Diff for /imach/src/imach.c between versions 1.17 and 1.89

version 1.17, 2002/02/20 17:15:02 version 1.89, 2003/06/24 12:30:52
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 1.89  2003/06/24 12:30:52  brouard
   individuals from different ages are interviewed on their health status    (Module): Some bugs corrected for windows. Also, when
   or degree of  disability. At least a second wave of interviews    mle=-1 a template is output in file "or"mypar.txt with the design
   ("longitudinal") should  measure each new individual health status.    of the covariance matrix to be input.
   Health expectancies are computed from the transistions observed between  
   waves and are computed for each degree of severity of disability (number    Revision 1.88  2003/06/23 17:54:56  brouard
   of life states). More degrees you consider, more time is necessary to    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
   reach the Maximum Likelihood of the parameters involved in the model.  
   The simplest model is the multinomial logistic model where pij is    Revision 1.87  2003/06/18 12:26:01  brouard
   the probabibility to be observed in state j at the second wave conditional    Version 0.96
   to be observed in state i at the first wave. Therefore the model is:  
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    Revision 1.86  2003/06/17 20:04:08  brouard
   is a covariate. If you want to have a more complex model than "constant and    (Module): Change position of html and gnuplot routines and added
   age", you should modify the program where the markup    routine fileappend.
     *Covariates have to be included here again* invites you to do it.  
   More covariates you add, less is the speed of the convergence.    Revision 1.85  2003/06/17 13:12:43  brouard
     * imach.c (Repository): Check when date of death was earlier that
   The advantage that this computer programme claims, comes from that if the    current date of interview. It may happen when the death was just
   delay between waves is not identical for each individual, or if some    prior to the death. In this case, dh was negative and likelihood
   individual missed an interview, the information is not rounded or lost, but    was wrong (infinity). We still send an "Error" but patch by
   taken into account using an interpolation or extrapolation.    assuming that the date of death was just one stepm after the
   hPijx is the probability to be    interview.
   observed in state i at age x+h conditional to the observed state i at age    (Repository): Because some people have very long ID (first column)
   x. The delay 'h' can be split into an exact number (nh*stepm) of    we changed int to long in num[] and we added a new lvector for
   unobserved intermediate  states. This elementary transition (by month or    memory allocation. But we also truncated to 8 characters (left
   quarter trimester, semester or year) is model as a multinomial logistic.    truncation)
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    (Repository): No more line truncation errors.
   and the contribution of each individual to the likelihood is simply hPijx.  
     Revision 1.84  2003/06/13 21:44:43  brouard
   Also this programme outputs the covariance matrix of the parameters but also    * imach.c (Repository): Replace "freqsummary" at a correct
   of the life expectancies. It also computes the prevalence limits.    place. It differs from routine "prevalence" which may be called
      many times. Probs is memory consuming and must be used with
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    parcimony.
            Institut national d'études démographiques, Paris.    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   This software have been partly granted by Euro-REVES, a concerted action  
   from the European Union.    Revision 1.83  2003/06/10 13:39:11  lievre
   It is copyrighted identically to a GNU software product, ie programme and    *** empty log message ***
   software can be distributed freely for non commercial use. Latest version  
   can be accessed at http://euroreves.ined.fr/imach .    Revision 1.82  2003/06/05 15:57:20  brouard
   **********************************************************************/    Add log in  imach.c and  fullversion number is now printed.
    
 #include <math.h>  */
 #include <stdio.h>  /*
 #include <stdlib.h>     Interpolated Markov Chain
 #include <unistd.h>  
     Short summary of the programme:
 #define MAXLINE 256    
 #define FILENAMELENGTH 80    This program computes Healthy Life Expectancies from
 /*#define DEBUG*/    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 #define windows    first survey ("cross") where individuals from different ages are
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    interviewed on their health status or degree of disability (in the
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    case of a health survey which is our main interest) -2- at least a
     second wave of interviews ("longitudinal") which measure each change
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    (if any) in individual health status.  Health expectancies are
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    computed from the time spent in each health state according to a
     model. More health states you consider, more time is necessary to reach the
 #define NINTERVMAX 8    Maximum Likelihood of the parameters involved in the model.  The
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    simplest model is the multinomial logistic model where pij is the
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    probability to be observed in state j at the second wave
 #define NCOVMAX 8 /* Maximum number of covariates */    conditional to be observed in state i at the first wave. Therefore
 #define MAXN 20000    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 #define YEARM 12. /* Number of months per year */    'age' is age and 'sex' is a covariate. If you want to have a more
 #define AGESUP 130    complex model than "constant and age", you should modify the program
 #define AGEBASE 40    where the markup *Covariates have to be included here again* invites
     you to do it.  More covariates you add, slower the
     convergence.
 int nvar;  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    The advantage of this computer programme, compared to a simple
 int npar=NPARMAX;    multinomial logistic model, is clear when the delay between waves is not
 int nlstate=2; /* Number of live states */    identical for each individual. Also, if a individual missed an
 int ndeath=1; /* Number of dead states */    intermediate interview, the information is lost, but taken into
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    account using an interpolation or extrapolation.  
 int popbased=0;  
     hPijx is the probability to be observed in state i at age x+h
 int *wav; /* Number of waves for this individuual 0 is possible */    conditional to the observed state i at age x. The delay 'h' can be
 int maxwav; /* Maxim number of waves */    split into an exact number (nh*stepm) of unobserved intermediate
 int jmin, jmax; /* min, max spacing between 2 waves */    states. This elementary transition (by month, quarter,
 int mle, weightopt;    semester or year) is modelled as a multinomial logistic.  The hPx
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    matrix is simply the matrix product of nh*stepm elementary matrices
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    and the contribution of each individual to the likelihood is simply
 double jmean; /* Mean space between 2 waves */    hPijx.
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Also this programme outputs the covariance matrix of the parameters but also
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    of the life expectancies. It also computes the stable prevalence. 
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;    
 FILE *ficreseij;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   char filerese[FILENAMELENGTH];             Institut national d'études démographiques, Paris.
  FILE  *ficresvij;    This software have been partly granted by Euro-REVES, a concerted action
   char fileresv[FILENAMELENGTH];    from the European Union.
  FILE  *ficresvpl;    It is copyrighted identically to a GNU software product, ie programme and
   char fileresvpl[FILENAMELENGTH];    software can be distributed freely for non commercial use. Latest version
     can be accessed at http://euroreves.ined.fr/imach .
 #define NR_END 1  
 #define FREE_ARG char*    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #define FTOL 1.0e-10    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
     
 #define NRANSI    **********************************************************************/
 #define ITMAX 200  /*
     main
 #define TOL 2.0e-4    read parameterfile
     read datafile
 #define CGOLD 0.3819660    concatwav
 #define ZEPS 1.0e-10    freqsummary
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    if (mle >= 1)
       mlikeli
 #define GOLD 1.618034    print results files
 #define GLIMIT 100.0    if mle==1 
 #define TINY 1.0e-20       computes hessian
     read end of parameter file: agemin, agemax, bage, fage, estepm
 static double maxarg1,maxarg2;        begin-prev-date,...
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    open gnuplot file
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    open html file
      stable prevalence
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))     for age prevalim()
 #define rint(a) floor(a+0.5)    h Pij x
     variance of p varprob
 static double sqrarg;    forecasting if prevfcast==1 prevforecast call prevalence()
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    health expectancies
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Variance-covariance of DFLE
     prevalence()
 int imx;     movingaverage()
 int stepm;    varevsij() 
 /* Stepm, step in month: minimum step interpolation*/    if popbased==1 varevsij(,popbased)
     total life expectancies
 int m,nb;    Variance of stable prevalence
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;   end
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  */
 double **pmmij, ***probs, ***mobaverage;  
   
 double *weight;  
 int **s; /* Status */   
 double *agedc, **covar, idx;  #include <math.h>
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  #include <stdio.h>
   #include <stdlib.h>
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  #include <unistd.h>
 double ftolhess; /* Tolerance for computing hessian */  
   #include <sys/time.h>
 /**************** split *************************/  #include <time.h>
 static  int split( char *path, char *dirc, char *name )  #include "timeval.h"
 {  
    char *s;                             /* pointer */  #define MAXLINE 256
    int  l1, l2;                         /* length counters */  #define GNUPLOTPROGRAM "gnuplot"
   /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
    l1 = strlen( path );                 /* length of path */  #define FILENAMELENGTH 132
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  /*#define DEBUG*/
    s = strrchr( path, '\\' );           /* find last / */  /*#define windows*/
    if ( s == NULL ) {                   /* no directory, so use current */  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #if     defined(__bsd__)                /* get current working directory */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
       extern char       *getwd( );  
   #define MAXPARM 30 /* Maximum number of parameters for the optimization */
       if ( getwd( dirc ) == NULL ) {  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 #else  
       extern char       *getcwd( );  #define NINTERVMAX 8
   #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #endif  #define NCOVMAX 8 /* Maximum number of covariates */
          return( GLOCK_ERROR_GETCWD );  #define MAXN 20000
       }  #define YEARM 12. /* Number of months per year */
       strcpy( name, path );             /* we've got it */  #define AGESUP 130
    } else {                             /* strip direcotry from path */  #define AGEBASE 40
       s++;                              /* after this, the filename */  #ifdef unix
       l2 = strlen( s );                 /* length of filename */  #define DIRSEPARATOR '/'
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  #define ODIRSEPARATOR '\\'
       strcpy( name, s );                /* save file name */  #else
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  #define DIRSEPARATOR '\\'
       dirc[l1-l2] = 0;                  /* add zero */  #define ODIRSEPARATOR '/'
    }  #endif
    l1 = strlen( dirc );                 /* length of directory */  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  /* $Id$ */
    return( 0 );                         /* we're done */  /* $State$ */
 }  
   char version[]="Imach version 0.96a, June 2003, INED-EUROREVES ";
   char fullversion[]="$Revision$ $Date$"; 
 /******************************************/  int erreur; /* Error number */
   int nvar;
 void replace(char *s, char*t)  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 {  int npar=NPARMAX;
   int i;  int nlstate=2; /* Number of live states */
   int lg=20;  int ndeath=1; /* Number of dead states */
   i=0;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   lg=strlen(t);  int popbased=0;
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);  int *wav; /* Number of waves for this individuual 0 is possible */
     if (t[i]== '\\') s[i]='/';  int maxwav; /* Maxim number of waves */
   }  int jmin, jmax; /* min, max spacing between 2 waves */
 }  int gipmx, gsw; /* Global variables on the number of contributions 
                      to the likelihood and the sum of weights (done by funcone)*/
 int nbocc(char *s, char occ)  int mle, weightopt;
 {  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   int i,j=0;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   int lg=20;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   i=0;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   lg=strlen(s);  double jmean; /* Mean space between 2 waves */
   for(i=0; i<= lg; i++) {  double **oldm, **newm, **savm; /* Working pointers to matrices */
   if  (s[i] == occ ) j++;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   }  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   return j;  FILE *ficlog, *ficrespow;
 }  int globpr; /* Global variable for printing or not */
   double fretone; /* Only one call to likelihood */
 void cutv(char *u,char *v, char*t, char occ)  long ipmx; /* Number of contributions */
 {  double sw; /* Sum of weights */
   int i,lg,j,p=0;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   i=0;  FILE *ficresilk;
   for(j=0; j<=strlen(t)-1; j++) {  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  FILE *ficresprobmorprev;
   }  FILE *fichtm; /* Html File */
   FILE *ficreseij;
   lg=strlen(t);  char filerese[FILENAMELENGTH];
   for(j=0; j<p; j++) {  FILE  *ficresvij;
     (u[j] = t[j]);  char fileresv[FILENAMELENGTH];
   }  FILE  *ficresvpl;
      u[p]='\0';  char fileresvpl[FILENAMELENGTH];
   char title[MAXLINE];
    for(j=0; j<= lg; j++) {  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
     if (j>=(p+1))(v[j-p-1] = t[j]);  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   }  char tmpout[FILENAMELENGTH]; 
 }  char command[FILENAMELENGTH];
   int  outcmd=0;
 /********************** nrerror ********************/  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 void nrerror(char error_text[])  char lfileres[FILENAMELENGTH];
 {  char filelog[FILENAMELENGTH]; /* Log file */
   fprintf(stderr,"ERREUR ...\n");  char filerest[FILENAMELENGTH];
   fprintf(stderr,"%s\n",error_text);  char fileregp[FILENAMELENGTH];
   exit(1);  char popfile[FILENAMELENGTH];
 }  
 /*********************** vector *******************/  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
 double *vector(int nl, int nh)  
 {  #define NR_END 1
   double *v;  #define FREE_ARG char*
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  #define FTOL 1.0e-10
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;  #define NRANSI 
 }  #define ITMAX 200 
   
 /************************ free vector ******************/  #define TOL 2.0e-4 
 void free_vector(double*v, int nl, int nh)  
 {  #define CGOLD 0.3819660 
   free((FREE_ARG)(v+nl-NR_END));  #define ZEPS 1.0e-10 
 }  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   
 /************************ivector *******************************/  #define GOLD 1.618034 
 int *ivector(long nl,long nh)  #define GLIMIT 100.0 
 {  #define TINY 1.0e-20 
   int *v;  
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  static double maxarg1,maxarg2;
   if (!v) nrerror("allocation failure in ivector");  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   return v-nl+NR_END;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 }    
   #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 /******************free ivector **************************/  #define rint(a) floor(a+0.5)
 void free_ivector(int *v, long nl, long nh)  
 {  static double sqrarg;
   free((FREE_ARG)(v+nl-NR_END));  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 }  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   
 /******************* imatrix *******************************/  int imx; 
 int **imatrix(long nrl, long nrh, long ncl, long nch)  int stepm;
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  /* Stepm, step in month: minimum step interpolation*/
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  int estepm;
   int **m;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
    
   /* allocate pointers to rows */  int m,nb;
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  long *num;
   if (!m) nrerror("allocation failure 1 in matrix()");  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
   m += NR_END;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   m -= nrl;  double **pmmij, ***probs;
    double dateintmean=0;
    
   /* allocate rows and set pointers to them */  double *weight;
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  int **s; /* Status */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  double *agedc, **covar, idx;
   m[nrl] += NR_END;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   m[nrl] -= ncl;  
    double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  double ftolhess; /* Tolerance for computing hessian */
    
   /* return pointer to array of pointers to rows */  /**************** split *************************/
   return m;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 }  {
     char  *ss;                            /* pointer */
 /****************** free_imatrix *************************/    int   l1, l2;                         /* length counters */
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;    l1 = strlen(path );                   /* length of path */
       long nch,ncl,nrh,nrl;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
      /* free an int matrix allocated by imatrix() */    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
 {    if ( ss == NULL ) {                   /* no directory, so use current */
   free((FREE_ARG) (m[nrl]+ncl-NR_END));      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   free((FREE_ARG) (m+nrl-NR_END));        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 }      /* get current working directory */
       /*    extern  char* getcwd ( char *buf , int len);*/
 /******************* matrix *******************************/      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 double **matrix(long nrl, long nrh, long ncl, long nch)        return( GLOCK_ERROR_GETCWD );
 {      }
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;      strcpy( name, path );               /* we've got it */
   double **m;    } else {                              /* strip direcotry from path */
       ss++;                               /* after this, the filename */
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));      l2 = strlen( ss );                  /* length of filename */
   if (!m) nrerror("allocation failure 1 in matrix()");      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   m += NR_END;      strcpy( name, ss );         /* save file name */
   m -= nrl;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       dirc[l1-l2] = 0;                    /* add zero */
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    }
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    l1 = strlen( dirc );                  /* length of directory */
   m[nrl] += NR_END;    /*#ifdef windows
   m[nrl] -= ncl;    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   #else
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   return m;  #endif
 }    */
     ss = strrchr( name, '.' );            /* find last / */
 /*************************free matrix ************************/    ss++;
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    strcpy(ext,ss);                       /* save extension */
 {    l1= strlen( name);
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    l2= strlen(ss)+1;
   free((FREE_ARG)(m+nrl-NR_END));    strncpy( finame, name, l1-l2);
 }    finame[l1-l2]= 0;
     return( 0 );                          /* we're done */
 /******************* ma3x *******************************/  }
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  /******************************************/
   double ***m;  
   void replace_back_to_slash(char *s, char*t)
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  {
   if (!m) nrerror("allocation failure 1 in matrix()");    int i;
   m += NR_END;    int lg=0;
   m -= nrl;    i=0;
     lg=strlen(t);
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    for(i=0; i<= lg; i++) {
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");      (s[i] = t[i]);
   m[nrl] += NR_END;      if (t[i]== '\\') s[i]='/';
   m[nrl] -= ncl;    }
   }
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   int nbocc(char *s, char occ)
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  {
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    int i,j=0;
   m[nrl][ncl] += NR_END;    int lg=20;
   m[nrl][ncl] -= nll;    i=0;
   for (j=ncl+1; j<=nch; j++)    lg=strlen(s);
     m[nrl][j]=m[nrl][j-1]+nlay;    for(i=0; i<= lg; i++) {
      if  (s[i] == occ ) j++;
   for (i=nrl+1; i<=nrh; i++) {    }
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    return j;
     for (j=ncl+1; j<=nch; j++)  }
       m[i][j]=m[i][j-1]+nlay;  
   }  void cutv(char *u,char *v, char*t, char occ)
   return m;  {
 }    /* cuts string t into u and v where u is ended by char occ excluding it
        and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
 /*************************free ma3x ************************/       gives u="abcedf" and v="ghi2j" */
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    int i,lg,j,p=0;
 {    i=0;
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    for(j=0; j<=strlen(t)-1; j++) {
   free((FREE_ARG)(m[nrl]+ncl-NR_END));      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   free((FREE_ARG)(m+nrl-NR_END));    }
 }  
     lg=strlen(t);
 /***************** f1dim *************************/    for(j=0; j<p; j++) {
 extern int ncom;      (u[j] = t[j]);
 extern double *pcom,*xicom;    }
 extern double (*nrfunc)(double []);       u[p]='\0';
    
