Diff for /imach/src/imach.c between versions 1.47 and 1.88

version 1.47, 2002/06/10 13:12:01 version 1.88, 2003/06/23 17:54:56
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.88  2003/06/23 17:54:56  brouard
      * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.87  2003/06/18 12:26:01  brouard
   first survey ("cross") where individuals from different ages are    Version 0.96
   interviewed on their health status or degree of disability (in the  
   case of a health survey which is our main interest) -2- at least a    Revision 1.86  2003/06/17 20:04:08  brouard
   second wave of interviews ("longitudinal") which measure each change    (Module): Change position of html and gnuplot routines and added
   (if any) in individual health status.  Health expectancies are    routine fileappend.
   computed from the time spent in each health state according to a  
   model. More health states you consider, more time is necessary to reach the    Revision 1.85  2003/06/17 13:12:43  brouard
   Maximum Likelihood of the parameters involved in the model.  The    * imach.c (Repository): Check when date of death was earlier that
   simplest model is the multinomial logistic model where pij is the    current date of interview. It may happen when the death was just
   probability to be observed in state j at the second wave    prior to the death. In this case, dh was negative and likelihood
   conditional to be observed in state i at the first wave. Therefore    was wrong (infinity). We still send an "Error" but patch by
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    assuming that the date of death was just one stepm after the
   'age' is age and 'sex' is a covariate. If you want to have a more    interview.
   complex model than "constant and age", you should modify the program    (Repository): Because some people have very long ID (first column)
   where the markup *Covariates have to be included here again* invites    we changed int to long in num[] and we added a new lvector for
   you to do it.  More covariates you add, slower the    memory allocation. But we also truncated to 8 characters (left
   convergence.    truncation)
     (Repository): No more line truncation errors.
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Revision 1.84  2003/06/13 21:44:43  brouard
   identical for each individual. Also, if a individual missed an    * imach.c (Repository): Replace "freqsummary" at a correct
   intermediate interview, the information is lost, but taken into    place. It differs from routine "prevalence" which may be called
   account using an interpolation or extrapolation.      many times. Probs is memory consuming and must be used with
     parcimony.
   hPijx is the probability to be observed in state i at age x+h    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   conditional to the observed state i at age x. The delay 'h' can be  
   split into an exact number (nh*stepm) of unobserved intermediate    Revision 1.83  2003/06/10 13:39:11  lievre
   states. This elementary transition (by month or quarter trimester,    *** empty log message ***
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.82  2003/06/05 15:57:20  brouard
   and the contribution of each individual to the likelihood is simply    Add log in  imach.c and  fullversion number is now printed.
   hPijx.  
   */
   Also this programme outputs the covariance matrix of the parameters but also  /*
   of the life expectancies. It also computes the prevalence limits.     Interpolated Markov Chain
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Short summary of the programme:
            Institut national d'études démographiques, Paris.    
   This software have been partly granted by Euro-REVES, a concerted action    This program computes Healthy Life Expectancies from
   from the European Union.    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   It is copyrighted identically to a GNU software product, ie programme and    first survey ("cross") where individuals from different ages are
   software can be distributed freely for non commercial use. Latest version    interviewed on their health status or degree of disability (in the
   can be accessed at http://euroreves.ined.fr/imach .    case of a health survey which is our main interest) -2- at least a
   **********************************************************************/    second wave of interviews ("longitudinal") which measure each change
      (if any) in individual health status.  Health expectancies are
 #include <math.h>    computed from the time spent in each health state according to a
 #include <stdio.h>    model. More health states you consider, more time is necessary to reach the
 #include <stdlib.h>    Maximum Likelihood of the parameters involved in the model.  The
 #include <unistd.h>    simplest model is the multinomial logistic model where pij is the
     probability to be observed in state j at the second wave
 #define MAXLINE 256    conditional to be observed in state i at the first wave. Therefore
 #define GNUPLOTPROGRAM "gnuplot"    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    '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
 #ifdef windows    and the contribution of each individual to the likelihood is simply
 #define DIRSEPARATOR '\\'    hPijx.
 #else  
 #define DIRSEPARATOR '/'    Also this programme outputs the covariance matrix of the parameters but also
 #endif    of the life expectancies. It also computes the stable prevalence. 
     
 char version[80]="Imach version 0.8g, May 2002, INED-EUROREVES ";    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 int erreur; /* Error number */             Institut national d'études démographiques, Paris.
 int nvar;    This software have been partly granted by Euro-REVES, a concerted action
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    from the European Union.
 int npar=NPARMAX;    It is copyrighted identically to a GNU software product, ie programme and
 int nlstate=2; /* Number of live states */    software can be distributed freely for non commercial use. Latest version
 int ndeath=1; /* Number of dead states */    can be accessed at http://euroreves.ined.fr/imach .
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 int *wav; /* Number of waves for this individuual 0 is possible */    
 int maxwav; /* Maxim number of waves */    **********************************************************************/
 int jmin, jmax; /* min, max spacing between 2 waves */  /*
 int mle, weightopt;    main
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    read parameterfile
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    read datafile
 double jmean; /* Mean space between 2 waves */    concatwav
 double **oldm, **newm, **savm; /* Working pointers to matrices */    freqsummary
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    if (mle >= 1)
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;      mlikeli
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;    print results files
 FILE *fichtm; /* Html File */    if mle==1 
 FILE *ficreseij;       computes hessian
 char filerese[FILENAMELENGTH];    read end of parameter file: agemin, agemax, bage, fage, estepm
 FILE  *ficresvij;        begin-prev-date,...
 char fileresv[FILENAMELENGTH];    open gnuplot file
 FILE  *ficresvpl;    open html file
 char fileresvpl[FILENAMELENGTH];    stable prevalence
 char title[MAXLINE];     for age prevalim()
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    h Pij x
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    variance of p varprob
     forecasting if prevfcast==1 prevforecast call prevalence()
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    health expectancies
     Variance-covariance of DFLE
 char filerest[FILENAMELENGTH];    prevalence()
 char fileregp[FILENAMELENGTH];     movingaverage()
 char popfile[FILENAMELENGTH];    varevsij() 
     if popbased==1 varevsij(,popbased)
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    total life expectancies
     Variance of stable prevalence
 #define NR_END 1   end
 #define FREE_ARG char*  */
 #define FTOL 1.0e-10  
   
 #define NRANSI  
 #define ITMAX 200   
   #include <math.h>
 #define TOL 2.0e-4  #include <stdio.h>
   #include <stdlib.h>
 #define CGOLD 0.3819660  #include <unistd.h>
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  #include <sys/time.h>
   #include <time.h>
 #define GOLD 1.618034  #include "timeval.h"
 #define GLIMIT 100.0  
 #define TINY 1.0e-20  #define MAXLINE 256
   #define GNUPLOTPROGRAM "gnuplot"
 static double maxarg1,maxarg2;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  #define FILENAMELENGTH 132
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  /*#define DEBUG*/
    /*#define windows*/
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #define rint(a) floor(a+0.5)  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
 static double sqrarg;  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
   #define NINTERVMAX 8
 int imx;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 int stepm;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 /* Stepm, step in month: minimum step interpolation*/  #define NCOVMAX 8 /* Maximum number of covariates */
   #define MAXN 20000
 int estepm;  #define YEARM 12. /* Number of months per year */
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  #define AGESUP 130
   #define AGEBASE 40
 int m,nb;  #ifdef unix
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  #define DIRSEPARATOR '/'
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  #define ODIRSEPARATOR '\\'
 double **pmmij, ***probs, ***mobaverage;  #else
 double dateintmean=0;  #define DIRSEPARATOR '\\'
   #define ODIRSEPARATOR '/'
 double *weight;  #endif
 int **s; /* Status */  
 double *agedc, **covar, idx;  /* $Id$ */
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  /* $State$ */
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  char version[]="Imach version 0.96a, June 2003, INED-EUROREVES ";
 double ftolhess; /* Tolerance for computing hessian */  char fullversion[]="$Revision$ $Date$"; 
   int erreur; /* Error number */
 /**************** split *************************/  int nvar;
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 {  int npar=NPARMAX;
    char *s;                             /* pointer */  int nlstate=2; /* Number of live states */
    int  l1, l2;                         /* length counters */  int ndeath=1; /* Number of dead states */
   int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
    l1 = strlen( path );                 /* length of path */  int popbased=0;
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
    s = strrchr( path,  DIRSEPARATOR );          /* find last / */  int *wav; /* Number of waves for this individuual 0 is possible */
    if ( s == NULL ) {                   /* no directory, so use current */  int maxwav; /* Maxim number of waves */
 #if     defined(__bsd__)                /* get current working directory */  int jmin, jmax; /* min, max spacing between 2 waves */
       extern char       *getwd( );  int gipmx, gsw; /* Global variables on the number of contributions 
                      to the likelihood and the sum of weights (done by funcone)*/
       if ( getwd( dirc ) == NULL ) {  int mle, weightopt;
 #else  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
       extern char       *getcwd( );  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 #endif  double jmean; /* Mean space between 2 waves */
          return( GLOCK_ERROR_GETCWD );  double **oldm, **newm, **savm; /* Working pointers to matrices */
       }  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
       strcpy( name, path );             /* we've got it */  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
    } else {                             /* strip direcotry from path */  FILE *ficlog, *ficrespow;
       s++;                              /* after this, the filename */  int globpr; /* Global variable for printing or not */
       l2 = strlen( s );                 /* length of filename */  double fretone; /* Only one call to likelihood */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  long ipmx; /* Number of contributions */
       strcpy( name, s );                /* save file name */  double sw; /* Sum of weights */
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
       dirc[l1-l2] = 0;                  /* add zero */  FILE *ficresilk;
    }  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
    l1 = strlen( dirc );                 /* length of directory */  FILE *ficresprobmorprev;
 #ifdef windows  FILE *fichtm; /* Html File */
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  FILE *ficreseij;
 #else  char filerese[FILENAMELENGTH];
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  FILE  *ficresvij;
 #endif  char fileresv[FILENAMELENGTH];
    s = strrchr( name, '.' );            /* find last / */  FILE  *ficresvpl;
    s++;  char fileresvpl[FILENAMELENGTH];
    strcpy(ext,s);                       /* save extension */  char title[MAXLINE];
    l1= strlen( name);  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
    l2= strlen( s)+1;  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
    strncpy( finame, name, l1-l2);  char tmpout[FILENAMELENGTH]; 
    finame[l1-l2]= 0;  char command[FILENAMELENGTH];
    return( 0 );                         /* we're done */  int  outcmd=0;
 }  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   char lfileres[FILENAMELENGTH];
 /******************************************/  char filelog[FILENAMELENGTH]; /* Log file */
   char filerest[FILENAMELENGTH];
 void replace(char *s, char*t)  char fileregp[FILENAMELENGTH];
 {  char popfile[FILENAMELENGTH];
   int i;  
   int lg=20;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
   i=0;  
   lg=strlen(t);  #define NR_END 1
   for(i=0; i<= lg; i++) {  #define FREE_ARG char*
     (s[i] = t[i]);  #define FTOL 1.0e-10
     if (t[i]== '\\') s[i]='/';  
   }  #define NRANSI 
 }  #define ITMAX 200 
   
 int nbocc(char *s, char occ)  #define TOL 2.0e-4 
 {  
   int i,j=0;  #define CGOLD 0.3819660 
   int lg=20;  #define ZEPS 1.0e-10 
   i=0;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   lg=strlen(s);  
   for(i=0; i<= lg; i++) {  #define GOLD 1.618034 
   if  (s[i] == occ ) j++;  #define GLIMIT 100.0 
   }  #define TINY 1.0e-20 
   return j;  
 }  static double maxarg1,maxarg2;
   #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 void cutv(char *u,char *v, char*t, char occ)  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 {    
   int i,lg,j,p=0;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   i=0;  #define rint(a) floor(a+0.5)
   for(j=0; j<=strlen(t)-1; j++) {  
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  static double sqrarg;
   }  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   lg=strlen(t);  
   for(j=0; j<p; j++) {  int imx; 
     (u[j] = t[j]);  int stepm;
   }  /* Stepm, step in month: minimum step interpolation*/
      u[p]='\0';  
   int estepm;
    for(j=0; j<= lg; j++) {  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
     if (j>=(p+1))(v[j-p-1] = t[j]);  
   }  int m,nb;
 }  long *num;
   int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 /********************** nrerror ********************/  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double **pmmij, ***probs;
 void nrerror(char error_text[])  double dateintmean=0;
 {  
   fprintf(stderr,"ERREUR ...\n");  double *weight;
   fprintf(stderr,"%s\n",error_text);  int **s; /* Status */
   exit(1);  double *agedc, **covar, idx;
 }  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 /*********************** vector *******************/  
 double *vector(int nl, int nh)  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 {  double ftolhess; /* Tolerance for computing hessian */
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  /**************** split *************************/
   if (!v) nrerror("allocation failure in vector");  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   return v-nl+NR_END;  {
 }    char  *ss;                            /* pointer */
     int   l1, l2;                         /* length counters */
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)    l1 = strlen(path );                   /* length of path */
 {    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   free((FREE_ARG)(v+nl-NR_END));    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
 }    if ( ss == NULL ) {                   /* no directory, so use current */
       /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 /************************ivector *******************************/        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 int *ivector(long nl,long nh)      /* get current working directory */
 {      /*    extern  char* getcwd ( char *buf , int len);*/
   int *v;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));        return( GLOCK_ERROR_GETCWD );
   if (!v) nrerror("allocation failure in ivector");      }
   return v-nl+NR_END;      strcpy( name, path );               /* we've got it */
 }    } else {                              /* strip direcotry from path */
       ss++;                               /* after this, the filename */
 /******************free ivector **************************/      l2 = strlen( ss );                  /* length of filename */
 void free_ivector(int *v, long nl, long nh)      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 {      strcpy( name, ss );         /* save file name */
   free((FREE_ARG)(v+nl-NR_END));      strncpy( dirc, path, l1 - l2 );     /* now the directory */
 }      dirc[l1-l2] = 0;                    /* add zero */
     }
 /******************* imatrix *******************************/    l1 = strlen( dirc );                  /* length of directory */
 int **imatrix(long nrl, long nrh, long ncl, long nch)    /*#ifdef windows
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
 {  #else
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   int **m;  #endif
      */
   /* allocate pointers to rows */    ss = strrchr( name, '.' );            /* find last / */
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    ss++;
   if (!m) nrerror("allocation failure 1 in matrix()");    strcpy(ext,ss);                       /* save extension */
   m += NR_END;    l1= strlen( name);
   m -= nrl;    l2= strlen(ss)+1;
      strncpy( finame, name, l1-l2);
      finame[l1-l2]= 0;
   /* allocate rows and set pointers to them */    return( 0 );                          /* we're done */
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  }
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  /******************************************/
    
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  void replace(char *s, char*t)
    {
   /* return pointer to array of pointers to rows */    int i;
   return m;    int lg=20;
 }    i=0;
     lg=strlen(t);
 /****************** free_imatrix *************************/    for(i=0; i<= lg; i++) {
 void free_imatrix(m,nrl,nrh,ncl,nch)      (s[i] = t[i]);
       int **m;      if (t[i]== '\\') s[i]='/';
       long nch,ncl,nrh,nrl;    }
      /* free an int matrix allocated by imatrix() */  }
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  int nbocc(char *s, char occ)
   free((FREE_ARG) (m+nrl-NR_END));  {
 }    int i,j=0;
     int lg=20;
 /******************* matrix *******************************/    i=0;
 double **matrix(long nrl, long nrh, long ncl, long nch)    lg=strlen(s);
 {    for(i=0; i<= lg; i++) {
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    if  (s[i] == occ ) j++;
   double **m;    }
     return j;
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  }
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  void cutv(char *u,char *v, char*t, char occ)
   m -= nrl;  {
     /* cuts string t into u and v where u is ended by char occ excluding it
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");       gives u="abcedf" and v="ghi2j" */
   m[nrl] += NR_END;    int i,lg,j,p=0;
   m[nrl] -= ncl;    i=0;
     for(j=0; j<=strlen(t)-1; j++) {
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   return m;    }
 }  
     lg=strlen(t);
 /*************************free matrix ************************/    for(j=0; j<p; j++) {
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)      (u[j] = t[j]);
 {    }
   free((FREE_ARG)(m[nrl]+ncl-NR_END));       u[p]='\0';
   free((FREE_ARG)(m+nrl-NR_END));  
 }     for(j=0; j<= lg; j++) {
       if (j>=(p+1))(v[j-p-1] = t[j]);
 /******************* ma3x *******************************/    }
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  }
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  /********************** nrerror ********************/
   double ***m;  
   void nrerror(char error_text[])
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  {
   if (!m) nrerror("allocation failure 1 in matrix()");    fprintf(stderr,"ERREUR ...\n");
   m += NR_END;    fprintf(stderr,"%s\n",error_text);
   m -= nrl;    exit(EXIT_FAILURE);
   }
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  /*********************** vector *******************/
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  double *vector(int nl, int nh)
   m[nrl] += NR_END;  {
   m[nrl] -= ncl;    double *v;
     v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    if (!v) nrerror("allocation failure in vector");
     return v-nl+NR_END;
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  }
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;  /************************ free vector ******************/
   m[nrl][ncl] -= nll;  void free_vector(double*v, int nl, int nh)
   for (j=ncl+1; j<=nch; j++)  {
     m[nrl][j]=m[nrl][j-1]+nlay;    free((FREE_ARG)(v+nl-NR_END));
    }
   for (i=nrl+1; i<=nrh; i++) {  
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  /************************ivector *******************************/
     for (j=ncl+1; j<=nch; j++)  int *ivector(long nl,long nh)
       m[i][j]=m[i][j-1]+nlay;  {
   }    int *v;
   return m;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
 }    if (!v) nrerror("allocation failure in ivector");
     return v-nl+NR_END;
 /*************************free ma3x ************************/  }
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {  /******************free ivector **************************/
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  void free_ivector(int *v, long nl, long nh)
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  {
   free((FREE_ARG)(m+nrl-NR_END));    free((FREE_ARG)(v+nl-NR_END));
 }  }
   
