrerror("allocation failure in vector");
     return v-nl+NR_END;
 /******************* ma3x *******************************/  }
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  
 {  /************************ free vector ******************/
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  void free_vector(double*v, int nl, int nh)
   double ***m;  {
     free((FREE_ARG)(v+nl-NR_END));
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  }
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  /************************ivector *******************************/
   m -= nrl;  int *ivector(long nl,long nh)
   {
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    int *v;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   m[nrl] += NR_END;    if (!v) nrerror("allocation failure in ivector");
   m[nrl] -= ncl;    return v-nl+NR_END;
   }
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   /******************free ivector **************************/
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  void free_ivector(int *v, long nl, long nh)
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  {
   m[nrl][ncl] += NR_END;    free((FREE_ARG)(v+nl-NR_END));
   m[nrl][ncl] -= nll;  }
   for (j=ncl+1; j<=nch; j++)  
     m[nrl][j]=m[nrl][j-1]+nlay;  /******************* imatrix *******************************/
    int **imatrix(long nrl, long nrh, long ncl, long nch) 
   for (i=nrl+1; i<=nrh; i++) {       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  { 
     for (j=ncl+1; j<=nch; j++)    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       m[i][j]=m[i][j-1]+nlay;    int **m; 
   }    
   return m;    /* allocate pointers to rows */ 
 }    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     if (!m) nrerror("allocation failure 1 in matrix()"); 
 /*************************free ma3x ************************/    m += NR_END; 
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    m -= nrl; 
 {    
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    /* allocate rows and set pointers to them */ 
   free((FREE_ARG)(m+nrl-NR_END));    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
 }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     m[nrl] += NR_END; 
 /***************** f1dim *************************/    m[nrl] -= ncl; 
 extern int ncom;    
 extern double *pcom,*xicom;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
 extern double (*nrfunc)(double []);    
      /* return pointer to array of pointers to rows */ 
 double f1dim(double x)    return m; 
 {  } 
   int j;  
   double f;  /****************** free_imatrix *************************/
   double *xt;  void free_imatrix(m,nrl,nrh,ncl,nch)
          int **m;
   xt=vector(1,ncom);        long nch,ncl,nrh,nrl; 
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];       /* free an int matrix allocated by imatrix() */ 
   f=(*nrfunc)(xt);  { 
   free_vector(xt,1,ncom);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   return f;    free((FREE_ARG) (m+nrl-NR_END)); 
 }  } 
   
 /*****************brent *************************/  /******************* matrix *******************************/
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  double **matrix(long nrl, long nrh, long ncl, long nch)
 {  {
   int iter;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   double a,b,d,etemp;    double **m;
   double fu,fv,fw,fx;  
   double ftemp;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double p,q,r,tol1,tol2,u,v,w,x,xm;    if (!m) nrerror("allocation failure 1 in matrix()");
   double e=0.0;    m += NR_END;
      m -= nrl;
   a=(ax < cx ? ax : cx);  
   b=(ax > cx ? ax : cx);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   x=w=v=bx;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   fw=fv=fx=(*f)(x);    m[nrl] += NR_END;
   for (iter=1;iter<=ITMAX;iter++) {    m[nrl] -= ncl;
     xm=0.5*(a+b);  
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    return m;
     printf(".");fflush(stdout);  }
 #ifdef DEBUG  
     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);  /*************************free matrix ************************/
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
 #endif  {
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       *xmin=x;    free((FREE_ARG)(m+nrl-NR_END));
       return fx;  }
     }  
     ftemp=fu;  /******************* ma3x *******************************/
     if (fabs(e) > tol1) {  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       r=(x-w)*(fx-fv);  {
       q=(x-v)*(fx-fw);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       p=(x-v)*q-(x-w)*r;    double ***m;
       q=2.0*(q-r);  
       if (q > 0.0) p = -p;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       q=fabs(q);    if (!m) nrerror("allocation failure 1 in matrix()");
       etemp=e;    m += NR_END;
       e=d;    m -= nrl;
       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));    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       else {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         d=p/q;    m[nrl] += NR_END;
         u=x+d;    m[nrl] -= ncl;
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       }  
     } else {    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     }    m[nrl][ncl] += NR_END;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    m[nrl][ncl] -= nll;
     fu=(*f)(u);    for (j=ncl+1; j<=nch; j++) 
     if (fu <= fx) {      m[nrl][j]=m[nrl][j-1]+nlay;
       if (u >= x) a=x; else b=x;    
       SHFT(v,w,x,u)    for (i=nrl+1; i<=nrh; i++) {
         SHFT(fv,fw,fx,fu)      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
         } else {      for (j=ncl+1; j<=nch; j++) 
           if (u < x) a=u; else b=u;        m[i][j]=m[i][j-1]+nlay;
           if (fu <= fw || w == x) {    }
             v=w;    return m;
             w=u;  }
             fv=fw;  
             fw=fu;  /*************************free ma3x ************************/
           } else if (fu <= fv || v == x || v == w) {  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
             v=u;  {
             fv=fu;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
           }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         }    free((FREE_ARG)(m+nrl-NR_END));
   }  }
   nrerror("Too many iterations in brent");  
   *xmin=x;  /***************** f1dim *************************/
   return fx;  extern int ncom; 
 }  extern double *pcom,*xicom;
   extern double (*nrfunc)(double []); 
 /****************** mnbrak ***********************/   
   double f1dim(double x) 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  { 
             double (*func)(double))    int j; 
 {    double f;
   double ulim,u,r,q, dum;    double *xt; 
   double fu;   
      xt=vector(1,ncom); 
   *fa=(*func)(*ax);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   *fb=(*func)(*bx);    f=(*nrfunc)(xt); 
   if (*fb > *fa) {    free_vector(xt,1,ncom); 
     SHFT(dum,*ax,*bx,dum)    return f; 
       SHFT(dum,*fb,*fa,dum)  } 
       }  
   *cx=(*bx)+GOLD*(*bx-*ax);  /*****************brent *************************/
   *fc=(*func)(*cx);  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   while (*fb > *fc) {  { 
     r=(*bx-*ax)*(*fb-*fc);    int iter; 
     q=(*bx-*cx)*(*fb-*fa);    double a,b,d,etemp;
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    double fu,fv,fw,fx;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    double ftemp;
     ulim=(*bx)+GLIMIT*(*cx-*bx);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     if ((*bx-u)*(u-*cx) > 0.0) {    double e=0.0; 
       fu=(*func)(u);   
     } else if ((*cx-u)*(u-ulim) > 0.0) {    a=(ax < cx ? ax : cx); 
       fu=(*func)(u);    b=(ax > cx ? ax : cx); 
       if (fu < *fc) {    x=w=v=bx; 
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    fw=fv=fx=(*f)(x); 
           SHFT(*fb,*fc,fu,(*func)(u))    for (iter=1;iter<=ITMAX;iter++) { 
           }      xm=0.5*(a+b); 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       u=ulim;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       fu=(*func)(u);      printf(".");fflush(stdout);
     } else {      fprintf(ficlog,".");fflush(ficlog);
       u=(*cx)+GOLD*(*cx-*bx);  #ifdef DEBUG
       fu=(*func)(u);      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     }      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     SHFT(*ax,*bx,*cx,u)      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       SHFT(*fa,*fb,*fc,fu)  #endif
       }      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
 }        *xmin=x; 
         return fx; 
 /*************** linmin ************************/      } 
       ftemp=fu;
 int ncom;      if (fabs(e) > tol1) { 
 double *pcom,*xicom;        r=(x-w)*(fx-fv); 
 double (*nrfunc)(double []);        q=(x-v)*(fx-fw); 
          p=(x-v)*q-(x-w)*r; 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))        q=2.0*(q-r); 
 {        if (q > 0.0) p = -p; 
   double brent(double ax, double bx, double cx,        q=fabs(q); 
                double (*f)(double), double tol, double *xmin);        etemp=e; 
   double f1dim(double x);        e=d; 
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
               double *fc, double (*func)(double));          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   int j;        else { 
   double xx,xmin,bx,ax;          d=p/q; 
   double fx,fb,fa;          u=x+d; 
            if (u-a < tol2 || b-u < tol2) 
   ncom=n;            d=SIGN(tol1,xm-x); 
   pcom=vector(1,n);        } 
   xicom=vector(1,n);      } else { 
   nrfunc=func;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   for (j=1;j<=n;j++) {      } 
     pcom[j]=p[j];      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     xicom[j]=xi[j];      fu=(*f)(u); 
   }      if (fu <= fx) { 
   ax=0.0;        if (u >= x) a=x; else b=x; 
   xx=1.0;        SHFT(v,w,x,u) 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);          SHFT(fv,fw,fx,fu) 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);          } else { 
 #ifdef DEBUG            if (u < x) a=u; else b=u; 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);            if (fu <= fw || w == x) { 
 #endif              v=w; 
   for (j=1;j<=n;j++) {              w=u; 
     xi[j] *= xmin;              fv=fw; 
     p[j] += xi[j];              fw=fu; 
   }            } else if (fu <= fv || v == x || v == w) { 
   free_vector(xicom,1,n);              v=u; 
   free_vector(pcom,1,n);              fv=fu; 
 }            } 
           } 
 /*************** powell ************************/    } 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    nrerror("Too many iterations in brent"); 
             double (*func)(double []))    *xmin=x; 
 {    return fx; 
   void linmin(double p[], double xi[], int n, double *fret,  } 
               double (*func)(double []));  
   int i,ibig,j;  /****************** mnbrak ***********************/
   double del,t,*pt,*ptt,*xit;  
   double fp,fptt;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   double *xits;              double (*func)(double)) 
   pt=vector(1,n);  { 
   ptt=vector(1,n);    double ulim,u,r,q, dum;
   xit=vector(1,n);    double fu; 
   xits=vector(1,n);   
   *fret=(*func)(p);    *fa=(*func)(*ax); 
   for (j=1;j<=n;j++) pt[j]=p[j];    *fb=(*func)(*bx); 
   for (*iter=1;;++(*iter)) {    if (*fb > *fa) { 
     fp=(*fret);      SHFT(dum,*ax,*bx,dum) 
     ibig=0;        SHFT(dum,*fb,*fa,dum) 
     del=0.0;        } 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    *cx=(*bx)+GOLD*(*bx-*ax); 
     for (i=1;i<=n;i++)    *fc=(*func)(*cx); 
       printf(" %d %.12f",i, p[i]);    while (*fb > *fc) { 
     printf("\n");      r=(*bx-*ax)*(*fb-*fc); 
     for (i=1;i<=n;i++) {      q=(*bx-*cx)*(*fb-*fa); 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       fptt=(*fret);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 #ifdef DEBUG      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       printf("fret=%lf \n",*fret);      if ((*bx-u)*(u-*cx) > 0.0) { 
 #endif        fu=(*func)(u); 
       printf("%d",i);fflush(stdout);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
       linmin(p,xit,n,fret,func);        fu=(*func)(u); 
       if (fabs(fptt-(*fret)) > del) {        if (fu < *fc) { 
         del=fabs(fptt-(*fret));          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
         ibig=i;            SHFT(*fb,*fc,fu,(*func)(u)) 
       }            } 
 #ifdef DEBUG      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       printf("%d %.12e",i,(*fret));        u=ulim; 
       for (j=1;j<=n;j++) {        fu=(*func)(u); 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);      } else { 
         printf(" x(%d)=%.12e",j,xit[j]);        u=(*cx)+GOLD*(*cx-*bx); 
       }        fu=(*func)(u); 
       for(j=1;j<=n;j++)      } 
         printf(" p=%.12e",p[j]);      SHFT(*ax,*bx,*cx,u) 
       printf("\n");        SHFT(*fa,*fb,*fc,fu) 
 #endif        } 
     }  } 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  
 #ifdef DEBUG  /*************** linmin ************************/
       int k[2],l;  
       k[0]=1;  int ncom; 
       k[1]=-1;  double *pcom,*xicom;
       printf("Max: %.12e",(*func)(p));  double (*nrfunc)(double []); 
       for (j=1;j<=n;j++)   
         printf(" %.12e",p[j]);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       printf("\n");  { 
       for(l=0;l<=1;l++) {    double brent(double ax, double bx, double cx, 
         for (j=1;j<=n;j++) {                 double (*f)(double), double tol, double *xmin); 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    double f1dim(double x); 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
         }                double *fc, double (*func)(double)); 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    int j; 
       }    double xx,xmin,bx,ax; 
 #endif    double fx,fb,fa;
    
