Diff for /imach/src/imach.c between versions 1.11 and 1.87

version 1.11, 2001/05/17 16:07:14 version 1.87, 2003/06/18 12:26:01
Line 1 Line 1
      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.87  2003/06/18 12:26:01  brouard
   individuals from different ages are interviewed on their health status    Version 0.96
   or degree of  disability. At least a second wave of interviews  
   ("longitudinal") should  measure each new individual health status.    Revision 1.86  2003/06/17 20:04:08  brouard
   Health expectancies are computed from the transistions observed between    (Module): Change position of html and gnuplot routines and added
   waves and are computed for each degree of severity of disability (number    routine fileappend.
   of life states). More degrees you consider, more time is necessary to  
   reach the Maximum Likelihood of the parameters involved in the model.    Revision 1.85  2003/06/17 13:12:43  brouard
   The simplest model is the multinomial logistic model where pij is    * imach.c (Repository): Check when date of death was earlier that
   the probabibility to be observed in state j at the second wave conditional    current date of interview. It may happen when the death was just
   to be observed in state i at the first wave. Therefore the model is:    prior to the death. In this case, dh was negative and likelihood
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    was wrong (infinity). We still send an "Error" but patch by
   is a covariate. If you want to have a more complex model than "constant and    assuming that the date of death was just one stepm after the
   age", you should modify the program where the markup    interview.
     *Covariates have to be included here again* invites you to do it.    (Repository): Because some people have very long ID (first column)
   More covariates you add, less is the speed of the convergence.    we changed int to long in num[] and we added a new lvector for
     memory allocation. But we also truncated to 8 characters (left
   The advantage that this computer programme claims, comes from that if the    truncation)
   delay between waves is not identical for each individual, or if some    (Repository): No more line truncation errors.
   individual missed an interview, the information is not rounded or lost, but  
   taken into account using an interpolation or extrapolation.    Revision 1.84  2003/06/13 21:44:43  brouard
   hPijx is the probability to be    * imach.c (Repository): Replace "freqsummary" at a correct
   observed in state i at age x+h conditional to the observed state i at age    place. It differs from routine "prevalence" which may be called
   x. The delay 'h' can be split into an exact number (nh*stepm) of    many times. Probs is memory consuming and must be used with
   unobserved intermediate  states. This elementary transition (by month or    parcimony.
   quarter trimester, semester or year) is model as a multinomial logistic.    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply hPijx.    Revision 1.83  2003/06/10 13:39:11  lievre
     *** empty log message ***
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.82  2003/06/05 15:57:20  brouard
      Add log in  imach.c and  fullversion number is now printed.
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.  */
   This software have been partly granted by Euro-REVES, a concerted action  /*
   from the European Union.     Interpolated Markov Chain
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Short summary of the programme:
   can be accessed at http://euroreves.ined.fr/imach .    
   **********************************************************************/    This program computes Healthy Life Expectancies from
      cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 #include <math.h>    first survey ("cross") where individuals from different ages are
 #include <stdio.h>    interviewed on their health status or degree of disability (in the
 #include <stdlib.h>    case of a health survey which is our main interest) -2- at least a
 #include <unistd.h>    second wave of interviews ("longitudinal") which measure each change
     (if any) in individual health status.  Health expectancies are
 #define MAXLINE 256    computed from the time spent in each health state according to a
 #define FILENAMELENGTH 80    model. More health states you consider, more time is necessary to reach the
 /*#define DEBUG*/    Maximum Likelihood of the parameters involved in the model.  The
 #define windows    simplest model is the multinomial logistic model where pij is the
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    probability to be observed in state j at the second wave
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    conditional to be observed in state i at the first wave. Therefore
     the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    'age' is age and 'sex' is a covariate. If you want to have a more
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    complex model than "constant and age", you should modify the program
     where the markup *Covariates have to be included here again* invites
 #define NINTERVMAX 8    you to do it.  More covariates you add, slower the
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    convergence.
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    The advantage of this computer programme, compared to a simple
 #define MAXN 20000    multinomial logistic model, is clear when the delay between waves is not
 #define YEARM 12. /* Number of months per year */    identical for each individual. Also, if a individual missed an
 #define AGESUP 130    intermediate interview, the information is lost, but taken into
 #define AGEBASE 40    account using an interpolation or extrapolation.  
   
     hPijx is the probability to be observed in state i at age x+h
 int nvar;    conditional to the observed state i at age x. The delay 'h' can be
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    split into an exact number (nh*stepm) of unobserved intermediate
 int npar=NPARMAX;    states. This elementary transition (by month, quarter,
 int nlstate=2; /* Number of live states */    semester or year) is modelled as a multinomial logistic.  The hPx
 int ndeath=1; /* Number of dead states */    matrix is simply the matrix product of nh*stepm elementary matrices
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    and the contribution of each individual to the likelihood is simply
     hPijx.
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Also this programme outputs the covariance matrix of the parameters but also
 int jmin, jmax; /* min, max spacing between 2 waves */    of the life expectancies. It also computes the stable prevalence. 
 int mle, weightopt;    
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */             Institut national d'études démographiques, Paris.
 double jmean; /* Mean space between 2 waves */    This software have been partly granted by Euro-REVES, a concerted action
 double **oldm, **newm, **savm; /* Working pointers to matrices */    from the European Union.
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    It is copyrighted identically to a GNU software product, ie programme and
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;    software can be distributed freely for non commercial use. Latest version
 FILE *ficgp, *fichtm;    can be accessed at http://euroreves.ined.fr/imach .
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
  FILE  *ficresvij;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   char fileresv[FILENAMELENGTH];    
  FILE  *ficresvpl;    **********************************************************************/
   char fileresvpl[FILENAMELENGTH];  /*
     main
 #define NR_END 1    read parameterfile
 #define FREE_ARG char*    read datafile
 #define FTOL 1.0e-10    concatwav
     freqsummary
 #define NRANSI    if (mle >= 1)
 #define ITMAX 200      mlikeli
     print results files
 #define TOL 2.0e-4    if mle==1 
        computes hessian
 #define CGOLD 0.3819660    read end of parameter file: agemin, agemax, bage, fage, estepm
 #define ZEPS 1.0e-10        begin-prev-date,...
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    open gnuplot file
     open html file
 #define GOLD 1.618034    stable prevalence
 #define GLIMIT 100.0     for age prevalim()
 #define TINY 1.0e-20    h Pij x
     variance of p varprob
 static double maxarg1,maxarg2;    forecasting if prevfcast==1 prevforecast call prevalence()
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    health expectancies
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Variance-covariance of DFLE
      prevalence()
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))     movingaverage()
 #define rint(a) floor(a+0.5)    varevsij() 
     if popbased==1 varevsij(,popbased)
 static double sqrarg;    total life expectancies
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Variance of stable prevalence
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}   end
   */
 int imx;  
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/  
    
 int m,nb;  #include <math.h>
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  #include <stdio.h>
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  #include <stdlib.h>
 double **pmmij;  #include <unistd.h>
   
 double *weight;  #include <sys/time.h>
 int **s; /* Status */  #include <time.h>
 double *agedc, **covar, idx;  #include "timeval.h"
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
   #define MAXLINE 256
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  #define GNUPLOTPROGRAM "gnuplot"
 double ftolhess; /* Tolerance for computing hessian */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   #define FILENAMELENGTH 132
 /**************** split *************************/  /*#define DEBUG*/
 static  int split( char *path, char *dirc, char *name )  /*#define windows*/
 {  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
    char *s;                             /* pointer */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
    int  l1, l2;                         /* length counters */  
   #define MAXPARM 30 /* Maximum number of parameters for the optimization */
    l1 = strlen( path );                 /* length of path */  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
    s = strrchr( path, '\\' );           /* find last / */  #define NINTERVMAX 8
    if ( s == NULL ) {                   /* no directory, so use current */  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #if     defined(__bsd__)                /* get current working directory */  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
       extern char       *getwd( );  #define NCOVMAX 8 /* Maximum number of covariates */
   #define MAXN 20000
       if ( getwd( dirc ) == NULL ) {  #define YEARM 12. /* Number of months per year */
 #else  #define AGESUP 130
       extern char       *getcwd( );  #define AGEBASE 40
   #ifdef unix
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  #define DIRSEPARATOR '/'
 #endif  #define ODIRSEPARATOR '\\'
          return( GLOCK_ERROR_GETCWD );  #else
       }  #define DIRSEPARATOR '\\'
       strcpy( name, path );             /* we've got it */  #define ODIRSEPARATOR '/'
    } else {                             /* strip direcotry from path */  #endif
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */  /* $Id$ */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  /* $State$ */
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  char version[]="Imach version 0.96, June 2003, INED-EUROREVES ";
       dirc[l1-l2] = 0;                  /* add zero */  char fullversion[]="$Revision$ $Date$"; 
    }  int erreur; /* Error number */
    l1 = strlen( dirc );                 /* length of directory */  int nvar;
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
    return( 0 );                         /* we're done */  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;
   
 void replace(char *s, char*t)  int *wav; /* Number of waves for this individuual 0 is possible */
 {  int maxwav; /* Maxim number of waves */
   int i;  int jmin, jmax; /* min, max spacing between 2 waves */
   int lg=20;  int gipmx, gsw; /* Global variables on the number of contributions 
   i=0;                     to the likelihood and the sum of weights (done by funcone)*/
   lg=strlen(t);  int mle, weightopt;
   for(i=0; i<= lg; i++) {  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
     (s[i] = t[i]);  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
     if (t[i]== '\\') s[i]='/';  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   }             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 }  double jmean; /* Mean space between 2 waves */
   double **oldm, **newm, **savm; /* Working pointers to matrices */
 int nbocc(char *s, char occ)  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 {  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   int i,j=0;  FILE *ficlog, *ficrespow;
   int lg=20;  int globpr; /* Global variable for printing or not */
   i=0;  double fretone; /* Only one call to likelihood */
   lg=strlen(s);  long ipmx; /* Number of contributions */
   for(i=0; i<= lg; i++) {  double sw; /* Sum of weights */
   if  (s[i] == occ ) j++;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   }  FILE *ficresilk;
   return j;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 }  FILE *ficresprobmorprev;
   FILE *fichtm; /* Html File */
 void cutv(char *u,char *v, char*t, char occ)  FILE *ficreseij;
 {  char filerese[FILENAMELENGTH];
   int i,lg,j,p=0;  FILE  *ficresvij;
   i=0;  char fileresv[FILENAMELENGTH];
   for(j=0; j<=strlen(t)-1; j++) {  FILE  *ficresvpl;
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  char fileresvpl[FILENAMELENGTH];
   }  char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   lg=strlen(t);  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   for(j=0; j<p; j++) {  
     (u[j] = t[j]);  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   }  char filelog[FILENAMELENGTH]; /* Log file */
      u[p]='\0';  char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
    for(j=0; j<= lg; j++) {  char popfile[FILENAMELENGTH];
     if (j>=(p+1))(v[j-p-1] = t[j]);  
   }  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
 }  
   #define NR_END 1
 /********************** nrerror ********************/  #define FREE_ARG char*
   #define FTOL 1.0e-10
 void nrerror(char error_text[])  
 {  #define NRANSI 
   fprintf(stderr,"ERREUR ...\n");  #define ITMAX 200 
   fprintf(stderr,"%s\n",error_text);  
   exit(1);  #define TOL 2.0e-4 
 }  
 /*********************** vector *******************/  #define CGOLD 0.3819660 
 double *vector(int nl, int nh)  #define ZEPS 1.0e-10 
 {  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  #define GOLD 1.618034 
   if (!v) nrerror("allocation failure in vector");  #define GLIMIT 100.0 
   return v-nl+NR_END;  #define TINY 1.0e-20 
 }  
   static double maxarg1,maxarg2;
 /************************ free vector ******************/  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 void free_vector(double*v, int nl, int nh)  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 {    
   free((FREE_ARG)(v+nl-NR_END));  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 }  #define rint(a) floor(a+0.5)
   