 /***************** f1dim *************************/  /************************lvector *******************************/
 extern int ncom;  long *lvector(long nl,long nh)
 extern double *pcom,*xicom;  {
 extern double (*nrfunc)(double []);    long *v;
      v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
 double f1dim(double x)    if (!v) nrerror("allocation failure in ivector");
 {    return v-nl+NR_END;
   int j;  }
   double f;  
   double *xt;  /******************free lvector **************************/
    void free_lvector(long *v, long nl, long nh)
   xt=vector(1,ncom);  {
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    free((FREE_ARG)(v+nl-NR_END));
   f=(*nrfunc)(xt);  }
   free_vector(xt,1,ncom);  
   return f;  /******************* imatrix *******************************/
 }  int **imatrix(long nrl, long nrh, long ncl, long nch) 
        /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 /*****************brent *************************/  { 
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
 {    int **m; 
   int iter;    
   double a,b,d,etemp;    /* allocate pointers to rows */ 
   double fu,fv,fw,fx;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   double ftemp;    if (!m) nrerror("allocation failure 1 in matrix()"); 
   double p,q,r,tol1,tol2,u,v,w,x,xm;    m += NR_END; 
   double e=0.0;    m -= nrl; 
      
   a=(ax < cx ? ax : cx);    
   b=(ax > cx ? ax : cx);    /* allocate rows and set pointers to them */ 
   x=w=v=bx;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   fw=fv=fx=(*f)(x);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   for (iter=1;iter<=ITMAX;iter++) {    m[nrl] += NR_END; 
     xm=0.5*(a+b);    m[nrl] -= ncl; 
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     printf(".");fflush(stdout);    
 #ifdef DEBUG    /* return pointer to array of pointers to rows */ 
     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);    return m; 
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  } 
 #endif  
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  /****************** free_imatrix *************************/
       *xmin=x;  void free_imatrix(m,nrl,nrh,ncl,nch)
       return fx;        int **m;
     }        long nch,ncl,nrh,nrl; 
     ftemp=fu;       /* free an int matrix allocated by imatrix() */ 
     if (fabs(e) > tol1) {  { 
       r=(x-w)*(fx-fv);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       q=(x-v)*(fx-fw);    free((FREE_ARG) (m+nrl-NR_END)); 
       p=(x-v)*q-(x-w)*r;  } 
       q=2.0*(q-r);  
       if (q > 0.0) p = -p;  /******************* matrix *******************************/
       q=fabs(q);  double **matrix(long nrl, long nrh, long ncl, long nch)
       etemp=e;  {
       e=d;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    double **m;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  
       else {    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
         d=p/q;    if (!m) nrerror("allocation failure 1 in matrix()");
         u=x+d;    m += NR_END;
         if (u-a < tol2 || b-u < tol2)    m -= nrl;
           d=SIGN(tol1,xm-x);  
       }    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     } else {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    m[nrl] += NR_END;
     }    m[nrl] -= ncl;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  
     fu=(*f)(u);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     if (fu <= fx) {    return m;
       if (u >= x) a=x; else b=x;    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       SHFT(v,w,x,u)     */
         SHFT(fv,fw,fx,fu)  }
         } else {  
           if (u < x) a=u; else b=u;  /*************************free matrix ************************/
           if (fu <= fw || w == x) {  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
             v=w;  {
             w=u;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
             fv=fw;    free((FREE_ARG)(m+nrl-NR_END));
             fw=fu;  }
           } else if (fu <= fv || v == x || v == w) {  
             v=u;  /******************* ma3x *******************************/
             fv=fu;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
           }  {
         }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   }    double ***m;
   nrerror("Too many iterations in brent");  
   *xmin=x;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   return fx;    if (!m) nrerror("allocation failure 1 in matrix()");
 }    m += NR_END;
     m -= nrl;
 /****************** mnbrak ***********************/  
     m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
             double (*func)(double))    m[nrl] += NR_END;
 {    m[nrl] -= ncl;
   double ulim,u,r,q, dum;  
   double fu;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
    
   *fa=(*func)(*ax);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   *fb=(*func)(*bx);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   if (*fb > *fa) {    m[nrl][ncl] += NR_END;
     SHFT(dum,*ax,*bx,dum)    m[nrl][ncl] -= nll;
       SHFT(dum,*fb,*fa,dum)    for (j=ncl+1; j<=nch; j++) 
       }      m[nrl][j]=m[nrl][j-1]+nlay;
   *cx=(*bx)+GOLD*(*bx-*ax);    
   *fc=(*func)(*cx);    for (i=nrl+1; i<=nrh; i++) {
   while (*fb > *fc) {      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     r=(*bx-*ax)*(*fb-*fc);      for (j=ncl+1; j<=nch; j++) 
     q=(*bx-*cx)*(*fb-*fa);        m[i][j]=m[i][j-1]+nlay;
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    }
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    return m; 
     ulim=(*bx)+GLIMIT*(*cx-*bx);    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     if ((*bx-u)*(u-*cx) > 0.0) {             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       fu=(*func)(u);    */
     } else if ((*cx-u)*(u-ulim) > 0.0) {  }
       fu=(*func)(u);  
       if (fu < *fc) {  /*************************free ma3x ************************/
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
           SHFT(*fb,*fc,fu,(*func)(u))  {
           }    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       u=ulim;    free((FREE_ARG)(m+nrl-NR_END));
       fu=(*func)(u);  }
     } else {  
       u=(*cx)+GOLD*(*cx-*bx);  /***************** f1dim *************************/
       fu=(*func)(u);  extern int ncom; 
     }  extern double *pcom,*xicom;
     SHFT(*ax,*bx,*cx,u)  extern double (*nrfunc)(double []); 
       SHFT(*fa,*fb,*fc,fu)   
       }  double f1dim(double x) 
 }  { 
     int j; 
 /*************** linmin ************************/    double f;
     double *xt; 
 int ncom;   
 double *pcom,*xicom;    xt=vector(1,ncom); 
 double (*nrfunc)(double []);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
      f=(*nrfunc)(xt); 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    free_vector(xt,1,ncom); 
 {    return f; 
   double brent(double ax, double bx, double cx,  } 
                double (*f)(double), double tol, double *xmin);  
   double f1dim(double x);  /*****************brent *************************/
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
               double *fc, double (*func)(double));  { 
   int j;    int iter; 
   double xx,xmin,bx,ax;    double a,b,d,etemp;
   double fx,fb,fa;    double fu,fv,fw,fx;
      double ftemp;
   ncom=n;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   pcom=vector(1,n);    double e=0.0; 
   xicom=vector(1,n);   
   nrfunc=func;    a=(ax < cx ? ax : cx); 
   for (j=1;j<=n;j++) {    b=(ax > cx ? ax : cx); 
     pcom[j]=p[j];    x=w=v=bx; 
     xicom[j]=xi[j];    fw=fv=fx=(*f)(x); 
   }    for (iter=1;iter<=ITMAX;iter++) { 
   ax=0.0;      xm=0.5*(a+b); 
   xx=1.0;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);      printf(".");fflush(stdout);
 #ifdef DEBUG      fprintf(ficlog,".");fflush(ficlog);
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  #ifdef DEBUG
 #endif      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);
   for (j=1;j<=n;j++) {      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     xi[j] *= xmin;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     p[j] += xi[j];  #endif
   }      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   free_vector(xicom,1,n);        *xmin=x; 
   free_vector(pcom,1,n);        return fx; 
 }      } 
       ftemp=fu;
 /*************** powell ************************/      if (fabs(e) > tol1) { 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,        r=(x-w)*(fx-fv); 
             double (*func)(double []))        q=(x-v)*(fx-fw); 
 {        p=(x-v)*q-(x-w)*r; 
   void linmin(double p[], double xi[], int n, double *fret,        q=2.0*(q-r); 
               double (*func)(double []));        if (q > 0.0) p = -p; 
   int i,ibig,j;        q=fabs(q); 
   double del,t,*pt,*ptt,*xit;        etemp=e; 
   double fp,fptt;        e=d; 
   double *xits;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   pt=vector(1,n);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   ptt=vector(1,n);        else { 
   xit=vector(1,n);          d=p/q; 
   xits=vector(1,n);          u=x+d; 
   *fret=(*func)(p);          if (u-a < tol2 || b-u < tol2) 
   for (j=1;j<=n;j++) pt[j]=p[j];            d=SIGN(tol1,xm-x); 
   for (*iter=1;;++(*iter)) {        } 
     fp=(*fret);      } else { 
     ibig=0;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     del=0.0;      } 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     for (i=1;i<=n;i++)      fu=(*f)(u); 
       printf(" %d %.12f",i, p[i]);      if (fu <= fx) { 
     printf("\n");        if (u >= x) a=x; else b=x; 
     for (i=1;i<=n;i++) {        SHFT(v,w,x,u) 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];          SHFT(fv,fw,fx,fu) 
       fptt=(*fret);          } else { 
 #ifdef DEBUG            if (u < x) a=u; else b=u; 
       printf("fret=%lf \n",*fret);            if (fu <= fw || w == x) { 
 #endif              v=w; 
       printf("%d",i);fflush(stdout);              w=u; 
       linmin(p,xit,n,fret,func);              fv=fw; 
       if (fabs(fptt-(*fret)) > del) {              fw=fu; 
         del=fabs(fptt-(*fret));            } else if (fu <= fv || v == x || v == w) { 
         ibig=i;              v=u; 
       }              fv=fu; 
 #ifdef DEBUG            } 
       printf("%d %.12e",i,(*fret));          } 
       for (j=1;j<=n;j++) {    } 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    nrerror("Too many iterations in brent"); 
         printf(" x(%d)=%.12e",j,xit[j]);    *xmin=x; 
       }    return fx; 
       for(j=1;j<=n;j++)  } 
         printf(" p=%.12e",p[j]);  
       printf("\n");  /****************** mnbrak ***********************/
 #endif  
     }  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {              double (*func)(double)) 
 #ifdef DEBUG  { 
       int k[2],l;    double ulim,u,r,q, dum;
       k[0]=1;    double fu; 
       k[1]=-1;   
       printf("Max: %.12e",(*func)(p));    *fa=(*func)(*ax); 
       for (j=1;j<=n;j++)    *fb=(*func)(*bx); 
         printf(" %.12e",p[j]);    if (*fb > *fa) { 
       printf("\n");      SHFT(dum,*ax,*bx,dum) 
       for(l=0;l<=1;l++) {        SHFT(dum,*fb,*fa,dum) 
         for (j=1;j<=n;j++) {        } 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    *cx=(*bx)+GOLD*(*bx-*ax); 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    *fc=(*func)(*cx); 
         }    while (*fb > *fc) { 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));      r=(*bx-*ax)*(*fb-*fc); 
       }      q=(*bx-*cx)*(*fb-*fa); 
 #endif      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       ulim=(*bx)+GLIMIT*(*cx-*bx); 
       free_vector(xit,1,n);      if ((*bx-u)*(u-*cx) > 0.0) { 
       free_vector(xits,1,n);        fu=(*func)(u); 
       free_vector(ptt,1,n);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
       free_vector(pt,1,n);        fu=(*func)(u); 
       return;        if (fu < *fc) { 
     }          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");            SHFT(*fb,*fc,fu,(*func)(u)) 
     for (j=1;j<=n;j++) {            } 
       ptt[j]=2.0*p[j]-pt[j];      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       xit[j]=p[j]-pt[j];        u=ulim; 
       pt[j]=p[j];        fu=(*func)(u); 
     }      } else { 
     fptt=(*func)(ptt);        u=(*cx)+GOLD*(*cx-*bx); 
     if (fptt < fp) {        fu=(*func)(u); 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);      } 
       if (t < 0.0) {      SHFT(*ax,*bx,*cx,u) 
         linmin(p,xit,n,fret,func);        SHFT(*fa,*fb,*fc,fu) 
         for (j=1;j<=n;j++) {        } 
           xi[j][ibig]=xi[j][n];  } 
           xi[j][n]=xit[j];  
         }  /*************** linmin ************************/
 #ifdef DEBUG  
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  int ncom; 
         for(j=1;j<=n;j++)  double *pcom,*xicom;
           printf(" %.12e",xit[j]);  double (*nrfunc)(double []); 
         printf("\n");   
 #endif  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       }  { 
     }    double brent(double ax, double bx, double cx, 
   }                 double (*f)(double), double tol, double *xmin); 
 }    double f1dim(double x); 
     void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
 /**** Prevalence limit ****************/                double *fc, double (*func)(double)); 
     int j; 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    double xx,xmin,bx,ax; 
 {    double fx,fb,fa;
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit   
      matrix by transitions matrix until convergence is reached */    ncom=n; 
     pcom=vector(1,n); 
   int i, ii,j,k;    xicom=vector(1,n); 
   double min, max, maxmin, maxmax,sumnew=0.;    nrfunc=func; 
   double **matprod2();    for (j=1;j<=n;j++) { 
   double **out, cov[NCOVMAX], **pmij();      pcom[j]=p[j]; 
   double **newm;      xicom[j]=xi[j]; 
   double agefin, delaymax=50 ; /* Max number of years to converge */    } 
     ax=0.0; 
   for (ii=1;ii<=nlstate+ndeath;ii++)    xx=1.0; 
     for (j=1;j<=nlstate+ndeath;j++){    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     }  #ifdef DEBUG
     printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
    cov[1]=1.;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
    #endif
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    for (j=1;j<=n;j++) { 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){      xi[j] *= xmin; 
     newm=savm;      p[j] += xi[j]; 
     /* Covariates have to be included here again */    } 
      cov[2]=agefin;    free_vector(xicom,1,n); 
      free_vector(pcom,1,n); 
       for (k=1; k<=cptcovn;k++) {  } 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  
         /*      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]]);*/  /*************** powell ************************/
       }  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];              double (*func)(double [])) 
       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]]];    void linmin(double p[], double xi[], int n, double *fret, 
                 double (*func)(double [])); 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    int i,ibig,j; 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    double del,t,*pt,*ptt,*xit;
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/    double fp,fptt;
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    double *xits;
     pt=vector(1,n); 
     savm=oldm;    ptt=vector(1,n); 
     oldm=newm;    xit=vector(1,n); 
     maxmax=0.;    xits=vector(1,n); 
     for(j=1;j<=nlstate;j++){    *fret=(*func)(p); 
       min=1.;    for (j=1;j<=n;j++) pt[j]=p[j]; 
       max=0.;    for (*iter=1;;++(*iter)) { 
       for(i=1; i<=nlstate; i++) {      fp=(*fret); 
         sumnew=0;      ibig=0; 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];      del=0.0; 
         prlim[i][j]= newm[i][j]/(1-sumnew);      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
         max=FMAX(max,prlim[i][j]);      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
         min=FMIN(min,prlim[i][j]);      fprintf(ficrespow,"%d %.12f",*iter,*fret);
       }      for (i=1;i<=n;i++) {
       maxmin=max-min;        printf(" %d %.12f",i, p[i]);
       maxmax=FMAX(maxmax,maxmin);        fprintf(ficlog," %d %.12lf",i, p[i]);
     }        fprintf(ficrespow," %.12lf", p[i]);
     if(maxmax < ftolpl){      }
       return prlim;      printf("\n");
     }      fprintf(ficlog,"\n");
   }      fprintf(ficrespow,"\n");
 }      for (i=1;i<=n;i++) { 
         for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
 /*************** transition probabilities ***************/        fptt=(*fret); 
   #ifdef DEBUG
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )        printf("fret=%lf \n",*fret);
 {        fprintf(ficlog,"fret=%lf \n",*fret);
   double s1, s2;  #endif
   /*double t34;*/        printf("%d",i);fflush(stdout);
   int i,j,j1, nc, ii, jj;        fprintf(ficlog,"%d",i);fflush(ficlog);
         linmin(p,xit,n,fret,func); 
     for(i=1; i<= nlstate; i++){        if (fabs(fptt-(*fret)) > del) { 
     for(j=1; j<i;j++){          del=fabs(fptt-(*fret)); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){          ibig=i; 
         /*s2 += param[i][j][nc]*cov[nc];*/        } 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  #ifdef DEBUG
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/        printf("%d %.12e",i,(*fret));
       }        fprintf(ficlog,"%d %.12e",i,(*fret));
       ps[i][j]=s2;        for (j=1;j<=n;j++) {
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     }          printf(" x(%d)=%.12e",j,xit[j]);
     for(j=i+1; j<=nlstate+ndeath;j++){          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       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];        for(j=1;j<=n;j++) {
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/          printf(" p=%.12e",p[j]);
       }          fprintf(ficlog," p=%.12e",p[j]);
       ps[i][j]=s2;        }
     }        printf("\n");
   }        fprintf(ficlog,"\n");
     /*ps[3][2]=1;*/  #endif
       } 
   for(i=1; i<= nlstate; i++){      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
      s1=0;  #ifdef DEBUG
     for(j=1; j<i; j++)        int k[2],l;
       s1+=exp(ps[i][j]);        k[0]=1;
     for(j=i+1; j<=nlstate+ndeath; j++)        k[1]=-1;
       s1+=exp(ps[i][j]);        printf("Max: %.12e",(*func)(p));
     ps[i][i]=1./(s1+1.);        fprintf(ficlog,"Max: %.12e",(*func)(p));
     for(j=1; j<i; j++)        for (j=1;j<=n;j++) {
       ps[i][j]= exp(ps[i][j])*ps[i][i];          printf(" %.12e",p[j]);
     for(j=i+1; j<=nlstate+ndeath; j++)          fprintf(ficlog," %.12e",p[j]);
       ps[i][j]= exp(ps[i][j])*ps[i][i];        }
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */        printf("\n");
   } /* end i */        fprintf(ficlog,"\n");
         for(l=0;l<=1;l++) {
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){          for (j=1;j<=n;j++) {
     for(jj=1; jj<= nlstate+ndeath; jj++){            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       ps[ii][jj]=0;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       ps[ii][ii]=1;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     }          }
   }          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         }
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  #endif
     for(jj=1; jj<= nlstate+ndeath; jj++){  
      printf("%lf ",ps[ii][jj]);  
    }        free_vector(xit,1,n); 
     printf("\n ");        free_vector(xits,1,n); 
     }        free_vector(ptt,1,n); 
     printf("\n ");printf("%lf ",cov[2]);*/        free_vector(pt,1,n); 
 /*        return; 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);      } 
   goto end;*/      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     return ps;      for (j=1;j<=n;j++) { 
 }        ptt[j]=2.0*p[j]-pt[j]; 
         xit[j]=p[j]-pt[j]; 
 /**************** Product of 2 matrices ******************/        pt[j]=p[j]; 
       } 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      fptt=(*func)(ptt); 
 {      if (fptt < fp) { 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */        if (t < 0.0) { 
   /* in, b, out are matrice of pointers which should have been initialized          linmin(p,xit,n,fret,func); 
      before: only the contents of out is modified. The function returns          for (j=1;j<=n;j++) { 
      a pointer to pointers identical to out */            xi[j][ibig]=xi[j][n]; 
   long i, j, k;            xi[j][n]=xit[j]; 
   for(i=nrl; i<= nrh; i++)          }
     for(k=ncolol; k<=ncoloh; k++)  #ifdef DEBUG
       for(j=ncl,out[i][k]=0.; j<=nch; j++)          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         out[i][k] +=in[i][j]*b[j][k];          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           for(j=1;j<=n;j++){
   return out;            printf(" %.12e",xit[j]);
 }            fprintf(ficlog," %.12e",xit[j]);
           }
           printf("\n");
 /************* Higher Matrix Product ***************/          fprintf(ficlog,"\n");
   #endif
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )        }
 {      } 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    } 
      duration (i.e. until  } 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  /**** Prevalence limit (stable prevalence)  ****************/
      (typically every 2 years instead of every month which is too big).  
      Model is determined by parameters x and covariates have to be  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
      included manually here.  {
     /* Computes the prevalence limit in each live state at age x by left multiplying the unit
      */       matrix by transitions matrix until convergence is reached */
   
   int i, j, d, h, k;    int i, ii,j,k;
   double **out, cov[NCOVMAX];    double min, max, maxmin, maxmax,sumnew=0.;
   double **newm;    double **matprod2();
     double **out, cov[NCOVMAX], **pmij();
   /* Hstepm could be zero and should return the unit matrix */    double **newm;
   for (i=1;i<=nlstate+ndeath;i++)    double agefin, delaymax=50 ; /* Max number of years to converge */
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[i][j]=(i==j ? 1.0 : 0.0);    for (ii=1;ii<=nlstate+ndeath;ii++)
       po[i][j][0]=(i==j ? 1.0 : 0.0);      for (j=1;j<=nlstate+ndeath;j++){
     }        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      }
   for(h=1; h <=nhstepm; h++){  
     for(d=1; d <=hstepm; d++){     cov[1]=1.;
       newm=savm;   
       /* Covariates have to be included here again */   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       cov[1]=1.;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      newm=savm;
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      /* Covariates have to be included here again */
       for (k=1; k<=cptcovage;k++)       cov[2]=agefin;
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    
       for (k=1; k<=cptcovprod;k++)        for (k=1; k<=cptcovn;k++) {
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
           /*      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]]);*/
         }
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        for (k=1; k<=cptcovprod;k++)
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  
       savm=oldm;        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       oldm=newm;        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     }        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     for(i=1; i<=nlstate+ndeath; i++)      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
       for(j=1;j<=nlstate+ndeath;j++) {  
         po[i][j][h]=newm[i][j];      savm=oldm;
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      oldm=newm;
          */      maxmax=0.;
       }      for(j=1;j<=nlstate;j++){
   } /* end h */        min=1.;
   return po;        max=0.;
 }        for(i=1; i<=nlstate; i++) {
           sumnew=0;
           for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
 /*************** log-likelihood *************/          prlim[i][j]= newm[i][j]/(1-sumnew);
 double func( double *x)          max=FMAX(max,prlim[i][j]);
 {          min=FMIN(min,prlim[i][j]);
   int i, ii, j, k, mi, d, kk;        }
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        maxmin=max-min;
   double **out;        maxmax=FMAX(maxmax,maxmin);
   double sw; /* Sum of weights */      }
   double lli; /* Individual log likelihood */      if(maxmax < ftolpl){
   long ipmx;        return prlim;
   /*extern weight */      }
   /* We are differentiating ll according to initial status */    }
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  }
   /*for(i=1;i<imx;i++)  
     printf(" %d\n",s[4][i]);  /*************** transition probabilities ***************/ 
   */  
   cov[1]=1.;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   {
   for(k=1; k<=nlstate; k++) ll[k]=0.;    double s1, s2;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    /*double t34;*/
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    int i,j,j1, nc, ii, jj;
     for(mi=1; mi<= wav[i]-1; mi++){  
       for (ii=1;ii<=nlstate+ndeath;ii++)      for(i=1; i<= nlstate; i++){
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      for(j=1; j<i;j++){
       for(d=0; d<dh[mi][i]; d++){        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
         newm=savm;          /*s2 += param[i][j][nc]*cov[nc];*/
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
         for (kk=1; kk<=cptcovage;kk++) {          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        }
         }        ps[i][j]=s2;
                /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      }
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      for(j=i+1; j<=nlstate+ndeath;j++){
         savm=oldm;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
         oldm=newm;          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
                  /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
                }
       } /* end mult */        ps[i][j]=s2;
            }
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    }
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/      /*ps[3][2]=1;*/
       ipmx +=1;  
       sw += weight[i];    for(i=1; i<= nlstate; i++){
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;       s1=0;
     } /* end of wave */      for(j=1; j<i; j++)
   } /* end of individual */        s1+=exp(ps[i][j]);
       for(j=i+1; j<=nlstate+ndeath; j++)
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        s1+=exp(ps[i][j]);
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      ps[i][i]=1./(s1+1.);
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      for(j=1; j<i; j++)
   return -l;        ps[i][j]= exp(ps[i][j])*ps[i][i];
 }      for(j=i+1; j<=nlstate+ndeath; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];
       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
 /*********** Maximum Likelihood Estimation ***************/    } /* end i */
   