     ncom=n; 
       free_vector(xit,1,n);    pcom=vector(1,n); 
       free_vector(xits,1,n);    xicom=vector(1,n); 
       free_vector(ptt,1,n);    nrfunc=func; 
       free_vector(pt,1,n);    for (j=1;j<=n;j++) { 
       return;      pcom[j]=p[j]; 
     }      xicom[j]=xi[j]; 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    } 
     for (j=1;j<=n;j++) {    ax=0.0; 
       ptt[j]=2.0*p[j]-pt[j];    xx=1.0; 
       xit[j]=p[j]-pt[j];    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       pt[j]=p[j];    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     }  #ifdef DEBUG
     fptt=(*func)(ptt);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     if (fptt < fp) {    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  #endif
       if (t < 0.0) {    for (j=1;j<=n;j++) { 
         linmin(p,xit,n,fret,func);      xi[j] *= xmin; 
         for (j=1;j<=n;j++) {      p[j] += xi[j]; 
           xi[j][ibig]=xi[j][n];    } 
           xi[j][n]=xit[j];    free_vector(xicom,1,n); 
         }    free_vector(pcom,1,n); 
 #ifdef DEBUG  } 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  
         for(j=1;j<=n;j++)  /*************** powell ************************/
           printf(" %.12e",xit[j]);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
         printf("\n");              double (*func)(double [])) 
 #endif  { 
       }    void linmin(double p[], double xi[], int n, double *fret, 
     }                double (*func)(double [])); 
   }    int i,ibig,j; 
 }    double del,t,*pt,*ptt,*xit;
     double fp,fptt;
 /**** Prevalence limit ****************/    double *xits;
     pt=vector(1,n); 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    ptt=vector(1,n); 
 {    xit=vector(1,n); 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    xits=vector(1,n); 
      matrix by transitions matrix until convergence is reached */    *fret=(*func)(p); 
     for (j=1;j<=n;j++) pt[j]=p[j]; 
   int i, ii,j,k;    for (*iter=1;;++(*iter)) { 
   double min, max, maxmin, maxmax,sumnew=0.;      fp=(*fret); 
   double **matprod2();      ibig=0; 
   double **out, cov[NCOVMAX], **pmij();      del=0.0; 
   double **newm;      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
   double agefin, delaymax=50 ; /* Max number of years to converge */      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       for (i=1;i<=n;i++) 
   for (ii=1;ii<=nlstate+ndeath;ii++)        printf(" %d %.12f",i, p[i]);
     for (j=1;j<=nlstate+ndeath;j++){      fprintf(ficlog," %d %.12f",i, p[i]);
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      printf("\n");
     }      fprintf(ficlog,"\n");
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      for (i=1;i<=n;i++) { 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     newm=savm;        fptt=(*fret); 
     /* Covariates have to be included here again */  #ifdef DEBUG
     cov[1]=1.;        printf("fret=%lf \n",*fret);
     cov[2]=agefin;        fprintf(ficlog,"fret=%lf \n",*fret);
     if (cptcovn>0){  #endif
       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]]);*/}        printf("%d",i);fflush(stdout);
     }        fprintf(ficlog,"%d",i);fflush(ficlog);
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);        linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
     savm=oldm;          del=fabs(fptt-(*fret)); 
     oldm=newm;          ibig=i; 
     maxmax=0.;        } 
     for(j=1;j<=nlstate;j++){  #ifdef DEBUG
       min=1.;        printf("%d %.12e",i,(*fret));
       max=0.;        fprintf(ficlog,"%d %.12e",i,(*fret));
       for(i=1; i<=nlstate; i++) {        for (j=1;j<=n;j++) {
         sumnew=0;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];          printf(" x(%d)=%.12e",j,xit[j]);
         prlim[i][j]= newm[i][j]/(1-sumnew);          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         max=FMAX(max,prlim[i][j]);        }
         min=FMIN(min,prlim[i][j]);        for(j=1;j<=n;j++) {
       }          printf(" p=%.12e",p[j]);
       maxmin=max-min;          fprintf(ficlog," p=%.12e",p[j]);
       maxmax=FMAX(maxmax,maxmin);        }
     }        printf("\n");
     if(maxmax < ftolpl){        fprintf(ficlog,"\n");
       return prlim;  #endif
     }      } 
   }      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
 }  #ifdef DEBUG
         int k[2],l;
 /*************** transition probabilities **********/        k[0]=1;
         k[1]=-1;
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )        printf("Max: %.12e",(*func)(p));
 {        fprintf(ficlog,"Max: %.12e",(*func)(p));
   double s1, s2;        for (j=1;j<=n;j++) {
   /*double t34;*/          printf(" %.12e",p[j]);
   int i,j,j1, nc, ii, jj;          fprintf(ficlog," %.12e",p[j]);
         }
     for(i=1; i<= nlstate; i++){        printf("\n");
     for(j=1; j<i;j++){        fprintf(ficlog,"\n");
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        for(l=0;l<=1;l++) {
         /*s2 += param[i][j][nc]*cov[nc];*/          for (j=1;j<=n;j++) {
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       }            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       ps[i][j]=s2;          }
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     }          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     for(j=i+1; j<=nlstate+ndeath;j++){        }
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  #endif
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  
       }        free_vector(xit,1,n); 
       ps[i][j]=s2;        free_vector(xits,1,n); 
     }        free_vector(ptt,1,n); 
   }        free_vector(pt,1,n); 
   for(i=1; i<= nlstate; i++){        return; 
      s1=0;      } 
     for(j=1; j<i; j++)      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       s1+=exp(ps[i][j]);      for (j=1;j<=n;j++) { 
     for(j=i+1; j<=nlstate+ndeath; j++)        ptt[j]=2.0*p[j]-pt[j]; 
       s1+=exp(ps[i][j]);        xit[j]=p[j]-pt[j]; 
     ps[i][i]=1./(s1+1.);        pt[j]=p[j]; 
     for(j=1; j<i; j++)      } 
       ps[i][j]= exp(ps[i][j])*ps[i][i];      fptt=(*func)(ptt); 
     for(j=i+1; j<=nlstate+ndeath; j++)      if (fptt < fp) { 
       ps[i][j]= exp(ps[i][j])*ps[i][i];        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        if (t < 0.0) { 
   } /* end i */          linmin(p,xit,n,fret,func); 
           for (j=1;j<=n;j++) { 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){            xi[j][ibig]=xi[j][n]; 
     for(jj=1; jj<= nlstate+ndeath; jj++){            xi[j][n]=xit[j]; 
       ps[ii][jj]=0;          }
       ps[ii][ii]=1;  #ifdef DEBUG
     }          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   }          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           for(j=1;j<=n;j++){
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){            printf(" %.12e",xit[j]);
     for(jj=1; jj<= nlstate+ndeath; jj++){            fprintf(ficlog," %.12e",xit[j]);
      printf("%lf ",ps[ii][jj]);          }
    }          printf("\n");
     printf("\n ");          fprintf(ficlog,"\n");
     }  #endif
     printf("\n ");printf("%lf ",cov[2]);*/        }
 /*      } 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    } 
   goto end;*/  } 
     return ps;  
 }  /**** Prevalence limit (stable prevalence)  ****************/
   
 /**************** Product of 2 matrices ******************/  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   {
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
 {       matrix by transitions matrix until convergence is reached */
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    int i, ii,j,k;
   /* in, b, out are matrice of pointers which should have been initialized    double min, max, maxmin, maxmax,sumnew=0.;
      before: only the contents of out is modified. The function returns    double **matprod2();
      a pointer to pointers identical to out */    double **out, cov[NCOVMAX], **pmij();
   long i, j, k;    double **newm;
   for(i=nrl; i<= nrh; i++)    double agefin, delaymax=50 ; /* Max number of years to converge */
     for(k=ncolol; k<=ncoloh; k++)  
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    for (ii=1;ii<=nlstate+ndeath;ii++)
         out[i][k] +=in[i][j]*b[j][k];      for (j=1;j<=nlstate+ndeath;j++){
         oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   return out;      }
 }  
      cov[1]=1.;
    
 /************* Higher Matrix Product ***************/   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      newm=savm;
 {      /* Covariates have to be included here again */
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month       cov[2]=agefin;
      duration (i.e. until    
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        for (k=1; k<=cptcovn;k++) {
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
      (typically every 2 years instead of every month which is too big).          /*      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]]);*/
      Model is determined by parameters x and covariates have to be        }
      included manually here.        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]]];
   
   int i, j, d, h, k;        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   double **out, cov[NCOVMAX];        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   double **newm;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   /* Hstepm could be zero and should return the unit matrix */  
   for (i=1;i<=nlstate+ndeath;i++)      savm=oldm;
     for (j=1;j<=nlstate+ndeath;j++){      oldm=newm;
       oldm[i][j]=(i==j ? 1.0 : 0.0);      maxmax=0.;
       po[i][j][0]=(i==j ? 1.0 : 0.0);      for(j=1;j<=nlstate;j++){
     }        min=1.;
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */        max=0.;
   for(h=1; h <=nhstepm; h++){        for(i=1; i<=nlstate; i++) {
     for(d=1; d <=hstepm; d++){          sumnew=0;
       newm=savm;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       /* Covariates have to be included here again */          prlim[i][j]= newm[i][j]/(1-sumnew);
       cov[1]=1.;          max=FMAX(max,prlim[i][j]);
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;          min=FMIN(min,prlim[i][j]);
       if (cptcovn>0){        }
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];        maxmin=max-min;
     }        maxmax=FMAX(maxmax,maxmin);
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      }
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      if(maxmax < ftolpl){
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,        return prlim;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      }
       savm=oldm;    }
       oldm=newm;  }
     }  
     for(i=1; i<=nlstate+ndeath; i++)  /*************** transition probabilities ***************/ 
       for(j=1;j<=nlstate+ndeath;j++) {  
         po[i][j][h]=newm[i][j];  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  {
          */    double s1, s2;
       }    /*double t34;*/
   } /* end h */    int i,j,j1, nc, ii, jj;
   return po;  
 }      for(i=1; i<= nlstate; i++){
       for(j=1; j<i;j++){
         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
 /*************** log-likelihood *************/          /*s2 += param[i][j][nc]*cov[nc];*/
 double func( double *x)          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
 {          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
   int i, ii, j, k, mi, d;        }
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        ps[i][j]=s2;
   double **out;        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
   double sw; /* Sum of weights */      }
   double lli; /* Individual log likelihood */      for(j=i+1; j<=nlstate+ndeath;j++){
   long ipmx;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   /*extern weight */          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   /* We are differentiating ll according to initial status */          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        }
   /*for(i=1;i<imx;i++)        ps[i][j]=s2;
 printf(" %d\n",s[4][i]);      }
   */    }
       /*ps[3][2]=1;*/
   for(k=1; k<=nlstate; k++) ll[k]=0.;  
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    for(i=1; i<= nlstate; i++){
        for(mi=1; mi<= wav[i]-1; mi++){       s1=0;
       for (ii=1;ii<=nlstate+ndeath;ii++)      for(j=1; j<i; j++)
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        s1+=exp(ps[i][j]);
             for(d=0; d<dh[mi][i]; d++){      for(j=i+1; j<=nlstate+ndeath; j++)
         newm=savm;        s1+=exp(ps[i][j]);
           cov[1]=1.;      ps[i][i]=1./(s1+1.);
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      for(j=1; j<i; j++)
           if (cptcovn>0){        ps[i][j]= exp(ps[i][j])*ps[i][i];
             for (k=1; k<=cptcovn;k++) {      for(j=i+1; j<=nlstate+ndeath; j++)
               cov[2+k]=covar[Tvar[k]][i];        ps[i][j]= exp(ps[i][j])*ps[i][i];
               /* printf("k=%d cptcovn=%d %lf\n",k,cptcovn,covar[Tvar[k]][i]);*/      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
             }    } /* end i */
             }  
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      for(jj=1; jj<= nlstate+ndeath; jj++){
           savm=oldm;        ps[ii][jj]=0;
           oldm=newm;        ps[ii][ii]=1;
       } /* end mult */      }
        }
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  
       ipmx +=1;    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
       sw += weight[i];      for(jj=1; jj<= nlstate+ndeath; jj++){
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;       printf("%lf ",ps[ii][jj]);
     } /* end of wave */     }
   } /* end of individual */      printf("\n ");
       }
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];      printf("\n ");printf("%lf ",cov[2]);*/
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  /*
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    for(i=1; i<= npar; i++) printf("%f ",x[i]);
     goto end;*/
   return -l;      return ps;
 }  }
   
   /**************** Product of 2 matrices ******************/
 /*********** Maximum Likelihood Estimation ***************/  
   double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  {
 {    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   int i,j, iter;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   double **xi,*delti;    /* in, b, out are matrice of pointers which should have been initialized 
   double fret;       before: only the contents of out is modified. The function returns
   xi=matrix(1,npar,1,npar);       a pointer to pointers identical to out */
   for (i=1;i<=npar;i++)    long i, j, k;
     for (j=1;j<=npar;j++)    for(i=nrl; i<= nrh; i++)
       xi[i][j]=(i==j ? 1.0 : 0.0);      for(k=ncolol; k<=ncoloh; k++)
   printf("Powell\n");        for(j=ncl,out[i][k]=0.; j<=nch; j++)
   powell(p,xi,npar,ftol,&iter,&fret,func);          out[i][k] +=in[i][j]*b[j][k];
   
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    return out;
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));  }
   
