Diff for /imach/src/imach.c between versions 1.20 and 1.85

version 1.20, 2002/02/20 17:22:01 version 1.85, 2003/06/17 13:12:43
Line 1 Line 1
      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.85  2003/06/17 13:12:43  brouard
   individuals from different ages are interviewed on their health status    * imach.c (Repository): Check when date of death was earlier that
   or degree of  disability. At least a second wave of interviews    current date of interview. It may happen when the death was just
   ("longitudinal") should  measure each new individual health status.    prior to the death. In this case, dh was negative and likelihood
   Health expectancies are computed from the transistions observed between    was wrong (infinity). We still send an "Error" but patch by
   waves and are computed for each degree of severity of disability (number    assuming that the date of death was just one stepm after the
   of life states). More degrees you consider, more time is necessary to    interview.
   reach the Maximum Likelihood of the parameters involved in the model.    (Repository): Because some people have very long ID (first column)
   The simplest model is the multinomial logistic model where pij is    we changed int to long in num[] and we added a new lvector for
   the probabibility to be observed in state j at the second wave conditional    memory allocation. But we also truncated to 8 characters (left
   to be observed in state i at the first wave. Therefore the model is:    truncation)
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    (Repository): No more line truncation errors.
   is a covariate. If you want to have a more complex model than "constant and  
   age", you should modify the program where the markup    Revision 1.84  2003/06/13 21:44:43  brouard
     *Covariates have to be included here again* invites you to do it.    * imach.c (Repository): Replace "freqsummary" at a correct
   More covariates you add, less is the speed of the convergence.    place. It differs from routine "prevalence" which may be called
     many times. Probs is memory consuming and must be used with
   The advantage that this computer programme claims, comes from that if the    parcimony.
   delay between waves is not identical for each individual, or if some    Version 0.95a2 (should output exactly the same maximization than 0.8a2)
   individual missed an interview, the information is not rounded or lost, but  
   taken into account using an interpolation or extrapolation.    Revision 1.83  2003/06/10 13:39:11  lievre
   hPijx is the probability to be    *** empty log message ***
   observed in state i at age x+h conditional to the observed state i at age  
   x. The delay 'h' can be split into an exact number (nh*stepm) of    Revision 1.82  2003/06/05 15:57:20  brouard
   unobserved intermediate  states. This elementary transition (by month or    Add log in  imach.c and  fullversion number is now printed.
   quarter trimester, semester or year) is model as a multinomial logistic.  
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices  */
   and the contribution of each individual to the likelihood is simply hPijx.  /*
      Interpolated Markov Chain
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Short summary of the programme:
      
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    This program computes Healthy Life Expectancies from
            Institut national d'études démographiques, Paris.    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   This software have been partly granted by Euro-REVES, a concerted action    first survey ("cross") where individuals from different ages are
   from the European Union.    interviewed on their health status or degree of disability (in the
   It is copyrighted identically to a GNU software product, ie programme and    case of a health survey which is our main interest) -2- at least a
   software can be distributed freely for non commercial use. Latest version    second wave of interviews ("longitudinal") which measure each change
   can be accessed at http://euroreves.ined.fr/imach .    (if any) in individual health status.  Health expectancies are
   **********************************************************************/    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
 #include <math.h>    Maximum Likelihood of the parameters involved in the model.  The
 #include <stdio.h>    simplest model is the multinomial logistic model where pij is the
 #include <stdlib.h>    probability to be observed in state j at the second wave
 #include <unistd.h>    conditional to be observed in state i at the first wave. Therefore
     the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 #define MAXLINE 256    'age' is age and 'sex' is a covariate. If you want to have a more
 #define FILENAMELENGTH 80    complex model than "constant and age", you should modify the program
 /*#define DEBUG*/    where the markup *Covariates have to be included here again* invites
 #define windows    you to do it.  More covariates you add, slower the
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    convergence.
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     The advantage of this computer programme, compared to a simple
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    multinomial logistic model, is clear when the delay between waves is not
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    identical for each individual. Also, if a individual missed an
     intermediate interview, the information is lost, but taken into
 #define NINTERVMAX 8    account using an interpolation or extrapolation.  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    hPijx is the probability to be observed in state i at age x+h
 #define NCOVMAX 8 /* Maximum number of covariates */    conditional to the observed state i at age x. The delay 'h' can be
 #define MAXN 20000    split into an exact number (nh*stepm) of unobserved intermediate
 #define YEARM 12. /* Number of months per year */    states. This elementary transition (by month, quarter,
 #define AGESUP 130    semester or year) is modelled as a multinomial logistic.  The hPx
 #define AGEBASE 40    matrix is simply the matrix product of nh*stepm elementary matrices
     and the contribution of each individual to the likelihood is simply
     hPijx.
 int nvar;  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Also this programme outputs the covariance matrix of the parameters but also
 int npar=NPARMAX;    of the life expectancies. It also computes the stable prevalence. 
 int nlstate=2; /* Number of live states */    
 int ndeath=1; /* Number of dead states */    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */             Institut national d'études démographiques, Paris.
 int popbased=0;    This software have been partly granted by Euro-REVES, a concerted action
     from the European Union.
 int *wav; /* Number of waves for this individuual 0 is possible */    It is copyrighted identically to a GNU software product, ie programme and
 int maxwav; /* Maxim number of waves */    software can be distributed freely for non commercial use. Latest version
 int jmin, jmax; /* min, max spacing between 2 waves */    can be accessed at http://euroreves.ined.fr/imach .
 int mle, weightopt;  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 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;    main
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;    read parameterfile
 FILE *ficreseij;    read datafile
   char filerese[FILENAMELENGTH];    concatwav
  FILE  *ficresvij;    freqsummary
   char fileresv[FILENAMELENGTH];    if (mle >= 1)
  FILE  *ficresvpl;      mlikeli
   char fileresvpl[FILENAMELENGTH];    print results files
     if mle==1 
 #define NR_END 1       computes hessian
 #define FREE_ARG char*    read end of parameter file: agemin, agemax, bage, fage, estepm
 #define FTOL 1.0e-10        begin-prev-date,...
     open gnuplot file
 #define NRANSI    open html file
 #define ITMAX 200    stable prevalence
      for age prevalim()
 #define TOL 2.0e-4    h Pij x
     variance of p varprob
 #define CGOLD 0.3819660    forecasting if prevfcast==1 prevforecast call prevalence()
 #define ZEPS 1.0e-10    health expectancies
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Variance-covariance of DFLE
     prevalence()
 #define GOLD 1.618034     movingaverage()
 #define GLIMIT 100.0    varevsij() 
 #define TINY 1.0e-20    if popbased==1 varevsij(,popbased)
     total life expectancies
 static double maxarg1,maxarg2;    Variance of stable prevalence
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))   end
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  */
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  
 #define rint(a) floor(a+0.5)  
    
 static double sqrarg;  #include <math.h>
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  #include <stdio.h>
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  #include <stdlib.h>
   #include <unistd.h>
 int imx;  
 int stepm;  #define MAXLINE 256
 /* Stepm, step in month: minimum step interpolation*/  #define GNUPLOTPROGRAM "gnuplot"
   /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 int m,nb;  #define FILENAMELENGTH 132
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  /*#define DEBUG*/
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  /*#define windows*/
 double **pmmij, ***probs, ***mobaverage;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 double dateintmean=0;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
 double *weight;  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 int **s; /* Status */  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  #define NINTERVMAX 8
   #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 double ftolhess; /* Tolerance for computing hessian */  #define NCOVMAX 8 /* Maximum number of covariates */
   #define MAXN 20000
 /**************** split *************************/  #define YEARM 12. /* Number of months per year */
 static  int split( char *path, char *dirc, char *name )  #define AGESUP 130
 {  #define AGEBASE 40
    char *s;                             /* pointer */  #ifdef unix
    int  l1, l2;                         /* length counters */  #define DIRSEPARATOR '/'
   #define ODIRSEPARATOR '\\'
    l1 = strlen( path );                 /* length of path */  #else
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  #define DIRSEPARATOR '\\'
    s = strrchr( path, '\\' );           /* find last / */  #define ODIRSEPARATOR '/'
    if ( s == NULL ) {                   /* no directory, so use current */  #endif
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );  /* $Id$ */
   /* $State$ */
       if ( getwd( dirc ) == NULL ) {  
 #else  char version[]="Imach version 0.95a2, June 2003, INED-EUROREVES ";
       extern char       *getcwd( );  char fullversion[]="$Revision$ $Date$"; 
   int erreur; /* Error number */
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  int nvar;
 #endif  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
          return( GLOCK_ERROR_GETCWD );  int npar=NPARMAX;
       }  int nlstate=2; /* Number of live states */
       strcpy( name, path );             /* we've got it */  int ndeath=1; /* Number of dead states */
    } else {                             /* strip direcotry from path */  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
       s++;                              /* after this, the filename */  int popbased=0;
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  int *wav; /* Number of waves for this individuual 0 is possible */
       strcpy( name, s );                /* save file name */  int maxwav; /* Maxim number of waves */
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  int jmin, jmax; /* min, max spacing between 2 waves */
       dirc[l1-l2] = 0;                  /* add zero */  int mle, weightopt;
    }  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
    l1 = strlen( dirc );                 /* length of directory */  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
    return( 0 );                         /* we're done */             * 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;
   FILE *ficlog, *ficrespow;
 void replace(char *s, char*t)  int globpr; /* Global variable for printing or not */
 {  double fretone; /* Only one call to likelihood */
   int i;  long ipmx; /* Number of contributions */
   int lg=20;  double sw; /* Sum of weights */
   i=0;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   lg=strlen(t);  FILE *ficresilk;
   for(i=0; i<= lg; i++) {  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
     (s[i] = t[i]);  FILE *ficresprobmorprev;
     if (t[i]== '\\') s[i]='/';  FILE *fichtm; /* Html File */
   }  FILE *ficreseij;
 }  char filerese[FILENAMELENGTH];
   FILE  *ficresvij;
 int nbocc(char *s, char occ)  char fileresv[FILENAMELENGTH];
 {  FILE  *ficresvpl;
   int i,j=0;  char fileresvpl[FILENAMELENGTH];
   int lg=20;  char title[MAXLINE];
   i=0;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   lg=strlen(s);  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   }  char filelog[FILENAMELENGTH]; /* Log file */
   return j;  char filerest[FILENAMELENGTH];
 }  char fileregp[FILENAMELENGTH];
   char popfile[FILENAMELENGTH];
 void cutv(char *u,char *v, char*t, char occ)  
 {  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
   int i,lg,j,p=0;  
   i=0;  #define NR_END 1
   for(j=0; j<=strlen(t)-1; j++) {  #define FREE_ARG char*
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  #define FTOL 1.0e-10
   }  
   #define NRANSI 
   lg=strlen(t);  #define ITMAX 200 
   for(j=0; j<p; j++) {  
     (u[j] = t[j]);  #define TOL 2.0e-4 
   }  
      u[p]='\0';  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
    for(j=0; j<= lg; j++) {  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
     if (j>=(p+1))(v[j-p-1] = t[j]);  
   }  #define GOLD 1.618034 
 }  #define GLIMIT 100.0 
   #define TINY 1.0e-20 
 /********************** nrerror ********************/  
   static double maxarg1,maxarg2;
 void nrerror(char error_text[])  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 {  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   fprintf(stderr,"ERREUR ...\n");    
   fprintf(stderr,"%s\n",error_text);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   exit(1);  #define rint(a) floor(a+0.5)
 }  
 /*********************** vector *******************/  static double sqrarg;
 double *vector(int nl, int nh)  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 {  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  int imx; 
   if (!v) nrerror("allocation failure in vector");  int stepm;
   return v-nl+NR_END;  /* Stepm, step in month: minimum step interpolation*/
 }  
   int estepm;
 /************************ free vector ******************/  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 void free_vector(double*v, int nl, int nh)  
 {  int m,nb;
   free((FREE_ARG)(v+nl-NR_END));  long *num;
 }  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
   double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 /************************ivector *******************************/  double **pmmij, ***probs;
 int *ivector(long nl,long nh)  double dateintmean=0;
 {  
   int *v;  double *weight;
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  int **s; /* Status */
   if (!v) nrerror("allocation failure in ivector");  double *agedc, **covar, idx;
   return v-nl+NR_END;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 }  
   double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 /******************free ivector **************************/  double ftolhess; /* Tolerance for computing hessian */
 void free_ivector(int *v, long nl, long nh)  
 {  /**************** split *************************/
   free((FREE_ARG)(v+nl-NR_END));  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 }  {
     char  *ss;                            /* pointer */
 /******************* imatrix *******************************/    int   l1, l2;                         /* length counters */
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    l1 = strlen(path );                   /* length of path */
 {    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   int **m;    if ( ss == NULL ) {                   /* no directory, so use current */
        /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   /* allocate pointers to rows */        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));      /* get current working directory */
   if (!m) nrerror("allocation failure 1 in matrix()");      /*    extern  char* getcwd ( char *buf , int len);*/
   m += NR_END;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   m -= nrl;        return( GLOCK_ERROR_GETCWD );
        }
        strcpy( name, path );               /* we've got it */
   /* allocate rows and set pointers to them */    } else {                              /* strip direcotry from path */
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));      ss++;                               /* after this, the filename */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");      l2 = strlen( ss );                  /* length of filename */
   m[nrl] += NR_END;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   m[nrl] -= ncl;      strcpy( name, ss );         /* save file name */
        strncpy( dirc, path, l1 - l2 );     /* now the directory */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;      dirc[l1-l2] = 0;                    /* add zero */
      }
   /* return pointer to array of pointers to rows */    l1 = strlen( dirc );                  /* length of directory */
   return m;    /*#ifdef windows
 }    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   #else
 /****************** free_imatrix *************************/    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
 void free_imatrix(m,nrl,nrh,ncl,nch)  #endif
       int **m;    */
       long nch,ncl,nrh,nrl;    ss = strrchr( name, '.' );            /* find last / */
      /* free an int matrix allocated by imatrix() */    ss++;
 {    strcpy(ext,ss);                       /* save extension */
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    l1= strlen( name);
   free((FREE_ARG) (m+nrl-NR_END));    l2= strlen(ss)+1;
 }    strncpy( finame, name, l1-l2);
     finame[l1-l2]= 0;
 /******************* matrix *******************************/    return( 0 );                          /* we're done */
 double **matrix(long nrl, long nrh, long ncl, long nch)  }
 {  
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;  /******************************************/
   
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  void replace(char *s, char*t)
   if (!m) nrerror("allocation failure 1 in matrix()");  {
   m += NR_END;    int i;
   m -= nrl;    int lg=20;
     i=0;
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    lg=strlen(t);
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    for(i=0; i<= lg; i++) {
   m[nrl] += NR_END;      (s[i] = t[i]);
   m[nrl] -= ncl;      if (t[i]== '\\') s[i]='/';
     }
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  }
   return m;  
 }  int nbocc(char *s, char occ)
   {
 /*************************free matrix ************************/    int i,j=0;
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    int lg=20;
 {    i=0;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    lg=strlen(s);
   free((FREE_ARG)(m+nrl-NR_END));    for(i=0; i<= lg; i++) {
 }    if  (s[i] == occ ) j++;
     }
 /******************* ma3x *******************************/    return j;
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  }
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  void cutv(char *u,char *v, char*t, char occ)
   double ***m;  {
     /* cuts string t into u and v where u is ended by char occ excluding it
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   if (!m) nrerror("allocation failure 1 in matrix()");       gives u="abcedf" and v="ghi2j" */
   m += NR_END;    int i,lg,j,p=0;
   m -= nrl;    i=0;
     for(j=0; j<=strlen(t)-1; j++) {
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    }
   m[nrl] += NR_END;  
   m[nrl] -= ncl;    lg=strlen(t);
     for(j=0; j<p; j++) {
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;      (u[j] = t[j]);
     }
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));       u[p]='\0';
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;     for(j=0; j<= lg; j++) {
   m[nrl][ncl] -= nll;      if (j>=(p+1))(v[j-p-1] = t[j]);
   for (j=ncl+1; j<=nch; j++)    }
     m[nrl][j]=m[nrl][j-1]+nlay;  }
    