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
 {      for(jj=1; jj<= nlstate+ndeath; jj++){
   int i,j, iter;        ps[ii][jj]=0;
   double **xi,*delti;        ps[ii][ii]=1;
   double fret;      }
   xi=matrix(1,npar,1,npar);    }
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++)  
       xi[i][j]=(i==j ? 1.0 : 0.0);    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   printf("Powell\n");      for(jj=1; jj<= nlstate+ndeath; jj++){
   powell(p,xi,npar,ftol,&iter,&fret,func);       printf("%lf ",ps[ii][jj]);
      }
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));      printf("\n ");
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      }
       printf("\n ");printf("%lf ",cov[2]);*/
 }  /*
     for(i=1; i<= npar; i++) printf("%f ",x[i]);
 /**** Computes Hessian and covariance matrix ***/    goto end;*/
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      return ps;
 {  }
   double  **a,**y,*x,pd;  
   double **hess;  /**************** Product of 2 matrices ******************/
   int i, j,jk;  
   int *indx;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   {
   double hessii(double p[], double delta, int theta, double delti[]);    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   double hessij(double p[], double delti[], int i, int j);       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   void lubksb(double **a, int npar, int *indx, double b[]) ;    /* in, b, out are matrice of pointers which should have been initialized 
   void ludcmp(double **a, int npar, int *indx, double *d) ;       before: only the contents of out is modified. The function returns
        a pointer to pointers identical to out */
   hess=matrix(1,npar,1,npar);    long i, j, k;
     for(i=nrl; i<= nrh; i++)
   printf("\nCalculation of the hessian matrix. Wait...\n");      for(k=ncolol; k<=ncoloh; k++)
   for (i=1;i<=npar;i++){        for(j=ncl,out[i][k]=0.; j<=nch; j++)
     printf("%d",i);fflush(stdout);          out[i][k] +=in[i][j]*b[j][k];
     hess[i][i]=hessii(p,ftolhess,i,delti);  
     /*printf(" %f ",p[i]);*/    return out;
     /*printf(" %lf ",hess[i][i]);*/  }
   }  
    
   for (i=1;i<=npar;i++) {  /************* Higher Matrix Product ***************/
     for (j=1;j<=npar;j++)  {  
       if (j>i) {  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
         printf(".%d%d",i,j);fflush(stdout);  {
         hess[i][j]=hessij(p,delti,i,j);    /* Computes the transition matrix starting at age 'age' over 
         hess[j][i]=hess[i][j];           'nhstepm*hstepm*stepm' months (i.e. until
         /*printf(" %lf ",hess[i][j]);*/       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");       for the memory).
        Model is determined by parameters x and covariates have to be 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");       included manually here. 
    
   a=matrix(1,npar,1,npar);       */
   y=matrix(1,npar,1,npar);  
   x=vector(1,npar);    int i, j, d, h, k;
   indx=ivector(1,npar);    double **out, cov[NCOVMAX];
   for (i=1;i<=npar;i++)    double **newm;
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  
   ludcmp(a,npar,indx,&pd);    /* Hstepm could be zero and should return the unit matrix */
     for (i=1;i<=nlstate+ndeath;i++)
   for (j=1;j<=npar;j++) {      for (j=1;j<=nlstate+ndeath;j++){
     for (i=1;i<=npar;i++) x[i]=0;        oldm[i][j]=(i==j ? 1.0 : 0.0);
     x[j]=1;        po[i][j][0]=(i==j ? 1.0 : 0.0);
     lubksb(a,npar,indx,x);      }
     for (i=1;i<=npar;i++){    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       matcov[i][j]=x[i];    for(h=1; h <=nhstepm; h++){
     }      for(d=1; d <=hstepm; d++){
   }        newm=savm;
         /* Covariates have to be included here again */
   printf("\n#Hessian matrix#\n");        cov[1]=1.;
   for (i=1;i<=npar;i++) {        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     for (j=1;j<=npar;j++) {        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       printf("%.3e ",hess[i][j]);        for (k=1; k<=cptcovage;k++)
     }          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     printf("\n");        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]]];
   
   /* Recompute Inverse */  
   for (i=1;i<=npar;i++)        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   ludcmp(a,npar,indx,&pd);        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                      pmij(pmmij,cov,ncovmodel,x,nlstate));
   /*  printf("\n#Hessian matrix recomputed#\n");        savm=oldm;
         oldm=newm;
   for (j=1;j<=npar;j++) {      }
     for (i=1;i<=npar;i++) x[i]=0;      for(i=1; i<=nlstate+ndeath; i++)
     x[j]=1;        for(j=1;j<=nlstate+ndeath;j++) {
     lubksb(a,npar,indx,x);          po[i][j][h]=newm[i][j];
     for (i=1;i<=npar;i++){          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
       y[i][j]=x[i];           */
       printf("%.3e ",y[i][j]);        }
     }    } /* end h */
     printf("\n");    return po;
   }  }
   */  
   
   free_matrix(a,1,npar,1,npar);  /*************** log-likelihood *************/
   free_matrix(y,1,npar,1,npar);  double func( double *x)
   free_vector(x,1,npar);  {
   free_ivector(indx,1,npar);    int i, ii, j, k, mi, d, kk;
   free_matrix(hess,1,npar,1,npar);    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     double **out;
     double sw; /* Sum of weights */
 }    double lli; /* Individual log likelihood */
     int s1, s2;
 /*************** hessian matrix ****************/    double bbh, survp;
 double hessii( double x[], double delta, int theta, double delti[])    long ipmx;
 {    /*extern weight */
   int i;    /* We are differentiating ll according to initial status */
   int l=1, lmax=20;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   double k1,k2;    /*for(i=1;i<imx;i++) 
   double p2[NPARMAX+1];      printf(" %d\n",s[4][i]);
   double res;    */
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    cov[1]=1.;
   double fx;  
   int k=0,kmax=10;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   double l1;  
     if(mle==1){
   fx=func(x);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   for (i=1;i<=npar;i++) p2[i]=x[i];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   for(l=0 ; l <=lmax; l++){        for(mi=1; mi<= wav[i]-1; mi++){
     l1=pow(10,l);          for (ii=1;ii<=nlstate+ndeath;ii++)
     delts=delt;            for (j=1;j<=nlstate+ndeath;j++){
     for(k=1 ; k <kmax; k=k+1){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       delt = delta*(l1*k);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       p2[theta]=x[theta] +delt;            }
       k1=func(p2)-fx;          for(d=0; d<dh[mi][i]; d++){
       p2[theta]=x[theta]-delt;            newm=savm;
       k2=func(p2)-fx;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       /*res= (k1-2.0*fx+k2)/delt/delt; */            for (kk=1; kk<=cptcovage;kk++) {
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                  }
 #ifdef DEBUG            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       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);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 #endif            savm=oldm;
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */            oldm=newm;
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          } /* end mult */
         k=kmax;        
       }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          /* But now since version 0.9 we anticipate for bias and large stepm.
         k=kmax; l=lmax*10.;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       }           * (in months) between two waves is not a multiple of stepm, we rounded to 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){           * the nearest (and in case of equal distance, to the lowest) interval but now
         delts=delt;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       }           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     }           * probability in order to take into account the bias as a fraction of the way
   }           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   delti[theta]=delts;           * -stepm/2 to stepm/2 .
   return res;           * 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. 
 }           */
           s1=s[mw[mi][i]][i];
 double hessij( double x[], double delti[], int thetai,int thetaj)          s2=s[mw[mi+1][i]][i];
 {          bbh=(double)bh[mi][i]/(double)stepm; 
   int i;          /* bias is positive if real duration
   int l=1, l1, lmax=20;           * is higher than the multiple of stepm and negative otherwise.
   double k1,k2,k3,k4,res,fx;           */
   double p2[NPARMAX+1];          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   int k;          if( s2 > nlstate){ 
             /* i.e. if s2 is a death state and if the date of death is known then the contribution
   fx=func(x);               to the likelihood is the probability to die between last step unit time and current 
   for (k=1; k<=2; k++) {               step unit time, which is also the differences between probability to die before dh 
     for (i=1;i<=npar;i++) p2[i]=x[i];               and probability to die before dh-stepm . 
     p2[thetai]=x[thetai]+delti[thetai]/k;               In version up to 0.92 likelihood was computed
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          as if date of death was unknown. Death was treated as any other
     k1=func(p2)-fx;          health state: the date of the interview describes the actual state
            and not the date of a change in health state. The former idea was
     p2[thetai]=x[thetai]+delti[thetai]/k;          to consider that at each interview the state was recorded
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          (healthy, disable or death) and IMaCh was corrected; but when we
     k2=func(p2)-fx;          introduced the exact date of death then we should have modified
            the contribution of an exact death to the likelihood. This new
     p2[thetai]=x[thetai]-delti[thetai]/k;          contribution is smaller and very dependent of the step unit
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          stepm. It is no more the probability to die between last interview
     k3=func(p2)-fx;          and month of death but the probability to survive from last
            interview up to one month before death multiplied by the
     p2[thetai]=x[thetai]-delti[thetai]/k;          probability to die within a month. Thanks to Chris
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          Jackson for correcting this bug.  Former versions increased
     k4=func(p2)-fx;          mortality artificially. The bad side is that we add another loop
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          which slows down the processing. The difference can be up to 10%
 #ifdef DEBUG          lower mortality.
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);            */
 #endif            lli=log(out[s1][s2] - savm[s1][s2]);
   }          }else{
   return res;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 }            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
           } 
 /************** Inverse of matrix **************/          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
 void ludcmp(double **a, int n, int *indx, double *d)          /*if(lli ==000.0)*/
 {          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
   int i,imax,j,k;          ipmx +=1;
   double big,dum,sum,temp;          sw += weight[i];
   double *vv;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          } /* end of wave */
   vv=vector(1,n);      } /* end of individual */
   *d=1.0;    }  else if(mle==2){
   for (i=1;i<=n;i++) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     big=0.0;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     for (j=1;j<=n;j++)        for(mi=1; mi<= wav[i]-1; mi++){
       if ((temp=fabs(a[i][j])) > big) big=temp;          for (ii=1;ii<=nlstate+ndeath;ii++)
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");            for (j=1;j<=nlstate+ndeath;j++){
     vv[i]=1.0/big;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (j=1;j<=n;j++) {            }
     for (i=1;i<j;i++) {          for(d=0; d<=dh[mi][i]; d++){
       sum=a[i][j];            newm=savm;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       a[i][j]=sum;            for (kk=1; kk<=cptcovage;kk++) {
     }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     big=0.0;            }
     for (i=j;i<=n;i++) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       sum=a[i][j];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for (k=1;k<j;k++)            savm=oldm;
         sum -= a[i][k]*a[k][j];            oldm=newm;
       a[i][j]=sum;          } /* end mult */
       if ( (dum=vv[i]*fabs(sum)) >= big) {        
         big=dum;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         imax=i;          /* But now since version 0.9 we anticipate for bias and large stepm.
       }           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     }           * (in months) between two waves is not a multiple of stepm, we rounded to 
     if (j != imax) {           * the nearest (and in case of equal distance, to the lowest) interval but now
       for (k=1;k<=n;k++) {           * we keep into memory the bias bh[mi][i] and also the previous matrix product
         dum=a[imax][k];           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
         a[imax][k]=a[j][k];           * probability in order to take into account the bias as a fraction of the way
         a[j][k]=dum;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
       }           * -stepm/2 to stepm/2 .
       *d = -(*d);           * For stepm=1 the results are the same as for previous versions of Imach.
       vv[imax]=vv[j];           * For stepm > 1 the results are less biased than in previous versions. 
     }           */
     indx[j]=imax;          s1=s[mw[mi][i]][i];
     if (a[j][j] == 0.0) a[j][j]=TINY;          s2=s[mw[mi+1][i]][i];
     if (j != n) {          bbh=(double)bh[mi][i]/(double)stepm; 
       dum=1.0/(a[j][j]);          /* bias is positive if real duration
       for (i=j+1;i<=n;i++) a[i][j] *= dum;           * is higher than the multiple of stepm and negative otherwise.
     }           */
   }          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 */
   free_vector(vv,1,n);  /* Doesn't work */          /* 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)*/
 void lubksb(double **a, int n, int *indx, double b[])          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
 {          ipmx +=1;
   int i,ii=0,ip,j;          sw += weight[i];
   double sum;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          } /* end of wave */
   for (i=1;i<=n;i++) {      } /* end of individual */
     ip=indx[i];    }  else if(mle==3){  /* exponential inter-extrapolation */
     sum=b[ip];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     b[ip]=b[i];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     if (ii)        for(mi=1; mi<= wav[i]-1; mi++){
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          for (ii=1;ii<=nlstate+ndeath;ii++)
     else if (sum) ii=i;            for (j=1;j<=nlstate+ndeath;j++){
     b[i]=sum;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (i=n;i>=1;i--) {            }
     sum=b[i];          for(d=0; d<dh[mi][i]; d++){
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];            newm=savm;
     b[i]=sum/a[i][i];            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];
             }
 /************ Frequencies ********************/            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 {  /* Some frequencies */            savm=oldm;
              oldm=newm;
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          } /* end mult */
   double ***freq; /* Frequencies */        
   double *pp;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   double pos, k2, dateintsum=0,k2cpt=0;          /* But now since version 0.9 we anticipate for bias and large stepm.
   FILE *ficresp;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   char fileresp[FILENAMELENGTH];           * (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
   pp=vector(1,nlstate);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   strcpy(fileresp,"p");           * probability in order to take into account the bias as a fraction of the way
   strcat(fileresp,fileres);           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   if((ficresp=fopen(fileresp,"w"))==NULL) {           * -stepm/2 to stepm/2 .
     printf("Problem with prevalence resultfile: %s\n", fileresp);           * For stepm=1 the results are the same as for previous versions of Imach.
     exit(0);           * For stepm > 1 the results are less biased than in previous versions. 
   }           */
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          s1=s[mw[mi][i]][i];
   j1=0;          s2=s[mw[mi+1][i]][i];
            bbh=(double)bh[mi][i]/(double)stepm; 
   j=cptcoveff;          /* bias is positive if real duration
   if (cptcovn<1) {j=1;ncodemax[1]=1;}           * is higher than the multiple of stepm and negative otherwise.
             */
   for(k1=1; k1<=j;k1++){          /* 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(i1=1; i1<=ncodemax[k1];i1++){          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 */
       j1++;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);          /*if(lli ==000.0)*/
         scanf("%d", 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); */
       for (i=-1; i<=nlstate+ndeath; i++)            ipmx +=1;
         for (jk=-1; jk<=nlstate+ndeath; jk++)            sw += weight[i];
           for(m=agemin; m <= agemax+3; m++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             freq[i][jk][m]=0;        } /* end of wave */
            } /* end of individual */
       dateintsum=0;    }else if (mle==4){  /* ml=4 no inter-extrapolation */
       k2cpt=0;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (i=1; i<=imx; i++) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         bool=1;        for(mi=1; mi<= wav[i]-1; mi++){
         if  (cptcovn>0) {          for (ii=1;ii<=nlstate+ndeath;ii++)
           for (z1=1; z1<=cptcoveff; z1++)            for (j=1;j<=nlstate+ndeath;j++){
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               bool=0;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         }            }
         if (bool==1) {          for(d=0; d<dh[mi][i]; d++){
           for(m=firstpass; m<=lastpass; m++){            newm=savm;
             k2=anint[m][i]+(mint[m][i]/12.);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {            for (kk=1; kk<=cptcovage;kk++) {
               if(agev[m][i]==0) agev[m][i]=agemax+1;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
               if(agev[m][i]==1) agev[m][i]=agemax+2;            }
               if (m<lastpass) {          
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
               }            savm=oldm;
                          oldm=newm;
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {          } /* end mult */
                 dateintsum=dateintsum+k2;        
                 k2cpt++;          s1=s[mw[mi][i]][i];
               }          s2=s[mw[mi+1][i]][i];
             }          if( s2 > nlstate){ 
           }            lli=log(out[s1][s2] - savm[s1][s2]);
         }          }else{
       }            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
                  }
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          ipmx +=1;
           sw += weight[i];
       if  (cptcovn>0) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         fprintf(ficresp, "\n#********** Variable ");  /*      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 (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        } /* end of wave */
         fprintf(ficresp, "**********\n#");      } /* end of individual */
       }    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       for(i=1; i<=nlstate;i++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       fprintf(ficresp, "\n");        for(mi=1; mi<= wav[i]-1; mi++){
                for (ii=1;ii<=nlstate+ndeath;ii++)
       for(i=(int)agemin; i <= (int)agemax+3; i++){            for (j=1;j<=nlstate+ndeath;j++){
         if(i==(int)agemax+3)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           printf("Total");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         else            }
           printf("Age %d", i);          for(d=0; d<dh[mi][i]; d++){
         for(jk=1; jk <=nlstate ; jk++){            newm=savm;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             pp[jk] += freq[jk][m][i];            for (kk=1; kk<=cptcovage;kk++) {
         }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         for(jk=1; jk <=nlstate ; jk++){            }
           for(m=-1, pos=0; m <=0 ; m++)          
             pos += freq[jk][m][i];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           if(pp[jk]>=1.e-10)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);            savm=oldm;
           else            oldm=newm;
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          } /* end mult */
         }        
           s1=s[mw[mi][i]][i];
         for(jk=1; jk <=nlstate ; jk++){          s2=s[mw[mi+1][i]][i];
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
             pp[jk] += freq[jk][m][i];          ipmx +=1;
         }          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         for(jk=1,pos=0; jk <=nlstate ; jk++)          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
           pos += pp[jk];        } /* end of wave */
         for(jk=1; jk <=nlstate ; jk++){      } /* end of individual */
           if(pos>=1.e-5)    } /* End of if */
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
           else    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
           if( i <= (int) agemax){    return -l;
             if(pos>=1.e-5){  }
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);  
               probs[i][jk][j1]= pp[jk]/pos;  /*************** log-likelihood *************/
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/  double funcone( double *x)
             }  {
             else    /* Same as likeli but slower because of a lot of printf and if */
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    int i, ii, j, k, mi, d, kk;
           }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
         }    double **out;
            double lli; /* Individual log likelihood */
         for(jk=-1; jk <=nlstate+ndeath; jk++)    double llt;
           for(m=-1; m <=nlstate+ndeath; m++)    int s1, s2;
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    double bbh, survp;
         if(i <= (int) agemax)    /*extern weight */
           fprintf(ficresp,"\n");    /* We are differentiating ll according to initial status */
         printf("\n");    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       }    /*for(i=1;i<imx;i++) 
     }      printf(" %d\n",s[4][i]);
   }    */
   dateintmean=dateintsum/k2cpt;    cov[1]=1.;
    