 }  
   /************* Higher Matrix Product ***************/
 /**** Computes Hessian and covariance matrix ***/  
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
 {  {
   double  **a,**y,*x,pd;    /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month 
   double **hess;       duration (i.e. until
   int i, j,jk;       age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices. 
   int *indx;       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).
   double hessii(double p[], double delta, int theta, double delti[]);       Model is determined by parameters x and covariates have to be 
   double hessij(double p[], double delti[], int i, int j);       included manually here. 
   void lubksb(double **a, int npar, int *indx, double b[]) ;  
   void ludcmp(double **a, int npar, int *indx, double *d) ;       */
   
     int i, j, d, h, k;
   hess=matrix(1,npar,1,npar);    double **out, cov[NCOVMAX];
     double **newm;
   printf("\nCalculation of the hessian matrix. Wait...\n");  
   for (i=1;i<=npar;i++){    /* Hstepm could be zero and should return the unit matrix */
     printf("%d",i);fflush(stdout);    for (i=1;i<=nlstate+ndeath;i++)
     hess[i][i]=hessii(p,ftolhess,i,delti);      for (j=1;j<=nlstate+ndeath;j++){
     /*printf(" %f ",p[i]);*/        oldm[i][j]=(i==j ? 1.0 : 0.0);
   }        po[i][j][0]=(i==j ? 1.0 : 0.0);
       }
   for (i=1;i<=npar;i++) {    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for (j=1;j<=npar;j++)  {    for(h=1; h <=nhstepm; h++){
       if (j>i) {      for(d=1; d <=hstepm; d++){
         printf(".%d%d",i,j);fflush(stdout);        newm=savm;
         hess[i][j]=hessij(p,delti,i,j);        /* Covariates have to be included here again */
         hess[j][i]=hess[i][j];        cov[1]=1.;
       }        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     }        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   }        for (k=1; k<=cptcovage;k++)
   printf("\n");          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++)
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
    
   a=matrix(1,npar,1,npar);  
   y=matrix(1,npar,1,npar);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   x=vector(1,npar);        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   indx=ivector(1,npar);        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   for (i=1;i<=npar;i++)                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        savm=oldm;
   ludcmp(a,npar,indx,&pd);        oldm=newm;
       }
   for (j=1;j<=npar;j++) {      for(i=1; i<=nlstate+ndeath; i++)
     for (i=1;i<=npar;i++) x[i]=0;        for(j=1;j<=nlstate+ndeath;j++) {
     x[j]=1;          po[i][j][h]=newm[i][j];
     lubksb(a,npar,indx,x);          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
     for (i=1;i<=npar;i++){           */
       matcov[i][j]=x[i];        }
     }    } /* end h */
   }    return po;
   }
   printf("\n#Hessian matrix#\n");  
   for (i=1;i<=npar;i++) {  
     for (j=1;j<=npar;j++) {  /*************** log-likelihood *************/
       printf("%.3e ",hess[i][j]);  double func( double *x)
     }  {
     printf("\n");    int i, ii, j, k, mi, d, kk;
   }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     double **out;
   /* Recompute Inverse */    double sw; /* Sum of weights */
   for (i=1;i<=npar;i++)    double lli; /* Individual log likelihood */
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    long ipmx;
   ludcmp(a,npar,indx,&pd);    /*extern weight */
     /* We are differentiating ll according to initial status */
   /*  printf("\n#Hessian matrix recomputed#\n");    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
   for (j=1;j<=npar;j++) {      printf(" %d\n",s[4][i]);
     for (i=1;i<=npar;i++) x[i]=0;    */
     x[j]=1;    cov[1]=1.;
     lubksb(a,npar,indx,x);  
     for (i=1;i<=npar;i++){    for(k=1; k<=nlstate; k++) ll[k]=0.;
       y[i][j]=x[i];    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       printf("%.3e ",y[i][j]);      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     }      for(mi=1; mi<= wav[i]-1; mi++){
     printf("\n");        for (ii=1;ii<=nlstate+ndeath;ii++)
   }          for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   */        for(d=0; d<dh[mi][i]; d++){
           newm=savm;
   free_matrix(a,1,npar,1,npar);          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   free_matrix(y,1,npar,1,npar);          for (kk=1; kk<=cptcovage;kk++) {
   free_vector(x,1,npar);            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   free_ivector(indx,1,npar);          }
   free_matrix(hess,1,npar,1,npar);          
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 }          savm=oldm;
           oldm=newm;
 /*************** hessian matrix ****************/          
 double hessii( double x[], double delta, int theta, double delti[])          
 {        } /* end mult */
   int i;        
   int l=1, lmax=20;        lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);
   double k1,k2;        /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/
   double p2[NPARMAX+1];        ipmx +=1;
   double res;        sw += weight[i];
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double fx;      } /* end of wave */
   int k=0,kmax=10;    } /* end of individual */
   double l1;  
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   fx=func(x);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   for (i=1;i<=npar;i++) p2[i]=x[i];    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   for(l=0 ; l <=lmax; l++){    return -l;
     l1=pow(10,l);  }
     delts=delt;  
     for(k=1 ; k <kmax; k=k+1){  
       delt = delta*(l1*k);  /*********** Maximum Likelihood Estimation ***************/
       p2[theta]=x[theta] +delt;  
       k1=func(p2)-fx;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       p2[theta]=x[theta]-delt;  {
       k2=func(p2)-fx;    int i,j, iter;
       /*res= (k1-2.0*fx+k2)/delt/delt; */    double **xi,*delti;
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    double fret;
          xi=matrix(1,npar,1,npar);
 #ifdef DEBUG    for (i=1;i<=npar;i++)
       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 (j=1;j<=npar;j++)
 #endif        xi[i][j]=(i==j ? 1.0 : 0.0);
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    printf("Powell\n");  fprintf(ficlog,"Powell\n");
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    powell(p,xi,npar,ftol,&iter,&fret,func);
         k=kmax;  
       }     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         k=kmax; l=lmax*10.;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
       }  
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  }
         delts=delt;  
       }  /**** Computes Hessian and covariance matrix ***/
     }  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   }  {
   delti[theta]=delts;    double  **a,**y,*x,pd;
   return res;      double **hess;
 }    int i, j,jk;
     int *indx;
 double hessij( double x[], double delti[], int thetai,int thetaj)  
 {    double hessii(double p[], double delta, int theta, double delti[]);
   int i;    double hessij(double p[], double delti[], int i, int j);
   int l=1, l1, lmax=20;    void lubksb(double **a, int npar, int *indx, double b[]) ;
   double k1,k2,k3,k4,res,fx;    void ludcmp(double **a, int npar, int *indx, double *d) ;
   double p2[NPARMAX+1];  
   int k;    hess=matrix(1,npar,1,npar);
   
   fx=func(x);    printf("\nCalculation of the hessian matrix. Wait...\n");
   for (k=1; k<=2; k++) {    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     for (i=1;i<=npar;i++) p2[i]=x[i];    for (i=1;i<=npar;i++){
     p2[thetai]=x[thetai]+delti[thetai]/k;      printf("%d",i);fflush(stdout);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      fprintf(ficlog,"%d",i);fflush(ficlog);
     k1=func(p2)-fx;      hess[i][i]=hessii(p,ftolhess,i,delti);
        /*printf(" %f ",p[i]);*/
     p2[thetai]=x[thetai]+delti[thetai]/k;      /*printf(" %lf ",hess[i][i]);*/
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    }
     k2=func(p2)-fx;    
      for (i=1;i<=npar;i++) {
     p2[thetai]=x[thetai]-delti[thetai]/k;      for (j=1;j<=npar;j++)  {
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        if (j>i) { 
     k3=func(p2)-fx;          printf(".%d%d",i,j);fflush(stdout);
            fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     p2[thetai]=x[thetai]-delti[thetai]/k;          hess[i][j]=hessij(p,delti,i,j);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          hess[j][i]=hess[i][j];    
     k4=func(p2)-fx;          /*printf(" %lf ",hess[i][j]);*/
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        }
 #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);    }
 #endif    printf("\n");
   }    fprintf(ficlog,"\n");
   return res;  
 }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
 /************** Inverse of matrix **************/    
 void ludcmp(double **a, int n, int *indx, double *d)    a=matrix(1,npar,1,npar);
 {    y=matrix(1,npar,1,npar);
   int i,imax,j,k;    x=vector(1,npar);
   double big,dum,sum,temp;    indx=ivector(1,npar);
   double *vv;    for (i=1;i<=npar;i++)
        for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   vv=vector(1,n);    ludcmp(a,npar,indx,&pd);
   *d=1.0;  
   for (i=1;i<=n;i++) {    for (j=1;j<=npar;j++) {
     big=0.0;      for (i=1;i<=npar;i++) x[i]=0;
     for (j=1;j<=n;j++)      x[j]=1;
       if ((temp=fabs(a[i][j])) > big) big=temp;      lubksb(a,npar,indx,x);
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");      for (i=1;i<=npar;i++){ 
     vv[i]=1.0/big;        matcov[i][j]=x[i];
   }      }
   for (j=1;j<=n;j++) {    }
     for (i=1;i<j;i++) {  
       sum=a[i][j];    printf("\n#Hessian matrix#\n");
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    fprintf(ficlog,"\n#Hessian matrix#\n");
       a[i][j]=sum;    for (i=1;i<=npar;i++) { 
     }      for (j=1;j<=npar;j++) { 
     big=0.0;        printf("%.3e ",hess[i][j]);
     for (i=j;i<=n;i++) {        fprintf(ficlog,"%.3e ",hess[i][j]);
       sum=a[i][j];      }
       for (k=1;k<j;k++)      printf("\n");
         sum -= a[i][k]*a[k][j];      fprintf(ficlog,"\n");
       a[i][j]=sum;    }
       if ( (dum=vv[i]*fabs(sum)) >= big) {  
         big=dum;    /* Recompute Inverse */
         imax=i;    for (i=1;i<=npar;i++)
       }      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     }    ludcmp(a,npar,indx,&pd);
     if (j != imax) {  
       for (k=1;k<=n;k++) {    /*  printf("\n#Hessian matrix recomputed#\n");
         dum=a[imax][k];  
         a[imax][k]=a[j][k];    for (j=1;j<=npar;j++) {
         a[j][k]=dum;      for (i=1;i<=npar;i++) x[i]=0;
       }      x[j]=1;
       *d = -(*d);      lubksb(a,npar,indx,x);
       vv[imax]=vv[j];      for (i=1;i<=npar;i++){ 
     }        y[i][j]=x[i];
     indx[j]=imax;        printf("%.3e ",y[i][j]);
     if (a[j][j] == 0.0) a[j][j]=TINY;        fprintf(ficlog,"%.3e ",y[i][j]);
     if (j != n) {      }
       dum=1.0/(a[j][j]);      printf("\n");
       for (i=j+1;i<=n;i++) a[i][j] *= dum;      fprintf(ficlog,"\n");
     }    }
   }    */
   free_vector(vv,1,n);  /* Doesn't work */  
 ;    free_matrix(a,1,npar,1,npar);
 }    free_matrix(y,1,npar,1,npar);
     free_vector(x,1,npar);
 void lubksb(double **a, int n, int *indx, double b[])    free_ivector(indx,1,npar);
 {    free_matrix(hess,1,npar,1,npar);
   int i,ii=0,ip,j;  
   double sum;  
    }
   for (i=1;i<=n;i++) {  
     ip=indx[i];  /*************** hessian matrix ****************/
     sum=b[ip];  double hessii( double x[], double delta, int theta, double delti[])
     b[ip]=b[i];  {
     if (ii)    int i;
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    int l=1, lmax=20;
     else if (sum) ii=i;    double k1,k2;
     b[i]=sum;    double p2[NPARMAX+1];
   }    double res;
   for (i=n;i>=1;i--) {    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     sum=b[i];    double fx;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    int k=0,kmax=10;
     b[i]=sum/a[i][i];    double l1;
   }  
 }    fx=func(x);
     for (i=1;i<=npar;i++) p2[i]=x[i];
 /************ Frequencies ********************/    for(l=0 ; l <=lmax; l++){
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)      l1=pow(10,l);
 {  /* Some frequencies */      delts=delt;
        for(k=1 ; k <kmax; k=k+1){
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;        delt = delta*(l1*k);
   double ***freq; /* Frequencies */        p2[theta]=x[theta] +delt;
   double *pp;        k1=func(p2)-fx;
   double pos;        p2[theta]=x[theta]-delt;
   FILE *ficresp;        k2=func(p2)-fx;
   char fileresp[FILENAMELENGTH];        /*res= (k1-2.0*fx+k2)/delt/delt; */
         res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   pp=vector(1,nlstate);        
   #ifdef DEBUG
   strcpy(fileresp,"p");        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);
   strcat(fileresp,fileres);        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);
   if((ficresp=fopen(fileresp,"w"))==NULL) {  #endif
     printf("Problem with prevalence resultfile: %s\n", fileresp);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
     exit(0);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   }          k=kmax;
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        }
   j1=0;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           k=kmax; l=lmax*10.;
   j=cptcovn;        }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           delts=delt;
   for(k1=1; k1<=j;k1++){        }
    for(i1=1; i1<=ncodemax[k1];i1++){      }
        j1++;    }
     delti[theta]=delts;
         for (i=-1; i<=nlstate+ndeath; i++)      return res; 
          for (jk=-1; jk<=nlstate+ndeath; jk++)      
            for(m=agemin; m <= agemax+3; m++)  }
              freq[i][jk][m]=0;  
          double hessij( double x[], double delti[], int thetai,int thetaj)
        for (i=1; i<=imx; i++) {  {
          bool=1;    int i;
          if  (cptcovn>0) {    int l=1, l1, lmax=20;
            for (z1=1; z1<=cptcovn; z1++)    double k1,k2,k3,k4,res,fx;
              if (covar[Tvar[z1]][i]!= nbcode[Tvar[z1]][codtab[j1][z1]]) bool=0;    double p2[NPARMAX+1];
          }    int k;
           if (bool==1) {  
            for(m=firstpass; m<=lastpass-1; m++){    fx=func(x);
              if(agev[m][i]==0) agev[m][i]=agemax+1;    for (k=1; k<=2; k++) {
              if(agev[m][i]==1) agev[m][i]=agemax+2;      for (i=1;i<=npar;i++) p2[i]=x[i];
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      p2[thetai]=x[thetai]+delti[thetai]/k;
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
            }      k1=func(p2)-fx;
          }    
        }      p2[thetai]=x[thetai]+delti[thetai]/k;
         if  (cptcovn>0) {      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
          fprintf(ficresp, "\n#Variable");      k2=func(p2)-fx;
          for (z1=1; z1<=cptcovn; z1++) fprintf(ficresp, " V%d=%d",Tvar[z1],nbcode[Tvar[z1]][codtab[j1][z1]]);    
        }      p2[thetai]=x[thetai]-delti[thetai]/k;
        fprintf(ficresp, "\n#");      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
        for(i=1; i<=nlstate;i++)      k3=func(p2)-fx;
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    
        fprintf(ficresp, "\n");      p2[thetai]=x[thetai]-delti[thetai]/k;
              p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   for(i=(int)agemin; i <= (int)agemax+3; i++){      k4=func(p2)-fx;
     if(i==(int)agemax+3)      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
       printf("Total");  #ifdef DEBUG
     else      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);
       printf("Age %d", i);      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(jk=1; jk <=nlstate ; jk++){  #endif
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    }
         pp[jk] += freq[jk][m][i];    return res;
     }  }
     for(jk=1; jk <=nlstate ; jk++){  
       for(m=-1, pos=0; m <=0 ; m++)  /************** Inverse of matrix **************/
         pos += freq[jk][m][i];  void ludcmp(double **a, int n, int *indx, double *d) 
       if(pp[jk]>=1.e-10)  { 
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    int i,imax,j,k; 
       else    double big,dum,sum,temp; 
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    double *vv; 
     }   
     for(jk=1; jk <=nlstate ; jk++){    vv=vector(1,n); 
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)    *d=1.0; 
         pp[jk] += freq[jk][m][i];    for (i=1;i<=n;i++) { 
     }      big=0.0; 
     for(jk=1,pos=0; jk <=nlstate ; jk++)      for (j=1;j<=n;j++) 
       pos += pp[jk];        if ((temp=fabs(a[i][j])) > big) big=temp; 
     for(jk=1; jk <=nlstate ; jk++){      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       if(pos>=1.e-5)      vv[i]=1.0/big; 
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    } 
       else    for (j=1;j<=n;j++) { 
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      for (i=1;i<j;i++) { 
       if( i <= (int) agemax){        sum=a[i][j]; 
         if(pos>=1.e-5)        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        a[i][j]=sum; 
       else      } 
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);      big=0.0; 
       }      for (i=j;i<=n;i++) { 
     }        sum=a[i][j]; 
     for(jk=-1; jk <=nlstate+ndeath; jk++)        for (k=1;k<j;k++) 
       for(m=-1; m <=nlstate+ndeath; m++)          sum -= a[i][k]*a[k][j]; 
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        a[i][j]=sum; 
     if(i <= (int) agemax)        if ( (dum=vv[i]*fabs(sum)) >= big) { 
       fprintf(ficresp,"\n");          big=dum; 
     printf("\n");          imax=i; 
     }        } 
     }      } 
  }      if (j != imax) { 
          for (k=1;k<=n;k++) { 
   fclose(ficresp);          dum=a[imax][k]; 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          a[imax][k]=a[j][k]; 
   free_vector(pp,1,nlstate);          a[j][k]=dum; 
         } 
 }  /* End of Freq */        *d = -(*d); 
         vv[imax]=vv[j]; 
 /************* Waves Concatenation ***************/      } 
       indx[j]=imax; 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)      if (a[j][j] == 0.0) a[j][j]=TINY; 
 {      if (j != n) { 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        dum=1.0/(a[j][j]); 
      Death is a valid wave (if date is known).        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      } 
      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.    free_vector(vv,1,n);  /* Doesn't work */
      */  ;
   } 
   int i, mi, m;  
   int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  void lubksb(double **a, int n, int *indx, double b[]) 
 float sum=0.;  { 
     int i,ii=0,ip,j; 
   for(i=1; i<=imx; i++){    double sum; 
     mi=0;   
     m=firstpass;    for (i=1;i<=n;i++) { 
     while(s[m][i] <= nlstate){      ip=indx[i]; 
       if(s[m][i]>=1)      sum=b[ip]; 
         mw[++mi][i]=m;      b[ip]=b[i]; 
       if(m >=lastpass)      if (ii) 
         break;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       else      else if (sum) ii=i; 
         m++;      b[i]=sum; 
     }/* end while */    } 
     if (s[m][i] > nlstate){    for (i=n;i>=1;i--) { 
       mi++;     /* Death is another wave */      sum=b[i]; 
       /* if(mi==0)  never been interviewed correctly before death */      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
          /* Only death is a correct wave */      b[i]=sum/a[i][i]; 
       mw[mi][i]=m;    } 
     }  } 
   