   for (i=nrl+1; i<=nrh; i++) {  /********************** nrerror ********************/
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)  void nrerror(char error_text[])
       m[i][j]=m[i][j-1]+nlay;  {
   }    fprintf(stderr,"ERREUR ...\n");
   return m;    fprintf(stderr,"%s\n",error_text);
 }    exit(EXIT_FAILURE);
   }
 /*************************free ma3x ************************/  /*********************** vector *******************/
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  double *vector(int nl, int nh)
 {  {
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    double *v;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   free((FREE_ARG)(m+nrl-NR_END));    if (!v) nrerror("allocation failure in vector");
 }    return v-nl+NR_END;
   }
 /***************** f1dim *************************/  
 extern int ncom;  /************************ free vector ******************/
 extern double *pcom,*xicom;  void free_vector(double*v, int nl, int nh)
 extern double (*nrfunc)(double []);  {
      free((FREE_ARG)(v+nl-NR_END));
 double f1dim(double x)  }
 {  
   int j;  /************************ivector *******************************/
   double f;  int *ivector(long nl,long nh)
   double *xt;  {
      int *v;
   xt=vector(1,ncom);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    if (!v) nrerror("allocation failure in ivector");
   f=(*nrfunc)(xt);    return v-nl+NR_END;
   free_vector(xt,1,ncom);  }
   return f;  
 }  /******************free ivector **************************/
   void free_ivector(int *v, long nl, long nh)
 /*****************brent *************************/  {
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    free((FREE_ARG)(v+nl-NR_END));
 {  }
   int iter;  
   double a,b,d,etemp;  /************************lvector *******************************/
   double fu,fv,fw,fx;  long *lvector(long nl,long nh)
   double ftemp;  {
   double p,q,r,tol1,tol2,u,v,w,x,xm;    long *v;
   double e=0.0;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
      if (!v) nrerror("allocation failure in ivector");
   a=(ax < cx ? ax : cx);    return v-nl+NR_END;
   b=(ax > cx ? ax : cx);  }
   x=w=v=bx;  
   fw=fv=fx=(*f)(x);  /******************free lvector **************************/
   for (iter=1;iter<=ITMAX;iter++) {  void free_lvector(long *v, long nl, long nh)
     xm=0.5*(a+b);  {
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    free((FREE_ARG)(v+nl-NR_END));
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  }
     printf(".");fflush(stdout);  
 #ifdef DEBUG  /******************* imatrix *******************************/
     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);  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 #endif  { 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       *xmin=x;    int **m; 
       return fx;    
     }    /* allocate pointers to rows */ 
     ftemp=fu;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     if (fabs(e) > tol1) {    if (!m) nrerror("allocation failure 1 in matrix()"); 
       r=(x-w)*(fx-fv);    m += NR_END; 
       q=(x-v)*(fx-fw);    m -= nrl; 
       p=(x-v)*q-(x-w)*r;    
       q=2.0*(q-r);    
       if (q > 0.0) p = -p;    /* allocate rows and set pointers to them */ 
       q=fabs(q);    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
       etemp=e;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       e=d;    m[nrl] += NR_END; 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    m[nrl] -= ncl; 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    
       else {    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
         d=p/q;    
         u=x+d;    /* return pointer to array of pointers to rows */ 
         if (u-a < tol2 || b-u < tol2)    return m; 
           d=SIGN(tol1,xm-x);  } 
       }  
     } else {  /****************** free_imatrix *************************/
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  void free_imatrix(m,nrl,nrh,ncl,nch)
     }        int **m;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));        long nch,ncl,nrh,nrl; 
     fu=(*f)(u);       /* free an int matrix allocated by imatrix() */ 
     if (fu <= fx) {  { 
       if (u >= x) a=x; else b=x;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       SHFT(v,w,x,u)    free((FREE_ARG) (m+nrl-NR_END)); 
         SHFT(fv,fw,fx,fu)  } 
         } else {  
           if (u < x) a=u; else b=u;  /******************* matrix *******************************/
           if (fu <= fw || w == x) {  double **matrix(long nrl, long nrh, long ncl, long nch)
             v=w;  {
             w=u;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
             fv=fw;    double **m;
             fw=fu;  
           } else if (fu <= fv || v == x || v == w) {    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
             v=u;    if (!m) nrerror("allocation failure 1 in matrix()");
             fv=fu;    m += NR_END;
           }    m -= nrl;
         }  
   }    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   nrerror("Too many iterations in brent");    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   *xmin=x;    m[nrl] += NR_END;
   return fx;    m[nrl] -= ncl;
 }  
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 /****************** mnbrak ***********************/    return m;
     /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,     */
             double (*func)(double))  }
 {  
   double ulim,u,r,q, dum;  /*************************free matrix ************************/
   double fu;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
    {
   *fa=(*func)(*ax);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   *fb=(*func)(*bx);    free((FREE_ARG)(m+nrl-NR_END));
   if (*fb > *fa) {  }
     SHFT(dum,*ax,*bx,dum)  
       SHFT(dum,*fb,*fa,dum)  /******************* ma3x *******************************/
       }  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   *cx=(*bx)+GOLD*(*bx-*ax);  {
   *fc=(*func)(*cx);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   while (*fb > *fc) {    double ***m;
     r=(*bx-*ax)*(*fb-*fc);  
     q=(*bx-*cx)*(*fb-*fa);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    if (!m) nrerror("allocation failure 1 in matrix()");
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    m += NR_END;
     ulim=(*bx)+GLIMIT*(*cx-*bx);    m -= nrl;
     if ((*bx-u)*(u-*cx) > 0.0) {  
       fu=(*func)(u);    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     } else if ((*cx-u)*(u-ulim) > 0.0) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       fu=(*func)(u);    m[nrl] += NR_END;
       if (fu < *fc) {    m[nrl] -= ncl;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
           }  
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       u=ulim;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       fu=(*func)(u);    m[nrl][ncl] += NR_END;
     } else {    m[nrl][ncl] -= nll;
       u=(*cx)+GOLD*(*cx-*bx);    for (j=ncl+1; j<=nch; j++) 
       fu=(*func)(u);      m[nrl][j]=m[nrl][j-1]+nlay;
     }    
     SHFT(*ax,*bx,*cx,u)    for (i=nrl+1; i<=nrh; i++) {
       SHFT(*fa,*fb,*fc,fu)      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       }      for (j=ncl+1; j<=nch; j++) 
 }        m[i][j]=m[i][j-1]+nlay;
     }
 /*************** linmin ************************/    return m; 
     /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
 int ncom;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
 double *pcom,*xicom;    */
 double (*nrfunc)(double []);  }
    
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  /*************************free ma3x ************************/
 {  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   double brent(double ax, double bx, double cx,  {
                double (*f)(double), double tol, double *xmin);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   double f1dim(double x);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    free((FREE_ARG)(m+nrl-NR_END));
               double *fc, double (*func)(double));  }
   int j;  
   double xx,xmin,bx,ax;  /***************** f1dim *************************/
   double fx,fb,fa;  extern int ncom; 
    extern double *pcom,*xicom;
   ncom=n;  extern double (*nrfunc)(double []); 
   pcom=vector(1,n);   
   xicom=vector(1,n);  double f1dim(double x) 
   nrfunc=func;  { 
   for (j=1;j<=n;j++) {    int j; 
     pcom[j]=p[j];    double f;
     xicom[j]=xi[j];    double *xt; 
   }   
   ax=0.0;    xt=vector(1,ncom); 
   xx=1.0;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    f=(*nrfunc)(xt); 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    free_vector(xt,1,ncom); 
 #ifdef DEBUG    return f; 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  } 
 #endif  
   for (j=1;j<=n;j++) {  /*****************brent *************************/
     xi[j] *= xmin;  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     p[j] += xi[j];  { 
   }    int iter; 
   free_vector(xicom,1,n);    double a,b,d,etemp;
   free_vector(pcom,1,n);    double fu,fv,fw,fx;
 }    double ftemp;
     double p,q,r,tol1,tol2,u,v,w,x,xm; 
 /*************** powell ************************/    double e=0.0; 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,   
             double (*func)(double []))    a=(ax < cx ? ax : cx); 
 {    b=(ax > cx ? ax : cx); 
   void linmin(double p[], double xi[], int n, double *fret,    x=w=v=bx; 
               double (*func)(double []));    fw=fv=fx=(*f)(x); 
   int i,ibig,j;    for (iter=1;iter<=ITMAX;iter++) { 
   double del,t,*pt,*ptt,*xit;      xm=0.5*(a+b); 
   double fp,fptt;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   double *xits;      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   pt=vector(1,n);      printf(".");fflush(stdout);
   ptt=vector(1,n);      fprintf(ficlog,".");fflush(ficlog);
   xit=vector(1,n);  #ifdef DEBUG
   xits=vector(1,n);      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);
   *fret=(*func)(p);      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);
   for (j=1;j<=n;j++) pt[j]=p[j];      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   for (*iter=1;;++(*iter)) {  #endif
     fp=(*fret);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
     ibig=0;        *xmin=x; 
     del=0.0;        return fx; 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      } 
     for (i=1;i<=n;i++)      ftemp=fu;
       printf(" %d %.12f",i, p[i]);      if (fabs(e) > tol1) { 
     printf("\n");        r=(x-w)*(fx-fv); 
     for (i=1;i<=n;i++) {        q=(x-v)*(fx-fw); 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];        p=(x-v)*q-(x-w)*r; 
       fptt=(*fret);        q=2.0*(q-r); 
 #ifdef DEBUG        if (q > 0.0) p = -p; 
       printf("fret=%lf \n",*fret);        q=fabs(q); 
 #endif        etemp=e; 
       printf("%d",i);fflush(stdout);        e=d; 
       linmin(p,xit,n,fret,func);        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
       if (fabs(fptt-(*fret)) > del) {          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         del=fabs(fptt-(*fret));        else { 
         ibig=i;          d=p/q; 
       }          u=x+d; 
 #ifdef DEBUG          if (u-a < tol2 || b-u < tol2) 
       printf("%d %.12e",i,(*fret));            d=SIGN(tol1,xm-x); 
       for (j=1;j<=n;j++) {        } 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);      } else { 
         printf(" x(%d)=%.12e",j,xit[j]);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       }      } 
       for(j=1;j<=n;j++)      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
         printf(" p=%.12e",p[j]);      fu=(*f)(u); 
       printf("\n");      if (fu <= fx) { 
 #endif        if (u >= x) a=x; else b=x; 
     }        SHFT(v,w,x,u) 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {          SHFT(fv,fw,fx,fu) 
 #ifdef DEBUG          } else { 
       int k[2],l;            if (u < x) a=u; else b=u; 
       k[0]=1;            if (fu <= fw || w == x) { 
       k[1]=-1;              v=w; 
       printf("Max: %.12e",(*func)(p));              w=u; 
       for (j=1;j<=n;j++)              fv=fw; 
         printf(" %.12e",p[j]);              fw=fu; 
       printf("\n");            } else if (fu <= fv || v == x || v == w) { 
       for(l=0;l<=1;l++) {              v=u; 
         for (j=1;j<=n;j++) {              fv=fu; 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];            } 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);          } 
         }    } 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    nrerror("Too many iterations in brent"); 
       }    *xmin=x; 
 #endif    return fx; 
   } 
   
       free_vector(xit,1,n);  /****************** mnbrak ***********************/
       free_vector(xits,1,n);  
       free_vector(ptt,1,n);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       free_vector(pt,1,n);              double (*func)(double)) 
       return;  { 
     }    double ulim,u,r,q, dum;
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    double fu; 
     for (j=1;j<=n;j++) {   
       ptt[j]=2.0*p[j]-pt[j];    *fa=(*func)(*ax); 
       xit[j]=p[j]-pt[j];    *fb=(*func)(*bx); 
       pt[j]=p[j];    if (*fb > *fa) { 
     }      SHFT(dum,*ax,*bx,dum) 
     fptt=(*func)(ptt);        SHFT(dum,*fb,*fa,dum) 
     if (fptt < fp) {        } 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    *cx=(*bx)+GOLD*(*bx-*ax); 
       if (t < 0.0) {    *fc=(*func)(*cx); 
         linmin(p,xit,n,fret,func);    while (*fb > *fc) { 
         for (j=1;j<=n;j++) {      r=(*bx-*ax)*(*fb-*fc); 
           xi[j][ibig]=xi[j][n];      q=(*bx-*cx)*(*fb-*fa); 
           xi[j][n]=xit[j];      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         }        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 #ifdef DEBUG      ulim=(*bx)+GLIMIT*(*cx-*bx); 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      if ((*bx-u)*(u-*cx) > 0.0) { 
         for(j=1;j<=n;j++)        fu=(*func)(u); 
           printf(" %.12e",xit[j]);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
         printf("\n");        fu=(*func)(u); 
 #endif        if (fu < *fc) { 
       }          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     }            SHFT(*fb,*fc,fu,(*func)(u)) 
   }            } 
 }      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
         u=ulim; 
 /**** Prevalence limit ****************/        fu=(*func)(u); 
       } else { 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)        u=(*cx)+GOLD*(*cx-*bx); 
 {        fu=(*func)(u); 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit      } 
      matrix by transitions matrix until convergence is reached */      SHFT(*ax,*bx,*cx,u) 
         SHFT(*fa,*fb,*fc,fu) 
   int i, ii,j,k;        } 
   double min, max, maxmin, maxmax,sumnew=0.;  } 
   double **matprod2();  
   double **out, cov[NCOVMAX], **pmij();  /*************** linmin ************************/
   double **newm;  
   double agefin, delaymax=50 ; /* Max number of years to converge */  int ncom; 
   double *pcom,*xicom;
   for (ii=1;ii<=nlstate+ndeath;ii++)  double (*nrfunc)(double []); 
     for (j=1;j<=nlstate+ndeath;j++){   
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     }  { 
     double brent(double ax, double bx, double cx, 
    cov[1]=1.;                 double (*f)(double), double tol, double *xmin); 
      double f1dim(double x); 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){                double *fc, double (*func)(double)); 
     newm=savm;    int j; 
     /* Covariates have to be included here again */    double xx,xmin,bx,ax; 
      cov[2]=agefin;    double fx,fb,fa;
     
       for (k=1; k<=cptcovn;k++) {    ncom=n; 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    pcom=vector(1,n); 
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/    xicom=vector(1,n); 
       }    nrfunc=func; 
       for (k=1; k<=cptcovage;k++)    for (j=1;j<=n;j++) { 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      pcom[j]=p[j]; 
       for (k=1; k<=cptcovprod;k++)      xicom[j]=xi[j]; 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    } 
     ax=0.0; 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    xx=1.0; 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  #ifdef DEBUG
     printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     savm=oldm;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     oldm=newm;  #endif
     maxmax=0.;    for (j=1;j<=n;j++) { 
     for(j=1;j<=nlstate;j++){      xi[j] *= xmin; 
       min=1.;      p[j] += xi[j]; 
       max=0.;    } 
       for(i=1; i<=nlstate; i++) {    free_vector(xicom,1,n); 
         sumnew=0;    free_vector(pcom,1,n); 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  } 
         prlim[i][j]= newm[i][j]/(1-sumnew);  
         max=FMAX(max,prlim[i][j]);  /*************** powell ************************/
         min=FMIN(min,prlim[i][j]);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       }              double (*func)(double [])) 
       maxmin=max-min;  { 
       maxmax=FMAX(maxmax,maxmin);    void linmin(double p[], double xi[], int n, double *fret, 
     }                double (*func)(double [])); 
     if(maxmax < ftolpl){    int i,ibig,j; 
       return prlim;    double del,t,*pt,*ptt,*xit;
     }    double fp,fptt;
   }    double *xits;
 }    pt=vector(1,n); 
     ptt=vector(1,n); 
 /*************** transition probabilities ***************/    xit=vector(1,n); 
     xits=vector(1,n); 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    *fret=(*func)(p); 
 {    for (j=1;j<=n;j++) pt[j]=p[j]; 
   double s1, s2;    for (*iter=1;;++(*iter)) { 
   /*double t34;*/      fp=(*fret); 
   int i,j,j1, nc, ii, jj;      ibig=0; 
       del=0.0; 
     for(i=1; i<= nlstate; i++){      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
     for(j=1; j<i;j++){      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      fprintf(ficrespow,"%d %.12f",*iter,*fret);
         /*s2 += param[i][j][nc]*cov[nc];*/      for (i=1;i<=n;i++) {
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        printf(" %d %.12f",i, p[i]);
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/        fprintf(ficlog," %d %.12lf",i, p[i]);
       }        fprintf(ficrespow," %.12lf", p[i]);
       ps[i][j]=s2;      }
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/      printf("\n");
     }      fprintf(ficlog,"\n");
     for(j=i+1; j<=nlstate+ndeath;j++){      fprintf(ficrespow,"\n");
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      for (i=1;i<=n;i++) { 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/        fptt=(*fret); 
       }  #ifdef DEBUG
       ps[i][j]=(s2);        printf("fret=%lf \n",*fret);
     }        fprintf(ficlog,"fret=%lf \n",*fret);
   }  #endif
     /*ps[3][2]=1;*/        printf("%d",i);fflush(stdout);
         fprintf(ficlog,"%d",i);fflush(ficlog);
   for(i=1; i<= nlstate; i++){        linmin(p,xit,n,fret,func); 
      s1=0;        if (fabs(fptt-(*fret)) > del) { 
     for(j=1; j<i; j++)          del=fabs(fptt-(*fret)); 
       s1+=exp(ps[i][j]);          ibig=i; 
     for(j=i+1; j<=nlstate+ndeath; j++)        } 
       s1+=exp(ps[i][j]);  #ifdef DEBUG
     ps[i][i]=1./(s1+1.);        printf("%d %.12e",i,(*fret));
     for(j=1; j<i; j++)        fprintf(ficlog,"%d %.12e",i,(*fret));
       ps[i][j]= exp(ps[i][j])*ps[i][i];        for (j=1;j<=n;j++) {
     for(j=i+1; j<=nlstate+ndeath; j++)          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       ps[i][j]= exp(ps[i][j])*ps[i][i];          printf(" x(%d)=%.12e",j,xit[j]);
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   } /* end i */        }
         for(j=1;j<=n;j++) {
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){          printf(" p=%.12e",p[j]);
     for(jj=1; jj<= nlstate+ndeath; jj++){          fprintf(ficlog," p=%.12e",p[j]);
       ps[ii][jj]=0;        }
       ps[ii][ii]=1;        printf("\n");
     }        fprintf(ficlog,"\n");
   }  #endif
       } 
       if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  #ifdef DEBUG
     for(jj=1; jj<= nlstate+ndeath; jj++){        int k[2],l;
      printf("%lf ",ps[ii][jj]);        k[0]=1;
    }        k[1]=-1;
     printf("\n ");        printf("Max: %.12e",(*func)(p));
     }        fprintf(ficlog,"Max: %.12e",(*func)(p));
     printf("\n ");printf("%lf ",cov[2]);*/        for (j=1;j<=n;j++) {
 /*          printf(" %.12e",p[j]);
   for(i=1; i<= npar; i++) printf("%f ",x[i]);          fprintf(ficlog," %.12e",p[j]);
   goto end;*/        }
     return ps;        printf("\n");
 }        fprintf(ficlog,"\n");
         for(l=0;l<=1;l++) {
 /**************** Product of 2 matrices ******************/          for (j=1;j<=n;j++) {
             ptt[j]=p[j]+(p[j]-pt[j])*k[l];
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 {            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times          }
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   /* in, b, out are matrice of pointers which should have been initialized          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
      before: only the contents of out is modified. The function returns        }
      a pointer to pointers identical to out */  #endif
   long i, j, k;  
   for(i=nrl; i<= nrh; i++)  
     for(k=ncolol; k<=ncoloh; k++)        free_vector(xit,1,n); 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        free_vector(xits,1,n); 
         out[i][k] +=in[i][j]*b[j][k];        free_vector(ptt,1,n); 
         free_vector(pt,1,n); 
   return out;        return; 
 }      } 
       if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       for (j=1;j<=n;j++) { 
 /************* Higher Matrix Product ***************/        ptt[j]=2.0*p[j]-pt[j]; 
         xit[j]=p[j]-pt[j]; 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )        pt[j]=p[j]; 
 {      } 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      fptt=(*func)(ptt); 
      duration (i.e. until      if (fptt < fp) { 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        if (t < 0.0) { 
      (typically every 2 years instead of every month which is too big).          linmin(p,xit,n,fret,func); 
      Model is determined by parameters x and covariates have to be          for (j=1;j<=n;j++) { 
      included manually here.            xi[j][ibig]=xi[j][n]; 
             xi[j][n]=xit[j]; 
      */          }
   #ifdef DEBUG
   int i, j, d, h, k;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   double **out, cov[NCOVMAX];          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   double **newm;          for(j=1;j<=n;j++){
             printf(" %.12e",xit[j]);
   /* Hstepm could be zero and should return the unit matrix */            fprintf(ficlog," %.12e",xit[j]);
   for (i=1;i<=nlstate+ndeath;i++)          }
     for (j=1;j<=nlstate+ndeath;j++){          printf("\n");
       oldm[i][j]=(i==j ? 1.0 : 0.0);          fprintf(ficlog,"\n");
       po[i][j][0]=(i==j ? 1.0 : 0.0);  #endif
     }        }
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      } 
   for(h=1; h <=nhstepm; h++){    } 
     for(d=1; d <=hstepm; d++){  } 
       newm=savm;  
       /* Covariates have to be included here again */  /**** Prevalence limit (stable prevalence)  ****************/
       cov[1]=1.;  
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  {
       for (k=1; k<=cptcovage;k++)    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];       matrix by transitions matrix until convergence is reached */
       for (k=1; k<=cptcovprod;k++)  
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    int i, ii,j,k;
     double min, max, maxmin, maxmax,sumnew=0.;
     double **matprod2();
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/    double **out, cov[NCOVMAX], **pmij();
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    double **newm;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,    double agefin, delaymax=50 ; /* Max number of years to converge */
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  
       savm=oldm;    for (ii=1;ii<=nlstate+ndeath;ii++)
       oldm=newm;      for (j=1;j<=nlstate+ndeath;j++){
     }        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(i=1; i<=nlstate+ndeath; i++)      }
       for(j=1;j<=nlstate+ndeath;j++) {  
         po[i][j][h]=newm[i][j];     cov[1]=1.;
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);   
          */   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       }    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   } /* end h */      newm=savm;
   return po;      /* Covariates have to be included here again */
 }       cov[2]=agefin;
     