 double f1dim(double x)     for(j=0; j<= lg; j++) {
 {      if (j>=(p+1))(v[j-p-1] = t[j]);
   int j;    }
   double f;  }
   double *xt;  
    /********************** nrerror ********************/
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  void nrerror(char error_text[])
   f=(*nrfunc)(xt);  {
   free_vector(xt,1,ncom);    fprintf(stderr,"ERREUR ...\n");
   return f;    fprintf(stderr,"%s\n",error_text);
 }    exit(EXIT_FAILURE);
   }
 /*****************brent *************************/  /*********************** vector *******************/
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  double *vector(int nl, int nh)
 {  {
   int iter;    double *v;
   double a,b,d,etemp;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   double fu,fv,fw,fx;    if (!v) nrerror("allocation failure in vector");
   double ftemp;    return v-nl+NR_END;
   double p,q,r,tol1,tol2,u,v,w,x,xm;  }
   double e=0.0;  
    /************************ free vector ******************/
   a=(ax < cx ? ax : cx);  void free_vector(double*v, int nl, int nh)
   b=(ax > cx ? ax : cx);  {
   x=w=v=bx;    free((FREE_ARG)(v+nl-NR_END));
   fw=fv=fx=(*f)(x);  }
   for (iter=1;iter<=ITMAX;iter++) {  
     xm=0.5*(a+b);  /************************ivector *******************************/
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  int *ivector(long nl,long nh)
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  {
     printf(".");fflush(stdout);    int *v;
 #ifdef DEBUG    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    if (!v) nrerror("allocation failure in ivector");
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    return v-nl+NR_END;
 #endif  }
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  
       *xmin=x;  /******************free ivector **************************/
       return fx;  void free_ivector(int *v, long nl, long nh)
     }  {
     ftemp=fu;    free((FREE_ARG)(v+nl-NR_END));
     if (fabs(e) > tol1) {  }
       r=(x-w)*(fx-fv);  
       q=(x-v)*(fx-fw);  /************************lvector *******************************/
       p=(x-v)*q-(x-w)*r;  long *lvector(long nl,long nh)
       q=2.0*(q-r);  {
       if (q > 0.0) p = -p;    long *v;
       q=fabs(q);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       etemp=e;    if (!v) nrerror("allocation failure in ivector");
       e=d;    return v-nl+NR_END;
       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));  
       else {  /******************free lvector **************************/
         d=p/q;  void free_lvector(long *v, long nl, long nh)
         u=x+d;  {
         if (u-a < tol2 || b-u < tol2)    free((FREE_ARG)(v+nl-NR_END));
           d=SIGN(tol1,xm-x);  }
       }  
     } else {  /******************* imatrix *******************************/
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     }       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  { 
     fu=(*f)(u);    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     if (fu <= fx) {    int **m; 
       if (u >= x) a=x; else b=x;    
       SHFT(v,w,x,u)    /* allocate pointers to rows */ 
         SHFT(fv,fw,fx,fu)    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
         } else {    if (!m) nrerror("allocation failure 1 in matrix()"); 
           if (u < x) a=u; else b=u;    m += NR_END; 
           if (fu <= fw || w == x) {    m -= nrl; 
             v=w;    
             w=u;    
             fv=fw;    /* allocate rows and set pointers to them */ 
             fw=fu;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
           } else if (fu <= fv || v == x || v == w) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
             v=u;    m[nrl] += NR_END; 
             fv=fu;    m[nrl] -= ncl; 
           }    
         }    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   }    
   nrerror("Too many iterations in brent");    /* return pointer to array of pointers to rows */ 
   *xmin=x;    return m; 
   return fx;  } 
 }  
   /****************** free_imatrix *************************/
 /****************** mnbrak ***********************/  void free_imatrix(m,nrl,nrh,ncl,nch)
         int **m;
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,        long nch,ncl,nrh,nrl; 
             double (*func)(double))       /* free an int matrix allocated by imatrix() */ 
 {  { 
   double ulim,u,r,q, dum;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   double fu;    free((FREE_ARG) (m+nrl-NR_END)); 
    } 
   *fa=(*func)(*ax);  
   *fb=(*func)(*bx);  /******************* matrix *******************************/
   if (*fb > *fa) {  double **matrix(long nrl, long nrh, long ncl, long nch)
     SHFT(dum,*ax,*bx,dum)  {
       SHFT(dum,*fb,*fa,dum)    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       }    double **m;
   *cx=(*bx)+GOLD*(*bx-*ax);  
   *fc=(*func)(*cx);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   while (*fb > *fc) {    if (!m) nrerror("allocation failure 1 in matrix()");
     r=(*bx-*ax)*(*fb-*fc);    m += NR_END;
     q=(*bx-*cx)*(*fb-*fa);    m -= nrl;
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     ulim=(*bx)+GLIMIT*(*cx-*bx);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     if ((*bx-u)*(u-*cx) > 0.0) {    m[nrl] += NR_END;
       fu=(*func)(u);    m[nrl] -= ncl;
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       if (fu < *fc) {    return m;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
           SHFT(*fb,*fc,fu,(*func)(u))     */
           }  }
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  
       u=ulim;  /*************************free matrix ************************/
       fu=(*func)(u);  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
     } else {  {
       u=(*cx)+GOLD*(*cx-*bx);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       fu=(*func)(u);    free((FREE_ARG)(m+nrl-NR_END));
     }  }
     SHFT(*ax,*bx,*cx,u)  
       SHFT(*fa,*fb,*fc,fu)  /******************* ma3x *******************************/
       }  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
 }  {
     long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
 /*************** linmin ************************/    double ***m;
   
 int ncom;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 double *pcom,*xicom;    if (!m) nrerror("allocation failure 1 in matrix()");
 double (*nrfunc)(double []);    m += NR_END;
      m -= nrl;
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  
 {    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   double brent(double ax, double bx, double cx,    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
                double (*f)(double), double tol, double *xmin);    m[nrl] += NR_END;
   double f1dim(double x);    m[nrl] -= ncl;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  
               double *fc, double (*func)(double));    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   int j;  
   double xx,xmin,bx,ax;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   double fx,fb,fa;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
      m[nrl][ncl] += NR_END;
   ncom=n;    m[nrl][ncl] -= nll;
   pcom=vector(1,n);    for (j=ncl+1; j<=nch; j++) 
   xicom=vector(1,n);      m[nrl][j]=m[nrl][j-1]+nlay;
   nrfunc=func;    
   for (j=1;j<=n;j++) {    for (i=nrl+1; i<=nrh; i++) {
     pcom[j]=p[j];      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     xicom[j]=xi[j];      for (j=ncl+1; j<=nch; j++) 
   }        m[i][j]=m[i][j-1]+nlay;
   ax=0.0;    }
   xx=1.0;    return m; 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
 #ifdef DEBUG    */
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  }
 #endif  
   for (j=1;j<=n;j++) {  /*************************free ma3x ************************/
     xi[j] *= xmin;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     p[j] += xi[j];  {
   }    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   free_vector(xicom,1,n);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   free_vector(pcom,1,n);    free((FREE_ARG)(m+nrl-NR_END));
 }  }
   
 /*************** powell ************************/  /***************** f1dim *************************/
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  extern int ncom; 
             double (*func)(double []))  extern double *pcom,*xicom;
 {  extern double (*nrfunc)(double []); 
   void linmin(double p[], double xi[], int n, double *fret,   
               double (*func)(double []));  double f1dim(double x) 
   int i,ibig,j;  { 
   double del,t,*pt,*ptt,*xit;    int j; 
   double fp,fptt;    double f;
   double *xits;    double *xt; 
   pt=vector(1,n);   
   ptt=vector(1,n);    xt=vector(1,ncom); 
   xit=vector(1,n);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   xits=vector(1,n);    f=(*nrfunc)(xt); 
   *fret=(*func)(p);    free_vector(xt,1,ncom); 
   for (j=1;j<=n;j++) pt[j]=p[j];    return f; 
   for (*iter=1;;++(*iter)) {  } 
     fp=(*fret);  
     ibig=0;  /*****************brent *************************/
     del=0.0;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  { 
     for (i=1;i<=n;i++)    int iter; 
       printf(" %d %.12f",i, p[i]);    double a,b,d,etemp;
     printf("\n");    double fu,fv,fw,fx;
     for (i=1;i<=n;i++) {    double ftemp;
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       fptt=(*fret);    double e=0.0; 
 #ifdef DEBUG   
       printf("fret=%lf \n",*fret);    a=(ax < cx ? ax : cx); 
 #endif    b=(ax > cx ? ax : cx); 
       printf("%d",i);fflush(stdout);    x=w=v=bx; 
       linmin(p,xit,n,fret,func);    fw=fv=fx=(*f)(x); 
       if (fabs(fptt-(*fret)) > del) {    for (iter=1;iter<=ITMAX;iter++) { 
         del=fabs(fptt-(*fret));      xm=0.5*(a+b); 
         ibig=i;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       }      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
 #ifdef DEBUG      printf(".");fflush(stdout);
       printf("%d %.12e",i,(*fret));      fprintf(ficlog,".");fflush(ficlog);
       for (j=1;j<=n;j++) {  #ifdef DEBUG
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
         printf(" x(%d)=%.12e",j,xit[j]);      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       }      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       for(j=1;j<=n;j++)  #endif
         printf(" p=%.12e",p[j]);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       printf("\n");        *xmin=x; 
 #endif        return fx; 
     }      } 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      ftemp=fu;
 #ifdef DEBUG      if (fabs(e) > tol1) { 
       int k[2],l;        r=(x-w)*(fx-fv); 
       k[0]=1;        q=(x-v)*(fx-fw); 
       k[1]=-1;        p=(x-v)*q-(x-w)*r; 
       printf("Max: %.12e",(*func)(p));        q=2.0*(q-r); 
       for (j=1;j<=n;j++)        if (q > 0.0) p = -p; 
         printf(" %.12e",p[j]);        q=fabs(q); 
       printf("\n");        etemp=e; 
       for(l=0;l<=1;l++) {        e=d; 
         for (j=1;j<=n;j++) {        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);        else { 
         }          d=p/q; 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));          u=x+d; 
       }          if (u-a < tol2 || b-u < tol2) 
 #endif            d=SIGN(tol1,xm-x); 
         } 
       } else { 
       free_vector(xit,1,n);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       free_vector(xits,1,n);      } 
       free_vector(ptt,1,n);      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       free_vector(pt,1,n);      fu=(*f)(u); 
       return;      if (fu <= fx) { 
     }        if (u >= x) a=x; else b=x; 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");        SHFT(v,w,x,u) 
     for (j=1;j<=n;j++) {          SHFT(fv,fw,fx,fu) 
       ptt[j]=2.0*p[j]-pt[j];          } else { 
       xit[j]=p[j]-pt[j];            if (u < x) a=u; else b=u; 
       pt[j]=p[j];            if (fu <= fw || w == x) { 
     }              v=w; 
     fptt=(*func)(ptt);              w=u; 
     if (fptt < fp) {              fv=fw; 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);              fw=fu; 
       if (t < 0.0) {            } else if (fu <= fv || v == x || v == w) { 
         linmin(p,xit,n,fret,func);              v=u; 
         for (j=1;j<=n;j++) {              fv=fu; 
           xi[j][ibig]=xi[j][n];            } 
           xi[j][n]=xit[j];          } 
         }    } 
 #ifdef DEBUG    nrerror("Too many iterations in brent"); 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    *xmin=x; 
         for(j=1;j<=n;j++)    return fx; 
           printf(" %.12e",xit[j]);  } 
         printf("\n");  
 #endif  /****************** mnbrak ***********************/
       }  
     }  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   }              double (*func)(double)) 
 }  { 
     double ulim,u,r,q, dum;
 /**** Prevalence limit ****************/    double fu; 
    
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    *fa=(*func)(*ax); 
 {    *fb=(*func)(*bx); 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    if (*fb > *fa) { 
      matrix by transitions matrix until convergence is reached */      SHFT(dum,*ax,*bx,dum) 
         SHFT(dum,*fb,*fa,dum) 
   int i, ii,j,k;        } 
   double min, max, maxmin, maxmax,sumnew=0.;    *cx=(*bx)+GOLD*(*bx-*ax); 
   double **matprod2();    *fc=(*func)(*cx); 
   double **out, cov[NCOVMAX], **pmij();    while (*fb > *fc) { 
   double **newm;      r=(*bx-*ax)*(*fb-*fc); 
   double agefin, delaymax=50 ; /* Max number of years to converge */      q=(*bx-*cx)*(*fb-*fa); 
       u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   for (ii=1;ii<=nlstate+ndeath;ii++)        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
     for (j=1;j<=nlstate+ndeath;j++){      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      if ((*bx-u)*(u-*cx) > 0.0) { 
     }        fu=(*func)(u); 
       } else if ((*cx-u)*(u-ulim) > 0.0) { 
    cov[1]=1.;        fu=(*func)(u); 
          if (fu < *fc) { 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){            SHFT(*fb,*fc,fu,(*func)(u)) 
     newm=savm;            } 
     /* Covariates have to be included here again */      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
      cov[2]=agefin;        u=ulim; 
          fu=(*func)(u); 
       for (k=1; k<=cptcovn;k++) {      } else { 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        u=(*cx)+GOLD*(*cx-*bx); 
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/        fu=(*func)(u); 
       }      } 
       for (k=1; k<=cptcovage;k++)      SHFT(*ax,*bx,*cx,u) 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        SHFT(*fa,*fb,*fc,fu) 
       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]]];  } 
   
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  /*************** linmin ************************/
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  
   int ncom; 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  double *pcom,*xicom;
   double (*nrfunc)(double []); 
     savm=oldm;   
     oldm=newm;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     maxmax=0.;  { 
     for(j=1;j<=nlstate;j++){    double brent(double ax, double bx, double cx, 
       min=1.;                 double (*f)(double), double tol, double *xmin); 
       max=0.;    double f1dim(double x); 
       for(i=1; i<=nlstate; i++) {    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
         sumnew=0;                double *fc, double (*func)(double)); 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    int j; 
         prlim[i][j]= newm[i][j]/(1-sumnew);    double xx,xmin,bx,ax; 
         max=FMAX(max,prlim[i][j]);    double fx,fb,fa;
         min=FMIN(min,prlim[i][j]);   
       }    ncom=n; 
       maxmin=max-min;    pcom=vector(1,n); 
       maxmax=FMAX(maxmax,maxmin);    xicom=vector(1,n); 
     }    nrfunc=func; 
     if(maxmax < ftolpl){    for (j=1;j<=n;j++) { 
       return prlim;      pcom[j]=p[j]; 
     }      xicom[j]=xi[j]; 
   }    } 
 }    ax=0.0; 
     xx=1.0; 
 /*************** transition probabilities ***************/    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  #ifdef DEBUG
 {    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   double s1, s2;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   /*double t34;*/  #endif
   int i,j,j1, nc, ii, jj;    for (j=1;j<=n;j++) { 
       xi[j] *= xmin; 
     for(i=1; i<= nlstate; i++){      p[j] += xi[j]; 
     for(j=1; j<i;j++){    } 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    free_vector(xicom,1,n); 
         /*s2 += param[i][j][nc]*cov[nc];*/    free_vector(pcom,1,n); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  } 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  
       }  /*************** powell ************************/
       ps[i][j]=s2;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/              double (*func)(double [])) 
     }  { 
     for(j=i+1; j<=nlstate+ndeath;j++){    void linmin(double p[], double xi[], int n, double *fret, 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){                double (*func)(double [])); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    int i,ibig,j; 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    double del,t,*pt,*ptt,*xit;
       }    double fp,fptt;
       ps[i][j]=(s2);    double *xits;
     }    pt=vector(1,n); 
   }    ptt=vector(1,n); 
     /*ps[3][2]=1;*/    xit=vector(1,n); 
     xits=vector(1,n); 
   for(i=1; i<= nlstate; i++){    *fret=(*func)(p); 
      s1=0;    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for(j=1; j<i; j++)    for (*iter=1;;++(*iter)) { 
       s1+=exp(ps[i][j]);      fp=(*fret); 
     for(j=i+1; j<=nlstate+ndeath; j++)      ibig=0; 
       s1+=exp(ps[i][j]);      del=0.0; 
     ps[i][i]=1./(s1+1.);      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
     for(j=1; j<i; j++)      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       ps[i][j]= exp(ps[i][j])*ps[i][i];      fprintf(ficrespow,"%d %.12f",*iter,*fret);
     for(j=i+1; j<=nlstate+ndeath; j++)      for (i=1;i<=n;i++) {
       ps[i][j]= exp(ps[i][j])*ps[i][i];        printf(" %d %.12f",i, p[i]);
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        fprintf(ficlog," %d %.12lf",i, p[i]);
   } /* end i */        fprintf(ficrespow," %.12lf", p[i]);
       }
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      printf("\n");
     for(jj=1; jj<= nlstate+ndeath; jj++){      fprintf(ficlog,"\n");
       ps[ii][jj]=0;      fprintf(ficrespow,"\n");
       ps[ii][ii]=1;      for (i=1;i<=n;i++) { 
     }        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   }        fptt=(*fret); 
   #ifdef DEBUG
         printf("fret=%lf \n",*fret);
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        fprintf(ficlog,"fret=%lf \n",*fret);
     for(jj=1; jj<= nlstate+ndeath; jj++){  #endif
      printf("%lf ",ps[ii][jj]);        printf("%d",i);fflush(stdout);
    }        fprintf(ficlog,"%d",i);fflush(ficlog);
     printf("\n ");        linmin(p,xit,n,fret,func); 
     }        if (fabs(fptt-(*fret)) > del) { 
     printf("\n ");printf("%lf ",cov[2]);*/          del=fabs(fptt-(*fret)); 
 /*          ibig=i; 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        } 
   goto end;*/  #ifdef DEBUG
     return ps;        printf("%d %.12e",i,(*fret));
 }        fprintf(ficlog,"%d %.12e",i,(*fret));
         for (j=1;j<=n;j++) {
 /**************** Product of 2 matrices ******************/          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
           printf(" x(%d)=%.12e",j,xit[j]);
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
 {        }
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        for(j=1;j<=n;j++) {
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */          printf(" p=%.12e",p[j]);
   /* in, b, out are matrice of pointers which should have been initialized          fprintf(ficlog," p=%.12e",p[j]);
      before: only the contents of out is modified. The function returns        }
      a pointer to pointers identical to out */        printf("\n");
   long i, j, k;        fprintf(ficlog,"\n");
   for(i=nrl; i<= nrh; i++)  #endif
     for(k=ncolol; k<=ncoloh; k++)      } 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
         out[i][k] +=in[i][j]*b[j][k];  #ifdef DEBUG
         int k[2],l;
   return out;        k[0]=1;
 }        k[1]=-1;
         printf("Max: %.12e",(*func)(p));
         fprintf(ficlog,"Max: %.12e",(*func)(p));
 /************* Higher Matrix Product ***************/        for (j=1;j<=n;j++) {
           printf(" %.12e",p[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," %.12e",p[j]);
 {        }
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month        printf("\n");
      duration (i.e. until        fprintf(ficlog,"\n");
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        for(l=0;l<=1;l++) {
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step          for (j=1;j<=n;j++) {
      (typically every 2 years instead of every month which is too big).            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
      Model is determined by parameters x and covariates have to be            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
      included manually here.            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
           }
      */          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   int i, j, d, h, k;        }
   double **out, cov[NCOVMAX];  #endif
   double **newm;  
   