   fclose(ficresp);    for(k=1; k<=nlstate; k++) ll[k]=0.;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  
   free_vector(pp,1,nlstate);    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   /* End of Freq */      for(mi=1; mi<= wav[i]-1; mi++){
 }        for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){
 /************ Prevalence ********************/            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)            savm[ii][j]=(ii==j ? 1.0 : 0.0);
 {  /* Some frequencies */          }
          for(d=0; d<dh[mi][i]; d++){
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          newm=savm;
   double ***freq; /* Frequencies */          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double *pp;          for (kk=1; kk<=cptcovage;kk++) {
   double pos, k2;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           }
   pp=vector(1,nlstate);          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
            savm=oldm;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          oldm=newm;
   j1=0;        } /* end mult */
          
   j=cptcoveff;        s1=s[mw[mi][i]][i];
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        s2=s[mw[mi+1][i]][i];
          bbh=(double)bh[mi][i]/(double)stepm; 
   for(k1=1; k1<=j;k1++){        /* bias is positive if real duration
     for(i1=1; i1<=ncodemax[k1];i1++){         * is higher than the multiple of stepm and negative otherwise.
       j1++;         */
              if( s2 > nlstate && (mle <5) ){  /* Jackson */
       for (i=-1; i<=nlstate+ndeath; i++)            lli=log(out[s1][s2] - savm[s1][s2]);
         for (jk=-1; jk<=nlstate+ndeath; jk++)          } else if (mle==1){
           for(m=agemin; m <= agemax+3; m++)          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
             freq[i][jk][m]=0;        } 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 (i=1; i<=imx; i++) {        } else if(mle==3){  /* exponential inter-extrapolation */
         bool=1;          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 */
         if  (cptcovn>0) {        } else if (mle==4){  /* mle=4 no inter-extrapolation */
           for (z1=1; z1<=cptcoveff; z1++)          lli=log(out[s1][s2]); /* Original formula */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
               bool=0;          lli=log(out[s1][s2]); /* Original formula */
         }        } /* End of if */
         if (bool==1) {        ipmx +=1;
           for(m=firstpass; m<=lastpass; m++){        sw += weight[i];
             k2=anint[m][i]+(mint[m][i]/12.);        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  /*       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(agev[m][i]==0) agev[m][i]=agemax+1;        if(globpr){
               if(agev[m][i]==1) agev[m][i]=agemax+2;          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
               if (m<lastpass) {   %10.6f %10.6f %10.6f ", \
                 if (calagedate>0)                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
                 else          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];            llt +=ll[k]*gipmx/gsw;
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
               }          }
             }          fprintf(ficresilk," %10.6f\n", -llt);
           }        }
         }      } /* end of wave */
       }    } /* end of individual */
       for(i=(int)agemin; i <= (int)agemax+3; i++){    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         for(jk=1; jk <=nlstate ; jk++){    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
             pp[jk] += freq[jk][m][i];    if(globpr==0){ /* First time we count the contributions and weights */
         }      gipmx=ipmx;
         for(jk=1; jk <=nlstate ; jk++){      gsw=sw;
           for(m=-1, pos=0; m <=0 ; m++)    }
             pos += freq[jk][m][i];    return -l;
         }  }
          
         for(jk=1; jk <=nlstate ; jk++){  char *subdirf(char fileres[])
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  {
             pp[jk] += freq[jk][m][i];    
         }    strcpy(tmpout,optionfilefiname);
            strcat(tmpout,"/"); /* Add to the right */
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    strcat(tmpout,fileres);
            return tmpout;
         for(jk=1; jk <=nlstate ; jk++){      }
           if( i <= (int) agemax){  
             if(pos>=1.e-5){  char *subdirf2(char fileres[], char *preop)
               probs[i][jk][j1]= pp[jk]/pos;  {
             }    
           }    strcpy(tmpout,optionfilefiname);
         }    strcat(tmpout,"/");
            strcat(tmpout,preop);
       }    strcat(tmpout,fileres);
     }    return tmpout;
   }  }
   char *subdirf3(char fileres[], char *preop, char *preop2)
    {
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    
   free_vector(pp,1,nlstate);    strcpy(tmpout,optionfilefiname);
      strcat(tmpout,"/");
 }  /* End of Freq */    strcat(tmpout,preop);
     strcat(tmpout,preop2);
 /************* Waves Concatenation ***************/    strcat(tmpout,fileres);
     return tmpout;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  }
 {  
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
      Death is a valid wave (if date is known).  {
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    /* This routine should help understanding what is done with 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]       the selection of individuals/waves and
      and mw[mi+1][i]. dh depends on stepm.       to check the exact contribution to the likelihood.
      */       Plotting could be done.
      */
   int i, mi, m;    int k;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  
      double sum=0., jmean=0.;*/    if(*globpri !=0){ /* Just counts and sums, no printings */
       strcpy(fileresilk,"ilk"); 
   int j, k=0,jk, ju, jl;      strcat(fileresilk,fileres);
   double sum=0.;      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   jmin=1e+5;        printf("Problem with resultfile: %s\n", fileresilk);
   jmax=-1;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   jmean=0.;      }
   for(i=1; i<=imx; i++){      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
     mi=0;      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     m=firstpass;      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     while(s[m][i] <= nlstate){      for(k=1; k<=nlstate; k++) 
       if(s[m][i]>=1)        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
         mw[++mi][i]=m;      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
       if(m >=lastpass)    }
         break;  
       else    *fretone=(*funcone)(p);
         m++;    if(*globpri !=0){
     }/* end while */      fclose(ficresilk);
     if (s[m][i] > nlstate){      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       mi++;     /* Death is another wave */      fflush(fichtm); 
       /* if(mi==0)  never been interviewed correctly before death */    } 
          /* Only death is a correct wave */    return;
       mw[mi][i]=m;  }
     }  
   
     wav[i]=mi;  /*********** Maximum Likelihood Estimation ***************/
     if(mi==0)  
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   }  {
     int i,j, iter;
   for(i=1; i<=imx; i++){    double **xi;
     for(mi=1; mi<wav[i];mi++){    double fret;
       if (stepm <=0)    double fretone; /* Only one call to likelihood */
         dh[mi][i]=1;    char filerespow[FILENAMELENGTH];
       else{    xi=matrix(1,npar,1,npar);
         if (s[mw[mi+1][i]][i] > nlstate) {    for (i=1;i<=npar;i++)
           if (agedc[i] < 2*AGESUP) {      for (j=1;j<=npar;j++)
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        xi[i][j]=(i==j ? 1.0 : 0.0);
           if(j==0) j=1;  /* Survives at least one month after exam */    printf("Powell\n");  fprintf(ficlog,"Powell\n");
           k=k+1;    strcpy(filerespow,"pow"); 
           if (j >= jmax) jmax=j;    strcat(filerespow,fileres);
           if (j <= jmin) jmin=j;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
           sum=sum+j;      printf("Problem with resultfile: %s\n", filerespow);
           /*if (j<0) printf("j=%d num=%d \n",j,i); */      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
           }    }
         }    fprintf(ficrespow,"# Powell\n# iter -2*LL");
         else{    for (i=1;i<=nlstate;i++)
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));      for(j=1;j<=nlstate+ndeath;j++)
           k=k+1;        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
           if (j >= jmax) jmax=j;    fprintf(ficrespow,"\n");
           else if (j <= jmin)jmin=j;  
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    powell(p,xi,npar,ftol,&iter,&fret,func);
           sum=sum+j;  
         }    fclose(ficrespow);
         jk= j/stepm;    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
         jl= j -jk*stepm;    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         ju= j -(jk+1)*stepm;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         if(jl <= -ju)  
           dh[mi][i]=jk;  }
         else  
           dh[mi][i]=jk+1;  /**** Computes Hessian and covariance matrix ***/
         if(dh[mi][i]==0)  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
           dh[mi][i]=1; /* At least one step */  {
       }    double  **a,**y,*x,pd;
     }    double **hess;
   }    int i, j,jk;
   jmean=sum/k;    int *indx;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);  
  }    double hessii(double p[], double delta, int theta, double delti[]);
 /*********** Tricode ****************************/    double hessij(double p[], double delti[], int i, int j);
 void tricode(int *Tvar, int **nbcode, int imx)    void lubksb(double **a, int npar, int *indx, double b[]) ;
 {    void ludcmp(double **a, int npar, int *indx, double *d) ;
   int Ndum[20],ij=1, k, j, i;  
   int cptcode=0;    hess=matrix(1,npar,1,npar);
   cptcoveff=0;  
      printf("\nCalculation of the hessian matrix. Wait...\n");
   for (k=0; k<19; k++) Ndum[k]=0;    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   for (k=1; k<=7; k++) ncodemax[k]=0;    for (i=1;i<=npar;i++){
       printf("%d",i);fflush(stdout);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {      fprintf(ficlog,"%d",i);fflush(ficlog);
     for (i=1; i<=imx; i++) {      hess[i][i]=hessii(p,ftolhess,i,delti);
       ij=(int)(covar[Tvar[j]][i]);      /*printf(" %f ",p[i]);*/
       Ndum[ij]++;      /*printf(" %lf ",hess[i][i]);*/
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    }
       if (ij > cptcode) cptcode=ij;    
     }    for (i=1;i<=npar;i++) {
       for (j=1;j<=npar;j++)  {
     for (i=0; i<=cptcode; i++) {        if (j>i) { 
       if(Ndum[i]!=0) ncodemax[j]++;          printf(".%d%d",i,j);fflush(stdout);
     }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     ij=1;          hess[i][j]=hessij(p,delti,i,j);
           hess[j][i]=hess[i][j];    
           /*printf(" %lf ",hess[i][j]);*/
     for (i=1; i<=ncodemax[j]; i++) {        }
       for (k=0; k<=19; k++) {      }
         if (Ndum[k] != 0) {    }
           nbcode[Tvar[j]][ij]=k;    printf("\n");
              fprintf(ficlog,"\n");
           ij++;  
         }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
         if (ij > ncodemax[j]) break;    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
       }      
     }    a=matrix(1,npar,1,npar);
   }      y=matrix(1,npar,1,npar);
     x=vector(1,npar);
  for (k=0; k<19; k++) Ndum[k]=0;    indx=ivector(1,npar);
     for (i=1;i<=npar;i++)
  for (i=1; i<=ncovmodel-2; i++) {      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
       ij=Tvar[i];    ludcmp(a,npar,indx,&pd);
       Ndum[ij]++;  
     }    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
  ij=1;      x[j]=1;
  for (i=1; i<=10; i++) {      lubksb(a,npar,indx,x);
    if((Ndum[i]!=0) && (i<=ncovcol)){      for (i=1;i<=npar;i++){ 
      Tvaraff[ij]=i;        matcov[i][j]=x[i];
      ij++;      }
    }    }
  }  
      printf("\n#Hessian matrix#\n");
     cptcoveff=ij-1;    fprintf(ficlog,"\n#Hessian matrix#\n");
 }    for (i=1;i<=npar;i++) { 
       for (j=1;j<=npar;j++) { 
 /*********** Health Expectancies ****************/        printf("%.3e ",hess[i][j]);
         fprintf(ficlog,"%.3e ",hess[i][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 )      }
       printf("\n");
 {      fprintf(ficlog,"\n");
   /* Health expectancies */    }
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;  
   double age, agelim, hf;    /* Recompute Inverse */
   double ***p3mat,***varhe;    for (i=1;i<=npar;i++)
   double **dnewm,**doldm;      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   double *xp;    ludcmp(a,npar,indx,&pd);
   double **gp, **gm;  
   double ***gradg, ***trgradg;    /*  printf("\n#Hessian matrix recomputed#\n");
   int theta;  
     for (j=1;j<=npar;j++) {
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);      for (i=1;i<=npar;i++) x[i]=0;
   xp=vector(1,npar);      x[j]=1;
   dnewm=matrix(1,nlstate*2,1,npar);      lubksb(a,npar,indx,x);
   doldm=matrix(1,nlstate*2,1,nlstate*2);      for (i=1;i<=npar;i++){ 
          y[i][j]=x[i];
   fprintf(ficreseij,"# Health expectancies\n");        printf("%.3e ",y[i][j]);
   fprintf(ficreseij,"# Age");        fprintf(ficlog,"%.3e ",y[i][j]);
   for(i=1; i<=nlstate;i++)      }
     for(j=1; j<=nlstate;j++)      printf("\n");
       fprintf(ficreseij," %1d-%1d (SE)",i,j);      fprintf(ficlog,"\n");
   fprintf(ficreseij,"\n");    }
     */
   if(estepm < stepm){  
     printf ("Problem %d lower than %d\n",estepm, stepm);    free_matrix(a,1,npar,1,npar);
   }    free_matrix(y,1,npar,1,npar);
   else  hstepm=estepm;      free_vector(x,1,npar);
   /* We compute the life expectancy from trapezoids spaced every estepm months    free_ivector(indx,1,npar);
    * This is mainly to measure the difference between two models: for example    free_matrix(hess,1,npar,1,npar);
    * if stepm=24 months pijx are given only every 2 years and by summing them  
    * we are calculating an estimate of the Life Expectancy assuming a linear  
    * progression inbetween and thus overestimating or underestimating according  }
    * to the curvature of the survival function. If, for the same date, we  
    * estimate the model with stepm=1 month, we can keep estepm to 24 months  /*************** hessian matrix ****************/
    * to compare the new estimate of Life expectancy with the same linear  double hessii( double x[], double delta, int theta, double delti[])
    * hypothesis. A more precise result, taking into account a more precise  {
    * curvature will be obtained if estepm is as small as stepm. */    int i;
     int l=1, lmax=20;
   /* For example we decided to compute the life expectancy with the smallest unit */    double k1,k2;
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    double p2[NPARMAX+1];
      nhstepm is the number of hstepm from age to agelim    double res;
      nstepm is the number of stepm from age to agelin.    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
      Look at hpijx to understand the reason of that which relies in memory size    double fx;
      and note for a fixed period like estepm months */    int k=0,kmax=10;
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    double l1;
      survival function given by stepm (the optimization length). Unfortunately it  
      means that if the survival funtion is printed only each two years of age and if    fx=func(x);
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    for (i=1;i<=npar;i++) p2[i]=x[i];
      results. So we changed our mind and took the option of the best precision.    for(l=0 ; l <=lmax; l++){
   */      l1=pow(10,l);
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */      delts=delt;
       for(k=1 ; k <kmax; k=k+1){
   agelim=AGESUP;        delt = delta*(l1*k);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        p2[theta]=x[theta] +delt;
     /* nhstepm age range expressed in number of stepm */        k1=func(p2)-fx;
     nstepm=(int) rint((agelim-age)*YEARM/stepm);        p2[theta]=x[theta]-delt;
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */        k2=func(p2)-fx;
     /* if (stepm >= YEARM) hstepm=1;*/        /*res= (k1-2.0*fx+k2)/delt/delt; */
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);  #ifdef DEBUG
     gp=matrix(0,nhstepm,1,nlstate*2);        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);
     gm=matrix(0,nhstepm,1,nlstate*2);        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);
   #endif
     /* Computed by stepm unit matrices, product of hstepm matrices, stored        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            k=kmax;
          }
         else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */          k=kmax; l=lmax*10.;
         }
     /* Computing Variances of health expectancies */        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           delts=delt;
      for(theta=1; theta <=npar; theta++){        }
       for(i=1; i<=npar; i++){      }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    }
       }    delti[theta]=delts;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      return res; 
      
       cptj=0;  }
       for(j=1; j<= nlstate; j++){  
         for(i=1; i<=nlstate; i++){  double hessij( double x[], double delti[], int thetai,int thetaj)
           cptj=cptj+1;  {
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){    int i;
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    int l=1, l1, lmax=20;
           }    double k1,k2,k3,k4,res,fx;
         }    double p2[NPARMAX+1];
       }    int k;
        
          fx=func(x);
       for(i=1; i<=npar; i++)    for (k=1; k<=2; k++) {
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      for (i=1;i<=npar;i++) p2[i]=x[i];
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        p2[thetai]=x[thetai]+delti[thetai]/k;
            p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       cptj=0;      k1=func(p2)-fx;
       for(j=1; j<= nlstate; j++){    
         for(i=1;i<=nlstate;i++){      p2[thetai]=x[thetai]+delti[thetai]/k;
           cptj=cptj+1;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){      k2=func(p2)-fx;
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    
           }      p2[thetai]=x[thetai]-delti[thetai]/k;
         }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       }      k3=func(p2)-fx;
       for(j=1; j<= nlstate*2; j++)    
         for(h=0; h<=nhstepm-1; h++){      p2[thetai]=x[thetai]-delti[thetai]/k;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         }      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
 /* End theta */      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       fprintf(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);
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);  #endif
     }
      for(h=0; h<=nhstepm-1; h++)    return res;
       for(j=1; j<=nlstate*2;j++)  }
         for(theta=1; theta <=npar; theta++)  
           trgradg[h][j][theta]=gradg[h][theta][j];  /************** Inverse of matrix **************/
        void ludcmp(double **a, int n, int *indx, double *d) 
   { 
      for(i=1;i<=nlstate*2;i++)    int i,imax,j,k; 
       for(j=1;j<=nlstate*2;j++)    double big,dum,sum,temp; 
         varhe[i][j][(int)age] =0.;    double *vv; 
    