         for (k=1; k<=cptcovn;k++) {
 /*************** log-likelihood *************/          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
 double func( double *x)          /*      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]]);*/
 {        }
   int i, ii, j, k, mi, d, kk;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        for (k=1; k<=cptcovprod;k++)
   double **out;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   double sw; /* Sum of weights */  
   double lli; /* Individual log likelihood */        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   long ipmx;        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   /*extern weight */        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   /* We are differentiating ll according to initial status */      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  
   /*for(i=1;i<imx;i++)      savm=oldm;
     printf(" %d\n",s[4][i]);      oldm=newm;
   */      maxmax=0.;
   cov[1]=1.;      for(j=1;j<=nlstate;j++){
         min=1.;
   for(k=1; k<=nlstate; k++) ll[k]=0.;        max=0.;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        for(i=1; i<=nlstate; i++) {
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];          sumnew=0;
     for(mi=1; mi<= wav[i]-1; mi++){          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       for (ii=1;ii<=nlstate+ndeath;ii++)          prlim[i][j]= newm[i][j]/(1-sumnew);
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);          max=FMAX(max,prlim[i][j]);
       for(d=0; d<dh[mi][i]; d++){          min=FMIN(min,prlim[i][j]);
         newm=savm;        }
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;        maxmin=max-min;
         for (kk=1; kk<=cptcovage;kk++) {        maxmax=FMAX(maxmax,maxmin);
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];      }
         }      if(maxmax < ftolpl){
                return prlim;
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      }
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    }
         savm=oldm;  }
         oldm=newm;  
          /*************** transition probabilities ***************/ 
          
       } /* end mult */  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
        {
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    double s1, s2;
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    /*double t34;*/
       ipmx +=1;    int i,j,j1, nc, ii, jj;
       sw += weight[i];  
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;      for(i=1; i<= nlstate; i++){
     } /* end of wave */      for(j=1; j<i;j++){
   } /* end of individual */        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
           /*s2 += param[i][j][nc]*cov[nc];*/
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        }
   return -l;        ps[i][j]=s2;
 }        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
       }
       for(j=i+1; j<=nlstate+ndeath;j++){
 /*********** Maximum Likelihood Estimation ***************/        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
           s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
 {        }
   int i,j, iter;        ps[i][j]=s2;
   double **xi,*delti;      }
   double fret;    }
   xi=matrix(1,npar,1,npar);      /*ps[3][2]=1;*/
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++)    for(i=1; i<= nlstate; i++){
       xi[i][j]=(i==j ? 1.0 : 0.0);       s1=0;
   printf("Powell\n");      for(j=1; j<i; j++)
   powell(p,xi,npar,ftol,&iter,&fret,func);        s1+=exp(ps[i][j]);
       for(j=i+1; j<=nlstate+ndeath; j++)
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        s1+=exp(ps[i][j]);
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));      ps[i][i]=1./(s1+1.);
       for(j=1; j<i; j++)
 }        ps[i][j]= exp(ps[i][j])*ps[i][i];
       for(j=i+1; j<=nlstate+ndeath; j++)
 /**** Computes Hessian and covariance matrix ***/        ps[i][j]= exp(ps[i][j])*ps[i][i];
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
 {    } /* end i */
   double  **a,**y,*x,pd;  
   double **hess;    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   int i, j,jk;      for(jj=1; jj<= nlstate+ndeath; jj++){
   int *indx;        ps[ii][jj]=0;
         ps[ii][ii]=1;
   double hessii(double p[], double delta, int theta, double delti[]);      }
   double hessij(double p[], double delti[], int i, int j);    }
   void lubksb(double **a, int npar, int *indx, double b[]) ;  
   void ludcmp(double **a, int npar, int *indx, double *d) ;  
     /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   hess=matrix(1,npar,1,npar);      for(jj=1; jj<= nlstate+ndeath; jj++){
        printf("%lf ",ps[ii][jj]);
   printf("\nCalculation of the hessian matrix. Wait...\n");     }
   for (i=1;i<=npar;i++){      printf("\n ");
     printf("%d",i);fflush(stdout);      }
     hess[i][i]=hessii(p,ftolhess,i,delti);      printf("\n ");printf("%lf ",cov[2]);*/
     /*printf(" %f ",p[i]);*/  /*
     /*printf(" %lf ",hess[i][i]);*/    for(i=1; i<= npar; i++) printf("%f ",x[i]);
   }    goto end;*/
        return ps;
   for (i=1;i<=npar;i++) {  }
     for (j=1;j<=npar;j++)  {  
       if (j>i) {  /**************** Product of 2 matrices ******************/
         printf(".%d%d",i,j);fflush(stdout);  
         hess[i][j]=hessij(p,delti,i,j);  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
         hess[j][i]=hess[i][j];      {
         /*printf(" %lf ",hess[i][j]);*/    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       }       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     }    /* in, b, out are matrice of pointers which should have been initialized 
   }       before: only the contents of out is modified. The function returns
   printf("\n");       a pointer to pointers identical to out */
     long i, j, k;
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    for(i=nrl; i<= nrh; i++)
        for(k=ncolol; k<=ncoloh; k++)
   a=matrix(1,npar,1,npar);        for(j=ncl,out[i][k]=0.; j<=nch; j++)
   y=matrix(1,npar,1,npar);          out[i][k] +=in[i][j]*b[j][k];
   x=vector(1,npar);  
   indx=ivector(1,npar);    return out;
   for (i=1;i<=npar;i++)  }
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  
   ludcmp(a,npar,indx,&pd);  
   /************* Higher Matrix Product ***************/
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     x[j]=1;  {
     lubksb(a,npar,indx,x);    /* Computes the transition matrix starting at age 'age' over 
     for (i=1;i<=npar;i++){       'nhstepm*hstepm*stepm' months (i.e. until
       matcov[i][j]=x[i];       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
     }       nhstepm*hstepm matrices. 
   }       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
        (typically every 2 years instead of every month which is too big 
   printf("\n#Hessian matrix#\n");       for the memory).
   for (i=1;i<=npar;i++) {       Model is determined by parameters x and covariates have to be 
     for (j=1;j<=npar;j++) {       included manually here. 
       printf("%.3e ",hess[i][j]);  
     }       */
     printf("\n");  
   }    int i, j, d, h, k;
     double **out, cov[NCOVMAX];
   /* Recompute Inverse */    double **newm;
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    /* Hstepm could be zero and should return the unit matrix */
   ludcmp(a,npar,indx,&pd);    for (i=1;i<=nlstate+ndeath;i++)
       for (j=1;j<=nlstate+ndeath;j++){
   /*  printf("\n#Hessian matrix recomputed#\n");        oldm[i][j]=(i==j ? 1.0 : 0.0);
         po[i][j][0]=(i==j ? 1.0 : 0.0);
   for (j=1;j<=npar;j++) {      }
     for (i=1;i<=npar;i++) x[i]=0;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     x[j]=1;    for(h=1; h <=nhstepm; h++){
     lubksb(a,npar,indx,x);      for(d=1; d <=hstepm; d++){
     for (i=1;i<=npar;i++){        newm=savm;
       y[i][j]=x[i];        /* Covariates have to be included here again */
       printf("%.3e ",y[i][j]);        cov[1]=1.;
     }        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     printf("\n");        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];
         for (k=1; k<=cptcovprod;k++)
   free_matrix(a,1,npar,1,npar);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   free_matrix(y,1,npar,1,npar);  
   free_vector(x,1,npar);  
   free_ivector(indx,1,npar);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   free_matrix(hess,1,npar,1,npar);        /*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, 
                      pmij(pmmij,cov,ncovmodel,x,nlstate));
 }        savm=oldm;
         oldm=newm;
 /*************** hessian matrix ****************/      }
 double hessii( double x[], double delta, int theta, double delti[])      for(i=1; i<=nlstate+ndeath; i++)
 {        for(j=1;j<=nlstate+ndeath;j++) {
   int i;          po[i][j][h]=newm[i][j];
   int l=1, lmax=20;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
   double k1,k2;           */
   double p2[NPARMAX+1];        }
   double res;    } /* end h */
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    return po;
   double fx;  }
   int k=0,kmax=10;  
   double l1;  
   /*************** log-likelihood *************/
   fx=func(x);  double func( double *x)
   for (i=1;i<=npar;i++) p2[i]=x[i];  {
   for(l=0 ; l <=lmax; l++){    int i, ii, j, k, mi, d, kk;
     l1=pow(10,l);    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     delts=delt;    double **out;
     for(k=1 ; k <kmax; k=k+1){    double sw; /* Sum of weights */
       delt = delta*(l1*k);    double lli; /* Individual log likelihood */
       p2[theta]=x[theta] +delt;    int s1, s2;
       k1=func(p2)-fx;    double bbh, survp;
       p2[theta]=x[theta]-delt;    long ipmx;
       k2=func(p2)-fx;    /*extern weight */
       /*res= (k1-2.0*fx+k2)/delt/delt; */    /* We are differentiating ll according to initial status */
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
          /*for(i=1;i<imx;i++) 
 #ifdef DEBUG      printf(" %d\n",s[4][i]);
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);    */
 #endif    cov[1]=1.;
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    for(k=1; k<=nlstate; k++) ll[k]=0.;
         k=kmax;  
       }    if(mle==1){
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         k=kmax; l=lmax*10.;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       }        for(mi=1; mi<= wav[i]-1; mi++){
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          for (ii=1;ii<=nlstate+ndeath;ii++)
         delts=delt;            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);
   }            }
   delti[theta]=delts;          for(d=0; d<dh[mi][i]; d++){
   return res;            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 }            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
 double hessij( double x[], double delti[], int thetai,int thetaj)            }
 {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int i;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   int l=1, l1, lmax=20;            savm=oldm;
   double k1,k2,k3,k4,res,fx;            oldm=newm;
   double p2[NPARMAX+1];          } /* end mult */
   int k;        
           /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   fx=func(x);          /* But now since version 0.9 we anticipate for bias and large stepm.
   for (k=1; k<=2; k++) {           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     for (i=1;i<=npar;i++) p2[i]=x[i];           * (in months) between two waves is not a multiple of stepm, we rounded to 
     p2[thetai]=x[thetai]+delti[thetai]/k;           * the nearest (and in case of equal distance, to the lowest) interval but now
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     k1=func(p2)-fx;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
             * probability in order to take into account the bias as a fraction of the way
     p2[thetai]=x[thetai]+delti[thetai]/k;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;           * -stepm/2 to stepm/2 .
     k2=func(p2)-fx;           * 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. 
     p2[thetai]=x[thetai]-delti[thetai]/k;           */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          s1=s[mw[mi][i]][i];
     k3=func(p2)-fx;          s2=s[mw[mi+1][i]][i];
            bbh=(double)bh[mi][i]/(double)stepm; 
     p2[thetai]=x[thetai]-delti[thetai]/k;          /* bias is positive if real duration
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;           * is higher than the multiple of stepm and negative otherwise.
     k4=func(p2)-fx;           */
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
 #ifdef DEBUG          if( s2 > nlstate){ 
     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);            /* i.e. if s2 is a death state and if the date of death is known then the contribution
 #endif               to the likelihood is the probability to die between last step unit time and current 
   }               step unit time, which is also the differences between probability to die before dh 
   return res;               and probability to die before dh-stepm . 
 }               In version up to 0.92 likelihood was computed
           as if date of death was unknown. Death was treated as any other
 /************** Inverse of matrix **************/          health state: the date of the interview describes the actual state
 void ludcmp(double **a, int n, int *indx, double *d)          and not the date of a change in health state. The former idea was
 {          to consider that at each interview the state was recorded
   int i,imax,j,k;          (healthy, disable or death) and IMaCh was corrected; but when we
   double big,dum,sum,temp;          introduced the exact date of death then we should have modified
   double *vv;          the contribution of an exact death to the likelihood. This new
            contribution is smaller and very dependent of the step unit
   vv=vector(1,n);          stepm. It is no more the probability to die between last interview
   *d=1.0;          and month of death but the probability to survive from last
   for (i=1;i<=n;i++) {          interview up to one month before death multiplied by the
     big=0.0;          probability to die within a month. Thanks to Chris
     for (j=1;j<=n;j++)          Jackson for correcting this bug.  Former versions increased
       if ((temp=fabs(a[i][j])) > big) big=temp;          mortality artificially. The bad side is that we add another loop
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          which slows down the processing. The difference can be up to 10%
     vv[i]=1.0/big;          lower mortality.
   }            */
   for (j=1;j<=n;j++) {            lli=log(out[s1][s2] - savm[s1][s2]);
     for (i=1;i<j;i++) {          }else{
       sum=a[i][j];            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][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 */
       a[i][j]=sum;          } 
     }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     big=0.0;          /*if(lli ==000.0)*/
     for (i=j;i<=n;i++) {          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
       sum=a[i][j];          ipmx +=1;
       for (k=1;k<j;k++)          sw += weight[i];
         sum -= a[i][k]*a[k][j];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       a[i][j]=sum;        } /* end of wave */
       if ( (dum=vv[i]*fabs(sum)) >= big) {      } /* end of individual */
         big=dum;    }  else if(mle==2){
         imax=i;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     }        for(mi=1; mi<= wav[i]-1; mi++){
     if (j != imax) {          for (ii=1;ii<=nlstate+ndeath;ii++)
       for (k=1;k<=n;k++) {            for (j=1;j<=nlstate+ndeath;j++){
         dum=a[imax][k];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         a[imax][k]=a[j][k];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         a[j][k]=dum;            }
       }          for(d=0; d<=dh[mi][i]; d++){
       *d = -(*d);            newm=savm;
       vv[imax]=vv[j];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     }            for (kk=1; kk<=cptcovage;kk++) {
     indx[j]=imax;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     if (a[j][j] == 0.0) a[j][j]=TINY;            }
     if (j != n) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       dum=1.0/(a[j][j]);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for (i=j+1;i<=n;i++) a[i][j] *= dum;            savm=oldm;
     }            oldm=newm;
   }          } /* end mult */
   free_vector(vv,1,n);  /* Doesn't work */        
 ;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
 }          /* But now since version 0.9 we anticipate for bias and large stepm.
            * If stepm is larger than one month (smallest stepm) and if the exact delay 
 void lubksb(double **a, int n, int *indx, double b[])           * (in months) between two waves is not a multiple of stepm, we rounded to 
 {           * the nearest (and in case of equal distance, to the lowest) interval but now
   int i,ii=0,ip,j;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   double sum;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
             * probability in order to take into account the bias as a fraction of the way
   for (i=1;i<=n;i++) {           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     ip=indx[i];           * -stepm/2 to stepm/2 .
     sum=b[ip];           * For stepm=1 the results are the same as for previous versions of Imach.
     b[ip]=b[i];           * For stepm > 1 the results are less biased than in previous versions. 
     if (ii)           */
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          s1=s[mw[mi][i]][i];
     else if (sum) ii=i;          s2=s[mw[mi+1][i]][i];
     b[i]=sum;          bbh=(double)bh[mi][i]/(double)stepm; 
   }          /* bias is positive if real duration
   for (i=n;i>=1;i--) {           * is higher than the multiple of stepm and negative otherwise.
     sum=b[i];           */
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[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 */
     b[i]=sum/a[i][i];          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   }          /*lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.-+bh)*out[s1][s2])); */ /* exponential interpolation */
 }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           /*if(lli ==000.0)*/
 /************ 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); */
 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)          ipmx +=1;
 {  /* Some frequencies */          sw += weight[i];
            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;        } /* end of wave */
   double ***freq; /* Frequencies */      } /* end of individual */
   double *pp;    }  else if(mle==3){  /* exponential inter-extrapolation */
   double pos, k2, dateintsum=0,k2cpt=0;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   FILE *ficresp;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   char fileresp[FILENAMELENGTH];        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
   pp=vector(1,nlstate);            for (j=1;j<=nlstate+ndeath;j++){
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   strcpy(fileresp,"p");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   strcat(fileresp,fileres);            }
   if((ficresp=fopen(fileresp,"w"))==NULL) {          for(d=0; d<dh[mi][i]; d++){
     printf("Problem with prevalence resultfile: %s\n", fileresp);            newm=savm;
     exit(0);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   }            for (kk=1; kk<=cptcovage;kk++) {
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   j1=0;            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   j=cptcoveff;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            savm=oldm;
             oldm=newm;
   for(k1=1; k1<=j;k1++){          } /* end mult */
    for(i1=1; i1<=ncodemax[k1];i1++){        
        j1++;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);          /* But now since version 0.9 we anticipate for bias and large stepm.
          scanf("%d", i);*/           * If stepm is larger than one month (smallest stepm) and if the exact delay 
         for (i=-1; i<=nlstate+ndeath; i++)             * (in months) between two waves is not a multiple of stepm, we rounded to 
          for (jk=-1; jk<=nlstate+ndeath; jk++)             * the nearest (and in case of equal distance, to the lowest) interval but now
            for(m=agemin; m <= agemax+3; m++)           * we keep into memory the bias bh[mi][i] and also the previous matrix product
              freq[i][jk][m]=0;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
            * probability in order to take into account the bias as a fraction of the way
         dateintsum=0;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
         k2cpt=0;           * -stepm/2 to stepm/2 .
        for (i=1; i<=imx; i++) {           * For stepm=1 the results are the same as for previous versions of Imach.
          bool=1;           * For stepm > 1 the results are less biased than in previous versions. 
          if  (cptcovn>0) {           */
            for (z1=1; z1<=cptcoveff; z1++)          s1=s[mw[mi][i]][i];
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          s2=s[mw[mi+1][i]][i];
                bool=0;          bbh=(double)bh[mi][i]/(double)stepm; 
          }          /* bias is positive if real duration
          if (bool==1) {           * is higher than the multiple of stepm and negative otherwise.
            for(m=firstpass; m<=lastpass; m++){           */
              k2=anint[m][i]+(mint[m][i]/12.);          /* 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 ((k2>=dateprev1) && (k2<=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])); /* exponential inter-extrapolation */
                if(agev[m][i]==0) agev[m][i]=agemax+1;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
                if(agev[m][i]==1) agev[m][i]=agemax+2;          /*if(lli ==000.0)*/
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          ipmx +=1;
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {          sw += weight[i];
                  dateintsum=dateintsum+k2;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                  k2cpt++;        } /* end of wave */
                }      } /* end of individual */
     }else if (mle==4){  /* ml=4 no inter-extrapolation */
              }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
            }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          }        for(mi=1; mi<= wav[i]-1; mi++){
        }          for (ii=1;ii<=nlstate+ndeath;ii++)
         if  (cptcovn>0) {            for (j=1;j<=nlstate+ndeath;j++){
          fprintf(ficresp, "\n#********** Variable ");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
        fprintf(ficresp, "**********\n#");            }
         }          for(d=0; d<dh[mi][i]; d++){
        for(i=1; i<=nlstate;i++)            newm=savm;
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
        fprintf(ficresp, "\n");            for (kk=1; kk<=cptcovage;kk++) {
                      cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   for(i=(int)agemin; i <= (int)agemax+3; i++){            }
     if(i==(int)agemax+3)          
       printf("Total");            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     else                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       printf("Age %d", i);            savm=oldm;
     for(jk=1; jk <=nlstate ; jk++){            oldm=newm;
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          } /* end mult */
         pp[jk] += freq[jk][m][i];        
     }          s1=s[mw[mi][i]][i];
     for(jk=1; jk <=nlstate ; jk++){          s2=s[mw[mi+1][i]][i];
       for(m=-1, pos=0; m <=0 ; m++)          if( s2 > nlstate){ 
         pos += freq[jk][m][i];            lli=log(out[s1][s2] - savm[s1][s2]);
       if(pp[jk]>=1.e-10)          }else{
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       else          }
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          ipmx +=1;
     }          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
      for(jk=1; 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]); */
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        } /* end of wave */
         pp[jk] += freq[jk][m][i];      } /* end of individual */
      }    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for(jk=1,pos=0; jk <=nlstate ; jk++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       pos += pp[jk];        for(mi=1; mi<= wav[i]-1; mi++){
     for(jk=1; jk <=nlstate ; jk++){          for (ii=1;ii<=nlstate+ndeath;ii++)
       if(pos>=1.e-5)            for (j=1;j<=nlstate+ndeath;j++){
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       else              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);            }
       if( i <= (int) agemax){          for(d=0; d<dh[mi][i]; d++){
         if(pos>=1.e-5){            newm=savm;
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           probs[i][jk][j1]= pp[jk]/pos;            for (kk=1; kk<=cptcovage;kk++) {
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         }            }
       else          
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     }            savm=oldm;
     for(jk=-1; jk <=nlstate+ndeath; jk++)            oldm=newm;
       for(m=-1; m <=nlstate+ndeath; m++)          } /* end mult */
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        
     if(i <= (int) agemax)          s1=s[mw[mi][i]][i];
       fprintf(ficresp,"\n");          s2=s[mw[mi+1][i]][i];
     printf("\n");          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     }          ipmx +=1;
     }          sw += weight[i];
  }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   dateintmean=dateintsum/k2cpt;          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
          } /* end of wave */
   fclose(ficresp);      } /* end of individual */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    } /* End of if */
   free_vector(pp,1,nlstate);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   /* End of Freq */    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
 }    return -l;
   }
 /************ Prevalence ********************/  
 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)  /*************** log-likelihood *************/
 {  /* Some frequencies */  double funcone( double *x)
    {
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;    int i, ii, j, k, mi, d, kk;
   double ***freq; /* Frequencies */    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   double *pp;    double **out;
   double pos, k2;    double lli; /* Individual log likelihood */
     int s1, s2;
   pp=vector(1,nlstate);    double bbh, survp;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    /*extern weight */
      /* We are differentiating ll according to initial status */
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   j1=0;    /*for(i=1;i<imx;i++) 
        printf(" %d\n",s[4][i]);
   j=cptcoveff;    */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    cov[1]=1.;
    