 /************************ivector *******************************/  static double sqrarg;
 int *ivector(long nl,long nh)  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 {  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   int *v;  
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  int imx; 
   if (!v) nrerror("allocation failure in ivector");  int stepm;
   return v-nl+NR_END;  /* Stepm, step in month: minimum step interpolation*/
 }  
   int estepm;
 /******************free ivector **************************/  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 void free_ivector(int *v, long nl, long nh)  
 {  int m,nb;
   free((FREE_ARG)(v+nl-NR_END));  long *num;
 }  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
   double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 /******************* imatrix *******************************/  double **pmmij, ***probs;
 int **imatrix(long nrl, long nrh, long ncl, long nch)  double dateintmean=0;
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {  double *weight;
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  int **s; /* Status */
   int **m;  double *agedc, **covar, idx;
    int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   if (!m) nrerror("allocation failure 1 in matrix()");  double ftolhess; /* Tolerance for computing hessian */
   m += NR_END;  
   m -= nrl;  /**************** split *************************/
    static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
    {
   /* allocate rows and set pointers to them */    char  *ss;                            /* pointer */
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    int   l1, l2;                         /* length counters */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;    l1 = strlen(path );                   /* length of path */
   m[nrl] -= ncl;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
      ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    if ( ss == NULL ) {                   /* no directory, so use current */
        /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   /* return pointer to array of pointers to rows */        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   return m;      /* get current working directory */
 }      /*    extern  char* getcwd ( char *buf , int len);*/
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 /****************** free_imatrix *************************/        return( GLOCK_ERROR_GETCWD );
 void free_imatrix(m,nrl,nrh,ncl,nch)      }
       int **m;      strcpy( name, path );               /* we've got it */
       long nch,ncl,nrh,nrl;    } else {                              /* strip direcotry from path */
      /* free an int matrix allocated by imatrix() */      ss++;                               /* after this, the filename */
 {      l2 = strlen( ss );                  /* length of filename */
   free((FREE_ARG) (m[nrl]+ncl-NR_END));      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   free((FREE_ARG) (m+nrl-NR_END));      strcpy( name, ss );         /* save file name */
 }      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       dirc[l1-l2] = 0;                    /* add zero */
 /******************* matrix *******************************/    }
 double **matrix(long nrl, long nrh, long ncl, long nch)    l1 = strlen( dirc );                  /* length of directory */
 {    /*#ifdef windows
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   double **m;  #else
     if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #endif
   if (!m) nrerror("allocation failure 1 in matrix()");    */
   m += NR_END;    ss = strrchr( name, '.' );            /* find last / */
   m -= nrl;    ss++;
     strcpy(ext,ss);                       /* save extension */
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    l1= strlen( name);
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    l2= strlen(ss)+1;
   m[nrl] += NR_END;    strncpy( finame, name, l1-l2);
   m[nrl] -= ncl;    finame[l1-l2]= 0;
     return( 0 );                          /* we're done */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  }
   return m;  
 }  
   /******************************************/
 /*************************free matrix ************************/  
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  void replace(char *s, char*t)
 {  {
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    int i;
   free((FREE_ARG)(m+nrl-NR_END));    int lg=20;
 }    i=0;
     lg=strlen(t);
 /******************* ma3x *******************************/    for(i=0; i<= lg; i++) {
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)      (s[i] = t[i]);
 {      if (t[i]== '\\') s[i]='/';
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    }
   double ***m;  }
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  int nbocc(char *s, char occ)
   if (!m) nrerror("allocation failure 1 in matrix()");  {
   m += NR_END;    int i,j=0;
   m -= nrl;    int lg=20;
     i=0;
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    lg=strlen(s);
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    for(i=0; i<= lg; i++) {
   m[nrl] += NR_END;    if  (s[i] == occ ) j++;
   m[nrl] -= ncl;    }
     return j;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  }
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  void cutv(char *u,char *v, char*t, char occ)
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  {
   m[nrl][ncl] += NR_END;    /* cuts string t into u and v where u is ended by char occ excluding it
   m[nrl][ncl] -= nll;       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   for (j=ncl+1; j<=nch; j++)       gives u="abcedf" and v="ghi2j" */
     m[nrl][j]=m[nrl][j-1]+nlay;    int i,lg,j,p=0;
      i=0;
   for (i=nrl+1; i<=nrh; i++) {    for(j=0; j<=strlen(t)-1; j++) {
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     for (j=ncl+1; j<=nch; j++)    }
       m[i][j]=m[i][j-1]+nlay;  
   }    lg=strlen(t);
   return m;    for(j=0; j<p; j++) {
 }      (u[j] = t[j]);
     }
 /*************************free ma3x ************************/       u[p]='\0';
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {     for(j=0; j<= lg; j++) {
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));      if (j>=(p+1))(v[j-p-1] = t[j]);
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    }
   free((FREE_ARG)(m+nrl-NR_END));  }
 }  
   /********************** nrerror ********************/
 /***************** f1dim *************************/  
 extern int ncom;  void nrerror(char error_text[])
 extern double *pcom,*xicom;  {
 extern double (*nrfunc)(double []);    fprintf(stderr,"ERREUR ...\n");
      fprintf(stderr,"%s\n",error_text);
 double f1dim(double x)    exit(EXIT_FAILURE);
 {  }
   int j;  /*********************** vector *******************/
   double f;  double *vector(int nl, int nh)
   double *xt;  {
      double *v;
   xt=vector(1,ncom);    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    if (!v) nrerror("allocation failure in vector");
   f=(*nrfunc)(xt);    return v-nl+NR_END;
   free_vector(xt,1,ncom);  }
   return f;  
 }  /************************ free vector ******************/
   void free_vector(double*v, int nl, int nh)
 /*****************brent *************************/  {
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    free((FREE_ARG)(v+nl-NR_END));
 {  }
   int iter;  
   double a,b,d,etemp;  /************************ivector *******************************/
   double fu,fv,fw,fx;  int *ivector(long nl,long nh)
   double ftemp;  {
   double p,q,r,tol1,tol2,u,v,w,x,xm;    int *v;
   double e=0.0;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
      if (!v) nrerror("allocation failure in ivector");
   a=(ax < cx ? ax : cx);    return v-nl+NR_END;
   b=(ax > cx ? ax : cx);  }
   x=w=v=bx;  
   fw=fv=fx=(*f)(x);  /******************free ivector **************************/
   for (iter=1;iter<=ITMAX;iter++) {  void free_ivector(int *v, long nl, long nh)
     xm=0.5*(a+b);  {
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    free((FREE_ARG)(v+nl-NR_END));
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  }
     printf(".");fflush(stdout);  
 #ifdef DEBUG  /************************lvector *******************************/
     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);  long *lvector(long nl,long nh)
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  {
 #endif    long *v;
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       *xmin=x;    if (!v) nrerror("allocation failure in ivector");
       return fx;    return v-nl+NR_END;
     }  }
     ftemp=fu;  
     if (fabs(e) > tol1) {  /******************free lvector **************************/
       r=(x-w)*(fx-fv);  void free_lvector(long *v, long nl, long nh)
       q=(x-v)*(fx-fw);  {
       p=(x-v)*q-(x-w)*r;    free((FREE_ARG)(v+nl-NR_END));
       q=2.0*(q-r);  }
       if (q > 0.0) p = -p;  
       q=fabs(q);  /******************* imatrix *******************************/
       etemp=e;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       e=d;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       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));    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       else {    int **m; 
         d=p/q;    
         u=x+d;    /* allocate pointers to rows */ 
         if (u-a < tol2 || b-u < tol2)    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
           d=SIGN(tol1,xm-x);    if (!m) nrerror("allocation failure 1 in matrix()"); 
       }    m += NR_END; 
     } else {    m -= nrl; 
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    
     }    
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    /* allocate rows and set pointers to them */ 
     fu=(*f)(u);    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     if (fu <= fx) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       if (u >= x) a=x; else b=x;    m[nrl] += NR_END; 
       SHFT(v,w,x,u)    m[nrl] -= ncl; 
         SHFT(fv,fw,fx,fu)    
         } else {    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
           if (u < x) a=u; else b=u;    
           if (fu <= fw || w == x) {    /* return pointer to array of pointers to rows */ 
             v=w;    return m; 
             w=u;  } 
             fv=fw;  
             fw=fu;  /****************** free_imatrix *************************/
           } else if (fu <= fv || v == x || v == w) {  void free_imatrix(m,nrl,nrh,ncl,nch)
             v=u;        int **m;
             fv=fu;        long nch,ncl,nrh,nrl; 
           }       /* free an int matrix allocated by imatrix() */ 
         }  { 
   }    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   nrerror("Too many iterations in brent");    free((FREE_ARG) (m+nrl-NR_END)); 
   *xmin=x;  } 
   return fx;  
 }  /******************* matrix *******************************/
   double **matrix(long nrl, long nrh, long ncl, long nch)
 /****************** mnbrak ***********************/  {
     long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    double **m;
             double (*func)(double))  
 {    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double ulim,u,r,q, dum;    if (!m) nrerror("allocation failure 1 in matrix()");
   double fu;    m += NR_END;
      m -= nrl;
   *fa=(*func)(*ax);  
   *fb=(*func)(*bx);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   if (*fb > *fa) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     SHFT(dum,*ax,*bx,dum)    m[nrl] += NR_END;
       SHFT(dum,*fb,*fa,dum)    m[nrl] -= ncl;
       }  
   *cx=(*bx)+GOLD*(*bx-*ax);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   *fc=(*func)(*cx);    return m;
   while (*fb > *fc) {    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
     r=(*bx-*ax)*(*fb-*fc);     */
     q=(*bx-*cx)*(*fb-*fa);  }
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  /*************************free matrix ************************/
     ulim=(*bx)+GLIMIT*(*cx-*bx);  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     if ((*bx-u)*(u-*cx) > 0.0) {  {
       fu=(*func)(u);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     } else if ((*cx-u)*(u-ulim) > 0.0) {    free((FREE_ARG)(m+nrl-NR_END));
       fu=(*func)(u);  }
       if (fu < *fc) {  
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  /******************* ma3x *******************************/
           SHFT(*fb,*fc,fu,(*func)(u))  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
           }  {
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       u=ulim;    double ***m;
       fu=(*func)(u);  
     } else {    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       u=(*cx)+GOLD*(*cx-*bx);    if (!m) nrerror("allocation failure 1 in matrix()");
       fu=(*func)(u);    m += NR_END;
     }    m -= nrl;
     SHFT(*ax,*bx,*cx,u)  
       SHFT(*fa,*fb,*fc,fu)    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 }    m[nrl] += NR_END;
     m[nrl] -= ncl;
 /*************** linmin ************************/  
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 int ncom;  
 double *pcom,*xicom;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
 double (*nrfunc)(double []);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
      m[nrl][ncl] += NR_END;
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    m[nrl][ncl] -= nll;
 {    for (j=ncl+1; j<=nch; j++) 
   double brent(double ax, double bx, double cx,      m[nrl][j]=m[nrl][j-1]+nlay;
                double (*f)(double), double tol, double *xmin);    
   double f1dim(double x);    for (i=nrl+1; i<=nrh; i++) {
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
               double *fc, double (*func)(double));      for (j=ncl+1; j<=nch; j++) 
   int j;        m[i][j]=m[i][j-1]+nlay;
   double xx,xmin,bx,ax;    }
   double fx,fb,fa;    return m; 
      /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   ncom=n;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   pcom=vector(1,n);    */
   xicom=vector(1,n);  }
   nrfunc=func;  
   for (j=1;j<=n;j++) {  /*************************free ma3x ************************/
     pcom[j]=p[j];  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     xicom[j]=xi[j];  {
   }    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   ax=0.0;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   xx=1.0;    free((FREE_ARG)(m+nrl-NR_END));
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  }
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  
 #ifdef DEBUG  /***************** f1dim *************************/
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  extern int ncom; 
 #endif  extern double *pcom,*xicom;
   for (j=1;j<=n;j++) {  extern double (*nrfunc)(double []); 
     xi[j] *= xmin;   
     p[j] += xi[j];  double f1dim(double x) 
   }  { 
   free_vector(xicom,1,n);    int j; 
   free_vector(pcom,1,n);    double f;
 }    double *xt; 
    
 /*************** powell ************************/    xt=vector(1,ncom); 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
             double (*func)(double []))    f=(*nrfunc)(xt); 
 {    free_vector(xt,1,ncom); 
   void linmin(double p[], double xi[], int n, double *fret,    return f; 
               double (*func)(double []));  } 
   int i,ibig,j;  
   double del,t,*pt,*ptt,*xit;  /*****************brent *************************/
   double fp,fptt;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   double *xits;  { 
   pt=vector(1,n);    int iter; 
   ptt=vector(1,n);    double a,b,d,etemp;
   xit=vector(1,n);    double fu,fv,fw,fx;
   xits=vector(1,n);    double ftemp;
   *fret=(*func)(p);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   for (j=1;j<=n;j++) pt[j]=p[j];    double e=0.0; 
   for (*iter=1;;++(*iter)) {   
     fp=(*fret);    a=(ax < cx ? ax : cx); 
     ibig=0;    b=(ax > cx ? ax : cx); 
     del=0.0;    x=w=v=bx; 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    fw=fv=fx=(*f)(x); 
     for (i=1;i<=n;i++)    for (iter=1;iter<=ITMAX;iter++) { 
       printf(" %d %.12f",i, p[i]);      xm=0.5*(a+b); 
     printf("\n");      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     for (i=1;i<=n;i++) {      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       for (j=1;j<=n;j++) xit[j]=xi[j][i];      printf(".");fflush(stdout);
       fptt=(*fret);      fprintf(ficlog,".");fflush(ficlog);
 #ifdef DEBUG  #ifdef DEBUG
       printf("fret=%lf \n",*fret);      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);
 #endif      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       printf("%d",i);fflush(stdout);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       linmin(p,xit,n,fret,func);  #endif
       if (fabs(fptt-(*fret)) > del) {      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         del=fabs(fptt-(*fret));        *xmin=x; 
         ibig=i;        return fx; 
       }      } 
 #ifdef DEBUG      ftemp=fu;
       printf("%d %.12e",i,(*fret));      if (fabs(e) > tol1) { 
       for (j=1;j<=n;j++) {        r=(x-w)*(fx-fv); 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);        q=(x-v)*(fx-fw); 
         printf(" x(%d)=%.12e",j,xit[j]);        p=(x-v)*q-(x-w)*r; 
       }        q=2.0*(q-r); 
       for(j=1;j<=n;j++)        if (q > 0.0) p = -p; 
         printf(" p=%.12e",p[j]);        q=fabs(q); 
       printf("\n");        etemp=e; 
 #endif        e=d; 
     }        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 #ifdef DEBUG        else { 
       int k[2],l;          d=p/q; 
       k[0]=1;          u=x+d; 
       k[1]=-1;          if (u-a < tol2 || b-u < tol2) 
       printf("Max: %.12e",(*func)(p));            d=SIGN(tol1,xm-x); 
       for (j=1;j<=n;j++)        } 
         printf(" %.12e",p[j]);      } else { 
       printf("\n");        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       for(l=0;l<=1;l++) {      } 
         for (j=1;j<=n;j++) {      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];      fu=(*f)(u); 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);      if (fu <= fx) { 
         }        if (u >= x) a=x; else b=x; 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));        SHFT(v,w,x,u) 
       }          SHFT(fv,fw,fx,fu) 
 #endif          } else { 
             if (u < x) a=u; else b=u; 
             if (fu <= fw || w == x) { 
       free_vector(xit,1,n);              v=w; 
       free_vector(xits,1,n);              w=u; 
       free_vector(ptt,1,n);              fv=fw; 
       free_vector(pt,1,n);              fw=fu; 
       return;            } else if (fu <= fv || v == x || v == w) { 
     }              v=u; 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");              fv=fu; 
     for (j=1;j<=n;j++) {            } 
       ptt[j]=2.0*p[j]-pt[j];          } 
       xit[j]=p[j]-pt[j];    } 
       pt[j]=p[j];    nrerror("Too many iterations in brent"); 
     }    *xmin=x; 
     fptt=(*func)(ptt);    return fx; 
     if (fptt < fp) {  } 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  
       if (t < 0.0) {  /****************** mnbrak ***********************/
         linmin(p,xit,n,fret,func);  
         for (j=1;j<=n;j++) {  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
           xi[j][ibig]=xi[j][n];              double (*func)(double)) 
           xi[j][n]=xit[j];  { 
         }    double ulim,u,r,q, dum;
 #ifdef DEBUG    double fu; 
         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++)    *fa=(*func)(*ax); 
           printf(" %.12e",xit[j]);    *fb=(*func)(*bx); 
         printf("\n");    if (*fb > *fa) { 
 #endif      SHFT(dum,*ax,*bx,dum) 
       }        SHFT(dum,*fb,*fa,dum) 
     }        } 
   }    *cx=(*bx)+GOLD*(*bx-*ax); 
 }    *fc=(*func)(*cx); 
     while (*fb > *fc) { 
 /**** Prevalence limit ****************/      r=(*bx-*ax)*(*fb-*fc); 
       q=(*bx-*cx)*(*fb-*fa); 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 {        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit      ulim=(*bx)+GLIMIT*(*cx-*bx); 
      matrix by transitions matrix until convergence is reached */      if ((*bx-u)*(u-*cx) > 0.0) { 
         fu=(*func)(u); 
   int i, ii,j,k;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   double min, max, maxmin, maxmax,sumnew=0.;        fu=(*func)(u); 
   double **matprod2();        if (fu < *fc) { 
   double **out, cov[NCOVMAX], **pmij();          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   double **newm;            SHFT(*fb,*fc,fu,(*func)(u)) 
   double agefin, delaymax=50 ; /* Max number of years to converge */            } 
       } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   for (ii=1;ii<=nlstate+ndeath;ii++)        u=ulim; 
     for (j=1;j<=nlstate+ndeath;j++){        fu=(*func)(u); 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      } else { 
     }        u=(*cx)+GOLD*(*cx-*bx); 
         fu=(*func)(u); 
    cov[1]=1.;      } 
        SHFT(*ax,*bx,*cx,u) 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */        SHFT(*fa,*fb,*fc,fu) 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        } 
     newm=savm;  } 
     /* Covariates have to be included here again */  
      cov[2]=agefin;  /*************** linmin ************************/
    