      printf("%d|",(int)age);fflush(stdout);    vv=vector(1,n); 
      for(h=0;h<=nhstepm-1;h++){    *d=1.0; 
       for(k=0;k<=nhstepm-1;k++){    for (i=1;i<=n;i++) { 
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);      big=0.0; 
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);      for (j=1;j<=n;j++) 
         for(i=1;i<=nlstate*2;i++)        if ((temp=fabs(a[i][j])) > big) big=temp; 
           for(j=1;j<=nlstate*2;j++)      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;      vv[i]=1.0/big; 
       }    } 
     }    for (j=1;j<=n;j++) { 
     /* Computing expectancies */      for (i=1;i<j;i++) { 
     for(i=1; i<=nlstate;i++)        sum=a[i][j]; 
       for(j=1; j<=nlstate;j++)        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){        a[i][j]=sum; 
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;      } 
                big=0.0; 
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/      for (i=j;i<=n;i++) { 
         sum=a[i][j]; 
         }        for (k=1;k<j;k++) 
           sum -= a[i][k]*a[k][j]; 
     fprintf(ficreseij,"%3.0f",age );        a[i][j]=sum; 
     cptj=0;        if ( (dum=vv[i]*fabs(sum)) >= big) { 
     for(i=1; i<=nlstate;i++)          big=dum; 
       for(j=1; j<=nlstate;j++){          imax=i; 
         cptj++;        } 
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );      } 
       }      if (j != imax) { 
     fprintf(ficreseij,"\n");        for (k=1;k<=n;k++) { 
              dum=a[imax][k]; 
     free_matrix(gm,0,nhstepm,1,nlstate*2);          a[imax][k]=a[j][k]; 
     free_matrix(gp,0,nhstepm,1,nlstate*2);          a[j][k]=dum; 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);        } 
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);        *d = -(*d); 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        vv[imax]=vv[j]; 
   }      } 
   printf("\n");      indx[j]=imax; 
       if (a[j][j] == 0.0) a[j][j]=TINY; 
   free_vector(xp,1,npar);      if (j != n) { 
   free_matrix(dnewm,1,nlstate*2,1,npar);        dum=1.0/(a[j][j]); 
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);      } 
 }    } 
     free_vector(vv,1,n);  /* Doesn't work */
 /************ Variance ******************/  ;
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)  } 
 {  
   /* Variance of health expectancies */  void lubksb(double **a, int n, int *indx, double b[]) 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  { 
   double **newm;    int i,ii=0,ip,j; 
   double **dnewm,**doldm;    double sum; 
   int i, j, nhstepm, hstepm, h, nstepm ;   
   int k, cptcode;    for (i=1;i<=n;i++) { 
   double *xp;      ip=indx[i]; 
   double **gp, **gm;      sum=b[ip]; 
   double ***gradg, ***trgradg;      b[ip]=b[i]; 
   double ***p3mat;      if (ii) 
   double age,agelim, hf;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   int theta;      else if (sum) ii=i; 
       b[i]=sum; 
   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");    for (i=n;i>=1;i--) { 
   for(i=1; i<=nlstate;i++)      sum=b[i]; 
     for(j=1; j<=nlstate;j++)      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      b[i]=sum/a[i][i]; 
   fprintf(ficresvij,"\n");    } 
   } 
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);  /************ Frequencies ********************/
   doldm=matrix(1,nlstate,1,nlstate);  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint)
    {  /* Some frequencies */
   if(estepm < stepm){    
     printf ("Problem %d lower than %d\n",estepm, stepm);    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   }    int first;
   else  hstepm=estepm;      double ***freq; /* Frequencies */
   /* For example we decided to compute the life expectancy with the smallest unit */    double *pp, **prop;
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    double pos,posprop, k2, dateintsum=0,k2cpt=0;
      nhstepm is the number of hstepm from age to agelim    FILE *ficresp;
      nstepm is the number of stepm from age to agelin.    char fileresp[FILENAMELENGTH];
      Look at hpijx to understand the reason of that which relies in memory size    
      and note for a fixed period like k years */    pp=vector(1,nlstate);
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    prop=matrix(1,nlstate,iagemin,iagemax+3);
      survival function given by stepm (the optimization length). Unfortunately it    strcpy(fileresp,"p");
      means that if the survival funtion is printed only each two years of age and if    strcat(fileresp,fileres);
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    if((ficresp=fopen(fileresp,"w"))==NULL) {
      results. So we changed our mind and took the option of the best precision.      printf("Problem with prevalence resultfile: %s\n", fileresp);
   */      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */      exit(0);
   agelim = AGESUP;    }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    j1=0;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    j=cptcoveff;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     gp=matrix(0,nhstepm,1,nlstate);  
     gm=matrix(0,nhstepm,1,nlstate);    first=1;
   
     for(theta=1; theta <=npar; theta++){    for(k1=1; k1<=j;k1++){
       for(i=1; i<=npar; i++){ /* Computes gradient */      for(i1=1; i1<=ncodemax[k1];i1++){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        j1++;
       }        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            scanf("%d", i);*/
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        for (i=-1; i<=nlstate+ndeath; i++)  
           for (jk=-1; jk<=nlstate+ndeath; jk++)  
       if (popbased==1) {            for(m=iagemin; m <= iagemax+3; m++)
         for(i=1; i<=nlstate;i++)              freq[i][jk][m]=0;
           prlim[i][i]=probs[(int)age][i][ij];  
       }      for (i=1; i<=nlstate; i++)  
          for(m=iagemin; m <= iagemax+3; m++)
       for(j=1; j<= nlstate; j++){          prop[i][m]=0;
         for(h=0; h<=nhstepm; h++){        
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)        dateintsum=0;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        k2cpt=0;
         }        for (i=1; i<=imx; i++) {
       }          bool=1;
              if  (cptcovn>0) {
       for(i=1; i<=npar; i++) /* Computes gradient */            for (z1=1; z1<=cptcoveff; z1++) 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                  bool=0;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          }
            if (bool==1){
       if (popbased==1) {            for(m=firstpass; m<=lastpass; m++){
         for(i=1; i<=nlstate;i++)              k2=anint[m][i]+(mint[m][i]/12.);
           prlim[i][i]=probs[(int)age][i][ij];              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
       }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
       for(j=1; j<= nlstate; j++){                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
         for(h=0; h<=nhstepm; h++){                if (m<lastpass) {
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
         }                }
       }                
                 if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
       for(j=1; j<= nlstate; j++)                  dateintsum=dateintsum+k2;
         for(h=0; h<=nhstepm; h++){                  k2cpt++;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];                }
         }                /*}*/
     } /* End theta */            }
           }
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);        }
          
     for(h=0; h<=nhstepm; h++)        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       for(j=1; j<=nlstate;j++)  
         for(theta=1; theta <=npar; theta++)        if  (cptcovn>0) {
           trgradg[h][j][theta]=gradg[h][theta][j];          fprintf(ficresp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */          fprintf(ficresp, "**********\n#");
     for(i=1;i<=nlstate;i++)        }
       for(j=1;j<=nlstate;j++)        for(i=1; i<=nlstate;i++) 
         vareij[i][j][(int)age] =0.;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         fprintf(ficresp, "\n");
     for(h=0;h<=nhstepm;h++){        
       for(k=0;k<=nhstepm;k++){        for(i=iagemin; i <= iagemax+3; i++){
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          if(i==iagemax+3){
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);            fprintf(ficlog,"Total");
         for(i=1;i<=nlstate;i++)          }else{
           for(j=1;j<=nlstate;j++)            if(first==1){
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;              first=0;
       }              printf("See log file for details...\n");
     }            }
             fprintf(ficlog,"Age %d", i);
     fprintf(ficresvij,"%.0f ",age );          }
     for(i=1; i<=nlstate;i++)          for(jk=1; jk <=nlstate ; jk++){
       for(j=1; j<=nlstate;j++){            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);              pp[jk] += freq[jk][m][i]; 
       }          }
     fprintf(ficresvij,"\n");          for(jk=1; jk <=nlstate ; jk++){
     free_matrix(gp,0,nhstepm,1,nlstate);            for(m=-1, pos=0; m <=0 ; m++)
     free_matrix(gm,0,nhstepm,1,nlstate);              pos += freq[jk][m][i];
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);            if(pp[jk]>=1.e-10){
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);              if(first==1){
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   } /* End age */              }
                fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   free_vector(xp,1,npar);            }else{
   free_matrix(doldm,1,nlstate,1,npar);              if(first==1)
   free_matrix(dnewm,1,nlstate,1,nlstate);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
 }            }
           }
 /************ Variance of prevlim ******************/  
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)          for(jk=1; jk <=nlstate ; jk++){
 {            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   /* Variance of prevalence limit */              pp[jk] += freq[jk][m][i];
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          }       
   double **newm;          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   double **dnewm,**doldm;            pos += pp[jk];
   int i, j, nhstepm, hstepm;            posprop += prop[jk][i];
   int k, cptcode;          }
   double *xp;          for(jk=1; jk <=nlstate ; jk++){
   double *gp, *gm;            if(pos>=1.e-5){
   double **gradg, **trgradg;              if(first==1)
   double age,agelim;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   int theta;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                }else{
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");              if(first==1)
   fprintf(ficresvpl,"# Age");                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   for(i=1; i<=nlstate;i++)              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       fprintf(ficresvpl," %1d-%1d",i,i);            }
   fprintf(ficresvpl,"\n");            if( i <= iagemax){
               if(pos>=1.e-5){
   xp=vector(1,npar);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   dnewm=matrix(1,nlstate,1,npar);                /*probs[i][jk][j1]= pp[jk]/pos;*/
   doldm=matrix(1,nlstate,1,nlstate);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
                }
   hstepm=1*YEARM; /* Every year of age */              else
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   agelim = AGESUP;            }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          
     if (stepm >= YEARM) hstepm=1;          for(jk=-1; jk <=nlstate+ndeath; jk++)
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            for(m=-1; m <=nlstate+ndeath; m++)
     gradg=matrix(1,npar,1,nlstate);              if(freq[jk][m][i] !=0 ) {
     gp=vector(1,nlstate);              if(first==1)
     gm=vector(1,nlstate);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                 fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     for(theta=1; theta <=npar; theta++){              }
       for(i=1; i<=npar; i++){ /* Computes gradient */          if(i <= iagemax)
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            fprintf(ficresp,"\n");
       }          if(first==1)
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            printf("Others in log...\n");
       for(i=1;i<=nlstate;i++)          fprintf(ficlog,"\n");
         gp[i] = prlim[i][i];        }
          }
       for(i=1; i<=npar; i++) /* Computes gradient */    }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    dateintmean=dateintsum/k2cpt; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);   
       for(i=1;i<=nlstate;i++)    fclose(ficresp);
         gm[i] = prlim[i][i];    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
     free_vector(pp,1,nlstate);
       for(i=1;i<=nlstate;i++)    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    /* End of Freq */
     } /* End theta */  }
   
     trgradg =matrix(1,nlstate,1,npar);  /************ Prevalence ********************/
   void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
     for(j=1; j<=nlstate;j++)  {  
       for(theta=1; theta <=npar; theta++)    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
         trgradg[j][theta]=gradg[theta][j];       in each health status at the date of interview (if between dateprev1 and dateprev2).
        We still use firstpass and lastpass as another selection.
     for(i=1;i<=nlstate;i++)    */
       varpl[i][(int)age] =0.;   
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    double ***freq; /* Frequencies */
     for(i=1;i<=nlstate;i++)    double *pp, **prop;
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    double pos,posprop; 
     double  y2; /* in fractional years */
     fprintf(ficresvpl,"%.0f ",age );    int iagemin, iagemax;
     for(i=1; i<=nlstate;i++)  
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    iagemin= (int) agemin;
     fprintf(ficresvpl,"\n");    iagemax= (int) agemax;
     free_vector(gp,1,nlstate);    /*pp=vector(1,nlstate);*/
     free_vector(gm,1,nlstate);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     free_matrix(gradg,1,npar,1,nlstate);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     free_matrix(trgradg,1,nlstate,1,npar);    j1=0;
   } /* End age */    
     j=cptcoveff;
   free_vector(xp,1,npar);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   free_matrix(doldm,1,nlstate,1,npar);    
   free_matrix(dnewm,1,nlstate,1,nlstate);    for(k1=1; k1<=j;k1++){
       for(i1=1; i1<=ncodemax[k1];i1++){
 }        j1++;
         
 /************ Variance of one-step probabilities  ******************/        for (i=1; i<=nlstate; i++)  
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)          for(m=iagemin; m <= iagemax+3; m++)
 {            prop[i][m]=0.0;
   int i, j,  i1, k1, l1;       
   int k2, l2, j1,  z1;        for (i=1; i<=imx; i++) { /* Each individual */
   int k=0,l, cptcode;          bool=1;
   int first=1;          if  (cptcovn>0) {
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;            for (z1=1; z1<=cptcoveff; z1++) 
   double **dnewm,**doldm;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   double *xp;                bool=0;
   double *gp, *gm;          } 
   double **gradg, **trgradg;          if (bool==1) { 
   double **mu;            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   double age,agelim, cov[NCOVMAX];              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   int theta;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   char fileresprob[FILENAMELENGTH];                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   char fileresprobcov[FILENAMELENGTH];                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); 
   char fileresprobcor[FILENAMELENGTH];                if (s[m][i]>0 && s[m][i]<=nlstate) { 
                   /*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 ***varpij;                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                   prop[s[m][i]][iagemax+3] += weight[i]; 
   strcpy(fileresprob,"prob");                } 
   strcat(fileresprob,fileres);              }
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {            } /* end selection of waves */
     printf("Problem with resultfile: %s\n", fileresprob);          }
   }        }
   strcpy(fileresprobcov,"probcov");        for(i=iagemin; i <= iagemax+3; i++){  
   strcat(fileresprobcov,fileres);          
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     printf("Problem with resultfile: %s\n", fileresprobcov);            posprop += prop[jk][i]; 
   }          } 
   strcpy(fileresprobcor,"probcor");  
   strcat(fileresprobcor,fileres);          for(jk=1; jk <=nlstate ; jk++){     
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {            if( i <=  iagemax){ 
     printf("Problem with resultfile: %s\n", fileresprobcor);              if(posprop>=1.e-5){ 
   }                probs[i][jk][j1]= prop[jk][i]/posprop;
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);              } 
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);            } 
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);          }/* end jk */ 
          }/* end i */ 
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");      } /* end i1 */
   fprintf(ficresprob,"# Age");    } /* end k1 */
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");    
   fprintf(ficresprobcov,"# Age");    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");    /*free_vector(pp,1,nlstate);*/
   fprintf(ficresprobcov,"# Age");    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  /* End of prevalence */
   