  for(k1=1; k1<=j;k1++){    for(k=1; k<=nlstate; k++) ll[k]=0.;
     for(i1=1; i1<=ncodemax[k1];i1++){  
       j1++;    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for (i=-1; i<=nlstate+ndeath; i++)        for(mi=1; mi<= wav[i]-1; mi++){
         for (jk=-1; jk<=nlstate+ndeath; jk++)          for (ii=1;ii<=nlstate+ndeath;ii++)
           for(m=agemin; m <= agemax+3; m++)          for (j=1;j<=nlstate+ndeath;j++){
             freq[i][jk][m]=0;            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                  savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for (i=1; i<=imx; i++) {          }
         bool=1;        for(d=0; d<dh[mi][i]; d++){
         if  (cptcovn>0) {          newm=savm;
           for (z1=1; z1<=cptcoveff; z1++)          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          for (kk=1; kk<=cptcovage;kk++) {
               bool=0;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         }          }
         if (bool==1) {          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           for(m=firstpass; m<=lastpass; m++){                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             k2=anint[m][i]+(mint[m][i]/12.);          savm=oldm;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          oldm=newm;
               if(agev[m][i]==0) agev[m][i]=agemax+1;        } /* end mult */
               if(agev[m][i]==1) agev[m][i]=agemax+2;        
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];        s1=s[mw[mi][i]][i];
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];          s2=s[mw[mi+1][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.
       }         */
              if( s2 > nlstate && (mle <5) ){  /* Jackson */
         for(i=(int)agemin; i <= (int)agemax+3; i++){          lli=log(out[s1][s2] - savm[s1][s2]);
           for(jk=1; jk <=nlstate ; jk++){        } else if (mle==1){
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
               pp[jk] += freq[jk][m][i];        } else if(mle==2){
           }          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(jk=1; jk <=nlstate ; jk++){        } else if(mle==3){  /* exponential inter-extrapolation */
             for(m=-1, pos=0; m <=0 ; m++)          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 */
             pos += freq[jk][m][i];        } else if (mle==4){  /* mle=4 no inter-extrapolation */
         }          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 */
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        } /* End of if */
              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++) pos += pp[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]); */
         if(globpr){
          for(jk=1; jk <=nlstate ; jk++){                    fprintf(ficresilk,"%6d %1d %1d %1d %1d %3d %10.6f %6.4f %10.6f %10.6f %10.6f ", \
            if( i <= (int) agemax){                  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
              if(pos>=1.e-5){          for(k=1,l=0.; k<=nlstate; k++) 
                probs[i][jk][j1]= pp[jk]/pos;            fprintf(ficresilk," %10.6f",ll[k]);
              }          fprintf(ficresilk,"\n");
            }        }
          }      } /* end of wave */
              } /* end of individual */
         }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   }    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
      return -l;
    }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  
   free_vector(pp,1,nlstate);  
    void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpr, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
 }  /* End of Freq */  {
     /* This routine should help understanding what is done with the selection of individuals/waves and
 /************* Waves Concatenation ***************/       to check the exact contribution to the likelihood.
        Plotting could be done.
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)     */
 {    int k;
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    if(globpr !=0){ /* Just counts and sums no printings */
      Death is a valid wave (if date is known).      strcpy(fileresilk,"ilk"); 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      strcat(fileresilk,fileres);
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
      and mw[mi+1][i]. dh depends on stepm.        printf("Problem with resultfile: %s\n", fileresilk);
      */        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }
   int i, mi, m;      fprintf(ficresilk, "# individual(line's record) s1 s2 wave# effective_wave# number_of_product_matrix pij weight 2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state");
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      fprintf(ficresilk, "# i s1 s2 mi mw dh likeli weight out sav ");
      double sum=0., jmean=0.;*/      /*  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; k<=nlstate; k++) 
   int j, k=0,jk, ju, jl;        fprintf(ficresilk," ll[%d]",k);
   double sum=0.;      fprintf(ficresilk,"\n");
   jmin=1e+5;    }
   jmax=-1;  
   jmean=0.;    *fretone=(*funcone)(p);
   for(i=1; i<=imx; i++){    if(globpr !=0)
     mi=0;      fclose(ficresilk);
     m=firstpass;    return;
     while(s[m][i] <= nlstate){  }
       if(s[m][i]>=1)  
         mw[++mi][i]=m;  /*********** Maximum Likelihood Estimation ***************/
       if(m >=lastpass)  
         break;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       else  {
         m++;    int i,j, iter;
     }/* end while */    double **xi;
     if (s[m][i] > nlstate){    double fret;
       mi++;     /* Death is another wave */    double fretone; /* Only one call to likelihood */
       /* if(mi==0)  never been interviewed correctly before death */    char filerespow[FILENAMELENGTH];
          /* Only death is a correct wave */    xi=matrix(1,npar,1,npar);
       mw[mi][i]=m;    for (i=1;i<=npar;i++)
     }      for (j=1;j<=npar;j++)
         xi[i][j]=(i==j ? 1.0 : 0.0);
     wav[i]=mi;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     if(mi==0)    strcpy(filerespow,"pow"); 
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);    strcat(filerespow,fileres);
   }    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
   for(i=1; i<=imx; i++){      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     for(mi=1; mi<wav[i];mi++){    }
       if (stepm <=0)    fprintf(ficrespow,"# Powell\n# iter -2*LL");
         dh[mi][i]=1;    for (i=1;i<=nlstate;i++)
       else{      for(j=1;j<=nlstate+ndeath;j++)
         if (s[mw[mi+1][i]][i] > nlstate) {        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
           if (agedc[i] < 2*AGESUP) {    fprintf(ficrespow,"\n");
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  
           if(j==0) j=1;  /* Survives at least one month after exam */    powell(p,xi,npar,ftol,&iter,&fret,func);
           k=k+1;  
           if (j >= jmax) jmax=j;    fclose(ficrespow);
           if (j <= jmin) jmin=j;    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
           sum=sum+j;    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
           /* if (j<10) printf("j=%d num=%d ",j,i); */    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
           }  
         }  }
         else{  
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));  /**** Computes Hessian and covariance matrix ***/
           k=k+1;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
           if (j >= jmax) jmax=j;  {
           else if (j <= jmin)jmin=j;    double  **a,**y,*x,pd;
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    double **hess;
           sum=sum+j;    int i, j,jk;
         }    int *indx;
         jk= j/stepm;  
         jl= j -jk*stepm;    double hessii(double p[], double delta, int theta, double delti[]);
         ju= j -(jk+1)*stepm;    double hessij(double p[], double delti[], int i, int j);
         if(jl <= -ju)    void lubksb(double **a, int npar, int *indx, double b[]) ;
           dh[mi][i]=jk;    void ludcmp(double **a, int npar, int *indx, double *d) ;
         else  
           dh[mi][i]=jk+1;    hess=matrix(1,npar,1,npar);
         if(dh[mi][i]==0)  
           dh[mi][i]=1; /* At least one step */    printf("\nCalculation of the hessian matrix. Wait...\n");
       }    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     }    for (i=1;i<=npar;i++){
   }      printf("%d",i);fflush(stdout);
   jmean=sum/k;      fprintf(ficlog,"%d",i);fflush(ficlog);
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);      hess[i][i]=hessii(p,ftolhess,i,delti);
  }      /*printf(" %f ",p[i]);*/
 /*********** Tricode ****************************/      /*printf(" %lf ",hess[i][i]);*/
 void tricode(int *Tvar, int **nbcode, int imx)    }
 {    
   int Ndum[20],ij=1, k, j, i;    for (i=1;i<=npar;i++) {
   int cptcode=0;      for (j=1;j<=npar;j++)  {
   cptcoveff=0;        if (j>i) { 
            printf(".%d%d",i,j);fflush(stdout);
   for (k=0; k<19; k++) Ndum[k]=0;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   for (k=1; k<=7; k++) ncodemax[k]=0;          hess[i][j]=hessij(p,delti,i,j);
           hess[j][i]=hess[i][j];    
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          /*printf(" %lf ",hess[i][j]);*/
     for (i=1; i<=imx; i++) {        }
       ij=(int)(covar[Tvar[j]][i]);      }
       Ndum[ij]++;    }
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    printf("\n");
       if (ij > cptcode) cptcode=ij;    fprintf(ficlog,"\n");
     }  
     printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     for (i=0; i<=cptcode; i++) {    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       if(Ndum[i]!=0) ncodemax[j]++;    
     }    a=matrix(1,npar,1,npar);
     ij=1;    y=matrix(1,npar,1,npar);
     x=vector(1,npar);
     indx=ivector(1,npar);
     for (i=1; i<=ncodemax[j]; i++) {    for (i=1;i<=npar;i++)
       for (k=0; k<=19; k++) {      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
         if (Ndum[k] != 0) {    ludcmp(a,npar,indx,&pd);
           nbcode[Tvar[j]][ij]=k;  
           ij++;    for (j=1;j<=npar;j++) {
         }      for (i=1;i<=npar;i++) x[i]=0;
         if (ij > ncodemax[j]) break;      x[j]=1;
       }        lubksb(a,npar,indx,x);
     }      for (i=1;i<=npar;i++){ 
   }          matcov[i][j]=x[i];
       }
  for (k=0; k<19; k++) Ndum[k]=0;    }
   
  for (i=1; i<=ncovmodel-2; i++) {    printf("\n#Hessian matrix#\n");
       ij=Tvar[i];    fprintf(ficlog,"\n#Hessian matrix#\n");
       Ndum[ij]++;    for (i=1;i<=npar;i++) { 
     }      for (j=1;j<=npar;j++) { 
         printf("%.3e ",hess[i][j]);
  ij=1;        fprintf(ficlog,"%.3e ",hess[i][j]);
  for (i=1; i<=10; i++) {      }
    if((Ndum[i]!=0) && (i<=ncov)){      printf("\n");
      Tvaraff[ij]=i;      fprintf(ficlog,"\n");
      ij++;    }
    }  
  }    /* Recompute Inverse */
      for (i=1;i<=npar;i++)
     cptcoveff=ij-1;      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
 }    ludcmp(a,npar,indx,&pd);
   
 /*********** Health Expectancies ****************/    /*  printf("\n#Hessian matrix recomputed#\n");
   