       for (k=1; k<=cptcovn;k++) {  int ncom; 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  double *pcom,*xicom;
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  double (*nrfunc)(double []); 
       }   
       for (k=1; k<=cptcovage;k++)  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  { 
       for (k=1; k<=cptcovprod;k++)    double brent(double ax, double bx, double cx, 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];                 double (*f)(double), double tol, double *xmin); 
     double f1dim(double x); 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/                double *fc, double (*func)(double)); 
     int j; 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    double xx,xmin,bx,ax; 
     double fx,fb,fa;
     savm=oldm;   
     oldm=newm;    ncom=n; 
     maxmax=0.;    pcom=vector(1,n); 
     for(j=1;j<=nlstate;j++){    xicom=vector(1,n); 
       min=1.;    nrfunc=func; 
       max=0.;    for (j=1;j<=n;j++) { 
       for(i=1; i<=nlstate; i++) {      pcom[j]=p[j]; 
         sumnew=0;      xicom[j]=xi[j]; 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    } 
         prlim[i][j]= newm[i][j]/(1-sumnew);    ax=0.0; 
         max=FMAX(max,prlim[i][j]);    xx=1.0; 
         min=FMIN(min,prlim[i][j]);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       }    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       maxmin=max-min;  #ifdef DEBUG
       maxmax=FMAX(maxmax,maxmin);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     }    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     if(maxmax < ftolpl){  #endif
       return prlim;    for (j=1;j<=n;j++) { 
     }      xi[j] *= xmin; 
   }      p[j] += xi[j]; 
 }    } 
     free_vector(xicom,1,n); 
 /*************** transition probabilities **********/    free_vector(pcom,1,n); 
   } 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  
 {  /*************** powell ************************/
   double s1, s2;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   /*double t34;*/              double (*func)(double [])) 
   int i,j,j1, nc, ii, jj;  { 
     void linmin(double p[], double xi[], int n, double *fret, 
     for(i=1; i<= nlstate; i++){                double (*func)(double [])); 
     for(j=1; j<i;j++){    int i,ibig,j; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    double del,t,*pt,*ptt,*xit;
         /*s2 += param[i][j][nc]*cov[nc];*/    double fp,fptt;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    double *xits;
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    pt=vector(1,n); 
       }    ptt=vector(1,n); 
       ps[i][j]=s2;    xit=vector(1,n); 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    xits=vector(1,n); 
     }    *fret=(*func)(p); 
     for(j=i+1; j<=nlstate+ndeath;j++){    for (j=1;j<=n;j++) pt[j]=p[j]; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    for (*iter=1;;++(*iter)) { 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      fp=(*fret); 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/      ibig=0; 
       }      del=0.0; 
       ps[i][j]=s2;      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
     }      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
   }      fprintf(ficrespow,"%d %.12f",*iter,*fret);
   for(i=1; i<= nlstate; i++){      for (i=1;i<=n;i++) {
      s1=0;        printf(" %d %.12f",i, p[i]);
     for(j=1; j<i; j++)        fprintf(ficlog," %d %.12lf",i, p[i]);
       s1+=exp(ps[i][j]);        fprintf(ficrespow," %.12lf", p[i]);
     for(j=i+1; j<=nlstate+ndeath; j++)      }
       s1+=exp(ps[i][j]);      printf("\n");
     ps[i][i]=1./(s1+1.);      fprintf(ficlog,"\n");
     for(j=1; j<i; j++)      fprintf(ficrespow,"\n");
       ps[i][j]= exp(ps[i][j])*ps[i][i];      for (i=1;i<=n;i++) { 
     for(j=i+1; j<=nlstate+ndeath; j++)        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];        fptt=(*fret); 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  #ifdef DEBUG
   } /* end i */        printf("fret=%lf \n",*fret);
         fprintf(ficlog,"fret=%lf \n",*fret);
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  #endif
     for(jj=1; jj<= nlstate+ndeath; jj++){        printf("%d",i);fflush(stdout);
       ps[ii][jj]=0;        fprintf(ficlog,"%d",i);fflush(ficlog);
       ps[ii][ii]=1;        linmin(p,xit,n,fret,func); 
     }        if (fabs(fptt-(*fret)) > del) { 
   }          del=fabs(fptt-(*fret)); 
           ibig=i; 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        } 
     for(jj=1; jj<= nlstate+ndeath; jj++){  #ifdef DEBUG
      printf("%lf ",ps[ii][jj]);        printf("%d %.12e",i,(*fret));
    }        fprintf(ficlog,"%d %.12e",i,(*fret));
     printf("\n ");        for (j=1;j<=n;j++) {
     }          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     printf("\n ");printf("%lf ",cov[2]);*/          printf(" x(%d)=%.12e",j,xit[j]);
 /*          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        }
   goto end;*/        for(j=1;j<=n;j++) {
     return ps;          printf(" p=%.12e",p[j]);
 }          fprintf(ficlog," p=%.12e",p[j]);
         }
 /**************** Product of 2 matrices ******************/        printf("\n");
         fprintf(ficlog,"\n");
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  #endif
 {      } 
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  #ifdef DEBUG
   /* in, b, out are matrice of pointers which should have been initialized        int k[2],l;
      before: only the contents of out is modified. The function returns        k[0]=1;
      a pointer to pointers identical to out */        k[1]=-1;
   long i, j, k;        printf("Max: %.12e",(*func)(p));
   for(i=nrl; i<= nrh; i++)        fprintf(ficlog,"Max: %.12e",(*func)(p));
     for(k=ncolol; k<=ncoloh; k++)        for (j=1;j<=n;j++) {
       for(j=ncl,out[i][k]=0.; j<=nch; j++)          printf(" %.12e",p[j]);
         out[i][k] +=in[i][j]*b[j][k];          fprintf(ficlog," %.12e",p[j]);
         }
   return out;        printf("\n");
 }        fprintf(ficlog,"\n");
         for(l=0;l<=1;l++) {
           for (j=1;j<=n;j++) {
 /************* Higher Matrix Product ***************/            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
             printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 {          }
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
      duration (i.e. until          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        }
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  #endif
      (typically every 2 years instead of every month which is too big).  
      Model is determined by parameters x and covariates have to be  
      included manually here.        free_vector(xit,1,n); 
         free_vector(xits,1,n); 
      */        free_vector(ptt,1,n); 
         free_vector(pt,1,n); 
   int i, j, d, h, k;        return; 
   double **out, cov[NCOVMAX];      } 
   double **newm;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       for (j=1;j<=n;j++) { 
   /* Hstepm could be zero and should return the unit matrix */        ptt[j]=2.0*p[j]-pt[j]; 
   for (i=1;i<=nlstate+ndeath;i++)        xit[j]=p[j]-pt[j]; 
     for (j=1;j<=nlstate+ndeath;j++){        pt[j]=p[j]; 
       oldm[i][j]=(i==j ? 1.0 : 0.0);      } 
       po[i][j][0]=(i==j ? 1.0 : 0.0);      fptt=(*func)(ptt); 
     }      if (fptt < fp) { 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   for(h=1; h <=nhstepm; h++){        if (t < 0.0) { 
     for(d=1; d <=hstepm; d++){          linmin(p,xit,n,fret,func); 
       newm=savm;          for (j=1;j<=n;j++) { 
       /* Covariates have to be included here again */            xi[j][ibig]=xi[j][n]; 
       cov[1]=1.;            xi[j][n]=xit[j]; 
       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]]];  #ifdef DEBUG
 for (k=1; k<=cptcovage;k++)          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
    for (k=1; k<=cptcovprod;k++)          for(j=1;j<=n;j++){
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];            printf(" %.12e",xit[j]);
             fprintf(ficlog," %.12e",xit[j]);
           }
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/          printf("\n");
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/          fprintf(ficlog,"\n");
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  #endif
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        }
       savm=oldm;      } 
       oldm=newm;    } 
     }  } 
     for(i=1; i<=nlstate+ndeath; i++)  
       for(j=1;j<=nlstate+ndeath;j++) {  /**** Prevalence limit (stable prevalence)  ****************/
         po[i][j][h]=newm[i][j];  
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
          */  {
       }    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   } /* end h */       matrix by transitions matrix until convergence is reached */
   return po;  
 }    int i, ii,j,k;
     double min, max, maxmin, maxmax,sumnew=0.;
     double **matprod2();
 /*************** log-likelihood *************/    double **out, cov[NCOVMAX], **pmij();
 double func( double *x)    double **newm;
 {    double agefin, delaymax=50 ; /* Max number of years to converge */
   int i, ii, j, k, mi, d, kk;  
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    for (ii=1;ii<=nlstate+ndeath;ii++)
   double **out;      for (j=1;j<=nlstate+ndeath;j++){
   double sw; /* Sum of weights */        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double lli; /* Individual log likelihood */      }
   long ipmx;  
   /*extern weight */     cov[1]=1.;
   /* We are differentiating ll according to initial status */   
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   /*for(i=1;i<imx;i++)    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     printf(" %d\n",s[4][i]);      newm=savm;
   */      /* Covariates have to be included here again */
   cov[1]=1.;       cov[2]=agefin;
     
   for(k=1; k<=nlstate; k++) ll[k]=0.;        for (k=1; k<=cptcovn;k++) {
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
     for(mi=1; mi<= wav[i]-1; mi++){        }
       for (ii=1;ii<=nlstate+ndeath;ii++)        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        for (k=1; k<=cptcovprod;k++)
       for(d=0; d<dh[mi][i]; d++){          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         newm=savm;  
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         for (kk=1; kk<=cptcovage;kk++) {        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        /*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);
          
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      savm=oldm;
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      oldm=newm;
         savm=oldm;      maxmax=0.;
         oldm=newm;      for(j=1;j<=nlstate;j++){
                min=1.;
                max=0.;
       } /* end mult */        for(i=1; i<=nlstate; i++) {
                sumnew=0;
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/          prlim[i][j]= newm[i][j]/(1-sumnew);
       ipmx +=1;          max=FMAX(max,prlim[i][j]);
       sw += weight[i];          min=FMIN(min,prlim[i][j]);
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        }
     } /* end of wave */        maxmin=max-min;
   } /* end of individual */        maxmax=FMAX(maxmax,maxmin);
       }
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];      if(maxmax < ftolpl){
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */        return prlim;
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      }
   return -l;    }
 }  }
   
   /*************** transition probabilities ***************/ 
 /*********** Maximum Likelihood Estimation ***************/  
   double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))  {
 {    double s1, s2;
   int i,j, iter;    /*double t34;*/
   double **xi,*delti;    int i,j,j1, nc, ii, jj;
   double fret;  
   xi=matrix(1,npar,1,npar);      for(i=1; i<= nlstate; i++){
   for (i=1;i<=npar;i++)      for(j=1; j<i;j++){
     for (j=1;j<=npar;j++)        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       xi[i][j]=(i==j ? 1.0 : 0.0);          /*s2 += param[i][j][nc]*cov[nc];*/
   printf("Powell\n");          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   powell(p,xi,npar,ftol,&iter,&fret,func);          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
         }
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        ps[i][j]=s2;
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
       }
 }      for(j=i+1; j<=nlstate+ndeath;j++){
         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
 /**** Computes Hessian and covariance matrix ***/          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
 {        }
   double  **a,**y,*x,pd;        ps[i][j]=s2;
   double **hess;      }
   int i, j,jk;    }
   int *indx;      /*ps[3][2]=1;*/
   
   double hessii(double p[], double delta, int theta, double delti[]);    for(i=1; i<= nlstate; i++){
   double hessij(double p[], double delti[], int i, int j);       s1=0;
   void lubksb(double **a, int npar, int *indx, double b[]) ;      for(j=1; j<i; j++)
   void ludcmp(double **a, int npar, int *indx, double *d) ;        s1+=exp(ps[i][j]);
       for(j=i+1; j<=nlstate+ndeath; j++)
         s1+=exp(ps[i][j]);
   hess=matrix(1,npar,1,npar);      ps[i][i]=1./(s1+1.);
       for(j=1; j<i; j++)
   printf("\nCalculation of the hessian matrix. Wait...\n");        ps[i][j]= exp(ps[i][j])*ps[i][i];
   for (i=1;i<=npar;i++){      for(j=i+1; j<=nlstate+ndeath; j++)
     printf("%d",i);fflush(stdout);        ps[i][j]= exp(ps[i][j])*ps[i][i];
     hess[i][i]=hessii(p,ftolhess,i,delti);      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     /*printf(" %f ",p[i]);*/    } /* end i */
   }  
     for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   for (i=1;i<=npar;i++) {      for(jj=1; jj<= nlstate+ndeath; jj++){
     for (j=1;j<=npar;j++)  {        ps[ii][jj]=0;
       if (j>i) {        ps[ii][ii]=1;
         printf(".%d%d",i,j);fflush(stdout);      }
         hess[i][j]=hessij(p,delti,i,j);    }
         hess[j][i]=hess[i][j];  
       }  
     }    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   }      for(jj=1; jj<= nlstate+ndeath; jj++){
   printf("\n");       printf("%lf ",ps[ii][jj]);
      }
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");      printf("\n ");
        }
   a=matrix(1,npar,1,npar);      printf("\n ");printf("%lf ",cov[2]);*/
   y=matrix(1,npar,1,npar);  /*
   x=vector(1,npar);    for(i=1; i<= npar; i++) printf("%f ",x[i]);
   indx=ivector(1,npar);    goto end;*/
   for (i=1;i<=npar;i++)      return ps;
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  }
   ludcmp(a,npar,indx,&pd);  
   /**************** Product of 2 matrices ******************/
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
     x[j]=1;  {
     lubksb(a,npar,indx,x);    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
     for (i=1;i<=npar;i++){       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       matcov[i][j]=x[i];    /* in, b, out are matrice of pointers which should have been initialized 
     }       before: only the contents of out is modified. The function returns
   }       a pointer to pointers identical to out */
     long i, j, k;
   printf("\n#Hessian matrix#\n");    for(i=nrl; i<= nrh; i++)
   for (i=1;i<=npar;i++) {      for(k=ncolol; k<=ncoloh; k++)
     for (j=1;j<=npar;j++) {        for(j=ncl,out[i][k]=0.; j<=nch; j++)
       printf("%.3e ",hess[i][j]);          out[i][k] +=in[i][j]*b[j][k];
     }  
     printf("\n");    return out;
   }  }
   
   /* Recompute Inverse */  
   for (i=1;i<=npar;i++)  /************* Higher Matrix Product ***************/
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  
   ludcmp(a,npar,indx,&pd);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   {
   /*  printf("\n#Hessian matrix recomputed#\n");    /* Computes the transition matrix starting at age 'age' over 
        'nhstepm*hstepm*stepm' months (i.e. until
   for (j=1;j<=npar;j++) {       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
     for (i=1;i<=npar;i++) x[i]=0;       nhstepm*hstepm matrices. 
     x[j]=1;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
     lubksb(a,npar,indx,x);       (typically every 2 years instead of every month which is too big 
     for (i=1;i<=npar;i++){       for the memory).
       y[i][j]=x[i];       Model is determined by parameters x and covariates have to be 
       printf("%.3e ",y[i][j]);       included manually here. 
     }  
     printf("\n");       */
   }  
   */    int i, j, d, h, k;
     double **out, cov[NCOVMAX];
   free_matrix(a,1,npar,1,npar);    double **newm;
   free_matrix(y,1,npar,1,npar);  
   free_vector(x,1,npar);    /* Hstepm could be zero and should return the unit matrix */
   free_ivector(indx,1,npar);    for (i=1;i<=nlstate+ndeath;i++)
   free_matrix(hess,1,npar,1,npar);      for (j=1;j<=nlstate+ndeath;j++){
         oldm[i][j]=(i==j ? 1.0 : 0.0);
         po[i][j][0]=(i==j ? 1.0 : 0.0);
 }      }
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 /*************** hessian matrix ****************/    for(h=1; h <=nhstepm; h++){
 double hessii( double x[], double delta, int theta, double delti[])      for(d=1; d <=hstepm; d++){
 {        newm=savm;
   int i;        /* Covariates have to be included here again */
   int l=1, lmax=20;        cov[1]=1.;
   double k1,k2;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   double p2[NPARMAX+1];        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   double res;        for (k=1; k<=cptcovage;k++)
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   double fx;        for (k=1; k<=cptcovprod;k++)
   int k=0,kmax=10;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   double l1;  
   