   for(i=1; i<=nlstate;i++)  /************* Waves Concatenation ***************/
     for(j=1; j<=(nlstate+ndeath);j++){  
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
       fprintf(ficresprobcov," p%1d-%1d ",i,j);  {
       fprintf(ficresprobcor," p%1d-%1d ",i,j);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     }         Death is a valid wave (if date is known).
   fprintf(ficresprob,"\n");       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   fprintf(ficresprobcov,"\n");       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   fprintf(ficresprobcor,"\n");       and mw[mi+1][i]. dh depends on stepm.
   xp=vector(1,npar);       */
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);  
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));    int i, mi, m;
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);       double sum=0., jmean=0.;*/
   first=1;    int first;
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    int j, k=0,jk, ju, jl;
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);    double sum=0.;
     exit(0);    first=0;
   }    jmin=1e+5;
   else{    jmax=-1;
     fprintf(ficgp,"\n# Routine varprob");    jmean=0.;
   }    for(i=1; i<=imx; i++){
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {      mi=0;
     printf("Problem with html file: %s\n", optionfilehtm);      m=firstpass;
     exit(0);      while(s[m][i] <= nlstate){
   }        if(s[m][i]>=1)
   else{          mw[++mi][i]=m;
     fprintf(fichtm,"\n<H2> Computing matrix of variance-covariance of step probabilities</h2>\n");        if(m >=lastpass)
     fprintf(fichtm,"\n<br> We 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");          break;
     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");        else
           m++;
   }      }/* end while */
   cov[1]=1;      if (s[m][i] > nlstate){
   j=cptcoveff;        mi++;     /* Death is another wave */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        /* if(mi==0)  never been interviewed correctly before death */
   j1=0;           /* Only death is a correct wave */
   for(k1=1; k1<=1;k1++){        mw[mi][i]=m;
     for(i1=1; i1<=ncodemax[k1];i1++){      }
     j1++;  
       wav[i]=mi;
     if  (cptcovn>0) {      if(mi==0){
       fprintf(ficresprob, "\n#********** Variable ");        if(first==0){
       fprintf(ficresprobcov, "\n#********** Variable ");          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
       fprintf(ficgp, "\n#********** Variable ");          first=1;
       fprintf(fichtm, "\n<h4>********** Variable</h4>\n ");        }
       fprintf(ficresprobcor, "\n#********** Variable ");        if(first==1){
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
       fprintf(ficresprob, "**********\n#");        }
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      } /* end mi==0 */
       fprintf(ficresprobcov, "**********\n#");    } /* End individuals */
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
       fprintf(ficgp, "**********\n#");    for(i=1; i<=imx; i++){
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      for(mi=1; mi<wav[i];mi++){
       fprintf(ficgp, "**********\n#");        if (stepm <=0)
       for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          dh[mi][i]=1;
       fprintf(fichtm, "**********\n#");        else{
     }          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
                if (agedc[i] < 2*AGESUP) {
       for (age=bage; age<=fage; age ++){              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
         cov[2]=age;              if(j==0) j=1;  /* Survives at least one month after exam */
         for (k=1; k<=cptcovn;k++) {              else if(j<0){
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];                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 */
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
         for (k=1; k<=cptcovprod;k++)                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]);
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];                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);
                      }
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));              k=k+1;
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);              if (j >= jmax) jmax=j;
         gp=vector(1,(nlstate)*(nlstate+ndeath));              if (j <= jmin) jmin=j;
         gm=vector(1,(nlstate)*(nlstate+ndeath));              sum=sum+j;
                  /*if (j<0) printf("j=%d num=%d \n",j,i);*/
         for(theta=1; theta <=npar; theta++){              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
           for(i=1; i<=npar; i++)            }
             xp[i] = x[i] + (i==theta ?delti[theta]:0);          }
                    else{
           pmij(pmmij,cov,ncovmodel,xp,nlstate);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
                      /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
           k=0;            k=k+1;
           for(i=1; i<= (nlstate); i++){            if (j >= jmax) jmax=j;
             for(j=1; j<=(nlstate+ndeath);j++){            else if (j <= jmin)jmin=j;
               k=k+1;            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
               gp[k]=pmmij[i][j];            /*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]);*/
             }            if(j<0){
           }              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                        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]);
           for(i=1; i<=npar; i++)            }
             xp[i] = x[i] - (i==theta ?delti[theta]:0);            sum=sum+j;
              }
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          jk= j/stepm;
           k=0;          jl= j -jk*stepm;
           for(i=1; i<=(nlstate); i++){          ju= j -(jk+1)*stepm;
             for(j=1; j<=(nlstate+ndeath);j++){          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
               k=k+1;            if(jl==0){
               gm[k]=pmmij[i][j];              dh[mi][i]=jk;
             }              bh[mi][i]=0;
           }            }else{ /* We want a negative bias in order to only have interpolation ie
                          * at the price of an extra matrix product in likelihood */
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)              dh[mi][i]=jk+1;
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];                bh[mi][i]=ju;
         }            }
           }else{
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)            if(jl <= -ju){
           for(theta=1; theta <=npar; theta++)              dh[mi][i]=jk;
             trgradg[j][theta]=gradg[theta][j];              bh[mi][i]=jl;       /* bias is positive if real duration
                                           * is higher than the multiple of stepm and negative otherwise.
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);                                   */
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);            }
                    else{
         pmij(pmmij,cov,ncovmodel,x,nlstate);              dh[mi][i]=jk+1;
                      bh[mi][i]=ju;
         k=0;            }
         for(i=1; i<=(nlstate); i++){            if(dh[mi][i]==0){
           for(j=1; j<=(nlstate+ndeath);j++){              dh[mi][i]=1; /* At least one step */
             k=k+1;              bh[mi][i]=ju; /* At least one step */
             mu[k][(int) age]=pmmij[i][j];              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
           }            }
         }          } /* end if mle */
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)        }
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)      } /* end wave */
             varpij[i][j][(int)age] = doldm[i][j];    }
     jmean=sum/k;
         /*printf("\n%d ",(int)age);    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));   }
      }*/  
   /*********** Tricode ****************************/
         fprintf(ficresprob,"\n%d ",(int)age);  void tricode(int *Tvar, int **nbcode, int imx)
         fprintf(ficresprobcov,"\n%d ",(int)age);  {
         fprintf(ficresprobcor,"\n%d ",(int)age);    
     int Ndum[20],ij=1, k, j, i, maxncov=19;
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)    int cptcode=0;
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));    cptcoveff=0; 
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){   
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);    for (k=0; k<maxncov; k++) Ndum[k]=0;
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);    for (k=1; k<=7; k++) ncodemax[k]=0;
         }  
         i=0;    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
         for (k=1; k<=(nlstate);k++){      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
           for (l=1; l<=(nlstate+ndeath);l++){                                 modality*/ 
             i=i++;        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);        Ndum[ij]++; /*store the modality */
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
             for (j=1; j<=i;j++){        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);                                         Tvar[j]. If V=sex and male is 0 and 
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));                                         female is 1, then  cptcode=1.*/
             }      }
           }  
         }/* end of loop for state */      for (i=0; i<=cptcode; i++) {
       } /* end of loop for age */        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 */
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/      }
       for (k1=1; k1<=(nlstate);k1++){  
         for (l1=1; l1<=(nlstate+ndeath);l1++){      ij=1; 
           if(l1==k1) continue;      for (i=1; i<=ncodemax[j]; i++) {
           i=(k1-1)*(nlstate+ndeath)+l1;        for (k=0; k<= maxncov; k++) {
           for (k2=1; k2<=(nlstate);k2++){          if (Ndum[k] != 0) {
             for (l2=1; l2<=(nlstate+ndeath);l2++){            nbcode[Tvar[j]][ij]=k; 
               if(l2==k2) continue;            /* 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; */
               j=(k2-1)*(nlstate+ndeath)+l2;            
               if(j<=i) continue;            ij++;
               for (age=bage; age<=fage; age ++){          }
                 if ((int)age %5==0){          if (ij > ncodemax[j]) break; 
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;        }  
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;      } 
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;    }  
                   mu1=mu[i][(int) age]/stepm*YEARM ;  
                   mu2=mu[j][(int) age]/stepm*YEARM;   for (k=0; k< maxncov; k++) Ndum[k]=0;
                   /* Computing eigen value of matrix of covariance */  
                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));   for (i=1; i<=ncovmodel-2; i++) { 
                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
                   printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);     ij=Tvar[i];
                   /* Eigen vectors */     Ndum[ij]++;
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));   }
                   v21=sqrt(1.-v11*v11);  
                   v12=-v21;   ij=1;
                   v22=v11;   for (i=1; i<= maxncov; i++) {
                   /*printf(fignu*/     if((Ndum[i]!=0) && (i<=ncovcol)){
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */       Tvaraff[ij]=i; /*For printing */
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */       ij++;
                   if(first==1){     }
                     first=0;   }
                     fprintf(ficgp,"\nset parametric;set nolabel");   
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);   cptcoveff=ij-1; /*Number of simple covariates*/
                     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%1d%1d-%1d%1d.png\">varpijgr%s%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1);  
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%1d%1d-%1d%1d.png\">, ",optionfilefiname,k2,l2,k1,l1);  /*********** Health Expectancies ****************/
                     fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\"",optionfilefiname,k2,l2,k1,l1);  
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);  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 )
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);  
                     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)) t \"%d\"",\  {
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    /* Health expectancies */
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
                   }else{    double age, agelim, hf;
                     first=0;    double ***p3mat,***varhe;
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);    double **dnewm,**doldm;
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);    double *xp;
                     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)) t \"%d\"",\    double **gp, **gm;
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    double ***gradg, ***trgradg;
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);    int theta;
                   }/* if first */  
                 } /* age mod 5 */    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
               } /* end loop age */    xp=vector(1,npar);
               fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\";replot;",optionfilefiname,k2,l2,k1,l1);    dnewm=matrix(1,nlstate*nlstate,1,npar);
               first=1;    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
             } /*l12 */    
           } /* k12 */    fprintf(ficreseij,"# Health expectancies\n");
         } /*l1 */    fprintf(ficreseij,"# Age");
       }/* k1 */    for(i=1; i<=nlstate;i++)
     } /* loop covariates */      for(j=1; j<=nlstate;j++)
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);        fprintf(ficreseij," %1d-%1d (SE)",i,j);
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    fprintf(ficreseij,"\n");
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));  
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);    if(estepm < stepm){
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      printf ("Problem %d lower than %d\n",estepm, stepm);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    }
   }    else  hstepm=estepm;   
   free_vector(xp,1,npar);    /* We compute the life expectancy from trapezoids spaced every estepm months
   fclose(ficresprob);     * This is mainly to measure the difference between two models: for example
   fclose(ficresprobcov);     * if stepm=24 months pijx are given only every 2 years and by summing them
   fclose(ficresprobcor);     * we are calculating an estimate of the Life Expectancy assuming a linear 
   fclose(ficgp);     * progression in between and thus overestimating or underestimating according
   fclose(fichtm);     * to the curvature of the survival function. If, for the same date, we 
 }     * estimate the model with stepm=1 month, we can keep estepm to 24 months
      * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
 /******************* Printing html file ***********/     * curvature will be obtained if estepm is as small as stepm. */
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \  
                   int lastpass, int stepm, int weightopt, char model[],\    /* For example we decided to compute the life expectancy with the smallest unit */
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
                   int popforecast, int estepm ,\       nhstepm is the number of hstepm from age to agelim 
                   double jprev1, double mprev1,double anprev1, \       nstepm is the number of stepm from age to agelin. 
                   double jprev2, double mprev2,double anprev2){       Look at hpijx to understand the reason of that which relies in memory size
   int jj1, k1, i1, cpt;       and note for a fixed period like estepm months */
   /*char optionfilehtm[FILENAMELENGTH];*/    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {       survival function given by stepm (the optimization length). Unfortunately it
     printf("Problem with %s \n",optionfilehtm), exit(0);       means that if the survival funtion is printed only each two years of age and if
   }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
    fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n    */
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n  
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n    agelim=AGESUP;
  - Life expectancies by age and initial health status (estepm=%2d months):    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
    <a href=\"e%s\">e%s</a> <br>\n</li>", \      /* nhstepm age range expressed in number of stepm */
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
  fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n      /* if (stepm >= YEARM) hstepm=1;*/
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n      gp=matrix(0,nhstepm,1,nlstate*nlstate);
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n      gm=matrix(0,nhstepm,1,nlstate*nlstate);
  - 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);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
          in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
  if(popforecast==1) fprintf(fichtm,"\n      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n   
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n  
         <br>",fileres,fileres,fileres,fileres);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
  else  
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);      /* Computing Variances of health expectancies */
 fprintf(fichtm," <li>Graphs</li><p>");  
        for(theta=1; theta <=npar; theta++){
  m=cptcoveff;        for(i=1; i<=npar; i++){ 
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
  jj1=0;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
  for(k1=1; k1<=m;k1++){    
    for(i1=1; i1<=ncodemax[k1];i1++){        cptj=0;
      jj1++;        for(j=1; j<= nlstate; j++){
      if (cptcovn > 0) {          for(i=1; i<=nlstate; i++){
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");            cptj=cptj+1;
        for (cpt=1; cpt<=cptcoveff;cpt++)            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");            }
      }          }
      /* Pij */        }
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>       
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);           
      /* Quasi-incidences */        for(i=1; i<=npar; i++) 
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>          xp[i] = x[i] - (i==theta ?delti[theta]:0);
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
        /* Stable prevalence in each health state */        
        for(cpt=1; cpt<nlstate;cpt++){        cptj=0;
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>        for(j=1; j<= nlstate; j++){
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          for(i=1;i<=nlstate;i++){
        }            cptj=cptj+1;
     for(cpt=1; cpt<=nlstate;cpt++) {            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident  
 interval) in state (%d): v%s%d%d.png <br>              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);              }
      }          }
      for(cpt=1; cpt<=nlstate;cpt++) {        }
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>        for(j=1; j<= nlstate*nlstate; j++)
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          for(h=0; h<=nhstepm-1; h++){
      }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
      fprintf(fichtm,"\n<br>- Total life expectancy by age and          }
 health expectancies in states (1) and (2): e%s%d.png<br>       } 
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     
    }  /* End theta */
  }  
 fclose(fichtm);       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
 }  
        for(h=0; h<=nhstepm-1; h++)
 /******************* Gnuplot file **************/        for(j=1; j<=nlstate*nlstate;j++)
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){          for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;       
   int ng;  
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {       for(i=1;i<=nlstate*nlstate;i++)
     printf("Problem with file %s",optionfilegnuplot);        for(j=1;j<=nlstate*nlstate;j++)
   }          varhe[i][j][(int)age] =0.;
   
 #ifdef windows       printf("%d|",(int)age);fflush(stdout);
     fprintf(ficgp,"cd \"%s\" \n",pathc);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
 #endif       for(h=0;h<=nhstepm-1;h++){
 m=pow(2,cptcoveff);        for(k=0;k<=nhstepm-1;k++){
            matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
  /* 1eme*/          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   for (cpt=1; cpt<= nlstate ; cpt ++) {          for(i=1;i<=nlstate*nlstate;i++)
    for (k1=1; k1<= m ; k1 ++) {            for(j=1;j<=nlstate*nlstate;j++)
               varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
 #ifdef windows        }
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);      }
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);      /* Computing expectancies */
 #endif      for(i=1; i<=nlstate;i++)
 #ifdef unix        for(j=1; j<=nlstate;j++)
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
 #endif            
   /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
 for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          }
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      fprintf(ficreseij,"%3.0f",age );
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);      cptj=0;
     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)");          cptj++;
 }          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);        }
      for (i=1; i<= nlstate ; i ++) {      fprintf(ficreseij,"\n");
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");     
   else fprintf(ficgp," \%%*lf (\%%*lf)");      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
 }        free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
 #ifdef unix      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 #endif    }
    }    printf("\n");
   }    fprintf(ficlog,"\n");
   /*2 eme*/  
     free_vector(xp,1,npar);
   for (k1=1; k1<= m ; k1 ++) {    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
      }
     for (i=1; i<= nlstate+1 ; i ++) {  
       k=2*i;  /************ Variance ******************/
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);  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)
       for (j=1; j<= nlstate+1 ; j ++) {  {
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    /* Variance of health expectancies */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
 }      /* double **newm;*/
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    double **dnewm,**doldm;
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    double **dnewmp,**doldmp;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    int i, j, nhstepm, hstepm, h, nstepm ;
       for (j=1; j<= nlstate+1 ; j ++) {    int k, cptcode;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    double *xp;
         else fprintf(ficgp," \%%*lf (\%%*lf)");    double **gp, **gm;  /* for var eij */
 }      double ***gradg, ***trgradg; /*for var eij */
       fprintf(ficgp,"\" t\"\" w l 0,");    double **gradgp, **trgradgp; /* for var p point j */
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    double *gpp, *gmp; /* for var p point j */
       for (j=1; j<= nlstate+1 ; j ++) {    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    double ***p3mat;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double age,agelim, hf;
 }      double ***mobaverage;
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    int theta;
       else fprintf(ficgp,"\" t\"\" w l 0,");    char digit[4];
     }    char digitp[25];
   }  
      char fileresprobmorprev[FILENAMELENGTH];
   /*3eme*/  
     if(popbased==1){
   for (k1=1; k1<= m ; k1 ++) {      if(mobilav!=0)
     for (cpt=1; cpt<= nlstate ; cpt ++) {        strcpy(digitp,"-populbased-mobilav-");
       k=2+nlstate*(2*cpt-2);      else strcpy(digitp,"-populbased-nomobil-");
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    }
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);    else 
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);      strcpy(digitp,"-stablbased-");
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");  
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    if (mobilav!=0) {
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
 */      }
       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);  
     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 */
      strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   /* CV preval stat */    strcat(fileresprobmorprev,fileres);
     for (k1=1; k1<= m ; k1 ++) {    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     for (cpt=1; cpt<nlstate ; cpt ++) {      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       k=3;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       for (i=1; i< nlstate ; i ++)    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
         fprintf(ficgp,"+$%d",k+i+1);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
            fprintf(ficresprobmorprev," p.%-d SE",j);
       l=3+(nlstate+ndeath)*cpt;      for(i=1; i<=nlstate;i++)
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
       for (i=1; i< nlstate ; i ++) {    }  
         l=3+(nlstate+ndeath)*cpt;    fprintf(ficresprobmorprev,"\n");
         fprintf(ficgp,"+$%d",l+i+1);    fprintf(ficgp,"\n# Routine varevsij");
       }    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(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
     }  /*   } */
   }      varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    
   /* proba elementaires */    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");
    for(i=1,jk=1; i <=nlstate; i++){    fprintf(ficresvij,"# Age");
     for(k=1; k <=(nlstate+ndeath); k++){    for(i=1; i<=nlstate;i++)
       if (k != i) {      for(j=1; j<=nlstate;j++)
         for(j=1; j <=ncovmodel; j++){        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
            fprintf(ficresvij,"\n");
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);  
           jk++;    xp=vector(1,npar);
           fprintf(ficgp,"\n");    dnewm=matrix(1,nlstate,1,npar);
         }    doldm=matrix(1,nlstate,1,nlstate);
       }    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     }    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    }  
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/    gpp=vector(nlstate+1,nlstate+ndeath);
      for(jk=1; jk <=m; jk++) {    gmp=vector(nlstate+1,nlstate+ndeath);
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
        if (ng==2)    
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");    if(estepm < stepm){
        else      printf ("Problem %d lower than %d\n",estepm, stepm);
          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);    else  hstepm=estepm;   
        i=1;    /* For example we decided to compute the life expectancy with the smallest unit */
        for(k2=1; k2<=nlstate; k2++) {    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
          k3=i;       nhstepm is the number of hstepm from age to agelim 
          for(k=1; k<=(nlstate+ndeath); k++) {       nstepm is the number of stepm from age to agelin. 
            if (k != k2){       Look at hpijx to understand the reason of that which relies in memory size
              if(ng==2)       and note for a fixed period like k years */
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
              else       survival function given by stepm (the optimization length). Unfortunately it
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);       means that if the survival funtion is printed every two years of age and if
              ij=1;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
              for(j=3; j <=ncovmodel; j++) {       results. So we changed our mind and took the option of the best precision.
                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]]]);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
                  ij++;    agelim = AGESUP;
                }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                else      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
              }      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
              fprintf(ficgp,")/(1");      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
                    gp=matrix(0,nhstepm,1,nlstate);
              for(k1=1; k1 <=nlstate; k1++){        gm=matrix(0,nhstepm,1,nlstate);
                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++){      for(theta=1; theta <=npar; theta++){
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
                    ij++;        }
                  }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
                  else        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  
                }        if (popbased==1) {
                fprintf(ficgp,")");          if(mobilav ==0){
              }            for(i=1; i<=nlstate;i++)
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);              prlim[i][i]=probs[(int)age][i][ij];
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");          }else{ /* mobilav */ 
              i=i+ncovmodel;            for(i=1; i<=nlstate;i++)
            }              prlim[i][i]=mobaverage[(int)age][i][ij];
          }          }
        }        }
      }    
    }        for(j=1; j<= nlstate; j++){
    fclose(ficgp);          for(h=0; h<=nhstepm; h++){
 }  /* end gnuplot */            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
 /*************** Moving average **************/        }
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){        /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
   int i, cpt, cptcod;           as a weighted average of prlim.
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)        */
       for (i=1; i<=nlstate;i++)        for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          for(i=1,gpp[j]=0.; i<= nlstate; i++)
           mobaverage[(int)agedeb][i][cptcod]=0.;            gpp[j] += prlim[i][i]*p3mat[i][j][1];
            }    
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){        /* end probability of death */
       for (i=1; i<=nlstate;i++){  
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           for (cpt=0;cpt<=4;cpt++){          xp[i] = x[i] - (i==theta ?delti[theta]:0);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;   
         }        if (popbased==1) {
       }          if(mobilav ==0){
     }            for(i=1; i<=nlstate;i++)
                  prlim[i][i]=probs[(int)age][i][ij];
 }          }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
 /************** Forecasting ******************/          }
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){        }
    
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        for(j=1; j<= nlstate; j++){
   int *popage;          for(h=0; h<=nhstepm; h++){
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   double *popeffectif,*popcount;              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   double ***p3mat;          }
   char fileresf[FILENAMELENGTH];        }
         /* This for computing probability of death (h=1 means
  agelim=AGESUP;           computed over hstepm matrices product = hstepm*stepm months) 
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;           as a weighted average of prlim.
         */
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
            for(i=1,gmp[j]=0.; i<= nlstate; i++)
             gmp[j] += prlim[i][i]*p3mat[i][j][1];
   strcpy(fileresf,"f");        }    
   strcat(fileresf,fileres);        /* end probability of death */
   if((ficresf=fopen(fileresf,"w"))==NULL) {  
     printf("Problem with forecast resultfile: %s\n", fileresf);        for(j=1; j<= nlstate; j++) /* vareij */
   }          for(h=0; h<=nhstepm; h++){
   printf("Computing forecasting: result on file '%s' \n", fileresf);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   if (mobilav==1) {          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        }
     movingaverage(agedeb, fage, ageminpar, mobaverage);  
   }      } /* End theta */
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   if (stepm<=12) stepsize=1;  
        for(h=0; h<=nhstepm; h++) /* veij */
   agelim=AGESUP;        for(j=1; j<=nlstate;j++)
            for(theta=1; theta <=npar; theta++)
   hstepm=1;            trgradg[h][j][theta]=gradg[h][theta][j];
   hstepm=hstepm/stepm;  
   yp1=modf(dateintmean,&yp);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   anprojmean=yp;        for(theta=1; theta <=npar; theta++)
   yp2=modf((yp1*12),&yp);          trgradgp[j][theta]=gradgp[theta][j];
   mprojmean=yp;    
   yp1=modf((yp2*30.5),&yp);  
   jprojmean=yp;      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   if(jprojmean==0) jprojmean=1;      for(i=1;i<=nlstate;i++)
   if(mprojmean==0) jprojmean=1;        for(j=1;j<=nlstate;j++)
            vareij[i][j][(int)age] =0.;
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);  
        for(h=0;h<=nhstepm;h++){
   for(cptcov=1;cptcov<=i2;cptcov++){        for(k=0;k<=nhstepm;k++){
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
       k=k+1;          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
       fprintf(ficresf,"\n#******");          for(i=1;i<=nlstate;i++)
       for(j=1;j<=cptcoveff;j++) {            for(j=1;j<=nlstate;j++)
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       }        }
       fprintf(ficresf,"******\n");      }
       fprintf(ficresf,"# StartingAge FinalAge");    
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);      /* pptj */
            matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
            matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {      for(j=nlstate+1;j<=nlstate+ndeath;j++)
         fprintf(ficresf,"\n");        for(i=nlstate+1;i<=nlstate+ndeath;i++)
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);            varppt[j][i]=doldmp[j][i];
       /* end ppptj */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      /*  x centered again */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
           nhstepm = nhstepm/hstepm;      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
             
