Diff for /imach/src/imach.c between versions 1.24 and 1.90

version 1.24, 2002/02/22 18:10:15 version 1.90, 2003/06/24 12:34:15
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.90  2003/06/24 12:34:15  brouard
      (Module): Some bugs corrected for windows. Also, when
   This program computes Healthy Life Expectancies from    mle=-1 a template is output in file "or"mypar.txt with the design
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    of the covariance matrix to be input.
   first survey ("cross") where individuals from different ages are  
   interviewed on their health status or degree of disability (in the    Revision 1.89  2003/06/24 12:30:52  brouard
   case of a health survey which is our main interest) -2- at least a    (Module): Some bugs corrected for windows. Also, when
   second wave of interviews ("longitudinal") which measure each change    mle=-1 a template is output in file "or"mypar.txt with the design
   (if any) in individual health status.  Health expectancies are    of the covariance matrix to be input.
   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    Revision 1.88  2003/06/23 17:54:56  brouard
   Maximum Likelihood of the parameters involved in the model.  The    * 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.
   simplest model is the multinomial logistic model where pij is the  
   probabibility to be observed in state j at the second wave    Revision 1.87  2003/06/18 12:26:01  brouard
   conditional to be observed in state i at the first wave. Therefore    Version 0.96
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where  
   'age' is age and 'sex' is a covariate. If you want to have a more    Revision 1.86  2003/06/17 20:04:08  brouard
   complex model than "constant and age", you should modify the program    (Module): Change position of html and gnuplot routines and added
   where the markup *Covariates have to be included here again* invites    routine fileappend.
   you to do it.  More covariates you add, slower 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 of this computer programme, compared to a simple    current date of interview. It may happen when the death was just
   multinomial logistic model, is clear when the delay between waves is not    prior to the death. In this case, dh was negative and likelihood
   identical for each individual. Also, if a individual missed an    was wrong (infinity). We still send an "Error" but patch by
   intermediate interview, the information is lost, but taken into    assuming that the date of death was just one stepm after the
   account using an interpolation or extrapolation.      interview.
     (Repository): Because some people have very long ID (first column)
   hPijx is the probability to be observed in state i at age x+h    we changed int to long in num[] and we added a new lvector for
   conditional to the observed state i at age x. The delay 'h' can be    memory allocation. But we also truncated to 8 characters (left
   split into an exact number (nh*stepm) of unobserved intermediate    truncation)
   states. This elementary transition (by month or quarter trimester,    (Repository): No more line truncation errors.
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.84  2003/06/13 21:44:43  brouard
   and the contribution of each individual to the likelihood is simply    * imach.c (Repository): Replace "freqsummary" at a correct
   hPijx.    place. It differs from routine "prevalence" which may be called
     many times. Probs is memory consuming and must be used with
   Also this programme outputs the covariance matrix of the parameters but also    parcimony.
   of the life expectancies. It also computes the prevalence limits.    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Revision 1.83  2003/06/10 13:39:11  lievre
            Institut national d'études démographiques, Paris.    *** empty log message ***
   This software have been partly granted by Euro-REVES, a concerted action  
   from the European Union.    Revision 1.82  2003/06/05 15:57:20  brouard
   It is copyrighted identically to a GNU software product, ie programme and    Add log in  imach.c and  fullversion number is now printed.
   software can be distributed freely for non commercial use. Latest version  
   can be accessed at http://euroreves.ined.fr/imach .  */
   **********************************************************************/  /*
       Interpolated Markov Chain
 #include <math.h>  
 #include <stdio.h>    Short summary of the programme:
 #include <stdlib.h>    
 #include <unistd.h>    This program computes Healthy Life Expectancies from
     cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 #define MAXLINE 256    first survey ("cross") where individuals from different ages are
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    interviewed on their health status or degree of disability (in the
 #define FILENAMELENGTH 80    case of a health survey which is our main interest) -2- at least a
 /*#define DEBUG*/    second wave of interviews ("longitudinal") which measure each change
 #define windows    (if any) in individual health status.  Health expectancies are
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    computed from the time spent in each health state according to a
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    model. More health states you consider, more time is necessary to reach the
     Maximum Likelihood of the parameters involved in the model.  The
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    simplest model is the multinomial logistic model where pij is the
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    probability to be observed in state j at the second wave
     conditional to be observed in state i at the first wave. Therefore
 #define NINTERVMAX 8    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    'age' is age and 'sex' is a covariate. If you want to have a more
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    complex model than "constant and age", you should modify the program
 #define NCOVMAX 8 /* Maximum number of covariates */    where the markup *Covariates have to be included here again* invites
 #define MAXN 20000    you to do it.  More covariates you add, slower the
 #define YEARM 12. /* Number of months per year */    convergence.
 #define AGESUP 130  
 #define AGEBASE 40    The advantage of this computer programme, compared to a simple
     multinomial logistic model, is clear when the delay between waves is not
     identical for each individual. Also, if a individual missed an
 int erreur; /* Error number */    intermediate interview, the information is lost, but taken into
 int nvar;    account using an interpolation or extrapolation.  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    hPijx is the probability to be observed in state i at age x+h
 int nlstate=2; /* Number of live states */    conditional to the observed state i at age x. The delay 'h' can be
 int ndeath=1; /* Number of dead states */    split into an exact number (nh*stepm) of unobserved intermediate
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    states. This elementary transition (by month, quarter,
 int popbased=0;    semester or year) is modelled as a multinomial logistic.  The hPx
     matrix is simply the matrix product of nh*stepm elementary matrices
 int *wav; /* Number of waves for this individuual 0 is possible */    and the contribution of each individual to the likelihood is simply
 int maxwav; /* Maxim number of waves */    hPijx.
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    Also this programme outputs the covariance matrix of the parameters but also
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    of the life expectancies. It also computes the stable prevalence. 
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    
 double jmean; /* Mean space between 2 waves */    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 double **oldm, **newm, **savm; /* Working pointers to matrices */             Institut national d'études démographiques, Paris.
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    This software have been partly granted by Euro-REVES, a concerted action
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    from the European Union.
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;    It is copyrighted identically to a GNU software product, ie programme and
 FILE *ficreseij;    software can be distributed freely for non commercial use. Latest version
   char filerese[FILENAMELENGTH];    can be accessed at http://euroreves.ined.fr/imach .
  FILE  *ficresvij;  
   char fileresv[FILENAMELENGTH];    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
  FILE  *ficresvpl;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   char fileresvpl[FILENAMELENGTH];    
     **********************************************************************/
 #define NR_END 1  /*
 #define FREE_ARG char*    main
 #define FTOL 1.0e-10    read parameterfile
     read datafile
 #define NRANSI    concatwav
 #define ITMAX 200    freqsummary
     if (mle >= 1)
 #define TOL 2.0e-4      mlikeli
     print results files
 #define CGOLD 0.3819660    if mle==1 
 #define ZEPS 1.0e-10       computes hessian
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    read end of parameter file: agemin, agemax, bage, fage, estepm
         begin-prev-date,...
 #define GOLD 1.618034    open gnuplot file
 #define GLIMIT 100.0    open html file
 #define TINY 1.0e-20    stable prevalence
      for age prevalim()
 static double maxarg1,maxarg2;    h Pij x
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    variance of p varprob
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    forecasting if prevfcast==1 prevforecast call prevalence()
      health expectancies
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Variance-covariance of DFLE
 #define rint(a) floor(a+0.5)    prevalence()
      movingaverage()
 static double sqrarg;    varevsij() 
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    if popbased==1 varevsij(,popbased)
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    total life expectancies
     Variance of stable prevalence
 int imx;   end
 int stepm;  */
 /* Stepm, step in month: minimum step interpolation*/  
   
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;   
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  #include <math.h>
 double **pmmij, ***probs, ***mobaverage;  #include <stdio.h>
 double dateintmean=0;  #include <stdlib.h>
   #include <unistd.h>
 double *weight;  
 int **s; /* Status */  #include <sys/time.h>
 double *agedc, **covar, idx;  #include <time.h>
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  #include "timeval.h"
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  #define MAXLINE 256
 double ftolhess; /* Tolerance for computing hessian */  #define GNUPLOTPROGRAM "gnuplot"
   /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 /**************** split *************************/  #define FILENAMELENGTH 132
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  /*#define DEBUG*/
 {  /*#define windows*/
    char *s;                             /* pointer */  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
    int  l1, l2;                         /* length counters */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
    l1 = strlen( path );                 /* length of path */  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 #ifdef windows  
    s = strrchr( path, '\\' );           /* find last / */  #define NINTERVMAX 8
 #else  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
    s = strrchr( path, '/' );            /* find last / */  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #endif  #define NCOVMAX 8 /* Maximum number of covariates */
    if ( s == NULL ) {                   /* no directory, so use current */  #define MAXN 20000
 #if     defined(__bsd__)                /* get current working directory */  #define YEARM 12. /* Number of months per year */
       extern char       *getwd( );  #define AGESUP 130
   #define AGEBASE 40
       if ( getwd( dirc ) == NULL ) {  #ifdef unix
 #else  #define DIRSEPARATOR '/'
       extern char       *getcwd( );  #define ODIRSEPARATOR '\\'
   #else
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  #define DIRSEPARATOR '\\'
 #endif  #define ODIRSEPARATOR '/'
          return( GLOCK_ERROR_GETCWD );  #endif
       }  
       strcpy( name, path );             /* we've got it */  /* $Id$ */
    } else {                             /* strip direcotry from path */  /* $State$ */
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */  char version[]="Imach version 0.96a, June 2003, INED-EUROREVES ";
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  char fullversion[]="$Revision$ $Date$"; 
       strcpy( name, s );                /* save file name */  int erreur; /* Error number */
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  int nvar;
       dirc[l1-l2] = 0;                  /* add zero */  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
    }  int npar=NPARMAX;
    l1 = strlen( dirc );                 /* length of directory */  int nlstate=2; /* Number of live states */
 #ifdef windows  int ndeath=1; /* Number of dead states */
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 #else  int popbased=0;
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  
 #endif  int *wav; /* Number of waves for this individuual 0 is possible */
    s = strrchr( name, '.' );            /* find last / */  int maxwav; /* Maxim number of waves */
    s++;  int jmin, jmax; /* min, max spacing between 2 waves */
    strcpy(ext,s);                       /* save extension */  int gipmx, gsw; /* Global variables on the number of contributions 
    l1= strlen( name);                     to the likelihood and the sum of weights (done by funcone)*/
    l2= strlen( s)+1;  int mle, weightopt;
    strncpy( finame, name, l1-l2);  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
    finame[l1-l2]= 0;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
    return( 0 );                         /* we're done */  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 }             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   double jmean; /* Mean space between 2 waves */
   double **oldm, **newm, **savm; /* Working pointers to matrices */
 /******************************************/  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 void replace(char *s, char*t)  FILE *ficlog, *ficrespow;
 {  int globpr; /* Global variable for printing or not */
   int i;  double fretone; /* Only one call to likelihood */
   int lg=20;  long ipmx; /* Number of contributions */
   i=0;  double sw; /* Sum of weights */
   lg=strlen(t);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   for(i=0; i<= lg; i++) {  FILE *ficresilk;
     (s[i] = t[i]);  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
     if (t[i]== '\\') s[i]='/';  FILE *ficresprobmorprev;
   }  FILE *fichtm; /* Html File */
 }  FILE *ficreseij;
   char filerese[FILENAMELENGTH];
 int nbocc(char *s, char occ)  FILE  *ficresvij;
 {  char fileresv[FILENAMELENGTH];
   int i,j=0;  FILE  *ficresvpl;
   int lg=20;  char fileresvpl[FILENAMELENGTH];
   i=0;  char title[MAXLINE];
   lg=strlen(s);  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   for(i=0; i<= lg; i++) {  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   if  (s[i] == occ ) j++;  char tmpout[FILENAMELENGTH]; 
   }  char command[FILENAMELENGTH];
   return j;  int  outcmd=0;
 }  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 void cutv(char *u,char *v, char*t, char occ)  char lfileres[FILENAMELENGTH];
 {  char filelog[FILENAMELENGTH]; /* Log file */
   int i,lg,j,p=0;  char filerest[FILENAMELENGTH];
   i=0;  char fileregp[FILENAMELENGTH];
   for(j=0; j<=strlen(t)-1; j++) {  char popfile[FILENAMELENGTH];
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
   
   lg=strlen(t);  #define NR_END 1
   for(j=0; j<p; j++) {  #define FREE_ARG char*
     (u[j] = t[j]);  #define FTOL 1.0e-10
   }  
      u[p]='\0';  #define NRANSI 
   #define ITMAX 200 
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);  #define TOL 2.0e-4 
   }  
 }  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
 /********************** nrerror ********************/  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   
 void nrerror(char error_text[])  #define GOLD 1.618034 
 {  #define GLIMIT 100.0 
   fprintf(stderr,"ERREUR ...\n");  #define TINY 1.0e-20 
   fprintf(stderr,"%s\n",error_text);  
   exit(1);  static double maxarg1,maxarg2;
 }  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 /*********************** vector *******************/  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 double *vector(int nl, int nh)    
 {  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   double *v;  #define rint(a) floor(a+0.5)
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");  static double sqrarg;
   return 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;} 
   
 /************************ free vector ******************/  int imx; 
 void free_vector(double*v, int nl, int nh)  int stepm;
 {  /* Stepm, step in month: minimum step interpolation*/
   free((FREE_ARG)(v+nl-NR_END));  
 }  int estepm;
   /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)  int m,nb;
 {  long *num;
   int *v;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   if (!v) nrerror("allocation failure in ivector");  double **pmmij, ***probs;
   return v-nl+NR_END;  double dateintmean=0;
 }  
   double *weight;
 /******************free ivector **************************/  int **s; /* Status */
 void free_ivector(int *v, long nl, long nh)  double *agedc, **covar, idx;
 {  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   free((FREE_ARG)(v+nl-NR_END));  
 }  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   double ftolhess; /* Tolerance for computing hessian */
 /******************* imatrix *******************************/  
 int **imatrix(long nrl, long nrh, long ncl, long nch)  /**************** split *************************/
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 {  {
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    char  *ss;                            /* pointer */
   int **m;    int   l1, l2;                         /* length counters */
    
   /* allocate pointers to rows */    l1 = strlen(path );                   /* length of path */
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   if (!m) nrerror("allocation failure 1 in matrix()");    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   m += NR_END;    if ( ss == NULL ) {                   /* no directory, so use current */
   m -= nrl;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
          printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
        /* get current working directory */
   /* allocate rows and set pointers to them */      /*    extern  char* getcwd ( char *buf , int len);*/
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");        return( GLOCK_ERROR_GETCWD );
   m[nrl] += NR_END;      }
   m[nrl] -= ncl;      strcpy( name, path );               /* we've got it */
      } else {                              /* strip direcotry from path */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;      ss++;                               /* after this, the filename */
        l2 = strlen( ss );                  /* length of filename */
   /* return pointer to array of pointers to rows */      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   return m;      strcpy( name, ss );         /* save file name */
 }      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       dirc[l1-l2] = 0;                    /* add zero */
 /****************** free_imatrix *************************/    }
 void free_imatrix(m,nrl,nrh,ncl,nch)    l1 = strlen( dirc );                  /* length of directory */
       int **m;    /*#ifdef windows
       long nch,ncl,nrh,nrl;    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
      /* free an int matrix allocated by imatrix() */  #else
 {    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  #endif
   free((FREE_ARG) (m+nrl-NR_END));    */
 }    ss = strrchr( name, '.' );            /* find last / */
     ss++;
 /******************* matrix *******************************/    strcpy(ext,ss);                       /* save extension */
 double **matrix(long nrl, long nrh, long ncl, long nch)    l1= strlen( name);
 {    l2= strlen(ss)+1;
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    strncpy( finame, name, l1-l2);
   double **m;    finame[l1-l2]= 0;
     return( 0 );                          /* we're done */
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  }
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  
   m -= nrl;  /******************************************/
   