   /* Hstepm could be zero and should return the unit matrix */        free_vector(xit,1,n); 
   for (i=1;i<=nlstate+ndeath;i++)        free_vector(xits,1,n); 
     for (j=1;j<=nlstate+ndeath;j++){        free_vector(ptt,1,n); 
       oldm[i][j]=(i==j ? 1.0 : 0.0);        free_vector(pt,1,n); 
       po[i][j][0]=(i==j ? 1.0 : 0.0);        return; 
     }      } 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   for(h=1; h <=nhstepm; h++){      for (j=1;j<=n;j++) { 
     for(d=1; d <=hstepm; d++){        ptt[j]=2.0*p[j]-pt[j]; 
       newm=savm;        xit[j]=p[j]-pt[j]; 
       /* Covariates have to be included here again */        pt[j]=p[j]; 
       cov[1]=1.;      } 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      fptt=(*func)(ptt); 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      if (fptt < fp) { 
       for (k=1; k<=cptcovage;k++)        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        if (t < 0.0) { 
       for (k=1; k<=cptcovprod;k++)          linmin(p,xit,n,fret,func); 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          for (j=1;j<=n;j++) { 
             xi[j][ibig]=xi[j][n]; 
             xi[j][n]=xit[j]; 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/          }
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  #ifdef DEBUG
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
                    pmij(pmmij,cov,ncovmodel,x,nlstate));          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       savm=oldm;          for(j=1;j<=n;j++){
       oldm=newm;            printf(" %.12e",xit[j]);
     }            fprintf(ficlog," %.12e",xit[j]);
     for(i=1; i<=nlstate+ndeath; i++)          }
       for(j=1;j<=nlstate+ndeath;j++) {          printf("\n");
         po[i][j][h]=newm[i][j];          fprintf(ficlog,"\n");
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  #endif
          */        }
       }      } 
   } /* end h */    } 
   return po;  } 
 }  
   /**** Prevalence limit (stable prevalence)  ****************/
   
 /*************** log-likelihood *************/  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
 double func( double *x)  {
 {    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   int i, ii, j, k, mi, d, kk;       matrix by transitions matrix until convergence is reached */
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  
   double **out;    int i, ii,j,k;
   double sw; /* Sum of weights */    double min, max, maxmin, maxmax,sumnew=0.;
   double lli; /* Individual log likelihood */    double **matprod2();
   long ipmx;    double **out, cov[NCOVMAX], **pmij();
   /*extern weight */    double **newm;
   /* We are differentiating ll according to initial status */    double agefin, delaymax=50 ; /* Max number of years to converge */
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  
   /*for(i=1;i<imx;i++)    for (ii=1;ii<=nlstate+ndeath;ii++)
     printf(" %d\n",s[4][i]);      for (j=1;j<=nlstate+ndeath;j++){
   */        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   cov[1]=1.;      }
   
   for(k=1; k<=nlstate; k++) ll[k]=0.;     cov[1]=1.;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){   
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(mi=1; mi<= wav[i]-1; mi++){    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       for (ii=1;ii<=nlstate+ndeath;ii++)      newm=savm;
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      /* Covariates have to be included here again */
       for(d=0; d<dh[mi][i]; d++){       cov[2]=agefin;
         newm=savm;    
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;        for (k=1; k<=cptcovn;k++) {
         for (kk=1; kk<=cptcovage;kk++) {          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
         }        }
                for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        for (k=1; k<=cptcovprod;k++)
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         savm=oldm;  
         oldm=newm;        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
                /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
                /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       } /* end mult */      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
        
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);      savm=oldm;
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/      oldm=newm;
       ipmx +=1;      maxmax=0.;
       sw += weight[i];      for(j=1;j<=nlstate;j++){
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        min=1.;
     } /* end of wave */        max=0.;
   } /* end of individual */        for(i=1; i<=nlstate; i++) {
           sumnew=0;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */          prlim[i][j]= newm[i][j]/(1-sumnew);
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */          max=FMAX(max,prlim[i][j]);
   return -l;          min=FMIN(min,prlim[i][j]);
 }        }
         maxmin=max-min;
         maxmax=FMAX(maxmax,maxmin);
 /*********** Maximum Likelihood Estimation ***************/      }
       if(maxmax < ftolpl){
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        return prlim;
 {      }
   int i,j, iter;    }
   double **xi,*delti;  }
   double fret;  
   xi=matrix(1,npar,1,npar);  /*************** transition probabilities ***************/ 
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++)  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       xi[i][j]=(i==j ? 1.0 : 0.0);  {
   printf("Powell\n");    double s1, s2;
   powell(p,xi,npar,ftol,&iter,&fret,func);    /*double t34;*/
     int i,j,j1, nc, ii, jj;
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));      for(i=1; i<= nlstate; i++){
       for(j=1; j<i;j++){
 }        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
           /*s2 += param[i][j][nc]*cov[nc];*/
 /**** Computes Hessian and covariance matrix ***/          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
 {        }
   double  **a,**y,*x,pd;        ps[i][j]=s2;
   double **hess;        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
   int i, j,jk;      }
   int *indx;      for(j=i+1; j<=nlstate+ndeath;j++){
         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   double hessii(double p[], double delta, int theta, double delti[]);          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   double hessij(double p[], double delti[], int i, int j);          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
   void lubksb(double **a, int npar, int *indx, double b[]) ;        }
   void ludcmp(double **a, int npar, int *indx, double *d) ;        ps[i][j]=s2;
       }
   hess=matrix(1,npar,1,npar);    }
       /*ps[3][2]=1;*/
   printf("\nCalculation of the hessian matrix. Wait...\n");  
   for (i=1;i<=npar;i++){    for(i=1; i<= nlstate; i++){
     printf("%d",i);fflush(stdout);       s1=0;
     hess[i][i]=hessii(p,ftolhess,i,delti);      for(j=1; j<i; j++)
     /*printf(" %f ",p[i]);*/        s1+=exp(ps[i][j]);
     /*printf(" %lf ",hess[i][i]);*/      for(j=i+1; j<=nlstate+ndeath; j++)
   }        s1+=exp(ps[i][j]);
        ps[i][i]=1./(s1+1.);
   for (i=1;i<=npar;i++) {      for(j=1; j<i; j++)
     for (j=1;j<=npar;j++)  {        ps[i][j]= exp(ps[i][j])*ps[i][i];
       if (j>i) {      for(j=i+1; j<=nlstate+ndeath; j++)
         printf(".%d%d",i,j);fflush(stdout);        ps[i][j]= exp(ps[i][j])*ps[i][i];
         hess[i][j]=hessij(p,delti,i,j);      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
         hess[j][i]=hess[i][j];        } /* end i */
         /*printf(" %lf ",hess[i][j]);*/  
       }    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     }      for(jj=1; jj<= nlstate+ndeath; jj++){
   }        ps[ii][jj]=0;
   printf("\n");        ps[ii][ii]=1;
       }
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    }
    
   a=matrix(1,npar,1,npar);  
   y=matrix(1,npar,1,npar);    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   x=vector(1,npar);      for(jj=1; jj<= nlstate+ndeath; jj++){
   indx=ivector(1,npar);       printf("%lf ",ps[ii][jj]);
   for (i=1;i<=npar;i++)     }
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];      printf("\n ");
   ludcmp(a,npar,indx,&pd);      }
       printf("\n ");printf("%lf ",cov[2]);*/
   for (j=1;j<=npar;j++) {  /*
     for (i=1;i<=npar;i++) x[i]=0;    for(i=1; i<= npar; i++) printf("%f ",x[i]);
     x[j]=1;    goto end;*/
     lubksb(a,npar,indx,x);      return ps;
     for (i=1;i<=npar;i++){  }
       matcov[i][j]=x[i];  
     }  /**************** Product of 2 matrices ******************/
   }  
   double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   printf("\n#Hessian matrix#\n");  {
   for (i=1;i<=npar;i++) {    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
     for (j=1;j<=npar;j++) {       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       printf("%.3e ",hess[i][j]);    /* in, b, out are matrice of pointers which should have been initialized 
     }       before: only the contents of out is modified. The function returns
     printf("\n");       a pointer to pointers identical to out */
   }    long i, j, k;
     for(i=nrl; i<= nrh; i++)
   /* Recompute Inverse */      for(k=ncolol; k<=ncoloh; k++)
   for (i=1;i<=npar;i++)        for(j=ncl,out[i][k]=0.; j<=nch; j++)
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];          out[i][k] +=in[i][j]*b[j][k];
   ludcmp(a,npar,indx,&pd);  
     return out;
   /*  printf("\n#Hessian matrix recomputed#\n");  }
   
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;  /************* Higher Matrix Product ***************/
     x[j]=1;  
     lubksb(a,npar,indx,x);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     for (i=1;i<=npar;i++){  {
       y[i][j]=x[i];    /* Computes the transition matrix starting at age 'age' over 
       printf("%.3e ",y[i][j]);       'nhstepm*hstepm*stepm' months (i.e. until
     }       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
     printf("\n");       nhstepm*hstepm matrices. 
   }       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   */       (typically every 2 years instead of every month which is too big 
        for the memory).
   free_matrix(a,1,npar,1,npar);       Model is determined by parameters x and covariates have to be 
   free_matrix(y,1,npar,1,npar);       included manually here. 
   free_vector(x,1,npar);  
   free_ivector(indx,1,npar);       */
   free_matrix(hess,1,npar,1,npar);  
     int i, j, d, h, k;
     double **out, cov[NCOVMAX];
 }    double **newm;
   