   fx=func(x);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   for (i=1;i<=npar;i++) p2[i]=x[i];        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   for(l=0 ; l <=lmax; l++){        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
     l1=pow(10,l);                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     delts=delt;        savm=oldm;
     for(k=1 ; k <kmax; k=k+1){        oldm=newm;
       delt = delta*(l1*k);      }
       p2[theta]=x[theta] +delt;      for(i=1; i<=nlstate+ndeath; i++)
       k1=func(p2)-fx;        for(j=1;j<=nlstate+ndeath;j++) {
       p2[theta]=x[theta]-delt;          po[i][j][h]=newm[i][j];
       k2=func(p2)-fx;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
       /*res= (k1-2.0*fx+k2)/delt/delt; */           */
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        }
          } /* end h */
 #ifdef DEBUG    return po;
       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);  }
 #endif  
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  /*************** log-likelihood *************/
         k=kmax;  double func( double *x)
       }  {
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    int i, ii, j, k, mi, d, kk;
         k=kmax; l=lmax*10.;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
       }    double **out;
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    double sw; /* Sum of weights */
         delts=delt;    double lli; /* Individual log likelihood */
       }    int s1, s2;
     }    double bbh, survp;
   }    long ipmx;
   delti[theta]=delts;    /*extern weight */
   return res;    /* We are differentiating ll according to initial status */
      /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 }    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
 double hessij( double x[], double delti[], int thetai,int thetaj)    */
 {    cov[1]=1.;
   int i;  
   int l=1, l1, lmax=20;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   double k1,k2,k3,k4,res,fx;  
   double p2[NPARMAX+1];    if(mle==1){
   int k;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   fx=func(x);        for(mi=1; mi<= wav[i]-1; mi++){
   for (k=1; k<=2; k++) {          for (ii=1;ii<=nlstate+ndeath;ii++)
     for (i=1;i<=npar;i++) p2[i]=x[i];            for (j=1;j<=nlstate+ndeath;j++){
     p2[thetai]=x[thetai]+delti[thetai]/k;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     k1=func(p2)-fx;            }
            for(d=0; d<dh[mi][i]; d++){
     p2[thetai]=x[thetai]+delti[thetai]/k;            newm=savm;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     k2=func(p2)-fx;            for (kk=1; kk<=cptcovage;kk++) {
                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     p2[thetai]=x[thetai]-delti[thetai]/k;            }
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     k3=func(p2)-fx;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              savm=oldm;
     p2[thetai]=x[thetai]-delti[thetai]/k;            oldm=newm;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          } /* end mult */
     k4=func(p2)-fx;        
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
 #ifdef DEBUG          /* But now since version 0.9 we anticipate for bias and large stepm.
     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);           * If stepm is larger than one month (smallest stepm) and if the exact delay 
 #endif           * (in months) between two waves is not a multiple of stepm, we rounded to 
   }           * the nearest (and in case of equal distance, to the lowest) interval but now
   return res;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
 }           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
            * probability in order to take into account the bias as a fraction of the way
 /************** Inverse of matrix **************/           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
 void ludcmp(double **a, int n, int *indx, double *d)           * -stepm/2 to stepm/2 .
 {           * For stepm=1 the results are the same as for previous versions of Imach.
   int i,imax,j,k;           * For stepm > 1 the results are less biased than in previous versions. 
   double big,dum,sum,temp;           */
   double *vv;          s1=s[mw[mi][i]][i];
            s2=s[mw[mi+1][i]][i];
   vv=vector(1,n);          bbh=(double)bh[mi][i]/(double)stepm; 
   *d=1.0;          /* bias is positive if real duration
   for (i=1;i<=n;i++) {           * is higher than the multiple of stepm and negative otherwise.
     big=0.0;           */
     for (j=1;j<=n;j++)          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
       if ((temp=fabs(a[i][j])) > big) big=temp;          if( s2 > nlstate){ 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");            /* i.e. if s2 is a death state and if the date of death is known then the contribution
     vv[i]=1.0/big;               to the likelihood is the probability to die between last step unit time and current 
   }               step unit time, which is also the differences between probability to die before dh 
   for (j=1;j<=n;j++) {               and probability to die before dh-stepm . 
     for (i=1;i<j;i++) {               In version up to 0.92 likelihood was computed
       sum=a[i][j];          as if date of death was unknown. Death was treated as any other
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];          health state: the date of the interview describes the actual state
       a[i][j]=sum;          and not the date of a change in health state. The former idea was
     }          to consider that at each interview the state was recorded
     big=0.0;          (healthy, disable or death) and IMaCh was corrected; but when we
     for (i=j;i<=n;i++) {          introduced the exact date of death then we should have modified
       sum=a[i][j];          the contribution of an exact death to the likelihood. This new
       for (k=1;k<j;k++)          contribution is smaller and very dependent of the step unit
         sum -= a[i][k]*a[k][j];          stepm. It is no more the probability to die between last interview
       a[i][j]=sum;          and month of death but the probability to survive from last
       if ( (dum=vv[i]*fabs(sum)) >= big) {          interview up to one month before death multiplied by the
         big=dum;          probability to die within a month. Thanks to Chris
         imax=i;          Jackson for correcting this bug.  Former versions increased
       }          mortality artificially. The bad side is that we add another loop
     }          which slows down the processing. The difference can be up to 10%
     if (j != imax) {          lower mortality.
       for (k=1;k<=n;k++) {            */
         dum=a[imax][k];            lli=log(out[s1][s2] - savm[s1][s2]);
         a[imax][k]=a[j][k];          }else{
         a[j][k]=dum;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       }            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
       *d = -(*d);          } 
       vv[imax]=vv[j];          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     }          /*if(lli ==000.0)*/
     indx[j]=imax;          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
     if (a[j][j] == 0.0) a[j][j]=TINY;          ipmx +=1;
     if (j != n) {          sw += weight[i];
       dum=1.0/(a[j][j]);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for (i=j+1;i<=n;i++) a[i][j] *= dum;        } /* end of wave */
     }      } /* end of individual */
   }    }  else if(mle==2){
   free_vector(vv,1,n);  /* Doesn't work */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 ;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 }        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
 void lubksb(double **a, int n, int *indx, double b[])            for (j=1;j<=nlstate+ndeath;j++){
 {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int i,ii=0,ip,j;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double sum;            }
            for(d=0; d<=dh[mi][i]; d++){
   for (i=1;i<=n;i++) {            newm=savm;
     ip=indx[i];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     sum=b[ip];            for (kk=1; kk<=cptcovage;kk++) {
     b[ip]=b[i];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     if (ii)            }
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     else if (sum) ii=i;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     b[i]=sum;            savm=oldm;
   }            oldm=newm;
   for (i=n;i>=1;i--) {          } /* end mult */
     sum=b[i];        
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     b[i]=sum/a[i][i];          /* But now since version 0.9 we anticipate for bias and large stepm.
   }           * If stepm is larger than one month (smallest stepm) and if the exact delay 
 }           * (in months) between two waves is not a multiple of stepm, we rounded to 
            * the nearest (and in case of equal distance, to the lowest) interval but now
 /************ Frequencies ********************/           * we keep into memory the bias bh[mi][i] and also the previous matrix product
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
 {  /* Some frequencies */           * probability in order to take into account the bias as a fraction of the way
             * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;           * -stepm/2 to stepm/2 .
   double ***freq; /* Frequencies */           * For stepm=1 the results are the same as for previous versions of Imach.
   double *pp;           * For stepm > 1 the results are less biased than in previous versions. 
   double pos;           */
   FILE *ficresp;          s1=s[mw[mi][i]][i];
   char fileresp[FILENAMELENGTH];          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
   pp=vector(1,nlstate);          /* bias is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
   strcpy(fileresp,"p");           */
   strcat(fileresp,fileres);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   if((ficresp=fopen(fileresp,"w"))==NULL) {          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     printf("Problem with prevalence resultfile: %s\n", fileresp);          /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
     exit(0);          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   }          /*if(lli ==000.0)*/
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   j1=0;          ipmx +=1;
           sw += weight[i];
   j=cptcoveff;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        } /* end of wave */
       } /* end of individual */
   for(k1=1; k1<=j;k1++){    }  else if(mle==3){  /* exponential inter-extrapolation */
    for(i1=1; i1<=ncodemax[k1];i1++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
        j1++;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);        for(mi=1; mi<= wav[i]-1; mi++){
          scanf("%d", i);*/          for (ii=1;ii<=nlstate+ndeath;ii++)
         for (i=-1; i<=nlstate+ndeath; i++)              for (j=1;j<=nlstate+ndeath;j++){
          for (jk=-1; jk<=nlstate+ndeath; jk++)                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
            for(m=agemin; m <= agemax+3; m++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              freq[i][jk][m]=0;            }
                  for(d=0; d<dh[mi][i]; d++){
        for (i=1; i<=imx; i++) {            newm=savm;
          bool=1;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
          if  (cptcovn>0) {            for (kk=1; kk<=cptcovage;kk++) {
            for (z1=1; z1<=cptcoveff; z1++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])            }
                bool=0;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
          }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           if (bool==1) {            savm=oldm;
            for(m=firstpass; m<=lastpass-1; m++){            oldm=newm;
              if(agev[m][i]==0) agev[m][i]=agemax+1;          } /* end mult */
              if(agev[m][i]==1) agev[m][i]=agemax+2;        
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          /* But now since version 0.9 we anticipate for bias and large stepm.
            }           * If stepm is larger than one month (smallest stepm) and if the exact delay 
          }           * (in months) between two waves is not a multiple of stepm, we rounded to 
        }           * the nearest (and in case of equal distance, to the lowest) interval but now
         if  (cptcovn>0) {           * we keep into memory the bias bh[mi][i] and also the previous matrix product
          fprintf(ficresp, "\n#********** Variable ");           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);           * probability in order to take into account the bias as a fraction of the way
        fprintf(ficresp, "**********\n#");           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
         }           * -stepm/2 to stepm/2 .
        for(i=1; i<=nlstate;i++)           * For stepm=1 the results are the same as for previous versions of Imach.
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);           * For stepm > 1 the results are less biased than in previous versions. 
        fprintf(ficresp, "\n");           */
                  s1=s[mw[mi][i]][i];
   for(i=(int)agemin; i <= (int)agemax+3; i++){          s2=s[mw[mi+1][i]][i];
     if(i==(int)agemax+3)          bbh=(double)bh[mi][i]/(double)stepm; 
       printf("Total");          /* bias is positive if real duration
     else           * is higher than the multiple of stepm and negative otherwise.
       printf("Age %d", i);           */
     for(jk=1; jk <=nlstate ; jk++){          /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
         pp[jk] += freq[jk][m][i];          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     }          /*if(lli ==000.0)*/
     for(jk=1; jk <=nlstate ; jk++){          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
       for(m=-1, pos=0; m <=0 ; m++)          ipmx +=1;
         pos += freq[jk][m][i];          sw += weight[i];
       if(pp[jk]>=1.e-10)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        } /* end of wave */
       else      } /* end of individual */
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);    }else if (mle==4){  /* ml=4 no inter-extrapolation */
     }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for(jk=1; jk <=nlstate ; jk++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)        for(mi=1; mi<= wav[i]-1; mi++){
         pp[jk] += freq[jk][m][i];          for (ii=1;ii<=nlstate+ndeath;ii++)
     }            for (j=1;j<=nlstate+ndeath;j++){
     for(jk=1,pos=0; jk <=nlstate ; jk++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       pos += pp[jk];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(jk=1; jk <=nlstate ; jk++){            }
       if(pos>=1.e-5)          for(d=0; d<dh[mi][i]; d++){
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);            newm=savm;
       else            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);            for (kk=1; kk<=cptcovage;kk++) {
       if( i <= (int) agemax){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         if(pos>=1.e-5)            }
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          
       else            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       }            savm=oldm;
     }            oldm=newm;
     for(jk=-1; jk <=nlstate+ndeath; jk++)          } /* end mult */
       for(m=-1; m <=nlstate+ndeath; m++)        
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          s1=s[mw[mi][i]][i];
     if(i <= (int) agemax)          s2=s[mw[mi+1][i]][i];
       fprintf(ficresp,"\n");          if( s2 > nlstate){ 
     printf("\n");            lli=log(out[s1][s2] - savm[s1][s2]);
     }          }else{
     }            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
  }          }
            ipmx +=1;
   fclose(ficresp);          sw += weight[i];
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   free_vector(pp,1,nlstate);  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         } /* end of wave */
 }  /* End of Freq */      } /* end of individual */
     }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
 /************* Waves Concatenation ***************/      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][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)        for(mi=1; mi<= wav[i]-1; mi++){
 {          for (ii=1;ii<=nlstate+ndeath;ii++)
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.            for (j=1;j<=nlstate+ndeath;j++){
      Death is a valid wave (if date is known).              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i              savm[ii][j]=(ii==j ? 1.0 : 0.0);
      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.          for(d=0; d<dh[mi][i]; d++){
      */            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   int i, mi, m;            for (kk=1; kk<=cptcovage;kk++) {
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
      double sum=0., jmean=0.;*/            }
           
   int j, k=0,jk, ju, jl;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double sum=0.;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   jmin=1e+5;            savm=oldm;
   jmax=-1;            oldm=newm;
   jmean=0.;          } /* end mult */
   for(i=1; i<=imx; i++){        
     mi=0;          s1=s[mw[mi][i]][i];
     m=firstpass;          s2=s[mw[mi+1][i]][i];
     while(s[m][i] <= nlstate){          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       if(s[m][i]>=1)          ipmx +=1;
         mw[++mi][i]=m;          sw += weight[i];
       if(m >=lastpass)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         break;          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
       else        } /* end of wave */
         m++;      } /* end of individual */
     }/* end while */    } /* End of if */
     if (s[m][i] > nlstate){    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       mi++;     /* Death is another wave */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
       /* if(mi==0)  never been interviewed correctly before death */    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
          /* Only death is a correct wave */    return -l;
       mw[mi][i]=m;  }
     }  
   /*************** log-likelihood *************/
     wav[i]=mi;  double funcone( double *x)
     if(mi==0)  {
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);    /* Same as likeli but slower because of a lot of printf and if */
   }    int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX], cov[NCOVMAX];
   for(i=1; i<=imx; i++){    double **out;
     for(mi=1; mi<wav[i];mi++){    double lli; /* Individual log likelihood */
       if (stepm <=0)    double llt;
         dh[mi][i]=1;    int s1, s2;
       else{    double bbh, survp;
         if (s[mw[mi+1][i]][i] > nlstate) {    /*extern weight */
           if (agedc[i] < 2*AGESUP) {    /* We are differentiating ll according to initial status */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
           if(j==0) j=1;  /* Survives at least one month after exam */    /*for(i=1;i<imx;i++) 
           k=k+1;      printf(" %d\n",s[4][i]);
           if (j >= jmax) jmax=j;    */
           if (j <= jmin) jmin=j;    cov[1]=1.;
           sum=sum+j;  
           if (j<0) printf("j=%d num=%d ",j,i);    for(k=1; k<=nlstate; k++) ll[k]=0.;
           }  
         }    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         else{      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));      for(mi=1; mi<= wav[i]-1; mi++){
           k=k+1;        for (ii=1;ii<=nlstate+ndeath;ii++)
           if (j >= jmax) jmax=j;          for (j=1;j<=nlstate+ndeath;j++){
           else if (j <= jmin)jmin=j;            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           sum=sum+j;            savm[ii][j]=(ii==j ? 1.0 : 0.0);
         }          }
         jk= j/stepm;        for(d=0; d<dh[mi][i]; d++){
         jl= j -jk*stepm;          newm=savm;
         ju= j -(jk+1)*stepm;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         if(jl <= -ju)          for (kk=1; kk<=cptcovage;kk++) {
           dh[mi][i]=jk;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         else          }
           dh[mi][i]=jk+1;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         if(dh[mi][i]==0)                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           dh[mi][i]=1; /* At least one step */          savm=oldm;
       }          oldm=newm;
     }        } /* end mult */
   }        
   jmean=sum/k;        s1=s[mw[mi][i]][i];
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        s2=s[mw[mi+1][i]][i];
 }        bbh=(double)bh[mi][i]/(double)stepm; 
 /*********** Tricode ****************************/        /* bias is positive if real duration
 void tricode(int *Tvar, int **nbcode, int imx)         * is higher than the multiple of stepm and negative otherwise.
 {         */
   int Ndum[20],ij=1, k, j, i;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   int cptcode=0;          lli=log(out[s1][s2] - savm[s1][s2]);
   cptcoveff=0;        } else if (mle==1){
            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   for (k=0; k<19; k++) Ndum[k]=0;        } else if(mle==2){
   for (k=1; k<=7; k++) ncodemax[k]=0;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
         } else if(mle==3){  /* exponential inter-extrapolation */
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
     for (i=1; i<=imx; i++) {        } else if (mle==4){  /* mle=4 no inter-extrapolation */
       ij=(int)(covar[Tvar[j]][i]);          lli=log(out[s1][s2]); /* Original formula */
       Ndum[ij]++;        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          lli=log(out[s1][s2]); /* Original formula */
       if (ij > cptcode) cptcode=ij;        } /* End of if */
     }        ipmx +=1;
         sw += weight[i];
     for (i=0; i<=cptcode; i++) {        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       if(Ndum[i]!=0) ncodemax[j]++;  /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
     }        if(globpr){
     ij=1;          fprintf(ficresilk,"%ld %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
    %10.6f %10.6f %10.6f ", \
                   num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
     for (i=1; i<=ncodemax[j]; i++) {                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
       for (k=0; k<=19; k++) {          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
         if (Ndum[k] != 0) {            llt +=ll[k]*gipmx/gsw;
           nbcode[Tvar[j]][ij]=k;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           ij++;          }
         }          fprintf(ficresilk," %10.6f\n", -llt);
         if (ij > ncodemax[j]) break;        }
       }        } /* end of wave */
     }    } /* end of individual */
   }      for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
  for (k=0; k<19; k++) Ndum[k]=0;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     if(globpr==0){ /* First time we count the contributions and weights */
  for (i=1; i<=ncovmodel; i++) {      gipmx=ipmx;
       ij=Tvar[i];      gsw=sw;
       Ndum[ij]++;    }
     }    return -l;
   }
  ij=1;  
  for (i=1; i<=10; i++) {  
    if((Ndum[i]!=0) && (i<=ncov)){  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
      Tvaraff[ij]=i;  {
      ij++;    /* This routine should help understanding what is done with 
    }       the selection of individuals/waves and
  }       to check the exact contribution to the likelihood.
         Plotting could be done.
     cptcoveff=ij-1;     */
 }    int k;
   