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  void replace_back_to_slash(char *s, char*t)
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  {
   m[nrl] += NR_END;    int i;
   m[nrl] -= ncl;    int lg=0;
     i=0;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    lg=strlen(t);
   return m;    for(i=0; i<= lg; i++) {
 }      (s[i] = t[i]);
       if (t[i]== '\\') s[i]='/';
 /*************************free matrix ************************/    }
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  }
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  int nbocc(char *s, char occ)
   free((FREE_ARG)(m+nrl-NR_END));  {
 }    int i,j=0;
     int lg=20;
 /******************* ma3x *******************************/    i=0;
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    lg=strlen(s);
 {    for(i=0; i<= lg; i++) {
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    if  (s[i] == occ ) j++;
   double ***m;    }
     return j;
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  }
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  void cutv(char *u,char *v, char*t, char occ)
   m -= nrl;  {
     /* cuts string t into u and v where u is ended by char occ excluding it
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");       gives u="abcedf" and v="ghi2j" */
   m[nrl] += NR_END;    int i,lg,j,p=0;
   m[nrl] -= ncl;    i=0;
     for(j=0; j<=strlen(t)-1; j++) {
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     }
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    lg=strlen(t);
   m[nrl][ncl] += NR_END;    for(j=0; j<p; j++) {
   m[nrl][ncl] -= nll;      (u[j] = t[j]);
   for (j=ncl+1; j<=nch; j++)    }
     m[nrl][j]=m[nrl][j-1]+nlay;       u[p]='\0';
    
   for (i=nrl+1; i<=nrh; i++) {     for(j=0; j<= lg; j++) {
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;      if (j>=(p+1))(v[j-p-1] = t[j]);
     for (j=ncl+1; j<=nch; j++)    }
       m[i][j]=m[i][j-1]+nlay;  }
   }  
   return m;  /********************** nrerror ********************/
 }  
   void nrerror(char error_text[])
 /*************************free ma3x ************************/  {
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    fprintf(stderr,"ERREUR ...\n");
 {    fprintf(stderr,"%s\n",error_text);
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    exit(EXIT_FAILURE);
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  }
   free((FREE_ARG)(m+nrl-NR_END));  /*********************** vector *******************/
 }  double *vector(int nl, int nh)
   {
 /***************** f1dim *************************/    double *v;
 extern int ncom;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 extern double *pcom,*xicom;    if (!v) nrerror("allocation failure in vector");
 extern double (*nrfunc)(double []);    return v-nl+NR_END;
    }
 double f1dim(double x)  
 {  /************************ free vector ******************/
   int j;  void free_vector(double*v, int nl, int nh)
   double f;  {
   double *xt;    free((FREE_ARG)(v+nl-NR_END));
    }
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  /************************ivector *******************************/
   f=(*nrfunc)(xt);  int *ivector(long nl,long nh)
   free_vector(xt,1,ncom);  {
   return f;    int *v;
 }    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     if (!v) nrerror("allocation failure in ivector");
 /*****************brent *************************/    return v-nl+NR_END;
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  }
 {  
   int iter;  /******************free ivector **************************/
   double a,b,d,etemp;  void free_ivector(int *v, long nl, long nh)
   double fu,fv,fw,fx;  {
   double ftemp;    free((FREE_ARG)(v+nl-NR_END));
   double p,q,r,tol1,tol2,u,v,w,x,xm;  }
   double e=0.0;  
    /************************lvector *******************************/
   a=(ax < cx ? ax : cx);  long *lvector(long nl,long nh)
   b=(ax > cx ? ax : cx);  {
   x=w=v=bx;    long *v;
   fw=fv=fx=(*f)(x);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   for (iter=1;iter<=ITMAX;iter++) {    if (!v) nrerror("allocation failure in ivector");
     xm=0.5*(a+b);    return v-nl+NR_END;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  }
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);  /******************free lvector **************************/
 #ifdef DEBUG  void free_lvector(long *v, long nl, long nh)
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  {
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    free((FREE_ARG)(v+nl-NR_END));
 #endif  }
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  
       *xmin=x;  /******************* imatrix *******************************/
       return fx;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     }       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     ftemp=fu;  { 
     if (fabs(e) > tol1) {    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       r=(x-w)*(fx-fv);    int **m; 
       q=(x-v)*(fx-fw);    
       p=(x-v)*q-(x-w)*r;    /* allocate pointers to rows */ 
       q=2.0*(q-r);    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       if (q > 0.0) p = -p;    if (!m) nrerror("allocation failure 1 in matrix()"); 
       q=fabs(q);    m += NR_END; 
       etemp=e;    m -= nrl; 
       e=d;    
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    /* allocate rows and set pointers to them */ 
       else {    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
         d=p/q;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
         u=x+d;    m[nrl] += NR_END; 
         if (u-a < tol2 || b-u < tol2)    m[nrl] -= ncl; 
           d=SIGN(tol1,xm-x);    
       }    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     } else {    
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    /* return pointer to array of pointers to rows */ 
     }    return m; 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  } 
     fu=(*f)(u);  
     if (fu <= fx) {  /****************** free_imatrix *************************/
       if (u >= x) a=x; else b=x;  void free_imatrix(m,nrl,nrh,ncl,nch)
       SHFT(v,w,x,u)        int **m;
         SHFT(fv,fw,fx,fu)        long nch,ncl,nrh,nrl; 
         } else {       /* free an int matrix allocated by imatrix() */ 
           if (u < x) a=u; else b=u;  { 
           if (fu <= fw || w == x) {    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
             v=w;    free((FREE_ARG) (m+nrl-NR_END)); 
             w=u;  } 
             fv=fw;  
             fw=fu;  /******************* matrix *******************************/
           } else if (fu <= fv || v == x || v == w) {  double **matrix(long nrl, long nrh, long ncl, long nch)
             v=u;  {
             fv=fu;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
           }    double **m;
         }  
   }    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   nrerror("Too many iterations in brent");    if (!m) nrerror("allocation failure 1 in matrix()");
   *xmin=x;    m += NR_END;
   return fx;    m -= nrl;
 }  
     m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 /****************** mnbrak ***********************/    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    m[nrl] -= ncl;
             double (*func)(double))  
 {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   double ulim,u,r,q, dum;    return m;
   double fu;    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       */
   *fa=(*func)(*ax);  }
   *fb=(*func)(*bx);  
   if (*fb > *fa) {  /*************************free matrix ************************/
     SHFT(dum,*ax,*bx,dum)  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       SHFT(dum,*fb,*fa,dum)  {
       }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   *cx=(*bx)+GOLD*(*bx-*ax);    free((FREE_ARG)(m+nrl-NR_END));
   *fc=(*func)(*cx);  }
   while (*fb > *fc) {  
     r=(*bx-*ax)*(*fb-*fc);  /******************* ma3x *******************************/
     q=(*bx-*cx)*(*fb-*fa);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  {
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     ulim=(*bx)+GLIMIT*(*cx-*bx);    double ***m;
     if ((*bx-u)*(u-*cx) > 0.0) {  
       fu=(*func)(u);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     } else if ((*cx-u)*(u-ulim) > 0.0) {    if (!m) nrerror("allocation failure 1 in matrix()");
       fu=(*func)(u);    m += NR_END;
       if (fu < *fc) {    m -= nrl;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
           }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    m[nrl] += NR_END;
       u=ulim;    m[nrl] -= ncl;
       fu=(*func)(u);  
     } else {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       u=(*cx)+GOLD*(*cx-*bx);  
       fu=(*func)(u);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     }    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     SHFT(*ax,*bx,*cx,u)    m[nrl][ncl] += NR_END;
       SHFT(*fa,*fb,*fc,fu)    m[nrl][ncl] -= nll;
       }    for (j=ncl+1; j<=nch; j++) 
 }      m[nrl][j]=m[nrl][j-1]+nlay;
     
 /*************** linmin ************************/    for (i=nrl+1; i<=nrh; i++) {
       m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
 int ncom;      for (j=ncl+1; j<=nch; j++) 
 double *pcom,*xicom;        m[i][j]=m[i][j-1]+nlay;
 double (*nrfunc)(double []);    }
      return m; 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
 {             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   double brent(double ax, double bx, double cx,    */
                double (*f)(double), double tol, double *xmin);  }
   double f1dim(double x);  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  /*************************free ma3x ************************/
               double *fc, double (*func)(double));  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   int j;  {
   double xx,xmin,bx,ax;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   double fx,fb,fa;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
      free((FREE_ARG)(m+nrl-NR_END));
   ncom=n;  }
   pcom=vector(1,n);  
   xicom=vector(1,n);  /***************** f1dim *************************/
   nrfunc=func;  extern int ncom; 
   for (j=1;j<=n;j++) {  extern double *pcom,*xicom;
     pcom[j]=p[j];  extern double (*nrfunc)(double []); 
     xicom[j]=xi[j];   
   }  double f1dim(double x) 
   ax=0.0;  { 
   xx=1.0;    int j; 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    double f;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    double *xt; 
 #ifdef DEBUG   
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    xt=vector(1,ncom); 
 #endif    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   for (j=1;j<=n;j++) {    f=(*nrfunc)(xt); 
     xi[j] *= xmin;    free_vector(xt,1,ncom); 
     p[j] += xi[j];    return f; 
   }  } 
   free_vector(xicom,1,n);  
   free_vector(pcom,1,n);  /*****************brent *************************/
 }  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   { 
 /*************** powell ************************/    int iter; 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    double a,b,d,etemp;
             double (*func)(double []))    double fu,fv,fw,fx;
 {    double ftemp;
   void linmin(double p[], double xi[], int n, double *fret,    double p,q,r,tol1,tol2,u,v,w,x,xm; 
               double (*func)(double []));    double e=0.0; 
   int i,ibig,j;   
   double del,t,*pt,*ptt,*xit;    a=(ax < cx ? ax : cx); 
   double fp,fptt;    b=(ax > cx ? ax : cx); 
   double *xits;    x=w=v=bx; 
   pt=vector(1,n);    fw=fv=fx=(*f)(x); 
   ptt=vector(1,n);    for (iter=1;iter<=ITMAX;iter++) { 
   xit=vector(1,n);      xm=0.5*(a+b); 
   xits=vector(1,n);      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   *fret=(*func)(p);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   for (j=1;j<=n;j++) pt[j]=p[j];      printf(".");fflush(stdout);
   for (*iter=1;;++(*iter)) {      fprintf(ficlog,".");fflush(ficlog);
     fp=(*fret);  #ifdef DEBUG
     ibig=0;      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     del=0.0;      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     for (i=1;i<=n;i++)  #endif
       printf(" %d %.12f",i, p[i]);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     printf("\n");        *xmin=x; 
     for (i=1;i<=n;i++) {        return fx; 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];      } 
       fptt=(*fret);      ftemp=fu;
 #ifdef DEBUG      if (fabs(e) > tol1) { 
       printf("fret=%lf \n",*fret);        r=(x-w)*(fx-fv); 
 #endif        q=(x-v)*(fx-fw); 
       printf("%d",i);fflush(stdout);        p=(x-v)*q-(x-w)*r; 
       linmin(p,xit,n,fret,func);        q=2.0*(q-r); 
       if (fabs(fptt-(*fret)) > del) {        if (q > 0.0) p = -p; 
         del=fabs(fptt-(*fret));        q=fabs(q); 
         ibig=i;        etemp=e; 
       }        e=d; 
 #ifdef DEBUG        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
       printf("%d %.12e",i,(*fret));          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       for (j=1;j<=n;j++) {        else { 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);          d=p/q; 
         printf(" x(%d)=%.12e",j,xit[j]);          u=x+d; 
       }          if (u-a < tol2 || b-u < tol2) 
       for(j=1;j<=n;j++)            d=SIGN(tol1,xm-x); 
         printf(" p=%.12e",p[j]);        } 
       printf("\n");      } else { 
 #endif        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     }      } 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
 #ifdef DEBUG      fu=(*f)(u); 
       int k[2],l;      if (fu <= fx) { 
       k[0]=1;        if (u >= x) a=x; else b=x; 
       k[1]=-1;        SHFT(v,w,x,u) 
       printf("Max: %.12e",(*func)(p));          SHFT(fv,fw,fx,fu) 
       for (j=1;j<=n;j++)          } else { 
         printf(" %.12e",p[j]);            if (u < x) a=u; else b=u; 
       printf("\n");            if (fu <= fw || w == x) { 
       for(l=0;l<=1;l++) {              v=w; 
         for (j=1;j<=n;j++) {              w=u; 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];              fv=fw; 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);              fw=fu; 
         }            } else if (fu <= fv || v == x || v == w) { 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));              v=u; 
       }              fv=fu; 
 #endif            } 
           } 
     } 
       free_vector(xit,1,n);    nrerror("Too many iterations in brent"); 
       free_vector(xits,1,n);    *xmin=x; 
       free_vector(ptt,1,n);    return fx; 
       free_vector(pt,1,n);  } 
       return;  
     }  /****************** mnbrak ***********************/
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  
     for (j=1;j<=n;j++) {  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       ptt[j]=2.0*p[j]-pt[j];              double (*func)(double)) 
       xit[j]=p[j]-pt[j];  { 
       pt[j]=p[j];    double ulim,u,r,q, dum;
     }    double fu; 
     fptt=(*func)(ptt);   
     if (fptt < fp) {    *fa=(*func)(*ax); 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    *fb=(*func)(*bx); 
       if (t < 0.0) {    if (*fb > *fa) { 
         linmin(p,xit,n,fret,func);      SHFT(dum,*ax,*bx,dum) 
         for (j=1;j<=n;j++) {        SHFT(dum,*fb,*fa,dum) 
           xi[j][ibig]=xi[j][n];        } 
           xi[j][n]=xit[j];    *cx=(*bx)+GOLD*(*bx-*ax); 
         }    *fc=(*func)(*cx); 
 #ifdef DEBUG    while (*fb > *fc) { 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      r=(*bx-*ax)*(*fb-*fc); 
         for(j=1;j<=n;j++)      q=(*bx-*cx)*(*fb-*fa); 
           printf(" %.12e",xit[j]);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         printf("\n");        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 #endif      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       }      if ((*bx-u)*(u-*cx) > 0.0) { 
     }        fu=(*func)(u); 
   }      } else if ((*cx-u)*(u-ulim) > 0.0) { 
 }        fu=(*func)(u); 
         if (fu < *fc) { 
 /**** Prevalence limit ****************/          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
             SHFT(*fb,*fc,fu,(*func)(u)) 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)            } 
 {      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit        u=ulim; 
      matrix by transitions matrix until convergence is reached */        fu=(*func)(u); 
       } else { 
   int i, ii,j,k;        u=(*cx)+GOLD*(*cx-*bx); 
   double min, max, maxmin, maxmax,sumnew=0.;        fu=(*func)(u); 
   double **matprod2();      } 
   double **out, cov[NCOVMAX], **pmij();      SHFT(*ax,*bx,*cx,u) 
   double **newm;        SHFT(*fa,*fb,*fc,fu) 
   double agefin, delaymax=50 ; /* Max number of years to converge */        } 
   } 
   for (ii=1;ii<=nlstate+ndeath;ii++)  
     for (j=1;j<=nlstate+ndeath;j++){  /*************** linmin ************************/
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  
     }  int ncom; 
   double *pcom,*xicom;
    cov[1]=1.;  double (*nrfunc)(double []); 
     
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  { 
     newm=savm;    double brent(double ax, double bx, double cx, 
     /* Covariates have to be included here again */                 double (*f)(double), double tol, double *xmin); 
      cov[2]=agefin;    double f1dim(double x); 
      void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       for (k=1; k<=cptcovn;k++) {                double *fc, double (*func)(double)); 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    int j; 
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/    double xx,xmin,bx,ax; 
       }    double fx,fb,fa;
       for (k=1; k<=cptcovage;k++)   
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    ncom=n; 
       for (k=1; k<=cptcovprod;k++)    pcom=vector(1,n); 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    xicom=vector(1,n); 
     nrfunc=func; 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    for (j=1;j<=n;j++) { 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/      pcom[j]=p[j]; 
       xicom[j]=xi[j]; 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    } 
     ax=0.0; 
     savm=oldm;    xx=1.0; 
     oldm=newm;    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     maxmax=0.;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     for(j=1;j<=nlstate;j++){  #ifdef DEBUG
       min=1.;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       max=0.;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       for(i=1; i<=nlstate; i++) {  #endif
         sumnew=0;    for (j=1;j<=n;j++) { 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];      xi[j] *= xmin; 
         prlim[i][j]= newm[i][j]/(1-sumnew);      p[j] += xi[j]; 
         max=FMAX(max,prlim[i][j]);    } 
         min=FMIN(min,prlim[i][j]);    free_vector(xicom,1,n); 
       }    free_vector(pcom,1,n); 
       maxmin=max-min;  } 
       maxmax=FMAX(maxmax,maxmin);  
     }  /*************** powell ************************/
     if(maxmax < ftolpl){  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       return prlim;              double (*func)(double [])) 
     }  { 
   }    void linmin(double p[], double xi[], int n, double *fret, 
 }                double (*func)(double [])); 
     int i,ibig,j; 
 /*************** transition probabilities ***************/    double del,t,*pt,*ptt,*xit;
     double fp,fptt;
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    double *xits;
 {    pt=vector(1,n); 
   double s1, s2;    ptt=vector(1,n); 
   /*double t34;*/    xit=vector(1,n); 
   int i,j,j1, nc, ii, jj;    xits=vector(1,n); 
     *fret=(*func)(p); 
     for(i=1; i<= nlstate; i++){    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for(j=1; j<i;j++){    for (*iter=1;;++(*iter)) { 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      fp=(*fret); 
         /*s2 += param[i][j][nc]*cov[nc];*/      ibig=0; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      del=0.0; 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       }      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       ps[i][j]=s2;      fprintf(ficrespow,"%d %.12f",*iter,*fret);
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/      for (i=1;i<=n;i++) {
     }        printf(" %d %.12f",i, p[i]);
     for(j=i+1; j<=nlstate+ndeath;j++){        fprintf(ficlog," %d %.12lf",i, p[i]);
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        fprintf(ficrespow," %.12lf", p[i]);
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      }
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/      printf("\n");
       }      fprintf(ficlog,"\n");
       ps[i][j]=s2;      fprintf(ficrespow,"\n");
     }      for (i=1;i<=n;i++) { 
   }        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     /*ps[3][2]=1;*/        fptt=(*fret); 
   #ifdef DEBUG
   for(i=1; i<= nlstate; i++){        printf("fret=%lf \n",*fret);
      s1=0;        fprintf(ficlog,"fret=%lf \n",*fret);
     for(j=1; j<i; j++)  #endif
       s1+=exp(ps[i][j]);        printf("%d",i);fflush(stdout);
     for(j=i+1; j<=nlstate+ndeath; j++)        fprintf(ficlog,"%d",i);fflush(ficlog);
       s1+=exp(ps[i][j]);        linmin(p,xit,n,fret,func); 
     ps[i][i]=1./(s1+1.);        if (fabs(fptt-(*fret)) > del) { 
     for(j=1; j<i; j++)          del=fabs(fptt-(*fret)); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];          ibig=i; 
     for(j=i+1; j<=nlstate+ndeath; j++)        } 
       ps[i][j]= exp(ps[i][j])*ps[i][i];  #ifdef DEBUG
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        printf("%d %.12e",i,(*fret));
   } /* end i */        fprintf(ficlog,"%d %.12e",i,(*fret));
         for (j=1;j<=n;j++) {
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     for(jj=1; jj<= nlstate+ndeath; jj++){          printf(" x(%d)=%.12e",j,xit[j]);
       ps[ii][jj]=0;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       ps[ii][ii]=1;        }
     }        for(j=1;j<=n;j++) {
   }          printf(" p=%.12e",p[j]);
           fprintf(ficlog," p=%.12e",p[j]);
         }
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        printf("\n");
     for(jj=1; jj<= nlstate+ndeath; jj++){        fprintf(ficlog,"\n");
      printf("%lf ",ps[ii][jj]);  #endif
    }      } 
     printf("\n ");      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     }  #ifdef DEBUG
     printf("\n ");printf("%lf ",cov[2]);*/        int k[2],l;
 /*        k[0]=1;
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        k[1]=-1;
   goto end;*/        printf("Max: %.12e",(*func)(p));
     return ps;        fprintf(ficlog,"Max: %.12e",(*func)(p));
 }        for (j=1;j<=n;j++) {
           printf(" %.12e",p[j]);
 /**************** Product of 2 matrices ******************/          fprintf(ficlog," %.12e",p[j]);
         }
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        printf("\n");
 {        fprintf(ficlog,"\n");
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        for(l=0;l<=1;l++) {
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */          for (j=1;j<=n;j++) {
   /* in, b, out are matrice of pointers which should have been initialized            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
      before: only the contents of out is modified. The function returns            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
      a pointer to pointers identical to out */            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   long i, j, k;          }
   for(i=nrl; i<= nrh; i++)          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     for(k=ncolol; k<=ncoloh; k++)          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        }
         out[i][k] +=in[i][j]*b[j][k];  #endif
   