 /*************** hessian matrix ****************/    /* Hstepm could be zero and should return the unit matrix */
 double hessii( double x[], double delta, int theta, double delti[])    for (i=1;i<=nlstate+ndeath;i++)
 {      for (j=1;j<=nlstate+ndeath;j++){
   int i;        oldm[i][j]=(i==j ? 1.0 : 0.0);
   int l=1, lmax=20;        po[i][j][0]=(i==j ? 1.0 : 0.0);
   double k1,k2;      }
   double p2[NPARMAX+1];    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   double res;    for(h=1; h <=nhstepm; h++){
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      for(d=1; d <=hstepm; d++){
   double fx;        newm=savm;
   int k=0,kmax=10;        /* Covariates have to be included here again */
   double l1;        cov[1]=1.;
         cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   fx=func(x);        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   for (i=1;i<=npar;i++) p2[i]=x[i];        for (k=1; k<=cptcovage;k++)
   for(l=0 ; l <=lmax; l++){          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     l1=pow(10,l);        for (k=1; k<=cptcovprod;k++)
     delts=delt;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     for(k=1 ; k <kmax; k=k+1){  
       delt = delta*(l1*k);  
       p2[theta]=x[theta] +delt;        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       k1=func(p2)-fx;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
       p2[theta]=x[theta]-delt;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
       k2=func(p2)-fx;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
       /*res= (k1-2.0*fx+k2)/delt/delt; */        savm=oldm;
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        oldm=newm;
            }
 #ifdef DEBUG      for(i=1; i<=nlstate+ndeath; i++)
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);        for(j=1;j<=nlstate+ndeath;j++) {
 #endif          po[i][j][h]=newm[i][j];
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){           */
         k=kmax;        }
       }    } /* end h */
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    return po;
         k=kmax; l=lmax*10.;  }
       }  
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  
         delts=delt;  /*************** log-likelihood *************/
       }  double func( double *x)
     }  {
   }    int i, ii, j, k, mi, d, kk;
   delti[theta]=delts;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   return res;    double **out;
      double sw; /* Sum of weights */
 }    double lli; /* Individual log likelihood */
     int s1, s2;
 double hessij( double x[], double delti[], int thetai,int thetaj)    double bbh, survp;
 {    long ipmx;
   int i;    /*extern weight */
   int l=1, l1, lmax=20;    /* We are differentiating ll according to initial status */
   double k1,k2,k3,k4,res,fx;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   double p2[NPARMAX+1];    /*for(i=1;i<imx;i++) 
   int k;      printf(" %d\n",s[4][i]);
     */
   fx=func(x);    cov[1]=1.;
   for (k=1; k<=2; k++) {  
     for (i=1;i<=npar;i++) p2[i]=x[i];    for(k=1; k<=nlstate; k++) ll[k]=0.;
     p2[thetai]=x[thetai]+delti[thetai]/k;  
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    if(mle==1){
     k1=func(p2)-fx;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     p2[thetai]=x[thetai]+delti[thetai]/k;        for(mi=1; mi<= wav[i]-1; mi++){
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          for (ii=1;ii<=nlstate+ndeath;ii++)
     k2=func(p2)-fx;            for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     p2[thetai]=x[thetai]-delti[thetai]/k;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;            }
     k3=func(p2)-fx;          for(d=0; d<dh[mi][i]; d++){
              newm=savm;
     p2[thetai]=x[thetai]-delti[thetai]/k;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;            for (kk=1; kk<=cptcovage;kk++) {
     k4=func(p2)-fx;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */            }
 #ifdef DEBUG            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     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);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 #endif            savm=oldm;
   }            oldm=newm;
   return res;          } /* end mult */
 }        
           /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
 /************** Inverse of matrix **************/          /* But now since version 0.9 we anticipate for bias and large stepm.
 void ludcmp(double **a, int n, int *indx, double *d)           * 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 
   int i,imax,j,k;           * the nearest (and in case of equal distance, to the lowest) interval but now
   double big,dum,sum,temp;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   double *vv;           * (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
   vv=vector(1,n);           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   *d=1.0;           * -stepm/2 to stepm/2 .
   for (i=1;i<=n;i++) {           * For stepm=1 the results are the same as for previous versions of Imach.
     big=0.0;           * For stepm > 1 the results are less biased than in previous versions. 
     for (j=1;j<=n;j++)           */
       if ((temp=fabs(a[i][j])) > big) big=temp;          s1=s[mw[mi][i]][i];
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          s2=s[mw[mi+1][i]][i];
     vv[i]=1.0/big;          bbh=(double)bh[mi][i]/(double)stepm; 
   }          /* bias is positive if real duration
   for (j=1;j<=n;j++) {           * is higher than the multiple of stepm and negative otherwise.
     for (i=1;i<j;i++) {           */
       sum=a[i][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]));*/
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];          if( s2 > nlstate){ 
       a[i][j]=sum;            /* i.e. if s2 is a death state and if the date of death is known then the contribution
     }               to the likelihood is the probability to die between last step unit time and current 
     big=0.0;               step unit time, which is also the differences between probability to die before dh 
     for (i=j;i<=n;i++) {               and probability to die before dh-stepm . 
       sum=a[i][j];               In version up to 0.92 likelihood was computed
       for (k=1;k<j;k++)          as if date of death was unknown. Death was treated as any other
         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
       if ( (dum=vv[i]*fabs(sum)) >= big) {          to consider that at each interview the state was recorded
         big=dum;          (healthy, disable or death) and IMaCh was corrected; but when we
         imax=i;          introduced the exact date of death then we should have modified
       }          the contribution of an exact death to the likelihood. This new
     }          contribution is smaller and very dependent of the step unit
     if (j != imax) {          stepm. It is no more the probability to die between last interview
       for (k=1;k<=n;k++) {          and month of death but the probability to survive from last
         dum=a[imax][k];          interview up to one month before death multiplied by the
         a[imax][k]=a[j][k];          probability to die within a month. Thanks to Chris
         a[j][k]=dum;          Jackson for correcting this bug.  Former versions increased
       }          mortality artificially. The bad side is that we add another loop
       *d = -(*d);          which slows down the processing. The difference can be up to 10%
       vv[imax]=vv[j];          lower mortality.
     }            */
     indx[j]=imax;            lli=log(out[s1][s2] - savm[s1][s2]);
     if (a[j][j] == 0.0) a[j][j]=TINY;          }else{
     if (j != n) {            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       dum=1.0/(a[j][j]);            /*  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 (i=j+1;i<=n;i++) a[i][j] *= dum;          } 
     }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   }          /*if(lli ==000.0)*/
   free_vector(vv,1,n);  /* Doesn't work */          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
 ;          ipmx +=1;
 }          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 void lubksb(double **a, int n, int *indx, double b[])        } /* end of wave */
 {      } /* end of individual */
   int i,ii=0,ip,j;    }  else if(mle==2){
   double sum;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   for (i=1;i<=n;i++) {        for(mi=1; mi<= wav[i]-1; mi++){
     ip=indx[i];          for (ii=1;ii<=nlstate+ndeath;ii++)
     sum=b[ip];            for (j=1;j<=nlstate+ndeath;j++){
     b[ip]=b[i];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     if (ii)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];            }
     else if (sum) ii=i;          for(d=0; d<=dh[mi][i]; d++){
     b[i]=sum;            newm=savm;
   }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   for (i=n;i>=1;i--) {            for (kk=1; kk<=cptcovage;kk++) {
     sum=b[i];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];            }
     b[i]=sum/a[i][i];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 }            savm=oldm;
             oldm=newm;
 /************ Frequencies ********************/          } /* end mult */
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1,double **mint,double **anint)        
 {  /* Some frequencies */          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
            /* But now since version 0.9 we anticipate for bias and large stepm.
   int i, m, jk, k1, k2,i1, j1, bool, z1,z2,j;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   double ***freq; /* Frequencies */           * (in months) between two waves is not a multiple of stepm, we rounded to 
   double *pp;           * the nearest (and in case of equal distance, to the lowest) interval but now
   double pos;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   FILE *ficresp;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   char fileresp[FILENAMELENGTH];           * 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
   pp=vector(1,nlstate);           * -stepm/2 to stepm/2 .
   probs= ma3x(1,130 ,1,8, 1,8);           * For stepm=1 the results are the same as for previous versions of Imach.
   strcpy(fileresp,"p");           * For stepm > 1 the results are less biased than in previous versions. 
   strcat(fileresp,fileres);           */
   if((ficresp=fopen(fileresp,"w"))==NULL) {          s1=s[mw[mi][i]][i];
     printf("Problem with prevalence resultfile: %s\n", fileresp);          s2=s[mw[mi+1][i]][i];
     exit(0);          bbh=(double)bh[mi][i]/(double)stepm; 
   }          /* bias is positive if real duration
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);           * is higher than the multiple of stepm and negative otherwise.
   j1=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 */
   j=cptcoveff;          /* 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 (cptcovn<1) {j=1;ncodemax[1]=1;}          /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
           /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   for(k1=1; k1<=j;k1++){          /*if(lli ==000.0)*/
    for(i1=1; i1<=ncodemax[k1];i1++){          /*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++;          ipmx +=1;
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);          sw += weight[i];
          scanf("%d", i);*/          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         for (i=-1; i<=nlstate+ndeath; i++)          } /* end of wave */
          for (jk=-1; jk<=nlstate+ndeath; jk++)        } /* end of individual */
            for(m=agemin; m <= agemax+3; m++)    }  else if(mle==3){  /* exponential inter-extrapolation */
              freq[i][jk][m]=0;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
        for (i=1; i<=imx; i++) {        for(mi=1; mi<= wav[i]-1; mi++){
          bool=1;          for (ii=1;ii<=nlstate+ndeath;ii++)
          if  (cptcovn>0) {            for (j=1;j<=nlstate+ndeath;j++){
            for (z1=1; z1<=cptcoveff; z1++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                bool=0;            }
          }          for(d=0; d<dh[mi][i]; d++){
           if (bool==1) {            newm=savm;
             for(m=fprev1; m<=lprev1; m++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
              k2=anint[m][i]+(mint[m][i]/12.);            for (kk=1; kk<=cptcovage;kk++) {
              if ((k2>=1984) && (k2<=1988.5)) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
              if(agev[m][i]==0) agev[m][i]=agemax+1;            }
              if(agev[m][i]==1) agev[m][i]=agemax+2;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];            savm=oldm;
              }            oldm=newm;
             }          } /* end mult */
           }        
        }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         if  (cptcovn>0) {          /* But now since version 0.9 we anticipate for bias and large stepm.
          fprintf(ficresp, "\n#********** Variable ");           * If stepm is larger than one month (smallest stepm) and if the exact delay 
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);           * (in months) between two waves is not a multiple of stepm, we rounded to 
        fprintf(ficresp, "**********\n#");           * the nearest (and in case of equal distance, to the lowest) interval but now
         }           * we keep into memory the bias bh[mi][i] and also the previous matrix product
        for(i=1; i<=nlstate;i++)           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);           * 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=(int)agemin; i <= (int)agemax+3; i++){           * For stepm=1 the results are the same as for previous versions of Imach.
     if(i==(int)agemax+3)           * For stepm > 1 the results are less biased than in previous versions. 
       printf("Total");           */
     else          s1=s[mw[mi][i]][i];
       printf("Age %d", i);          s2=s[mw[mi+1][i]][i];
     for(jk=1; jk <=nlstate ; jk++){          bbh=(double)bh[mi][i]/(double)stepm; 
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          /* bias is positive if real duration
         pp[jk] += freq[jk][m][i];           * is higher than the multiple of stepm and negative otherwise.
     }           */
     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, pos=0; m <=0 ; 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 */
         pos += freq[jk][m][i];          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       if(pp[jk]>=1.e-10)          /*if(lli ==000.0)*/
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[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); */
       else          ipmx +=1;
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          sw += weight[i];
     }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
      for(jk=1; jk <=nlstate ; jk++){      } /* end of individual */
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    }else if (mle==4){  /* ml=4 no inter-extrapolation */
         pp[jk] += freq[jk][m][i];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
     for(jk=1,pos=0; jk <=nlstate ; jk++)          for (ii=1;ii<=nlstate+ndeath;ii++)
       pos += pp[jk];            for (j=1;j<=nlstate+ndeath;j++){
     for(jk=1; jk <=nlstate ; jk++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       if(pos>=1.e-5)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);            }
       else          for(d=0; d<dh[mi][i]; d++){
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);            newm=savm;
       if( i <= (int) agemax){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         if(pos>=1.e-5){            for (kk=1; kk<=cptcovage;kk++) {
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           probs[i][jk][j1]= pp[jk]/pos;            }
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/          
         }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       else                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);            savm=oldm;
       }            oldm=newm;
     }          } /* end mult */
     for(jk=-1; jk <=nlstate+ndeath; jk++)        
       for(m=-1; m <=nlstate+ndeath; m++)          s1=s[mw[mi][i]][i];
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          s2=s[mw[mi+1][i]][i];
     if(i <= (int) agemax)          if( s2 > nlstate){ 
       fprintf(ficresp,"\n");            lli=log(out[s1][s2] - savm[s1][s2]);
     printf("\n");          }else{
     }            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     }          }
  }          ipmx +=1;
            sw += weight[i];
   fclose(ficresp);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  /*      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]); */
   free_vector(pp,1,nlstate);        } /* end of wave */
       } /* end of individual */
 }  /* End of Freq */    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 /************ Prevalence ********************/        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax, int fprev1,int lprev1)        for(mi=1; mi<= wav[i]-1; mi++){
 {  /* Some frequencies */          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double ***freq; /* Frequencies */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double *pp;            }
   double pos;          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
   pp=vector(1,nlstate);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   probs= ma3x(1,130 ,1,8, 1,8);            for (kk=1; kk<=cptcovage;kk++) {
                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);            }
   j1=0;          
              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   j=cptcoveff;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            savm=oldm;
              oldm=newm;
  for(k1=1; k1<=j;k1++){          } /* end mult */
     for(i1=1; i1<=ncodemax[k1];i1++){        
       j1++;          s1=s[mw[mi][i]][i];
            s2=s[mw[mi+1][i]][i];
       for (i=-1; i<=nlstate+ndeath; i++)            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         for (jk=-1; jk<=nlstate+ndeath; jk++)            ipmx +=1;
           for(m=agemin; m <= agemax+3; m++)          sw += weight[i];
           freq[i][jk][m]=0;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
       for (i=1; i<=imx; i++) {        } /* end of wave */
         bool=1;      } /* end of individual */
         if  (cptcovn>0) {    } /* End of if */
           for (z1=1; z1<=cptcoveff; z1++)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
               bool=0;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
               }    return -l;
         if (bool==1) {  }
           for(m=fprev1; m<=lprev1; m++){  
             if(agev[m][i]==0) agev[m][i]=agemax+1;  /*************** log-likelihood *************/
             if(agev[m][i]==1) agev[m][i]=agemax+2;  double funcone( double *x)
             freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  {
             freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[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];
       }    double **out;
        for(i=(int)agemin; i <= (int)agemax+3; i++){    double lli; /* Individual log likelihood */
         for(jk=1; jk <=nlstate ; jk++){    double llt;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    int s1, s2;
             pp[jk] += freq[jk][m][i];    double bbh, survp;
         }    /*extern weight */
         for(jk=1; jk <=nlstate ; jk++){    /* We are differentiating ll according to initial status */
           for(m=-1, pos=0; m <=0 ; m++)    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
             pos += freq[jk][m][i];    /*for(i=1;i<imx;i++) 
         }      printf(" %d\n",s[4][i]);
            */
          for(jk=1; jk <=nlstate ; jk++){    cov[1]=1.;
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  
              pp[jk] += freq[jk][m][i];    for(k=1; k<=nlstate; k++) ll[k]=0.;
          }  
              for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){
          for(jk=1; jk <=nlstate ; jk++){                  for (ii=1;ii<=nlstate+ndeath;ii++)
            if( i <= (int) agemax){          for (j=1;j<=nlstate+ndeath;j++){
              if(pos>=1.e-5){            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                probs[i][jk][j1]= pp[jk]/pos;            savm[ii][j]=(ii==j ? 1.0 : 0.0);
              }          }
            }        for(d=0; d<dh[mi][i]; d++){
          }          newm=savm;
                    cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
          }          for (kk=1; kk<=cptcovage;kk++) {
     }            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   }          }
            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          savm=oldm;
   free_vector(pp,1,nlstate);          oldm=newm;
          } /* end mult */
 }  /* End of Freq */        
 /************* Waves Concatenation ***************/        s1=s[mw[mi][i]][i];
         s2=s[mw[mi+1][i]][i];
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)        bbh=(double)bh[mi][i]/(double)stepm; 
 {        /* bias is positive if real duration
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.         * is higher than the multiple of stepm and negative otherwise.
      Death is a valid wave (if date is known).         */
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i        if( s2 > nlstate && (mle <5) ){  /* Jackson */
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          lli=log(out[s1][s2] - savm[s1][s2]);
      and mw[mi+1][i]. dh depends on stepm.        } else if (mle==1){
      */          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         } else if(mle==2){
   int i, mi, m;          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 */
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        } else if(mle==3){  /* exponential inter-extrapolation */
      double sum=0., jmean=0.;*/          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
         } else if (mle==4){  /* mle=4 no inter-extrapolation */
   int j, k=0,jk, ju, jl;          lli=log(out[s1][s2]); /* Original formula */
   double sum=0.;        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
   jmin=1e+5;          lli=log(out[s1][s2]); /* Original formula */
   jmax=-1;        } /* End of if */
   jmean=0.;        ipmx +=1;
   for(i=1; i<=imx; i++){        sw += weight[i];
     mi=0;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     m=firstpass;  /*       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]); */
     while(s[m][i] <= nlstate){        if(globpr){
       if(s[m][i]>=1)          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
         mw[++mi][i]=m;   %10.6f %10.6f %10.6f ", \
       if(m >=lastpass)                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
         break;                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
       else          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
         m++;            llt +=ll[k]*gipmx/gsw;
     }/* end while */            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
     if (s[m][i] > nlstate){          }
       mi++;     /* Death is another wave */          fprintf(ficresilk," %10.6f\n", -llt);
       /* if(mi==0)  never been interviewed correctly before death */        }
          /* Only death is a correct wave */      } /* end of wave */
       mw[mi][i]=m;    } /* end of individual */
     }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     wav[i]=mi;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     if(mi==0)    if(globpr==0){ /* First time we count the contributions and weights */
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);      gipmx=ipmx;
   }      gsw=sw;
     }
   for(i=1; i<=imx; i++){    return -l;
     for(mi=1; mi<wav[i];mi++){  }
       if (stepm <=0)  
         dh[mi][i]=1;  char *subdirf(char fileres[])
       else{  {
         if (s[mw[mi+1][i]][i] > nlstate) {    
           if (agedc[i] < 2*AGESUP) {    strcpy(tmpout,optionfilefiname);
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    strcat(tmpout,"/"); /* Add to the right */
           if(j==0) j=1;  /* Survives at least one month after exam */    strcat(tmpout,fileres);
           k=k+1;    return tmpout;
           if (j >= jmax) jmax=j;  }
           if (j <= jmin) jmin=j;  
           sum=sum+j;  char *subdirf2(char fileres[], char *preop)
           /* if (j<10) printf("j=%d num=%d ",j,i); */  {
           }    
         }    strcpy(tmpout,optionfilefiname);
         else{    strcat(tmpout,"/");
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    strcat(tmpout,preop);
           k=k+1;    strcat(tmpout,fileres);
           if (j >= jmax) jmax=j;    return tmpout;
           else if (j <= jmin)jmin=j;  }
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */  char *subdirf3(char fileres[], char *preop, char *preop2)
           sum=sum+j;  {
         }    
         jk= j/stepm;    strcpy(tmpout,optionfilefiname);
         jl= j -jk*stepm;    strcat(tmpout,"/");
         ju= j -(jk+1)*stepm;    strcat(tmpout,preop);
         if(jl <= -ju)    strcat(tmpout,preop2);
           dh[mi][i]=jk;    strcat(tmpout,fileres);
         else    return tmpout;
           dh[mi][i]=jk+1;  }
         if(dh[mi][i]==0)  
           dh[mi][i]=1; /* At least one step */  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
       }  {
     }    /* This routine should help understanding what is done with 
   }       the selection of individuals/waves and
   jmean=sum/k;       to check the exact contribution to the likelihood.
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);       Plotting could be done.
  }     */
 /*********** Tricode ****************************/    int k;
 void tricode(int *Tvar, int **nbcode, int imx)  
 {    if(*globpri !=0){ /* Just counts and sums, no printings */
   int Ndum[20],ij=1, k, j, i;      strcpy(fileresilk,"ilk"); 
   int cptcode=0;      strcat(fileresilk,fileres);
   cptcoveff=0;      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
          printf("Problem with resultfile: %s\n", fileresilk);
   for (k=0; k<19; k++) Ndum[k]=0;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   for (k=1; k<=7; k++) ncodemax[k]=0;      }
       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");
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     for (i=1; i<=imx; i++) {      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       ij=(int)(covar[Tvar[j]][i]);      for(k=1; k<=nlstate; k++) 
       Ndum[ij]++;        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
       if (ij > cptcode) cptcode=ij;    }
     }  
     *fretone=(*funcone)(p);
     for (i=0; i<=cptcode; i++) {    if(*globpri !=0){
       if(Ndum[i]!=0) ncodemax[j]++;      fclose(ficresilk);
     }      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
     ij=1;      fflush(fichtm); 
     } 
     return;
     for (i=1; i<=ncodemax[j]; i++) {  }
       for (k=0; k<=19; k++) {  
         if (Ndum[k] != 0) {  
           nbcode[Tvar[j]][ij]=k;  /*********** Maximum Likelihood Estimation ***************/
           ij++;  
         }  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
         if (ij > ncodemax[j]) break;  {
       }      int i,j, iter;
     }    double **xi;
   }      double fret;
     double fretone; /* Only one call to likelihood */
  for (k=0; k<19; k++) Ndum[k]=0;    char filerespow[FILENAMELENGTH];
     xi=matrix(1,npar,1,npar);
  for (i=1; i<=ncovmodel-2; i++) {    for (i=1;i<=npar;i++)
       ij=Tvar[i];      for (j=1;j<=npar;j++)
       Ndum[ij]++;        xi[i][j]=(i==j ? 1.0 : 0.0);
     }    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow"); 
  ij=1;    strcat(filerespow,fileres);
  for (i=1; i<=10; i++) {    if((ficrespow=fopen(filerespow,"w"))==NULL) {
    if((Ndum[i]!=0) && (i<=ncov)){      printf("Problem with resultfile: %s\n", filerespow);
      Tvaraff[ij]=i;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
      ij++;    }
    }    fprintf(ficrespow,"# Powell\n# iter -2*LL");
  }    for (i=1;i<=nlstate;i++)
        for(j=1;j<=nlstate+ndeath;j++)
     cptcoveff=ij-1;        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
 }    fprintf(ficrespow,"\n");
   
 /*********** Health Expectancies ****************/    powell(p,xi,npar,ftol,&iter,&fret,func);
   
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)    fclose(ficrespow);
 {    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   /* Health expectancies */    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   int i, j, nhstepm, hstepm, h;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   double age, agelim,hf;  
   double ***p3mat;  }
    