 /*********** Health Expectancies ****************/    if(*globpri !=0){ /* Just counts and sums no printings */
       strcpy(fileresilk,"ilk"); 
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)      strcat(fileresilk,fileres);
 {      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   /* Health expectancies */        printf("Problem with resultfile: %s\n", fileresilk);
   int i, j, nhstepm, hstepm, h;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   double age, agelim,hf;      }
   double ***p3mat;      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
        fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight out sav ");
   fprintf(ficreseij,"# Health expectancies\n");      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   fprintf(ficreseij,"# Age");      for(k=1; k<=nlstate; k++) 
   for(i=1; i<=nlstate;i++)        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
     for(j=1; j<=nlstate;j++)      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
       fprintf(ficreseij," %1d-%1d",i,j);    }
   fprintf(ficreseij,"\n");  
     *fretone=(*funcone)(p);
   hstepm=1*YEARM; /*  Every j years of age (in month) */    if(*globpri !=0){
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      fclose(ficresilk);
       fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",fileresilk,fileresilk);
   agelim=AGESUP;      fflush(fichtm); 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    } 
     /* nhstepm age range expressed in number of stepm */    return;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);  }
     /* Typically if 20 years = 20*12/6=40 stepm */  
     if (stepm >= YEARM) hstepm=1;  /*********** Maximum Likelihood Estimation ***************/
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */  
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
     /* Computed by stepm unit matrices, product of hstepm matrices, stored  {
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    int i,j, iter;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      double **xi;
     double fret;
     double fretone; /* Only one call to likelihood */
     for(i=1; i<=nlstate;i++)    char filerespow[FILENAMELENGTH];
       for(j=1; j<=nlstate;j++)    xi=matrix(1,npar,1,npar);
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){    for (i=1;i<=npar;i++)
           eij[i][j][(int)age] +=p3mat[i][j][h];      for (j=1;j<=npar;j++)
         }        xi[i][j]=(i==j ? 1.0 : 0.0);
        printf("Powell\n");  fprintf(ficlog,"Powell\n");
     hf=1;    strcpy(filerespow,"pow"); 
     if (stepm >= YEARM) hf=stepm/YEARM;    strcat(filerespow,fileres);
     fprintf(ficreseij,"%.0f",age );    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     for(i=1; i<=nlstate;i++)      printf("Problem with resultfile: %s\n", filerespow);
       for(j=1; j<=nlstate;j++){      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);    }
       }    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     fprintf(ficreseij,"\n");    for (i=1;i<=nlstate;i++)
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for(j=1;j<=nlstate+ndeath;j++)
   }        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
 }    fprintf(ficrespow,"\n");
   
 /************ Variance ******************/    powell(p,xi,npar,ftol,&iter,&fret,func);
 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)  
 {    fclose(ficrespow);
   /* Variance of health expectancies */    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   double **newm;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   double **dnewm,**doldm;  
   int i, j, nhstepm, hstepm, h;  }
   int k, cptcode;  
    double *xp;  /**** Computes Hessian and covariance matrix ***/
   double **gp, **gm;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   double ***gradg, ***trgradg;  {
   double ***p3mat;    double  **a,**y,*x,pd;
   double age,agelim;    double **hess;
   int theta;    int i, j,jk;
     int *indx;
    fprintf(ficresvij,"# Covariances of life expectancies\n");  
   fprintf(ficresvij,"# Age");    double hessii(double p[], double delta, int theta, double delti[]);
   for(i=1; i<=nlstate;i++)    double hessij(double p[], double delti[], int i, int j);
     for(j=1; j<=nlstate;j++)    void lubksb(double **a, int npar, int *indx, double b[]) ;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    void ludcmp(double **a, int npar, int *indx, double *d) ;
   fprintf(ficresvij,"\n");  
     hess=matrix(1,npar,1,npar);
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);    printf("\nCalculation of the hessian matrix. Wait...\n");
   doldm=matrix(1,nlstate,1,nlstate);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
      for (i=1;i<=npar;i++){
   hstepm=1*YEARM; /* Every year of age */      printf("%d",i);fflush(stdout);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      fprintf(ficlog,"%d",i);fflush(ficlog);
   agelim = AGESUP;      hess[i][i]=hessii(p,ftolhess,i,delti);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      /*printf(" %f ",p[i]);*/
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      /*printf(" %lf ",hess[i][i]);*/
     if (stepm >= YEARM) hstepm=1;    }
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for (i=1;i<=npar;i++) {
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      for (j=1;j<=npar;j++)  {
     gp=matrix(0,nhstepm,1,nlstate);        if (j>i) { 
     gm=matrix(0,nhstepm,1,nlstate);          printf(".%d%d",i,j);fflush(stdout);
           fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     for(theta=1; theta <=npar; theta++){          hess[i][j]=hessij(p,delti,i,j);
       for(i=1; i<=npar; i++){ /* Computes gradient */          hess[j][i]=hess[i][j];    
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          /*printf(" %lf ",hess[i][j]);*/
       }        }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    }
       for(j=1; j<= nlstate; j++){    printf("\n");
         for(h=0; h<=nhstepm; h++){    fprintf(ficlog,"\n");
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
         }    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       }    
        a=matrix(1,npar,1,npar);
       for(i=1; i<=npar; i++) /* Computes gradient */    y=matrix(1,npar,1,npar);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    x=vector(1,npar);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      indx=ivector(1,npar);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    for (i=1;i<=npar;i++)
       for(j=1; j<= nlstate; j++){      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
         for(h=0; h<=nhstepm; h++){    ludcmp(a,npar,indx,&pd);
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)  
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    for (j=1;j<=npar;j++) {
         }      for (i=1;i<=npar;i++) x[i]=0;
       }      x[j]=1;
       for(j=1; j<= nlstate; j++)      lubksb(a,npar,indx,x);
         for(h=0; h<=nhstepm; h++){      for (i=1;i<=npar;i++){ 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        matcov[i][j]=x[i];
         }      }
     } /* End theta */    }
   
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    printf("\n#Hessian matrix#\n");
     fprintf(ficlog,"\n#Hessian matrix#\n");
     for(h=0; h<=nhstepm; h++)    for (i=1;i<=npar;i++) { 
       for(j=1; j<=nlstate;j++)      for (j=1;j<=npar;j++) { 
         for(theta=1; theta <=npar; theta++)        printf("%.3e ",hess[i][j]);
           trgradg[h][j][theta]=gradg[h][theta][j];        fprintf(ficlog,"%.3e ",hess[i][j]);
       }
     for(i=1;i<=nlstate;i++)      printf("\n");
       for(j=1;j<=nlstate;j++)      fprintf(ficlog,"\n");
         vareij[i][j][(int)age] =0.;    }
     for(h=0;h<=nhstepm;h++){  
       for(k=0;k<=nhstepm;k++){    /* Recompute Inverse */
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    for (i=1;i<=npar;i++)
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
         for(i=1;i<=nlstate;i++)    ludcmp(a,npar,indx,&pd);
           for(j=1;j<=nlstate;j++)  
             vareij[i][j][(int)age] += doldm[i][j];    /*  printf("\n#Hessian matrix recomputed#\n");
       }  
     }    for (j=1;j<=npar;j++) {
     h=1;      for (i=1;i<=npar;i++) x[i]=0;
     if (stepm >= YEARM) h=stepm/YEARM;      x[j]=1;
     fprintf(ficresvij,"%.0f ",age );      lubksb(a,npar,indx,x);
     for(i=1; i<=nlstate;i++)      for (i=1;i<=npar;i++){ 
       for(j=1; j<=nlstate;j++){        y[i][j]=x[i];
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);        printf("%.3e ",y[i][j]);
       }        fprintf(ficlog,"%.3e ",y[i][j]);
     fprintf(ficresvij,"\n");      }
     free_matrix(gp,0,nhstepm,1,nlstate);      printf("\n");
     free_matrix(gm,0,nhstepm,1,nlstate);      fprintf(ficlog,"\n");
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    }
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   } /* End age */    free_matrix(a,1,npar,1,npar);
      free_matrix(y,1,npar,1,npar);
   free_vector(xp,1,npar);    free_vector(x,1,npar);
   free_matrix(doldm,1,nlstate,1,npar);    free_ivector(indx,1,npar);
   free_matrix(dnewm,1,nlstate,1,nlstate);    free_matrix(hess,1,npar,1,npar);
   
 }  
   }
 /************ Variance of prevlim ******************/  
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)  /*************** hessian matrix ****************/
 {  double hessii( double x[], double delta, int theta, double delti[])
   /* Variance of prevalence limit */  {
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    int i;
   double **newm;    int l=1, lmax=20;
   double **dnewm,**doldm;    double k1,k2;
   int i, j, nhstepm, hstepm;    double p2[NPARMAX+1];
   int k, cptcode;    double res;
   double *xp;    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   double *gp, *gm;    double fx;
   double **gradg, **trgradg;    int k=0,kmax=10;
   double age,agelim;    double l1;
   int theta;  
        fx=func(x);
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    for (i=1;i<=npar;i++) p2[i]=x[i];
   fprintf(ficresvpl,"# Age");    for(l=0 ; l <=lmax; l++){
   for(i=1; i<=nlstate;i++)      l1=pow(10,l);
       fprintf(ficresvpl," %1d-%1d",i,i);      delts=delt;
   fprintf(ficresvpl,"\n");      for(k=1 ; k <kmax; k=k+1){
         delt = delta*(l1*k);
   xp=vector(1,npar);        p2[theta]=x[theta] +delt;
   dnewm=matrix(1,nlstate,1,npar);        k1=func(p2)-fx;
   doldm=matrix(1,nlstate,1,nlstate);        p2[theta]=x[theta]-delt;
          k2=func(p2)-fx;
   hstepm=1*YEARM; /* Every year of age */        /*res= (k1-2.0*fx+k2)/delt/delt; */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   agelim = AGESUP;        
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  #ifdef DEBUG
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        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);
     if (stepm >= YEARM) hstepm=1;        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);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  #endif
     gradg=matrix(1,npar,1,nlstate);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
     gp=vector(1,nlstate);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     gm=vector(1,nlstate);          k=kmax;
         }
     for(theta=1; theta <=npar; theta++){        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       for(i=1; i<=npar; i++){ /* Computes gradient */          k=kmax; l=lmax*10.;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        }
       }        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          delts=delt;
       for(i=1;i<=nlstate;i++)        }
         gp[i] = prlim[i][i];      }
        }
       for(i=1; i<=npar; i++) /* Computes gradient */    delti[theta]=delts;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    return res; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    
       for(i=1;i<=nlstate;i++)  }
         gm[i] = prlim[i][i];  
   double hessij( double x[], double delti[], int thetai,int thetaj)
       for(i=1;i<=nlstate;i++)  {
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    int i;
     } /* End theta */    int l=1, l1, lmax=20;
     double k1,k2,k3,k4,res,fx;
     trgradg =matrix(1,nlstate,1,npar);    double p2[NPARMAX+1];
     int k;
     for(j=1; j<=nlstate;j++)  
       for(theta=1; theta <=npar; theta++)    fx=func(x);
         trgradg[j][theta]=gradg[theta][j];    for (k=1; k<=2; k++) {
       for (i=1;i<=npar;i++) p2[i]=x[i];
     for(i=1;i<=nlstate;i++)      p2[thetai]=x[thetai]+delti[thetai]/k;
       varpl[i][(int)age] =0.;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      k1=func(p2)-fx;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    
     for(i=1;i<=nlstate;i++)      p2[thetai]=x[thetai]+delti[thetai]/k;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k2=func(p2)-fx;
     fprintf(ficresvpl,"%.0f ",age );    
     for(i=1; i<=nlstate;i++)      p2[thetai]=x[thetai]-delti[thetai]/k;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     fprintf(ficresvpl,"\n");      k3=func(p2)-fx;
     free_vector(gp,1,nlstate);    
     free_vector(gm,1,nlstate);      p2[thetai]=x[thetai]-delti[thetai]/k;
     free_matrix(gradg,1,npar,1,nlstate);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     free_matrix(trgradg,1,nlstate,1,npar);      k4=func(p2)-fx;
   } /* End age */      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   #ifdef DEBUG
   free_vector(xp,1,npar);      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   free_matrix(doldm,1,nlstate,1,npar);      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);
   free_matrix(dnewm,1,nlstate,1,nlstate);  #endif
     }
 }    return res;
   }
   
   /************** Inverse of matrix **************/
 /***********************************************/  void ludcmp(double **a, int n, int *indx, double *d) 
 /**************** Main Program *****************/  { 
 /***********************************************/    int i,imax,j,k; 
     double big,dum,sum,temp; 
 /*int main(int argc, char *argv[])*/    double *vv; 
 int main()   
 {    vv=vector(1,n); 
     *d=1.0; 
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    for (i=1;i<=n;i++) { 
   double agedeb, agefin,hf;      big=0.0; 
   double agemin=1.e20, agemax=-1.e20;      for (j=1;j<=n;j++) 
         if ((temp=fabs(a[i][j])) > big) big=temp; 
   double fret;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   double **xi,tmp,delta;      vv[i]=1.0/big; 
     } 
   double dum; /* Dummy variable */    for (j=1;j<=n;j++) { 
   double ***p3mat;      for (i=1;i<j;i++) { 
   int *indx;        sum=a[i][j]; 
   char line[MAXLINE], linepar[MAXLINE];        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   char title[MAXLINE];        a[i][j]=sum; 
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];      } 
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];      big=0.0; 
   char filerest[FILENAMELENGTH];      for (i=j;i<=n;i++) { 
   char fileregp[FILENAMELENGTH];        sum=a[i][j]; 
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];        for (k=1;k<j;k++) 
   int firstobs=1, lastobs=10;          sum -= a[i][k]*a[k][j]; 
   int sdeb, sfin; /* Status at beginning and end */        a[i][j]=sum; 
   int c,  h , cpt,l;        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   int ju,jl, mi;          big=dum; 
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;          imax=i; 
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;        } 
        } 
   int hstepm, nhstepm;      if (j != imax) { 
   double bage, fage, age, agelim, agebase;        for (k=1;k<=n;k++) { 
   double ftolpl=FTOL;          dum=a[imax][k]; 
   double **prlim;          a[imax][k]=a[j][k]; 
   double *severity;          a[j][k]=dum; 
   double ***param; /* Matrix of parameters */        } 
   double  *p;        *d = -(*d); 
   double **matcov; /* Matrix of covariance */        vv[imax]=vv[j]; 
   double ***delti3; /* Scale */      } 
   double *delti; /* Scale */      indx[j]=imax; 
   double ***eij, ***vareij;      if (a[j][j] == 0.0) a[j][j]=TINY; 
   double **varpl; /* Variances of prevalence limits by age */      if (j != n) { 
   double *epj, vepp;        dum=1.0/(a[j][j]); 
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   char *alph[]={"a","a","b","c","d","e"}, str[4];      } 
     } 
   char z[1]="c", occ;    free_vector(vv,1,n);  /* Doesn't work */
 #include <sys/time.h>  ;
 #include <time.h>  } 
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  
   /* long total_usecs;  void lubksb(double **a, int n, int *indx, double b[]) 
   struct timeval start_time, end_time;  { 
      int i,ii=0,ip,j; 
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    double sum; 
    