   return out;  
 }        free_vector(xit,1,n); 
         free_vector(xits,1,n); 
         free_vector(ptt,1,n); 
 /************* Higher Matrix Product ***************/        free_vector(pt,1,n); 
         return; 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      } 
 {      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      for (j=1;j<=n;j++) { 
      duration (i.e. until        ptt[j]=2.0*p[j]-pt[j]; 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        xit[j]=p[j]-pt[j]; 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        pt[j]=p[j]; 
      (typically every 2 years instead of every month which is too big).      } 
      Model is determined by parameters x and covariates have to be      fptt=(*func)(ptt); 
      included manually here.      if (fptt < fp) { 
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
      */        if (t < 0.0) { 
           linmin(p,xit,n,fret,func); 
   int i, j, d, h, k;          for (j=1;j<=n;j++) { 
   double **out, cov[NCOVMAX];            xi[j][ibig]=xi[j][n]; 
   double **newm;            xi[j][n]=xit[j]; 
           }
   /* Hstepm could be zero and should return the unit matrix */  #ifdef DEBUG
   for (i=1;i<=nlstate+ndeath;i++)          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     for (j=1;j<=nlstate+ndeath;j++){          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       oldm[i][j]=(i==j ? 1.0 : 0.0);          for(j=1;j<=n;j++){
       po[i][j][0]=(i==j ? 1.0 : 0.0);            printf(" %.12e",xit[j]);
     }            fprintf(ficlog," %.12e",xit[j]);
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */          }
   for(h=1; h <=nhstepm; h++){          printf("\n");
     for(d=1; d <=hstepm; d++){          fprintf(ficlog,"\n");
       newm=savm;  #endif
       /* Covariates have to be included here again */        }
       cov[1]=1.;      } 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    } 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  } 
       for (k=1; k<=cptcovage;k++)  
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  /**** Prevalence limit (stable prevalence)  ****************/
       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]]];  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   {
     /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/       matrix by transitions matrix until convergence is reached */
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    int i, ii,j,k;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    double min, max, maxmin, maxmax,sumnew=0.;
       savm=oldm;    double **matprod2();
       oldm=newm;    double **out, cov[NCOVMAX], **pmij();
     }    double **newm;
     for(i=1; i<=nlstate+ndeath; i++)    double agefin, delaymax=50 ; /* Max number of years to converge */
       for(j=1;j<=nlstate+ndeath;j++) {  
         po[i][j][h]=newm[i][j];    for (ii=1;ii<=nlstate+ndeath;ii++)
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      for (j=1;j<=nlstate+ndeath;j++){
          */        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }      }
   } /* end h */  
   return po;     cov[1]=1.;
 }   
    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
 /*************** log-likelihood *************/      newm=savm;
 double func( double *x)      /* Covariates have to be included here again */
 {       cov[2]=agefin;
   int i, ii, j, k, mi, d, kk;    
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        for (k=1; k<=cptcovn;k++) {
   double **out;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   double sw; /* Sum of weights */          /*      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]]);*/
   double lli; /* Individual log likelihood */        }
   long ipmx;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   /*extern weight */        for (k=1; k<=cptcovprod;k++)
   /* We are differentiating ll according to initial status */          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<=npar;i++) printf("%f ", x[i]);*/  
   /*for(i=1;i<imx;i++)        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     printf(" %d\n",s[4][i]);        /*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]);*/
   cov[1]=1.;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   
   for(k=1; k<=nlstate; k++) ll[k]=0.;      savm=oldm;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      oldm=newm;
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      maxmax=0.;
     for(mi=1; mi<= wav[i]-1; mi++){      for(j=1;j<=nlstate;j++){
       for (ii=1;ii<=nlstate+ndeath;ii++)        min=1.;
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        max=0.;
       for(d=0; d<dh[mi][i]; d++){        for(i=1; i<=nlstate; i++) {
         newm=savm;          sumnew=0;
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
         for (kk=1; kk<=cptcovage;kk++) {          prlim[i][j]= newm[i][j]/(1-sumnew);
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];          max=FMAX(max,prlim[i][j]);
         }          min=FMIN(min,prlim[i][j]);
                }
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        maxmin=max-min;
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        maxmax=FMAX(maxmax,maxmin);
         savm=oldm;      }
         oldm=newm;      if(maxmax < ftolpl){
                return prlim;
              }
       } /* end mult */    }
        }
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  /*************** transition probabilities ***************/ 
       ipmx +=1;  
       sw += weight[i];  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  {
     } /* end of wave */    double s1, s2;
   } /* end of individual */    /*double t34;*/
     int i,j,j1, nc, ii, jj;
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      for(i=1; i<= nlstate; i++){
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      for(j=1; j<i;j++){
   return -l;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
 }          /*s2 += param[i][j][nc]*cov[nc];*/
           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);*/
 /*********** Maximum Likelihood Estimation ***************/        }
         ps[i][j]=s2;
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
 {      }
   int i,j, iter;      for(j=i+1; j<=nlstate+ndeath;j++){
   double **xi,*delti;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   double fret;          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   xi=matrix(1,npar,1,npar);          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
   for (i=1;i<=npar;i++)        }
     for (j=1;j<=npar;j++)        ps[i][j]=s2;
       xi[i][j]=(i==j ? 1.0 : 0.0);      }
   printf("Powell\n");    }
   powell(p,xi,npar,ftol,&iter,&fret,func);      /*ps[3][2]=1;*/
   
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    for(i=1; i<= nlstate; i++){
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));       s1=0;
       for(j=1; j<i; j++)
 }        s1+=exp(ps[i][j]);
       for(j=i+1; j<=nlstate+ndeath; j++)
 /**** Computes Hessian and covariance matrix ***/        s1+=exp(ps[i][j]);
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      ps[i][i]=1./(s1+1.);
 {      for(j=1; j<i; j++)
   double  **a,**y,*x,pd;        ps[i][j]= exp(ps[i][j])*ps[i][i];
   double **hess;      for(j=i+1; j<=nlstate+ndeath; j++)
   int i, j,jk;        ps[i][j]= exp(ps[i][j])*ps[i][i];
   int *indx;      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     } /* end i */
   double hessii(double p[], double delta, int theta, double delti[]);  
   double hessij(double p[], double delti[], int i, int j);    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   void lubksb(double **a, int npar, int *indx, double b[]) ;      for(jj=1; jj<= nlstate+ndeath; jj++){
   void ludcmp(double **a, int npar, int *indx, double *d) ;        ps[ii][jj]=0;
         ps[ii][ii]=1;
   hess=matrix(1,npar,1,npar);      }
     }
   printf("\nCalculation of the hessian matrix. Wait...\n");  
   for (i=1;i<=npar;i++){  
     printf("%d",i);fflush(stdout);    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
     hess[i][i]=hessii(p,ftolhess,i,delti);      for(jj=1; jj<= nlstate+ndeath; jj++){
     /*printf(" %f ",p[i]);*/       printf("%lf ",ps[ii][jj]);
     /*printf(" %lf ",hess[i][i]);*/     }
   }      printf("\n ");
        }
   for (i=1;i<=npar;i++) {      printf("\n ");printf("%lf ",cov[2]);*/
     for (j=1;j<=npar;j++)  {  /*
       if (j>i) {    for(i=1; i<= npar; i++) printf("%f ",x[i]);
         printf(".%d%d",i,j);fflush(stdout);    goto end;*/
         hess[i][j]=hessij(p,delti,i,j);      return ps;
         hess[j][i]=hess[i][j];      }
         /*printf(" %lf ",hess[i][j]);*/  
       }  /**************** 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");  {
     /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
      /* in, b, out are matrice of pointers which should have been initialized 
   a=matrix(1,npar,1,npar);       before: only the contents of out is modified. The function returns
   y=matrix(1,npar,1,npar);       a pointer to pointers identical to out */
   x=vector(1,npar);    long i, j, k;
   indx=ivector(1,npar);    for(i=nrl; i<= nrh; i++)
   for (i=1;i<=npar;i++)      for(k=ncolol; k<=ncoloh; k++)
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        for(j=ncl,out[i][k]=0.; j<=nch; j++)
   ludcmp(a,npar,indx,&pd);          out[i][k] +=in[i][j]*b[j][k];
   
   for (j=1;j<=npar;j++) {    return out;
     for (i=1;i<=npar;i++) x[i]=0;  }
     x[j]=1;  
     lubksb(a,npar,indx,x);  
     for (i=1;i<=npar;i++){  /************* Higher Matrix Product ***************/
       matcov[i][j]=x[i];  
     }  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   }  {
     /* Computes the transition matrix starting at age 'age' over 
   printf("\n#Hessian matrix#\n");       'nhstepm*hstepm*stepm' months (i.e. until
   for (i=1;i<=npar;i++) {       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
     for (j=1;j<=npar;j++) {       nhstepm*hstepm matrices. 
       printf("%.3e ",hess[i][j]);       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 
     printf("\n");       for the memory).
   }       Model is determined by parameters x and covariates have to be 
        included manually here. 
   /* Recompute Inverse */  
   for (i=1;i<=npar;i++)       */
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  
   ludcmp(a,npar,indx,&pd);    int i, j, d, h, k;
     double **out, cov[NCOVMAX];
   /*  printf("\n#Hessian matrix recomputed#\n");    double **newm;
   
   for (j=1;j<=npar;j++) {    /* Hstepm could be zero and should return the unit matrix */
     for (i=1;i<=npar;i++) x[i]=0;    for (i=1;i<=nlstate+ndeath;i++)
     x[j]=1;      for (j=1;j<=nlstate+ndeath;j++){
     lubksb(a,npar,indx,x);        oldm[i][j]=(i==j ? 1.0 : 0.0);
     for (i=1;i<=npar;i++){        po[i][j][0]=(i==j ? 1.0 : 0.0);
       y[i][j]=x[i];      }
       printf("%.3e ",y[i][j]);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     }    for(h=1; h <=nhstepm; h++){
     printf("\n");      for(d=1; d <=hstepm; d++){
   }        newm=savm;
   */        /* Covariates have to be included here again */
         cov[1]=1.;
   free_matrix(a,1,npar,1,npar);        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   free_matrix(y,1,npar,1,npar);        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   free_vector(x,1,npar);        for (k=1; k<=cptcovage;k++)
   free_ivector(indx,1,npar);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   free_matrix(hess,1,npar,1,npar);        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("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
 /*************** hessian matrix ****************/        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
 double hessii( double x[], double delta, int theta, double delti[])        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
 {                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   int i;        savm=oldm;
   int l=1, lmax=20;        oldm=newm;
   double k1,k2;      }
   double p2[NPARMAX+1];      for(i=1; i<=nlstate+ndeath; i++)
   double res;        for(j=1;j<=nlstate+ndeath;j++) {
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;          po[i][j][h]=newm[i][j];
   double fx;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
   int k=0,kmax=10;           */
   double l1;        }
     } /* end h */
   fx=func(x);    return po;
   for (i=1;i<=npar;i++) p2[i]=x[i];  }
   for(l=0 ; l <=lmax; l++){  
     l1=pow(10,l);  
     delts=delt;  /*************** log-likelihood *************/
     for(k=1 ; k <kmax; k=k+1){  double func( double *x)
       delt = delta*(l1*k);  {
       p2[theta]=x[theta] +delt;    int i, ii, j, k, mi, d, kk;
       k1=func(p2)-fx;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
       p2[theta]=x[theta]-delt;    double **out;
       k2=func(p2)-fx;    double sw; /* Sum of weights */
       /*res= (k1-2.0*fx+k2)/delt/delt; */    double lli; /* Individual log likelihood */
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    int s1, s2;
          double bbh, survp;
 #ifdef DEBUG    long ipmx;
       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);    /*extern weight */
 #endif    /* We are differentiating ll according to initial status */
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    /*for(i=1;i<imx;i++) 
         k=kmax;      printf(" %d\n",s[4][i]);
       }    */
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    cov[1]=1.;
         k=kmax; l=lmax*10.;  
       }    for(k=1; k<=nlstate; k++) ll[k]=0.;
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  
         delts=delt;    if(mle==1){
       }      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++){
   delti[theta]=delts;          for (ii=1;ii<=nlstate+ndeath;ii++)
   return res;            for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
 double hessij( double x[], double delti[], int thetai,int thetaj)          for(d=0; d<dh[mi][i]; d++){
 {            newm=savm;
   int i;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   int l=1, l1, lmax=20;            for (kk=1; kk<=cptcovage;kk++) {
   double k1,k2,k3,k4,res,fx;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double p2[NPARMAX+1];            }
   int k;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   fx=func(x);            savm=oldm;
   for (k=1; k<=2; k++) {            oldm=newm;
     for (i=1;i<=npar;i++) p2[i]=x[i];          } /* end mult */
     p2[thetai]=x[thetai]+delti[thetai]/k;        
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     k1=func(p2)-fx;          /* But now since version 0.9 we anticipate for bias and large stepm.
             * If stepm is larger than one month (smallest stepm) and if the exact delay 
     p2[thetai]=x[thetai]+delti[thetai]/k;           * (in months) between two waves is not a multiple of stepm, we rounded to 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;           * the nearest (and in case of equal distance, to the lowest) interval but now
     k2=func(p2)-fx;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
             * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     p2[thetai]=x[thetai]-delti[thetai]/k;           * probability in order to take into account the bias as a fraction of the way
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     k3=func(p2)-fx;           * -stepm/2 to stepm/2 .
             * For stepm=1 the results are the same as for previous versions of Imach.
     p2[thetai]=x[thetai]-delti[thetai]/k;           * For stepm > 1 the results are less biased than in previous versions. 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;           */
     k4=func(p2)-fx;          s1=s[mw[mi][i]][i];
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          s2=s[mw[mi+1][i]][i];
 #ifdef DEBUG          bbh=(double)bh[mi][i]/(double)stepm; 
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);          /* bias is positive if real duration
 #endif           * is higher than the multiple of stepm and negative otherwise.
   }           */
   return res;          /* 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( s2 > nlstate){ 
             /* i.e. if s2 is a death state and if the date of death is known then the contribution
 /************** Inverse of matrix **************/               to the likelihood is the probability to die between last step unit time and current 
 void ludcmp(double **a, int n, int *indx, double *d)               step unit time, which is also the differences between probability to die before dh 
 {               and probability to die before dh-stepm . 
   int i,imax,j,k;               In version up to 0.92 likelihood was computed
   double big,dum,sum,temp;          as if date of death was unknown. Death was treated as any other
   double *vv;          health state: the date of the interview describes the actual state
            and not the date of a change in health state. The former idea was
   vv=vector(1,n);          to consider that at each interview the state was recorded
   *d=1.0;          (healthy, disable or death) and IMaCh was corrected; but when we
   for (i=1;i<=n;i++) {          introduced the exact date of death then we should have modified
     big=0.0;          the contribution of an exact death to the likelihood. This new
     for (j=1;j<=n;j++)          contribution is smaller and very dependent of the step unit
       if ((temp=fabs(a[i][j])) > big) big=temp;          stepm. It is no more the probability to die between last interview
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          and month of death but the probability to survive from last
     vv[i]=1.0/big;          interview up to one month before death multiplied by the
   }          probability to die within a month. Thanks to Chris
   for (j=1;j<=n;j++) {          Jackson for correcting this bug.  Former versions increased
     for (i=1;i<j;i++) {          mortality artificially. The bad side is that we add another loop
       sum=a[i][j];          which slows down the processing. The difference can be up to 10%
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];          lower mortality.
       a[i][j]=sum;            */
     }            lli=log(out[s1][s2] - savm[s1][s2]);
     big=0.0;          }else{
     for (i=j;i<=n;i++) {            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       sum=a[i][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 (k=1;k<j;k++)          } 
         sum -= a[i][k]*a[k][j];          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       a[i][j]=sum;          /*if(lli ==000.0)*/
       if ( (dum=vv[i]*fabs(sum)) >= big) {          /*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); */
         big=dum;          ipmx +=1;
         imax=i;          sw += weight[i];
       }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }        } /* end of wave */
     if (j != imax) {      } /* end of individual */
       for (k=1;k<=n;k++) {    }  else if(mle==2){
         dum=a[imax][k];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         a[imax][k]=a[j][k];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         a[j][k]=dum;        for(mi=1; mi<= wav[i]-1; mi++){
       }          for (ii=1;ii<=nlstate+ndeath;ii++)
       *d = -(*d);            for (j=1;j<=nlstate+ndeath;j++){
       vv[imax]=vv[j];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     indx[j]=imax;            }
     if (a[j][j] == 0.0) a[j][j]=TINY;          for(d=0; d<=dh[mi][i]; d++){
     if (j != n) {            newm=savm;
       dum=1.0/(a[j][j]);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for (i=j+1;i<=n;i++) a[i][j] *= dum;            for (kk=1; kk<=cptcovage;kk++) {
     }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   }            }
   free_vector(vv,1,n);  /* Doesn't work */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 ;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 }            savm=oldm;
             oldm=newm;
 void lubksb(double **a, int n, int *indx, double b[])          } /* end mult */
 {        
   int i,ii=0,ip,j;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   double sum;          /* But now since version 0.9 we anticipate for bias and large stepm.
             * If stepm is larger than one month (smallest stepm) and if the exact delay 
   for (i=1;i<=n;i++) {           * (in months) between two waves is not a multiple of stepm, we rounded to 
     ip=indx[i];           * the nearest (and in case of equal distance, to the lowest) interval but now
     sum=b[ip];           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     b[ip]=b[i];           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     if (ii)           * probability in order to take into account the bias as a fraction of the way
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     else if (sum) ii=i;           * -stepm/2 to stepm/2 .
     b[i]=sum;           * For stepm=1 the results are the same as for previous versions of Imach.
   }           * For stepm > 1 the results are less biased than in previous versions. 
   for (i=n;i>=1;i--) {           */
     sum=b[i];          s1=s[mw[mi][i]][i];
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          s2=s[mw[mi+1][i]][i];
     b[i]=sum/a[i][i];          bbh=(double)bh[mi][i]/(double)stepm; 
   }          /* bias is positive if real duration
 }           * is higher than the multiple of stepm and negative otherwise.
            */
 /************ Frequencies ********************/          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 */
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2)          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
 {  /* Some frequencies */          /*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]);*/
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          /*if(lli ==000.0)*/
   double ***freq; /* Frequencies */          /*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); */
   double *pp;          ipmx +=1;
   double pos, k2, dateintsum=0,k2cpt=0;          sw += weight[i];
   FILE *ficresp;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   char fileresp[FILENAMELENGTH];        } /* end of wave */
       } /* end of individual */
   pp=vector(1,nlstate);    }  else if(mle==3){  /* exponential inter-extrapolation */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   strcpy(fileresp,"p");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   strcat(fileresp,fileres);        for(mi=1; mi<= wav[i]-1; mi++){
   if((ficresp=fopen(fileresp,"w"))==NULL) {          for (ii=1;ii<=nlstate+ndeath;ii++)
     printf("Problem with prevalence resultfile: %s\n", fileresp);            for (j=1;j<=nlstate+ndeath;j++){
     exit(0);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);            }
   j1=0;          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
   j=cptcoveff;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   for(k1=1; k1<=j;k1++){            }
    for(i1=1; i1<=ncodemax[k1];i1++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
        j1++;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);            savm=oldm;
          scanf("%d", i);*/            oldm=newm;
         for (i=-1; i<=nlstate+ndeath; i++)            } /* end mult */
          for (jk=-1; jk<=nlstate+ndeath; jk++)          
            for(m=agemin; m <= agemax+3; m++)          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
              freq[i][jk][m]=0;          /* But now since version 0.9 we anticipate for bias and large stepm.
            * If stepm is larger than one month (smallest stepm) and if the exact delay 
         dateintsum=0;           * (in months) between two waves is not a multiple of stepm, we rounded to 
         k2cpt=0;           * the nearest (and in case of equal distance, to the lowest) interval but now
        for (i=1; i<=imx; i++) {           * we keep into memory the bias bh[mi][i] and also the previous matrix product
          bool=1;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
          if  (cptcovn>0) {           * probability in order to take into account the bias as a fraction of the way
            for (z1=1; z1<=cptcoveff; z1++)           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])           * -stepm/2 to stepm/2 .
                bool=0;           * For stepm=1 the results are the same as for previous versions of Imach.
          }           * For stepm > 1 the results are less biased than in previous versions. 
          if (bool==1) {           */
            for(m=firstpass; m<=lastpass; m++){          s1=s[mw[mi][i]][i];
              k2=anint[m][i]+(mint[m][i]/12.);          s2=s[mw[mi+1][i]][i];
              if ((k2>=dateprev1) && (k2<=dateprev2)) {          bbh=(double)bh[mi][i]/(double)stepm; 
                if(agev[m][i]==0) agev[m][i]=agemax+1;          /* bias is positive if real duration
                if(agev[m][i]==1) agev[m][i]=agemax+2;           * is higher than the multiple of stepm and negative otherwise.
                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];          /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {          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 */
                  dateintsum=dateintsum+k2;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
                  k2cpt++;          /*if(lli ==000.0)*/
                }          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
           ipmx +=1;
              }          sw += weight[i];
            }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          }        } /* end of wave */
        }      } /* end of individual */
         if  (cptcovn>0) {    }else if (mle==4){  /* ml=4 no inter-extrapolation */
          fprintf(ficresp, "\n#********** Variable ");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
        fprintf(ficresp, "**********\n#");        for(mi=1; mi<= wav[i]-1; mi++){
         }          for (ii=1;ii<=nlstate+ndeath;ii++)
        for(i=1; i<=nlstate;i++)            for (j=1;j<=nlstate+ndeath;j++){
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
        fprintf(ficresp, "\n");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                    }
   for(i=(int)agemin; i <= (int)agemax+3; i++){          for(d=0; d<dh[mi][i]; d++){
     if(i==(int)agemax+3)            newm=savm;
       printf("Total");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     else            for (kk=1; kk<=cptcovage;kk++) {
       printf("Age %d", i);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for(jk=1; jk <=nlstate ; jk++){            }
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          
         pp[jk] += freq[jk][m][i];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(jk=1; jk <=nlstate ; jk++){            savm=oldm;
       for(m=-1, pos=0; m <=0 ; m++)            oldm=newm;
         pos += freq[jk][m][i];          } /* end mult */
       if(pp[jk]>=1.e-10)        
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          s1=s[mw[mi][i]][i];
       else          s2=s[mw[mi+1][i]][i];
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          if( s2 > nlstate){ 
     }            lli=log(out[s1][s2] - savm[s1][s2]);
           }else{
      for(jk=1; jk <=nlstate ; jk++){            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          }
         pp[jk] += freq[jk][m][i];          ipmx +=1;
      }          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(jk=1,pos=0; jk <=nlstate ; jk++)  /*      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]); */
       pos += pp[jk];        } /* end of wave */
     for(jk=1; jk <=nlstate ; jk++){      } /* end of individual */
       if(pos>=1.e-5)    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       else        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        for(mi=1; mi<= wav[i]-1; mi++){
       if( i <= (int) agemax){          for (ii=1;ii<=nlstate+ndeath;ii++)
         if(pos>=1.e-5){            for (j=1;j<=nlstate+ndeath;j++){
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);              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);
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/            }
         }          for(d=0; d<dh[mi][i]; d++){
       else            newm=savm;
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);            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];
     for(jk=-1; jk <=nlstate+ndeath; jk++)            }
       for(m=-1; m <=nlstate+ndeath; m++)          
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     if(i <= (int) agemax)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       fprintf(ficresp,"\n");            savm=oldm;
     printf("\n");            oldm=newm;
     }          } /* end mult */
     }        
  }          s1=s[mw[mi][i]][i];
   dateintmean=dateintsum/k2cpt;          s2=s[mw[mi+1][i]][i];
            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   fclose(ficresp);          ipmx +=1;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          sw += weight[i];
   free_vector(pp,1,nlstate);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
   /* End of Freq */        } /* end of wave */
 }      } /* end of individual */
     } /* End of if */
 /************ Prevalence ********************/    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
 {  /* Some frequencies */    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
      return -l;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  }
   double ***freq; /* Frequencies */  
   double *pp;  /*************** log-likelihood *************/
   double pos, k2;  double funcone( double *x)
   {
   pp=vector(1,nlstate);    /* Same as likeli but slower because of a lot of printf and if */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    int i, ii, j, k, mi, d, kk;
      double l, ll[NLSTATEMAX], cov[NCOVMAX];
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    double **out;
   j1=0;    double lli; /* Individual log likelihood */
      double llt;
   j=cptcoveff;    int s1, s2;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    double bbh, survp;
      /*extern weight */
  for(k1=1; k1<=j;k1++){    /* We are differentiating ll according to initial status */
     for(i1=1; i1<=ncodemax[k1];i1++){    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       j1++;    /*for(i=1;i<imx;i++) 
        printf(" %d\n",s[4][i]);
       for (i=-1; i<=nlstate+ndeath; i++)      */
         for (jk=-1; jk<=nlstate+ndeath; jk++)      cov[1]=1.;
           for(m=agemin; m <= agemax+3; m++)  
             freq[i][jk][m]=0;    for(k=1; k<=nlstate; k++) ll[k]=0.;
        