   fprintf(ficreseij,"# Health expectancies\n");  /**** Computes Hessian and covariance matrix ***/
   fprintf(ficreseij,"# Age");  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   for(i=1; i<=nlstate;i++)  {
     for(j=1; j<=nlstate;j++)    double  **a,**y,*x,pd;
       fprintf(ficreseij," %1d-%1d",i,j);    double **hess;
   fprintf(ficreseij,"\n");    int i, j,jk;
     int *indx;
   hstepm=1*YEARM; /*  Every j years of age (in month) */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    double hessii(double p[], double delta, int theta, double delti[]);
     double hessij(double p[], double delti[], int i, int j);
   agelim=AGESUP;    void lubksb(double **a, int npar, int *indx, double b[]) ;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    void ludcmp(double **a, int npar, int *indx, double *d) ;
     /* nhstepm age range expressed in number of stepm */  
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);    hess=matrix(1,npar,1,npar);
     /* Typically if 20 years = 20*12/6=40 stepm */  
     if (stepm >= YEARM) hstepm=1;    printf("\nCalculation of the hessian matrix. Wait...\n");
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for (i=1;i<=npar;i++){
     /* Computed by stepm unit matrices, product of hstepm matrices, stored      printf("%d",i);fflush(stdout);
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */      fprintf(ficlog,"%d",i);fflush(ficlog);
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);        hess[i][i]=hessii(p,ftolhess,i,delti);
       /*printf(" %f ",p[i]);*/
       /*printf(" %lf ",hess[i][i]);*/
     for(i=1; i<=nlstate;i++)    }
       for(j=1; j<=nlstate;j++)    
         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++)  {
         }        if (j>i) { 
              printf(".%d%d",i,j);fflush(stdout);
     hf=1;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     if (stepm >= YEARM) hf=stepm/YEARM;          hess[i][j]=hessij(p,delti,i,j);
     fprintf(ficreseij,"%.0f",age );          hess[j][i]=hess[i][j];    
     for(i=1; i<=nlstate;i++)          /*printf(" %lf ",hess[i][j]);*/
       for(j=1; j<=nlstate;j++){        }
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);      }
       }    }
     fprintf(ficreseij,"\n");    printf("\n");
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficlog,"\n");
   }  
 }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
 /************ Variance ******************/    
 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)    a=matrix(1,npar,1,npar);
 {    y=matrix(1,npar,1,npar);
   /* Variance of health expectancies */    x=vector(1,npar);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    indx=ivector(1,npar);
   double **newm;    for (i=1;i<=npar;i++)
   double **dnewm,**doldm;      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   int i, j, nhstepm, hstepm, h;    ludcmp(a,npar,indx,&pd);
   int k, cptcode;  
   double *xp;    for (j=1;j<=npar;j++) {
   double **gp, **gm;      for (i=1;i<=npar;i++) x[i]=0;
   double ***gradg, ***trgradg;      x[j]=1;
   double ***p3mat;      lubksb(a,npar,indx,x);
   double age,agelim;      for (i=1;i<=npar;i++){ 
   int theta;        matcov[i][j]=x[i];
       }
    fprintf(ficresvij,"# Covariances of life expectancies\n");    }
   fprintf(ficresvij,"# Age");  
   for(i=1; i<=nlstate;i++)    printf("\n#Hessian matrix#\n");
     for(j=1; j<=nlstate;j++)    fprintf(ficlog,"\n#Hessian matrix#\n");
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    for (i=1;i<=npar;i++) { 
   fprintf(ficresvij,"\n");      for (j=1;j<=npar;j++) { 
         printf("%.3e ",hess[i][j]);
   xp=vector(1,npar);        fprintf(ficlog,"%.3e ",hess[i][j]);
   dnewm=matrix(1,nlstate,1,npar);      }
   doldm=matrix(1,nlstate,1,nlstate);      printf("\n");
        fprintf(ficlog,"\n");
   hstepm=1*YEARM; /* Every year of age */    }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  
   agelim = AGESUP;    /* Recompute Inverse */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    for (i=1;i<=npar;i++)
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     if (stepm >= YEARM) hstepm=1;    ludcmp(a,npar,indx,&pd);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /*  printf("\n#Hessian matrix recomputed#\n");
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);  
     gp=matrix(0,nhstepm,1,nlstate);    for (j=1;j<=npar;j++) {
     gm=matrix(0,nhstepm,1,nlstate);      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
     for(theta=1; theta <=npar; theta++){      lubksb(a,npar,indx,x);
       for(i=1; i<=npar; i++){ /* Computes gradient */      for (i=1;i<=npar;i++){ 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        y[i][j]=x[i];
       }        printf("%.3e ",y[i][j]);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          fprintf(ficlog,"%.3e ",y[i][j]);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      }
       printf("\n");
       if (popbased==1) {      fprintf(ficlog,"\n");
         for(i=1; i<=nlstate;i++)    }
           prlim[i][i]=probs[(int)age][i][ij];    */
       }  
          free_matrix(a,1,npar,1,npar);
       for(j=1; j<= nlstate; j++){    free_matrix(y,1,npar,1,npar);
         for(h=0; h<=nhstepm; h++){    free_vector(x,1,npar);
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    free_ivector(indx,1,npar);
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    free_matrix(hess,1,npar,1,npar);
         }  
       }  
      }
       for(i=1; i<=npar; i++) /* Computes gradient */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  /*************** hessian matrix ****************/
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    double hessii( double x[], double delta, int theta, double delti[])
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  {
     int i;
       if (popbased==1) {    int l=1, lmax=20;
         for(i=1; i<=nlstate;i++)    double k1,k2;
           prlim[i][i]=probs[(int)age][i][ij];    double p2[NPARMAX+1];
       }    double res;
     double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
       for(j=1; j<= nlstate; j++){    double fx;
         for(h=0; h<=nhstepm; h++){    int k=0,kmax=10;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    double l1;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];  
         }    fx=func(x);
       }    for (i=1;i<=npar;i++) p2[i]=x[i];
     for(l=0 ; l <=lmax; l++){
       for(j=1; j<= nlstate; j++)      l1=pow(10,l);
         for(h=0; h<=nhstepm; h++){      delts=delt;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      for(k=1 ; k <kmax; k=k+1){
         }        delt = delta*(l1*k);
     } /* End theta */        p2[theta]=x[theta] +delt;
         k1=func(p2)-fx;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);        p2[theta]=x[theta]-delt;
         k2=func(p2)-fx;
     for(h=0; h<=nhstepm; h++)        /*res= (k1-2.0*fx+k2)/delt/delt; */
       for(j=1; j<=nlstate;j++)        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         for(theta=1; theta <=npar; theta++)        
           trgradg[h][j][theta]=gradg[h][theta][j];  #ifdef DEBUG
         printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
     for(i=1;i<=nlstate;i++)        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);
       for(j=1;j<=nlstate;j++)  #endif
         vareij[i][j][(int)age] =0.;        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
     for(h=0;h<=nhstepm;h++){        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
       for(k=0;k<=nhstepm;k++){          k=kmax;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);        }
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
         for(i=1;i<=nlstate;i++)          k=kmax; l=lmax*10.;
           for(j=1;j<=nlstate;j++)        }
             vareij[i][j][(int)age] += doldm[i][j];        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       }          delts=delt;
     }        }
     h=1;      }
     if (stepm >= YEARM) h=stepm/YEARM;    }
     fprintf(ficresvij,"%.0f ",age );    delti[theta]=delts;
     for(i=1; i<=nlstate;i++)    return res; 
       for(j=1; j<=nlstate;j++){    
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);  }
       }  
     fprintf(ficresvij,"\n");  double hessij( double x[], double delti[], int thetai,int thetaj)
     free_matrix(gp,0,nhstepm,1,nlstate);  {
     free_matrix(gm,0,nhstepm,1,nlstate);    int i;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    int l=1, l1, lmax=20;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    double k1,k2,k3,k4,res,fx;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double p2[NPARMAX+1];
   } /* End age */    int k;
    
   free_vector(xp,1,npar);    fx=func(x);
   free_matrix(doldm,1,nlstate,1,npar);    for (k=1; k<=2; k++) {
   free_matrix(dnewm,1,nlstate,1,nlstate);      for (i=1;i<=npar;i++) p2[i]=x[i];
       p2[thetai]=x[thetai]+delti[thetai]/k;
 }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k1=func(p2)-fx;
 /************ 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)      p2[thetai]=x[thetai]+delti[thetai]/k;
 {      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   /* Variance of prevalence limit */      k2=func(p2)-fx;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    
   double **newm;      p2[thetai]=x[thetai]-delti[thetai]/k;
   double **dnewm,**doldm;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   int i, j, nhstepm, hstepm;      k3=func(p2)-fx;
   int k, cptcode;    
   double *xp;      p2[thetai]=x[thetai]-delti[thetai]/k;
   double *gp, *gm;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   double **gradg, **trgradg;      k4=func(p2)-fx;
   double age,agelim;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   int theta;  #ifdef DEBUG
          printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");      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);
   fprintf(ficresvpl,"# Age");  #endif
   for(i=1; i<=nlstate;i++)    }
       fprintf(ficresvpl," %1d-%1d",i,i);    return res;
   fprintf(ficresvpl,"\n");  }
   
   xp=vector(1,npar);  /************** Inverse of matrix **************/
   dnewm=matrix(1,nlstate,1,npar);  void ludcmp(double **a, int n, int *indx, double *d) 
   doldm=matrix(1,nlstate,1,nlstate);  { 
      int i,imax,j,k; 
   hstepm=1*YEARM; /* Every year of age */    double big,dum,sum,temp; 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    double *vv; 
   agelim = AGESUP;   
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    vv=vector(1,n); 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    *d=1.0; 
     if (stepm >= YEARM) hstepm=1;    for (i=1;i<=n;i++) { 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      big=0.0; 
     gradg=matrix(1,npar,1,nlstate);      for (j=1;j<=n;j++) 
     gp=vector(1,nlstate);        if ((temp=fabs(a[i][j])) > big) big=temp; 
     gm=vector(1,nlstate);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       vv[i]=1.0/big; 
     for(theta=1; theta <=npar; theta++){    } 
       for(i=1; i<=npar; i++){ /* Computes gradient */    for (j=1;j<=n;j++) { 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      for (i=1;i<j;i++) { 
       }        sum=a[i][j]; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
       for(i=1;i<=nlstate;i++)        a[i][j]=sum; 
         gp[i] = prlim[i][i];      } 
          big=0.0; 
       for(i=1; i<=npar; i++) /* Computes gradient */      for (i=j;i<=n;i++) { 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        sum=a[i][j]; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        for (k=1;k<j;k++) 
       for(i=1;i<=nlstate;i++)          sum -= a[i][k]*a[k][j]; 
         gm[i] = prlim[i][i];        a[i][j]=sum; 
         if ( (dum=vv[i]*fabs(sum)) >= big) { 
       for(i=1;i<=nlstate;i++)          big=dum; 
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          imax=i; 
     } /* End theta */        } 
       } 
     trgradg =matrix(1,nlstate,1,npar);      if (j != imax) { 
         for (k=1;k<=n;k++) { 
     for(j=1; j<=nlstate;j++)          dum=a[imax][k]; 
       for(theta=1; theta <=npar; theta++)          a[imax][k]=a[j][k]; 
         trgradg[j][theta]=gradg[theta][j];          a[j][k]=dum; 
         } 
     for(i=1;i<=nlstate;i++)        *d = -(*d); 
       varpl[i][(int)age] =0.;        vv[imax]=vv[j]; 
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      } 
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      indx[j]=imax; 
     for(i=1;i<=nlstate;i++)      if (a[j][j] == 0.0) a[j][j]=TINY; 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      if (j != n) { 
         dum=1.0/(a[j][j]); 
     fprintf(ficresvpl,"%.0f ",age );        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     for(i=1; i<=nlstate;i++)      } 
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    } 
     fprintf(ficresvpl,"\n");    free_vector(vv,1,n);  /* Doesn't work */
     free_vector(gp,1,nlstate);  ;
     free_vector(gm,1,nlstate);  } 
     free_matrix(gradg,1,npar,1,nlstate);  
     free_matrix(trgradg,1,nlstate,1,npar);  void lubksb(double **a, int n, int *indx, double b[]) 
   } /* End age */  { 
     int i,ii=0,ip,j; 
   free_vector(xp,1,npar);    double sum; 
   free_matrix(doldm,1,nlstate,1,npar);   
   free_matrix(dnewm,1,nlstate,1,nlstate);    for (i=1;i<=n;i++) { 
       ip=indx[i]; 
 }      sum=b[ip]; 
       b[ip]=b[i]; 
 /************ Variance of one-step probabilities  ******************/      if (ii) 
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
 {      else if (sum) ii=i; 
   int i, j;      b[i]=sum; 
   int k=0, cptcode;    } 
   double **dnewm,**doldm;    for (i=n;i>=1;i--) { 
   double *xp;      sum=b[i]; 
   double *gp, *gm;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   double **gradg, **trgradg;      b[i]=sum/a[i][i]; 
   double age,agelim, cov[NCOVMAX];    } 
   int theta;  } 
   char fileresprob[FILENAMELENGTH];  
   /************ Frequencies ********************/
   strcpy(fileresprob,"prob");  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)
   strcat(fileresprob,fileres);  {  /* Some frequencies */
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    
     printf("Problem with resultfile: %s\n", fileresprob);    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   }    int first;
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);    double ***freq; /* Frequencies */
      double *pp, **prop;
     double pos,posprop, k2, dateintsum=0,k2cpt=0;
   xp=vector(1,npar);    FILE *ficresp;
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    char fileresp[FILENAMELENGTH];
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    
      pp=vector(1,nlstate);
   cov[1]=1;    prop=matrix(1,nlstate,iagemin,iagemax+3);
   for (age=bage; age<=fage; age ++){    strcpy(fileresp,"p");
     cov[2]=age;    strcat(fileresp,fileres);
     gradg=matrix(1,npar,1,9);    if((ficresp=fopen(fileresp,"w"))==NULL) {
     trgradg=matrix(1,9,1,npar);      printf("Problem with prevalence resultfile: %s\n", fileresp);
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      exit(0);
        }
     for(theta=1; theta <=npar; theta++){    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
       for(i=1; i<=npar; i++)    j1=0;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    
          j=cptcoveff;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
      
       k=0;    first=1;
       for(i=1; i<= (nlstate+ndeath); i++){  
         for(j=1; j<=(nlstate+ndeath);j++){    for(k1=1; k1<=j;k1++){
            k=k+1;      for(i1=1; i1<=ncodemax[k1];i1++){
           gp[k]=pmmij[i][j];        j1++;
         }        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       }          scanf("%d", i);*/
         for (i=-1; i<=nlstate+ndeath; i++)  
       for(i=1; i<=npar; i++)          for (jk=-1; jk<=nlstate+ndeath; jk++)  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            for(m=iagemin; m <= iagemax+3; m++)
                  freq[i][jk][m]=0;
   
       pmij(pmmij,cov,ncovmodel,xp,nlstate);      for (i=1; i<=nlstate; i++)  
       k=0;        for(m=iagemin; m <= iagemax+3; m++)
       for(i=1; i<=(nlstate+ndeath); i++){          prop[i][m]=0;
         for(j=1; j<=(nlstate+ndeath);j++){        
           k=k+1;        dateintsum=0;
           gm[k]=pmmij[i][j];        k2cpt=0;
         }        for (i=1; i<=imx; i++) {
       }          bool=1;
                if  (cptcovn>0) {
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)            for (z1=1; z1<=cptcoveff; z1++) 
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];                if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     }                bool=0;
           }
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)          if (bool==1){
       for(theta=1; theta <=npar; theta++)            for(m=firstpass; m<=lastpass; m++){
       trgradg[j][theta]=gradg[theta][j];              k2=anint[m][i]+(mint[m][i]/12.);
                /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
      pmij(pmmij,cov,ncovmodel,x,nlstate);                if (m<lastpass) {
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
      k=0;                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
      for(i=1; i<=(nlstate+ndeath); i++){                }
        for(j=1; j<=(nlstate+ndeath);j++){                
          k=k+1;                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
          gm[k]=pmmij[i][j];                  dateintsum=dateintsum+k2;
         }                  k2cpt++;
      }                }
                      /*}*/
      /*printf("\n%d ",(int)age);            }
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){          }
                }
          
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
      }*/  
         if  (cptcovn>0) {
   fprintf(ficresprob,"\n%d ",(int)age);          fprintf(ficresp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){          fprintf(ficresp, "**********\n#");
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);        }
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);        for(i=1; i<=nlstate;i++) 
   }          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         fprintf(ficresp, "\n");
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));        
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));        for(i=iagemin; i <= iagemax+3; i++){
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          if(i==iagemax+3){
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            fprintf(ficlog,"Total");
 }          }else{
  free_vector(xp,1,npar);            if(first==1){
 fclose(ficresprob);              first=0;
  exit(0);              printf("See log file for details...\n");
 }            }
             fprintf(ficlog,"Age %d", i);
 /***********************************************/          }
 /**************** Main Program *****************/          for(jk=1; jk <=nlstate ; jk++){
 /***********************************************/            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
               pp[jk] += freq[jk][m][i]; 
 /*int main(int argc, char *argv[])*/          }
 int main()          for(jk=1; jk <=nlstate ; jk++){
 {            for(m=-1, pos=0; m <=0 ; m++)
               pos += freq[jk][m][i];
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;            if(pp[jk]>=1.e-10){
   double agedeb, agefin,hf;              if(first==1){
   double agemin=1.e20, agemax=-1.e20;              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
               }
   double fret;              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   double **xi,tmp,delta;            }else{
               if(first==1)
   double dum; /* Dummy variable */                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   double ***p3mat;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   int *indx;            }
   char line[MAXLINE], linepar[MAXLINE];          }
   char title[MAXLINE];  
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];          for(jk=1; jk <=nlstate ; jk++){
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   char filerest[FILENAMELENGTH];              pp[jk] += freq[jk][m][i];
   char fileregp[FILENAMELENGTH];          }       
   char popfile[FILENAMELENGTH];          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];            pos += pp[jk];
   int firstobs=1, lastobs=10;            posprop += prop[jk][i];
   int sdeb, sfin; /* Status at beginning and end */          }
   int c,  h , cpt,l;          for(jk=1; jk <=nlstate ; jk++){
   int ju,jl, mi;            if(pos>=1.e-5){
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;              if(first==1)
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   int mobilav=0, fprev, lprev ,fprevfore=1, lprevfore=1,nforecast,popforecast=0;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   int hstepm, nhstepm;            }else{
   int *popage;              if(first==1)
                 printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   double bage, fage, age, agelim, agebase;              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   double ftolpl=FTOL;            }
   double **prlim;            if( i <= iagemax){
   double *severity;              if(pos>=1.e-5){
   double ***param; /* Matrix of parameters */                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   double  *p;                /*probs[i][jk][j1]= pp[jk]/pos;*/
   double **matcov; /* Matrix of covariance */                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   double ***delti3; /* Scale */              }
   double *delti; /* Scale */              else
   double ***eij, ***vareij;                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   double **varpl; /* Variances of prevalence limits by age */            }
   double *epj, vepp;          }
   double kk1, kk2;          
   double *popeffectif,*popcount;          for(jk=-1; jk <=nlstate+ndeath; jk++)
             for(m=-1; m <=nlstate+ndeath; m++)
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";              if(freq[jk][m][i] !=0 ) {
   char *alph[]={"a","a","b","c","d","e"}, str[4];              if(first==1)
                 printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                 fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   char z[1]="c", occ;              }
 #include <sys/time.h>          if(i <= iagemax)
 #include <time.h>            fprintf(ficresp,"\n");
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];          if(first==1)
   /* long total_usecs;            printf("Others in log...\n");
   struct timeval start_time, end_time;          fprintf(ficlog,"\n");
          }
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      }
     }
     dateintmean=dateintsum/k2cpt; 
   printf("\nIMACH, Version 0.7");   
   printf("\nEnter the parameter file name: ");    fclose(ficresp);
     free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
 #ifdef windows    free_vector(pp,1,nlstate);
   scanf("%s",pathtot);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   getcwd(pathcd, size);    /* End of Freq */
   /*cygwin_split_path(pathtot,path,optionfile);  }
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/  
   /* cutv(path,optionfile,pathtot,'\\');*/  /************ 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)
 split(pathtot, path,optionfile);  {  
   chdir(path);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   replace(pathc,path);       in each health status at the date of interview (if between dateprev1 and dateprev2).
 #endif       We still use firstpass and lastpass as another selection.
 #ifdef unix    */
   scanf("%s",optionfile);   
 #endif    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     double ***freq; /* Frequencies */
 /*-------- arguments in the command line --------*/    double *pp, **prop;
     double pos,posprop; 
   strcpy(fileres,"r");    double  y2; /* in fractional years */
   strcat(fileres, optionfile);    int iagemin, iagemax;
   