     for (i=1;i<=n;i++) { 
   printf("\nIMACH, Version 0.64b");      ip=indx[i]; 
   printf("\nEnter the parameter file name: ");      sum=b[ip]; 
       b[ip]=b[i]; 
 #ifdef windows      if (ii) 
   scanf("%s",pathtot);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   getcwd(pathcd, size);      else if (sum) ii=i; 
   /*cygwin_split_path(pathtot,path,optionfile);      b[i]=sum; 
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    } 
   /* cutv(path,optionfile,pathtot,'\\');*/    for (i=n;i>=1;i--) { 
       sum=b[i]; 
 split(pathtot, path,optionfile);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   chdir(path);      b[i]=sum/a[i][i]; 
   replace(pathc,path);    } 
 #endif  } 
 #ifdef unix  
   scanf("%s",optionfile);  /************ Frequencies ********************/
 #endif  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint)
   {  /* Some frequencies */
 /*-------- arguments in the command line --------*/    
     int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   strcpy(fileres,"r");    int first;
   strcat(fileres, optionfile);    double ***freq; /* Frequencies */
     double *pp, **prop;
   /*---------arguments file --------*/    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     FILE *ficresp;
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    char fileresp[FILENAMELENGTH];
     printf("Problem with optionfile %s\n",optionfile);    
     goto end;    pp=vector(1,nlstate);
   }    prop=matrix(1,nlstate,iagemin,iagemax+3);
     strcpy(fileresp,"p");
   strcpy(filereso,"o");    strcat(fileresp,fileres);
   strcat(filereso,fileres);    if((ficresp=fopen(fileresp,"w"))==NULL) {
   if((ficparo=fopen(filereso,"w"))==NULL) {      printf("Problem with prevalence resultfile: %s\n", fileresp);
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   }      exit(0);
     }
   /* Reads comments: lines beginning with '#' */    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
   while((c=getc(ficpar))=='#' && c!= EOF){    j1=0;
     ungetc(c,ficpar);    
     fgets(line, MAXLINE, ficpar);    j=cptcoveff;
     puts(line);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     fputs(line,ficparo);  
   }    first=1;
   ungetc(c,ficpar);  
     for(k1=1; k1<=j;k1++){
   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);      for(i1=1; i1<=ncodemax[k1];i1++){
   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);        j1++;
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           scanf("%d", i);*/
   covar=matrix(0,NCOVMAX,1,n);        for (i=-1; i<=nlstate+ndeath; i++)  
   cptcovn=0;          for (jk=-1; jk<=nlstate+ndeath; jk++)  
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;            for(m=iagemin; m <= iagemax+3; m++)
               freq[i][jk][m]=0;
   ncovmodel=2+cptcovn;  
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      for (i=1; i<=nlstate; i++)  
          for(m=iagemin; m <= iagemax+3; m++)
   /* Read guess parameters */          prop[i][m]=0;
   /* Reads comments: lines beginning with '#' */        
   while((c=getc(ficpar))=='#' && c!= EOF){        dateintsum=0;
     ungetc(c,ficpar);        k2cpt=0;
     fgets(line, MAXLINE, ficpar);        for (i=1; i<=imx; i++) {
     puts(line);          bool=1;
     fputs(line,ficparo);          if  (cptcovn>0) {
   }            for (z1=1; z1<=cptcoveff; z1++) 
   ungetc(c,ficpar);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                  bool=0;
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          }
     for(i=1; i <=nlstate; i++)          if (bool==1){
     for(j=1; j <=nlstate+ndeath-1; j++){            for(m=firstpass; m<=lastpass; m++){
       fscanf(ficpar,"%1d%1d",&i1,&j1);              k2=anint[m][i]+(mint[m][i]/12.);
       fprintf(ficparo,"%1d%1d",i1,j1);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
       printf("%1d%1d",i,j);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       for(k=1; k<=ncovmodel;k++){                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         fscanf(ficpar," %lf",&param[i][j][k]);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
         printf(" %lf",param[i][j][k]);                if (m<lastpass) {
         fprintf(ficparo," %lf",param[i][j][k]);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
       }                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
       fscanf(ficpar,"\n");                }
       printf("\n");                
       fprintf(ficparo,"\n");                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
     }                  dateintsum=dateintsum+k2;
                    k2cpt++;
   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);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
     puts(line);  
     fputs(line,ficparo);        if  (cptcovn>0) {
   }          fprintf(ficresp, "\n#********** Variable "); 
   ungetc(c,ficpar);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresp, "**********\n#");
   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(i=1; i <=nlstate; i++){          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     for(j=1; j <=nlstate+ndeath-1; j++){        fprintf(ficresp, "\n");
       fscanf(ficpar,"%1d%1d",&i1,&j1);        
       printf("%1d%1d",i,j);        for(i=iagemin; i <= iagemax+3; i++){
       fprintf(ficparo,"%1d%1d",i1,j1);          if(i==iagemax+3){
       for(k=1; k<=ncovmodel;k++){            fprintf(ficlog,"Total");
         fscanf(ficpar,"%le",&delti3[i][j][k]);          }else{
         printf(" %le",delti3[i][j][k]);            if(first==1){
         fprintf(ficparo," %le",delti3[i][j][k]);              first=0;
       }              printf("See log file for details...\n");
       fscanf(ficpar,"\n");            }
       printf("\n");            fprintf(ficlog,"Age %d", i);
       fprintf(ficparo,"\n");          }
     }          for(jk=1; jk <=nlstate ; jk++){
   }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   delti=delti3[1][1];              pp[jk] += freq[jk][m][i]; 
            }
   /* Reads comments: lines beginning with '#' */          for(jk=1; jk <=nlstate ; jk++){
   while((c=getc(ficpar))=='#' && c!= EOF){            for(m=-1, pos=0; m <=0 ; m++)
     ungetc(c,ficpar);              pos += freq[jk][m][i];
     fgets(line, MAXLINE, ficpar);            if(pp[jk]>=1.e-10){
     puts(line);              if(first==1){
     fputs(line,ficparo);              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   }              }
   ungetc(c,ficpar);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
              }else{
   matcov=matrix(1,npar,1,npar);              if(first==1)
   for(i=1; i <=npar; i++){                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     fscanf(ficpar,"%s",&str);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     printf("%s",str);            }
     fprintf(ficparo,"%s",str);          }
     for(j=1; j <=i; j++){  
       fscanf(ficpar," %le",&matcov[i][j]);          for(jk=1; jk <=nlstate ; jk++){
       printf(" %.5le",matcov[i][j]);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
       fprintf(ficparo," %.5le",matcov[i][j]);              pp[jk] += freq[jk][m][i];
     }          }       
     fscanf(ficpar,"\n");          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
     printf("\n");            pos += pp[jk];
     fprintf(ficparo,"\n");            posprop += prop[jk][i];
   }          }
   for(i=1; i <=npar; i++)          for(jk=1; jk <=nlstate ; jk++){
     for(j=i+1;j<=npar;j++)            if(pos>=1.e-5){
       matcov[i][j]=matcov[j][i];              if(first==1)
                    printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   printf("\n");              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
             }else{
               if(first==1)
     /*-------- data file ----------*/                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     if((ficres =fopen(fileres,"w"))==NULL) {              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       printf("Problem with resultfile: %s\n", fileres);goto end;            }
     }            if( i <= iagemax){
     fprintf(ficres,"#%s\n",version);              if(pos>=1.e-5){
                    fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
     if((fic=fopen(datafile,"r"))==NULL)    {                /*probs[i][jk][j1]= pp[jk]/pos;*/
       printf("Problem with datafile: %s\n", datafile);goto end;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     }              }
               else
     n= lastobs;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     severity = vector(1,maxwav);            }
     outcome=imatrix(1,maxwav+1,1,n);          }
     num=ivector(1,n);          
     moisnais=vector(1,n);          for(jk=-1; jk <=nlstate+ndeath; jk++)
     annais=vector(1,n);            for(m=-1; m <=nlstate+ndeath; m++)
     moisdc=vector(1,n);              if(freq[jk][m][i] !=0 ) {
     andc=vector(1,n);              if(first==1)
     agedc=vector(1,n);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     cod=ivector(1,n);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     weight=vector(1,n);              }
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */          if(i <= iagemax)
     mint=matrix(1,maxwav,1,n);            fprintf(ficresp,"\n");
     anint=matrix(1,maxwav,1,n);          if(first==1)
     s=imatrix(1,maxwav+1,1,n);            printf("Others in log...\n");
     adl=imatrix(1,maxwav+1,1,n);              fprintf(ficlog,"\n");
     tab=ivector(1,NCOVMAX);        }
     ncodemax=ivector(1,8);      }
     }
     i=1;    dateintmean=dateintsum/k2cpt; 
     while (fgets(line, MAXLINE, fic) != NULL)    {   
       if ((i >= firstobs) && (i <=lastobs)) {    fclose(ficresp);
            free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
         for (j=maxwav;j>=1;j--){    free_vector(pp,1,nlstate);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
           strcpy(line,stra);    /* End of Freq */
           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);  
         }  /************ Prevalence ********************/
          void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);  {  
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
        in each health status at the date of interview (if between dateprev1 and dateprev2).
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);       We still use firstpass and lastpass as another selection.
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    */
    