       for (i=1; i<=imx; i++) {    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         bool=1;      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         if  (cptcovn>0) {      for(mi=1; mi<= wav[i]-1; mi++){
           for (z1=1; z1<=cptcoveff; z1++)        for (ii=1;ii<=nlstate+ndeath;ii++)
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          for (j=1;j<=nlstate+ndeath;j++){
               bool=0;            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         }            savm[ii][j]=(ii==j ? 1.0 : 0.0);
         if (bool==1) {          }
           for(m=firstpass; m<=lastpass; m++){        for(d=0; d<dh[mi][i]; d++){
             k2=anint[m][i]+(mint[m][i]/12.);          newm=savm;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
               if(agev[m][i]==0) agev[m][i]=agemax+1;          for (kk=1; kk<=cptcovage;kk++) {
               if(agev[m][i]==1) agev[m][i]=agemax+2;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          }
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             }                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           }          savm=oldm;
         }          oldm=newm;
       }        } /* end mult */
              
         for(i=(int)agemin; i <= (int)agemax+3; i++){        s1=s[mw[mi][i]][i];
           for(jk=1; jk <=nlstate ; jk++){        s2=s[mw[mi+1][i]][i];
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        bbh=(double)bh[mi][i]/(double)stepm; 
               pp[jk] += freq[jk][m][i];        /* bias is positive if real duration
           }         * is higher than the multiple of stepm and negative otherwise.
           for(jk=1; jk <=nlstate ; jk++){         */
             for(m=-1, pos=0; m <=0 ; m++)        if( s2 > nlstate && (mle <5) ){  /* Jackson */
             pos += freq[jk][m][i];          lli=log(out[s1][s2] - savm[s1][s2]);
         }        } else if (mle==1){
                  lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
          for(jk=1; jk <=nlstate ; jk++){        } else if(mle==2){
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; 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 */
              pp[jk] += freq[jk][m][i];        } else if(mle==3){  /* exponential inter-extrapolation */
          }          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
                  } else if (mle==4){  /* mle=4 no inter-extrapolation */
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          lli=log(out[s1][s2]); /* Original formula */
         } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
          for(jk=1; jk <=nlstate ; jk++){                    lli=log(out[s1][s2]); /* Original formula */
            if( i <= (int) agemax){        } /* End of if */
              if(pos>=1.e-5){        ipmx +=1;
                probs[i][jk][j1]= pp[jk]/pos;        sw += weight[i];
              }        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
            }  /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
          }        if(globpr){
                    fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
         }   %10.6f %10.6f %10.6f ", \
     }                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   }                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
            for(k=1,llt=0.,l=0.; k<=nlstate; k++){
              llt +=ll[k]*gipmx/gsw;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   free_vector(pp,1,nlstate);          }
            fprintf(ficresilk," %10.6f\n", -llt);
 }  /* End of Freq */        }
       } /* end of wave */
 /************* Waves Concatenation ***************/    } /* end of individual */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
 {    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    if(globpr==0){ /* First time we count the contributions and weights */
      Death is a valid wave (if date is known).      gipmx=ipmx;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      gsw=sw;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    }
      and mw[mi+1][i]. dh depends on stepm.    return -l;
      */  }
   
   int i, mi, m;  char *subdirf(char fileres[])
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  {
      double sum=0., jmean=0.;*/    
     strcpy(tmpout,optionfilefiname);
   int j, k=0,jk, ju, jl;    strcat(tmpout,"/"); /* Add to the right */
   double sum=0.;    strcat(tmpout,fileres);
   jmin=1e+5;    return tmpout;
   jmax=-1;  }
   jmean=0.;  
   for(i=1; i<=imx; i++){  char *subdirf2(char fileres[], char *preop)
     mi=0;  {
     m=firstpass;    
     while(s[m][i] <= nlstate){    strcpy(tmpout,optionfilefiname);
       if(s[m][i]>=1)    strcat(tmpout,"/");
         mw[++mi][i]=m;    strcat(tmpout,preop);
       if(m >=lastpass)    strcat(tmpout,fileres);
         break;    return tmpout;
       else  }
         m++;  char *subdirf3(char fileres[], char *preop, char *preop2)
     }/* end while */  {
     if (s[m][i] > nlstate){    
       mi++;     /* Death is another wave */    strcpy(tmpout,optionfilefiname);
       /* if(mi==0)  never been interviewed correctly before death */    strcat(tmpout,"/");
          /* Only death is a correct wave */    strcat(tmpout,preop);
       mw[mi][i]=m;    strcat(tmpout,preop2);
     }    strcat(tmpout,fileres);
     return tmpout;
     wav[i]=mi;  }
     if(mi==0)  
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  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 
   for(i=1; i<=imx; i++){       the selection of individuals/waves and
     for(mi=1; mi<wav[i];mi++){       to check the exact contribution to the likelihood.
       if (stepm <=0)       Plotting could be done.
         dh[mi][i]=1;     */
       else{    int k;
         if (s[mw[mi+1][i]][i] > nlstate) {  
           if (agedc[i] < 2*AGESUP) {    if(*globpri !=0){ /* Just counts and sums, no printings */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);      strcpy(fileresilk,"ilk"); 
           if(j==0) j=1;  /* Survives at least one month after exam */      strcat(fileresilk,fileres);
           k=k+1;      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
           if (j >= jmax) jmax=j;        printf("Problem with resultfile: %s\n", fileresilk);
           if (j <= jmin) jmin=j;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
           sum=sum+j;      }
           /* if (j<10) printf("j=%d num=%d ",j,i); */      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
           }      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
         }      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
         else{      for(k=1; k<=nlstate; k++) 
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
           k=k+1;      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
           if (j >= jmax) jmax=j;    }
           else if (j <= jmin)jmin=j;  
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    *fretone=(*funcone)(p);
           sum=sum+j;    if(*globpri !=0){
         }      fclose(ficresilk);
         jk= j/stepm;      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
         jl= j -jk*stepm;      fflush(fichtm); 
         ju= j -(jk+1)*stepm;    } 
         if(jl <= -ju)    return;
           dh[mi][i]=jk;  }
         else  
           dh[mi][i]=jk+1;  
         if(dh[mi][i]==0)  /*********** Maximum Likelihood Estimation ***************/
           dh[mi][i]=1; /* At least one step */  
       }  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
     }  {
   }    int i,j, iter;
   jmean=sum/k;    double **xi;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    double fret;
  }    double fretone; /* Only one call to likelihood */
 /*********** Tricode ****************************/    char filerespow[FILENAMELENGTH];
 void tricode(int *Tvar, int **nbcode, int imx)    xi=matrix(1,npar,1,npar);
 {    for (i=1;i<=npar;i++)
   int Ndum[20],ij=1, k, j, i;      for (j=1;j<=npar;j++)
   int cptcode=0;        xi[i][j]=(i==j ? 1.0 : 0.0);
   cptcoveff=0;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
      strcpy(filerespow,"pow"); 
   for (k=0; k<19; k++) Ndum[k]=0;    strcat(filerespow,fileres);
   for (k=1; k<=7; k++) ncodemax[k]=0;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     for (i=1; i<=imx; i++) {    }
       ij=(int)(covar[Tvar[j]][i]);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
       Ndum[ij]++;    for (i=1;i<=nlstate;i++)
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/      for(j=1;j<=nlstate+ndeath;j++)
       if (ij > cptcode) cptcode=ij;        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     }    fprintf(ficrespow,"\n");
   
     for (i=0; i<=cptcode; i++) {    powell(p,xi,npar,ftol,&iter,&fret,func);
       if(Ndum[i]!=0) ncodemax[j]++;  
     }    fclose(ficrespow);
     ij=1;    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     for (i=1; i<=ncodemax[j]; i++) {  
       for (k=0; k<=19; k++) {  }
         if (Ndum[k] != 0) {  
           nbcode[Tvar[j]][ij]=k;  /**** Computes Hessian and covariance matrix ***/
           ij++;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
         }  {
         if (ij > ncodemax[j]) break;    double  **a,**y,*x,pd;
       }      double **hess;
     }    int i, j,jk;
   }      int *indx;
   
  for (k=0; k<19; k++) Ndum[k]=0;    double hessii(double p[], double delta, int theta, double delti[]);
     double hessij(double p[], double delti[], int i, int j);
  for (i=1; i<=ncovmodel-2; i++) {    void lubksb(double **a, int npar, int *indx, double b[]) ;
       ij=Tvar[i];    void ludcmp(double **a, int npar, int *indx, double *d) ;
       Ndum[ij]++;  
     }    hess=matrix(1,npar,1,npar);
   