   /*---------arguments file --------*/    iagemin= (int) agemin;
     iagemax= (int) agemax;
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    /*pp=vector(1,nlstate);*/
     printf("Problem with optionfile %s\n",optionfile);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     goto end;    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   }    j1=0;
     
   strcpy(filereso,"o");    j=cptcoveff;
   strcat(filereso,fileres);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   if((ficparo=fopen(filereso,"w"))==NULL) {    
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    for(k1=1; k1<=j;k1++){
   }      for(i1=1; i1<=ncodemax[k1];i1++){
         j1++;
   /* Reads comments: lines beginning with '#' */        
   while((c=getc(ficpar))=='#' && c!= EOF){        for (i=1; i<=nlstate; i++)  
     ungetc(c,ficpar);          for(m=iagemin; m <= iagemax+3; m++)
     fgets(line, MAXLINE, ficpar);            prop[i][m]=0.0;
     puts(line);       
     fputs(line,ficparo);        for (i=1; i<=imx; i++) { /* Each individual */
   }          bool=1;
   ungetc(c,ficpar);          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
   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);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   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);                bool=0;
   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);          } 
 while((c=getc(ficpar))=='#' && c!= EOF){          if (bool==1) { 
     ungetc(c,ficpar);            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     fgets(line, MAXLINE, ficpar);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     puts(line);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
     fputs(line,ficparo);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   ungetc(c,ficpar);                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); 
                  if (s[m][i]>0 && s[m][i]<=nlstate) { 
   fscanf(ficpar,"fprevalence=%d lprevalence=%d pop_based=%d\n",&fprev,&lprev,&popbased);                  /*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]]);*/
   fprintf(ficparo,"fprevalence=%d lprevalence=%d pop_based=%d\n",fprev,lprev,popbased);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                    prop[s[m][i]][iagemax+3] += weight[i]; 
  while((c=getc(ficpar))=='#' && c!= EOF){                } 
     ungetc(c,ficpar);              }
     fgets(line, MAXLINE, ficpar);            } /* end selection of waves */
     puts(line);          }
     fputs(line,ficparo);        }
   }        for(i=iagemin; i <= iagemax+3; i++){  
   ungetc(c,ficpar);          
            for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   fscanf(ficpar,"fprevalence=%d lprevalence=%d nforecast=%d mob_average=%d\n",&fprevfore,&lprevfore,&nforecast,&mobilav);            posprop += prop[jk][i]; 
   fprintf(ficparo,"fprevalence=%d lprevalence=%d nforecast=%d mob_average=%d\n",fprevfore,lprevfore,nforecast,mobilav);          } 
        
            for(jk=1; jk <=nlstate ; jk++){     
 while((c=getc(ficpar))=='#' && c!= EOF){            if( i <=  iagemax){ 
     ungetc(c,ficpar);              if(posprop>=1.e-5){ 
     fgets(line, MAXLINE, ficpar);                probs[i][jk][j1]= prop[jk][i]/posprop;
     puts(line);              } 
     fputs(line,ficparo);            } 
   }          }/* end jk */ 
   ungetc(c,ficpar);        }/* end i */ 
        } /* end i1 */
   fscanf(ficpar,"popforecast=%d popfile=%s\n",&popforecast,popfile);    } /* end k1 */
      
   covar=matrix(0,NCOVMAX,1,n);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   cptcovn=0;    /*free_vector(pp,1,nlstate);*/
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  /* End of prevalence */
   ncovmodel=2+cptcovn;  
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  /************* Waves Concatenation ***************/
    
   /* Read guess parameters */  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)
   /* Reads comments: lines beginning with '#' */  {
   while((c=getc(ficpar))=='#' && c!= EOF){    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     ungetc(c,ficpar);       Death is a valid wave (if date is known).
     fgets(line, MAXLINE, ficpar);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     puts(line);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
     fputs(line,ficparo);       and mw[mi+1][i]. dh depends on stepm.
   }       */
   ungetc(c,ficpar);  
      int i, mi, m;
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     for(i=1; i <=nlstate; i++)       double sum=0., jmean=0.;*/
     for(j=1; j <=nlstate+ndeath-1; j++){    int first;
       fscanf(ficpar,"%1d%1d",&i1,&j1);    int j, k=0,jk, ju, jl;
       fprintf(ficparo,"%1d%1d",i1,j1);    double sum=0.;
       printf("%1d%1d",i,j);    first=0;
       for(k=1; k<=ncovmodel;k++){    jmin=1e+5;
         fscanf(ficpar," %lf",&param[i][j][k]);    jmax=-1;
         printf(" %lf",param[i][j][k]);    jmean=0.;
         fprintf(ficparo," %lf",param[i][j][k]);    for(i=1; i<=imx; i++){
       }      mi=0;
       fscanf(ficpar,"\n");      m=firstpass;
       printf("\n");      while(s[m][i] <= nlstate){
       fprintf(ficparo,"\n");        if(s[m][i]>=1)
     }          mw[++mi][i]=m;
          if(m >=lastpass)
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;          break;
         else
   p=param[1][1];          m++;
        }/* end while */
   /* Reads comments: lines beginning with '#' */      if (s[m][i] > nlstate){
   while((c=getc(ficpar))=='#' && c!= EOF){        mi++;     /* Death is another wave */
     ungetc(c,ficpar);        /* if(mi==0)  never been interviewed correctly before death */
     fgets(line, MAXLINE, ficpar);           /* Only death is a correct wave */
     puts(line);        mw[mi][i]=m;
     fputs(line,ficparo);      }
   }  
   ungetc(c,ficpar);      wav[i]=mi;
       if(mi==0){
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        if(first==0){
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
   for(i=1; i <=nlstate; i++){          first=1;
     for(j=1; j <=nlstate+ndeath-1; j++){        }
       fscanf(ficpar,"%1d%1d",&i1,&j1);        if(first==1){
       printf("%1d%1d",i,j);          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
       fprintf(ficparo,"%1d%1d",i1,j1);        }
       for(k=1; k<=ncovmodel;k++){      } /* end mi==0 */
         fscanf(ficpar,"%le",&delti3[i][j][k]);    } /* End individuals */
         printf(" %le",delti3[i][j][k]);  
         fprintf(ficparo," %le",delti3[i][j][k]);    for(i=1; i<=imx; i++){
       }      for(mi=1; mi<wav[i];mi++){
       fscanf(ficpar,"\n");        if (stepm <=0)
       printf("\n");          dh[mi][i]=1;
       fprintf(ficparo,"\n");        else{
     }          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   }            if (agedc[i] < 2*AGESUP) {
   delti=delti3[1][1];              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
                if(j==0) j=1;  /* Survives at least one month after exam */
   /* Reads comments: lines beginning with '#' */              else if(j<0){
   while((c=getc(ficpar))=='#' && c!= EOF){                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]);
     ungetc(c,ficpar);                j=1; /* Careful Patch */
     fgets(line, MAXLINE, ficpar);                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);
     puts(line);                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]);
     fputs(line,ficparo);                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);
   }              }
   ungetc(c,ficpar);              k=k+1;
                if (j >= jmax) jmax=j;
   matcov=matrix(1,npar,1,npar);              if (j <= jmin) jmin=j;
   for(i=1; i <=npar; i++){              sum=sum+j;
     fscanf(ficpar,"%s",&str);              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
     printf("%s",str);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     fprintf(ficparo,"%s",str);            }
     for(j=1; j <=i; j++){          }
       fscanf(ficpar," %le",&matcov[i][j]);          else{
       printf(" %.5le",matcov[i][j]);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
       fprintf(ficparo," %.5le",matcov[i][j]);            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     }            k=k+1;
     fscanf(ficpar,"\n");            if (j >= jmax) jmax=j;
     printf("\n");            else if (j <= jmin)jmin=j;
     fprintf(ficparo,"\n");            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   }            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
   for(i=1; i <=npar; i++)            if(j<0){
     for(j=i+1;j<=npar;j++)              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]);
       matcov[i][j]=matcov[j][i];              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                }
   printf("\n");            sum=sum+j;
           }
           jk= j/stepm;
     /*-------- data file ----------*/          jl= j -jk*stepm;
     if((ficres =fopen(fileres,"w"))==NULL) {          ju= j -(jk+1)*stepm;
       printf("Problem with resultfile: %s\n", fileres);goto end;          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
     }            if(jl==0){
     fprintf(ficres,"#%s\n",version);              dh[mi][i]=jk;
                  bh[mi][i]=0;
     if((fic=fopen(datafile,"r"))==NULL)    {            }else{ /* We want a negative bias in order to only have interpolation ie
       printf("Problem with datafile: %s\n", datafile);goto end;                    * at the price of an extra matrix product in likelihood */
     }              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
     n= lastobs;            }
     severity = vector(1,maxwav);          }else{
     outcome=imatrix(1,maxwav+1,1,n);            if(jl <= -ju){
     num=ivector(1,n);              dh[mi][i]=jk;
     moisnais=vector(1,n);              bh[mi][i]=jl;       /* bias is positive if real duration
     annais=vector(1,n);                                   * is higher than the multiple of stepm and negative otherwise.
     moisdc=vector(1,n);                                   */
     andc=vector(1,n);            }
     agedc=vector(1,n);            else{
     cod=ivector(1,n);              dh[mi][i]=jk+1;
     weight=vector(1,n);              bh[mi][i]=ju;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */            }
     mint=matrix(1,maxwav,1,n);            if(dh[mi][i]==0){
     anint=matrix(1,maxwav,1,n);              dh[mi][i]=1; /* At least one step */
     s=imatrix(1,maxwav+1,1,n);              bh[mi][i]=ju; /* At least one step */
     adl=imatrix(1,maxwav+1,1,n);                  /*  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);*/
     tab=ivector(1,NCOVMAX);            }
     ncodemax=ivector(1,8);          } /* end if mle */
         }
     i=1;      } /* end wave */
     while (fgets(line, MAXLINE, fic) != NULL)    {    }
       if ((i >= firstobs) && (i <=lastobs)) {    jmean=sum/k;
            printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
         for (j=maxwav;j>=1;j--){    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
           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);  /*********** Tricode ****************************/
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  void tricode(int *Tvar, int **nbcode, int imx)
         }  {
            
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    int Ndum[20],ij=1, k, j, i, maxncov=19;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    int cptcode=0;
     cptcoveff=0; 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);   
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    for (k=0; k<maxncov; k++) Ndum[k]=0;
     for (k=1; k<=7; k++) ncodemax[k]=0;
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);  
         for (j=ncov;j>=1;j--){    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
         }                                 modality*/ 
         num[i]=atol(stra);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
                Ndum[ij]++; /*store the modality */
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
                                          Tvar[j]. If V=sex and male is 0 and 
         i=i+1;                                         female is 1, then  cptcode=1.*/
       }      }
     }  
     /* printf("ii=%d", ij);      for (i=0; i<=cptcode; i++) {
        scanf("%d",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 */
   imx=i-1; /* Number of individuals */      }
   
   /* for (i=1; i<=imx; i++){      ij=1; 
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;      for (i=1; i<=ncodemax[j]; i++) {
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;        for (k=0; k<= maxncov; k++) {
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;          if (Ndum[k] != 0) {
     }            nbcode[Tvar[j]][ij]=k; 
     for (i=1; i<=imx; i++) 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]));*/            /* 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; */
             
   /* Calculation of the number of parameter from char model*/            ij++;
   Tvar=ivector(1,15);          }
   Tprod=ivector(1,15);          if (ij > ncodemax[j]) break; 
   Tvaraff=ivector(1,15);        }  
   Tvard=imatrix(1,15,1,2);      } 
   Tage=ivector(1,15);          }  
      
   if (strlen(model) >1){   for (k=0; k< maxncov; k++) Ndum[k]=0;
     j=0, j1=0, k1=1, k2=1;  
     j=nbocc(model,'+');   for (i=1; i<=ncovmodel-2; i++) { 
     j1=nbocc(model,'*');     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     cptcovn=j+1;     ij=Tvar[i];
     cptcovprod=j1;     Ndum[ij]++;
       }
      
     strcpy(modelsav,model);   ij=1;
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){   for (i=1; i<= maxncov; i++) {
       printf("Error. Non available option model=%s ",model);     if((Ndum[i]!=0) && (i<=ncovcol)){
       goto end;       Tvaraff[ij]=i; /*For printing */
     }       ij++;
         }
     for(i=(j+1); i>=1;i--){   }
       cutv(stra,strb,modelsav,'+');   
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);   cptcoveff=ij-1; /*Number of simple covariates*/
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/  }
       /*scanf("%d",i);*/  
       if (strchr(strb,'*')) {  /*********** Health Expectancies ****************/
         cutv(strd,strc,strb,'*');  
         if (strcmp(strc,"age")==0) {  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 )
           cptcovprod--;  
           cutv(strb,stre,strd,'V');  {
           Tvar[i]=atoi(stre);    /* Health expectancies */
           cptcovage++;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
             Tage[cptcovage]=i;    double age, agelim, hf;
             /*printf("stre=%s ", stre);*/    double ***p3mat,***varhe;
         }    double **dnewm,**doldm;
         else if (strcmp(strd,"age")==0) {    double *xp;
           cptcovprod--;    double **gp, **gm;
           cutv(strb,stre,strc,'V');    double ***gradg, ***trgradg;
           Tvar[i]=atoi(stre);    int theta;
           cptcovage++;  
           Tage[cptcovage]=i;    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
         }    xp=vector(1,npar);
         else {    dnewm=matrix(1,nlstate*nlstate,1,npar);
           cutv(strb,stre,strc,'V');    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
           Tvar[i]=ncov+k1;    
           cutv(strb,strc,strd,'V');    fprintf(ficreseij,"# Health expectancies\n");
           Tprod[k1]=i;    fprintf(ficreseij,"# Age");
           Tvard[k1][1]=atoi(strc);    for(i=1; i<=nlstate;i++)
           Tvard[k1][2]=atoi(stre);      for(j=1; j<=nlstate;j++)
           Tvar[cptcovn+k2]=Tvard[k1][1];        fprintf(ficreseij," %1d-%1d (SE)",i,j);
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    fprintf(ficreseij,"\n");
           for (k=1; k<=lastobs;k++)  
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    if(estepm < stepm){
           k1++;      printf ("Problem %d lower than %d\n",estepm, stepm);
           k2=k2+2;    }
         }    else  hstepm=estepm;   
       }    /* We compute the life expectancy from trapezoids spaced every estepm months
       else {     * This is mainly to measure the difference between two models: for example
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/     * if stepm=24 months pijx are given only every 2 years and by summing them
        /*  scanf("%d",i);*/     * we are calculating an estimate of the Life Expectancy assuming a linear 
       cutv(strd,strc,strb,'V');     * progression in between and thus overestimating or underestimating according
       Tvar[i]=atoi(strc);     * to the curvature of the survival function. If, for the same date, we 
       }     * estimate the model with stepm=1 month, we can keep estepm to 24 months
       strcpy(modelsav,stra);       * to compare the new estimate of Life expectancy with the same linear 
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);     * hypothesis. A more precise result, taking into account a more precise
         scanf("%d",i);*/     * curvature will be obtained if estepm is as small as stepm. */
     }  
 }    /* For example we decided to compute the life expectancy with the smallest unit */
      /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);       nhstepm is the number of hstepm from age to agelim 
   printf("cptcovprod=%d ", cptcovprod);       nstepm is the number of stepm from age to agelin. 
   scanf("%d ",i);*/       Look at hpijx to understand the reason of that which relies in memory size
     fclose(fic);       and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     /*  if(mle==1){*/       survival function given by stepm (the optimization length). Unfortunately it
     if (weightopt != 1) { /* Maximisation without weights*/       means that if the survival funtion is printed only each two years of age and if
       for(i=1;i<=n;i++) weight[i]=1.0;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     }       results. So we changed our mind and took the option of the best precision.
     /*-calculation of age at interview from date of interview and age at death -*/    */
     agev=matrix(1,maxwav,1,imx);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
    for (i=1; i<=imx; i++)    agelim=AGESUP;
      for(m=2; (m<= maxwav); m++)    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){      /* nhstepm age range expressed in number of stepm */
          anint[m][i]=9999;      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
          s[m][i]=-1;      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
        }      /* if (stepm >= YEARM) hstepm=1;*/
          nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     for (i=1; i<=imx; i++)  {      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
       for(m=1; (m<= maxwav); m++){      gp=matrix(0,nhstepm,1,nlstate*nlstate);
         if(s[m][i] >0){      gm=matrix(0,nhstepm,1,nlstate*nlstate);
           if (s[m][i] == nlstate+1) {  
             if(agedc[i]>0)      /* Computed by stepm unit matrices, product of hstepm matrices, stored
               if(moisdc[i]!=99 && andc[i]!=9999)         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
               agev[m][i]=agedc[i];      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
             else {   
               if (andc[i]!=9999){  
               printf("Warning negative age at death: %d line:%d\n",num[i],i);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
               agev[m][i]=-1;  
               }      /* Computing Variances of health expectancies */
             }  
           }       for(theta=1; theta <=npar; theta++){
           else if(s[m][i] !=9){ /* Should no more exist */        for(i=1; i<=npar; i++){ 
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
             if(mint[m][i]==99 || anint[m][i]==9999)        }
               agev[m][i]=1;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
             else if(agev[m][i] <agemin){    
               agemin=agev[m][i];        cptj=0;
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/        for(j=1; j<= nlstate; j++){
             }          for(i=1; i<=nlstate; i++){
             else if(agev[m][i] >agemax){            cptj=cptj+1;
               agemax=agev[m][i];            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
             }            }
             /*agev[m][i]=anint[m][i]-annais[i];*/          }
             /*   agev[m][i] = age[i]+2*m;*/        }
           }       
           else { /* =9 */       
             agev[m][i]=1;        for(i=1; i<=npar; i++) 
             s[m][i]=-1;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
           }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         }        
         else /*= 0 Unknown */        cptj=0;
           agev[m][i]=1;        for(j=1; j<= nlstate; j++){
       }          for(i=1;i<=nlstate;i++){
                cptj=cptj+1;
     }            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
     for (i=1; i<=imx; i++)  {  
       for(m=1; (m<= maxwav); m++){              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
         if (s[m][i] > (nlstate+ndeath)) {            }
           printf("Error: Wrong value in nlstate or ndeath\n");            }
           goto end;        }
         }        for(j=1; j<= nlstate*nlstate; j++)
       }          for(h=0; h<=nhstepm-1; h++){
     }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);       } 
      
     free_vector(severity,1,maxwav);  /* End theta */
     free_imatrix(outcome,1,maxwav+1,1,n);  
     free_vector(moisnais,1,n);       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     free_vector(annais,1,n);  
     /* free_matrix(mint,1,maxwav,1,n);       for(h=0; h<=nhstepm-1; h++)
        free_matrix(anint,1,maxwav,1,n);*/        for(j=1; j<=nlstate*nlstate;j++)
     free_vector(moisdc,1,n);          for(theta=1; theta <=npar; theta++)
     free_vector(andc,1,n);            trgradg[h][j][theta]=gradg[h][theta][j];
        
      
     wav=ivector(1,imx);       for(i=1;i<=nlstate*nlstate;i++)
     dh=imatrix(1,lastpass-firstpass+1,1,imx);        for(j=1;j<=nlstate*nlstate;j++)
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          varhe[i][j][(int)age] =0.;
      