     wav[i]=mi;  /************ Frequencies ********************/
     if(mi==0)  void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  {  /* Some frequencies */
   }    
     int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   for(i=1; i<=imx; i++){    int first;
     for(mi=1; mi<wav[i];mi++){    double ***freq; /* Frequencies */
       if (stepm <=0)    double *pp;
         dh[mi][i]=1;    double pos, k2, dateintsum=0,k2cpt=0;
       else{    FILE *ficresp;
         if (s[mw[mi+1][i]][i] > nlstate) {    char fileresp[FILENAMELENGTH];
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    
           if(j=0) j=1;  /* Survives at least one month after exam */    pp=vector(1,nlstate);
         }    probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
         else{    strcpy(fileresp,"p");
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    strcat(fileresp,fileres);
           /*printf("i=%d agevi+1=%lf agevi=%lf j=%d\n", i,agev[mw[mi+1][i]][i],agev[mw[mi][i]][i],j);*/    if((ficresp=fopen(fileresp,"w"))==NULL) {
       printf("Problem with prevalence resultfile: %s\n", fileresp);
           k=k+1;      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
           if (j >= jmax) jmax=j;      exit(0);
           else if (j <= jmin)jmin=j;    }
           sum=sum+j;    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
         }    j1=0;
         jk= j/stepm;    
         jl= j -jk*stepm;    j=cptcoveff;
         ju= j -(jk+1)*stepm;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         if(jl <= -ju)  
           dh[mi][i]=jk;    first=1;
         else  
           dh[mi][i]=jk+1;    for(k1=1; k1<=j;k1++){
         if(dh[mi][i]==0)      for(i1=1; i1<=ncodemax[k1];i1++){
           dh[mi][i]=1; /* At least one step */        j1++;
       }        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     }          scanf("%d", i);*/
   }        for (i=-1; i<=nlstate+ndeath; i++)  
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);          for (jk=-1; jk<=nlstate+ndeath; jk++)  
 }            for(m=agemin; m <= agemax+3; m++)
 /*********** Tricode ****************************/              freq[i][jk][m]=0;
 void tricode(int *Tvar, int **nbcode, int imx)        
 {        dateintsum=0;
   int Ndum[80],ij, k, j, i;        k2cpt=0;
   int cptcode=0;        for (i=1; i<=imx; i++) {
   for (k=0; k<79; k++) Ndum[k]=0;          bool=1;
   for (k=1; k<=7; k++) ncodemax[k]=0;          if  (cptcovn>0) {
              for (z1=1; z1<=cptcoveff; z1++) 
   for (j=1; j<=cptcovn; j++) {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     for (i=1; i<=imx; i++) {                bool=0;
       ij=(int)(covar[Tvar[j]][i]);          }
       Ndum[ij]++;          if (bool==1) {
       if (ij > cptcode) cptcode=ij;            for(m=firstpass; m<=lastpass; m++){
     }              k2=anint[m][i]+(mint[m][i]/12.);
     /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/              if ((k2>=dateprev1) && (k2<=dateprev2)) {
     for (i=0; i<=cptcode; i++) {                if(agev[m][i]==0) agev[m][i]=agemax+1;
       if(Ndum[i]!=0) ncodemax[j]++;                if(agev[m][i]==1) agev[m][i]=agemax+2;
     }                if (m<lastpass) {
                    freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     ij=1;                  freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];
     for (i=1; i<=ncodemax[j]; i++) {                }
       for (k=0; k<=79; k++) {                
         if (Ndum[k] != 0) {                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {
           nbcode[Tvar[j]][ij]=k;                  dateintsum=dateintsum+k2;
           ij++;                  k2cpt++;
         }                }
         if (ij > ncodemax[j]) break;              }
       }              }
     }          }
   }          }
          
   }        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);
   
 /*********** Health Expectancies ****************/        if  (cptcovn>0) {
           fprintf(ficresp, "\n#********** Variable "); 
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 {          fprintf(ficresp, "**********\n#");
   /* Health expectancies */        }
   int i, j, nhstepm, hstepm, h;        for(i=1; i<=nlstate;i++) 
   double age, agelim,hf;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   double ***p3mat;        fprintf(ficresp, "\n");
          
   fprintf(ficreseij,"# Health expectancies\n");        for(i=(int)agemin; i <= (int)agemax+3; i++){
   fprintf(ficreseij,"# Age");          if(i==(int)agemax+3){
   for(i=1; i<=nlstate;i++)            fprintf(ficlog,"Total");
     for(j=1; j<=nlstate;j++)          }else{
       fprintf(ficreseij," %1d-%1d",i,j);            if(first==1){
   fprintf(ficreseij,"\n");              first=0;
               printf("See log file for details...\n");
   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 */            fprintf(ficlog,"Age %d", i);
           }
   agelim=AGESUP;          for(jk=1; jk <=nlstate ; jk++){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     /* nhstepm age range expressed in number of stepm */              pp[jk] += freq[jk][m][i]; 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);          }
     /* Typically if 20 years = 20*12/6=40 stepm */          for(jk=1; jk <=nlstate ; jk++){
     if (stepm >= YEARM) hstepm=1;            for(m=-1, pos=0; m <=0 ; m++)
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */              pos += freq[jk][m][i];
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            if(pp[jk]>=1.e-10){
     /* Computed by stepm unit matrices, product of hstepm matrices, stored              if(first==1){
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);                }
               fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             }else{
     for(i=1; i<=nlstate;i++)              if(first==1)
       for(j=1; j<=nlstate;j++)                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
           eij[i][j][(int)age] +=p3mat[i][j][h];            }
         }          }
      
     hf=1;          for(jk=1; jk <=nlstate ; jk++){
     if (stepm >= YEARM) hf=stepm/YEARM;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     fprintf(ficreseij,"%.0f",age );              pp[jk] += freq[jk][m][i];
     for(i=1; i<=nlstate;i++)          }
       for(j=1; j<=nlstate;j++){  
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);          for(jk=1,pos=0; jk <=nlstate ; jk++)
       }            pos += pp[jk];
     fprintf(ficreseij,"\n");          for(jk=1; jk <=nlstate ; jk++){
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            if(pos>=1.e-5){
   }              if(first==1)
 }                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
               fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
 /************ Variance ******************/            }else{
 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)              if(first==1)
 {                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   /* Variance of health expectancies */              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            }
   double **newm;            if( i <= (int) agemax){
   double **dnewm,**doldm;              if(pos>=1.e-5){
   int i, j, nhstepm, hstepm, h;                fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);
   int k, cptcode;                probs[i][jk][j1]= pp[jk]/pos;
    double *xp;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   double **gp, **gm;              }
   double ***gradg, ***trgradg;              else
   double ***p3mat;                fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);
   double age,agelim;            }
   int theta;          }
           