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)    for (j=1;j<=npar;j++) {
 {      for (i=1;i<=npar;i++) x[i]=0;
   /* Health expectancies */      x[j]=1;
   int i, j, nhstepm, hstepm, h;      lubksb(a,npar,indx,x);
   double age, agelim,hf;      for (i=1;i<=npar;i++){ 
   double ***p3mat;        y[i][j]=x[i];
          printf("%.3e ",y[i][j]);
   fprintf(ficreseij,"# Health expectancies\n");        fprintf(ficlog,"%.3e ",y[i][j]);
   fprintf(ficreseij,"# Age");      }
   for(i=1; i<=nlstate;i++)      printf("\n");
     for(j=1; j<=nlstate;j++)      fprintf(ficlog,"\n");
       fprintf(ficreseij," %1d-%1d",i,j);    }
   fprintf(ficreseij,"\n");    */
   
   hstepm=1*YEARM; /*  Every j years of age (in month) */    free_matrix(a,1,npar,1,npar);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    free_matrix(y,1,npar,1,npar);
     free_vector(x,1,npar);
   agelim=AGESUP;    free_ivector(indx,1,npar);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    free_matrix(hess,1,npar,1,npar);
     /* nhstepm age range expressed in number of stepm */  
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);  
     /* Typically if 20 years = 20*12/6=40 stepm */  }
     if (stepm >= YEARM) hstepm=1;  
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */  /*************** hessian matrix ****************/
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  double hessii( double x[], double delta, int theta, double delti[])
     /* Computed by stepm unit matrices, product of hstepm matrices, stored  {
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    int i;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      int l=1, lmax=20;
     double k1,k2;
     double p2[NPARMAX+1];
     for(i=1; i<=nlstate;i++)    double res;
       for(j=1; j<=nlstate;j++)    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){    double fx;
           eij[i][j][(int)age] +=p3mat[i][j][h];    int k=0,kmax=10;
         }    double l1;
      
     hf=1;    fx=func(x);
     if (stepm >= YEARM) hf=stepm/YEARM;    for (i=1;i<=npar;i++) p2[i]=x[i];
     fprintf(ficreseij,"%.0f",age );    for(l=0 ; l <=lmax; l++){
     for(i=1; i<=nlstate;i++)      l1=pow(10,l);
       for(j=1; j<=nlstate;j++){      delts=delt;
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);      for(k=1 ; k <kmax; k=k+1){
       }        delt = delta*(l1*k);
     fprintf(ficreseij,"\n");        p2[theta]=x[theta] +delt;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        k1=func(p2)-fx;
   }        p2[theta]=x[theta]-delt;
 }        k2=func(p2)-fx;
         /*res= (k1-2.0*fx+k2)/delt/delt; */
 /************ Variance ******************/        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
 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)        
 {  #ifdef DEBUG
   /* Variance of health expectancies */        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);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        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);
   double **newm;  #endif
   double **dnewm,**doldm;        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   int i, j, nhstepm, hstepm, h;        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   int k, cptcode;          k=kmax;
   double *xp;        }
   double **gp, **gm;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
   double ***gradg, ***trgradg;          k=kmax; l=lmax*10.;
   double ***p3mat;        }
   double age,agelim;        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   int theta;          delts=delt;
         }
    fprintf(ficresvij,"# Covariances of life expectancies\n");      }
   fprintf(ficresvij,"# Age");    }
   for(i=1; i<=nlstate;i++)    delti[theta]=delts;
     for(j=1; j<=nlstate;j++)    return res; 
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    
   fprintf(ficresvij,"\n");  }
   
   xp=vector(1,npar);  double hessij( double x[], double delti[], int thetai,int thetaj)
   dnewm=matrix(1,nlstate,1,npar);  {
   doldm=matrix(1,nlstate,1,nlstate);    int i;
      int l=1, l1, lmax=20;
   hstepm=1*YEARM; /* Every year of age */    double k1,k2,k3,k4,res,fx;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    double p2[NPARMAX+1];
   agelim = AGESUP;    int k;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    fx=func(x);
     if (stepm >= YEARM) hstepm=1;    for (k=1; k<=2; k++) {
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      for (i=1;i<=npar;i++) p2[i]=x[i];
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      p2[thetai]=x[thetai]+delti[thetai]/k;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     gp=matrix(0,nhstepm,1,nlstate);      k1=func(p2)-fx;
     gm=matrix(0,nhstepm,1,nlstate);    
       p2[thetai]=x[thetai]+delti[thetai]/k;
     for(theta=1; theta <=npar; theta++){      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       for(i=1; i<=npar; i++){ /* Computes gradient */      k2=func(p2)-fx;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    
       }      p2[thetai]=x[thetai]-delti[thetai]/k;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      k3=func(p2)-fx;
     
       if (popbased==1) {      p2[thetai]=x[thetai]-delti[thetai]/k;
         for(i=1; i<=nlstate;i++)      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
           prlim[i][i]=probs[(int)age][i][ij];      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
       for(j=1; j<= nlstate; j++){      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);
         for(h=0; h<=nhstepm; h++){      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  #endif
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    }
         }    return res;
       }  }
      
       for(i=1; i<=npar; i++) /* Computes gradient */  /************** Inverse of matrix **************/
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  void ludcmp(double **a, int n, int *indx, double *d) 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    { 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    int i,imax,j,k; 
     double big,dum,sum,temp; 
       if (popbased==1) {    double *vv; 
         for(i=1; i<=nlstate;i++)   
           prlim[i][i]=probs[(int)age][i][ij];    vv=vector(1,n); 
       }    *d=1.0; 
     for (i=1;i<=n;i++) { 
       for(j=1; j<= nlstate; j++){      big=0.0; 
         for(h=0; h<=nhstepm; h++){      for (j=1;j<=n;j++) 
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        if ((temp=fabs(a[i][j])) > big) big=temp; 
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
         }      vv[i]=1.0/big; 
       }    } 
     for (j=1;j<=n;j++) { 
       for(j=1; j<= nlstate; j++)      for (i=1;i<j;i++) { 
         for(h=0; h<=nhstepm; h++){        sum=a[i][j]; 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         }        a[i][j]=sum; 
     } /* End theta */      } 
       big=0.0; 
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);      for (i=j;i<=n;i++) { 
         sum=a[i][j]; 
     for(h=0; h<=nhstepm; h++)        for (k=1;k<j;k++) 
       for(j=1; j<=nlstate;j++)          sum -= a[i][k]*a[k][j]; 
         for(theta=1; theta <=npar; theta++)        a[i][j]=sum; 
           trgradg[h][j][theta]=gradg[h][theta][j];        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           big=dum; 
     for(i=1;i<=nlstate;i++)          imax=i; 
       for(j=1;j<=nlstate;j++)        } 
         vareij[i][j][(int)age] =0.;      } 
     for(h=0;h<=nhstepm;h++){      if (j != imax) { 
       for(k=0;k<=nhstepm;k++){        for (k=1;k<=n;k++) { 
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          dum=a[imax][k]; 
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          a[imax][k]=a[j][k]; 
         for(i=1;i<=nlstate;i++)          a[j][k]=dum; 
           for(j=1;j<=nlstate;j++)        } 
             vareij[i][j][(int)age] += doldm[i][j];        *d = -(*d); 
       }        vv[imax]=vv[j]; 
     }      } 
     h=1;      indx[j]=imax; 
     if (stepm >= YEARM) h=stepm/YEARM;      if (a[j][j] == 0.0) a[j][j]=TINY; 
     fprintf(ficresvij,"%.0f ",age );      if (j != n) { 
     for(i=1; i<=nlstate;i++)        dum=1.0/(a[j][j]); 
       for(j=1; j<=nlstate;j++){        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);      } 
       }    } 
     fprintf(ficresvij,"\n");    free_vector(vv,1,n);  /* Doesn't work */
     free_matrix(gp,0,nhstepm,1,nlstate);  ;
     free_matrix(gm,0,nhstepm,1,nlstate);  } 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);  
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);  void lubksb(double **a, int n, int *indx, double b[]) 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  { 
   } /* End age */    int i,ii=0,ip,j; 
      double sum; 
   free_vector(xp,1,npar);   
   free_matrix(doldm,1,nlstate,1,npar);    for (i=1;i<=n;i++) { 
   free_matrix(dnewm,1,nlstate,1,nlstate);      ip=indx[i]; 
       sum=b[ip]; 
 }      b[ip]=b[i]; 
       if (ii) 
 /************ Variance of prevlim ******************/        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
 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)      else if (sum) ii=i; 
 {      b[i]=sum; 
   /* Variance of prevalence limit */    } 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    for (i=n;i>=1;i--) { 
   double **newm;      sum=b[i]; 
   double **dnewm,**doldm;      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   int i, j, nhstepm, hstepm;      b[i]=sum/a[i][i]; 
   int k, cptcode;    } 
   double *xp;  } 
   double *gp, *gm;  
   double **gradg, **trgradg;  /************ Frequencies ********************/
   double age,agelim;  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)
   int theta;  {  /* Some frequencies */
        
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   fprintf(ficresvpl,"# Age");    int first;
   for(i=1; i<=nlstate;i++)    double ***freq; /* Frequencies */
       fprintf(ficresvpl," %1d-%1d",i,i);    double *pp, **prop;
   fprintf(ficresvpl,"\n");    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     FILE *ficresp;
   xp=vector(1,npar);    char fileresp[FILENAMELENGTH];
   dnewm=matrix(1,nlstate,1,npar);    
   doldm=matrix(1,nlstate,1,nlstate);    pp=vector(1,nlstate);
      prop=matrix(1,nlstate,iagemin,iagemax+3);
   hstepm=1*YEARM; /* Every year of age */    strcpy(fileresp,"p");
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    strcat(fileresp,fileres);
   agelim = AGESUP;    if((ficresp=fopen(fileresp,"w"))==NULL) {
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      printf("Problem with prevalence resultfile: %s\n", fileresp);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     if (stepm >= YEARM) hstepm=1;      exit(0);
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    }
     gradg=matrix(1,npar,1,nlstate);    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
     gp=vector(1,nlstate);    j1=0;
     gm=vector(1,nlstate);    
     j=cptcoveff;
     for(theta=1; theta <=npar; theta++){    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       for(i=1; i<=npar; i++){ /* Computes gradient */  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    first=1;
       }  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    for(k1=1; k1<=j;k1++){
       for(i=1;i<=nlstate;i++)      for(i1=1; i1<=ncodemax[k1];i1++){
         gp[i] = prlim[i][i];        j1++;
            /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       for(i=1; i<=npar; i++) /* Computes gradient */          scanf("%d", i);*/
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        for (i=-1; i<=nlstate+ndeath; i++)  
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          for (jk=-1; jk<=nlstate+ndeath; jk++)  
       for(i=1;i<=nlstate;i++)            for(m=iagemin; m <= iagemax+3; m++)
         gm[i] = prlim[i][i];              freq[i][jk][m]=0;
   
       for(i=1;i<=nlstate;i++)      for (i=1; i<=nlstate; i++)  
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        for(m=iagemin; m <= iagemax+3; m++)
     } /* End theta */          prop[i][m]=0;
         
     trgradg =matrix(1,nlstate,1,npar);        dateintsum=0;
         k2cpt=0;
     for(j=1; j<=nlstate;j++)        for (i=1; i<=imx; i++) {
       for(theta=1; theta <=npar; theta++)          bool=1;
         trgradg[j][theta]=gradg[theta][j];          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
     for(i=1;i<=nlstate;i++)              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       varpl[i][(int)age] =0.;                bool=0;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          }
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          if (bool==1){
     for(i=1;i<=nlstate;i++)            for(m=firstpass; m<=lastpass; m++){
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */              k2=anint[m][i]+(mint[m][i]/12.);
               /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     fprintf(ficresvpl,"%.0f ",age );                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     for(i=1; i<=nlstate;i++)                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     fprintf(ficresvpl,"\n");                if (m<lastpass) {
     free_vector(gp,1,nlstate);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     free_vector(gm,1,nlstate);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
     free_matrix(gradg,1,npar,1,nlstate);                }
     free_matrix(trgradg,1,nlstate,1,npar);                
   } /* End age */                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                   dateintsum=dateintsum+k2;
   free_vector(xp,1,npar);                  k2cpt++;
   free_matrix(doldm,1,nlstate,1,npar);                }
   free_matrix(dnewm,1,nlstate,1,nlstate);                /*}*/
             }
 }          }
         }
 /************ Variance of one-step probabilities  ******************/         
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
 {  
   int i, j;        if  (cptcovn>0) {
   int k=0, cptcode;          fprintf(ficresp, "\n#********** Variable "); 
   double **dnewm,**doldm;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   double *xp;          fprintf(ficresp, "**********\n#");
   double *gp, *gm;        }
   double **gradg, **trgradg;        for(i=1; i<=nlstate;i++) 
   double age,agelim, cov[NCOVMAX];          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   int theta;        fprintf(ficresp, "\n");
   char fileresprob[FILENAMELENGTH];        
         for(i=iagemin; i <= iagemax+3; i++){
   strcpy(fileresprob,"prob");          if(i==iagemax+3){
   strcat(fileresprob,fileres);            fprintf(ficlog,"Total");
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {          }else{
     printf("Problem with resultfile: %s\n", fileresprob);            if(first==1){
   }              first=0;
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);              printf("See log file for details...\n");
              }
             fprintf(ficlog,"Age %d", i);
   xp=vector(1,npar);          }
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          for(jk=1; jk <=nlstate ; jk++){
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
                pp[jk] += freq[jk][m][i]; 
   cov[1]=1;          }
   for (age=bage; age<=fage; age ++){          for(jk=1; jk <=nlstate ; jk++){
     cov[2]=age;            for(m=-1, pos=0; m <=0 ; m++)
     gradg=matrix(1,npar,1,9);              pos += freq[jk][m][i];
     trgradg=matrix(1,9,1,npar);            if(pp[jk]>=1.e-10){
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));              if(first==1){
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                  }
     for(theta=1; theta <=npar; theta++){              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       for(i=1; i<=npar; i++)            }else{
         xp[i] = x[i] + (i==theta ?delti[theta]:0);              if(first==1)
                      printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       pmij(pmmij,cov,ncovmodel,xp,nlstate);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                }
       k=0;          }
       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=0, pp[jk]=0; m <=nlstate+ndeath; m++)
           gp[k]=pmmij[i][j];              pp[jk] += freq[jk][m][i];
         }          }       
       }          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
             pos += pp[jk];
       for(i=1; i<=npar; i++)            posprop += prop[jk][i];
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          }
              for(jk=1; jk <=nlstate ; jk++){
             if(pos>=1.e-5){
       pmij(pmmij,cov,ncovmodel,xp,nlstate);              if(first==1)
       k=0;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       for(i=1; i<=(nlstate+ndeath); i++){              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         for(j=1; j<=(nlstate+ndeath);j++){            }else{
           k=k+1;              if(first==1)
           gm[k]=pmmij[i][j];                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
         }              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       }            }
                  if( i <= iagemax){
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)              if(pos>=1.e-5){
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];                  fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
     }                /*probs[i][jk][j1]= pp[jk]/pos;*/
                 /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)              }
       for(theta=1; theta <=npar; theta++)              else
       trgradg[j][theta]=gradg[theta][j];                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
              }
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);          }
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);          
           for(jk=-1; jk <=nlstate+ndeath; jk++)
      pmij(pmmij,cov,ncovmodel,x,nlstate);            for(m=-1; m <=nlstate+ndeath; m++)
               if(freq[jk][m][i] !=0 ) {
      k=0;              if(first==1)
      for(i=1; i<=(nlstate+ndeath); i++){                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
        for(j=1; j<=(nlstate+ndeath);j++){                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
          k=k+1;              }
          gm[k]=pmmij[i][j];          if(i <= iagemax)
         }            fprintf(ficresp,"\n");
      }          if(first==1)
                  printf("Others in log...\n");
      /*printf("\n%d ",(int)age);          fprintf(ficlog,"\n");
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){        }
              }
     }
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    dateintmean=dateintsum/k2cpt; 
      }*/   
     fclose(ficresp);
   fprintf(ficresprob,"\n%d ",(int)age);    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
     free_vector(pp,1,nlstate);
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    /* End of Freq */
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  }
   }  
   /************ Prevalence ********************/
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));  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)
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));  {  
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);       in each health status at the date of interview (if between dateprev1 and dateprev2).
 }       We still use firstpass and lastpass as another selection.
  free_vector(xp,1,npar);    */
 fclose(ficresprob);   
  exit(0);    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
 }    double ***freq; /* Frequencies */
     double *pp, **prop;
 /***********************************************/    double pos,posprop; 
 /**************** Main Program *****************/    double  y2; /* in fractional years */
 /***********************************************/    int iagemin, iagemax;
   
 /*int main(int argc, char *argv[])*/    iagemin= (int) agemin;
 int main()    iagemax= (int) agemax;
 {    /*pp=vector(1,nlstate);*/
     prop=matrix(1,nlstate,iagemin,iagemax+3); 
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   double agedeb, agefin,hf;    j1=0;
   double agemin=1.e20, agemax=-1.e20;    
     j=cptcoveff;
   double fret;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   double **xi,tmp,delta;    
     for(k1=1; k1<=j;k1++){
   double dum; /* Dummy variable */      for(i1=1; i1<=ncodemax[k1];i1++){
   double ***p3mat;        j1++;
   int *indx;        
   char line[MAXLINE], linepar[MAXLINE];        for (i=1; i<=nlstate; i++)  
   char title[MAXLINE];          for(m=iagemin; m <= iagemax+3; m++)
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];            prop[i][m]=0.0;
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];       
   char filerest[FILENAMELENGTH];        for (i=1; i<=imx; i++) { /* Each individual */
   char fileregp[FILENAMELENGTH];          bool=1;
   char popfile[FILENAMELENGTH];          if  (cptcovn>0) {
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];            for (z1=1; z1<=cptcoveff; z1++) 
   int firstobs=1, lastobs=10;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   int sdeb, sfin; /* Status at beginning and end */                bool=0;
   int c,  h , cpt,l;          } 
   int ju,jl, mi;          if (bool==1) { 
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   int mobilav=0,popforecast=0;              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   int hstepm, nhstepm;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   int *popage;/*boolprev=0 if date and zero if wave*/                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
                 if (s[m][i]>0 && s[m][i]<=nlstate) { 
   double bage, fage, age, agelim, agebase;                  /*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]]);*/
   double ftolpl=FTOL;                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   double **prlim;                  prop[s[m][i]][iagemax+3] += weight[i]; 
   double *severity;                } 
   double ***param; /* Matrix of parameters */              }
   double  *p;            } /* end selection of waves */
   double **matcov; /* Matrix of covariance */          }
   double ***delti3; /* Scale */        }
   double *delti; /* Scale */        for(i=iagemin; i <= iagemax+3; i++){  
   double ***eij, ***vareij;          
   double **varpl; /* Variances of prevalence limits by age */          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   double *epj, vepp;            posprop += prop[jk][i]; 
   double kk1, kk2;          } 
   double *popeffectif,*popcount;  
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;          for(jk=1; jk <=nlstate ; jk++){     
   double yp,yp1,yp2;            if( i <=  iagemax){ 
               if(posprop>=1.e-5){ 
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";                probs[i][jk][j1]= prop[jk][i]/posprop;
   char *alph[]={"a","a","b","c","d","e"}, str[4];              } 
             } 
           }/* end jk */ 
   char z[1]="c", occ;        }/* end i */ 
 #include <sys/time.h>      } /* end i1 */
 #include <time.h>    } /* end k1 */
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    
      /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   /* long total_usecs;    /*free_vector(pp,1,nlstate);*/
   struct timeval start_time, end_time;    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
    }  /* End of prevalence */
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */  
   /************* Waves Concatenation ***************/
   