     /* Concatenates waves */       printf("%d|",(int)age);fflush(stdout);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
       Tcode=ivector(1,100);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
       ncodemax[1]=1;          for(i=1;i<=nlstate*nlstate;i++)
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);            for(j=1;j<=nlstate*nlstate;j++)
                    varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
    codtab=imatrix(1,100,1,10);        }
    h=0;      }
    m=pow(2,cptcoveff);      /* Computing expectancies */
        for(i=1; i<=nlstate;i++)
    for(k=1;k<=cptcoveff; k++){        for(j=1; j<=nlstate;j++)
      for(i=1; i <=(m/pow(2,k));i++){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
        for(j=1; j <= ncodemax[k]; j++){            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){            
            h++;  /* 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]);*/
            if (h>m) h=1;codtab[h][k]=j;  
          }          }
        }  
      }      fprintf(ficreseij,"%3.0f",age );
    }      cptj=0;
          for(i=1; i<=nlstate;i++)
    /* Calculates basic frequencies. Computes observed prevalence at single age        for(j=1; j<=nlstate;j++){
        and prints on file fileres'p'. */          cptj++;
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprev, lprev,mint,anint);          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
          }
   free_matrix(mint,1,maxwav,1,n);      fprintf(ficreseij,"\n");
   free_matrix(anint,1,maxwav,1,n);     
        free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    }
          printf("\n");
     /* For Powell, parameters are in a vector p[] starting at p[1]    fprintf(ficlog,"\n");
        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) */    free_vector(xp,1,npar);
     free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     if(mle==1){    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
     }  }
      
     /*--------- results files --------------*/  /************ Variance ******************/
     fprintf(ficres,"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);  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)
    fprintf(ficres,"fprevalence=%d lprevalence=%d pop_based=%d\n",fprev,lprev,popbased);  {
    fprintf(ficres,"fprevalence=%d lprevalence=%d nforecast=%d mob_average=%d\n",fprevfore,lprevfore,nforecast,mobilav);    /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
    jk=1;    /* double **newm;*/
    fprintf(ficres,"# Parameters\n");    double **dnewm,**doldm;
    printf("# Parameters\n");    double **dnewmp,**doldmp;
    for(i=1,jk=1; i <=nlstate; i++){    int i, j, nhstepm, hstepm, h, nstepm ;
      for(k=1; k <=(nlstate+ndeath); k++){    int k, cptcode;
        if (k != i)    double *xp;
          {    double **gp, **gm;  /* for var eij */
            printf("%d%d ",i,k);    double ***gradg, ***trgradg; /*for var eij */
            fprintf(ficres,"%1d%1d ",i,k);    double **gradgp, **trgradgp; /* for var p point j */
            for(j=1; j <=ncovmodel; j++){    double *gpp, *gmp; /* for var p point j */
              printf("%f ",p[jk]);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
              fprintf(ficres,"%f ",p[jk]);    double ***p3mat;
              jk++;    double age,agelim, hf;
            }    double ***mobaverage;
            printf("\n");    int theta;
            fprintf(ficres,"\n");    char digit[4];
          }    char digitp[25];
      }  
    }    char fileresprobmorprev[FILENAMELENGTH];
  if(mle==1){  
     /* Computing hessian and covariance matrix */    if(popbased==1){
     ftolhess=ftol; /* Usually correct */      if(mobilav!=0)
     hesscov(matcov, p, npar, delti, ftolhess, func);        strcpy(digitp,"-populbased-mobilav-");
  }      else strcpy(digitp,"-populbased-nomobil-");
     fprintf(ficres,"# Scales\n");    }
     printf("# Scales\n");    else 
      for(i=1,jk=1; i <=nlstate; i++){      strcpy(digitp,"-stablbased-");
       for(j=1; j <=nlstate+ndeath; j++){  
         if (j!=i) {    if (mobilav!=0) {
           fprintf(ficres,"%1d%1d",i,j);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           printf("%1d%1d",i,j);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           for(k=1; k<=ncovmodel;k++){        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
             printf(" %.5e",delti[jk]);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
             fprintf(ficres," %.5e",delti[jk]);      }
             jk++;    }
           }  
           printf("\n");    strcpy(fileresprobmorprev,"prmorprev"); 
           fprintf(ficres,"\n");    sprintf(digit,"%-d",ij);
         }    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
       }    strcat(fileresprobmorprev,digit); /* Tvar to be done */
       }    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
        strcat(fileresprobmorprev,fileres);
     k=1;    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     fprintf(ficres,"# Covariance\n");      printf("Problem with resultfile: %s\n", fileresprobmorprev);
     printf("# Covariance\n");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     for(i=1;i<=npar;i++){    }
       /*  if (k>nlstate) k=1;    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       i1=(i-1)/(ncovmodel*nlstate)+1;    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    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);
       printf("%s%d%d",alph[k],i1,tab[i]);*/    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
       fprintf(ficres,"%3d",i);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       printf("%3d",i);      fprintf(ficresprobmorprev," p.%-d SE",j);
       for(j=1; j<=i;j++){      for(i=1; i<=nlstate;i++)
         fprintf(ficres," %.5e",matcov[i][j]);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
         printf(" %.5e",matcov[i][j]);    }  
       }    fprintf(ficresprobmorprev,"\n");
       fprintf(ficres,"\n");    fprintf(ficgp,"\n# Routine varevsij");
       printf("\n");    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");
       k++;    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
     }  /*   } */
        varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     while((c=getc(ficpar))=='#' && c!= EOF){  
       ungetc(c,ficpar);    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");
       fgets(line, MAXLINE, ficpar);    fprintf(ficresvij,"# Age");
       puts(line);    for(i=1; i<=nlstate;i++)
       fputs(line,ficparo);      for(j=1; j<=nlstate;j++)
     }        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
     ungetc(c,ficpar);    fprintf(ficresvij,"\n");
    
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    xp=vector(1,npar);
        dnewm=matrix(1,nlstate,1,npar);
     if (fage <= 2) {    doldm=matrix(1,nlstate,1,nlstate);
       bage = agemin;    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
       fage = agemax;    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     }  
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    gpp=vector(nlstate+1,nlstate+ndeath);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
        
 /*------------ gnuplot -------------*/    if(estepm < stepm){
 chdir(pathcd);      printf ("Problem %d lower than %d\n",estepm, stepm);
   if((ficgp=fopen("graph.plt","w"))==NULL) {    }
     printf("Problem with file graph.gp");goto end;    else  hstepm=estepm;   
   }    /* For example we decided to compute the life expectancy with the smallest unit */
 #ifdef windows    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   fprintf(ficgp,"cd \"%s\" \n",pathc);       nhstepm is the number of hstepm from age to agelim 
 #endif       nstepm is the number of stepm from age to agelin. 
 m=pow(2,cptcoveff);       Look at hpijx to understand the reason of that which relies in memory size
         and note for a fixed period like k years */
  /* 1eme*/    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   for (cpt=1; cpt<= nlstate ; cpt ++) {       survival function given by stepm (the optimization length). Unfortunately it
    for (k1=1; k1<= m ; k1 ++) {       means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
 #ifdef windows       results. So we changed our mind and took the option of the best precision.
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);    */
 #endif    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
 #ifdef unix    agelim = AGESUP;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 #endif      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
 for (i=1; i<= nlstate ; i ++) {      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   else fprintf(ficgp," \%%*lf (\%%*lf)");      gp=matrix(0,nhstepm,1,nlstate);
 }      gm=matrix(0,nhstepm,1,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);  
     for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      for(theta=1; theta <=npar; theta++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
 }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);        }
      for (i=1; i<= nlstate ; i ++) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }          if (popbased==1) {
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));          if(mobilav ==0){
 #ifdef unix            for(i=1; i<=nlstate;i++)
 fprintf(ficgp,"\nset ter gif small size 400,300");              prlim[i][i]=probs[(int)age][i][ij];
 #endif          }else{ /* mobilav */ 
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            for(i=1; i<=nlstate;i++)
    }              prlim[i][i]=mobaverage[(int)age][i][ij];
   }          }
   /*2 eme*/        }
     
   for (k1=1; k1<= m ; k1 ++) {        for(j=1; j<= nlstate; j++){
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);          for(h=0; h<=nhstepm; h++){
                for(i=1, gp[h][j]=0.;i<=nlstate;i++)
     for (i=1; i<= nlstate+1 ; i ++) {              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
       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 ++) {        /* This for computing probability of death (h=1 means
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");           computed over hstepm matrices product = hstepm*stepm months) 
   else fprintf(ficgp," \%%*lf (\%%*lf)");           as a weighted average of prlim.
 }          */
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        for(j=nlstate+1;j<=nlstate+ndeath;j++){
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
       for (j=1; j<= nlstate+1 ; j ++) {        }    
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        /* end probability of death */
         else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }          for(i=1; i<=npar; i++) /* Computes gradient x - delta */
       fprintf(ficgp,"\" t\"\" w l 0,");          xp[i] = x[i] - (i==theta ?delti[theta]:0);
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       for (j=1; j<= nlstate+1 ; j ++) {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");   
   else fprintf(ficgp," \%%*lf (\%%*lf)");        if (popbased==1) {
 }            if(mobilav ==0){
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");            for(i=1; i<=nlstate;i++)
       else fprintf(ficgp,"\" t\"\" w l 0,");              prlim[i][i]=probs[(int)age][i][ij];
     }          }else{ /* mobilav */ 
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);            for(i=1; i<=nlstate;i++)
   }              prlim[i][i]=mobaverage[(int)age][i][ij];
            }
   /*3eme*/        }
   
   for (k1=1; k1<= m ; k1 ++) {        for(j=1; j<= nlstate; j++){
     for (cpt=1; cpt<= nlstate ; cpt ++) {          for(h=0; h<=nhstepm; h++){
       k=2+nlstate*(cpt-1);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
       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);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
       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+i,cpt,i+1);        }
       }        /* This for computing probability of death (h=1 means
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);           computed over hstepm matrices product = hstepm*stepm months) 
     }           as a weighted average of prlim.
   }        */
          for(j=nlstate+1;j<=nlstate+ndeath;j++){
   /* CV preval stat */          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   for (k1=1; k1<= m ; k1 ++) {           gmp[j] += prlim[i][i]*p3mat[i][j][1];
     for (cpt=1; cpt<nlstate ; cpt ++) {        }    
       k=3;        /* end probability of death */
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);  
       for (i=1; i< nlstate ; i ++)        for(j=1; j<= nlstate; j++) /* vareij */
         fprintf(ficgp,"+$%d",k+i+1);          for(h=0; h<=nhstepm; h++){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
                }
       l=3+(nlstate+ndeath)*cpt;  
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
       for (i=1; i< nlstate ; i ++) {          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         l=3+(nlstate+ndeath)*cpt;        }
         fprintf(ficgp,"+$%d",l+i+1);  
       }      } /* End theta */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);    
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
     }  
   }        for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
   /* proba elementaires */          for(theta=1; theta <=npar; theta++)
    for(i=1,jk=1; i <=nlstate; i++){            trgradg[h][j][theta]=gradg[h][theta][j];
     for(k=1; k <=(nlstate+ndeath); k++){  
       if (k != i) {      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(j=1; j <=ncovmodel; j++){        for(theta=1; theta <=npar; theta++)
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/          trgradgp[j][theta]=gradgp[theta][j];
           /*fprintf(ficgp,"%s",alph[1]);*/    
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);  
           jk++;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           fprintf(ficgp,"\n");      for(i=1;i<=nlstate;i++)
         }        for(j=1;j<=nlstate;j++)
       }          vareij[i][j][(int)age] =0.;
     }  
     }      for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
   for(jk=1; jk <=m; jk++) {          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
    i=1;          for(i=1;i<=nlstate;i++)
    for(k2=1; k2<=nlstate; k2++) {            for(j=1;j<=nlstate;j++)
      k3=i;              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
      for(k=1; k<=(nlstate+ndeath); k++) {        }
        if (k != k2){      }
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    
 ij=1;      /* pptj */
         for(j=3; j <=ncovmodel; j++) {      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
             ij++;        for(i=nlstate+1;i<=nlstate+ndeath;i++)
           }          varppt[j][i]=doldmp[j][i];
           else      /* end ppptj */
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      /*  x centered again */
         }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
           fprintf(ficgp,")/(1");      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
           
         for(k1=1; k1 <=nlstate; k1++){        if (popbased==1) {
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);        if(mobilav ==0){
 ij=1;          for(i=1; i<=nlstate;i++)
           for(j=3; j <=ncovmodel; j++){            prlim[i][i]=probs[(int)age][i][ij];
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        }else{ /* mobilav */ 
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          for(i=1; i<=nlstate;i++)
             ij++;            prlim[i][i]=mobaverage[(int)age][i][ij];
           }        }
           else      }
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);               
           }      /* This for computing probability of death (h=1 means
           fprintf(ficgp,")");         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
         }         as a weighted average of prlim.
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);      */
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");      for(j=nlstate+1;j<=nlstate+ndeath;j++){
         i=i+ncovmodel;        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
        }          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
      }      }    
    }      /* end probability of death */
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);  
   }      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
          for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   fclose(ficgp);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
            for(i=1; i<=nlstate;i++){
 chdir(path);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
            }
     free_ivector(wav,1,imx);      } 
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      fprintf(ficresprobmorprev,"\n");
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);    
     free_ivector(num,1,n);      fprintf(ficresvij,"%.0f ",age );
     free_vector(agedc,1,n);      for(i=1; i<=nlstate;i++)
     /*free_matrix(covar,1,NCOVMAX,1,n);*/        for(j=1; j<=nlstate;j++){
     fclose(ficparo);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
     fclose(ficres);        }
     /*  }*/      fprintf(ficresvij,"\n");
          free_matrix(gp,0,nhstepm,1,nlstate);
    /*________fin mle=1_________*/      free_matrix(gm,0,nhstepm,1,nlstate);
          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);
     /* No more information from the sample is required now */    } /* End age */
   /* Reads comments: lines beginning with '#' */    free_vector(gpp,nlstate+1,nlstate+ndeath);
   while((c=getc(ficpar))=='#' && c!= EOF){    free_vector(gmp,nlstate+1,nlstate+ndeath);
     ungetc(c,ficpar);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     fgets(line, MAXLINE, ficpar);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     puts(line);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     fputs(line,ficparo);    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
   }    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   ungetc(c,ficpar);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
    /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
 /*--------- index.htm --------*/    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
   strcpy(optionfilehtm,optionfile);    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   strcat(optionfilehtm,".htm");    /*  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);
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {  */
     printf("Problem with %s \n",optionfilehtm);goto end;  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
   }    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">    free_vector(xp,1,npar);
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>    free_matrix(doldm,1,nlstate,1,nlstate);
 Total number of observations=%d <br>    free_matrix(dnewm,1,nlstate,1,npar);
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
 <hr  size=\"2\" color=\"#EC5E5E\">    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
 <li>Outputs files<br><br>\n    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>    fclose(ficresprobmorprev);
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>    fflush(ficgp);
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>    fflush(fichtm); 
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>  }  /* end varevsij */
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>  
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>  /************ Variance of prevlim ******************/
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>  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)
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>  {
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>    /* Variance of prevalence limit */
 <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,fileres,fileres);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     double **newm;
  fprintf(fichtm," <li>Graphs</li><p>");    double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
  m=cptcoveff;    int k, cptcode;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    double *xp;
     double *gp, *gm;
  j1=0;    double **gradg, **trgradg;
  for(k1=1; k1<=m;k1++){    double age,agelim;
    for(i1=1; i1<=ncodemax[k1];i1++){    int theta;
        j1++;     
        if (cptcovn > 0) {    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    fprintf(ficresvpl,"# Age");
          for (cpt=1; cpt<=cptcoveff;cpt++)    for(i=1; i<=nlstate;i++)
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);        fprintf(ficresvpl," %1d-%1d",i,i);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    fprintf(ficresvpl,"\n");
        }  
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    xp=vector(1,npar);
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);        dnewm=matrix(1,nlstate,1,npar);
        for(cpt=1; cpt<nlstate;cpt++){    doldm=matrix(1,nlstate,1,nlstate);
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    hstepm=1*YEARM; /* Every year of age */
        }    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     for(cpt=1; cpt<=nlstate;cpt++) {    agelim = AGESUP;
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 interval) in state (%d): v%s%d%d.gif <br>      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        if (stepm >= YEARM) hstepm=1;
      }      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
      for(cpt=1; cpt<=nlstate;cpt++) {      gradg=matrix(1,npar,1,nlstate);
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>      gp=vector(1,nlstate);
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      gm=vector(1,nlstate);
      }  
      fprintf(fichtm,"\n<br>- Total life expectancy by age and      for(theta=1; theta <=npar; theta++){
 health expectancies in states (1) and (2): e%s%d.gif<br>        for(i=1; i<=npar; i++){ /* Computes gradient */
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
 fprintf(fichtm,"\n</body>");        }
    }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
  }        for(i=1;i<=nlstate;i++)
 fclose(fichtm);          gp[i] = prlim[i][i];
       