    fprintf(ficresvij,"# Covariances of life expectancies\n");          for(jk=-1; jk <=nlstate+ndeath; jk++)
   fprintf(ficresvij,"# Age");            for(m=-1; m <=nlstate+ndeath; m++)
   for(i=1; i<=nlstate;i++)              if(freq[jk][m][i] !=0 ) {
     for(j=1; j<=nlstate;j++)              if(first==1)
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   fprintf(ficresvij,"\n");                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
               }
   xp=vector(1,npar);          if(i <= (int) agemax)
   dnewm=matrix(1,nlstate,1,npar);            fprintf(ficresp,"\n");
   doldm=matrix(1,nlstate,1,nlstate);          if(first==1)
              printf("Others in log...\n");
   hstepm=1*YEARM; /* Every year of age */          fprintf(ficlog,"\n");
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        }
   agelim = AGESUP;      }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    dateintmean=dateintsum/k2cpt; 
     if (stepm >= YEARM) hstepm=1;   
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    fclose(ficresp);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    free_vector(pp,1,nlstate);
     gp=matrix(0,nhstepm,1,nlstate);    
     gm=matrix(0,nhstepm,1,nlstate);    /* End of Freq */
   }
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient */  /************ Prevalence ********************/
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)
       }  {  /* Some frequencies */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);     
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
       for(j=1; j<= nlstate; j++){    double ***freq; /* Frequencies */
         for(h=0; h<=nhstepm; h++){    double *pp;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    double pos, k2;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];  
         }    pp=vector(1,nlstate);
       }    
        freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);
       for(i=1; i<=npar; i++) /* Computes gradient */    j1=0;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      j=cptcoveff;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       for(j=1; j<= nlstate; j++){    
         for(h=0; h<=nhstepm; h++){    for(k1=1; k1<=j;k1++){
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      for(i1=1; i1<=ncodemax[k1];i1++){
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        j1++;
         }        
       }        for (i=-1; i<=nlstate+ndeath; i++)  
       for(j=1; j<= nlstate; j++)          for (jk=-1; jk<=nlstate+ndeath; jk++)  
         for(h=0; h<=nhstepm; h++){            for(m=agemin; m <= agemax+3; m++)
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];              freq[i][jk][m]=0;
         }       
     } /* End theta */        for (i=1; i<=imx; i++) {
           bool=1;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
     for(h=0; h<=nhstepm; h++)              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       for(j=1; j<=nlstate;j++)                bool=0;
         for(theta=1; theta <=npar; theta++)          } 
           trgradg[h][j][theta]=gradg[h][theta][j];          if (bool==1) { 
             for(m=firstpass; m<=lastpass; m++){
     for(i=1;i<=nlstate;i++)              k2=anint[m][i]+(mint[m][i]/12.);
       for(j=1;j<=nlstate;j++)              if ((k2>=dateprev1) && (k2<=dateprev2)) {
         vareij[i][j][(int)age] =0.;                if(agev[m][i]==0) agev[m][i]=agemax+1;
     for(h=0;h<=nhstepm;h++){                if(agev[m][i]==1) agev[m][i]=agemax+2;
       for(k=0;k<=nhstepm;k++){                if (m<lastpass) {
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);                  if (calagedate>0) 
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);                    freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];
         for(i=1;i<=nlstate;i++)                  else
           for(j=1;j<=nlstate;j++)                    freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
             vareij[i][j][(int)age] += doldm[i][j];                  freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i]; 
       }                }
     }              }
     h=1;            }
     if (stepm >= YEARM) h=stepm/YEARM;          }
     fprintf(ficresvij,"%.0f ",age );        }
     for(i=1; i<=nlstate;i++)        for(i=(int)agemin; i <= (int)agemax+3; i++){ 
       for(j=1; j<=nlstate;j++){          for(jk=1; jk <=nlstate ; jk++){
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
       }              pp[jk] += freq[jk][m][i]; 
     fprintf(ficresvij,"\n");          }
     free_matrix(gp,0,nhstepm,1,nlstate);          for(jk=1; jk <=nlstate ; jk++){
     free_matrix(gm,0,nhstepm,1,nlstate);            for(m=-1, pos=0; m <=0 ; m++)
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);              pos += freq[jk][m][i];
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          
   } /* End age */          for(jk=1; jk <=nlstate ; jk++){
              for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   free_vector(xp,1,npar);              pp[jk] += freq[jk][m][i];
   free_matrix(doldm,1,nlstate,1,npar);          }
   free_matrix(dnewm,1,nlstate,1,nlstate);          
           for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];
 }          
           for(jk=1; jk <=nlstate ; jk++){    
 /************ Variance of prevlim ******************/            if( i <= (int) agemax){
 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)              if(pos>=1.e-5){
 {                probs[i][jk][j1]= pp[jk]/pos;
   /* Variance of prevalence limit */              }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            }
   double **newm;          }/* end jk */
   double **dnewm,**doldm;        }/* end i */
   int i, j, nhstepm, hstepm;      } /* end i1 */
   int k, cptcode;    } /* end k1 */
   double *xp;  
   double *gp, *gm;    
   double **gradg, **trgradg;    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);
   double age,agelim;    free_vector(pp,1,nlstate);
   int theta;    
      }  /* End of Freq */
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");  
   fprintf(ficresvpl,"# Age");  /************* Waves Concatenation ***************/
   for(i=1; i<=nlstate;i++)  
       fprintf(ficresvpl," %1d-%1d",i,i);  void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
   fprintf(ficresvpl,"\n");  {
     /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   xp=vector(1,npar);       Death is a valid wave (if date is known).
   dnewm=matrix(1,nlstate,1,npar);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   doldm=matrix(1,nlstate,1,nlstate);       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.
   hstepm=1*YEARM; /* Every year of age */       */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  
   agelim = AGESUP;    int i, mi, m;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */       double sum=0., jmean=0.;*/
     if (stepm >= YEARM) hstepm=1;    int first;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    int j, k=0,jk, ju, jl;
     gradg=matrix(1,npar,1,nlstate);    double sum=0.;
     gp=vector(1,nlstate);    first=0;
     gm=vector(1,nlstate);    jmin=1e+5;
     jmax=-1;
     for(theta=1; theta <=npar; theta++){    jmean=0.;
       for(i=1; i<=npar; i++){ /* Computes gradient */    for(i=1; i<=imx; i++){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      mi=0;
       }      m=firstpass;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      while(s[m][i] <= nlstate){
       for(i=1;i<=nlstate;i++)        if(s[m][i]>=1)
         gp[i] = prlim[i][i];          mw[++mi][i]=m;
            if(m >=lastpass)
       for(i=1; i<=npar; i++) /* Computes gradient */          break;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        else
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          m++;
       for(i=1;i<=nlstate;i++)      }/* end while */
         gm[i] = prlim[i][i];      if (s[m][i] > nlstate){
         mi++;     /* Death is another wave */
       for(i=1;i<=nlstate;i++)        /* if(mi==0)  never been interviewed correctly before death */
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];           /* Only death is a correct wave */
     } /* End theta */        mw[mi][i]=m;
       }
     trgradg =matrix(1,nlstate,1,npar);  
       wav[i]=mi;
     for(j=1; j<=nlstate;j++)      if(mi==0){
       for(theta=1; theta <=npar; theta++)        if(first==0){
         trgradg[j][theta]=gradg[theta][j];          printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);
           first=1;
     for(i=1;i<=nlstate;i++)        }
       varpl[i][(int)age] =0.;        if(first==1){
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        }
     for(i=1;i<=nlstate;i++)      } /* end mi==0 */
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    }
   
     fprintf(ficresvpl,"%.0f ",age );    for(i=1; i<=imx; i++){
     for(i=1; i<=nlstate;i++)      for(mi=1; mi<wav[i];mi++){
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        if (stepm <=0)
     fprintf(ficresvpl,"\n");          dh[mi][i]=1;
     free_vector(gp,1,nlstate);        else{
     free_vector(gm,1,nlstate);          if (s[mw[mi+1][i]][i] > nlstate) {
     free_matrix(gradg,1,npar,1,nlstate);            if (agedc[i] < 2*AGESUP) {
     free_matrix(trgradg,1,nlstate,1,npar);            j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   } /* End age */            if(j==0) j=1;  /* Survives at least one month after exam */
             k=k+1;
   free_vector(xp,1,npar);            if (j >= jmax) jmax=j;
   free_matrix(doldm,1,nlstate,1,npar);            if (j <= jmin) jmin=j;
   free_matrix(dnewm,1,nlstate,1,nlstate);            sum=sum+j;
             /*if (j<0) printf("j=%d num=%d \n",j,i); */
 }            }
           }
           else{
             j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
 /***********************************************/            k=k+1;
 /**************** Main Program *****************/            if (j >= jmax) jmax=j;
 /***********************************************/            else if (j <= jmin)jmin=j;
             /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
 /*int main(int argc, char *argv[])*/            sum=sum+j;
 int main()          }
 {          jk= j/stepm;
           jl= j -jk*stepm;
   int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;          ju= j -(jk+1)*stepm;
   double agedeb, agefin,hf;          if(jl <= -ju)
   double agemin=1.e20, agemax=-1.e20;            dh[mi][i]=jk;
           else
   double fret;            dh[mi][i]=jk+1;
   double **xi,tmp,delta;          if(dh[mi][i]==0)
             dh[mi][i]=1; /* At least one step */
   double dum; /* Dummy variable */        }
   double ***p3mat;      }
   int *indx;    }
   char line[MAXLINE], linepar[MAXLINE];    jmean=sum/k;
   char title[MAXLINE];    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];   }
   char filerest[FILENAMELENGTH];  
   char fileregp[FILENAMELENGTH];  /*********** Tricode ****************************/
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];  void tricode(int *Tvar, int **nbcode, int imx)
   int firstobs=1, lastobs=10;  {
   int sdeb, sfin; /* Status at beginning and end */    int Ndum[20],ij=1, k, j, i;
   int c,  h , cpt,l;    int cptcode=0;
   int ju,jl, mi;    cptcoveff=0; 
   int i1,j1, k1,jk,aa,bb, stepsize;   
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    for (k=0; k<19; k++) Ndum[k]=0;
      for (k=1; k<=7; k++) ncodemax[k]=0;
   int hstepm, nhstepm;  
   double bage, fage, age, agelim, agebase;    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   double ftolpl=FTOL;      for (i=1; i<=imx; i++) {
   double **prlim;        ij=(int)(covar[Tvar[j]][i]);
   double *severity;        Ndum[ij]++; 
   double ***param; /* Matrix of parameters */        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   double  *p;        if (ij > cptcode) cptcode=ij; 
   double **matcov; /* Matrix of covariance */      }
   double ***delti3; /* Scale */  
   double *delti; /* Scale */      for (i=0; i<=cptcode; i++) {
   double ***eij, ***vareij;        if(Ndum[i]!=0) ncodemax[j]++;
   double **varpl; /* Variances of prevalence limits by age */      }
   double *epj, vepp;      ij=1; 
   char version[80]="Imach version 62c, May 1999, INED-EUROREVES ";  
   char *alph[]={"a","a","b","c","d","e"}, str[4];  
   char z[1]="c", occ;      for (i=1; i<=ncodemax[j]; i++) {
 #include <sys/time.h>        for (k=0; k<=19; k++) {
 #include <time.h>          if (Ndum[k] != 0) {
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];            nbcode[Tvar[j]][ij]=k; 
   /* long total_usecs;            
   struct timeval start_time, end_time;            ij++;
            }
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */          if (ij > ncodemax[j]) break; 
         }  
       } 
   printf("\nIMACH, Version 0.63");    }  
   printf("\nEnter the parameter file name: ");  
    for (k=0; k<19; k++) Ndum[k]=0;
 #ifdef windows  
   scanf("%s",pathtot);   for (i=1; i<=ncovmodel-2; i++) {
   getcwd(pathcd, size);     ij=Tvar[i];
   cutv(path,optionfile,pathtot,'\\');     Ndum[ij]++; 
   chdir(path);   }
   replace(pathc,path);  
 #endif   ij=1;
 #ifdef unix   for (i=1; i<=10; i++) {
   scanf("%s",optionfile);     if((Ndum[i]!=0) && (i<=ncovcol)){
 #endif       Tvaraff[ij]=i; 
        ij++;
 /*-------- arguments in the command line --------*/     }
    }
   strcpy(fileres,"r");   
   strcat(fileres, optionfile);   cptcoveff=ij-1;
   }
   /*---------arguments file --------*/  
   /*********** Health Expectancies ****************/
   if((ficpar=fopen(optionfile,"r"))==NULL)    {  
     printf("Problem with optionfile %s\n",optionfile);  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 )
     goto end;  
   }  {
     /* Health expectancies */
   strcpy(filereso,"o");    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
   strcat(filereso,fileres);    double age, agelim, hf;
   if((ficparo=fopen(filereso,"w"))==NULL) {    double ***p3mat,***varhe;
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    double **dnewm,**doldm;
   }    double *xp;
     double **gp, **gm;
   /* Reads comments: lines beginning with '#' */    double ***gradg, ***trgradg;
   while((c=getc(ficpar))=='#' && c!= EOF){    int theta;
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);
     puts(line);    xp=vector(1,npar);
     fputs(line,ficparo);    dnewm=matrix(1,nlstate*2,1,npar);
   }    doldm=matrix(1,nlstate*2,1,nlstate*2);
   ungetc(c,ficpar);    
     fprintf(ficreseij,"# Health expectancies\n");
   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(ficreseij,"# Age");
   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);    for(i=1; i<=nlstate;i++)
   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);      for(j=1; j<=nlstate;j++)
         fprintf(ficreseij," %1d-%1d (SE)",i,j);
   covar=matrix(1,NCOVMAX,1,n);        fprintf(ficreseij,"\n");
   if (strlen(model)<=1) cptcovn=0;  
   else {    if(estepm < stepm){
     j=0;      printf ("Problem %d lower than %d\n",estepm, stepm);
     j=nbocc(model,'+');    }
     cptcovn=j+1;    else  hstepm=estepm;   
   }    /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
   ncovmodel=2+cptcovn;     * if stepm=24 months pijx are given only every 2 years and by summing them
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */     * we are calculating an estimate of the Life Expectancy assuming a linear 
       * progression inbetween and thus overestimating or underestimating according
   /* Read guess parameters */     * to the curvature of the survival function. If, for the same date, we 
   /* Reads comments: lines beginning with '#' */     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   while((c=getc(ficpar))=='#' && c!= EOF){     * to compare the new estimate of Life expectancy with the same linear 
     ungetc(c,ficpar);     * hypothesis. A more precise result, taking into account a more precise
     fgets(line, MAXLINE, ficpar);     * curvature will be obtained if estepm is as small as stepm. */
     puts(line);  
     fputs(line,ficparo);    /* 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. 
   ungetc(c,ficpar);       nhstepm is the number of hstepm from age to agelim 
         nstepm is the number of stepm from age to agelin. 
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);       Look at hpijx to understand the reason of that which relies in memory size
     for(i=1; i <=nlstate; i++)       and note for a fixed period like estepm months */
     for(j=1; j <=nlstate+ndeath-1; j++){    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       fscanf(ficpar,"%1d%1d",&i1,&j1);       survival function given by stepm (the optimization length). Unfortunately it
       fprintf(ficparo,"%1d%1d",i1,j1);       means that if the survival funtion is printed only each two years of age and if
       printf("%1d%1d",i,j);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       for(k=1; k<=ncovmodel;k++){       results. So we changed our mind and took the option of the best precision.
         fscanf(ficpar," %lf",&param[i][j][k]);    */
         printf(" %lf",param[i][j][k]);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         fprintf(ficparo," %lf",param[i][j][k]);  
       }    agelim=AGESUP;
       fscanf(ficpar,"\n");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       printf("\n");      /* nhstepm age range expressed in number of stepm */
       fprintf(ficparo,"\n");      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
     }      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
        /* if (stepm >= YEARM) hstepm=1;*/
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   p=param[1][1];      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);
   /* Reads comments: lines beginning with '#' */      gp=matrix(0,nhstepm,1,nlstate*2);
   while((c=getc(ficpar))=='#' && c!= EOF){      gm=matrix(0,nhstepm,1,nlstate*2);
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
     puts(line);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     fputs(line,ficparo);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
   }   
   ungetc(c,ficpar);  
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      /* Computing Variances of health expectancies */
   for(i=1; i <=nlstate; i++){  
     for(j=1; j <=nlstate+ndeath-1; j++){       for(theta=1; theta <=npar; theta++){
       fscanf(ficpar,"%1d%1d",&i1,&j1);        for(i=1; i<=npar; i++){ 
       printf("%1d%1d",i,j);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       fprintf(ficparo,"%1d%1d",i1,j1);        }
       for(k=1; k<=ncovmodel;k++){        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         fscanf(ficpar,"%le",&delti3[i][j][k]);    
         printf(" %le",delti3[i][j][k]);        cptj=0;
         fprintf(ficparo," %le",delti3[i][j][k]);        for(j=1; j<= nlstate; j++){
       }          for(i=1; i<=nlstate; i++){
       fscanf(ficpar,"\n");            cptj=cptj+1;
       printf("\n");            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
       fprintf(ficparo,"\n");              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     }            }
   }          }
   delti=delti3[1][1];        }
         