  ij=1;    printf("\nCalculation of the hessian matrix. Wait...\n");
  for (i=1; i<=10; i++) {    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
    if((Ndum[i]!=0) && (i<=ncov)){    for (i=1;i<=npar;i++){
      Tvaraff[ij]=i;      printf("%d",i);fflush(stdout);
      ij++;      fprintf(ficlog,"%d",i);fflush(ficlog);
    }      hess[i][i]=hessii(p,ftolhess,i,delti);
  }      /*printf(" %f ",p[i]);*/
        /*printf(" %lf ",hess[i][i]);*/
     cptcoveff=ij-1;    }
 }    
     for (i=1;i<=npar;i++) {
 /*********** Health Expectancies ****************/      for (j=1;j<=npar;j++)  {
         if (j>i) { 
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)          printf(".%d%d",i,j);fflush(stdout);
 {          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   /* Health expectancies */          hess[i][j]=hessij(p,delti,i,j);
   int i, j, nhstepm, hstepm, h;          hess[j][i]=hess[i][j];    
   double age, agelim,hf;          /*printf(" %lf ",hess[i][j]);*/
   double ***p3mat;        }
        }
   fprintf(ficreseij,"# Health expectancies\n");    }
   fprintf(ficreseij,"# Age");    printf("\n");
   for(i=1; i<=nlstate;i++)    fprintf(ficlog,"\n");
     for(j=1; j<=nlstate;j++)  
       fprintf(ficreseij," %1d-%1d",i,j);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   fprintf(ficreseij,"\n");    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     
   hstepm=1*YEARM; /*  Every j years of age (in month) */    a=matrix(1,npar,1,npar);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    y=matrix(1,npar,1,npar);
     x=vector(1,npar);
   agelim=AGESUP;    indx=ivector(1,npar);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    for (i=1;i<=npar;i++)
     /* nhstepm age range expressed in number of stepm */      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);    ludcmp(a,npar,indx,&pd);
     /* Typically if 20 years = 20*12/6=40 stepm */  
     if (stepm >= YEARM) hstepm=1;    for (j=1;j<=npar;j++) {
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */      for (i=1;i<=npar;i++) x[i]=0;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      x[j]=1;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored      lubksb(a,npar,indx,x);
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */      for (i=1;i<=npar;i++){ 
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);          matcov[i][j]=x[i];
       }
     }
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++)    printf("\n#Hessian matrix#\n");
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){    fprintf(ficlog,"\n#Hessian matrix#\n");
           eij[i][j][(int)age] +=p3mat[i][j][h];    for (i=1;i<=npar;i++) { 
         }      for (j=1;j<=npar;j++) { 
            printf("%.3e ",hess[i][j]);
     hf=1;        fprintf(ficlog,"%.3e ",hess[i][j]);
     if (stepm >= YEARM) hf=stepm/YEARM;      }
     fprintf(ficreseij,"%.0f",age );      printf("\n");
     for(i=1; i<=nlstate;i++)      fprintf(ficlog,"\n");
       for(j=1; j<=nlstate;j++){    }
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);  
       }    /* Recompute Inverse */
     fprintf(ficreseij,"\n");    for (i=1;i<=npar;i++)
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   }    ludcmp(a,npar,indx,&pd);
 }  
     /*  printf("\n#Hessian matrix recomputed#\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)    for (j=1;j<=npar;j++) {
 {      for (i=1;i<=npar;i++) x[i]=0;
   /* Variance of health expectancies */      x[j]=1;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      lubksb(a,npar,indx,x);
   double **newm;      for (i=1;i<=npar;i++){ 
   double **dnewm,**doldm;        y[i][j]=x[i];
   int i, j, nhstepm, hstepm, h;        printf("%.3e ",y[i][j]);
   int k, cptcode;        fprintf(ficlog,"%.3e ",y[i][j]);
   double *xp;      }
   double **gp, **gm;      printf("\n");
   double ***gradg, ***trgradg;      fprintf(ficlog,"\n");
   double ***p3mat;    }
   double age,agelim;    */
   int theta;  
     free_matrix(a,1,npar,1,npar);
    fprintf(ficresvij,"# Covariances of life expectancies\n");    free_matrix(y,1,npar,1,npar);
   fprintf(ficresvij,"# Age");    free_vector(x,1,npar);
   for(i=1; i<=nlstate;i++)    free_ivector(indx,1,npar);
     for(j=1; j<=nlstate;j++)    free_matrix(hess,1,npar,1,npar);
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);  
   fprintf(ficresvij,"\n");  
   }
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);  /*************** hessian matrix ****************/
   doldm=matrix(1,nlstate,1,nlstate);  double hessii( double x[], double delta, int theta, double delti[])
    {
   hstepm=1*YEARM; /* Every year of age */    int i;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    int l=1, lmax=20;
   agelim = AGESUP;    double k1,k2;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    double p2[NPARMAX+1];
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    double res;
     if (stepm >= YEARM) hstepm=1;    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    double fx;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int k=0,kmax=10;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    double l1;
     gp=matrix(0,nhstepm,1,nlstate);  
     gm=matrix(0,nhstepm,1,nlstate);    fx=func(x);
     for (i=1;i<=npar;i++) p2[i]=x[i];
     for(theta=1; theta <=npar; theta++){    for(l=0 ; l <=lmax; l++){
       for(i=1; i<=npar; i++){ /* Computes gradient */      l1=pow(10,l);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      delts=delt;
       }      for(k=1 ; k <kmax; k=k+1){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          delt = delta*(l1*k);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        p2[theta]=x[theta] +delt;
         k1=func(p2)-fx;
       if (popbased==1) {        p2[theta]=x[theta]-delt;
         for(i=1; i<=nlstate;i++)        k2=func(p2)-fx;
           prlim[i][i]=probs[(int)age][i][ij];        /*res= (k1-2.0*fx+k2)/delt/delt; */
       }        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
              
       for(j=1; j<= nlstate; j++){  #ifdef DEBUG
         for(h=0; h<=nhstepm; h++){        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, gp[h][j]=0.;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);
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];  #endif
         }        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
       }        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
              k=kmax;
       for(i=1; i<=npar; i++) /* Computes gradient */        }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            k=kmax; l=lmax*10.;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        }
         else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       if (popbased==1) {          delts=delt;
         for(i=1; i<=nlstate;i++)        }
           prlim[i][i]=probs[(int)age][i][ij];      }
       }    }
     delti[theta]=delts;
       for(j=1; j<= nlstate; j++){    return res; 
         for(h=0; h<=nhstepm; h++){    
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)  }
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];  
         }  double hessij( double x[], double delti[], int thetai,int thetaj)
       }  {
     int i;
       for(j=1; j<= nlstate; j++)    int l=1, l1, lmax=20;
         for(h=0; h<=nhstepm; h++){    double k1,k2,k3,k4,res,fx;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    double p2[NPARMAX+1];
         }    int k;
     } /* End theta */  
     fx=func(x);
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    for (k=1; k<=2; k++) {
       for (i=1;i<=npar;i++) p2[i]=x[i];
     for(h=0; h<=nhstepm; h++)      p2[thetai]=x[thetai]+delti[thetai]/k;
       for(j=1; j<=nlstate;j++)      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         for(theta=1; theta <=npar; theta++)      k1=func(p2)-fx;
           trgradg[h][j][theta]=gradg[h][theta][j];    
       p2[thetai]=x[thetai]+delti[thetai]/k;
     for(i=1;i<=nlstate;i++)      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       for(j=1;j<=nlstate;j++)      k2=func(p2)-fx;
         vareij[i][j][(int)age] =0.;    
     for(h=0;h<=nhstepm;h++){      p2[thetai]=x[thetai]-delti[thetai]/k;
       for(k=0;k<=nhstepm;k++){      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      k3=func(p2)-fx;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    
         for(i=1;i<=nlstate;i++)      p2[thetai]=x[thetai]-delti[thetai]/k;
           for(j=1;j<=nlstate;j++)      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
             vareij[i][j][(int)age] += doldm[i][j];      k4=func(p2)-fx;
       }      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     }  #ifdef DEBUG
     h=1;      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
     if (stepm >= YEARM) h=stepm/YEARM;      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(ficresvij,"%.0f ",age );  #endif
     for(i=1; i<=nlstate;i++)    }
       for(j=1; j<=nlstate;j++){    return res;
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);  }
       }  
     fprintf(ficresvij,"\n");  /************** Inverse of matrix **************/
     free_matrix(gp,0,nhstepm,1,nlstate);  void ludcmp(double **a, int n, int *indx, double *d) 
     free_matrix(gm,0,nhstepm,1,nlstate);  { 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    int i,imax,j,k; 
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    double big,dum,sum,temp; 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double *vv; 
   } /* End age */   
      vv=vector(1,n); 
   free_vector(xp,1,npar);    *d=1.0; 
   free_matrix(doldm,1,nlstate,1,npar);    for (i=1;i<=n;i++) { 
   free_matrix(dnewm,1,nlstate,1,nlstate);      big=0.0; 
       for (j=1;j<=n;j++) 
 }        if ((temp=fabs(a[i][j])) > big) big=temp; 
       if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
 /************ Variance of prevlim ******************/      vv[i]=1.0/big; 
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)    } 
 {    for (j=1;j<=n;j++) { 
   /* Variance of prevalence limit */      for (i=1;i<j;i++) { 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        sum=a[i][j]; 
   double **newm;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   double **dnewm,**doldm;        a[i][j]=sum; 
   int i, j, nhstepm, hstepm;      } 
   int k, cptcode;      big=0.0; 
   double *xp;      for (i=j;i<=n;i++) { 
   double *gp, *gm;        sum=a[i][j]; 
   double **gradg, **trgradg;        for (k=1;k<j;k++) 
   double age,agelim;          sum -= a[i][k]*a[k][j]; 
   int theta;        a[i][j]=sum; 
            if ( (dum=vv[i]*fabs(sum)) >= big) { 
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");          big=dum; 
   fprintf(ficresvpl,"# Age");          imax=i; 
   for(i=1; i<=nlstate;i++)        } 
       fprintf(ficresvpl," %1d-%1d",i,i);      } 
   fprintf(ficresvpl,"\n");      if (j != imax) { 
         for (k=1;k<=n;k++) { 
   xp=vector(1,npar);          dum=a[imax][k]; 
   dnewm=matrix(1,nlstate,1,npar);          a[imax][k]=a[j][k]; 
   doldm=matrix(1,nlstate,1,nlstate);          a[j][k]=dum; 
          } 
   hstepm=1*YEARM; /* Every year of age */        *d = -(*d); 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        vv[imax]=vv[j]; 
   agelim = AGESUP;      } 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      indx[j]=imax; 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      if (a[j][j] == 0.0) a[j][j]=TINY; 
     if (stepm >= YEARM) hstepm=1;      if (j != n) { 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        dum=1.0/(a[j][j]); 
     gradg=matrix(1,npar,1,nlstate);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     gp=vector(1,nlstate);      } 
     gm=vector(1,nlstate);    } 
     free_vector(vv,1,n);  /* Doesn't work */
     for(theta=1; theta <=npar; theta++){  ;
       for(i=1; i<=npar; i++){ /* Computes gradient */  } 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
       }  void lubksb(double **a, int n, int *indx, double b[]) 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  { 
       for(i=1;i<=nlstate;i++)    int i,ii=0,ip,j; 
         gp[i] = prlim[i][i];    double sum; 
       
       for(i=1; i<=npar; i++) /* Computes gradient */    for (i=1;i<=n;i++) { 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      ip=indx[i]; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      sum=b[ip]; 
       for(i=1;i<=nlstate;i++)      b[ip]=b[i]; 
         gm[i] = prlim[i][i];      if (ii) 
         for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       for(i=1;i<=nlstate;i++)      else if (sum) ii=i; 
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];      b[i]=sum; 
     } /* End theta */    } 
     for (i=n;i>=1;i--) { 
     trgradg =matrix(1,nlstate,1,npar);      sum=b[i]; 
       for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     for(j=1; j<=nlstate;j++)      b[i]=sum/a[i][i]; 
       for(theta=1; theta <=npar; theta++)    } 
         trgradg[j][theta]=gradg[theta][j];  } 
   
     for(i=1;i<=nlstate;i++)  /************ Frequencies ********************/
       varpl[i][(int)age] =0.;  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)
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);  {  /* Some frequencies */
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    
     for(i=1;i<=nlstate;i++)    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    int first;
     double ***freq; /* Frequencies */
     fprintf(ficresvpl,"%.0f ",age );    double *pp, **prop;
     for(i=1; i<=nlstate;i++)    double pos,posprop, k2, dateintsum=0,k2cpt=0;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    FILE *ficresp;
     fprintf(ficresvpl,"\n");    char fileresp[FILENAMELENGTH];
     free_vector(gp,1,nlstate);    
     free_vector(gm,1,nlstate);    pp=vector(1,nlstate);
     free_matrix(gradg,1,npar,1,nlstate);    prop=matrix(1,nlstate,iagemin,iagemax+3);
     free_matrix(trgradg,1,nlstate,1,npar);    strcpy(fileresp,"p");
   } /* End age */    strcat(fileresp,fileres);
     if((ficresp=fopen(fileresp,"w"))==NULL) {
   free_vector(xp,1,npar);      printf("Problem with prevalence resultfile: %s\n", fileresp);
   free_matrix(doldm,1,nlstate,1,npar);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   free_matrix(dnewm,1,nlstate,1,nlstate);      exit(0);
     }
 }    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
     j1=0;
 /************ Variance of one-step probabilities  ******************/    
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)    j=cptcoveff;
 {    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   int i, j;  
   int k=0, cptcode;    first=1;
   double **dnewm,**doldm;  
   double *xp;    for(k1=1; k1<=j;k1++){
   double *gp, *gm;      for(i1=1; i1<=ncodemax[k1];i1++){
   double **gradg, **trgradg;        j1++;
   double age,agelim, cov[NCOVMAX];        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   int theta;          scanf("%d", i);*/
   char fileresprob[FILENAMELENGTH];        for (i=-1; i<=nlstate+ndeath; i++)  
           for (jk=-1; jk<=nlstate+ndeath; jk++)  
   strcpy(fileresprob,"prob");            for(m=iagemin; m <= iagemax+3; m++)
   strcat(fileresprob,fileres);              freq[i][jk][m]=0;
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {  
     printf("Problem with resultfile: %s\n", fileresprob);      for (i=1; i<=nlstate; i++)  
   }        for(m=iagemin; m <= iagemax+3; m++)
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);          prop[i][m]=0;
          
         dateintsum=0;
   xp=vector(1,npar);        k2cpt=0;
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        for (i=1; i<=imx; i++) {
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));          bool=1;
            if  (cptcovn>0) {
   cov[1]=1;            for (z1=1; z1<=cptcoveff; z1++) 
   for (age=bage; age<=fage; age ++){              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     cov[2]=age;                bool=0;
     gradg=matrix(1,npar,1,9);          }
     trgradg=matrix(1,9,1,npar);          if (bool==1){
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));            for(m=firstpass; m<=lastpass; m++){
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));              k2=anint[m][i]+(mint[m][i]/12.);
                  /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     for(theta=1; theta <=npar; theta++){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       for(i=1; i<=npar; i++)                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
                      if (m<lastpass) {
       pmij(pmmij,cov,ncovmodel,xp,nlstate);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                      freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
       k=0;                }
       for(i=1; i<= (nlstate+ndeath); i++){                
         for(j=1; j<=(nlstate+ndeath);j++){                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
            k=k+1;                  dateintsum=dateintsum+k2;
           gp[k]=pmmij[i][j];                  k2cpt++;
         }                }
       }                /*}*/
             }
       for(i=1; i<=npar; i++)          }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        }
             
         /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       pmij(pmmij,cov,ncovmodel,xp,nlstate);  
       k=0;        if  (cptcovn>0) {
       for(i=1; i<=(nlstate+ndeath); i++){          fprintf(ficresp, "\n#********** Variable "); 
         for(j=1; j<=(nlstate+ndeath);j++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           k=k+1;          fprintf(ficresp, "**********\n#");
           gm[k]=pmmij[i][j];        }
         }        for(i=1; i<=nlstate;i++) 
       }          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
              fprintf(ficresp, "\n");
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)        
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];          for(i=iagemin; i <= iagemax+3; i++){
     }          if(i==iagemax+3){
             fprintf(ficlog,"Total");
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)          }else{
       for(theta=1; theta <=npar; theta++)            if(first==1){
       trgradg[j][theta]=gradg[theta][j];              first=0;
                printf("See log file for details...\n");
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);            }
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);            fprintf(ficlog,"Age %d", i);
           }
      pmij(pmmij,cov,ncovmodel,x,nlstate);          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
      k=0;              pp[jk] += freq[jk][m][i]; 
      for(i=1; i<=(nlstate+ndeath); i++){          }
        for(j=1; j<=(nlstate+ndeath);j++){          for(jk=1; jk <=nlstate ; jk++){
          k=k+1;            for(m=-1, pos=0; m <=0 ; m++)
          gm[k]=pmmij[i][j];              pos += freq[jk][m][i];
         }            if(pp[jk]>=1.e-10){
      }              if(first==1){
                    printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
      /*printf("\n%d ",(int)age);              }
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                    }else{
               if(first==1)
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
      }*/              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             }
   fprintf(ficresprob,"\n%d ",(int)age);          }
   
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){          for(jk=1; jk <=nlstate ; jk++){
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);              pp[jk] += freq[jk][m][i];
   }          }       
           for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));            pos += pp[jk];
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));            posprop += prop[jk][i];
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          }
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          for(jk=1; jk <=nlstate ; jk++){
 }            if(pos>=1.e-5){
  free_vector(xp,1,npar);              if(first==1)
 fclose(ficresprob);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
  exit(0);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
 }            }else{
               if(first==1)
 /***********************************************/                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 /**************** Main Program *****************/              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 /***********************************************/            }
             if( i <= iagemax){
 int main(int argc, char *argv[])              if(pos>=1.e-5){
 {                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                 /*probs[i][jk][j1]= pp[jk]/pos;*/
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;                /*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 agedeb, agefin,hf;              }
   double agemin=1.e20, agemax=-1.e20;              else
                 fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   double fret;            }
   double **xi,tmp,delta;          }
           
   double dum; /* Dummy variable */          for(jk=-1; jk <=nlstate+ndeath; jk++)
   double ***p3mat;            for(m=-1; m <=nlstate+ndeath; m++)
   int *indx;              if(freq[jk][m][i] !=0 ) {
   char line[MAXLINE], linepar[MAXLINE];              if(first==1)
   char title[MAXLINE];                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];              }
            if(i <= iagemax)
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];            fprintf(ficresp,"\n");
           if(first==1)
   char filerest[FILENAMELENGTH];            printf("Others in log...\n");
   char fileregp[FILENAMELENGTH];          fprintf(ficlog,"\n");
   char popfile[FILENAMELENGTH];        }
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];      }
   int firstobs=1, lastobs=10;    }
   int sdeb, sfin; /* Status at beginning and end */    dateintmean=dateintsum/k2cpt; 
   int c,  h , cpt,l;   
   int ju,jl, mi;    fclose(ficresp);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    free_vector(pp,1,nlstate);
   int mobilav=0,popforecast=0;    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   int hstepm, nhstepm;    /* End of Freq */
   int *popage;/*boolprev=0 if date and zero if wave*/  }
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;  
   /************ Prevalence ********************/
   double bage, fage, age, agelim, agebase;  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)
   double ftolpl=FTOL;  {  
   double **prlim;    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   double *severity;       in each health status at the date of interview (if between dateprev1 and dateprev2).
   double ***param; /* Matrix of parameters */       We still use firstpass and lastpass as another selection.
   double  *p;    */
   double **matcov; /* Matrix of covariance */   
   double ***delti3; /* Scale */    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   double *delti; /* Scale */    double ***freq; /* Frequencies */
   double ***eij, ***vareij;    double *pp, **prop;
   double **varpl; /* Variances of prevalence limits by age */    double pos,posprop; 
   double *epj, vepp;    double  y2; /* in fractional years */
   double kk1, kk2;    int iagemin, iagemax;
   double *popeffectif,*popcount;  
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;    iagemin= (int) agemin;
   double yp,yp1,yp2;    iagemax= (int) agemax;
     /*pp=vector(1,nlstate);*/
   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";    prop=matrix(1,nlstate,iagemin,iagemax+3); 
   char *alph[]={"a","a","b","c","d","e"}, str[4];    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     j1=0;
     
   char z[1]="c", occ;    j=cptcoveff;
 #include <sys/time.h>    if (cptcovn<1) {j=1;ncodemax[1]=1;}
 #include <time.h>    
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    for(k1=1; k1<=j;k1++){
        for(i1=1; i1<=ncodemax[k1];i1++){
   /* long total_usecs;        j1++;
   struct timeval start_time, end_time;        
          for (i=1; i<=nlstate; i++)  
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */          for(m=iagemin; m <= iagemax+3; m++)
             prop[i][m]=0.0;
        