   /*--------------- Prevalence limit --------------*/        for(i=1; i<=npar; i++) /* Computes gradient */
            xp[i] = x[i] - (i==theta ?delti[theta]:0);
   strcpy(filerespl,"pl");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   strcat(filerespl,fileres);        for(i=1;i<=nlstate;i++)
   if((ficrespl=fopen(filerespl,"w"))==NULL) {          gm[i] = prlim[i][i];
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;  
   }        for(i=1;i<=nlstate;i++)
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   fprintf(ficrespl,"#Prevalence limit\n");      } /* End theta */
   fprintf(ficrespl,"#Age ");  
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      trgradg =matrix(1,nlstate,1,npar);
   fprintf(ficrespl,"\n");  
        for(j=1; j<=nlstate;j++)
   prlim=matrix(1,nlstate,1,nlstate);        for(theta=1; theta <=npar; theta++)
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          trgradg[j][theta]=gradg[theta][j];
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for(i=1;i<=nlstate;i++)
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        varpl[i][(int)age] =0.;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   k=0;      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   agebase=agemin;      for(i=1;i<=nlstate;i++)
   agelim=agemax;        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   ftolpl=1.e-10;  
   i1=cptcoveff;      fprintf(ficresvpl,"%.0f ",age );
   if (cptcovn < 1){i1=1;}      for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   for(cptcov=1;cptcov<=i1;cptcov++){      fprintf(ficresvpl,"\n");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      free_vector(gp,1,nlstate);
         k=k+1;      free_vector(gm,1,nlstate);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/      free_matrix(gradg,1,npar,1,nlstate);
         fprintf(ficrespl,"\n#******");      free_matrix(trgradg,1,nlstate,1,npar);
         for(j=1;j<=cptcoveff;j++)    } /* End age */
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
         fprintf(ficrespl,"******\n");    free_vector(xp,1,npar);
            free_matrix(doldm,1,nlstate,1,npar);
         for (age=agebase; age<=agelim; age++){    free_matrix(dnewm,1,nlstate,1,nlstate);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  
           fprintf(ficrespl,"%.0f",age );  }
           for(i=1; i<=nlstate;i++)  
           fprintf(ficrespl," %.5f", prlim[i][i]);  /************ Variance of one-step probabilities  ******************/
           fprintf(ficrespl,"\n");  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
         }  {
       }    int i, j=0,  i1, k1, l1, t, tj;
     }    int k2, l2, j1,  z1;
   fclose(ficrespl);    int k=0,l, cptcode;
     int first=1, first1;
   /*------------- h Pij x at various ages ------------*/    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
      double **dnewm,**doldm;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    double *xp;
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    double *gp, *gm;
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    double **gradg, **trgradg;
   }    double **mu;
   printf("Computing pij: result on file '%s' \n", filerespij);    double age,agelim, cov[NCOVMAX];
      double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   stepsize=(int) (stepm+YEARM-1)/YEARM;    int theta;
   /*if (stepm<=24) stepsize=2;*/    char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
   agelim=AGESUP;    char fileresprobcor[FILENAMELENGTH];
   hstepm=stepsize*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    double ***varpij;
    
   k=0;    strcpy(fileresprob,"prob"); 
   for(cptcov=1;cptcov<=i1;cptcov++){    strcat(fileresprob,fileres);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       k=k+1;      printf("Problem with resultfile: %s\n", fileresprob);
         fprintf(ficrespij,"\n#****** ");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
         for(j=1;j<=cptcoveff;j++)    }
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    strcpy(fileresprobcov,"probcov"); 
         fprintf(ficrespij,"******\n");    strcat(fileresprobcov,fileres);
            if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */      printf("Problem with resultfile: %s\n", fileresprobcov);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    strcpy(fileresprobcor,"probcor"); 
           oldm=oldms;savm=savms;    strcat(fileresprobcor,fileres);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
           fprintf(ficrespij,"# Age");      printf("Problem with resultfile: %s\n", fileresprobcor);
           for(i=1; i<=nlstate;i++)      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
             for(j=1; j<=nlstate+ndeath;j++)    }
               fprintf(ficrespij," %1d-%1d",i,j);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
           fprintf(ficrespij,"\n");    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
           for (h=0; h<=nhstepm; h++){    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
             for(i=1; i<=nlstate;i++)    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
               for(j=1; j<=nlstate+ndeath;j++)    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    
             fprintf(ficrespij,"\n");    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
           }    fprintf(ficresprob,"# Age");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
           fprintf(ficrespij,"\n");    fprintf(ficresprobcov,"# Age");
         }    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     }    fprintf(ficresprobcov,"# Age");
   }  
   
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/    for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
   fclose(ficrespij);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
   /*---------- Forecasting ------------------*/        fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
   strcpy(fileresf,"f");   /* fprintf(ficresprob,"\n");
   strcat(fileresf,fileres);    fprintf(ficresprobcov,"\n");
   if((ficresf=fopen(fileresf,"w"))==NULL) {    fprintf(ficresprobcor,"\n");
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;   */
   }   xp=vector(1,npar);
   printf("Computing forecasting: result on file '%s' \n", fileresf);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax, fprevfore, lprevfore);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
  free_matrix(agev,1,maxwav,1,imx);    first=1;
   /* Mobile average */    fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    fprintf(fichtm,"\n");
   
   if (mobilav==1) {    fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    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");
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)    fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
       for (i=1; i<=nlstate;i++)  
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    cov[1]=1;
           mobaverage[(int)agedeb][i][cptcod]=0.;    tj=cptcoveff;
        if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     for (agedeb=bage+4; agedeb<=fage; agedeb++){    j1=0;
       for (i=1; i<=nlstate;i++){    for(t=1; t<=tj;t++){
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      for(i1=1; i1<=ncodemax[t];i1++){ 
           for (cpt=0;cpt<=4;cpt++){        j1++;
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];        if  (cptcovn>0) {
           }          fprintf(ficresprob, "\n#********** Variable "); 
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;          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");
           
   stepsize=(int) (stepm+YEARM-1)/YEARM;          fprintf(ficgp, "\n#********** Variable "); 
   if (stepm<=12) stepsize=1;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficgp, "**********\n#\n");
   agelim=AGESUP;          
   hstepm=stepsize*YEARM; /* Every year of age */          
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */          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]]);
   if (popforecast==1) {          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     if((ficpop=fopen(popfile,"r"))==NULL)    {          
       printf("Problem with population file : %s\n",popfile);goto end;          fprintf(ficresprobcor, "\n#********** Variable ");    
     }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     popage=ivector(0,AGESUP);          fprintf(ficresprobcor, "**********\n#");    
     popeffectif=vector(0,AGESUP);        }
     popcount=vector(0,AGESUP);        
         for (age=bage; age<=fage; age ++){ 
     i=1;            cov[2]=age;
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)          for (k=1; k<=cptcovn;k++) {
       {            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
         i=i+1;          }
       }          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     imx=i;          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]]];
   for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];          
   }          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   for(cptcov=1;cptcov<=i1;cptcov++){          gp=vector(1,(nlstate)*(nlstate+ndeath));
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          gm=vector(1,(nlstate)*(nlstate+ndeath));
       k=k+1;      
       fprintf(ficresf,"\n#****** ");          for(theta=1; theta <=npar; theta++){
       for(j=1;j<=cptcoveff;j++) {            for(i=1; i<=npar; i++)
         fprintf(ficresf,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
       }            
       fprintf(ficresf,"******\n");            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       fprintf(ficresf,"# StartingAge FinalAge Horizon(in years)");            
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);            k=0;
       if (popforecast==1)  fprintf(ficresf," [Population]");            for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
       for (agedeb=fage; agedeb>=bage; agedeb--){                k=k+1;
         fprintf(ficresf,"\n%.f %.f 0",agedeb, agedeb);                gp[k]=pmmij[i][j];
        if (mobilav==1) {              }
         for(j=1; j<=nlstate;j++)            }
           fprintf(ficresf," %.3f",mobaverage[(int)agedeb][j][cptcod]);            
         }            for(i=1; i<=npar; i++)
         else {              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
           for(j=1; j<=nlstate;j++)      
           fprintf(ficresf," %.3f",probs[(int)agedeb][j][cptcod]);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
         }              k=0;
             for(i=1; i<=(nlstate); i++){
        for(j=1; j<=ndeath;j++) fprintf(ficresf," 0.00000");              for(j=1; j<=(nlstate+ndeath);j++){
        if (popforecast==1) fprintf(ficresf," [%.f] ",popeffectif[(int)agedeb]);                k=k+1;
       }                gm[k]=pmmij[i][j];
                    }
       for (cpt=1; cpt<=nforecast;cpt++) {            }
         fprintf(ficresf,"\n");       
       for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
         nhstepm = nhstepm/hstepm;          }
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/  
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for(theta=1; theta <=npar; theta++)
         oldm=oldms;savm=savms;              trgradg[j][theta]=gradg[theta][j];
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            
                          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
         for (h=0; h<=nhstepm; h++){          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
                  free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
          if (h*hstepm/YEARM*stepm==cpt)          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
             fprintf(ficresf,"\n%.f %.f %.f",agedeb, agedeb+ h*hstepm/YEARM*stepm, h*hstepm/YEARM*stepm);          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
                    free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
            
          for(j=1; j<=nlstate+ndeath;j++) {          pmij(pmmij,cov,ncovmodel,x,nlstate);
            kk1=0.;kk2=0;          
            for(i=1; i<=nlstate;i++) {                  k=0;
              if (mobilav==1)          for(i=1; i<=(nlstate); i++){
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb][i][cptcod];            for(j=1; j<=(nlstate+ndeath);j++){
              else kk1=kk1+p3mat[i][j][h]*probs[(int)agedeb][i][cptcod];              k=k+1;
              if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];              mu[k][(int) age]=pmmij[i][j];
             }            }
            if (h*hstepm/YEARM*stepm==cpt) {          }
              fprintf(ficresf," %.3f", kk1);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
                if (popforecast==1) fprintf(ficresf," [%.f]", kk2);            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
            }              varpij[i][j][(int)age] = doldm[i][j];
           }  
         }          /*printf("\n%d ",(int)age);
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            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);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          fprintf(ficresprobcov,"\n%d ",(int)age);
   if (popforecast==1) {          fprintf(ficresprobcor,"\n%d ",(int)age);
     free_ivector(popage,0,AGESUP);  
     free_vector(popeffectif,0,AGESUP);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
     free_vector(popcount,0,AGESUP);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
   }          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   free_imatrix(s,1,maxwav+1,1,n);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   free_vector(weight,1,n);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
   fclose(ficresf);          }
   /*---------- Health expectancies and variances ------------*/          i=0;
           for (k=1; k<=(nlstate);k++){
   strcpy(filerest,"t");            for (l=1; l<=(nlstate+ndeath);l++){ 
   strcat(filerest,fileres);              i=i++;
   if((ficrest=fopen(filerest,"w"))==NULL) {              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
   }              for (j=1; j<=i;j++){
   printf("Computing Total LEs with variances: file '%s' \n", filerest);                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]));
               }
   strcpy(filerese,"e");            }
   strcat(filerese,fileres);          }/* end of loop for state */
   if((ficreseij=fopen(filerese,"w"))==NULL) {        } /* end of loop for age */
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);  
   }        /* Confidence intervalle of pij  */
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);        /*
           fprintf(ficgp,"\nset noparametric;unset label");
  strcpy(fileresv,"v");          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   strcat(fileresv,fileres);          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   if((ficresvij=fopen(fileresv,"w"))==NULL) {          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
   }          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        first1=1;
       k=k+1;        for (k2=1; k2<=(nlstate);k2++){
       fprintf(ficrest,"\n#****** ");          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
       for(j=1;j<=cptcoveff;j++)            if(l2==k2) continue;
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            j=(k2-1)*(nlstate+ndeath)+l2;
       fprintf(ficrest,"******\n");            for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
       fprintf(ficreseij,"\n#****** ");                if(l1==k1) continue;
       for(j=1;j<=cptcoveff;j++)                i=(k1-1)*(nlstate+ndeath)+l1;
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);                if(i<=j) continue;
       fprintf(ficreseij,"******\n");                for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
       fprintf(ficresvij,"\n#****** ");                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
       for(j=1;j<=cptcoveff;j++)                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
       fprintf(ficresvij,"******\n");                    mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                    c12=cv12/sqrt(v1*v2);
       oldm=oldms;savm=savms;                    /* Computing eigen value of matrix of covariance */
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);                      lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       oldm=oldms;savm=savms;                    /* Eigen vectors */
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                          /*v21=sqrt(1.-v11*v11); *//* error */
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");                    v21=(lc1-v1)/cv12*v11;
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);                    v12=-v21;
       fprintf(ficrest,"\n");                    v22=v11;
                            tnalp=v21/v11;
       hf=1;                    if(first1==1){
       if (stepm >= YEARM) hf=stepm/YEARM;                      first1=0;
       epj=vector(1,nlstate+1);                      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);
       for(age=bage; age <=fage ;age++){                    }
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                    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);
         if (popbased==1) {                    /*printf(fignu*/
           for(i=1; i<=nlstate;i++)                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
             prlim[i][i]=probs[(int)age][i][k];                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
         }                    if(first==1){
                              first=0;
         fprintf(ficrest," %.0f",age);                      fprintf(ficgp,"\nset parametric;unset label");
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];                      fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
           }   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
           epj[nlstate+1] +=epj[j];  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
         }                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
         for(i=1, vepp=0.;i <=nlstate;i++)                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
           for(j=1;j <=nlstate;j++)                      fprintf(fichtm,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
             vepp += vareij[i][j][(int)age];                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
         for(j=1;j <=nlstate;j++){                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
         }                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
         fprintf(ficrest,"\n");                              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",\
  fclose(ficreseij);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
  fclose(ficresvij);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   fclose(ficrest);                    }/* if first */
   fclose(ficpar);                  } /* age mod 5 */
   free_vector(epj,1,nlstate+1);                } /* end loop age */
   /*  scanf("%d ",i); */                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
   /*------- Variance limit prevalence------*/                } /*l12 */
             } /* k12 */
 strcpy(fileresvpl,"vpl");          } /*l1 */
   strcat(fileresvpl,fileres);        }/* k1 */
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      } /* loop covariates */
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    }
     exit(0);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   }    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    free_vector(xp,1,npar);
     fclose(ficresprob);
  k=0;    fclose(ficresprobcov);
  for(cptcov=1;cptcov<=i1;cptcov++){    fclose(ficresprobcor);
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    /*  fclose(ficgp);*/
      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]]);  /******************* Printing html file ***********/
      fprintf(ficresvpl,"******\n");  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                          int lastpass, int stepm, int weightopt, char model[],\
      varpl=matrix(1,nlstate,(int) bage, (int) fage);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
      oldm=oldms;savm=savms;                    int popforecast, int estepm ,\
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);                    double jprev1, double mprev1,double anprev1, \
    }                    double jprev2, double mprev2,double anprev2){
  }    int jj1, k1, i1, cpt;
     /*char optionfilehtm[FILENAMELENGTH];*/
   fclose(ficresvpl);  /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    { */
   /*     printf("Problem with %s \n",optionfilehtm), exit(0); */
   /*---------- End : free ----------------*/  /*     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  /*   } */
    
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n \
     - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n \
     - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n \
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);   - Life expectancies by age and initial health status (estepm=%2d months): \
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);     <a href=\"%s\">%s</a> <br>\n</li>", \
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
               subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
   free_matrix(matcov,1,npar,1,npar);             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   free_vector(delti,1,npar);  
    fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);  
    m=cptcoveff;
   printf("End of Imach\n");   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */  
     jj1=0;
   /* 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);*/   for(k1=1; k1<=m;k1++){
   /*printf("Total time was %d uSec.\n", total_usecs);*/     for(i1=1; i1<=ncodemax[k1];i1++){
   /*------ End -----------*/       jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
  end:         for (cpt=1; cpt<=cptcoveff;cpt++) 
 #ifdef windows           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
  chdir(pathcd);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
 #endif       }
         /* Pij */
  system("..\\gp37mgw\\wgnuplot graph.plt");       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
 #ifdef windows       /* Quasi-incidences */
   while (z[0] != 'q') {       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
     chdir(pathcd);   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
     printf("\nType e to edit output files, c to start again, and q for exiting: ");  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
     scanf("%s",z);         /* Stable prevalence in each health state */
     if (z[0] == 'c') system("./imach");         for(cpt=1; cpt<nlstate;cpt++){
     else if (z[0] == 'e') {           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
       chdir(path);  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
       system(optionfilehtm);         }
     }       for(cpt=1; cpt<=nlstate;cpt++) {
     else if (z[0] == 'q') exit(0);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
   }  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
 #endif       }
 }       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2): %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End 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=\"%s\">%s</a> <br>\n\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
    - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n\
    - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n\
    - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
            rfileres,rfileres,\
            subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
            subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
            subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  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): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"vr"),cpt,jj1,subdirf2(optionfilefiname,"vr"),cpt,jj1);  
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int 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);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),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,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),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,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),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 \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           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," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
           
         } 
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%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 \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),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 */
      fflush(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);
   }
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     }
   
   } /* end of prwizard */
   
   /***********************************************/
   /**************** 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, imk;
     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[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE]; 
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   
     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 strstart[80], *strt, strtend[80];
     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);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     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, MAXLINE)!= 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);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* 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\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Localtime (at start):%s",strstart);
     fprintf(ficlog,"Localtime (at start): %s",strstart);
     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) { /* opened on subdirectory */
       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 */
    
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     /* 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,strstart);
     /*fclose(fichtm);*/
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     strcpy(lfileres,fileres);
     strcat(lfileres,"/");
     strcat(lfileres,optionfilefiname);
     
     /* 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);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       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);*/
   
     replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
     printinggnuplot(fileres, optionfilefiname,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);
   
     fflush(fichtm);
     fflush(ficgp);
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Localtime at start %s\nLocaltime at end   %s",strstart, strtend); 
     fprintf(ficlog,"Localtime at start %s\nLocal time at end   %s",strstart, 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>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
     fclose(fichtm);
     fclose(ficgp);
     /*------ End -----------*/
   
     end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
     chdir(path);
    /*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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  Added in v.1.89


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