   /* Reads comments: lines beginning with '#' */       
   while((c=getc(ficpar))=='#' && c!= EOF){        for(i=1; i<=npar; i++) 
     ungetc(c,ficpar);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     fgets(line, MAXLINE, ficpar);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     puts(line);        
     fputs(line,ficparo);        cptj=0;
   }        for(j=1; j<= nlstate; j++){
   ungetc(c,ficpar);          for(i=1;i<=nlstate;i++){
              cptj=cptj+1;
   matcov=matrix(1,npar,1,npar);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   for(i=1; i <=npar; i++){              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     fscanf(ficpar,"%s",&str);            }
     printf("%s",str);          }
     fprintf(ficparo,"%s",str);        }
     for(j=1; j <=i; j++){        for(j=1; j<= nlstate*2; j++)
       fscanf(ficpar," %le",&matcov[i][j]);          for(h=0; h<=nhstepm-1; h++){
       printf(" %.5le",matcov[i][j]);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
       fprintf(ficparo," %.5le",matcov[i][j]);          }
     }       } 
     fscanf(ficpar,"\n");     
     printf("\n");  /* End theta */
     fprintf(ficparo,"\n");  
   }       trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);
   for(i=1; i <=npar; i++)  
     for(j=i+1;j<=npar;j++)       for(h=0; h<=nhstepm-1; h++)
       matcov[i][j]=matcov[j][i];        for(j=1; j<=nlstate*2;j++)
              for(theta=1; theta <=npar; theta++)
   printf("\n");            trgradg[h][j][theta]=gradg[h][theta][j];
        
   
    if(mle==1){       for(i=1;i<=nlstate*2;i++)
     /*-------- data file ----------*/        for(j=1;j<=nlstate*2;j++)
     if((ficres =fopen(fileres,"w"))==NULL) {          varhe[i][j][(int)age] =0.;
       printf("Problem with resultfile: %s\n", fileres);goto end;  
     }       printf("%d|",(int)age);fflush(stdout);
     fprintf(ficres,"#%s\n",version);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
           for(h=0;h<=nhstepm-1;h++){
     if((fic=fopen(datafile,"r"))==NULL)    {        for(k=0;k<=nhstepm-1;k++){
       printf("Problem with datafile: %s\n", datafile);goto end;          matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);
     }          matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);
           for(i=1;i<=nlstate*2;i++)
     n= lastobs;            for(j=1;j<=nlstate*2;j++)
     severity = vector(1,maxwav);              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
     outcome=imatrix(1,maxwav+1,1,n);        }
     num=ivector(1,n);      }
     moisnais=vector(1,n);      /* Computing expectancies */
     annais=vector(1,n);      for(i=1; i<=nlstate;i++)
     moisdc=vector(1,n);        for(j=1; j<=nlstate;j++)
     andc=vector(1,n);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     agedc=vector(1,n);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     cod=ivector(1,n);            
     weight=vector(1,n);  /* 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]);*/
     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);      fprintf(ficreseij,"%3.0f",age );
     adl=imatrix(1,maxwav+1,1,n);          cptj=0;
     tab=ivector(1,NCOVMAX);      for(i=1; i<=nlstate;i++)
     ncodemax=ivector(1,NCOVMAX);        for(j=1; j<=nlstate;j++){
           cptj++;
     i=1;          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
     while (fgets(line, MAXLINE, fic) != NULL)    {        }
       if ((i >= firstobs) && (i <=lastobs)) {      fprintf(ficreseij,"\n");
             
         for (j=maxwav;j>=1;j--){      free_matrix(gm,0,nhstepm,1,nlstate*2);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);      free_matrix(gp,0,nhstepm,1,nlstate*2);
           strcpy(line,stra);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         }    }
            printf("\n");
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficlog,"\n");
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);  
     free_vector(xp,1,npar);
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    free_matrix(dnewm,1,nlstate*2,1,npar);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    free_matrix(doldm,1,nlstate*2,1,nlstate*2);
     free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);  }
         for (j=ncov;j>=1;j--){  
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);  /************ 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)
         num[i]=atol(stra);  {
     /* Variance of health expectancies */
         /* 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]));*/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
         /*printf("%d %.lf %.lf %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),(covar[3][i]), (covar[4][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]));*/    double **dnewm,**doldm;
     double **dnewmp,**doldmp;
         i=i+1;    int i, j, nhstepm, hstepm, h, nstepm ;
       }    int k, cptcode;
     }    double *xp;
     /*scanf("%d",i);*/    double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
   imx=i-1; /* Number of individuals */    double **gradgp, **trgradgp; /* for var p point j */
      double *gpp, *gmp; /* for var p point j */
   /* Calculation of the number of parameter from char model*/    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   Tvar=ivector(1,8);        double ***p3mat;
        double age,agelim, hf;
   if (strlen(model) >1){    double ***mobaverage;
     j=0;    int theta;
     j=nbocc(model,'+');    char digit[4];
     cptcovn=j+1;    char digitp[25];
    
     strcpy(modelsav,model);    char fileresprobmorprev[FILENAMELENGTH];
     if (j==0) {  
       cutv(stra,strb,modelsav,'V'); Tvar[1]=atoi(strb);    if(popbased==1){
     }      if(mobilav==1)
     else {        strcpy(digitp,"-populbased-mobilav-");
       for(i=j; i>=1;i--){      else strcpy(digitp,"-populbased-nomobil-");
         cutv(stra,strb,modelsav,'+');    }
         if (strchr(strb,'*')) {    else 
           cutv(strd,strc,strb,'*');      strcpy(digitp,"-stablbased-");
           cutv(strb,stre,strc,'V');Tvar[i+1]=ncov+1;  
           cutv(strb,strc,strd,'V');    if (mobilav!=0) {
           for (k=1; k<=lastobs;k++)      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
             covar[ncov+1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         }        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         else {        printf(" Error in movingaverage mobilav=%d\n",mobilav);
           cutv(strd,strc,strb,'V');      }
           Tvar[i+1]=atoi(strc);    }
         }  
         strcpy(modelsav,stra);      strcpy(fileresprobmorprev,"prmorprev"); 
       }    sprintf(digit,"%-d",ij);
       /*cutv(strd,strc,stra,'V');*/    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
       Tvar[1]=atoi(strc);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     }    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   }    strcat(fileresprobmorprev,fileres);
   /*printf("tvar=%d ",Tvar[1]);*/    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   /*scanf("%d ",i);*/      printf("Problem with resultfile: %s\n", fileresprobmorprev);
     fclose(fic);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
     if (weightopt != 1) { /* Maximisation without weights*/    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       for(i=1;i<=n;i++) weight[i]=1.0;    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     }    fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");
     /*-calculation of age at interview from date of interview and age at death -*/    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     agev=matrix(1,maxwav,1,imx);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
          fprintf(ficresprobmorprev," p.%-d SE",j);
     for (i=1; i<=imx; i++)  {      for(i=1; i<=nlstate;i++)
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
       for(m=1; (m<= maxwav); m++){    }  
         if (mint[m][i]==99 || anint[m][i]==9999) s[m][i]=-1;      fprintf(ficresprobmorprev,"\n");
         if(s[m][i] >0){    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
           if (s[m][i] == nlstate+1) {      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
             if(agedc[i]>0)      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
               if(moisdc[i]!=99 && andc[i]!=9999)      exit(0);
               agev[m][i]=agedc[i];    }
             else{    else{
               printf("Warning negative age at death: %d line:%d\n",num[i],i);      fprintf(ficgp,"\n# Routine varevsij");
               agev[m][i]=-1;    }
             }    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
           }      printf("Problem with html file: %s\n", optionfilehtm);
           else if(s[m][i] !=9){ /* Should no more exist */      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);      exit(0);
             if(mint[m][i]==99 || anint[m][i]==9999){    }
               agev[m][i]=1;    else{
               /* printf("i=%d m=%d agev=%lf \n",i,m, agev[m][i]);    */      fprintf(fichtm,"\n<li><h4> Computing probabilities of dying as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
             }      fprintf(fichtm,"\n<br>%s (à revoir) <br>\n",digitp);
             else if(agev[m][i] <agemin){    }
               agemin=agev[m][i];    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/  
             }    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");
             else if(agev[m][i] >agemax){    fprintf(ficresvij,"# Age");
               agemax=agev[m][i];    for(i=1; i<=nlstate;i++)
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/      for(j=1; j<=nlstate;j++)
             }        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
             /*agev[m][i]=anint[m][i]-annais[i];*/    fprintf(ficresvij,"\n");
             /*   agev[m][i] = age[i]+2*m;*/  
           }    xp=vector(1,npar);
           else { /* =9 */    dnewm=matrix(1,nlstate,1,npar);
             agev[m][i]=1;    doldm=matrix(1,nlstate,1,nlstate);
             s[m][i]=-1;    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
           }    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         }  
         else /*= 0 Unknown */    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
           agev[m][i]=1;    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*/
     }    
     for (i=1; i<=imx; i++)  {    if(estepm < stepm){
       for(m=1; (m<= maxwav); m++){      printf ("Problem %d lower than %d\n",estepm, stepm);
         if (s[m][i] > (nlstate+ndeath)) {    }
           printf("Error: Wrong value in nlstate or ndeath\n");      else  hstepm=estepm;   
           goto end;    /* 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. 
       }       nhstepm is the number of hstepm from age to agelim 
     }       nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);       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_vector(severity,1,maxwav);       survival function given by stepm (the optimization length). Unfortunately it
     free_imatrix(outcome,1,maxwav+1,1,n);       means that if the survival funtion is printed only each two years of age and if
     free_vector(moisnais,1,n);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     free_vector(annais,1,n);       results. So we changed our mind and took the option of the best precision.
     free_matrix(mint,1,maxwav,1,n);    */
     free_matrix(anint,1,maxwav,1,n);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     free_vector(moisdc,1,n);    agelim = AGESUP;
     free_vector(andc,1,n);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       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 */
     wav=ivector(1,imx);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);      gp=matrix(0,nhstepm,1,nlstate);
          gm=matrix(0,nhstepm,1,nlstate);
     /* Concatenates waves */  
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
 Tcode=ivector(1,100);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
    nbcode=imatrix(1,nvar,1,8);          }
    ncodemax[1]=1;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
    if (cptcovn > 0) tricode(Tvar,nbcode,imx);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
    codtab=imatrix(1,100,1,10);        if (popbased==1) {
    h=0;          if(mobilav ==0){
    m=pow(2,cptcovn);            for(i=1; i<=nlstate;i++)
                prlim[i][i]=probs[(int)age][i][ij];
    for(k=1;k<=cptcovn; k++){          }else{ /* mobilav */ 
      for(i=1; i <=(m/pow(2,k));i++){            for(i=1; i<=nlstate;i++)
        for(j=1; j <= ncodemax[k]; j++){              prlim[i][i]=mobaverage[(int)age][i][ij];
          for(cpt=1; cpt <=(m/pow(2,cptcovn+1-k)); cpt++){          }
            h++;        }
            if (h>m) h=1;codtab[h][k]=j;    
          }        for(j=1; j<= nlstate; j++){
        }          for(h=0; h<=nhstepm; h++){
      }            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
    }              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
    /*for(i=1; i <=m ;i++){        }
      for(k=1; k <=cptcovn; k++){        /* This for computing forces of mortality (h=1)as a weighted average */
        printf("i=%d k=%d %d ",i,k,codtab[i][k]);        for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){
      }          for(i=1; i<= nlstate; i++)
      printf("\n");            gpp[j] += prlim[i][i]*p3mat[i][j][1];
    }        }    
   scanf("%d",i);*/        /* end force of mortality */
      