   printf("\nIMACH, Version 0.7");  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)
   printf("\nEnter the parameter file name: ");  {
     /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
 #ifdef windows       Death is a valid wave (if date is known).
   scanf("%s",pathtot);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   getcwd(pathcd, size);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   /*cygwin_split_path(pathtot,path,optionfile);       and mw[mi+1][i]. dh depends on stepm.
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/       */
   /* cutv(path,optionfile,pathtot,'\\');*/  
     int i, mi, m;
 split(pathtot, path,optionfile);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   chdir(path);       double sum=0., jmean=0.;*/
   replace(pathc,path);    int first;
 #endif    int j, k=0,jk, ju, jl;
 #ifdef unix    double sum=0.;
   scanf("%s",optionfile);    first=0;
 #endif    jmin=1e+5;
     jmax=-1;
 /*-------- arguments in the command line --------*/    jmean=0.;
     for(i=1; i<=imx; i++){
   strcpy(fileres,"r");      mi=0;
   strcat(fileres, optionfile);      m=firstpass;
       while(s[m][i] <= nlstate){
   /*---------arguments file --------*/        if(s[m][i]>=1)
           mw[++mi][i]=m;
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        if(m >=lastpass)
     printf("Problem with optionfile %s\n",optionfile);          break;
     goto end;        else
   }          m++;
       }/* end while */
   strcpy(filereso,"o");      if (s[m][i] > nlstate){
   strcat(filereso,fileres);        mi++;     /* Death is another wave */
   if((ficparo=fopen(filereso,"w"))==NULL) {        /* if(mi==0)  never been interviewed correctly before death */
     printf("Problem with Output resultfile: %s\n", filereso);goto end;           /* Only death is a correct wave */
   }        mw[mi][i]=m;
       }
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){      wav[i]=mi;
     ungetc(c,ficpar);      if(mi==0){
     fgets(line, MAXLINE, ficpar);        if(first==0){
     puts(line);          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
     fputs(line,ficparo);          first=1;
   }        }
   ungetc(c,ficpar);        if(first==1){
           fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
   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);      } /* end mi==0 */
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);    } /* End individuals */
 while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    for(i=1; i<=imx; i++){
     fgets(line, MAXLINE, ficpar);      for(mi=1; mi<wav[i];mi++){
     puts(line);        if (stepm <=0)
     fputs(line,ficparo);          dh[mi][i]=1;
   }        else{
   ungetc(c,ficpar);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
              if (agedc[i] < 2*AGESUP) {
                  j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   covar=matrix(0,NCOVMAX,1,n);              if(j==0) j=1;  /* Survives at least one month after exam */
   cptcovn=0;              else if(j<0){
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;                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]);
                 j=1; /* Careful Patch */
   ncovmodel=2+cptcovn;                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 fixe the contradiction between dates.\n",stepm);
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                  fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
   /* Read guess parameters */              }
   /* Reads comments: lines beginning with '#' */              k=k+1;
   while((c=getc(ficpar))=='#' && c!= EOF){              if (j >= jmax) jmax=j;
     ungetc(c,ficpar);              if (j <= jmin) jmin=j;
     fgets(line, MAXLINE, ficpar);              sum=sum+j;
     puts(line);              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
     fputs(line,ficparo);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   }            }
   ungetc(c,ficpar);          }
            else{
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     for(i=1; i <=nlstate; i++)            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     for(j=1; j <=nlstate+ndeath-1; j++){            k=k+1;
       fscanf(ficpar,"%1d%1d",&i1,&j1);            if (j >= jmax) jmax=j;
       fprintf(ficparo,"%1d%1d",i1,j1);            else if (j <= jmin)jmin=j;
       printf("%1d%1d",i,j);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
       for(k=1; k<=ncovmodel;k++){            /*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]);*/
         fscanf(ficpar," %lf",&param[i][j][k]);            if(j<0){
         printf(" %lf",param[i][j][k]);              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]);
         fprintf(ficparo," %lf",param[i][j][k]);              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]);
       }            }
       fscanf(ficpar,"\n");            sum=sum+j;
       printf("\n");          }
       fprintf(ficparo,"\n");          jk= j/stepm;
     }          jl= j -jk*stepm;
            ju= j -(jk+1)*stepm;
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
             if(jl==0){
   p=param[1][1];              dh[mi][i]=jk;
                bh[mi][i]=0;
   /* Reads comments: lines beginning with '#' */            }else{ /* We want a negative bias in order to only have interpolation ie
   while((c=getc(ficpar))=='#' && c!= EOF){                    * at the price of an extra matrix product in likelihood */
     ungetc(c,ficpar);              dh[mi][i]=jk+1;
     fgets(line, MAXLINE, ficpar);              bh[mi][i]=ju;
     puts(line);            }
     fputs(line,ficparo);          }else{
   }            if(jl <= -ju){
   ungetc(c,ficpar);              dh[mi][i]=jk;
               bh[mi][i]=jl;       /* bias is positive if real duration
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);                                   * is higher than the multiple of stepm and negative otherwise.
   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++){            else{
       fscanf(ficpar,"%1d%1d",&i1,&j1);              dh[mi][i]=jk+1;
       printf("%1d%1d",i,j);              bh[mi][i]=ju;
       fprintf(ficparo,"%1d%1d",i1,j1);            }
       for(k=1; k<=ncovmodel;k++){            if(dh[mi][i]==0){
         fscanf(ficpar,"%le",&delti3[i][j][k]);              dh[mi][i]=1; /* At least one step */
         printf(" %le",delti3[i][j][k]);              bh[mi][i]=ju; /* At least one step */
         fprintf(ficparo," %le",delti3[i][j][k]);              /*  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);*/
       }            }
       fscanf(ficpar,"\n");          } /* end if mle */
       printf("\n");        }
       fprintf(ficparo,"\n");      } /* end wave */
     }    }
   }    jmean=sum/k;
   delti=delti3[1][1];    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
      fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   /* Reads comments: lines beginning with '#' */   }
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  /*********** Tricode ****************************/
     fgets(line, MAXLINE, ficpar);  void tricode(int *Tvar, int **nbcode, int imx)
     puts(line);  {
     fputs(line,ficparo);    
   }    int Ndum[20],ij=1, k, j, i, maxncov=19;
   ungetc(c,ficpar);    int cptcode=0;
      cptcoveff=0; 
   matcov=matrix(1,npar,1,npar);   
   for(i=1; i <=npar; i++){    for (k=0; k<maxncov; k++) Ndum[k]=0;
     fscanf(ficpar,"%s",&str);    for (k=1; k<=7; k++) ncodemax[k]=0;
     printf("%s",str);  
     fprintf(ficparo,"%s",str);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
     for(j=1; j <=i; j++){      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
       fscanf(ficpar," %le",&matcov[i][j]);                                 modality*/ 
       printf(" %.5le",matcov[i][j]);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
       fprintf(ficparo," %.5le",matcov[i][j]);        Ndum[ij]++; /*store the modality */
     }        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
     fscanf(ficpar,"\n");        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
     printf("\n");                                         Tvar[j]. If V=sex and male is 0 and 
     fprintf(ficparo,"\n");                                         female is 1, then  cptcode=1.*/
   }      }
   for(i=1; i <=npar; i++)  
     for(j=i+1;j<=npar;j++)      for (i=0; i<=cptcode; i++) {
       matcov[i][j]=matcov[j][i];        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
          }
   printf("\n");  
       ij=1; 
       for (i=1; i<=ncodemax[j]; i++) {
     /*-------- data file ----------*/        for (k=0; k<= maxncov; k++) {
     if((ficres =fopen(fileres,"w"))==NULL) {          if (Ndum[k] != 0) {
       printf("Problem with resultfile: %s\n", fileres);goto end;            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; */
     fprintf(ficres,"#%s\n",version);            
                ij++;
     if((fic=fopen(datafile,"r"))==NULL)    {          }
       printf("Problem with datafile: %s\n", datafile);goto end;          if (ij > ncodemax[j]) break; 
     }        }  
       } 
     n= lastobs;    }  
     severity = vector(1,maxwav);  
     outcome=imatrix(1,maxwav+1,1,n);   for (k=0; k< maxncov; k++) Ndum[k]=0;
     num=ivector(1,n);  
     moisnais=vector(1,n);   for (i=1; i<=ncovmodel-2; i++) { 
     annais=vector(1,n);     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     moisdc=vector(1,n);     ij=Tvar[i];
     andc=vector(1,n);     Ndum[ij]++;
     agedc=vector(1,n);   }
     cod=ivector(1,n);  
     weight=vector(1,n);   ij=1;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */   for (i=1; i<= maxncov; i++) {
     mint=matrix(1,maxwav,1,n);     if((Ndum[i]!=0) && (i<=ncovcol)){
     anint=matrix(1,maxwav,1,n);       Tvaraff[ij]=i; /*For printing */
     s=imatrix(1,maxwav+1,1,n);       ij++;
     adl=imatrix(1,maxwav+1,1,n);         }
     tab=ivector(1,NCOVMAX);   }
     ncodemax=ivector(1,8);   
    cptcoveff=ij-1; /*Number of simple covariates*/
     i=1;  }
     while (fgets(line, MAXLINE, fic) != NULL)    {  
       if ((i >= firstobs) && (i <=lastobs)) {  /*********** Health Expectancies ****************/
          
         for (j=maxwav;j>=1;j--){  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 )
           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);    /* Health expectancies */
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
         }    double age, agelim, hf;
            double ***p3mat,***varhe;
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    double **dnewm,**doldm;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    double *xp;
     double **gp, **gm;
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    double ***gradg, ***trgradg;
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    int theta;
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
         for (j=ncov;j>=1;j--){    xp=vector(1,npar);
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    dnewm=matrix(1,nlstate*nlstate,1,npar);
         }    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
         num[i]=atol(stra);    
            fprintf(ficreseij,"# Health expectancies\n");
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    fprintf(ficreseij,"# Age");
           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;}*/    for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
         i=i+1;        fprintf(ficreseij," %1d-%1d (SE)",i,j);
       }    fprintf(ficreseij,"\n");
     }  
     /* printf("ii=%d", ij);    if(estepm < stepm){
        scanf("%d",i);*/      printf ("Problem %d lower than %d\n",estepm, stepm);
   imx=i-1; /* Number of individuals */    }
     else  hstepm=estepm;   
   /* for (i=1; i<=imx; i++){    /* We compute the life expectancy from trapezoids spaced every estepm months
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;     * This is mainly to measure the difference between two models: for example
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;     * if stepm=24 months pijx are given only every 2 years and by summing them
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;     * we are calculating an estimate of the Life Expectancy assuming a linear 
     }     * progression in between and thus overestimating or underestimating according
      * to the curvature of the survival function. If, for the same date, we 
     for (i=1; i<=imx; i++)     * estimate the model with stepm=1 month, we can keep estepm to 24 months
     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]));*/     * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
   /* Calculation of the number of parameter from char model*/     * curvature will be obtained if estepm is as small as stepm. */
   Tvar=ivector(1,15);  
   Tprod=ivector(1,15);    /* For example we decided to compute the life expectancy with the smallest unit */
   Tvaraff=ivector(1,15);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   Tvard=imatrix(1,15,1,2);       nhstepm is the number of hstepm from age to agelim 
   Tage=ivector(1,15);             nstepm is the number of stepm from age to agelin. 
           Look at hpijx to understand the reason of that which relies in memory size
   if (strlen(model) >1){       and note for a fixed period like estepm months */
     j=0, j1=0, k1=1, k2=1;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     j=nbocc(model,'+');       survival function given by stepm (the optimization length). Unfortunately it
     j1=nbocc(model,'*');       means that if the survival funtion is printed only each two years of age and if
     cptcovn=j+1;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     cptcovprod=j1;       results. So we changed our mind and took the option of the best precision.
        */
        hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     strcpy(modelsav,model);  
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    agelim=AGESUP;
       printf("Error. Non available option model=%s ",model);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       goto end;      /* nhstepm age range expressed in number of stepm */
     }      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
          /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     for(i=(j+1); i>=1;i--){      /* if (stepm >= YEARM) hstepm=1;*/
       cutv(stra,strb,modelsav,'+');      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
       /*scanf("%d",i);*/      gp=matrix(0,nhstepm,1,nlstate*nlstate);
       if (strchr(strb,'*')) {      gm=matrix(0,nhstepm,1,nlstate*nlstate);
         cutv(strd,strc,strb,'*');  
         if (strcmp(strc,"age")==0) {      /* Computed by stepm unit matrices, product of hstepm matrices, stored
           cptcovprod--;         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
           cutv(strb,stre,strd,'V');      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
           Tvar[i]=atoi(stre);   
           cptcovage++;  
             Tage[cptcovage]=i;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
             /*printf("stre=%s ", stre);*/  
         }      /* Computing Variances of health expectancies */
         else if (strcmp(strd,"age")==0) {  
           cptcovprod--;       for(theta=1; theta <=npar; theta++){
           cutv(strb,stre,strc,'V');        for(i=1; i<=npar; i++){ 
           Tvar[i]=atoi(stre);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
           cptcovage++;        }
           Tage[cptcovage]=i;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         }    
         else {        cptj=0;
           cutv(strb,stre,strc,'V');        for(j=1; j<= nlstate; j++){
           Tvar[i]=ncov+k1;          for(i=1; i<=nlstate; i++){
           cutv(strb,strc,strd,'V');            cptj=cptj+1;
           Tprod[k1]=i;            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
           Tvard[k1][1]=atoi(strc);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
           Tvard[k1][2]=atoi(stre);            }
           Tvar[cptcovn+k2]=Tvard[k1][1];          }
           Tvar[cptcovn+k2+1]=Tvard[k1][2];        }
           for (k=1; k<=lastobs;k++)       
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];       
           k1++;        for(i=1; i<=npar; i++) 
           k2=k2+2;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       }        
       else {        cptj=0;
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/        for(j=1; j<= nlstate; j++){
        /*  scanf("%d",i);*/          for(i=1;i<=nlstate;i++){
       cutv(strd,strc,strb,'V');            cptj=cptj+1;
       Tvar[i]=atoi(strc);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
       }  
       strcpy(modelsav,stra);                gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);            }
         scanf("%d",i);*/          }
     }        }
 }        for(j=1; j<= nlstate*nlstate; j++)
            for(h=0; h<=nhstepm-1; h++){
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   printf("cptcovprod=%d ", cptcovprod);          }
   scanf("%d ",i);*/       } 
     fclose(fic);     
   /* End theta */
     /*  if(mle==1){*/  
     if (weightopt != 1) { /* Maximisation without weights*/       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
       for(i=1;i<=n;i++) weight[i]=1.0;  
     }       for(h=0; h<=nhstepm-1; h++)
     /*-calculation of age at interview from date of interview and age at death -*/        for(j=1; j<=nlstate*nlstate;j++)
     agev=matrix(1,maxwav,1,imx);          for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
    for (i=1; i<=imx; i++)       
      for(m=2; (m<= maxwav); m++)  
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){       for(i=1;i<=nlstate*nlstate;i++)
          anint[m][i]=9999;        for(j=1;j<=nlstate*nlstate;j++)
          s[m][i]=-1;          varhe[i][j][(int)age] =0.;
        }  
           printf("%d|",(int)age);fflush(stdout);
     for (i=1; i<=imx; i++)  {       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);       for(h=0;h<=nhstepm-1;h++){
       for(m=1; (m<= maxwav); m++){        for(k=0;k<=nhstepm-1;k++){
         if(s[m][i] >0){          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
           if (s[m][i] == nlstate+1) {          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
             if(agedc[i]>0)          for(i=1;i<=nlstate*nlstate;i++)
               if(moisdc[i]!=99 && andc[i]!=9999)            for(j=1;j<=nlstate*nlstate;j++)
               agev[m][i]=agedc[i];              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
             else {        }
               if (andc[i]!=9999){      }
               printf("Warning negative age at death: %d line:%d\n",num[i],i);      /* Computing expectancies */
               agev[m][i]=-1;      for(i=1; i<=nlstate;i++)
               }        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;
           else if(s[m][i] !=9){ /* Should no more exist */            
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
             if(mint[m][i]==99 || anint[m][i]==9999)  
               agev[m][i]=1;          }
             else if(agev[m][i] <agemin){  
               agemin=agev[m][i];      fprintf(ficreseij,"%3.0f",age );
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/      cptj=0;
             }      for(i=1; i<=nlstate;i++)
             else if(agev[m][i] >agemax){        for(j=1; j<=nlstate;j++){
               agemax=agev[m][i];          cptj++;
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
             }        }
             /*agev[m][i]=anint[m][i]-annais[i];*/      fprintf(ficreseij,"\n");
             /*   agev[m][i] = age[i]+2*m;*/     
           }      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
           else { /* =9 */      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
             agev[m][i]=1;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
             s[m][i]=-1;      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
           }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         }    }
         else /*= 0 Unknown */    printf("\n");
           agev[m][i]=1;    fprintf(ficlog,"\n");
       }  
        free_vector(xp,1,npar);
     }    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     for (i=1; i<=imx; i++)  {    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
       for(m=1; (m<= maxwav); m++){    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
         if (s[m][i] > (nlstate+ndeath)) {  }
           printf("Error: Wrong value in nlstate or ndeath\n");    
           goto end;  /************ Variance ******************/
         }  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
       }  {
     }    /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    /* double **newm;*/
     double **dnewm,**doldm;
     free_vector(severity,1,maxwav);    double **dnewmp,**doldmp;
     free_imatrix(outcome,1,maxwav+1,1,n);    int i, j, nhstepm, hstepm, h, nstepm ;
     free_vector(moisnais,1,n);    int k, cptcode;
     free_vector(annais,1,n);    double *xp;
     /* free_matrix(mint,1,maxwav,1,n);    double **gp, **gm;  /* for var eij */
        free_matrix(anint,1,maxwav,1,n);*/    double ***gradg, ***trgradg; /*for var eij */
     free_vector(moisdc,1,n);    double **gradgp, **trgradgp; /* for var p point j */
     free_vector(andc,1,n);    double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
        double ***p3mat;
     wav=ivector(1,imx);    double age,agelim, hf;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    double ***mobaverage;
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    int theta;
        char digit[4];
     /* Concatenates waves */    char digitp[25];
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);  
     char fileresprobmorprev[FILENAMELENGTH];
   