   printf("\n%s",version);        for (i=1; i<=imx; i++) { /* Each individual */
   if(argc <=1){          bool=1;
     printf("\nEnter the parameter file name: ");          if  (cptcovn>0) {
     scanf("%s",pathtot);            for (z1=1; z1<=cptcoveff; z1++) 
   }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   else{                bool=0;
     strcpy(pathtot,argv[1]);          } 
   }          if (bool==1) { 
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   /*cygwin_split_path(pathtot,path,optionfile);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   /* cutv(path,optionfile,pathtot,'\\');*/                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   chdir(path);                  /*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]]);*/
   replace(pathc,path);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                   prop[s[m][i]][iagemax+3] += weight[i]; 
 /*-------- arguments in the command line --------*/                } 
               }
   strcpy(fileres,"r");            } /* end selection of waves */
   strcat(fileres, optionfilefiname);          }
   strcat(fileres,".txt");    /* Other files have txt extension */        }
         for(i=iagemin; i <= iagemax+3; i++){  
   /*---------arguments file --------*/          
           for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   if((ficpar=fopen(optionfile,"r"))==NULL)    {            posprop += prop[jk][i]; 
     printf("Problem with optionfile %s\n",optionfile);          } 
     goto end;  
   }          for(jk=1; jk <=nlstate ; jk++){     
             if( i <=  iagemax){ 
   strcpy(filereso,"o");              if(posprop>=1.e-5){ 
   strcat(filereso,fileres);                probs[i][jk][j1]= prop[jk][i]/posprop;
   if((ficparo=fopen(filereso,"w"))==NULL) {              } 
     printf("Problem with Output resultfile: %s\n", filereso);goto end;            } 
   }          }/* end jk */ 
         }/* end i */ 
   /* Reads comments: lines beginning with '#' */      } /* end i1 */
   while((c=getc(ficpar))=='#' && c!= EOF){    } /* end k1 */
     ungetc(c,ficpar);    
     fgets(line, MAXLINE, ficpar);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     puts(line);    /*free_vector(pp,1,nlstate);*/
     fputs(line,ficparo);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  }  /* End of prevalence */
   ungetc(c,ficpar);  
   /************* Waves Concatenation ***************/
   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);  
   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);  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)
   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){    /* 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;
        /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   covar=matrix(0,NCOVMAX,1,n);       double sum=0., jmean=0.;*/
   cptcovn=0;    int first;
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    int j, k=0,jk, ju, jl;
     double sum=0.;
   ncovmodel=2+cptcovn;    first=0;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    jmin=1e+5;
      jmax=-1;
   /* Read guess parameters */    jmean=0.;
   /* Reads comments: lines beginning with '#' */    for(i=1; i<=imx; i++){
   while((c=getc(ficpar))=='#' && c!= EOF){      mi=0;
     ungetc(c,ficpar);      m=firstpass;
     fgets(line, MAXLINE, ficpar);      while(s[m][i] <= nlstate){
     puts(line);        if(s[m][i]>=1)
     fputs(line,ficparo);          mw[++mi][i]=m;
   }        if(m >=lastpass)
   ungetc(c,ficpar);          break;
          else
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          m++;
     for(i=1; i <=nlstate; i++)      }/* end while */
     for(j=1; j <=nlstate+ndeath-1; j++){      if (s[m][i] > nlstate){
       fscanf(ficpar,"%1d%1d",&i1,&j1);        mi++;     /* Death is another wave */
       fprintf(ficparo,"%1d%1d",i1,j1);        /* if(mi==0)  never been interviewed correctly before death */
       printf("%1d%1d",i,j);           /* Only death is a correct wave */
       for(k=1; k<=ncovmodel;k++){        mw[mi][i]=m;
         fscanf(ficpar," %lf",&param[i][j][k]);      }
         printf(" %lf",param[i][j][k]);  
         fprintf(ficparo," %lf",param[i][j][k]);      wav[i]=mi;
       }      if(mi==0){
       fscanf(ficpar,"\n");        if(first==0){
       printf("\n");          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
       fprintf(ficparo,"\n");          first=1;
     }        }
          if(first==1){
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
         }
   p=param[1][1];      } /* end mi==0 */
      } /* End individuals */
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){    for(i=1; i<=imx; i++){
     ungetc(c,ficpar);      for(mi=1; mi<wav[i];mi++){
     fgets(line, MAXLINE, ficpar);        if (stepm <=0)
     puts(line);          dh[mi][i]=1;
     fputs(line,ficparo);        else{
   }          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   ungetc(c,ficpar);            if (agedc[i] < 2*AGESUP) {
               j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);              if(j==0) j=1;  /* Survives at least one month after exam */
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */              else if(j<0){
   for(i=1; i <=nlstate; i++){                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]);
     for(j=1; j <=nlstate+ndeath-1; j++){                j=1; /* Careful Patch */
       fscanf(ficpar,"%1d%1d",&i1,&j1);                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
       printf("%1d%1d",i,j);                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       fprintf(ficparo,"%1d%1d",i1,j1);                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
       for(k=1; k<=ncovmodel;k++){              }
         fscanf(ficpar,"%le",&delti3[i][j][k]);              k=k+1;
         printf(" %le",delti3[i][j][k]);              if (j >= jmax) jmax=j;
         fprintf(ficparo," %le",delti3[i][j][k]);              if (j <= jmin) jmin=j;
       }              sum=sum+j;
       fscanf(ficpar,"\n");              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
       printf("\n");              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       fprintf(ficparo,"\n");            }
     }          }
   }          else{
   delti=delti3[1][1];            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
              /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   /* Reads comments: lines beginning with '#' */            k=k+1;
   while((c=getc(ficpar))=='#' && c!= EOF){            if (j >= jmax) jmax=j;
     ungetc(c,ficpar);            else if (j <= jmin)jmin=j;
     fgets(line, MAXLINE, ficpar);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     puts(line);            /*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]);*/
     fputs(line,ficparo);            if(j<0){
   }              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]);
   ungetc(c,ficpar);              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]);
              }
   matcov=matrix(1,npar,1,npar);            sum=sum+j;
   for(i=1; i <=npar; i++){          }
     fscanf(ficpar,"%s",&str);          jk= j/stepm;
     printf("%s",str);          jl= j -jk*stepm;
     fprintf(ficparo,"%s",str);          ju= j -(jk+1)*stepm;
     for(j=1; j <=i; j++){          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
       fscanf(ficpar," %le",&matcov[i][j]);            if(jl==0){
       printf(" %.5le",matcov[i][j]);              dh[mi][i]=jk;
       fprintf(ficparo," %.5le",matcov[i][j]);              bh[mi][i]=0;
     }            }else{ /* We want a negative bias in order to only have interpolation ie
     fscanf(ficpar,"\n");                    * at the price of an extra matrix product in likelihood */
     printf("\n");              dh[mi][i]=jk+1;
     fprintf(ficparo,"\n");              bh[mi][i]=ju;
   }            }
   for(i=1; i <=npar; i++)          }else{
     for(j=i+1;j<=npar;j++)            if(jl <= -ju){
       matcov[i][j]=matcov[j][i];              dh[mi][i]=jk;
                  bh[mi][i]=jl;       /* bias is positive if real duration
   printf("\n");                                   * is higher than the multiple of stepm and negative otherwise.
                                    */
             }
     /*-------- data file ----------*/            else{
     if((ficres =fopen(fileres,"w"))==NULL) {              dh[mi][i]=jk+1;
       printf("Problem with resultfile: %s\n", fileres);goto end;              bh[mi][i]=ju;
     }            }
     fprintf(ficres,"#%s\n",version);            if(dh[mi][i]==0){
                  dh[mi][i]=1; /* At least one step */
     if((fic=fopen(datafile,"r"))==NULL)    {              bh[mi][i]=ju; /* At least one step */
       printf("Problem with datafile: %s\n", datafile);goto end;              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
     }            }
           } /* end if mle */
     n= lastobs;        }
     severity = vector(1,maxwav);      } /* end wave */
     outcome=imatrix(1,maxwav+1,1,n);    }
     num=ivector(1,n);    jmean=sum/k;
     moisnais=vector(1,n);    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     annais=vector(1,n);    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     moisdc=vector(1,n);   }
     andc=vector(1,n);  
     agedc=vector(1,n);  /*********** Tricode ****************************/
     cod=ivector(1,n);  void tricode(int *Tvar, int **nbcode, int imx)
     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);    int Ndum[20],ij=1, k, j, i, maxncov=19;
     anint=matrix(1,maxwav,1,n);    int cptcode=0;
     s=imatrix(1,maxwav+1,1,n);    cptcoveff=0; 
     adl=imatrix(1,maxwav+1,1,n);       
     tab=ivector(1,NCOVMAX);    for (k=0; k<maxncov; k++) Ndum[k]=0;
     ncodemax=ivector(1,8);    for (k=1; k<=7; k++) ncodemax[k]=0;
   
     i=1;    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
     while (fgets(line, MAXLINE, fic) != NULL)    {      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
       if ((i >= firstobs) && (i <=lastobs)) {                                 modality*/ 
                ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
         for (j=maxwav;j>=1;j--){        Ndum[ij]++; /*store the modality */
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
           strcpy(line,stra);        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                                         Tvar[j]. If V=sex and male is 0 and 
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                                         female is 1, then  cptcode=1.*/
         }      }
          
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);      for (i=0; i<=cptcode; i++) {
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);        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 */
       }
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);  
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);      ij=1; 
       for (i=1; i<=ncodemax[j]; i++) {
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);        for (k=0; k<= maxncov; k++) {
         for (j=ncov;j>=1;j--){          if (Ndum[k] != 0) {
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);            nbcode[Tvar[j]][ij]=k; 
         }            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
         num[i]=atol(stra);            
                    ij++;
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){          }
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/          if (ij > ncodemax[j]) break; 
         }  
         i=i+1;      } 
       }    }  
     }  
     /* printf("ii=%d", ij);   for (k=0; k< maxncov; k++) Ndum[k]=0;
        scanf("%d",i);*/  
   imx=i-1; /* Number of individuals */   for (i=1; i<=ncovmodel-2; i++) { 
      /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
   /* for (i=1; i<=imx; i++){     ij=Tvar[i];
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;     Ndum[ij]++;
     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;  
     }   ij=1;
    for (i=1; i<= maxncov; i++) {
     for (i=1; i<=imx; i++)     if((Ndum[i]!=0) && (i<=ncovcol)){
     if (covar[1][i]==0) 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]));*/       Tvaraff[ij]=i; /*For printing */
        ij++;
   /* Calculation of the number of parameter from char model*/     }
   Tvar=ivector(1,15);   }
   Tprod=ivector(1,15);   
   Tvaraff=ivector(1,15);   cptcoveff=ij-1; /*Number of simple covariates*/
   Tvard=imatrix(1,15,1,2);  }
   Tage=ivector(1,15);        
      /*********** Health Expectancies ****************/
   if (strlen(model) >1){  
     j=0, j1=0, k1=1, k2=1;  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 )
     j=nbocc(model,'+');  
     j1=nbocc(model,'*');  {
     cptcovn=j+1;    /* Health expectancies */
     cptcovprod=j1;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
        double age, agelim, hf;
        double ***p3mat,***varhe;
     strcpy(modelsav,model);    double **dnewm,**doldm;
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    double *xp;
       printf("Error. Non available option model=%s ",model);    double **gp, **gm;
       goto end;    double ***gradg, ***trgradg;
     }    int theta;
      
     for(i=(j+1); i>=1;i--){    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
       cutv(stra,strb,modelsav,'+');    xp=vector(1,npar);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    dnewm=matrix(1,nlstate*nlstate,1,npar);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
       /*scanf("%d",i);*/    
       if (strchr(strb,'*')) {    fprintf(ficreseij,"# Health expectancies\n");
         cutv(strd,strc,strb,'*');    fprintf(ficreseij,"# Age");
         if (strcmp(strc,"age")==0) {    for(i=1; i<=nlstate;i++)
           cptcovprod--;      for(j=1; j<=nlstate;j++)
           cutv(strb,stre,strd,'V');        fprintf(ficreseij," %1d-%1d (SE)",i,j);
           Tvar[i]=atoi(stre);    fprintf(ficreseij,"\n");
           cptcovage++;  
             Tage[cptcovage]=i;    if(estepm < stepm){
             /*printf("stre=%s ", stre);*/      printf ("Problem %d lower than %d\n",estepm, stepm);
         }    }
         else if (strcmp(strd,"age")==0) {    else  hstepm=estepm;   
           cptcovprod--;    /* We compute the life expectancy from trapezoids spaced every estepm months
           cutv(strb,stre,strc,'V');     * This is mainly to measure the difference between two models: for example
           Tvar[i]=atoi(stre);     * if stepm=24 months pijx are given only every 2 years and by summing them
           cptcovage++;     * we are calculating an estimate of the Life Expectancy assuming a linear 
           Tage[cptcovage]=i;     * progression in between and thus overestimating or underestimating according
         }     * to the curvature of the survival function. If, for the same date, we 
         else {     * estimate the model with stepm=1 month, we can keep estepm to 24 months
           cutv(strb,stre,strc,'V');     * to compare the new estimate of Life expectancy with the same linear 
           Tvar[i]=ncov+k1;     * hypothesis. A more precise result, taking into account a more precise
           cutv(strb,strc,strd,'V');     * curvature will be obtained if estepm is as small as stepm. */
           Tprod[k1]=i;  
           Tvard[k1][1]=atoi(strc);    /* For example we decided to compute the life expectancy with the smallest unit */
           Tvard[k1][2]=atoi(stre);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           Tvar[cptcovn+k2]=Tvard[k1][1];       nhstepm is the number of hstepm from age to agelim 
           Tvar[cptcovn+k2+1]=Tvard[k1][2];       nstepm is the number of stepm from age to agelin. 
           for (k=1; k<=lastobs;k++)       Look at hpijx to understand the reason of that which relies in memory size
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];       and note for a fixed period like estepm months */
           k1++;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           k2=k2+2;       survival function given by stepm (the optimization length). Unfortunately it
         }       means that if the survival funtion is printed only each two years of age and if
       }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       else {       results. So we changed our mind and took the option of the best precision.
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    */
        /*  scanf("%d",i);*/    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       cutv(strd,strc,strb,'V');  
       Tvar[i]=atoi(strc);    agelim=AGESUP;
       }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       strcpy(modelsav,stra);        /* nhstepm age range expressed in number of stepm */
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
         scanf("%d",i);*/      /* 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 */
        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   printf("cptcovprod=%d ", cptcovprod);      gp=matrix(0,nhstepm,1,nlstate*nlstate);
   scanf("%d ",i);*/      gm=matrix(0,nhstepm,1,nlstate*nlstate);
     fclose(fic);  
       /* Computed by stepm unit matrices, product of hstepm matrices, stored
     /*  if(mle==1){*/         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
     if (weightopt != 1) { /* Maximisation without weights*/      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
       for(i=1;i<=n;i++) weight[i]=1.0;   
     }  
     /*-calculation of age at interview from date of interview and age at death -*/      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     agev=matrix(1,maxwav,1,imx);  
       /* Computing Variances of health expectancies */
    for (i=1; i<=imx; i++)  
      for(m=2; (m<= maxwav); m++)       for(theta=1; theta <=npar; theta++){
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){        for(i=1; i<=npar; i++){ 
          anint[m][i]=9999;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
          s[m][i]=-1;        }
        }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
        
     for (i=1; i<=imx; i++)  {        cptj=0;
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        for(j=1; j<= nlstate; j++){
       for(m=1; (m<= maxwav); m++){          for(i=1; i<=nlstate; i++){
         if(s[m][i] >0){            cptj=cptj+1;
           if (s[m][i] == nlstate+1) {            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
             if(agedc[i]>0)              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
               if(moisdc[i]!=99 && andc[i]!=9999)            }
               agev[m][i]=agedc[i];          }
             else {        }
               if (andc[i]!=9999){       
               printf("Warning negative age at death: %d line:%d\n",num[i],i);       
               agev[m][i]=-1;        for(i=1; i<=npar; i++) 
               }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
             }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           }        
           else if(s[m][i] !=9){ /* Should no more exist */        cptj=0;
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);        for(j=1; j<= nlstate; j++){
             if(mint[m][i]==99 || anint[m][i]==9999)          for(i=1;i<=nlstate;i++){
               agev[m][i]=1;            cptj=cptj+1;
             else if(agev[m][i] <agemin){            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
               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);*/              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
             }            }
             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);*/        for(j=1; j<= nlstate*nlstate; j++)
             }          for(h=0; h<=nhstepm-1; h++){
             /*agev[m][i]=anint[m][i]-annais[i];*/            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
             /*   agev[m][i] = age[i]+2*m;*/          }
           }       } 
           else { /* =9 */     
             agev[m][i]=1;  /* End theta */
             s[m][i]=-1;  
           }       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
         }  
         else /*= 0 Unknown */       for(h=0; h<=nhstepm-1; h++)
           agev[m][i]=1;        for(j=1; j<=nlstate*nlstate;j++)
       }          for(theta=1; theta <=npar; theta++)
                trgradg[h][j][theta]=gradg[h][theta][j];
     }       
     for (i=1; i<=imx; i++)  {  
       for(m=1; (m<= maxwav); m++){       for(i=1;i<=nlstate*nlstate;i++)
         if (s[m][i] > (nlstate+ndeath)) {        for(j=1;j<=nlstate*nlstate;j++)
           printf("Error: Wrong value in nlstate or ndeath\n");            varhe[i][j][(int)age] =0.;
           goto end;  
         }       printf("%d|",(int)age);fflush(stdout);
       }       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     }       for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
     free_vector(severity,1,maxwav);          for(i=1;i<=nlstate*nlstate;i++)
     free_imatrix(outcome,1,maxwav+1,1,n);            for(j=1;j<=nlstate*nlstate;j++)
     free_vector(moisnais,1,n);              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
     free_vector(annais,1,n);        }
     /* free_matrix(mint,1,maxwav,1,n);      }
        free_matrix(anint,1,maxwav,1,n);*/      /* Computing expectancies */
     free_vector(moisdc,1,n);      for(i=1; i<=nlstate;i++)
     free_vector(andc,1,n);        for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
                eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
     wav=ivector(1,imx);            
     dh=imatrix(1,lastpass-firstpass+1,1,imx);  /* 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]);*/
     mw=imatrix(1,lastpass-firstpass+1,1,imx);  
              }
     /* Concatenates waves */  
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      fprintf(ficreseij,"%3.0f",age );
       cptj=0;
       for(i=1; i<=nlstate;i++)
       Tcode=ivector(1,100);        for(j=1; j<=nlstate;j++){
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);          cptj++;
       ncodemax[1]=1;          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);        }
            fprintf(ficreseij,"\n");
    codtab=imatrix(1,100,1,10);     
    h=0;      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
    m=pow(2,cptcoveff);      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
        free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
    for(k=1;k<=cptcoveff; k++){      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
      for(i=1; i <=(m/pow(2,k));i++){      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        for(j=1; j <= ncodemax[k]; j++){    }
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    printf("\n");
            h++;    fprintf(ficlog,"\n");
            if (h>m) h=1;codtab[h][k]=j;  
          }    free_vector(xp,1,npar);
        }    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
      }    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
    }    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   }
   