    /* Calculates basic frequencies. Computes observed prevalence at single age        for(i=1; i<=npar; i++) /* Computes gradient */
        and prints on file fileres'p'. */          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        if (popbased==1) {
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          if(mobilav ==0){
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            for(i=1; i<=nlstate;i++)
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */              prlim[i][i]=probs[(int)age][i][ij];
              }else{ /* mobilav */ 
     /* For Powell, parameters are in a vector p[] starting at p[1]            for(i=1; i<=nlstate;i++)
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */              prlim[i][i]=mobaverage[(int)age][i][ij];
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */          }
     /*scanf("%d",i);*/        }
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  
         for(j=1; j<= nlstate; j++){
              for(h=0; h<=nhstepm; h++){
     /*--------- results files --------------*/            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
     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);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
              }
    jk=1;        }
    fprintf(ficres,"# Parameters\n");        /* This for computing force of mortality (h=1)as a weighted average */
    printf("# Parameters\n");        for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
    for(i=1,jk=1; i <=nlstate; i++){          for(i=1; i<= nlstate; i++)
      for(k=1; k <=(nlstate+ndeath); k++){            gmp[j] += prlim[i][i]*p3mat[i][j][1];
        if (k != i)        }    
          {        /* end force of mortality */
            printf("%d%d ",i,k);  
            fprintf(ficres,"%1d%1d ",i,k);        for(j=1; j<= nlstate; j++) /* vareij */
            for(j=1; j <=ncovmodel; j++){          for(h=0; h<=nhstepm; h++){
              printf("%f ",p[jk]);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
              fprintf(ficres,"%f ",p[jk]);          }
              jk++;        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
            }          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
            printf("\n");        }
            fprintf(ficres,"\n");  
          }      } /* End theta */
      }  
    }      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
     /* Computing hessian and covariance matrix */      for(h=0; h<=nhstepm; h++) /* veij */
     ftolhess=ftol; /* Usually correct */        for(j=1; j<=nlstate;j++)
     hesscov(matcov, p, npar, delti, ftolhess, func);          for(theta=1; theta <=npar; theta++)
     fprintf(ficres,"# Scales\n");            trgradg[h][j][theta]=gradg[h][theta][j];
     printf("# Scales\n");  
      for(i=1,jk=1; i <=nlstate; i++){      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
       for(j=1; j <=nlstate+ndeath; j++){        for(theta=1; theta <=npar; theta++)
         if (j!=i) {          trgradgp[j][theta]=gradgp[theta][j];
           fprintf(ficres,"%1d%1d",i,j);  
           printf("%1d%1d",i,j);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           for(k=1; k<=ncovmodel;k++){      for(i=1;i<=nlstate;i++)
             printf(" %.5e",delti[jk]);        for(j=1;j<=nlstate;j++)
             fprintf(ficres," %.5e",delti[jk]);          vareij[i][j][(int)age] =0.;
             jk++;  
           }      for(h=0;h<=nhstepm;h++){
           printf("\n");        for(k=0;k<=nhstepm;k++){
           fprintf(ficres,"\n");          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
         }          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
       }          for(i=1;i<=nlstate;i++)
       }            for(j=1;j<=nlstate;j++)
                  vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
     k=1;        }
     fprintf(ficres,"# Covariance\n");      }
     printf("# Covariance\n");  
     for(i=1;i<=npar;i++){      /* pptj */
       /*  if (k>nlstate) k=1;      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       i1=(i-1)/(ncovmodel*nlstate)+1;      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
       printf("%s%d%d",alph[k],i1,tab[i]);*/        for(i=nlstate+1;i<=nlstate+ndeath;i++)
       fprintf(ficres,"%3d",i);          varppt[j][i]=doldmp[j][i];
       printf("%3d",i);      /* end ppptj */
       for(j=1; j<=i;j++){      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
         fprintf(ficres," %.5e",matcov[i][j]);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
         printf(" %.5e",matcov[i][j]);   
       }      if (popbased==1) {
       fprintf(ficres,"\n");        if(mobilav ==0){
       printf("\n");          for(i=1; i<=nlstate;i++)
       k++;            prlim[i][i]=probs[(int)age][i][ij];
     }        }else{ /* mobilav */ 
              for(i=1; i<=nlstate;i++)
     while((c=getc(ficpar))=='#' && c!= EOF){            prlim[i][i]=mobaverage[(int)age][i][ij];
       ungetc(c,ficpar);        }
       fgets(line, MAXLINE, ficpar);      }
       puts(line);      
       fputs(line,ficparo);      /* This for computing force of mortality (h=1)as a weighted average */
     }      for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){
     ungetc(c,ficpar);        for(i=1; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);      }    
          /* end force of mortality */
     if (fage <= 2) {  
       bage = agemin;      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       fage = agemax;      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     }        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);        }
 /*------------ gnuplot -------------*/      } 
 chdir(pathcd);      fprintf(ficresprobmorprev,"\n");
   if((ficgp=fopen("graph.plt","w"))==NULL) {  
     printf("Problem with file graph.gp");goto end;      fprintf(ficresvij,"%.0f ",age );
   }      for(i=1; i<=nlstate;i++)
 #ifdef windows        for(j=1; j<=nlstate;j++){
   fprintf(ficgp,"cd \"%s\" \n",pathc);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
 #endif        }
 m=pow(2,cptcovn);      fprintf(ficresvij,"\n");
        free_matrix(gp,0,nhstepm,1,nlstate);
  /* 1eme*/      free_matrix(gm,0,nhstepm,1,nlstate);
   for (cpt=1; cpt<= nlstate ; cpt ++) {      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
    for (k1=1; k1<= m ; k1 ++) {      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 #ifdef windows    } /* End 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);    free_vector(gpp,nlstate+1,nlstate+ndeath);
 #endif    free_vector(gmp,nlstate+1,nlstate+ndeath);
 #ifdef unix    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
 #endif    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 */
 for (i=1; i<= nlstate ; i ++) {    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);
 }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
     for (i=1; i<= nlstate ; i ++) {    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,digitp,digit);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    /*  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);
   else fprintf(ficgp," \%%*lf (\%%*lf)");  */
 }    fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  
      for (i=1; i<= nlstate ; i ++) {    free_vector(xp,1,npar);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    free_matrix(doldm,1,nlstate,1,nlstate);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    free_matrix(dnewm,1,nlstate,1,npar);
 }      free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
 #ifdef unix    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
 fprintf(ficgp,"\nset ter gif small size 400,300");    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 #endif    fclose(ficresprobmorprev);
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    fclose(ficgp);
    }    fclose(fichtm);
   }  }
   /*2 eme*/  
   /************ Variance of prevlim ******************/
   for (k1=1; k1<= m ; k1 ++) {  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)
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);  {
        /* Variance of prevalence limit */
     for (i=1; i<= nlstate+1 ; i ++) {    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
       k=2*i;    double **newm;
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    double **dnewm,**doldm;
       for (j=1; j<= nlstate+1 ; j ++) {    int i, j, nhstepm, hstepm;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    int k, cptcode;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double *xp;
 }      double *gp, *gm;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    double **gradg, **trgradg;
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    double age,agelim;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    int theta;
       for (j=1; j<= nlstate+1 ; j ++) {     
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
         else fprintf(ficgp," \%%*lf (\%%*lf)");    fprintf(ficresvpl,"# Age");
 }      for(i=1; i<=nlstate;i++)
       fprintf(ficgp,"\" t\"\" w l 0,");        fprintf(ficresvpl," %1d-%1d",i,i);
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    fprintf(ficresvpl,"\n");
       for (j=1; j<= nlstate+1 ; j ++) {  
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    xp=vector(1,npar);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    dnewm=matrix(1,nlstate,1,npar);
 }      doldm=matrix(1,nlstate,1,nlstate);
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    
       else fprintf(ficgp,"\" t\"\" w l 0,");    hstepm=1*YEARM; /* Every year of age */
     }    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    agelim = AGESUP;
   }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
        nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   /*3eme*/      if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   for (k1=1; k1<= m ; k1 ++) {      gradg=matrix(1,npar,1,nlstate);
     for (cpt=1; cpt<= nlstate ; cpt ++) {      gp=vector(1,nlstate);
       k=2+nlstate*(cpt-1);      gm=vector(1,nlstate);
       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);  
       for (i=1; i< nlstate ; i ++) {      for(theta=1; theta <=npar; theta++){
         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);        for(i=1; i<=npar; i++){ /* Computes gradient */
       }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        }
     }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   }        for(i=1;i<=nlstate;i++)
            gp[i] = prlim[i][i];
   /* CV preval stat */      
   for (k1=1; k1<= m ; k1 ++) {        for(i=1; i<=npar; i++) /* Computes gradient */
     for (cpt=1; cpt<nlstate ; cpt ++) {          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       k=3;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);        for(i=1;i<=nlstate;i++)
       for (i=1; i< nlstate ; i ++)          gm[i] = prlim[i][i];
         fprintf(ficgp,"+$%d",k+i+1);  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);        for(i=1;i<=nlstate;i++)
                gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       l=3+(nlstate+ndeath)*cpt;      } /* End theta */
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);  
       for (i=1; i< nlstate ; i ++) {      trgradg =matrix(1,nlstate,1,npar);
         l=3+(nlstate+ndeath)*cpt;  
         fprintf(ficgp,"+$%d",l+i+1);      for(j=1; j<=nlstate;j++)
       }        for(theta=1; theta <=npar; theta++)
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            trgradg[j][theta]=gradg[theta][j];
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
     }      for(i=1;i<=nlstate;i++)
   }        varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   /* proba elementaires */      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   for(i=1,jk=1; i <=nlstate; i++){      for(i=1;i<=nlstate;i++)
     for(k=1; k <=(nlstate+ndeath); k++){        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
       if (k != i) {  
         /*  fprintf(ficgp,"%1d%1d ",i,k);*/      fprintf(ficresvpl,"%.0f ",age );
         for(j=1; j <=ncovmodel; j++){      for(i=1; i<=nlstate;i++)
           fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
           jk++;      fprintf(ficresvpl,"\n");
           fprintf(ficgp,"\n");      free_vector(gp,1,nlstate);
         }      free_vector(gm,1,nlstate);
       }      free_matrix(gradg,1,npar,1,nlstate);
     }      free_matrix(trgradg,1,nlstate,1,npar);
   }    } /* End age */
   for(jk=1; jk <=m; jk++) {  
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    free_vector(xp,1,npar);
   for(i=1; i <=nlstate; i++) {    free_matrix(doldm,1,nlstate,1,npar);
     for(k=1; k <=(nlstate+ndeath); k++){    free_matrix(dnewm,1,nlstate,1,nlstate);
       if (k != i) {  
         fprintf(ficgp," exp(a%d%d+b%d%d*x",i,k,i,k);  }
         for(j=3; j <=ncovmodel; j++)  
           fprintf(ficgp,"+%s%d%d*%d",alph[j],i,k,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  /************ Variance of one-step probabilities  ******************/
         fprintf(ficgp,")/(1");  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
         for(k1=1; k1 <=(nlstate+ndeath); k1++)  {
           if (k1 != i) {    int i, j=0,  i1, k1, l1, t, tj;
             fprintf(ficgp,"+exp(a%d%d+b%d%d*x",i,k1,i,k1);    int k2, l2, j1,  z1;
             for(j=3; j <=ncovmodel; j++)    int k=0,l, cptcode;
               fprintf(ficgp,"+%s%d%d*%d",alph[j],i,k,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    int first=1, first1;
             fprintf(ficgp,")");    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
           }    double **dnewm,**doldm;
         fprintf(ficgp,") t \"p%d%d\" ", i,k);    double *xp;
       if ((i+k)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    double *gp, *gm;
       }    double **gradg, **trgradg;
     }    double **mu;
   }    double age,agelim, cov[NCOVMAX];
 fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);      double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   }    int theta;
   fclose(ficgp);    char fileresprob[FILENAMELENGTH];
        char fileresprobcov[FILENAMELENGTH];
 chdir(path);    char fileresprobcor[FILENAMELENGTH];
     free_matrix(agev,1,maxwav,1,imx);  
     free_ivector(wav,1,imx);    double ***varpij;
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);  
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);    strcpy(fileresprob,"prob"); 
        strcat(fileresprob,fileres);
     free_imatrix(s,1,maxwav+1,1,n);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
          printf("Problem with resultfile: %s\n", fileresprob);
          fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     free_ivector(num,1,n);    }
     free_vector(agedc,1,n);    strcpy(fileresprobcov,"probcov"); 
     free_vector(weight,1,n);    strcat(fileresprobcov,fileres);
     /*free_matrix(covar,1,NCOVMAX,1,n);*/    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     fclose(ficparo);      printf("Problem with resultfile: %s\n", fileresprobcov);
     fclose(ficres);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
    }    }
        strcpy(fileresprobcor,"probcor"); 
    /*________fin mle=1_________*/    strcat(fileresprobcor,fileres);
        if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     /* No more information from the sample is required now */    }
   /* Reads comments: lines beginning with '#' */    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     ungetc(c,ficpar);    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fgets(line, MAXLINE, ficpar);    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     puts(line);    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fputs(line,ficparo);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   }    
   ungetc(c,ficpar);    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
      fprintf(ficresprob,"# Age");
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);    fprintf(ficresprobcov,"# Age");
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
 /*--------- index.htm --------*/    fprintf(ficresprobcov,"# Age");
   
   if((fichtm=fopen("index.htm","w"))==NULL)    {  
     printf("Problem with index.htm \n");goto end;    for(i=1; i<=nlstate;i++)
   }      for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
  fprintf(fichtm,"<body><ul> Imach, Version 0.63<hr> <li>Outputs files<br><br>\n        fprintf(ficresprobcov," p%1d-%1d ",i,j);
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n        fprintf(ficresprobcor," p%1d-%1d ",i,j);
 - 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>    fprintf(ficresprob,"\n");
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>    fprintf(ficresprobcov,"\n");
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    fprintf(ficresprobcor,"\n");
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>    xp=vector(1,npar);
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
         - 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);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
  fprintf(fichtm," <li>Graphs</li>\n<p>");    first=1;
     if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
  m=cptcovn;      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
       exit(0);
  j1=0;    }
  for(k1=1; k1<=m;k1++){    else{
    for(i1=1; i1<=ncodemax[k1];i1++){      fprintf(ficgp,"\n# Routine varprob");
        j1++;    }
        if (cptcovn > 0) {    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
          fprintf(fichtm,"<hr>************ Results for covariates");      printf("Problem with html file: %s\n", optionfilehtm);
          for (cpt=1; cpt<=cptcovn;cpt++)      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
            fprintf(fichtm," V%d=%d ",Tvar[cpt],nbcode[Tvar[cpt]][codtab[j1][cpt]]);      exit(0);
          fprintf(fichtm," ************\n<hr>");    }
        }    else{
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);          fprintf(fichtm,"\n");
        for(cpt=1; cpt<nlstate;cpt++){  
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>      fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      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");
     for(cpt=1; cpt<=nlstate;cpt++) {  
        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);     
      }    cov[1]=1;
      for(cpt=1; cpt<=nlstate;cpt++) {    tj=cptcoveff;
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    j1=0;
      }    for(t=1; t<=tj;t++){
      fprintf(fichtm,"\n<br>- Total life expectancy by age and      for(i1=1; i1<=ncodemax[t];i1++){ 
 health expectancies in states (1) and (2): e%s%d.gif<br>        j1++;
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);        
 fprintf(fichtm,"\n</body>");        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]]);
 fclose(fichtm);          fprintf(ficresprob, "**********\n#");
           fprintf(ficresprobcov, "\n#********** Variable "); 
   /*--------------- Prevalence limit --------------*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficresprobcov, "**********\n#");
   strcpy(filerespl,"pl");          
   strcat(filerespl,fileres);          fprintf(ficgp, "\n#********** Variable "); 
   if((ficrespl=fopen(filerespl,"w"))==NULL) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;          fprintf(ficgp, "**********\n#");
   }          
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);          
   fprintf(ficrespl,"#Prevalence limit\n");          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   fprintf(ficrespl,"#Age ");          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
   fprintf(ficrespl,"\n");          
            fprintf(ficresprobcor, "\n#********** Variable ");    
   prlim=matrix(1,nlstate,1,nlstate);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fprintf(ficgp, "**********\n#");    
   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 */        for (age=bage; age<=fage; age ++){ 
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          cov[2]=age;
   k=0;          for (k=1; k<=cptcovn;k++) {
   agebase=agemin;            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
   agelim=agemax;          }
   ftolpl=1.e-10;          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   i1=cptcovn;          for (k=1; k<=cptcovprod;k++)
   if (cptcovn < 1){i1=1;}            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
   for(cptcov=1;cptcov<=i1;cptcov++){          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         k=k+1;          gp=vector(1,(nlstate)*(nlstate+ndeath));
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/          gm=vector(1,(nlstate)*(nlstate+ndeath));
         fprintf(ficrespl,"\n#****** ");      
         for(j=1;j<=cptcovn;j++)          for(theta=1; theta <=npar; theta++){
           fprintf(ficrespl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);            for(i=1; i<=npar; i++)
         fprintf(ficrespl,"******\n");              xp[i] = x[i] + (i==theta ?delti[theta]:0);
                    