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      if (popbased==1) {
           oldm=oldms;savm=savms;        if(mobilav ==0){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            for(i=1; i<=nlstate;i++)
                    prlim[i][i]=probs[(int)age][i][ij];
           for (h=0; h<=nhstepm; h++){        }else{ /* mobilav */ 
             if (h==(int) (calagedate+YEARM*cpt)) {          for(i=1; i<=nlstate;i++)
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);            prlim[i][i]=mobaverage[(int)age][i][ij];
             }        }
             for(j=1; j<=nlstate+ndeath;j++) {      }
               kk1=0.;kk2=0;               
               for(i=1; i<=nlstate;i++) {                    /* This for computing probability of death (h=1 means
                 if (mobilav==1)         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];         as a weighted average of prlim.
                 else {      */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      for(j=nlstate+1;j<=nlstate+ndeath;j++){
                 }        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
                          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
               }      }    
               if (h==(int)(calagedate+12*cpt)){      /* end probability of death */
                 fprintf(ficresf," %.3f", kk1);  
                              fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
               }      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
             }        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
           }        for(i=1; i<=nlstate;i++){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }        }
       }      } 
     }      fprintf(ficresprobmorprev,"\n");
   }  
              fprintf(ficresvij,"%.0f ",age );
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
   fclose(ficresf);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
 }        }
 /************** Forecasting ******************/      fprintf(ficresvij,"\n");
 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){      free_matrix(gp,0,nhstepm,1,nlstate);
        free_matrix(gm,0,nhstepm,1,nlstate);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   int *popage;      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   double *popeffectif,*popcount;    } /* End age */
   double ***p3mat,***tabpop,***tabpopprev;    free_vector(gpp,nlstate+1,nlstate+ndeath);
   char filerespop[FILENAMELENGTH];    free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
   agelim=AGESUP;    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
    /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
    /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
      fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
   strcpy(filerespop,"pop");    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
   strcat(filerespop,fileres);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     printf("Problem with forecast resultfile: %s\n", filerespop);    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   }    /*  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);
   printf("Computing forecasting: result on file '%s' \n", filerespop);  */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    fprintf(ficgp,"\nset out \"%s%s.png\";replot;",digitp,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
   if (mobilav==1) {    free_vector(xp,1,npar);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    free_matrix(doldm,1,nlstate,1,nlstate);
     movingaverage(agedeb, fage, ageminpar, mobaverage);    free_matrix(dnewm,1,nlstate,1,npar);
   }    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   if (stepm<=12) stepsize=1;    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      fclose(ficresprobmorprev);
   agelim=AGESUP;    fflush(ficgp);
      fflush(fichtm); 
   hstepm=1;  }  /* end varevsij */
   hstepm=hstepm/stepm;  
    /************ Variance of prevlim ******************/
   if (popforecast==1) {  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
     if((ficpop=fopen(popfile,"r"))==NULL) {  {
       printf("Problem with population file : %s\n",popfile);exit(0);    /* Variance of prevalence limit */
     }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     popage=ivector(0,AGESUP);    double **newm;
     popeffectif=vector(0,AGESUP);    double **dnewm,**doldm;
     popcount=vector(0,AGESUP);    int i, j, nhstepm, hstepm;
        int k, cptcode;
     i=1;      double *xp;
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    double *gp, *gm;
        double **gradg, **trgradg;
     imx=i;    double age,agelim;
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    int theta;
   }     
     fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
   for(cptcov=1;cptcov<=i2;cptcov++){    fprintf(ficresvpl,"# Age");
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    for(i=1; i<=nlstate;i++)
       k=k+1;        fprintf(ficresvpl," %1d-%1d",i,i);
       fprintf(ficrespop,"\n#******");    fprintf(ficresvpl,"\n");
       for(j=1;j<=cptcoveff;j++) {  
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    xp=vector(1,npar);
       }    dnewm=matrix(1,nlstate,1,npar);
       fprintf(ficrespop,"******\n");    doldm=matrix(1,nlstate,1,nlstate);
       fprintf(ficrespop,"# Age");    
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    hstepm=1*YEARM; /* Every year of age */
       if (popforecast==1)  fprintf(ficrespop," [Population]");    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
          agelim = AGESUP;
       for (cpt=0; cpt<=0;cpt++) {    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);        nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
              if (stepm >= YEARM) hstepm=1;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      gradg=matrix(1,npar,1,nlstate);
           nhstepm = nhstepm/hstepm;      gp=vector(1,nlstate);
                gm=vector(1,nlstate);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;      for(theta=1; theta <=npar; theta++){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          for(i=1; i<=npar; i++){ /* Computes gradient */
                  xp[i] = x[i] + (i==theta ?delti[theta]:0);
           for (h=0; h<=nhstepm; h++){        }
             if (h==(int) (calagedate+YEARM*cpt)) {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        for(i=1;i<=nlstate;i++)
             }          gp[i] = prlim[i][i];
             for(j=1; j<=nlstate+ndeath;j++) {      
               kk1=0.;kk2=0;        for(i=1; i<=npar; i++) /* Computes gradient */
               for(i=1; i<=nlstate;i++) {                        xp[i] = x[i] - (i==theta ?delti[theta]:0);
                 if (mobilav==1)        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        for(i=1;i<=nlstate;i++)
                 else {          gm[i] = prlim[i][i];
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];  
                 }        for(i=1;i<=nlstate;i++)
               }          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
               if (h==(int)(calagedate+12*cpt)){      } /* End theta */
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;  
                   /*fprintf(ficrespop," %.3f", kk1);      trgradg =matrix(1,nlstate,1,npar);
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/  
               }      for(j=1; j<=nlstate;j++)
             }        for(theta=1; theta <=npar; theta++)
             for(i=1; i<=nlstate;i++){          trgradg[j][theta]=gradg[theta][j];
               kk1=0.;  
                 for(j=1; j<=nlstate;j++){      for(i=1;i<=nlstate;i++)
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];        varpl[i][(int)age] =0.;
                 }      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
             }      for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)  
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);      fprintf(ficresvpl,"%.0f ",age );
           }      for(i=1; i<=nlstate;i++)
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
         }      fprintf(ficresvpl,"\n");
       }      free_vector(gp,1,nlstate);
        free_vector(gm,1,nlstate);
   /******/      free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    } /* End age */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    free_vector(xp,1,npar);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    free_matrix(doldm,1,nlstate,1,npar);
           nhstepm = nhstepm/hstepm;    free_matrix(dnewm,1,nlstate,1,nlstate);
            
           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);    /************ Variance of one-step probabilities  ******************/
           for (h=0; h<=nhstepm; h++){  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
             if (h==(int) (calagedate+YEARM*cpt)) {  {
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    int i, j=0,  i1, k1, l1, t, tj;
             }    int k2, l2, j1,  z1;
             for(j=1; j<=nlstate+ndeath;j++) {    int k=0,l, cptcode;
               kk1=0.;kk2=0;    int first=1, first1;
               for(i=1; i<=nlstate;i++) {                  double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        double **dnewm,**doldm;
               }    double *xp;
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    double *gp, *gm;
             }    double **gradg, **trgradg;
           }    double **mu;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double age,agelim, cov[NCOVMAX];
         }    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
       }    int theta;
    }    char fileresprob[FILENAMELENGTH];
   }    char fileresprobcov[FILENAMELENGTH];
      char fileresprobcor[FILENAMELENGTH];
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
     double ***varpij;
   if (popforecast==1) {  
     free_ivector(popage,0,AGESUP);    strcpy(fileresprob,"prob"); 
     free_vector(popeffectif,0,AGESUP);    strcat(fileresprob,fileres);
     free_vector(popcount,0,AGESUP);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   }      printf("Problem with resultfile: %s\n", fileresprob);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    }
   fclose(ficrespop);    strcpy(fileresprobcov,"probcov"); 
 }    strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
 /***********************************************/      printf("Problem with resultfile: %s\n", fileresprobcov);
 /**************** Main Program *****************/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
 /***********************************************/    }
     strcpy(fileresprobcor,"probcor"); 
 int main(int argc, char *argv[])    strcat(fileresprobcor,fileres);
 {    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   double agedeb, agefin,hf;    }
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    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);
   double fret;    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   double **xi,tmp,delta;    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   double dum; /* Dummy variable */    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   double ***p3mat;    
   int *indx;    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   char line[MAXLINE], linepar[MAXLINE];    fprintf(ficresprob,"# Age");
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   int firstobs=1, lastobs=10;    fprintf(ficresprobcov,"# Age");
   int sdeb, sfin; /* Status at beginning and end */    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   int c,  h , cpt,l;    fprintf(ficresprobcov,"# Age");
   int ju,jl, mi;  
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;  
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    for(i=1; i<=nlstate;i++)
   int mobilav=0,popforecast=0;      for(j=1; j<=(nlstate+ndeath);j++){
   int hstepm, nhstepm;        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;        fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
   double bage, fage, age, agelim, agebase;      }  
   double ftolpl=FTOL;   /* fprintf(ficresprob,"\n");
   double **prlim;    fprintf(ficresprobcov,"\n");
   double *severity;    fprintf(ficresprobcor,"\n");
   double ***param; /* Matrix of parameters */   */
   double  *p;   xp=vector(1,npar);
   double **matcov; /* Matrix of covariance */    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   double ***delti3; /* Scale */    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
   double *delti; /* Scale */    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
   double ***eij, ***vareij;    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
   double **varpl; /* Variances of prevalence limits by age */    first=1;
   double *epj, vepp;    fprintf(ficgp,"\n# Routine varprob");
   double kk1, kk2;    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    fprintf(fichtm,"\n");
    
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
   char *alph[]={"a","a","b","c","d","e"}, str[4];    fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
   
   char z[1]="c", occ;    cov[1]=1;
 #include <sys/time.h>    tj=cptcoveff;
 #include <time.h>    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    j1=0;
      for(t=1; t<=tj;t++){
   /* long total_usecs;      for(i1=1; i1<=ncodemax[t];i1++){ 
   struct timeval start_time, end_time;        j1++;
          if  (cptcovn>0) {
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */          fprintf(ficresprob, "\n#********** Variable "); 
   getcwd(pathcd, size);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
   printf("\n%s",version);          fprintf(ficresprobcov, "\n#********** Variable "); 
   if(argc <=1){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     printf("\nEnter the parameter file name: ");          fprintf(ficresprobcov, "**********\n#\n");
     scanf("%s",pathtot);          
   }          fprintf(ficgp, "\n#********** Variable "); 
   else{          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     strcpy(pathtot,argv[1]);          fprintf(ficgp, "**********\n#\n");
   }          
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/          
   /*cygwin_split_path(pathtot,path,optionfile);          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   /* cutv(path,optionfile,pathtot,'\\');*/          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);          fprintf(ficresprobcor, "\n#********** Variable ");    
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   chdir(path);          fprintf(ficresprobcor, "**********\n#");    
   replace(pathc,path);        }
         
 /*-------- arguments in the command line --------*/        for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
   strcpy(fileres,"r");          for (k=1; k<=cptcovn;k++) {
   strcat(fileres, optionfilefiname);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
   strcat(fileres,".txt");    /* Other files have txt extension */          }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   /*---------arguments file --------*/          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]]];
   if((ficpar=fopen(optionfile,"r"))==NULL)    {          
     printf("Problem with optionfile %s\n",optionfile);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
     goto end;          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   }          gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
   strcpy(filereso,"o");      
   strcat(filereso,fileres);          for(theta=1; theta <=npar; theta++){
   if((ficparo=fopen(filereso,"w"))==NULL) {            for(i=1; i<=npar; i++)
     printf("Problem with Output resultfile: %s\n", filereso);goto end;              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
   }            
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
   /* Reads comments: lines beginning with '#' */            
   while((c=getc(ficpar))=='#' && c!= EOF){            k=0;
     ungetc(c,ficpar);            for(i=1; i<= (nlstate); i++){
     fgets(line, MAXLINE, ficpar);              for(j=1; j<=(nlstate+ndeath);j++){
     puts(line);                k=k+1;
     fputs(line,ficparo);                gp[k]=pmmij[i][j];
   }              }
   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\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);            for(i=1; i<=npar; i++)
   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);              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);      
 while((c=getc(ficpar))=='#' && c!= EOF){            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     ungetc(c,ficpar);            k=0;
     fgets(line, MAXLINE, ficpar);            for(i=1; i<=(nlstate); i++){
     puts(line);              for(j=1; j<=(nlstate+ndeath);j++){
     fputs(line,ficparo);                k=k+1;
   }                gm[k]=pmmij[i][j];
   ungetc(c,ficpar);              }
              }
           
   covar=matrix(0,NCOVMAX,1,n);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
   cptcovn=0;              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;          }
   
   ncovmodel=2+cptcovn;          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */            for(theta=1; theta <=npar; theta++)
                trgradg[j][theta]=gradg[theta][j];
   /* Read guess parameters */          
   /* Reads comments: lines beginning with '#' */          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
   while((c=getc(ficpar))=='#' && c!= EOF){          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
     ungetc(c,ficpar);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
     fgets(line, MAXLINE, ficpar);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
     puts(line);          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     fputs(line,ficparo);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   }  
   ungetc(c,ficpar);          pmij(pmmij,cov,ncovmodel,x,nlstate);
            
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          k=0;
     for(i=1; i <=nlstate; i++)          for(i=1; i<=(nlstate); i++){
     for(j=1; j <=nlstate+ndeath-1; j++){            for(j=1; j<=(nlstate+ndeath);j++){
       fscanf(ficpar,"%1d%1d",&i1,&j1);              k=k+1;
       fprintf(ficparo,"%1d%1d",i1,j1);              mu[k][(int) age]=pmmij[i][j];
       printf("%1d%1d",i,j);            }
       for(k=1; k<=ncovmodel;k++){          }
         fscanf(ficpar," %lf",&param[i][j][k]);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
         printf(" %lf",param[i][j][k]);            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
         fprintf(ficparo," %lf",param[i][j][k]);              varpij[i][j][(int)age] = doldm[i][j];
       }  
       fscanf(ficpar,"\n");          /*printf("\n%d ",(int)age);
       printf("\n");            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
       fprintf(ficparo,"\n");            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     }            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
              }*/
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;  
           fprintf(ficresprob,"\n%d ",(int)age);
   p=param[1][1];          fprintf(ficresprobcov,"\n%d ",(int)age);
            fprintf(ficresprobcor,"\n%d ",(int)age);
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
     ungetc(c,ficpar);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
     fgets(line, MAXLINE, ficpar);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     puts(line);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
     fputs(line,ficparo);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
   }          }
   ungetc(c,ficpar);          i=0;
           for (k=1; k<=(nlstate);k++){
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);            for (l=1; l<=(nlstate+ndeath);l++){ 
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */              i=i++;
   for(i=1; i <=nlstate; i++){              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
     for(j=1; j <=nlstate+ndeath-1; j++){              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
       fscanf(ficpar,"%1d%1d",&i1,&j1);              for (j=1; j<=i;j++){
       printf("%1d%1d",i,j);                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
       fprintf(ficparo,"%1d%1d",i1,j1);                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
       for(k=1; k<=ncovmodel;k++){              }
         fscanf(ficpar,"%le",&delti3[i][j][k]);            }
         printf(" %le",delti3[i][j][k]);          }/* end of loop for state */
         fprintf(ficparo," %le",delti3[i][j][k]);        } /* end of loop for age */
       }  
       fscanf(ficpar,"\n");        /* Confidence intervalle of pij  */
       printf("\n");        /*
       fprintf(ficparo,"\n");          fprintf(ficgp,"\nset noparametric;unset label");
     }          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   }          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   delti=delti3[1][1];          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
            fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
   /* Reads comments: lines beginning with '#' */          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
   while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
     ungetc(c,ficpar);        */
     fgets(line, MAXLINE, ficpar);  
     puts(line);        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
     fputs(line,ficparo);        first1=1;
   }        for (k2=1; k2<=(nlstate);k2++){
   ungetc(c,ficpar);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
              if(l2==k2) continue;
   matcov=matrix(1,npar,1,npar);            j=(k2-1)*(nlstate+ndeath)+l2;
   for(i=1; i <=npar; i++){            for (k1=1; k1<=(nlstate);k1++){
     fscanf(ficpar,"%s",&str);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
     printf("%s",str);                if(l1==k1) continue;
     fprintf(ficparo,"%s",str);                i=(k1-1)*(nlstate+ndeath)+l1;
     for(j=1; j <=i; j++){                if(i<=j) continue;
       fscanf(ficpar," %le",&matcov[i][j]);                for (age=bage; age<=fage; age ++){ 
       printf(" %.5le",matcov[i][j]);                  if ((int)age %5==0){
       fprintf(ficparo," %.5le",matcov[i][j]);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
     }                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
     fscanf(ficpar,"\n");                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
     printf("\n");                    mu1=mu[i][(int) age]/stepm*YEARM ;
     fprintf(ficparo,"\n");                    mu2=mu[j][(int) age]/stepm*YEARM;
   }                    c12=cv12/sqrt(v1*v2);
   for(i=1; i <=npar; i++)                    /* Computing eigen value of matrix of covariance */
     for(j=i+1;j<=npar;j++)                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       matcov[i][j]=matcov[j][i];                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                        /* Eigen vectors */
   printf("\n");                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
     /*-------- Rewriting paramater file ----------*/                    v12=-v21;
      strcpy(rfileres,"r");    /* "Rparameterfile */                    v22=v11;
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/                    tnalp=v21/v11;
      strcat(rfileres,".");    /* */                    if(first1==1){
      strcat(rfileres,optionfilext);    /* Other files have txt extension */                      first1=0;
     if((ficres =fopen(rfileres,"w"))==NULL) {                      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);
       printf("Problem writing new parameter file: %s\n", fileres);goto end;                    }
     }                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
     fprintf(ficres,"#%s\n",version);                    /*printf(fignu*/
                        /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
     /*-------- data file ----------*/                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
     if((fic=fopen(datafile,"r"))==NULL)    {                    if(first==1){
       printf("Problem with datafile: %s\n", datafile);goto end;                      first=0;
     }                      fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
     n= lastobs;                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     severity = vector(1,maxwav);                      fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
     outcome=imatrix(1,maxwav+1,1,n);   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
     num=ivector(1,n);  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
     moisnais=vector(1,n);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
     annais=vector(1,n);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     moisdc=vector(1,n);                      fprintf(fichtm,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     andc=vector(1,n);                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
     agedc=vector(1,n);                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     cod=ivector(1,n);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     weight=vector(1,n);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */                      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",\
     mint=matrix(1,maxwav,1,n);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     anint=matrix(1,maxwav,1,n);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     s=imatrix(1,maxwav+1,1,n);                    }else{
     adl=imatrix(1,maxwav+1,1,n);                          first=0;
     tab=ivector(1,NCOVMAX);                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
     ncodemax=ivector(1,8);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     i=1;                      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",\
     while (fgets(line, MAXLINE, fic) != NULL)    {                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
       if ((i >= firstobs) && (i <=lastobs)) {                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                            }/* if first */
         for (j=maxwav;j>=1;j--){                  } /* age mod 5 */
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);                } /* end loop age */
           strcpy(line,stra);                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                first=1;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);              } /*l12 */
         }            } /* k12 */
                  } /*l1 */
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        }/* k1 */
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);      } /* loop covariates */
     }
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_vector(xp,1,npar);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    fclose(ficresprob);
         for (j=ncovcol;j>=1;j--){    fclose(ficresprobcov);
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    fclose(ficresprobcor);
         }    /*  fclose(ficgp);*/
         num[i]=atol(stra);  }
          