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
         for (j=ncov;j>=1;j--){    double ***freq; /* Frequencies */
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    double *pp, **prop;
         }    double pos,posprop; 
         num[i]=atol(stra);    double  y2; /* in fractional years */
     int iagemin, iagemax;
         /*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]));*/  
     iagemin= (int) agemin;
         i=i+1;    iagemax= (int) agemax;
       }    /*pp=vector(1,nlstate);*/
     }    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     /*scanf("%d",i);*/    j1=0;
   imx=i-1; /* Number of individuals */    
     j=cptcoveff;
   /* Calculation of the number of parameter from char model*/    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   Tvar=ivector(1,15);    
   Tprod=ivector(1,15);    for(k1=1; k1<=j;k1++){
   Tvaraff=ivector(1,15);      for(i1=1; i1<=ncodemax[k1];i1++){
   Tvard=imatrix(1,15,1,2);        j1++;
   Tage=ivector(1,15);              
            for (i=1; i<=nlstate; i++)  
   if (strlen(model) >1){          for(m=iagemin; m <= iagemax+3; m++)
     j=0, j1=0, k1=1, k2=1;            prop[i][m]=0.0;
     j=nbocc(model,'+');       
     j1=nbocc(model,'*');        for (i=1; i<=imx; i++) { /* Each individual */
     cptcovn=j+1;          bool=1;
     cptcovprod=j1;          if  (cptcovn>0) {
                for (z1=1; z1<=cptcoveff; z1++) 
                  if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     strcpy(modelsav,model);                bool=0;
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){          } 
       printf("Error. Non available option model=%s ",model);          if (bool==1) { 
       goto end;            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     }              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
                  if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
     for(i=(j+1); i>=1;i--){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       cutv(stra,strb,modelsav,'+');                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/                if (s[m][i]>0 && s[m][i]<=nlstate) { 
       /*scanf("%d",i);*/                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
       if (strchr(strb,'*')) {                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
         cutv(strd,strc,strb,'*');                  prop[s[m][i]][iagemax+3] += weight[i]; 
         if (strcmp(strc,"age")==0) {                } 
           cptcovprod--;              }
           cutv(strb,stre,strd,'V');            } /* end selection of waves */
           Tvar[i]=atoi(stre);          }
           cptcovage++;        }
             Tage[cptcovage]=i;        for(i=iagemin; i <= iagemax+3; i++){  
             /*printf("stre=%s ", stre);*/          
         }          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
         else if (strcmp(strd,"age")==0) {            posprop += prop[jk][i]; 
           cptcovprod--;          } 
           cutv(strb,stre,strc,'V');  
           Tvar[i]=atoi(stre);          for(jk=1; jk <=nlstate ; jk++){     
           cptcovage++;            if( i <=  iagemax){ 
           Tage[cptcovage]=i;              if(posprop>=1.e-5){ 
         }                probs[i][jk][j1]= prop[jk][i]/posprop;
         else {              } 
           cutv(strb,stre,strc,'V');            } 
           Tvar[i]=ncov+k1;          }/* end jk */ 
           cutv(strb,strc,strd,'V');        }/* end i */ 
           Tprod[k1]=i;      } /* end i1 */
           Tvard[k1][1]=atoi(strc);    } /* end k1 */
           Tvard[k1][2]=atoi(stre);    
           Tvar[cptcovn+k2]=Tvard[k1][1];    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    /*free_vector(pp,1,nlstate);*/
           for (k=1; k<=lastobs;k++)    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];  }  /* End of prevalence */
           k1++;  
           k2=k2+2;  /************* Waves Concatenation ***************/
         }  
       }  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
       else {  {
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
        /*  scanf("%d",i);*/       Death is a valid wave (if date is known).
       cutv(strd,strc,strb,'V');       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
       Tvar[i]=atoi(strc);       dh[m][i] or 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.
       strcpy(modelsav,stra);         */
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);  
         scanf("%d",i);*/    int i, mi, m;
     }    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
 }       double sum=0., jmean=0.;*/
      int first;
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    int j, k=0,jk, ju, jl;
   printf("cptcovprod=%d ", cptcovprod);    double sum=0.;
   scanf("%d ",i);*/    first=0;
     fclose(fic);    jmin=1e+5;
     jmax=-1;
     /*  if(mle==1){*/    jmean=0.;
     if (weightopt != 1) { /* Maximisation without weights*/    for(i=1; i<=imx; i++){
       for(i=1;i<=n;i++) weight[i]=1.0;      mi=0;
     }      m=firstpass;
     /*-calculation of age at interview from date of interview and age at death -*/      while(s[m][i] <= nlstate){
     agev=matrix(1,maxwav,1,imx);        if(s[m][i]>=1)
              mw[++mi][i]=m;
     for (i=1; i<=imx; i++)  {        if(m >=lastpass)
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);          break;
       for(m=1; (m<= maxwav); m++){        else
         if(s[m][i] >0){          m++;
           if (s[m][i] == nlstate+1) {      }/* end while */
             if(agedc[i]>0)      if (s[m][i] > nlstate){
               if(moisdc[i]!=99 && andc[i]!=9999)        mi++;     /* Death is another wave */
               agev[m][i]=agedc[i];        /* if(mi==0)  never been interviewed correctly before death */
             else {           /* Only death is a correct wave */
               if (andc[i]!=9999){        mw[mi][i]=m;
               printf("Warning negative age at death: %d line:%d\n",num[i],i);      }
               agev[m][i]=-1;  
               }      wav[i]=mi;
             }      if(mi==0){
           }        if(first==0){
           else if(s[m][i] !=9){ /* Should no more exist */          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);          first=1;
             if(mint[m][i]==99 || anint[m][i]==9999)        }
               agev[m][i]=1;        if(first==1){
             else if(agev[m][i] <agemin){          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
               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);*/      } /* end mi==0 */
             }    } /* End individuals */
             else if(agev[m][i] >agemax){  
               agemax=agev[m][i];    for(i=1; i<=imx; i++){
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/      for(mi=1; mi<wav[i];mi++){
             }        if (stepm <=0)
             /*agev[m][i]=anint[m][i]-annais[i];*/          dh[mi][i]=1;
             /*   agev[m][i] = age[i]+2*m;*/        else{
           }          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
           else { /* =9 */            if (agedc[i] < 2*AGESUP) {
             agev[m][i]=1;              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
             s[m][i]=-1;              if(j==0) j=1;  /* Survives at least one month after exam */
           }              else if(j<0){
         }                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
         else /*= 0 Unknown */                j=1; /* Careful Patch */
           agev[m][i]=1;                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
       }                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                    fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
     }              }
     for (i=1; i<=imx; i++)  {              k=k+1;
       for(m=1; (m<= maxwav); m++){              if (j >= jmax) jmax=j;
         if (s[m][i] > (nlstate+ndeath)) {              if (j <= jmin) jmin=j;
           printf("Error: Wrong value in nlstate or ndeath\n");                sum=sum+j;
           goto end;              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
         }              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       }            }
     }          }
           else{
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
             /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     free_vector(severity,1,maxwav);            k=k+1;
     free_imatrix(outcome,1,maxwav+1,1,n);            if (j >= jmax) jmax=j;
     free_vector(moisnais,1,n);            else if (j <= jmin)jmin=j;
     free_vector(annais,1,n);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     free_matrix(mint,1,maxwav,1,n);            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
     free_matrix(anint,1,maxwav,1,n);            if(j<0){
     free_vector(moisdc,1,n);              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     free_vector(andc,1,n);              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             }
                sum=sum+j;
     wav=ivector(1,imx);          }
     dh=imatrix(1,lastpass-firstpass+1,1,imx);          jk= j/stepm;
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          jl= j -jk*stepm;
              ju= j -(jk+1)*stepm;
     /* Concatenates waves */          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);            if(jl==0){
               dh[mi][i]=jk;
               bh[mi][i]=0;
       Tcode=ivector(1,100);            }else{ /* We want a negative bias in order to only have interpolation ie
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);                    * at the price of an extra matrix product in likelihood */
       ncodemax[1]=1;              dh[mi][i]=jk+1;
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);              bh[mi][i]=ju;
                  }
    codtab=imatrix(1,100,1,10);          }else{
    h=0;            if(jl <= -ju){
    m=pow(2,cptcoveff);              dh[mi][i]=jk;
                bh[mi][i]=jl;       /* bias is positive if real duration
    for(k=1;k<=cptcoveff; k++){                                   * is higher than the multiple of stepm and negative otherwise.
      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++){            else{
            h++;              dh[mi][i]=jk+1;
            if (h>m) h=1;codtab[h][k]=j;              bh[mi][i]=ju;
          }            }
        }            if(dh[mi][i]==0){
      }              dh[mi][i]=1; /* At least one step */
    }              bh[mi][i]=ju; /* At least one step */
               /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
             }
    /*for(i=1; i <=m ;i++){          } /* end if mle */
      for(k=1; k <=cptcovn; k++){        }
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);      } /* end wave */
      }    }
      printf("\n");    jmean=sum/k;
    }    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
    scanf("%d",i);*/    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
       }
    /* Calculates basic frequencies. Computes observed prevalence at single age  
        and prints on file fileres'p'. */  /*********** Tricode ****************************/
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);  void tricode(int *Tvar, int **nbcode, int imx)
   {
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int Ndum[20],ij=1, k, j, i, maxncov=19;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int cptcode=0;
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    cptcoveff=0; 
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */   
        for (k=0; k<maxncov; k++) Ndum[k]=0;
     /* For Powell, parameters are in a vector p[] starting at p[1]    for (k=1; k<=7; k++) ncodemax[k]=0;
        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) */    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
       for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
     if(mle==1){                                 modality*/ 
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
     }        Ndum[ij]++; /*store the modality */
            /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
     /*--------- results files --------------*/        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
     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);                                         Tvar[j]. If V=sex and male is 0 and 
                                             female is 1, then  cptcode=1.*/
    jk=1;      }
    fprintf(ficres,"# Parameters\n");  
    printf("# Parameters\n");      for (i=0; i<=cptcode; i++) {
    for(i=1,jk=1; i <=nlstate; i++){        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
      for(k=1; k <=(nlstate+ndeath); k++){      }
        if (k != i)  
          {      ij=1; 
            printf("%d%d ",i,k);      for (i=1; i<=ncodemax[j]; i++) {
            fprintf(ficres,"%1d%1d ",i,k);        for (k=0; k<= maxncov; k++) {
            for(j=1; j <=ncovmodel; j++){          if (Ndum[k] != 0) {
              printf("%f ",p[jk]);            nbcode[Tvar[j]][ij]=k; 
              fprintf(ficres,"%f ",p[jk]);            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
              jk++;            
            }            ij++;
            printf("\n");          }
            fprintf(ficres,"\n");          if (ij > ncodemax[j]) break; 
          }        }  
      }      } 
    }    }  
  if(mle==1){  
     /* Computing hessian and covariance matrix */   for (k=0; k< maxncov; k++) Ndum[k]=0;
     ftolhess=ftol; /* Usually correct */  
     hesscov(matcov, p, npar, delti, ftolhess, func);   for (i=1; i<=ncovmodel-2; i++) { 
  }     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     fprintf(ficres,"# Scales\n");     ij=Tvar[i];
     printf("# Scales\n");     Ndum[ij]++;
      for(i=1,jk=1; i <=nlstate; i++){   }
       for(j=1; j <=nlstate+ndeath; j++){  
         if (j!=i) {   ij=1;
           fprintf(ficres,"%1d%1d",i,j);   for (i=1; i<= maxncov; i++) {
           printf("%1d%1d",i,j);     if((Ndum[i]!=0) && (i<=ncovcol)){
           for(k=1; k<=ncovmodel;k++){       Tvaraff[ij]=i; /*For printing */
             printf(" %.5e",delti[jk]);       ij++;
             fprintf(ficres," %.5e",delti[jk]);     }
             jk++;   }
           }   
           printf("\n");   cptcoveff=ij-1; /*Number of simple covariates*/
           fprintf(ficres,"\n");  }
         }  
       }  /*********** Health Expectancies ****************/
       }  
      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 )
     k=1;  
     fprintf(ficres,"# Covariance\n");  {
     printf("# Covariance\n");    /* Health expectancies */
     for(i=1;i<=npar;i++){    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
       /*  if (k>nlstate) k=1;    double age, agelim, hf;
       i1=(i-1)/(ncovmodel*nlstate)+1;    double ***p3mat,***varhe;
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    double **dnewm,**doldm;
       printf("%s%d%d",alph[k],i1,tab[i]);*/    double *xp;
       fprintf(ficres,"%3d",i);    double **gp, **gm;
       printf("%3d",i);    double ***gradg, ***trgradg;
       for(j=1; j<=i;j++){    int theta;
         fprintf(ficres," %.5e",matcov[i][j]);  
         printf(" %.5e",matcov[i][j]);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
       }    xp=vector(1,npar);
       fprintf(ficres,"\n");    dnewm=matrix(1,nlstate*nlstate,1,npar);
       printf("\n");    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
       k++;    
     }    fprintf(ficreseij,"# Health expectancies\n");
        fprintf(ficreseij,"# Age");
     while((c=getc(ficpar))=='#' && c!= EOF){    for(i=1; i<=nlstate;i++)
       ungetc(c,ficpar);      for(j=1; j<=nlstate;j++)
       fgets(line, MAXLINE, ficpar);        fprintf(ficreseij," %1d-%1d (SE)",i,j);
       puts(line);    fprintf(ficreseij,"\n");
       fputs(line,ficparo);  
     }    if(estepm < stepm){
     ungetc(c,ficpar);      printf ("Problem %d lower than %d\n",estepm, stepm);
      }
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    else  hstepm=estepm;   
        /* We compute the life expectancy from trapezoids spaced every estepm months
     if (fage <= 2) {     * This is mainly to measure the difference between two models: for example
       bage = agemin;     * if stepm=24 months pijx are given only every 2 years and by summing them
       fage = agemax;     * we are calculating an estimate of the Life Expectancy assuming a linear 
     }     * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");     * estimate the model with stepm=1 month, we can keep estepm to 24 months
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);     * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
         * curvature will be obtained if estepm is as small as stepm. */
 /*------------ gnuplot -------------*/  
 chdir(pathcd);    /* For example we decided to compute the life expectancy with the smallest unit */
   if((ficgp=fopen("graph.plt","w"))==NULL) {    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     printf("Problem with file graph.gp");goto end;       nhstepm is the number of hstepm from age to agelim 
   }       nstepm is the number of stepm from age to agelin. 
 #ifdef windows       Look at hpijx to understand the reason of that which relies in memory size
   fprintf(ficgp,"cd \"%s\" \n",pathc);       and note for a fixed period like estepm months */
 #endif    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 m=pow(2,cptcoveff);       survival function given by stepm (the optimization length). Unfortunately it
         means that if the survival funtion is printed only each two years of age and if
  /* 1eme*/       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   for (cpt=1; cpt<= nlstate ; cpt ++) {       results. So we changed our mind and took the option of the best precision.
    for (k1=1; k1<= m ; k1 ++) {    */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
 #ifdef windows  
     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);    agelim=AGESUP;
 #endif    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 #ifdef unix      /* nhstepm age range expressed in number of stepm */
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
 #endif      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
       /* if (stepm >= YEARM) hstepm=1;*/
 for (i=1; i<= nlstate ; i ++) {      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
 }      gp=matrix(0,nhstepm,1,nlstate*nlstate);
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);      gm=matrix(0,nhstepm,1,nlstate*nlstate);
     for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   else fprintf(ficgp," \%%*lf (\%%*lf)");         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
 }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);   
      for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }        /* Computing Variances of health expectancies */
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));  
 #ifdef unix       for(theta=1; theta <=npar; theta++){
 fprintf(ficgp,"\nset ter gif small size 400,300");        for(i=1; i<=npar; i++){ 
 #endif          xp[i] = x[i] + (i==theta ?delti[theta]:0);
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        }
    }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   }    
   /*2 eme*/        cptj=0;
         for(j=1; j<= nlstate; j++){
   for (k1=1; k1<= m ; k1 ++) {          for(i=1; i<=nlstate; i++){
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);            cptj=cptj+1;
                for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
     for (i=1; i<= nlstate+1 ; i ++) {              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
       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)");       
 }          for(i=1; i<=npar; i++) 
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     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 ++) {        cptj=0;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        for(j=1; j<= nlstate; j++){
         else fprintf(ficgp," \%%*lf (\%%*lf)");          for(i=1;i<=nlstate;i++){
 }              cptj=cptj+1;
       fprintf(ficgp,"\" t\"\" w l 0,");            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
      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 ++) {              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            }
   else fprintf(ficgp," \%%*lf (\%%*lf)");          }
 }          }
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        for(j=1; j<= nlstate*nlstate; j++)
       else fprintf(ficgp,"\" t\"\" w l 0,");          for(h=0; h<=nhstepm-1; h++){
     }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);          }
   }       } 
       
   /*3eme*/  /* End theta */
   
   for (k1=1; k1<= m ; k1 ++) {       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     for (cpt=1; cpt<= nlstate ; cpt ++) {  
       k=2+nlstate*(cpt-1);       for(h=0; h<=nhstepm-1; h++)
       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(j=1; j<=nlstate*nlstate;j++)
       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);            trgradg[h][j][theta]=gradg[h][theta][j];
       }       
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
     }       for(i=1;i<=nlstate*nlstate;i++)
   }        for(j=1;j<=nlstate*nlstate;j++)
            varhe[i][j][(int)age] =0.;
   /* CV preval stat */  
   for (k1=1; k1<= m ; k1 ++) {       printf("%d|",(int)age);fflush(stdout);
     for (cpt=1; cpt<nlstate ; cpt ++) {       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       k=3;       for(h=0;h<=nhstepm-1;h++){
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);        for(k=0;k<=nhstepm-1;k++){
       for (i=1; i< nlstate ; i ++)          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
         fprintf(ficgp,"+$%d",k+i+1);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);          for(i=1;i<=nlstate*nlstate;i++)
                  for(j=1;j<=nlstate*nlstate;j++)
       l=3+(nlstate+ndeath)*cpt;              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        }
       for (i=1; i< nlstate ; i ++) {      }
         l=3+(nlstate+ndeath)*cpt;      /* Computing expectancies */
         fprintf(ficgp,"+$%d",l+i+1);      for(i=1; i<=nlstate;i++)
       }        for(j=1; j<=nlstate;j++)
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     }            
   }  /* 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]);*/
   
   /* proba elementaires */          }
    for(i=1,jk=1; i <=nlstate; i++){  
     for(k=1; k <=(nlstate+ndeath); k++){      fprintf(ficreseij,"%3.0f",age );
       if (k != i) {      cptj=0;
         for(j=1; j <=ncovmodel; j++){      for(i=1; i<=nlstate;i++)
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/        for(j=1; j<=nlstate;j++){
           /*fprintf(ficgp,"%s",alph[1]);*/          cptj++;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
           jk++;        }
           fprintf(ficgp,"\n");      fprintf(ficreseij,"\n");
         }     
       }      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     }      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   for(jk=1; jk <=m; jk++) {      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    }
    i=1;    printf("\n");
    for(k2=1; k2<=nlstate; k2++) {    fprintf(ficlog,"\n");
      k3=i;  
      for(k=1; k<=(nlstate+ndeath); k++) {    free_vector(xp,1,npar);
        if (k != k2){    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
 ij=1;    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
         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]]]);  /************ Variance ******************/
             ij++;  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)
           }  {
           else    /* Variance of health expectancies */
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
         }    /* double **newm;*/
           fprintf(ficgp,")/(1");    double **dnewm,**doldm;
            double **dnewmp,**doldmp;
         for(k1=1; k1 <=nlstate; k1++){      int i, j, nhstepm, hstepm, h, nstepm ;
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    int k, cptcode;
 ij=1;    double *xp;
           for(j=3; j <=ncovmodel; j++){    double **gp, **gm;  /* for var eij */
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    double ***gradg, ***trgradg; /*for var eij */
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    double **gradgp, **trgradgp; /* for var p point j */
             ij++;    double *gpp, *gmp; /* for var p point j */
           }    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
           else    double ***p3mat;
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    double age,agelim, hf;
           }    double ***mobaverage;
           fprintf(ficgp,")");    int theta;
         }    char digit[4];
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    char digitp[25];
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");  
         i=i+ncovmodel;    char fileresprobmorprev[FILENAMELENGTH];
        }  
      }    if(popbased==1){
    }      if(mobilav!=0)
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);        strcpy(digitp,"-populbased-mobilav-");
   }      else strcpy(digitp,"-populbased-nomobil-");
        }
   fclose(ficgp);    else 
          strcpy(digitp,"-stablbased-");
 chdir(path);  
     free_matrix(agev,1,maxwav,1,imx);    if (mobilav!=0) {
     free_ivector(wav,1,imx);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
            printf(" Error in movingaverage mobilav=%d\n",mobilav);
     free_imatrix(s,1,maxwav+1,1,n);      }
        }
      