    /*for(i=1; i <=m ;i++){  /************ Variance ******************/
      for(k=1; k <=cptcovn; k++){  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)
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);  {
      }    /* Variance of health expectancies */
      printf("\n");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
    }    /* double **newm;*/
    scanf("%d",i);*/    double **dnewm,**doldm;
        double **dnewmp,**doldmp;
    /* Calculates basic frequencies. Computes observed prevalence at single age    int i, j, nhstepm, hstepm, h, nstepm ;
        and prints on file fileres'p'. */    int k, cptcode;
     double *xp;
        double **gp, **gm;  /* for var eij */
        double ***gradg, ***trgradg; /*for var eij */
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double **gradgp, **trgradgp; /* for var p point j */
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double *gpp, *gmp; /* for var p point j */
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    double ***p3mat;
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    double age,agelim, hf;
          double ***mobaverage;
     /* For Powell, parameters are in a vector p[] starting at p[1]    int theta;
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */    char digit[4];
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    char digitp[25];
   
     if(mle==1){    char fileresprobmorprev[FILENAMELENGTH];
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  
     }    if(popbased==1){
          if(mobilav!=0)
     /*--------- results files --------------*/        strcpy(digitp,"-populbased-mobilav-");
     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);      else strcpy(digitp,"-populbased-nomobil-");
      }
     else 
    jk=1;      strcpy(digitp,"-stablbased-");
    fprintf(ficres,"# Parameters\n");  
    printf("# Parameters\n");    if (mobilav!=0) {
    for(i=1,jk=1; i <=nlstate; i++){      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      for(k=1; k <=(nlstate+ndeath); k++){      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
        if (k != i)        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
          {        printf(" Error in movingaverage mobilav=%d\n",mobilav);
            printf("%d%d ",i,k);      }
            fprintf(ficres,"%1d%1d ",i,k);    }
            for(j=1; j <=ncovmodel; j++){  
              printf("%f ",p[jk]);    strcpy(fileresprobmorprev,"prmorprev"); 
              fprintf(ficres,"%f ",p[jk]);    sprintf(digit,"%-d",ij);
              jk++;    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
            }    strcat(fileresprobmorprev,digit); /* Tvar to be done */
            printf("\n");    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
            fprintf(ficres,"\n");    strcat(fileresprobmorprev,fileres);
          }    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
      }      printf("Problem with resultfile: %s\n", fileresprobmorprev);
    }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
  if(mle==1){    }
     /* Computing hessian and covariance matrix */    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     ftolhess=ftol; /* Usually correct */    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     hesscov(matcov, p, npar, delti, ftolhess, func);    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
  }    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     fprintf(ficres,"# Scales\n");    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     printf("# Scales\n");      fprintf(ficresprobmorprev," p.%-d SE",j);
      for(i=1,jk=1; i <=nlstate; i++){      for(i=1; i<=nlstate;i++)
       for(j=1; j <=nlstate+ndeath; j++){        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
         if (j!=i) {    }  
           fprintf(ficres,"%1d%1d",i,j);    fprintf(ficresprobmorprev,"\n");
           printf("%1d%1d",i,j);    fprintf(ficgp,"\n# Routine varevsij");
           for(k=1; k<=ncovmodel;k++){    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");
             printf(" %.5e",delti[jk]);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
             fprintf(ficres," %.5e",delti[jk]);  /*   } */
             jk++;    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           }  
           printf("\n");    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
           fprintf(ficres,"\n");    fprintf(ficresvij,"# Age");
         }    for(i=1; i<=nlstate;i++)
       }      for(j=1; j<=nlstate;j++)
      }        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
        fprintf(ficresvij,"\n");
     k=1;  
     fprintf(ficres,"# Covariance\n");    xp=vector(1,npar);
     printf("# Covariance\n");    dnewm=matrix(1,nlstate,1,npar);
     for(i=1;i<=npar;i++){    doldm=matrix(1,nlstate,1,nlstate);
       /*  if (k>nlstate) k=1;    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
       i1=(i-1)/(ncovmodel*nlstate)+1;    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);  
       printf("%s%d%d",alph[k],i1,tab[i]);*/    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
       fprintf(ficres,"%3d",i);    gpp=vector(nlstate+1,nlstate+ndeath);
       printf("%3d",i);    gmp=vector(nlstate+1,nlstate+ndeath);
       for(j=1; j<=i;j++){    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
         fprintf(ficres," %.5e",matcov[i][j]);    
         printf(" %.5e",matcov[i][j]);    if(estepm < stepm){
       }      printf ("Problem %d lower than %d\n",estepm, stepm);
       fprintf(ficres,"\n");    }
       printf("\n");    else  hstepm=estepm;   
       k++;    /* For example we decided to compute the life expectancy with the smallest unit */
     }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           nhstepm is the number of hstepm from age to agelim 
     while((c=getc(ficpar))=='#' && c!= EOF){       nstepm is the number of stepm from age to agelin. 
       ungetc(c,ficpar);       Look at hpijx to understand the reason of that which relies in memory size
       fgets(line, MAXLINE, ficpar);       and note for a fixed period like k years */
       puts(line);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       fputs(line,ficparo);       survival function given by stepm (the optimization length). Unfortunately it
     }       means that if the survival funtion is printed every two years of age and if
     ungetc(c,ficpar);       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.
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    */
        hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     if (fage <= 2) {    agelim = AGESUP;
       bage = agemin;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       fage = agemax;      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     }      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
          p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);      gp=matrix(0,nhstepm,1,nlstate);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);      gm=matrix(0,nhstepm,1,nlstate);
    
     while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      for(theta=1; theta <=npar; theta++){
     fgets(line, MAXLINE, ficpar);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
     puts(line);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     fputs(line,ficparo);        }
   }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   ungetc(c,ficpar);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mob_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);        if (popbased==1) {
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);          if(mobilav ==0){
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);            for(i=1; i<=nlstate;i++)
                    prlim[i][i]=probs[(int)age][i][ij];
   while((c=getc(ficpar))=='#' && c!= EOF){          }else{ /* mobilav */ 
     ungetc(c,ficpar);            for(i=1; i<=nlstate;i++)
     fgets(line, MAXLINE, ficpar);              prlim[i][i]=mobaverage[(int)age][i][ij];
     puts(line);          }
     fputs(line,ficparo);        }
   }    
   ungetc(c,ficpar);        for(j=1; j<= nlstate; j++){
            for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
    dateprev1=anprev1+mprev1/12.+jprev1/365.;              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
    dateprev2=anprev2+mprev2/12.+jprev2/365.;          }
         }
   fscanf(ficpar,"pop_based=%d\n",&popbased);        /* This for computing probability of death (h=1 means
    fprintf(ficparo,"pop_based=%d\n",popbased);             computed over hstepm matrices product = hstepm*stepm months) 
    fprintf(ficres,"pop_based=%d\n",popbased);             as a weighted average of prlim.
         */
   while((c=getc(ficpar))=='#' && c!= EOF){        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     ungetc(c,ficpar);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
     fgets(line, MAXLINE, ficpar);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     puts(line);        }    
     fputs(line,ficparo);        /* end probability of death */
   }  
   ungetc(c,ficpar);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);        if (popbased==1) {
           if(mobilav ==0){
                for(i=1; i<=nlstate;i++)
     /*------------ gnuplot -------------*/              prlim[i][i]=probs[(int)age][i][ij];
     /*chdir(pathcd);*/          }else{ /* mobilav */ 
     strcpy(optionfilegnuplot,optionfilefiname);            for(i=1; i<=nlstate;i++)
     strcat(optionfilegnuplot,".plt");              prlim[i][i]=mobaverage[(int)age][i][ij];
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {          }
       printf("Problem with file %s",optionfilegnuplot);goto end;        }
     }  
 #ifdef windows        for(j=1; j<= nlstate; j++){
     fprintf(ficgp,"cd \"%s\" \n",pathc);          for(h=0; h<=nhstepm; h++){
 #endif            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
 m=pow(2,cptcoveff);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
            }
  /* 1eme*/        }
   for (cpt=1; cpt<= nlstate ; cpt ++) {        /* This for computing probability of death (h=1 means
    for (k1=1; k1<= m ; k1 ++) {           computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
 #ifdef windows        */
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
 #endif          for(i=1,gmp[j]=0.; i<= nlstate; i++)
 #ifdef unix           gmp[j] += prlim[i][i]*p3mat[i][j][1];
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);        }    
 #endif        /* end probability of death */
   
 for (i=1; i<= nlstate ; i ++) {        for(j=1; j<= nlstate; j++) /* vareij */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          for(h=0; h<=nhstepm; h++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
 }          }
     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 ++) {        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   else fprintf(ficgp," \%%*lf (\%%*lf)");        }
 }  
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      } /* End theta */
      for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }        for(h=0; h<=nhstepm; h++) /* veij */
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));        for(j=1; j<=nlstate;j++)
 #ifdef unix          for(theta=1; theta <=npar; theta++)
 fprintf(ficgp,"\nset ter gif small size 400,300");            trgradg[h][j][theta]=gradg[h][theta][j];
 #endif  
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
    }        for(theta=1; theta <=npar; theta++)
   }          trgradgp[j][theta]=gradgp[theta][j];
   /*2 eme*/    
   
   for (k1=1; k1<= m ; k1 ++) {      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);      for(i=1;i<=nlstate;i++)
            for(j=1;j<=nlstate;j++)
     for (i=1; i<= nlstate+1 ; i ++) {          vareij[i][j][(int)age] =0.;
       k=2*i;  
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);      for(h=0;h<=nhstepm;h++){
       for (j=1; j<= nlstate+1 ; j ++) {        for(k=0;k<=nhstepm;k++){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   else fprintf(ficgp," \%%*lf (\%%*lf)");          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
 }            for(i=1;i<=nlstate;i++)
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");            for(j=1;j<=nlstate;j++)
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);        }
       for (j=1; j<= nlstate+1 ; j ++) {      }
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    
         else fprintf(ficgp," \%%*lf (\%%*lf)");      /* pptj */
 }        matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       fprintf(ficgp,"\" t\"\" w l 0,");      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
       for (j=1; j<= nlstate+1 ; j ++) {        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          varppt[j][i]=doldmp[j][i];
   else fprintf(ficgp," \%%*lf (\%%*lf)");      /* end ppptj */
 }        /*  x centered again */
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       else fprintf(ficgp,"\" t\"\" w l 0,");      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
     }   
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);      if (popbased==1) {
   }        if(mobilav ==0){
            for(i=1; i<=nlstate;i++)
   /*3eme*/            prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
   for (k1=1; k1<= m ; k1 ++) {          for(i=1; i<=nlstate;i++)
     for (cpt=1; cpt<= nlstate ; cpt ++) {            prlim[i][i]=mobaverage[(int)age][i][ij];
       k=2+nlstate*(cpt-1);        }
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);      }
       for (i=1; i< nlstate ; i ++) {               
         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
       }         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);         as a weighted average of prlim.
     }      */
   }      for(j=nlstate+1;j<=nlstate+ndeath;j++){
          for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   /* CV preval stat */          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   for (k1=1; k1<= m ; k1 ++) {      }    
     for (cpt=1; cpt<nlstate ; cpt ++) {      /* end probability of death */
       k=3;  
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for (i=1; i< nlstate ; i ++)      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficgp,"+$%d",k+i+1);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);        for(i=1; i<=nlstate;i++){
                fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
       l=3+(nlstate+ndeath)*cpt;        }
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);      } 
       for (i=1; i< nlstate ; i ++) {      fprintf(ficresprobmorprev,"\n");
         l=3+(nlstate+ndeath)*cpt;  
         fprintf(ficgp,"+$%d",l+i+1);      fprintf(ficresvij,"%.0f ",age );
       }      for(i=1; i<=nlstate;i++)
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);          for(j=1; j<=nlstate;j++){
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
     }        }
   }        fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
   /* proba elementaires */      free_matrix(gm,0,nhstepm,1,nlstate);
    for(i=1,jk=1; i <=nlstate; i++){      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
     for(k=1; k <=(nlstate+ndeath); k++){      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       if (k != i) {      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         for(j=1; j <=ncovmodel; j++){    } /* End age */
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/    free_vector(gpp,nlstate+1,nlstate+ndeath);
           /*fprintf(ficgp,"%s",alph[1]);*/    free_vector(gmp,nlstate+1,nlstate+ndeath);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
           jk++;    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
           fprintf(ficgp,"\n");    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
         }    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
       }    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
     }  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
     }  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   for(jk=1; jk <=m; jk++) {    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
    i=1;    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
    for(k2=1; k2<=nlstate; k2++) {    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
      k3=i;    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);
      for(k=1; k<=(nlstate+ndeath); k++) {    /*  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 (k != k2){  */
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
 ij=1;    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
         for(j=3; j <=ncovmodel; j++) {  
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    free_vector(xp,1,npar);
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    free_matrix(doldm,1,nlstate,1,nlstate);
             ij++;    free_matrix(dnewm,1,nlstate,1,npar);
           }    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           else    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         }    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           fprintf(ficgp,")/(1");    fclose(ficresprobmorprev);
            fflush(ficgp);
         for(k1=1; k1 <=nlstate; k1++){      fflush(fichtm); 
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);  }  /* end varevsij */
 ij=1;  
           for(j=3; j <=ncovmodel; j++){  /************ Variance of prevlim ******************/
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  {
             ij++;    /* Variance of prevalence limit */
           }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
           else    double **newm;
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    double **dnewm,**doldm;
           }    int i, j, nhstepm, hstepm;
           fprintf(ficgp,")");    int k, cptcode;
         }    double *xp;
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    double *gp, *gm;
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    double **gradg, **trgradg;
         i=i+ncovmodel;    double age,agelim;
        }    int theta;
      }     
    }    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    fprintf(ficresvpl,"# Age");
   }    for(i=1; i<=nlstate;i++)
            fprintf(ficresvpl," %1d-%1d",i,i);
   fclose(ficgp);    fprintf(ficresvpl,"\n");
   /* end gnuplot */  
        xp=vector(1,npar);
 chdir(path);    dnewm=matrix(1,nlstate,1,npar);
        doldm=matrix(1,nlstate,1,nlstate);
     free_ivector(wav,1,imx);    
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    hstepm=1*YEARM; /* Every year of age */
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     free_ivector(num,1,n);    agelim = AGESUP;
     free_vector(agedc,1,n);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
     /*free_matrix(covar,1,NCOVMAX,1,n);*/      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     fclose(ficparo);      if (stepm >= YEARM) hstepm=1;
     fclose(ficres);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
     /*  }*/      gradg=matrix(1,npar,1,nlstate);
          gp=vector(1,nlstate);
    /*________fin mle=1_________*/      gm=vector(1,nlstate);
      
       for(theta=1; theta <=npar; theta++){
          for(i=1; i<=npar; i++){ /* Computes gradient */
     /* No more information from the sample is required now */          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   /* Reads comments: lines beginning with '#' */        }
   while((c=getc(ficpar))=='#' && c!= EOF){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     ungetc(c,ficpar);        for(i=1;i<=nlstate;i++)
     fgets(line, MAXLINE, ficpar);          gp[i] = prlim[i][i];
     puts(line);      
     fputs(line,ficparo);        for(i=1; i<=npar; i++) /* Computes gradient */
   }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   ungetc(c,ficpar);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
          for(i=1;i<=nlstate;i++)
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);          gm[i] = prlim[i][i];
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);  
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);        for(i=1;i<=nlstate;i++)
 /*--------- index.htm --------*/          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   strcpy(optionfilehtm,optionfile);  
   strcat(optionfilehtm,".htm");      trgradg =matrix(1,nlstate,1,npar);
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {  
     printf("Problem with %s \n",optionfilehtm);goto end;      for(j=1; j<=nlstate;j++)
   }        for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">  
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>      for(i=1;i<=nlstate;i++)
 Total number of observations=%d <br>        varpl[i][(int)age] =0.;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
 <hr  size=\"2\" color=\"#EC5E5E\">      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
 <li>Outputs files<br><br>\n      for(i=1;i<=nlstate;i++)
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>  
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>      fprintf(ficresvpl,"%.0f ",age );
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>      for(i=1; i<=nlstate;i++)
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>      fprintf(ficresvpl,"\n");
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>      free_vector(gp,1,nlstate);
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>      free_vector(gm,1,nlstate);
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>      free_matrix(gradg,1,npar,1,nlstate);
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>      free_matrix(trgradg,1,nlstate,1,npar);
 <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);    } /* End age */
   