       Tcode=ivector(1,100);    if(popbased==1){
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);      if(mobilav!=0)
       ncodemax[1]=1;        strcpy(digitp,"-populbased-mobilav-");
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);      else strcpy(digitp,"-populbased-nomobil-");
          }
    codtab=imatrix(1,100,1,10);    else 
    h=0;      strcpy(digitp,"-stablbased-");
    m=pow(2,cptcoveff);  
      if (mobilav!=0) {
    for(k=1;k<=cptcoveff; k++){      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      for(i=1; i <=(m/pow(2,k));i++){      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
        for(j=1; j <= ncodemax[k]; j++){        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){        printf(" Error in movingaverage mobilav=%d\n",mobilav);
            h++;      }
            if (h>m) h=1;codtab[h][k]=j;    }
          }  
        }    strcpy(fileresprobmorprev,"prmorprev"); 
      }    sprintf(digit,"%-d",ij);
    }    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
        strcat(fileresprobmorprev,digit); /* Tvar to be done */
    /* Calculates basic frequencies. Computes observed prevalence at single age    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
        and prints on file fileres'p'. */    strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
          printf("Problem with resultfile: %s\n", fileresprobmorprev);
          fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    }
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    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);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
          for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     /* For Powell, parameters are in a vector p[] starting at p[1]      fprintf(ficresprobmorprev," p.%-d SE",j);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */      for(i=1; i<=nlstate;i++)
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
     if(mle==1){    fprintf(ficresprobmorprev,"\n");
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
     }      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
          fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
     /*--------- results files --------------*/      exit(0);
     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{
       fprintf(ficgp,"\n# Routine varevsij");
    jk=1;    }
    fprintf(ficres,"# Parameters\n");    if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
    printf("# Parameters\n");      printf("Problem with html file: %s\n", optionfilehtm);
    for(i=1,jk=1; i <=nlstate; i++){      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
      for(k=1; k <=(nlstate+ndeath); k++){      exit(0);
        if (k != i)    }
          {    else{
            printf("%d%d ",i,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");
            fprintf(ficres,"%1d%1d ",i,k);      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
            for(j=1; j <=ncovmodel; j++){    }
              printf("%f ",p[jk]);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
              fprintf(ficres,"%f ",p[jk]);  
              jk++;    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(ficresvij,"# Age");
            printf("\n");    for(i=1; i<=nlstate;i++)
            fprintf(ficres,"\n");      for(j=1; j<=nlstate;j++)
          }        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
      }    fprintf(ficresvij,"\n");
    }  
  if(mle==1){    xp=vector(1,npar);
     /* Computing hessian and covariance matrix */    dnewm=matrix(1,nlstate,1,npar);
     ftolhess=ftol; /* Usually correct */    doldm=matrix(1,nlstate,1,nlstate);
     hesscov(matcov, p, npar, delti, ftolhess, func);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
  }    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     fprintf(ficres,"# Scales\n");  
     printf("# Scales\n");    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
      for(i=1,jk=1; i <=nlstate; i++){    gpp=vector(nlstate+1,nlstate+ndeath);
       for(j=1; j <=nlstate+ndeath; j++){    gmp=vector(nlstate+1,nlstate+ndeath);
         if (j!=i) {    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
           fprintf(ficres,"%1d%1d",i,j);    
           printf("%1d%1d",i,j);    if(estepm < stepm){
           for(k=1; k<=ncovmodel;k++){      printf ("Problem %d lower than %d\n",estepm, stepm);
             printf(" %.5e",delti[jk]);    }
             fprintf(ficres," %.5e",delti[jk]);    else  hstepm=estepm;   
             jk++;    /* For example we decided to compute the life expectancy with the smallest unit */
           }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           printf("\n");       nhstepm is the number of hstepm from age to agelim 
           fprintf(ficres,"\n");       nstepm is the number of stepm from age to agelin. 
         }       Look at hpijx to understand the reason of that which relies in memory size
       }       and note for a fixed period like k years */
      }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           survival function given by stepm (the optimization length). Unfortunately it
     k=1;       means that if the survival funtion is printed every two years of age and if
     fprintf(ficres,"# Covariance\n");       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     printf("# Covariance\n");       results. So we changed our mind and took the option of the best precision.
     for(i=1;i<=npar;i++){    */
       /*  if (k>nlstate) k=1;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       i1=(i-1)/(ncovmodel*nlstate)+1;    agelim = AGESUP;
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       printf("%s%d%d",alph[k],i1,tab[i]);*/      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       fprintf(ficres,"%3d",i);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       printf("%3d",i);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       for(j=1; j<=i;j++){      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
         fprintf(ficres," %.5e",matcov[i][j]);      gp=matrix(0,nhstepm,1,nlstate);
         printf(" %.5e",matcov[i][j]);      gm=matrix(0,nhstepm,1,nlstate);
       }  
       fprintf(ficres,"\n");  
       printf("\n");      for(theta=1; theta <=npar; theta++){
       k++;        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
     }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
            }
     while((c=getc(ficpar))=='#' && c!= EOF){        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       ungetc(c,ficpar);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       fgets(line, MAXLINE, ficpar);  
       puts(line);        if (popbased==1) {
       fputs(line,ficparo);          if(mobilav ==0){
     }            for(i=1; i<=nlstate;i++)
     ungetc(c,ficpar);              prlim[i][i]=probs[(int)age][i][ij];
            }else{ /* mobilav */ 
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);            for(i=1; i<=nlstate;i++)
                  prlim[i][i]=mobaverage[(int)age][i][ij];
     if (fage <= 2) {          }
       bage = agemin;        }
       fage = agemax;    
     }        for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
     fprintf(ficres,"# agemin agemax for life expectancy.\n");            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
     fprintf(ficres,"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);        }
          /* This for computing probability of death (h=1 means
     while((c=getc(ficpar))=='#' && c!= EOF){           computed over hstepm matrices product = hstepm*stepm months) 
     ungetc(c,ficpar);           as a weighted average of prlim.
     fgets(line, MAXLINE, ficpar);        */
     puts(line);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     fputs(line,ficparo);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
   }            gpp[j] += prlim[i][i]*p3mat[i][j][1];
   ungetc(c,ficpar);        }    
          /* end probability of death */
   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);  
   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);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
  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);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
              hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   while((c=getc(ficpar))=='#' && c!= EOF){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     ungetc(c,ficpar);   
     fgets(line, MAXLINE, ficpar);        if (popbased==1) {
     puts(line);          if(mobilav ==0){
     fputs(line,ficparo);            for(i=1; i<=nlstate;i++)
   }              prlim[i][i]=probs[(int)age][i][ij];
   ungetc(c,ficpar);          }else{ /* mobilav */ 
              for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
    dateprev1=anprev1+mprev1/12.+jprev1/365.;          }
    dateprev2=anprev2+mprev2/12.+jprev2/365.;        }
   
   fscanf(ficpar,"pop_based=%d\n",&popbased);        for(j=1; j<= nlstate; j++){
    fprintf(ficparo,"pop_based=%d\n",popbased);            for(h=0; h<=nhstepm; h++){
    fprintf(ficres,"pop_based=%d\n",popbased);              for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   while((c=getc(ficpar))=='#' && c!= EOF){          }
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);        /* This for computing probability of death (h=1 means
     puts(line);           computed over hstepm matrices product = hstepm*stepm months) 
     fputs(line,ficparo);           as a weighted average of prlim.
   }        */
   ungetc(c,ficpar);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   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);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
 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);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
 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);        }    
         /* end probability of death */
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);  
         for(j=1; j<= nlstate; j++) /* vareij */
  /*------------ gnuplot -------------*/          for(h=0; h<=nhstepm; h++){
 chdir(pathcd);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   if((ficgp=fopen("graph.plt","w"))==NULL) {          }
     printf("Problem with file graph.gp");goto end;  
   }        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
 #ifdef windows          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   fprintf(ficgp,"cd \"%s\" \n",pathc);        }
 #endif  
 m=pow(2,cptcoveff);      } /* End theta */
    
  /* 1eme*/      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   for (cpt=1; cpt<= nlstate ; cpt ++) {  
    for (k1=1; k1<= m ; k1 ++) {      for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
 #ifdef windows          for(theta=1; theta <=npar; theta++)
     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);            trgradg[h][j][theta]=gradg[h][theta][j];
 #endif  
 #ifdef unix      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);        for(theta=1; theta <=npar; theta++)
 #endif          trgradgp[j][theta]=gradgp[theta][j];
     
 for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for(i=1;i<=nlstate;i++)
 }        for(j=1;j<=nlstate;j++)
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);          vareij[i][j][(int)age] =0.;
     for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      for(h=0;h<=nhstepm;h++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for(k=0;k<=nhstepm;k++){
 }          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
      for (i=1; i<= nlstate ; i ++) {          for(i=1;i<=nlstate;i++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            for(j=1;j<=nlstate;j++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
 }          }
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      }
 #ifdef unix    
 fprintf(ficgp,"\nset ter gif small size 400,300");      /* pptj */
 #endif      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
    }      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   }        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   /*2 eme*/          varppt[j][i]=doldmp[j][i];
       /* end ppptj */
   for (k1=1; k1<= m ; k1 ++) {      /*  x centered again */
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
          prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
     for (i=1; i<= nlstate+1 ; i ++) {   
       k=2*i;      if (popbased==1) {
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);        if(mobilav ==0){
       for (j=1; j<= nlstate+1 ; j ++) {          for(i=1; i<=nlstate;i++)
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            prlim[i][i]=probs[(int)age][i][ij];
   else fprintf(ficgp," \%%*lf (\%%*lf)");        }else{ /* mobilav */ 
 }            for(i=1; i<=nlstate;i++)
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");            prlim[i][i]=mobaverage[(int)age][i][ij];
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        }
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);      }
       for (j=1; j<= nlstate+1 ; j ++) {               
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      /* This for computing probability of death (h=1 means
         else fprintf(ficgp," \%%*lf (\%%*lf)");         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
 }           as a weighted average of prlim.
       fprintf(ficgp,"\" t\"\" w l 0,");      */
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
       for (j=1; j<= nlstate+1 ; j ++) {        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");      }    
 }        /* end probability of death */
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");  
       else fprintf(ficgp,"\" t\"\" w l 0,");      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
     }      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
   }        for(i=1; i<=nlstate;i++){
            fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   /*3eme*/        }
       } 
   for (k1=1; k1<= m ; k1 ++) {      fprintf(ficresprobmorprev,"\n");
     for (cpt=1; cpt<= nlstate ; cpt ++) {  
       k=2+nlstate*(cpt-1);      fprintf(ficresvij,"%.0f ",age );
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);      for(i=1; i<=nlstate;i++)
       for (i=1; i< nlstate ; i ++) {        for(j=1; j<=nlstate;j++){
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
       }        }
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      fprintf(ficresvij,"\n");
     }      free_matrix(gp,0,nhstepm,1,nlstate);
   }      free_matrix(gm,0,nhstepm,1,nlstate);
        free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   /* CV preval stat */      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
   for (k1=1; k1<= m ; k1 ++) {      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     for (cpt=1; cpt<nlstate ; cpt ++) {    } /* End age */
       k=3;    free_vector(gpp,nlstate+1,nlstate+ndeath);
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);    free_vector(gmp,nlstate+1,nlstate+ndeath);
       for (i=1; i< nlstate ; i ++)    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
         fprintf(ficgp,"+$%d",k+i+1);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    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 */
       l=3+(nlstate+ndeath)*cpt;    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
       for (i=1; i< nlstate ; i ++) {  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
         l=3+(nlstate+ndeath)*cpt;  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
         fprintf(ficgp,"+$%d",l+i+1);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",fileresprobmorprev);
       }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",fileresprobmorprev);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",fileresprobmorprev);
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);
     }    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"varmuptjgr%s%s%s.png\"> <br>\n", estepm,digitp,optionfilefiname,digit);
   }      /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   /* proba elementaires */    fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit);
    for(i=1,jk=1; i <=nlstate; i++){  
     for(k=1; k <=(nlstate+ndeath); k++){    free_vector(xp,1,npar);
       if (k != i) {    free_matrix(doldm,1,nlstate,1,nlstate);
         for(j=1; j <=ncovmodel; j++){    free_matrix(dnewm,1,nlstate,1,npar);
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           /*fprintf(ficgp,"%s",alph[1]);*/    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           jk++;    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           fprintf(ficgp,"\n");    fclose(ficresprobmorprev);
         }    fclose(ficgp);
       }    fclose(fichtm);
     }  }  /* end varevsij */
     }  
   /************ Variance of prevlim ******************/
   for(jk=1; jk <=m; jk++) {  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,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);  {
    i=1;    /* Variance of prevalence limit */
    for(k2=1; k2<=nlstate; k2++) {    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
      k3=i;    double **newm;
      for(k=1; k<=(nlstate+ndeath); k++) {    double **dnewm,**doldm;
        if (k != k2){    int i, j, nhstepm, hstepm;
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    int k, cptcode;
 ij=1;    double *xp;
         for(j=3; j <=ncovmodel; j++) {    double *gp, *gm;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    double **gradg, **trgradg;
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    double age,agelim;
             ij++;    int theta;
           }     
           else    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    fprintf(ficresvpl,"# Age");
         }    for(i=1; i<=nlstate;i++)
           fprintf(ficgp,")/(1");        fprintf(ficresvpl," %1d-%1d",i,i);
            fprintf(ficresvpl,"\n");
         for(k1=1; k1 <=nlstate; k1++){    
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    xp=vector(1,npar);
 ij=1;    dnewm=matrix(1,nlstate,1,npar);
           for(j=3; j <=ncovmodel; j++){    doldm=matrix(1,nlstate,1,nlstate);
           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]]]);    hstepm=1*YEARM; /* Every year of age */
             ij++;    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
           }    agelim = AGESUP;
           else    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           }      if (stepm >= YEARM) hstepm=1;
           fprintf(ficgp,")");      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
         }      gradg=matrix(1,npar,1,nlstate);
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);      gp=vector(1,nlstate);
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");      gm=vector(1,nlstate);
         i=i+ncovmodel;  
        }      for(theta=1; theta <=npar; theta++){
      }        for(i=1; i<=npar; i++){ /* Computes gradient */
    }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);        }
   }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
            for(i=1;i<=nlstate;i++)
   fclose(ficgp);          gp[i] = prlim[i][i];
          
 chdir(path);        for(i=1; i<=npar; i++) /* Computes gradient */
              xp[i] = x[i] - (i==theta ?delti[theta]:0);
     free_ivector(wav,1,imx);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        for(i=1;i<=nlstate;i++)
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);            gm[i] = prlim[i][i];
     free_ivector(num,1,n);  
     free_vector(agedc,1,n);        for(i=1;i<=nlstate;i++)
     /*free_matrix(covar,1,NCOVMAX,1,n);*/          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
     fclose(ficparo);      } /* End theta */
     fclose(ficres);  
     /*  }*/      trgradg =matrix(1,nlstate,1,npar);
      
    /*________fin mle=1_________*/      for(j=1; j<=nlstate;j++)
            for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
    
     /* No more information from the sample is required now */      for(i=1;i<=nlstate;i++)
   /* Reads comments: lines beginning with '#' */        varpl[i][(int)age] =0.;
   while((c=getc(ficpar))=='#' && c!= EOF){      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
     ungetc(c,ficpar);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
     fgets(line, MAXLINE, ficpar);      for(i=1;i<=nlstate;i++)
     puts(line);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
     fputs(line,ficparo);  
   }      fprintf(ficresvpl,"%.0f ",age );
   ungetc(c,ficpar);      for(i=1; i<=nlstate;i++)
          fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);      fprintf(ficresvpl,"\n");
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);      free_vector(gp,1,nlstate);
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);      free_vector(gm,1,nlstate);
 /*--------- index.htm --------*/      free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
   strcpy(optionfilehtm,optionfile);    } /* End age */
   strcat(optionfilehtm,".htm");  
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    free_vector(xp,1,npar);
     printf("Problem with %s \n",optionfilehtm);goto end;    free_matrix(doldm,1,nlstate,1,npar);
   }    free_matrix(dnewm,1,nlstate,1,nlstate);
   
  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>  
 Total number of observations=%d <br>  /************ Variance of one-step probabilities  ******************/
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
 <hr  size=\"2\" color=\"#EC5E5E\">  {
 <li>Outputs files<br><br>\n    int i, j=0,  i1, k1, l1, t, tj;
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    int k2, l2, j1,  z1;
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>    int k=0,l, cptcode;
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>    int first=1, first1;
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    double **dnewm,**doldm;
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>    double *xp;
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>    double *gp, *gm;
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    double **gradg, **trgradg;
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>    double **mu;
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>    double age,agelim, cov[NCOVMAX];
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
  fprintf(fichtm," <li>Graphs</li><p>");    char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
  m=cptcoveff;    char fileresprobcor[FILENAMELENGTH];
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}  
     double ***varpij;
  j1=0;  
  for(k1=1; k1<=m;k1++){    strcpy(fileresprob,"prob"); 
    for(i1=1; i1<=ncodemax[k1];i1++){    strcat(fileresprob,fileres);
        j1++;    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
        if (cptcovn > 0) {      printf("Problem with resultfile: %s\n", fileresprob);
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
          for (cpt=1; cpt<=cptcoveff;cpt++)    }
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);    strcpy(fileresprobcov,"probcov"); 
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    strcat(fileresprobcov,fileres);
        }    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>      printf("Problem with resultfile: %s\n", fileresprobcov);
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);          fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
        for(cpt=1; cpt<nlstate;cpt++){    }
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    strcpy(fileresprobcor,"probcor"); 
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    strcat(fileresprobcor,fileres);
        }    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
     for(cpt=1; cpt<=nlstate;cpt++) {      printf("Problem with resultfile: %s\n", fileresprobcor);
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
 interval) in state (%d): v%s%d%d.gif <br>    }
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
      }    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
      for(cpt=1; cpt<=nlstate;cpt++) {    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
      }    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    
 health expectancies in states (1) and (2): e%s%d.gif<br>    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);    fprintf(ficresprob,"# Age");
 fprintf(fichtm,"\n</body>");    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
    }    fprintf(ficresprobcov,"# Age");
  }    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
 fclose(fichtm);    fprintf(ficresprobcov,"# Age");
   