         for (age=agebase; age<=agelim; age++){            pmij(pmmij,cov,ncovmodel,xp,nlstate);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);            
           fprintf(ficrespl,"%.0f",age );            k=0;
           for(i=1; i<=nlstate;i++)            for(i=1; i<= (nlstate); i++){
           fprintf(ficrespl," %.5f", prlim[i][i]);              for(j=1; j<=(nlstate+ndeath);j++){
           fprintf(ficrespl,"\n");                k=k+1;
         }                gp[k]=pmmij[i][j];
       }              }
     }            }
   fclose(ficrespl);            
   /*------------- h Pij x at various ages ------------*/            for(i=1; i<=npar; i++)
                xp[i] = x[i] - (i==theta ?delti[theta]:0);
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);      
   if((ficrespij=fopen(filerespij,"w"))==NULL) {            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;            k=0;
   }            for(i=1; i<=(nlstate); i++){
   printf("Computing pij: result on file '%s' \n", filerespij);              for(j=1; j<=(nlstate+ndeath);j++){
                  k=k+1;
   stepsize=(int) (stepm+YEARM-1)/YEARM;                gm[k]=pmmij[i][j];
   if (stepm<=24) stepsize=2;              }
             }
   agelim=AGESUP;       
   hstepm=stepsize*YEARM; /* Every year of age */            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */              gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];  
            }
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            for(theta=1; theta <=npar; theta++)
       k=k+1;              trgradg[j][theta]=gradg[theta][j];
         fprintf(ficrespij,"\n#****** ");          
         for(j=1;j<=cptcovn;j++)          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           fprintf(ficrespij,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
         fprintf(ficrespij,"******\n");          
                  pmij(pmmij,cov,ncovmodel,x,nlstate);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          k=0;
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          for(i=1; i<=(nlstate); i++){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for(j=1; j<=(nlstate+ndeath);j++){
           oldm=oldms;savm=savms;              k=k+1;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                mu[k][(int) age]=pmmij[i][j];
           fprintf(ficrespij,"# Age");            }
           for(i=1; i<=nlstate;i++)          }
             for(j=1; j<=nlstate+ndeath;j++)          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
               fprintf(ficrespij," %1d-%1d",i,j);            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
           fprintf(ficrespij,"\n");              varpij[i][j][(int)age] = doldm[i][j];
           for (h=0; h<=nhstepm; h++){  
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );          /*printf("\n%d ",(int)age);
             for(i=1; i<=nlstate;i++)       for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
               for(j=1; j<=nlstate+ndeath;j++)         printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);         fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficrespij,"\n");       }*/
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficrespij,"\n");          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]));
   fclose(ficrespij);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   /*---------- Health expectancies and variances ------------*/            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
   strcpy(filerest,"t");          i=0;
   strcat(filerest,fileres);          for (k=1; k<=(nlstate);k++){
   if((ficrest=fopen(filerest,"w"))==NULL) {            for (l=1; l<=(nlstate+ndeath);l++){ 
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;              i=i++;
   }              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);              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]);
   strcpy(filerese,"e");                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
   strcat(filerese,fileres);              }
   if((ficreseij=fopen(filerese,"w"))==NULL) {            }
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);          }/* end of loop for state */
   }        } /* end of loop for age */
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);  
         /* Confidence intervalle of pij  */
  strcpy(fileresv,"v");        /*
   strcat(fileresv,fileres);        fprintf(ficgp,"\nset noparametric;unset label");
   if((ficresvij=fopen(fileresv,"w"))==NULL) {        fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        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);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);        fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
         fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
   k=0;        fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
   for(cptcov=1;cptcov<=i1;cptcov++){        */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
       fprintf(ficrest,"\n#****** ");        first1=1;
       for(j=1;j<=cptcovn;j++)        for (k2=1; k2<=(nlstate);k2++){
         fprintf(ficrest,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
       fprintf(ficrest,"******\n");            if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
       fprintf(ficreseij,"\n#****** ");            for (k1=1; k1<=(nlstate);k1++){
       for(j=1;j<=cptcovn;j++)              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);                if(l1==k1) continue;
       fprintf(ficreseij,"******\n");                i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
       fprintf(ficresvij,"\n#****** ");                for (age=bage; age<=fage; age ++){ 
       for(j=1;j<=cptcovn;j++)                  if ((int)age %5==0){
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
       fprintf(ficresvij,"******\n");                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                    mu1=mu[i][(int) age]/stepm*YEARM ;
       oldm=oldms;savm=savms;                    mu2=mu[j][(int) age]/stepm*YEARM;
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);                      c12=cv12/sqrt(v1*v2);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                    /* Computing eigen value of matrix of covariance */
       oldm=oldms;savm=savms;                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                          /* Eigen vectors */
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);                    /*v21=sqrt(1.-v11*v11); *//* error */
       fprintf(ficrest,"\n");                    v21=(lc1-v1)/cv12*v11;
                            v12=-v21;
       hf=1;                    v22=v11;
       if (stepm >= YEARM) hf=stepm/YEARM;                    tnalp=v21/v11;
       epj=vector(1,nlstate+1);                    if(first1==1){
       for(age=bage; age <=fage ;age++){                      first1=0;
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                      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(ficrest," %.0f",age);                    }
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){                    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);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {                    /*printf(fignu*/
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
           }                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
           epj[nlstate+1] +=epj[j];                    if(first==1){
         }                      first=0;
         for(i=1, vepp=0.;i <=nlstate;i++)                      fprintf(ficgp,"\nset parametric;unset label");
           for(j=1;j <=nlstate;j++)                      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);
             vepp += vareij[i][j][(int)age];                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));                      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);
         for(j=1;j <=nlstate;j++){                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));                      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(ficrest,"\n");                      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));
  fclose(ficreseij);                    }else{
  fclose(ficresvij);                      first=0;
   fclose(ficrest);                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
   fclose(ficpar);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   free_vector(epj,1,nlstate+1);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   /*  scanf("%d ",i); */                      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),\
   /*------- Variance limit prevalence------*/                                mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
 strcpy(fileresvpl,"vpl");                  } /* age mod 5 */
   strcat(fileresvpl,fileres);                } /* end loop age */
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);                first=1;
     exit(0);              } /*l12 */
   }            } /* k12 */
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);          } /*l1 */
         }/* k1 */
  k=0;      } /* loop covariates */
  for(cptcov=1;cptcov<=i1;cptcov++){      free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
      k=k+1;      free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
      fprintf(ficresvpl,"\n#****** ");      free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
      for(j=1;j<=cptcovn;j++)      free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
        fprintf(ficresvpl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);      free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
      fprintf(ficresvpl,"******\n");    }
          free_vector(xp,1,npar);
      varpl=matrix(1,nlstate,(int) bage, (int) fage);    fclose(ficresprob);
      oldm=oldms;savm=savms;    fclose(ficresprobcov);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    fclose(ficresprobcor);
    }    fclose(ficgp);
  }    fclose(fichtm);
   }
   fclose(ficresvpl);  
   
   /*---------- End : free ----------------*/  /******************* Printing html file ***********/
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                      int lastpass, int stepm, int weightopt, char model[],\
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);                    int popforecast, int estepm ,\
                      double jprev1, double mprev1,double anprev1, \
                      double jprev2, double mprev2,double anprev2){
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    int jj1, k1, i1, cpt;
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    /*char optionfilehtm[FILENAMELENGTH];*/
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);      printf("Problem with %s \n",optionfilehtm), exit(0);
        fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);
   free_matrix(matcov,1,npar,1,npar);    }
   free_vector(delti,1,npar);  
       fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);   - 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
   printf("End of Imach\n");   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */   - Life expectancies by age and initial health status (estepm=%2d months): 
       <a href=\"e%s\">e%s</a> <br>\n</li>", \
   /* 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);*/    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
   /*printf("Total time was %d uSec.\n", total_usecs);*/  
   /*------ End -----------*/  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
  end:   m=cptcoveff;
 #ifdef windows   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
  chdir(pathcd);  
 #endif   jj1=0;
  system("wgnuplot ../gp37mgw/graph.plt");   for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
 #ifdef windows       jj1++;
   while (z[0] != 'q') {       if (cptcovn > 0) {
     chdir(pathcd);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     printf("\nType e to edit output files, c to start again, and q for exiting: ");         for (cpt=1; cpt<=cptcoveff;cpt++) 
     scanf("%s",z);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     if (z[0] == 'c') system("./imach");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     else if (z[0] == 'e') {       }
       chdir(path);       /* Pij */
       system("index.htm");       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);     
     else if (z[0] == 'q') exit(0);       /* 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>
 #endif  <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 stationary 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+2*$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:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%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 stat */
     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 mobilavrange, mob;
     double age;
     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<=ncodemax[cptcov];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<=ncodemax[cptcoveff];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 agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
    agelim=AGESUP;
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;
   
     prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
    
    
     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;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);
     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;
     
     fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean); 
     
     for(cptcov=1;cptcov<=i2;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 ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# StartingAge FinalAge");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);
         
         
         for (cpt=0; cpt<=(anproj2-anproj1);cpt++) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);   
   
           for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %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) (calagedate+YEARM*cpt)) {
                 fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,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)(calagedate+12*cpt)){
                   fprintf(ficresf," %.3f", kk1);
                           
                 }
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
       }
     }
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   /************** Forecasting ******************/
   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 calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     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;
     calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
     
     
     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;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)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %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) (calagedate+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)(calagedate+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+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedate+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)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %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) (calagedate+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)(calagedate+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 i,j, k, n=MAXN,iter,m,size,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,**adl,*tab; 
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;
   
     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,mproj1,anproj1,jproj2,mproj2,anproj2;
     
   
     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",version);
     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; 
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn;
     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;
   
     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];
     
     /* 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);
       adl=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]));}*/
     
    
     /* 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){
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+');
       j1=nbocc(model,'*');
       cptcovn=j+1;
       cptcovprod=j1;
       
       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;
       }
       
       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 analyze 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 */
     
     /* 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 ((mint[m][i]== 99) && (s[m][i] <= nlstate)){
            anint[m][i]=9999;
            s[m][i]=-1;
          }
        if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;
         }
       }
   
       for (i=1; i<=imx; i++)  {
         agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
         for(m=1; (m<= maxwav); m++){
           if(s[m][i] >0){
             if (s[m][i] >= nlstate+1) {
               if(agedc[i]>0)
                 if(moisdc[i]!=99 && andc[i]!=9999)
                   agev[m][i]=agedc[i];
               /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
              else {
                 if (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){ /* Should no more exist */
               agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
               if(mint[m][i]==99 || 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=1; (m<= maxwav); 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;
           }
         }
       }
   
   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);
       mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
       /* Concatenates waves */
         concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
   
         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);
      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){
       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");
          }
        }
      }
      
      k=1;
      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;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);
      
      while((c=getc(ficpar))=='#' && c!= EOF){
        ungetc(c,ficpar);
        fgets(line, MAXLINE, ficpar);
        puts(line);
        fputs(line,ficparo);
      }
      ungetc(c,ficpar);
    
   
      dateprev1=anprev1+mprev1/12.+jprev1/365.;
      dateprev2=anprev2+mprev2/12.+jprev2/365.;
   
     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,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);
   fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);
   fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",jproj1,mproj1,anproj1,jproj2,mproj2,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);
   
    freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,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
   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,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(mw,1,lastpass-firstpass+1,1,imx);   
    free_ivector(num,1,n);
    free_vector(agedc,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);
     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 */
     k=0;
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1;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(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*/
   
     k=0;
     for(cptcov=1;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,"# Age");
             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 %f %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, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
   
     /*---------- Forecasting ------------------*/
     if((stepm == 1) && (strcmp(model,".")==0)){
       prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);
       if (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);
     calagedate=-1;
     prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);
     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);
       }
     }
   
     k=0;
     for(cptcov=1;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_matrix(mint,1,maxwav,1,n);
       free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);
       free_vector(weight,1,n);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     free_vector(epj,1,nlstate+1);
     
     /*------- 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);
   
     k=0;
     for(cptcov=1;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);
       }
    }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
     
     free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
     free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
     
     
     free_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(matcov,1,npar,1,npar);
     free_vector(delti,1,npar);
     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);
   
     fprintf(fichtm,"\n</body>");
     fclose(fichtm);
     fclose(ficgp);
     
   
     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: %s\n",plotcmd);fflush(stdout);
    system(plotcmd);
   
    /*#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.1.2  
changed lines
  Added in v.1.56


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