  fprintf(fichtm," <li>Graphs</li><p>");    free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
  m=cptcoveff;    free_matrix(dnewm,1,nlstate,1,nlstate);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  
   }
  j1=0;  
  for(k1=1; k1<=m;k1++){  /************ Variance of one-step probabilities  ******************/
    for(i1=1; i1<=ncodemax[k1];i1++){  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
        j1++;  {
        if (cptcovn > 0) {    int i, j=0,  i1, k1, l1, t, tj;
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    int k2, l2, j1,  z1;
          for (cpt=1; cpt<=cptcoveff;cpt++)    int k=0,l, cptcode;
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);    int first=1, first1;
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
        }    double **dnewm,**doldm;
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    double *xp;
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);        double *gp, *gm;
        for(cpt=1; cpt<nlstate;cpt++){    double **gradg, **trgradg;
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    double **mu;
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    double age,agelim, cov[NCOVMAX];
        }    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     for(cpt=1; cpt<=nlstate;cpt++) {    int theta;
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    char fileresprob[FILENAMELENGTH];
 interval) in state (%d): v%s%d%d.gif <br>    char fileresprobcov[FILENAMELENGTH];
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      char fileresprobcor[FILENAMELENGTH];
      }  
      for(cpt=1; cpt<=nlstate;cpt++) {    double ***varpij;
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>  
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    strcpy(fileresprob,"prob"); 
      }    strcat(fileresprob,fileres);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
 health expectancies in states (1) and (2): e%s%d.gif<br>      printf("Problem with resultfile: %s\n", fileresprob);
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
 fprintf(fichtm,"\n</body>");    }
    }    strcpy(fileresprobcov,"probcov"); 
  }    strcat(fileresprobcov,fileres);
 fclose(fichtm);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
   /*--------------- Prevalence limit --------------*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
      }
   strcpy(filerespl,"pl");    strcpy(fileresprobcor,"probcor"); 
   strcat(filerespl,fileres);    strcat(fileresprobcor,fileres);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;      printf("Problem with resultfile: %s\n", fileresprobcor);
   }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    }
   fprintf(ficrespl,"#Prevalence limit\n");    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   fprintf(ficrespl,"#Age ");    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   fprintf(ficrespl,"\n");    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
      printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   prlim=matrix(1,nlstate,1,nlstate);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficresprob,"# Age");
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    fprintf(ficresprobcov,"# Age");
   k=0;    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   agebase=agemin;    fprintf(ficresprobcov,"# Age");
   agelim=agemax;  
   ftolpl=1.e-10;  
   i1=cptcoveff;    for(i=1; i<=nlstate;i++)
   if (cptcovn < 1){i1=1;}      for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   for(cptcov=1;cptcov<=i1;cptcov++){        fprintf(ficresprobcov," p%1d-%1d ",i,j);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        fprintf(ficresprobcor," p%1d-%1d ",i,j);
         k=k+1;      }  
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/   /* fprintf(ficresprob,"\n");
         fprintf(ficrespl,"\n#******");    fprintf(ficresprobcov,"\n");
         for(j=1;j<=cptcoveff;j++)    fprintf(ficresprobcor,"\n");
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   */
         fprintf(ficrespl,"******\n");   xp=vector(1,npar);
            dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
         for (age=agebase; age<=agelim; age++){    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
           fprintf(ficrespl,"%.0f",age );    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
           for(i=1; i<=nlstate;i++)    first=1;
           fprintf(ficrespl," %.5f", prlim[i][i]);    fprintf(ficgp,"\n# Routine varprob");
           fprintf(ficrespl,"\n");    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
         }    fprintf(fichtm,"\n");
       }  
     }    fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
   fclose(ficrespl);    fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
   /*------------- h Pij x at various ages ------------*/  
      cov[1]=1;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    tj=cptcoveff;
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    j1=0;
   }    for(t=1; t<=tj;t++){
   printf("Computing pij: result on file '%s' \n", filerespij);      for(i1=1; i1<=ncodemax[t];i1++){ 
          j1++;
   stepsize=(int) (stepm+YEARM-1)/YEARM;        if  (cptcovn>0) {
   /*if (stepm<=24) stepsize=2;*/          fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   agelim=AGESUP;          fprintf(ficresprob, "**********\n#\n");
   hstepm=stepsize*YEARM; /* Every year of age */          fprintf(ficresprobcov, "\n#********** Variable "); 
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficresprobcov, "**********\n#\n");
   k=0;          
   for(cptcov=1;cptcov<=i1;cptcov++){          fprintf(ficgp, "\n#********** Variable "); 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       k=k+1;          fprintf(ficgp, "**********\n#\n");
         fprintf(ficrespij,"\n#****** ");          
         for(j=1;j<=cptcoveff;j++)          
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
         fprintf(ficrespij,"******\n");          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
                  fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          fprintf(ficresprobcor, "\n#********** Variable ");    
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficresprobcor, "**********\n#");    
           oldm=oldms;savm=savms;        }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          
           fprintf(ficrespij,"# Age");        for (age=bage; age<=fage; age ++){ 
           for(i=1; i<=nlstate;i++)          cov[2]=age;
             for(j=1; j<=nlstate+ndeath;j++)          for (k=1; k<=cptcovn;k++) {
               fprintf(ficrespij," %1d-%1d",i,j);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           fprintf(ficrespij,"\n");          }
           for (h=0; h<=nhstepm; h++){          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );          for (k=1; k<=cptcovprod;k++)
             for(i=1; i<=nlstate;i++)            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<=nlstate+ndeath;j++)          
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
             fprintf(ficrespij,"\n");          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           }          gp=vector(1,(nlstate)*(nlstate+ndeath));
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          gm=vector(1,(nlstate)*(nlstate+ndeath));
           fprintf(ficrespij,"\n");      
         }          for(theta=1; theta <=npar; theta++){
     }            for(i=1; i<=npar; i++)
   }              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/            pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
   fclose(ficrespij);            k=0;
             for(i=1; i<= (nlstate); i++){
   if(stepm == 1) {              for(j=1; j<=(nlstate+ndeath);j++){
   /*---------- Forecasting ------------------*/                k=k+1;
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;                gp[k]=pmmij[i][j];
               }
   /*printf("calage= %f", calagedate);*/            }
              
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);            for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
   strcpy(fileresf,"f");            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   strcat(fileresf,fileres);            k=0;
   if((ficresf=fopen(fileresf,"w"))==NULL) {            for(i=1; i<=(nlstate); i++){
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;              for(j=1; j<=(nlstate+ndeath);j++){
   }                k=k+1;
   printf("Computing forecasting: result on file '%s' \n", fileresf);                gm[k]=pmmij[i][j];
               }
   free_matrix(mint,1,maxwav,1,n);            }
   free_matrix(anint,1,maxwav,1,n);       
   free_matrix(agev,1,maxwav,1,imx);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
   /* Mobile average */              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
   if (mobilav==1) {            for(theta=1; theta <=npar; theta++)
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              trgradg[j][theta]=gradg[theta][j];
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)          
       for (i=1; i<=nlstate;i++)          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           mobaverage[(int)agedeb][i][cptcod]=0.;          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
              free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
     for (agedeb=bage+4; agedeb<=fage; agedeb++){          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       for (i=1; i<=nlstate;i++){          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
           for (cpt=0;cpt<=4;cpt++){          pmij(pmmij,cov,ncovmodel,x,nlstate);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];          
           }          k=0;
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;          for(i=1; i<=(nlstate); i++){
         }            for(j=1; j<=(nlstate+ndeath);j++){
       }              k=k+1;
     }                mu[k][(int) age]=pmmij[i][j];
   }            }
           }
   stepsize=(int) (stepm+YEARM-1)/YEARM;          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   if (stepm<=12) stepsize=1;            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   agelim=AGESUP;  
   /*hstepm=stepsize*YEARM; *//* Every year of age */          /*printf("\n%d ",(int)age);
   hstepm=1;            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   yp1=modf(dateintmean,&yp);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   anprojmean=yp;            }*/
   yp2=modf((yp1*12),&yp);  
   mprojmean=yp;          fprintf(ficresprob,"\n%d ",(int)age);
   yp1=modf((yp2*30.5),&yp);          fprintf(ficresprobcov,"\n%d ",(int)age);
   jprojmean=yp;          fprintf(ficresprobcor,"\n%d ",(int)age);
   if(jprojmean==0) jprojmean=1;  
   if(mprojmean==0) jprojmean=1;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   if (popforecast==1) {            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
     if((ficpop=fopen(popfile,"r"))==NULL)    {          }
       printf("Problem with population file : %s\n",popfile);goto end;          i=0;
     }          for (k=1; k<=(nlstate);k++){
     popage=ivector(0,AGESUP);            for (l=1; l<=(nlstate+ndeath);l++){ 
     popeffectif=vector(0,AGESUP);              i=i++;
     popcount=vector(0,AGESUP);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
     i=1;                for (j=1; j<=i;j++){
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)                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]));
         i=i+1;              }
       }            }
     imx=i;          }/* end of loop for state */
            } /* end of loop for age */
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];  
   }        /* Confidence intervalle of pij  */
         /*
   for(cptcov=1;cptcov<=i1;cptcov++){          fprintf(ficgp,"\nset noparametric;unset label");
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
       k=k+1;          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
       fprintf(ficresf,"\n#******");          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);
       for(j=1;j<=cptcoveff;j++) {          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
       }          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
       fprintf(ficresf,"******\n");        */
       fprintf(ficresf,"# StartingAge FinalAge");  
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
       if (popforecast==1)  fprintf(ficresf," [Population]");        first1=1;
            for (k2=1; k2<=(nlstate);k2++){
       for (cpt=0; cpt<4;cpt++) {          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
         fprintf(ficresf,"\n");            if(l2==k2) continue;
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);              j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(bage-((int)calagedate %12)/12.); agedeb--){ /* If stepm=6 months */              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);                if(l1==k1) continue;
         nhstepm = nhstepm/hstepm;                i=(k1-1)*(nlstate+ndeath)+l1;
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/                if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                  if ((int)age %5==0){
         oldm=oldms;savm=savms;                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                      v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                            cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
         for (h=0; h<=nhstepm; h++){                    mu1=mu[i][(int) age]/stepm*YEARM ;
           if (h==(int) (calagedate+YEARM*cpt)) {                    mu2=mu[j][(int) age]/stepm*YEARM;
             fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);                    c12=cv12/sqrt(v1*v2);
           }                    /* Computing eigen value of matrix of covariance */
           for(j=1; j<=nlstate+ndeath;j++) {                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
             kk1=0.;kk2=0;                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
             for(i=1; i<=nlstate;i++) {                            /* Eigen vectors */
               if (mobilav==1)                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];                    /*v21=sqrt(1.-v11*v11); *//* error */
               else {                    v21=(lc1-v1)/cv12*v11;
                 kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];                    v12=-v21;
                 /* fprintf(ficresf," p3=%.3f p=%.3f ", p3mat[i][j][h], probs[(int)(agedeb)+1][i][cptcod]);*/                    v22=v11;
               }                    tnalp=v21/v11;
                     if(first1==1){
               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];                      first1=0;
             }                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                              }
             if (h==(int)(calagedate+12*cpt)){                    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);
               fprintf(ficresf," %.3f", kk1);                    /*printf(fignu*/
                                  /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
             }                    if(first==1){
           }                      first=0;
         }                      fprintf(ficgp,"\nset parametric;unset label");
         /*      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);*/                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
       }                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
       }                      fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
     }   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   }  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
   /*  if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
   if (popforecast==1) {                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     free_ivector(popage,0,AGESUP);                      fprintf(fichtm,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     free_vector(popeffectif,0,AGESUP);                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
     free_vector(popcount,0,AGESUP);                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   }                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   free_imatrix(s,1,maxwav+1,1,n);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   free_vector(weight,1,n);*/                      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",\
   fclose(ficresf);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   }/* End forecasting */                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   else{                    }else{
     erreur=108;                      first=0;
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);                      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);
   /*---------- Health expectancies and variances ------------*/                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   strcpy(filerest,"t");                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   strcat(filerest,fileres);                    }/* if first */
   if((ficrest=fopen(filerest,"w"))==NULL) {                  } /* age mod 5 */
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;                } /* end loop age */
   }                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);                first=1;
               } /*l12 */
             } /* k12 */
   strcpy(filerese,"e");          } /*l1 */
   strcat(filerese,fileres);        }/* k1 */
   if((ficreseij=fopen(filerese,"w"))==NULL) {      } /* loop covariates */
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    }
   }    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_vector(xp,1,npar);
  strcpy(fileresv,"v");    fclose(ficresprob);
   strcat(fileresv,fileres);    fclose(ficresprobcov);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    fclose(ficresprobcor);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    /*  fclose(ficgp);*/
   }  }
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);  
   
   k=0;  /******************* Printing html file ***********/
   for(cptcov=1;cptcov<=i1;cptcov++){  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                    int lastpass, int stepm, int weightopt, char model[],\
       k=k+1;                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
       fprintf(ficrest,"\n#****** ");                    int popforecast, int estepm ,\
       for(j=1;j<=cptcoveff;j++)                    double jprev1, double mprev1,double anprev1, \
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    double jprev2, double mprev2,double anprev2){
       fprintf(ficrest,"******\n");    int jj1, k1, i1, cpt;
     /*char optionfilehtm[FILENAMELENGTH];*/
       fprintf(ficreseij,"\n#****** ");  /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    { */
       for(j=1;j<=cptcoveff;j++)  /*     printf("Problem with %s \n",optionfilehtm), exit(0); */
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);  /*     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
       fprintf(ficreseij,"******\n");  /*   } */
   
       fprintf(ficresvij,"\n#****** ");     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
       for(j=1;j<=cptcoveff;j++)   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n \
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n \
       fprintf(ficresvij,"******\n");   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n \
    - Life expectancies by age and initial health status (estepm=%2d months): \
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);     <a href=\"%s\">%s</a> <br>\n</li>", \
       oldm=oldms;savm=savms;             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);               stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
       oldm=oldms;savm=savms;             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  
        fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");  
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);   m=cptcoveff;
       fprintf(ficrest,"\n");   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
          
       hf=1;   jj1=0;
       if (stepm >= YEARM) hf=stepm/YEARM;   for(k1=1; k1<=m;k1++){
       epj=vector(1,nlstate+1);     for(i1=1; i1<=ncodemax[k1];i1++){
       for(age=bage; age <=fage ;age++){       jj1++;
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);       if (cptcovn > 0) {
         if (popbased==1) {         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
           for(i=1; i<=nlstate;i++)         for (cpt=1; cpt<=cptcoveff;cpt++) 
             prlim[i][i]=probs[(int)age][i][k];           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
         }         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
               }
         fprintf(ficrest," %.0f",age);       /* Pij */
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){       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> \
           for(i=1, epj[j]=0.;i <=nlstate;i++) {  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];       /* Quasi-incidences */
           }       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
           epj[nlstate+1] +=epj[j];   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
         }  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
         for(i=1, vepp=0.;i <=nlstate;i++)         /* Stable prevalence in each health state */
           for(j=1;j <=nlstate;j++)         for(cpt=1; cpt<nlstate;cpt++){
             vepp += vareij[i][j][(int)age];           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
         for(j=1;j <=nlstate;j++){         }
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));       for(cpt=1; cpt<=nlstate;cpt++) {
         }          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
         fprintf(ficrest,"\n");  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
       }       }
     }       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   }  health expectancies in states (1) and (2): %s%d.png<br>\
          <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
             } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
  fclose(ficreseij);  
  fclose(ficresvij);  
   fclose(ficrest);   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
   fclose(ficpar);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
   free_vector(epj,1,nlstate+1);   - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
   /*  scanf("%d ",i); */   - 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\
   /*------- Variance limit prevalence------*/     - 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\
 strcpy(fileresvpl,"vpl");   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
   strcat(fileresvpl,fileres);           rfileres,rfileres,\
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
     exit(0);           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
   }           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);           subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
  k=0;  
  for(cptcov=1;cptcov<=i1;cptcov++){  /*  if(popforecast==1) fprintf(fichtm,"\n */
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
      k=k+1;  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
      fprintf(ficresvpl,"\n#****** ");  /*      <br>",fileres,fileres,fileres,fileres); */
      for(j=1;j<=cptcoveff;j++)  /*  else  */
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  /*    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(ficresvpl,"******\n");  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
        
      varpl=matrix(1,nlstate,(int) bage, (int) fage);   m=cptcoveff;
      oldm=oldms;savm=savms;   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  
    }   jj1=0;
  }   for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
   fclose(ficresvpl);       jj1++;
        if (cptcovn > 0) {
   /*---------- End : free ----------------*/         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);         for (cpt=1; cpt<=cptcoveff;cpt++) 
             fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);       }
         for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);  interval) in state (%d): %s%d%d.png <br>\
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);       }
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);     } /* end i1 */
     }/* End k1 */
   free_matrix(matcov,1,npar,1,npar);   fprintf(fichtm,"</ul>");
   free_vector(delti,1,npar);   fflush(fichtm);
    }
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);  
   /******************* Gnuplot file **************/
   if(erreur >0)  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
     printf("End of Imach with error %d\n",erreur);  
   else   printf("End of Imach\n");    char dirfileres[132],optfileres[132];
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
      int ng;
   /* 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);*/  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*printf("Total time was %d uSec.\n", total_usecs);*/  /*     printf("Problem with file %s",optionfilegnuplot); */
   /*------ End -----------*/  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
  end:    /*#ifdef windows */
 #ifdef windows    fprintf(ficgp,"cd \"%s\" \n",pathc);
   /* chdir(pathcd);*/      /*#endif */
 #endif    m=pow(2,cptcoveff);
  /*system("wgnuplot graph.plt");*/  
  /*system("../gp37mgw/wgnuplot graph.plt");*/    strcpy(dirfileres,optionfilefiname);
  /*system("cd ../gp37mgw");*/    strcpy(optfileres,"vpl");
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/   /* 1eme*/
  strcpy(plotcmd,GNUPLOTPROGRAM);    for (cpt=1; cpt<= nlstate ; cpt ++) {
  strcat(plotcmd," ");     for (k1=1; k1<= m ; k1 ++) {
  strcat(plotcmd,optionfilegnuplot);       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
  system(plotcmd);       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
 #ifdef windows  set ylabel \"Probability\" \n\
   while (z[0] != 'q') {  set ter png small\n\
     chdir(path);  set size 0.65,0.65\n\
     printf("\nType e to edit output files, c to start again, and q for exiting: ");  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
     scanf("%s",z);  
     if (z[0] == 'c') system("./imach");       for (i=1; i<= nlstate ; i ++) {
     else if (z[0] == 'e') {         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
       chdir(path);         else fprintf(ficgp," \%%*lf (\%%*lf)");
       system(optionfilehtm);       }
     }       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);
     else if (z[0] == 'q') exit(0);       for (i=1; i<= nlstate ; i ++) {
   }         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
 #endif         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.1.90


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