   /*--------------- Prevalence limit --------------*/  
      for(i=1; i<=nlstate;i++)
   strcpy(filerespl,"pl");      for(j=1; j<=(nlstate+ndeath);j++){
   strcat(filerespl,fileres);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {        fprintf(ficresprobcov," p%1d-%1d ",i,j);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;        fprintf(ficresprobcor," p%1d-%1d ",i,j);
   }      }  
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);   /* fprintf(ficresprob,"\n");
   fprintf(ficrespl,"#Prevalence limit\n");    fprintf(ficresprobcov,"\n");
   fprintf(ficrespl,"#Age ");    fprintf(ficresprobcor,"\n");
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);   */
   fprintf(ficrespl,"\n");   xp=vector(1,npar);
      dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   prlim=matrix(1,nlstate,1,nlstate);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    first=1;
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      printf("Problem with gnuplot file: %s\n", optionfilegnuplot);
   k=0;      fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);
   agebase=agemin;      exit(0);
   agelim=agemax;    }
   ftolpl=1.e-10;    else{
   i1=cptcoveff;      fprintf(ficgp,"\n# Routine varprob");
   if (cptcovn < 1){i1=1;}    }
     if((fichtm=fopen(optionfilehtm,"a"))==NULL) {
   for(cptcov=1;cptcov<=i1;cptcov++){      printf("Problem with html file: %s\n", optionfilehtm);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);
         k=k+1;      exit(0);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    }
         fprintf(ficrespl,"\n#******");    else{
         for(j=1;j<=cptcoveff;j++)      fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      fprintf(fichtm,"\n");
         fprintf(ficrespl,"******\n");  
              fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
         for (age=agebase; age<=agelim; age++){      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");
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      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");
           fprintf(ficrespl,"%.0f",age );  
           for(i=1; i<=nlstate;i++)    }
           fprintf(ficrespl," %.5f", prlim[i][i]);  
           fprintf(ficrespl,"\n");    cov[1]=1;
         }    tj=cptcoveff;
       }    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     }    j1=0;
   fclose(ficrespl);    for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
   /*------------- h Pij x at various ages ------------*/        j1++;
          if  (cptcovn>0) {
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);          fprintf(ficresprob, "\n#********** Variable "); 
   if((ficrespij=fopen(filerespij,"w"))==NULL) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;          fprintf(ficresprob, "**********\n#\n");
   }          fprintf(ficresprobcov, "\n#********** Variable "); 
   printf("Computing pij: result on file '%s' \n", filerespij);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficresprobcov, "**********\n#\n");
   stepsize=(int) (stepm+YEARM-1)/YEARM;          
   /*if (stepm<=24) stepsize=2;*/          fprintf(ficgp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   agelim=AGESUP;          fprintf(ficgp, "**********\n#\n");
   hstepm=stepsize*YEARM; /* Every year of age */          
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */          
            fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   k=0;          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   for(cptcov=1;cptcov<=i1;cptcov++){          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          
       k=k+1;          fprintf(ficresprobcor, "\n#********** Variable ");    
         fprintf(ficrespij,"\n#****** ");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         for(j=1;j<=cptcoveff;j++)          fprintf(ficresprobcor, "**********\n#");    
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        }
         fprintf(ficrespij,"******\n");        
                for (age=bage; age<=fage; age ++){ 
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          cov[2]=age;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          for (k=1; k<=cptcovn;k++) {
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
           oldm=oldms;savm=savms;          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            for (k=1; k<=cptcovprod;k++)
           fprintf(ficrespij,"# Age");            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<=nlstate;i++)          
             for(j=1; j<=nlstate+ndeath;j++)          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
               fprintf(ficrespij," %1d-%1d",i,j);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           fprintf(ficrespij,"\n");          gp=vector(1,(nlstate)*(nlstate+ndeath));
           for (h=0; h<=nhstepm; h++){          gm=vector(1,(nlstate)*(nlstate+ndeath));
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );      
             for(i=1; i<=nlstate;i++)          for(theta=1; theta <=npar; theta++){
               for(j=1; j<=nlstate+ndeath;j++)            for(i=1; i<=npar; i++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             fprintf(ficrespij,"\n");            
           }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            
           fprintf(ficrespij,"\n");            k=0;
         }            for(i=1; i<= (nlstate); i++){
     }              for(j=1; j<=(nlstate+ndeath);j++){
   }                k=k+1;
                 gp[k]=pmmij[i][j];
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/              }
             }
   fclose(ficrespij);            
             for(i=1; i<=npar; i++)
   /*---------- Forecasting ------------------*/              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;      
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);            k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
   strcpy(fileresf,"f");                k=k+1;
   strcat(fileresf,fileres);                gm[k]=pmmij[i][j];
   if((ficresf=fopen(fileresf,"w"))==NULL) {              }
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;            }
   }       
   printf("Computing forecasting: result on file '%s' \n", fileresf);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
   free_matrix(mint,1,maxwav,1,n);          }
   free_matrix(anint,1,maxwav,1,n);  
   free_matrix(agev,1,maxwav,1,imx);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
   /* Mobile average */            for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          
           matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
   if (mobilav==1) {          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
       for (i=1; i<=nlstate;i++)          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           mobaverage[(int)agedeb][i][cptcod]=0.;  
              pmij(pmmij,cov,ncovmodel,x,nlstate);
     for (agedeb=bage+4; agedeb<=fage; agedeb++){          
       for (i=1; i<=nlstate;i++){          k=0;
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          for(i=1; i<=(nlstate); i++){
           for (cpt=0;cpt<=4;cpt++){            for(j=1; j<=(nlstate+ndeath);j++){
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];              k=k+1;
           }              mu[k][(int) age]=pmmij[i][j];
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;            }
         }          }
       }          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
     }              for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
   }              varpij[i][j][(int)age] = doldm[i][j];
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;          /*printf("\n%d ",(int)age);
   if (stepm<=12) stepsize=1;            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   agelim=AGESUP;            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   /*hstepm=stepsize*YEARM; *//* Every year of age */            }*/
   hstepm=1;  
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */          fprintf(ficresprob,"\n%d ",(int)age);
   yp1=modf(dateintmean,&yp);          fprintf(ficresprobcov,"\n%d ",(int)age);
   anprojmean=yp;          fprintf(ficresprobcor,"\n%d ",(int)age);
   yp2=modf((yp1*12),&yp);  
   mprojmean=yp;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
   yp1=modf((yp2*30.5),&yp);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
   jprojmean=yp;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   if(jprojmean==0) jprojmean=1;            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   if(mprojmean==0) jprojmean=1;            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);          i=0;
           for (k=1; k<=(nlstate);k++){
   if (popforecast==1) {            for (l=1; l<=(nlstate+ndeath);l++){ 
     if((ficpop=fopen(popfile,"r"))==NULL)    {              i=i++;
       printf("Problem with population file : %s\n",popfile);goto end;              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
     }              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
     popage=ivector(0,AGESUP);              for (j=1; j<=i;j++){
     popeffectif=vector(0,AGESUP);                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
     popcount=vector(0,AGESUP);                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
     i=1;              }
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)          }/* end of loop for state */
       {        } /* end of loop for age */
         i=i+1;  
       }        /* Confidence intervalle of pij  */
     imx=i;        /*
              fprintf(ficgp,"\nset noparametric;unset label");
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   }          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
   for(cptcov=1;cptcov<=i1;cptcov++){          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
       k=k+1;          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
       fprintf(ficresf,"\n#******");        */
       for(j=1;j<=cptcoveff;j++) {  
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
       }        first1=1;
       fprintf(ficresf,"******\n");        for (k2=1; k2<=(nlstate);k2++){
       fprintf(ficresf,"# StartingAge FinalAge");          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);            if(l2==k2) continue;
       if (popforecast==1)  fprintf(ficresf," [Population]");            j=(k2-1)*(nlstate+ndeath)+l2;
              for (k1=1; k1<=(nlstate);k1++){
       for (cpt=0; cpt<=5;cpt++) {              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
         fprintf(ficresf,"\n");                if(l1==k1) continue;
   fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);                  i=(k1-1)*(nlstate+ndeath)+l1;
       for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(bage-((int)calagedate %12)/12.); agedeb--){ /* If stepm=6 months */                if(i<=j) continue;
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);                for (age=bage; age<=fage; age ++){ 
         nhstepm = nhstepm/hstepm;                  if ((int)age %5==0){
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
         oldm=oldms;savm=savms;                    mu1=mu[i][(int) age]/stepm*YEARM ;
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                      mu2=mu[j][(int) age]/stepm*YEARM;
                                    c12=cv12/sqrt(v1*v2);
         for (h=0; h<=nhstepm; h++){                    /* Computing eigen value of matrix of covariance */
           if (h==(int) (calagedate+YEARM*cpt)) {                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
             fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
           }                    /* Eigen vectors */
           for(j=1; j<=nlstate+ndeath;j++) {                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
             kk1=0.;kk2=0;                    /*v21=sqrt(1.-v11*v11); *//* error */
             for(i=1; i<=nlstate;i++) {                            v21=(lc1-v1)/cv12*v11;
               if (mobilav==1)                    v12=-v21;
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];                    v22=v11;
               else {                    tnalp=v21/v11;
                 kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];                    if(first1==1){
                 /* fprintf(ficresf," p3=%.3f p=%.3f ", p3mat[i][j][h], probs[(int)(agedeb)+1][i][cptcod]);*/                      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 (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
             }                    /*printf(fignu*/
                              /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
             if (h==(int)(calagedate+12*cpt)){                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
               fprintf(ficresf," %.3f", kk1);                    if(first==1){
                                    first=0;
               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);                      fprintf(ficgp,"\nset parametric;unset label");
             }                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
           }                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
         }                      fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                      fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);
       }                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
       }                      fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);
     }                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   }                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                      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",\
   if (popforecast==1) {                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     free_ivector(popage,0,AGESUP);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     free_vector(popeffectif,0,AGESUP);                    }else{
     free_vector(popcount,0,AGESUP);                      first=0;
   }                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
   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,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   fclose(ficresf);                      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",\
   /*---------- Health expectancies and variances ------------*/                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   strcpy(filerest,"t");                    }/* if first */
   strcat(filerest,fileres);                  } /* age mod 5 */
   if((ficrest=fopen(filerest,"w"))==NULL) {                } /* end loop age */
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;                fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);
   }                first=1;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);              } /*l12 */
             } /* k12 */
           } /*l1 */
   strcpy(filerese,"e");        }/* k1 */
   strcat(filerese,fileres);      } /* loop covariates */
   if((ficreseij=fopen(filerese,"w"))==NULL) {    }
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   }    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    free_vector(xp,1,npar);
     fclose(ficresprob);
  strcpy(fileresv,"v");    fclose(ficresprobcov);
   strcat(fileresv,fileres);    fclose(ficresprobcor);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    fclose(ficgp);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    fclose(fichtm);
   }  }
   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=\"p%s\">p%s</a> <br>\n \
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);   - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n \
       fprintf(ficresvij,"******\n");   - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n \
    - Life expectancies by age and initial health status (estepm=%2d months): \
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);     <a href=\"e%s\">e%s</a> <br>\n</li>", \
       oldm=oldms;savm=savms;    jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);    
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
       oldm=oldms;savm=savms;  
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);   m=cptcoveff;
         if (cptcovn < 1) {m=1;ncodemax[1]=1;}
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");  
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);   jj1=0;
       fprintf(ficrest,"\n");   for(k1=1; k1<=m;k1++){
             for(i1=1; i1<=ncodemax[k1];i1++){
       hf=1;       jj1++;
       if (stepm >= YEARM) hf=stepm/YEARM;       if (cptcovn > 0) {
       epj=vector(1,nlstate+1);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
       for(age=bage; age <=fage ;age++){         for (cpt=1; cpt<=cptcoveff;cpt++) 
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
         if (popbased==1) {         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
           for(i=1; i<=nlstate;i++)       }
             prlim[i][i]=probs[(int)age][i][k];       /* Pij */
         }       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: pe%s%d1.png<br> \
          <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
         fprintf(ficrest," %.0f",age);       /* Quasi-incidences */
         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\
           for(i=1, epj[j]=0.;i <=nlstate;i++) {   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br> \
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];  <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1); 
           }         /* Stable prevalence in each health state */
           epj[nlstate+1] +=epj[j];         for(cpt=1; cpt<nlstate;cpt++){
         }           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
         for(i=1, vepp=0.;i <=nlstate;i++)  <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
           for(j=1;j <=nlstate;j++)         }
             vepp += vareij[i][j][(int)age];       for(cpt=1; cpt<=nlstate;cpt++) {
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br> \
         for(j=1;j <=nlstate;j++){  <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));       }
         }       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
         fprintf(ficrest,"\n");  health expectancies in states (1) and (2): e%s%d.png<br>\
       }  <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);
     }     } /* end i1 */
   }   }/* End k1 */
           fprintf(fichtm,"</ul>");
          
   
    fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
  fclose(ficreseij);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
  fclose(ficresvij);   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n\
   fclose(ficrest);   - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n\
   fclose(ficpar);   - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n\
   free_vector(epj,1,nlstate+1);   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n\
   /*  scanf("%d ",i); */   - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n\
    - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);
   /*------- Variance limit prevalence------*/    
   /*  if(popforecast==1) fprintf(fichtm,"\n */
 strcpy(fileresvpl,"vpl");  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   strcat(fileresvpl,fileres);  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  /*      <br>",fileres,fileres,fileres,fileres); */
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);  /*  else  */
     exit(0);  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
   }  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);  
    m=cptcoveff;
  k=0;   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
  for(cptcov=1;cptcov<=i1;cptcov++){  
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){   jj1=0;
      k=k+1;   for(k1=1; k1<=m;k1++){
      fprintf(ficresvpl,"\n#****** ");     for(i1=1; i1<=ncodemax[k1];i1++){
      for(j=1;j<=cptcoveff;j++)       jj1++;
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       if (cptcovn > 0) {
      fprintf(ficresvpl,"******\n");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
               for (cpt=1; cpt<=cptcoveff;cpt++) 
      varpl=matrix(1,nlstate,(int) bage, (int) fage);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
      oldm=oldms;savm=savms;         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);       }
    }       for(cpt=1; cpt<=nlstate;cpt++) {
  }         fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
   interval) in state (%d): v%s%d%d.png <br>\
   fclose(ficresvpl);  <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
        }
   /*---------- End : free ----------------*/     } /* end i1 */
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);   }/* End k1 */
     fprintf(fichtm,"</ul>");
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  fclose(fichtm);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);  }
    
    /******************* Gnuplot file **************/
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);  void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    int ng;
      if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {
   free_matrix(matcov,1,npar,1,npar);      printf("Problem with file %s",optionfilegnuplot);
   free_vector(delti,1,npar);      fprintf(ficlog,"Problem with file %s",optionfilegnuplot);
      }
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);  
     /*#ifdef windows */
   printf("End of Imach\n");      fprintf(ficgp,"cd \"%s\" \n",pathc);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      /*#endif */
    m=pow(2,cptcoveff);
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/    
   /*printf("Total time was %d uSec.\n", total_usecs);*/   /* 1eme*/
   /*------ End -----------*/    for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
  end:       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);
 #ifdef windows  
  chdir(pathcd);       for (i=1; i<= nlstate ; i ++) {
 #endif         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
  system("..\\gp37mgw\\wgnuplot graph.plt");       }
        fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",fileres,k1-1,k1-1);
 #ifdef windows       for (i=1; i<= nlstate ; i ++) {
   while (z[0] != 'q') {         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     chdir(pathcd);         else fprintf(ficgp," \%%*lf (\%%*lf)");
     printf("\nType e to edit output files, c to start again, and q for exiting: ");       } 
     scanf("%s",z);       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",fileres,k1-1,k1-1); 
     if (z[0] == 'c') system("./imach");       for (i=1; i<= nlstate ; i ++) {
     else if (z[0] == 'e') {         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
       chdir(path);         else fprintf(ficgp," \%%*lf (\%%*lf)");
       system(optionfilehtm);       }  
     }       fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));
     else if (z[0] == 'q') exit(0);     }
   }    }
 #endif    /*2 eme*/
 }    
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
         fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);
           
         } 
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fclose(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int jj;
     int numlinepar=0; /* Current linenumber of parameter file */
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[132],pathc[132],pathcd[132],pathtot[132],model[132];
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   
     char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
     char z[1]="c", occ;
   #include <sys/time.h>
   #include <time.h>
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char *strt, *strtend;
     char *stratrunc;
     int lstra;
   
     long total_usecs;
     struct timeval start_time, end_time, curr_time;
     struct timezone tzp;
     extern int gettimeofday();
     struct tm tmg, tm, *gmtime(), *localtime();
     long time_value;
     extern long time();
    
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strt=asctime(&tm);
   /*  printf("Localtime (at start)=%s",strt); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strt);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strt=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strt); 
   */
   
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, 132)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     replace(pathc,path);
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: ");
     fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("Localtime (at start)=%s",strt); 
     fprintf(ficlog,"Localtime (at start)=%s",strt); 
     fflush(ficlog);
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) {
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     
     /* Read guess parameters */
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++){
       j=0;
       for(jj=1; jj <=nlstate+ndeath; jj++){
         if(jj==i) continue;
         j++;
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1 != i) && (j1 != j)){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);
         }
         fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)
           printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);
           if(mle==1){
             printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);
           }
           else
             fprintf(ficlog," %lf",param[i][j][k]);
           fprintf(ficparo," %lf",param[i][j][k]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     }  
     fflush(ficlog);
   
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1-i)*(j1-j)!=0){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);
         }
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         fprintf(ficlog,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);
           fprintf(ficlog," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
         fprintf(ficlog,"\n");
       }
     }
     fflush(ficlog);
   
     delti=delti3[1][1];
   
   
     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);
       if(mle==1)
         printf("%s",str);
       fprintf(ficlog,"%s",str);
       fprintf(ficparo,"%s",str);
       for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
           printf(" %.5le",matcov[i][j]);
         }
         fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       numlinepar++;
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
     for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];
      
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
   
     fflush(ficlog);
   
     /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         lstra=strlen(stra);
         if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
           stratrunc = &(stra[lstra-9]);
           num[i]=atol(stratrunc);
         }
         else
           num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /* 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);
   
       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 ipmx number of contributions and 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);*/
   
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     fclose(ficgp);
     printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfile);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",\
             version,title,datafile,firstpass,lastpass,stepm, weightopt,\
             model,imx,agemin,agemax,jmin,jmax,jmean,fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot);
     fclose(fichtm);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     chdir(path);
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_lvector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
   /*      }  */
   /*      else{ */
   /*        erreur=108; */
   /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*      } */
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     /*  fclose(fichtm);*/
     /*  fclose(ficgp);*/ /* ALready done */
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strtend=asctime(&tm);
     printf("Localtime at start %s and at end=%s",strt, strtend); 
     fprintf(ficlog,"Localtime at start %s and at end=%s",strt, strtend); 
     /*  printf("Total time used %d Sec\n", asc_time(end_time.tv_sec -start_time.tv_sec);*/
   
     printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
     fprintf(ficlog,"Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
     /*------ End -----------*/
   
     end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
    /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     system(plotcmd);
     printf(" Wait...");
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   

Removed from v.1.20  
changed lines
  Added in v.1.85


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