     free_ivector(num,1,n);    strcpy(fileresprobmorprev,"prmorprev"); 
     free_vector(agedc,1,n);    sprintf(digit,"%-d",ij);
     free_vector(weight,1,n);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     fclose(ficparo);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     fclose(ficres);    strcat(fileresprobmorprev,fileres);
     /*  }*/    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
          printf("Problem with resultfile: %s\n", fileresprobmorprev);
    /*________fin mle=1_________*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
        }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
      fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     /* No more information from the sample is required now */    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
   /* Reads comments: lines beginning with '#' */    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   while((c=getc(ficpar))=='#' && c!= EOF){    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     ungetc(c,ficpar);      fprintf(ficresprobmorprev," p.%-d SE",j);
     fgets(line, MAXLINE, ficpar);      for(i=1; i<=nlstate;i++)
     puts(line);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     fputs(line,ficparo);    }  
   }    fprintf(ficresprobmorprev,"\n");
   ungetc(c,ficpar);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
        printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);      exit(0);
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    }
 /*--------- index.htm --------*/    else{
       fprintf(ficgp,"\n# Routine varevsij");
   strcpy(optionfilehtm,optionfile);    }
   strcat(optionfilehtm,".htm");  /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL) { */
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {  /*     printf("Problem with html file: %s\n", optionfilehtm); */
     printf("Problem with %s \n",optionfilehtm);goto end;  /*     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm); */
   }  /*     exit(0); */
   /*   } */
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.64b </font> <hr size=\"2\" color=\"#EC5E5E\">  /*   else{ */
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
 Total number of observations=%d <br>    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>  /*   } */
 <hr  size=\"2\" color=\"#EC5E5E\">    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
 <li>Outputs files<br><br>\n  
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>    fprintf(ficresvij,"# Age");
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>    for(i=1; i<=nlstate;i++)
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>      for(j=1; j<=nlstate;j++)
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>    fprintf(ficresvij,"\n");
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>  
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    xp=vector(1,npar);
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);    dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
  fprintf(fichtm," <li>Graphs</li><p>");    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
  m=cptcoveff;  
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
  j1=0;    gmp=vector(nlstate+1,nlstate+ndeath);
  for(k1=1; k1<=m;k1++){    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
    for(i1=1; i1<=ncodemax[k1];i1++){    
        j1++;    if(estepm < stepm){
        if (cptcovn > 0) {      printf ("Problem %d lower than %d\n",estepm, stepm);
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    }
          for (cpt=1; cpt<=cptcoveff;cpt++)    else  hstepm=estepm;   
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);    /* For example we decided to compute the life expectancy with the smallest unit */
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    /* 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 
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>       nstepm is the number of stepm from age to agelin. 
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);           Look at hpijx to understand the reason of that which relies in memory size
        for(cpt=1; cpt<nlstate;cpt++){       and note for a fixed period like k years */
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);       survival function given by stepm (the optimization length). Unfortunately it
        }       means that if the survival funtion is printed every two years of age and if
     for(cpt=1; cpt<=nlstate;cpt++) {       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident       results. So we changed our mind and took the option of the best precision.
 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);      hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
      }    agelim = AGESUP;
      for(cpt=1; cpt<=nlstate;cpt++) {    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
      }      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
 health expectancies in states (1) and (2): e%s%d.gif<br>      gp=matrix(0,nhstepm,1,nlstate);
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);      gm=matrix(0,nhstepm,1,nlstate);
 fprintf(fichtm,"\n</body>");  
    }  
  }      for(theta=1; theta <=npar; theta++){
 fclose(fichtm);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
   /*--------------- Prevalence limit --------------*/        }
          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   strcpy(filerespl,"pl");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   strcat(filerespl,fileres);  
   if((ficrespl=fopen(filerespl,"w"))==NULL) {        if (popbased==1) {
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;          if(mobilav ==0){
   }            for(i=1; i<=nlstate;i++)
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);              prlim[i][i]=probs[(int)age][i][ij];
   fprintf(ficrespl,"#Prevalence limit\n");          }else{ /* mobilav */ 
   fprintf(ficrespl,"#Age ");            for(i=1; i<=nlstate;i++)
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);              prlim[i][i]=mobaverage[(int)age][i][ij];
   fprintf(ficrespl,"\n");          }
          }
   prlim=matrix(1,nlstate,1,nlstate);    
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(j=1; j<= nlstate; j++){
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for(h=0; h<=nhstepm; h++){
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          }
   k=0;        }
   agebase=agemin;        /* This for computing probability of death (h=1 means
   agelim=agemax;           computed over hstepm matrices product = hstepm*stepm months) 
   ftolpl=1.e-10;           as a weighted average of prlim.
   i1=cptcoveff;        */
   if (cptcovn < 1){i1=1;}        for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
   for(cptcov=1;cptcov<=i1;cptcov++){            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        }    
         k=k+1;        /* end probability of death */
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/  
         fprintf(ficrespl,"\n#******");        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
         for(j=1;j<=cptcoveff;j++)          xp[i] = x[i] - (i==theta ?delti[theta]:0);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         fprintf(ficrespl,"******\n");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           
         for (age=agebase; age<=agelim; age++){        if (popbased==1) {
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);          if(mobilav ==0){
           fprintf(ficrespl,"%.0f",age );            for(i=1; i<=nlstate;i++)
           for(i=1; i<=nlstate;i++)              prlim[i][i]=probs[(int)age][i][ij];
           fprintf(ficrespl," %.5f", prlim[i][i]);          }else{ /* mobilav */ 
           fprintf(ficrespl,"\n");            for(i=1; i<=nlstate;i++)
         }              prlim[i][i]=mobaverage[(int)age][i][ij];
       }          }
     }        }
   fclose(ficrespl);  
   /*------------- h Pij x at various ages ------------*/        for(j=1; j<= nlstate; j++){
            for(h=0; h<=nhstepm; h++){
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   if((ficrespij=fopen(filerespij,"w"))==NULL) {              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;          }
   }        }
   printf("Computing pij: result on file '%s' \n", filerespij);        /* This for computing probability of death (h=1 means
             computed over hstepm matrices product = hstepm*stepm months) 
   stepsize=(int) (stepm+YEARM-1)/YEARM;           as a weighted average of prlim.
   if (stepm<=24) stepsize=2;        */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
   agelim=AGESUP;          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   hstepm=stepsize*YEARM; /* Every year of age */           gmp[j] += prlim[i][i]*p3mat[i][j][1];
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */        }    
          /* end probability of death */
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){        for(j=1; j<= nlstate; j++) /* vareij */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          for(h=0; h<=nhstepm; h++){
       k=k+1;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
         fprintf(ficrespij,"\n#****** ");          }
         for(j=1;j<=cptcoveff;j++)  
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
         fprintf(ficrespij,"******\n");          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
                }
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      } /* End theta */
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        for(h=0; h<=nhstepm; h++) /* veij */
           fprintf(ficrespij,"# Age");        for(j=1; j<=nlstate;j++)
           for(i=1; i<=nlstate;i++)          for(theta=1; theta <=npar; theta++)
             for(j=1; j<=nlstate+ndeath;j++)            trgradg[h][j][theta]=gradg[h][theta][j];
               fprintf(ficrespij," %1d-%1d",i,j);  
           fprintf(ficrespij,"\n");      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
           for (h=0; h<=nhstepm; h++){        for(theta=1; theta <=npar; theta++)
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );          trgradgp[j][theta]=gradgp[theta][j];
             for(i=1; i<=nlstate;i++)    
               for(j=1; j<=nlstate+ndeath;j++)  
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
             fprintf(ficrespij,"\n");      for(i=1;i<=nlstate;i++)
           }        for(j=1;j<=nlstate;j++)
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          vareij[i][j][(int)age] =0.;
           fprintf(ficrespij,"\n");  
         }      for(h=0;h<=nhstepm;h++){
     }        for(k=0;k<=nhstepm;k++){
   }          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   fclose(ficrespij);          for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
   /*---------- Health expectancies and variances ------------*/              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
   strcpy(filerest,"t");      }
   strcat(filerest,fileres);    
   if((ficrest=fopen(filerest,"w"))==NULL) {      /* pptj */
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   }      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
   strcpy(filerese,"e");      /* end ppptj */
   strcat(filerese,fileres);      /*  x centered again */
   if((ficreseij=fopen(filerese,"w"))==NULL) {      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   }   
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      if (popbased==1) {
         if(mobilav ==0){
  strcpy(fileresv,"v");          for(i=1; i<=nlstate;i++)
   strcat(fileresv,fileres);            prlim[i][i]=probs[(int)age][i][ij];
   if((ficresvij=fopen(fileresv,"w"))==NULL) {        }else{ /* mobilav */ 
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);          for(i=1; i<=nlstate;i++)
   }            prlim[i][i]=mobaverage[(int)age][i][ij];
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);        }
       }
   k=0;               
   for(cptcov=1;cptcov<=i1;cptcov++){      /* This for computing probability of death (h=1 means
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
       k=k+1;         as a weighted average of prlim.
       fprintf(ficrest,"\n#****** ");      */
       for(j=1;j<=cptcoveff;j++)      for(j=nlstate+1;j<=nlstate+ndeath;j++){
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
       fprintf(ficrest,"******\n");          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       fprintf(ficreseij,"\n#****** ");      /* end probability of death */
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       fprintf(ficreseij,"******\n");      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
       fprintf(ficresvij,"\n#****** ");        for(i=1; i<=nlstate;i++){
       for(j=1;j<=cptcoveff;j++)          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);        }
       fprintf(ficresvij,"******\n");      } 
       fprintf(ficresprobmorprev,"\n");
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;      fprintf(ficresvij,"%.0f ",age );
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);        for(i=1; i<=nlstate;i++)
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        for(j=1; j<=nlstate;j++){
       oldm=oldms;savm=savms;          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        }
            fprintf(ficresvij,"\n");
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      free_matrix(gp,0,nhstepm,1,nlstate);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      free_matrix(gm,0,nhstepm,1,nlstate);
       fprintf(ficrest,"\n");      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
              free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       hf=1;      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       if (stepm >= YEARM) hf=stepm/YEARM;    } /* End age */
       epj=vector(1,nlstate+1);    free_vector(gpp,nlstate+1,nlstate+ndeath);
       for(age=bage; age <=fage ;age++){    free_vector(gmp,nlstate+1,nlstate+ndeath);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
         fprintf(ficrest," %.0f",age);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
           }  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
           epj[nlstate+1] +=epj[j];  /*   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); */
         for(i=1, vepp=0.;i <=nlstate;i++)    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
           for(j=1;j <=nlstate;j++)    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
             vepp += vareij[i][j][(int)age];    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
         for(j=1;j <=nlstate;j++){    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
         }  */
         fprintf(ficrest,"\n");    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
       }  
     }    free_vector(xp,1,npar);
   }    free_matrix(doldm,1,nlstate,1,nlstate);
            free_matrix(dnewm,1,nlstate,1,npar);
  fclose(ficreseij);    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
  fclose(ficresvij);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   fclose(ficrest);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   fclose(ficpar);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   free_vector(epj,1,nlstate+1);    fclose(ficresprobmorprev);
   /*  scanf("%d ",i); */    fclose(ficgp);
   /*   fclose(fichtm); */
   /*------- Variance limit prevalence------*/    }  /* end varevsij */
   
 strcpy(fileresvpl,"vpl");  /************ Variance of prevlim ******************/
   strcat(fileresvpl,fileres);  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((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  {
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    /* Variance of prevalence limit */
     exit(0);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   }    double **newm;
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
  k=0;    int k, cptcode;
  for(cptcov=1;cptcov<=i1;cptcov++){    double *xp;
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    double *gp, *gm;
      k=k+1;    double **gradg, **trgradg;
      fprintf(ficresvpl,"\n#****** ");    double age,agelim;
      for(j=1;j<=cptcoveff;j++)    int theta;
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);     
      fprintf(ficresvpl,"******\n");    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
          fprintf(ficresvpl,"# Age");
      varpl=matrix(1,nlstate,(int) bage, (int) fage);    for(i=1; i<=nlstate;i++)
      oldm=oldms;savm=savms;        fprintf(ficresvpl," %1d-%1d",i,i);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    fprintf(ficresvpl,"\n");
    }  
  }    xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
   fclose(ficresvpl);    doldm=matrix(1,nlstate,1,nlstate);
     
   /*---------- End : free ----------------*/    hstepm=1*YEARM; /* Every year of age */
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
      agelim = AGESUP;
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
        if (stepm >= YEARM) hstepm=1;
        nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      gradg=matrix(1,npar,1,nlstate);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);      gp=vector(1,nlstate);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);      gm=vector(1,nlstate);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);  
        for(theta=1; theta <=npar; theta++){
   free_matrix(matcov,1,npar,1,npar);        for(i=1; i<=npar; i++){ /* Computes gradient */
   free_vector(delti,1,npar);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
          }
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
   printf("End of Imach\n");          gp[i] = prlim[i][i];
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      
          for(i=1; i<=npar; i++) /* Computes gradient */
   /* 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);*/          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   /*printf("Total time was %d uSec.\n", total_usecs);*/        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   /*------ End -----------*/        for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
  end:  
 #ifdef windows        for(i=1;i<=nlstate;i++)
  chdir(pathcd);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
 #endif      } /* End theta */
  /*system("wgnuplot graph.plt");*/  
  /*system("../gp37mgw/wgnuplot graph.plt");*/      trgradg =matrix(1,nlstate,1,npar);
  /*system("cd ../gp37mgw");*/  
  system("..\\gp37mgw\\wgnuplot graph.plt");      for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
 #ifdef windows          trgradg[j][theta]=gradg[theta][j];
   while (z[0] != 'q') {  
     chdir(pathcd);      for(i=1;i<=nlstate;i++)
     printf("\nType e to edit output files, c to start again, and q for exiting: ");        varpl[i][(int)age] =0.;
     scanf("%s",z);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
     if (z[0] == 'c') system("./imach");      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
     else if (z[0] == 'e') {      for(i=1;i<=nlstate;i++)
       chdir(path);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
       system(optionfilehtm);  
     }      fprintf(ficresvpl,"%.0f ",age );
     else if (z[0] == 'q') exit(0);      for(i=1; i<=nlstate;i++)
   }        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
 #endif      fprintf(ficresvpl,"\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 */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
   {
     int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
     int k=0,l, cptcode;
     int first=1, first1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age,agelim, cov[NCOVMAX];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
   
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcov,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
    xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
       fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
       exit(0);
     }
     else{
       fprintf(ficgp,"\n# Routine varprob");
     }
   /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL) { */
   /*     printf("Problem with html file: %s\n", optionfilehtm); */
   /*     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm); */
   /*     exit(0); */
   /*   } */
   /*   else{ */
       fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
       fprintf(fichtm,"\n");
   
       fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
       fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
       fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
   
   /*   } */
   
     cov[1]=1;
     tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
         j1++;
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
           
           fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
             cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
   
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nset noparametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     }
                     fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                     /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
                       fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
                       fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtm," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fclose(ficgp);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
     /*char optionfilehtm[FILENAMELENGTH];*/
   /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    { */
   /*     printf("Problem with %s \n",optionfilehtm), exit(0); */
   /*     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
   /*   } */
   
      fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n \
    - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n \
    - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n \
    - Life expectancies by age and initial health status (estepm=%2d months): \
      <a href=\"e%s\">e%s</a> <br>\n</li>", \
     jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: pe%s%d1.png<br> \
   <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br> \
   <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
          /* Stable prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
   <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br> \
   <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2): e%s%d.png<br>\
   <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
    - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n\
    - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n\
    - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n\
    - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n\
    - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n\
    - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
   interval) in state (%d): v%s%d%d.png <br>\
   <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
     if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
       fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
     }
   
     /*#ifdef windows */
       fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   m=pow(2,cptcoveff);
     
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
         fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
           
         } 
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fclose(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int jj;
     int numlinepar=0; /* Current linenumber of parameter file */
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[132],pathc[132],pathcd[132],pathtot[132],model[132];
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   
     char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char *strt, *strtend;
     char *stratrunc;
     int lstra;
   
     long total_usecs;
     struct timeval start_time, end_time, curr_time;
     struct timezone tzp;
     extern int gettimeofday();
     struct tm tmg, tm, *gmtime(), *localtime();
     long time_value;
     extern long time();
    
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strt=asctime(&tm);
   
   /*  printf("Localtime (at start)=%s",strt); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strt);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strt=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strt); 
   */
   
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, 132)!= 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,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%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\n%s",version,fullversion);
     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);
   
     printf("Localtime (at start)=%s",strt);
     fprintf(ficlog,"Localtime (at start)=%s",strt);
     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);
       fflush(ficlog);
       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);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     
     /* Read guess parameters */
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++){
       j=0;
       for(jj=1; jj <=nlstate+ndeath; jj++){
         if(jj==i) continue;
         j++;
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1 != i) && (j1 != j)){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);
         }
         fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)
           printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);
           if(mle==1){
             printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);
           }
           else
             fprintf(ficlog," %lf",param[i][j][k]);
           fprintf(ficparo," %lf",param[i][j][k]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     }  
     fflush(ficlog);
   
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     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);
         if ((i1-i)*(j1-j)!=0){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);
         }
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         fprintf(ficlog,"%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]);
           fprintf(ficlog," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
         fprintf(ficlog,"\n");
       }
     }
     fflush(ficlog);
   
     delti=delti3[1][1];
   
   
     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     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]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       numlinepar++;
       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");
   
     fflush(ficlog);
   
     /*-------- 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=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         lstra=strlen(stra);
         if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
           stratrunc = &(stra[lstra-9]);
           num[i]=atol(stratrunc);
         }
         else
           num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* 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("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ 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);
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt,\
             model,fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strt);
     /*fclose(fichtm);*/
     fflush(fichtm);
   
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
   
   /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL) { */
   /*     printf("Problem with file: %s\n", optionfilehtm); */
   /*     fprintf(ficlog,"Problem with file: %s\n", optionfilehtm); */
   /*   } */
   
   
   /*   if(fileappend(fichtm, optionfilehtm)){ */
       fprintf(fichtm,"\n");
       fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
           imx,agemin,agemax,jmin,jmax,jmean);
   /*     fclose(fichtm); */
   /*   } */
   
       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) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);
     printf("\n");
     globpr=1; /* to print the contributions */
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);
     printf("\n");
     if(mle>=1){ /* Could be 1 or 2 */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
       
     /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
     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!=0){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);
             jk++;
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle==1)
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
           i1=(i-1)/(ncovmodel*nlstate)+1; 
           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
           printf("%s%d%d",alph[k],i1,tab[i]);
       */
       fprintf(ficres,"%3d",i);
       if(mle==1)
         printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   
     printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     chdir(path);
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_lvector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
   /*      }  */
   /*      else{ */
   /*        erreur=108; */
   /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*      } */
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     /*  fclose(fichtm);*/
     /*  fclose(ficgp);*/ /* ALready done */
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strtend=asctime(&tm);
     printf("Localtime at start %s and at end=%s",strt, strtend); 
     fprintf(ficlog,"Localtime at start %s and at end=%s",strt, strtend); 
     /*  printf("Total time used %d Sec\n", asc_time(end_time.tv_sec -start_time.tv_sec);*/
   
     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);
     fprintf(ficlog,"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);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Localtime at start %s and at end=%s<br>",strt, strtend);
     fclose(fichtm);
     /*------ End -----------*/
   
     end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
    /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     system(plotcmd);
     printf(" Wait...");
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   

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changed lines
  Added in v.1.87


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