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){  
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/  /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
         i=i+1;                    int lastpass, int stepm, int weightopt, char model[],\
       }                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
     }                    int popforecast, int estepm ,\
     /* printf("ii=%d", ij);                    double jprev1, double mprev1,double anprev1, \
        scanf("%d",i);*/                    double jprev2, double mprev2,double anprev2){
   imx=i-1; /* Number of individuals */    int jj1, k1, i1, cpt;
     /*char optionfilehtm[FILENAMELENGTH];*/
   /* for (i=1; i<=imx; i++){  /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    { */
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;  /*     printf("Problem with %s \n",optionfilehtm), exit(0); */
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;  /*     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;  /*   } */
     }*/  
    /*  for (i=1; i<=imx; i++){     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
      if (s[4][i]==9)  s[4][i]=-1;   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n \
      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]));}*/   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n \
     - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n \
     - Life expectancies by age and initial health status (estepm=%2d months): \
   /* Calculation of the number of parameter from char model*/     <a href=\"%s\">%s</a> <br>\n</li>", \
   Tvar=ivector(1,15);             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
   Tprod=ivector(1,15);             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
   Tvaraff=ivector(1,15);             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
   Tvard=imatrix(1,15,1,2);             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   Tage=ivector(1,15);        
      fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   if (strlen(model) >1){  
     j=0, j1=0, k1=1, k2=1;   m=cptcoveff;
     j=nbocc(model,'+');   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     j1=nbocc(model,'*');  
     cptcovn=j+1;   jj1=0;
     cptcovprod=j1;   for(k1=1; k1<=m;k1++){
         for(i1=1; i1<=ncodemax[k1];i1++){
     strcpy(modelsav,model);       jj1++;
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){       if (cptcovn > 0) {
       printf("Error. Non available option model=%s ",model);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
       goto end;         for (cpt=1; cpt<=cptcoveff;cpt++) 
     }           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
             fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     for(i=(j+1); i>=1;i--){       }
       cutv(stra,strb,modelsav,'+');       /* Pij */
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
       /*scanf("%d",i);*/       /* Quasi-incidences */
       if (strchr(strb,'*')) {       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
         cutv(strd,strc,strb,'*');   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
         if (strcmp(strc,"age")==0) {  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
           cptcovprod--;         /* Stable prevalence in each health state */
           cutv(strb,stre,strd,'V');         for(cpt=1; cpt<nlstate;cpt++){
           Tvar[i]=atoi(stre);           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
           cptcovage++;  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
             Tage[cptcovage]=i;         }
             /*printf("stre=%s ", stre);*/       for(cpt=1; cpt<=nlstate;cpt++) {
         }          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
         else if (strcmp(strd,"age")==0) {  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exo"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
           cptcovprod--;       }
           cutv(strb,stre,strc,'V');       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
           Tvar[i]=atoi(stre);  health expectancies in states (1) and (2): %s%d.png<br>\
           cptcovage++;  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
           Tage[cptcovage]=i;     } /* end i1 */
         }   }/* End k1 */
         else {   fprintf(fichtm,"</ul>");
           cutv(strb,stre,strc,'V');  
           Tvar[i]=ncovcol+k1;  
           cutv(strb,strc,strd,'V');   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
           Tprod[k1]=i;   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
           Tvard[k1][1]=atoi(strc);   - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
           Tvard[k1][2]=atoi(stre);   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
           Tvar[cptcovn+k2]=Tvard[k1][1];   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
           Tvar[cptcovn+k2+1]=Tvard[k1][2];   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n\
           for (k=1; k<=lastobs;k++)   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n\
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
           k1++;           rfileres,rfileres,\
           k2=k2+2;           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
         }           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
       }           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
       else {           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/           subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
        /*  scanf("%d",i);*/           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
       cutv(strd,strc,strb,'V');  
       Tvar[i]=atoi(strc);  /*  if(popforecast==1) fprintf(fichtm,"\n */
       }  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
       strcpy(modelsav,stra);    /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);  /*      <br>",fileres,fileres,fileres,fileres); */
         scanf("%d",i);*/  /*  else  */
     }  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
 }  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
    
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);   m=cptcoveff;
   printf("cptcovprod=%d ", cptcovprod);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   scanf("%d ",i);*/  
     fclose(fic);   jj1=0;
    for(k1=1; k1<=m;k1++){
     /*  if(mle==1){*/     for(i1=1; i1<=ncodemax[k1];i1++){
     if (weightopt != 1) { /* Maximisation without weights*/       jj1++;
       for(i=1;i<=n;i++) weight[i]=1.0;       if (cptcovn > 0) {
     }         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     /*-calculation of age at interview from date of interview and age at death -*/         for (cpt=1; cpt<=cptcoveff;cpt++) 
     agev=matrix(1,maxwav,1,imx);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     for (i=1; i<=imx; i++) {       }
       for(m=2; (m<= maxwav); m++) {       for(cpt=1; cpt<=nlstate;cpt++) {
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){         fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
          anint[m][i]=9999;  interval) in state (%d): %s%d%d.png <br>\
          s[m][i]=-1;  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"pe"),cpt,jj1,subdirf2(optionfilefiname,"pe"),cpt,jj1);  
        }       }
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;     } /* end i1 */
       }   }/* End k1 */
     }   fprintf(fichtm,"</ul>");
    fflush(fichtm);
     for (i=1; i<=imx; i++)  {  }
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  
       for(m=1; (m<= maxwav); m++){  /******************* Gnuplot file **************/
         if(s[m][i] >0){  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char path[], double p[]){
           if (s[m][i] >= nlstate+1) {  
             if(agedc[i]>0)    char dirfileres[132],optfileres[132];
               if(moisdc[i]!=99 && andc[i]!=9999)    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
                 agev[m][i]=agedc[i];    int ng;
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
            else {  /*     printf("Problem with file %s",optionfilegnuplot); */
               if (andc[i]!=9999){  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  /*   } */
               agev[m][i]=-1;  
               }    /*#ifdef windows */
             }    fprintf(ficgp,"cd \"%s\" \n",path);
           }      /*#endif */
           else if(s[m][i] !=9){ /* Should no more exist */    m=pow(2,cptcoveff);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);  
             if(mint[m][i]==99 || anint[m][i]==9999)    strcpy(dirfileres,optionfilefiname);
               agev[m][i]=1;    strcpy(optfileres,"vpl");
             else if(agev[m][i] <agemin){   /* 1eme*/
               agemin=agev[m][i];    for (cpt=1; cpt<= nlstate ; cpt ++) {
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/     for (k1=1; k1<= m ; k1 ++) {
             }       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
             else if(agev[m][i] >agemax){       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
               agemax=agev[m][i];       fprintf(ficgp,"set xlabel \"Age\" \n\
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/  set ylabel \"Probability\" \n\
             }  set ter png small\n\
             /*agev[m][i]=anint[m][i]-annais[i];*/  set size 0.65,0.65\n\
             /*   agev[m][i] = age[i]+2*m;*/  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
           }  
           else { /* =9 */       for (i=1; i<= nlstate ; i ++) {
             agev[m][i]=1;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
             s[m][i]=-1;         else fprintf(ficgp," \%%*lf (\%%*lf)");
           }       }
         }       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
         else /*= 0 Unknown */       for (i=1; i<= nlstate ; i ++) {
           agev[m][i]=1;         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
       }         else fprintf(ficgp," \%%*lf (\%%*lf)");
           } 
     }       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
     for (i=1; i<=imx; i++)  {       for (i=1; i<= nlstate ; i ++) {
       for(m=1; (m<= maxwav); m++){         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         if (s[m][i] > (nlstate+ndeath)) {         else fprintf(ficgp," \%%*lf (\%%*lf)");
           printf("Error: Wrong value in nlstate or ndeath\n");         }  
           goto end;       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
         }     }
       }    }
     }    /*2 eme*/
     
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
     free_vector(severity,1,maxwav);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
     free_imatrix(outcome,1,maxwav+1,1,n);      
     free_vector(moisnais,1,n);      for (i=1; i<= nlstate+1 ; i ++) {
     free_vector(annais,1,n);        k=2*i;
     /* free_matrix(mint,1,maxwav,1,n);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
        free_matrix(anint,1,maxwav,1,n);*/        for (j=1; j<= nlstate+1 ; j ++) {
     free_vector(moisdc,1,n);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     free_vector(andc,1,n);          else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
            if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
     wav=ivector(1,imx);        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);        for (j=1; j<= nlstate+1 ; j ++) {
              if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     /* Concatenates waves */          else fprintf(ficgp," \%%*lf (\%%*lf)");
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);        }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       Tcode=ivector(1,100);        for (j=1; j<= nlstate+1 ; j ++) {
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       ncodemax[1]=1;          else fprintf(ficgp," \%%*lf (\%%*lf)");
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);        }   
              if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
    codtab=imatrix(1,100,1,10);        else fprintf(ficgp,"\" t\"\" w l 0,");
    h=0;      }
    m=pow(2,cptcoveff);    }
      
    for(k=1;k<=cptcoveff; k++){    /*3eme*/
      for(i=1; i <=(m/pow(2,k));i++){    
        for(j=1; j <= ncodemax[k]; j++){    for (k1=1; k1<= m ; k1 ++) { 
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){      for (cpt=1; cpt<= nlstate ; cpt ++) {
            h++;        k=2+nlstate*(2*cpt-2);
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/        fprintf(ficgp,"set ter png small\n\
          }  set size 0.65,0.65\n\
        }  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
      }        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
    }          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
       codtab[1][2]=1;codtab[2][2]=2; */          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 <=m ;i++){          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
       for(k=1; k <=cptcovn; k++){          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);          
       }        */
       printf("\n");        for (i=1; i< nlstate ; i ++) {
       }          fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
       scanf("%d",i);*/          
            } 
    /* Calculates basic frequencies. Computes observed prevalence at single age      }
        and prints on file fileres'p'. */    }
     
        /* CV preval stable (period) */
        for (k1=1; k1<= m ; k1 ++) { 
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for (cpt=1; cpt<=nlstate ; cpt ++) {
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        k=3;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  set ter png small\nset size 0.65,0.65\n\
        plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
     /* For Powell, parameters are in a vector p[] starting at p[1]        
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */        for (i=1; i< nlstate ; i ++)
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */          fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
     if(mle==1){        
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        l=3+(nlstate+ndeath)*cpt;
     }        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
            for (i=1; i< nlstate ; i ++) {
     /*--------- results files --------------*/          l=3+(nlstate+ndeath)*cpt;
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);          fprintf(ficgp,"+$%d",l+i+1);
          }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
    jk=1;      } 
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    }  
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    
    for(i=1,jk=1; i <=nlstate; i++){    /* proba elementaires */
      for(k=1; k <=(nlstate+ndeath); k++){    for(i=1,jk=1; i <=nlstate; i++){
        if (k != i)      for(k=1; k <=(nlstate+ndeath); k++){
          {        if (k != i) {
            printf("%d%d ",i,k);          for(j=1; j <=ncovmodel; j++){
            fprintf(ficres,"%1d%1d ",i,k);            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
            for(j=1; j <=ncovmodel; j++){            jk++; 
              printf("%f ",p[jk]);            fprintf(ficgp,"\n");
              fprintf(ficres,"%f ",p[jk]);          }
              jk++;        }
            }      }
            printf("\n");     }
            fprintf(ficres,"\n");  
          }     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
      }       for(jk=1; jk <=m; jk++) {
    }         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
  if(mle==1){         if (ng==2)
     /* Computing hessian and covariance matrix */           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
     ftolhess=ftol; /* Usually correct */         else
     hesscov(matcov, p, npar, delti, ftolhess, func);           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);
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");         i=1;
     printf("# Scales (for hessian or gradient estimation)\n");         for(k2=1; k2<=nlstate; k2++) {
      for(i=1,jk=1; i <=nlstate; i++){           k3=i;
       for(j=1; j <=nlstate+ndeath; j++){           for(k=1; k<=(nlstate+ndeath); k++) {
         if (j!=i) {             if (k != k2){
           fprintf(ficres,"%1d%1d",i,j);               if(ng==2)
           printf("%1d%1d",i,j);                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
           for(k=1; k<=ncovmodel;k++){               else
             printf(" %.5e",delti[jk]);                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
             fprintf(ficres," %.5e",delti[jk]);               ij=1;
             jk++;               for(j=3; j <=ncovmodel; j++) {
           }                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
           printf("\n");                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
           fprintf(ficres,"\n");                   ij++;
         }                 }
       }                 else
      }                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                   }
     k=1;               fprintf(ficgp,")/(1");
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");               
     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");               for(k1=1; k1 <=nlstate; k1++){   
     for(i=1;i<=npar;i++){                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
       /*  if (k>nlstate) k=1;                 ij=1;
       i1=(i-1)/(ncovmodel*nlstate)+1;                 for(j=3; j <=ncovmodel; j++){
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
       printf("%s%d%d",alph[k],i1,tab[i]);*/                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
       fprintf(ficres,"%3d",i);                     ij++;
       printf("%3d",i);                   }
       for(j=1; j<=i;j++){                   else
         fprintf(ficres," %.5e",matcov[i][j]);                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
         printf(" %.5e",matcov[i][j]);                 }
       }                 fprintf(ficgp,")");
       fprintf(ficres,"\n");               }
       printf("\n");               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
       k++;               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
     }               i=i+ncovmodel;
                 }
     while((c=getc(ficpar))=='#' && c!= EOF){           } /* end k */
       ungetc(c,ficpar);         } /* end k2 */
       fgets(line, MAXLINE, ficpar);       } /* end jk */
       puts(line);     } /* end ng */
       fputs(line,ficparo);     fflush(ficgp); 
     }  }  /* end gnuplot */
     ungetc(c,ficpar);  
     estepm=0;  
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);  /*************** Moving average **************/
     if (estepm==0 || estepm < stepm) estepm=stepm;  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
     if (fage <= 2) {  
       bage = ageminpar;    int i, cpt, cptcod;
       fage = agemaxpar;    int modcovmax =1;
     }    int mobilavrange, mob;
        double age;
     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);    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                             a covariate has 2 modalities */
      if (cptcovn<1) modcovmax=1; /* At least 1 pass */
     while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
     fgets(line, MAXLINE, ficpar);      if(mobilav==1) mobilavrange=5; /* default */
     puts(line);      else mobilavrange=mobilav;
     fputs(line,ficparo);      for (age=bage; age<=fage; age++)
   }        for (i=1; i<=nlstate;i++)
   ungetc(c,ficpar);          for (cptcod=1;cptcod<=modcovmax;cptcod++)
              mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);      /* We keep the original values on the extreme ages bage, fage and for 
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);         fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);         we use a 5 terms etc. until the borders are no more concerned. 
            */ 
   while((c=getc(ficpar))=='#' && c!= EOF){      for (mob=3;mob <=mobilavrange;mob=mob+2){
     ungetc(c,ficpar);        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
     fgets(line, MAXLINE, ficpar);          for (i=1; i<=nlstate;i++){
     puts(line);            for (cptcod=1;cptcod<=modcovmax;cptcod++){
     fputs(line,ficparo);              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
   }                for (cpt=1;cpt<=(mob-1)/2;cpt++){
   ungetc(c,ficpar);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                    mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
    dateprev1=anprev1+mprev1/12.+jprev1/365.;              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
    dateprev2=anprev2+mprev2/12.+jprev2/365.;            }
           }
   fscanf(ficpar,"pop_based=%d\n",&popbased);        }/* end age */
   fprintf(ficparo,"pop_based=%d\n",popbased);        }/* end mob */
   fprintf(ficres,"pop_based=%d\n",popbased);      }else return -1;
      return 0;
   while((c=getc(ficpar))=='#' && c!= EOF){  }/* End movingaverage */
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  
     puts(line);  /************** Forecasting ******************/
     fputs(line,ficparo);  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 
   ungetc(c,ficpar);       agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);       anproj2 year of en of projection (same day and month as proj1).
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);    */
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
 while((c=getc(ficpar))=='#' && c!= EOF){    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     ungetc(c,ficpar);    double *popeffectif,*popcount;
     fgets(line, MAXLINE, ficpar);    double ***p3mat;
     puts(line);    double ***mobaverage;
     fputs(line,ficparo);    char fileresf[FILENAMELENGTH];
   }  
   ungetc(c,ficpar);    agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   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);    strcpy(fileresf,"f"); 
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
 /*------------ gnuplot -------------*/    }
   strcpy(optionfilegnuplot,optionfilefiname);    printf("Computing forecasting: result on file '%s' \n", fileresf);
   strcat(optionfilegnuplot,".gp");    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {  
     printf("Problem with file %s",optionfilegnuplot);    if (cptcoveff==0) ncodemax[cptcoveff]=1;
   }  
   fclose(ficgp);    if (mobilav!=0) {
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 /*--------- index.htm --------*/      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   strcpy(optionfilehtm,optionfile);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   strcat(optionfilehtm,".htm");      }
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    }
     printf("Problem with %s \n",optionfilehtm), exit(0);  
   }    stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n    if(estepm < stepm){
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n      printf ("Problem %d lower than %d\n",estepm, stepm);
 \n    }
 Total number of observations=%d <br>\n    else  hstepm=estepm;   
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n  
 <hr  size=\"2\" color=\"#EC5E5E\">    hstepm=hstepm/stepm; 
  <ul><li>Parameter files<br>\n    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n                                 fractional in yp1 */
  - Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);    anprojmean=yp;
   fclose(fichtm);    yp2=modf((yp1*12),&yp);
     mprojmean=yp;
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);    yp1=modf((yp2*30.5),&yp);
      jprojmean=yp;
 /*------------ free_vector  -------------*/    if(jprojmean==0) jprojmean=1;
  chdir(path);    if(mprojmean==0) jprojmean=1;
    
  free_ivector(wav,1,imx);    i1=cptcoveff;
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    if (cptcovn < 1){i1=1;}
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);      
  free_ivector(num,1,n);    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
  free_vector(agedc,1,n);    
  /*free_matrix(covar,1,NCOVMAX,1,n);*/    fprintf(ficresf,"#****** Routine prevforecast **\n");
  fclose(ficparo);  
  fclose(ficres);  /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   /*--------------- Prevalence limit --------------*/        k=k+1;
          fprintf(ficresf,"\n#******");
   strcpy(filerespl,"pl");        for(j=1;j<=cptcoveff;j++) {
   strcat(filerespl,fileres);          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]]);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {        }
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;        fprintf(ficresf,"******\n");
   }        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);        for(j=1; j<=nlstate+ndeath;j++){ 
   fprintf(ficrespl,"#Prevalence limit\n");          for(i=1; i<=nlstate;i++)              
   fprintf(ficrespl,"#Age ");            fprintf(ficresf," p%d%d",i,j);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);          fprintf(ficresf," p.%d",j);
   fprintf(ficrespl,"\n");        }
          for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
   prlim=matrix(1,nlstate,1,nlstate);          fprintf(ficresf,"\n");
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for (agec=fage; agec>=(ageminpar-1); agec--){ 
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */            nhstepm = nhstepm/hstepm; 
   k=0;            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   agebase=ageminpar;            oldm=oldms;savm=savms;
   agelim=agemaxpar;            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
   ftolpl=1.e-10;          
   i1=cptcoveff;            for (h=0; h<=nhstepm; h++){
   if (cptcovn < 1){i1=1;}              if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
   for(cptcov=1;cptcov<=i1;cptcov++){                for(j=1;j<=cptcoveff;j++) 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         k=k+1;                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/              } 
         fprintf(ficrespl,"\n#******");              for(j=1; j<=nlstate+ndeath;j++) {
         for(j=1;j<=cptcoveff;j++)                ppij=0.;
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                for(i=1; i<=nlstate;i++) {
         fprintf(ficrespl,"******\n");                  if (mobilav==1) 
                            ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
         for (age=agebase; age<=agelim; age++){                  else {
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
           fprintf(ficrespl,"%.0f",age );                  }
           for(i=1; i<=nlstate;i++)                  if (h*hstepm/YEARM*stepm== yearp) {
           fprintf(ficrespl," %.5f", prlim[i][i]);                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
           fprintf(ficrespl,"\n");                  }
         }                } /* end i */
       }                if (h*hstepm/YEARM*stepm==yearp) {
     }                  fprintf(ficresf," %.3f", ppij);
   fclose(ficrespl);                }
               }/* end j */
   /*------------- h Pij x at various ages ------------*/            } /* end h */
              free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);          } /* end agec */
   if((ficrespij=fopen(filerespij,"w"))==NULL) {        } /* end yearp */
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;      } /* end cptcod */
   }    } /* end  cptcov */
   printf("Computing pij: result on file '%s' \n", filerespij);         
      if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   /*if (stepm<=24) stepsize=2;*/    fclose(ficresf);
   }
   agelim=AGESUP;  
   hstepm=stepsize*YEARM; /* Every year of age */  /************** Forecasting *****not tested NB*************/
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */  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){
      
   k=0;    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
   for(cptcov=1;cptcov<=i1;cptcov++){    int *popage;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    double calagedatem, agelim, kk1, kk2;
       k=k+1;    double *popeffectif,*popcount;
         fprintf(ficrespij,"\n#****** ");    double ***p3mat,***tabpop,***tabpopprev;
         for(j=1;j<=cptcoveff;j++)    double ***mobaverage;
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    char filerespop[FILENAMELENGTH];
         fprintf(ficrespij,"******\n");  
            tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    agelim=AGESUP;
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    
           oldm=oldms;savm=savms;    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      
           fprintf(ficrespij,"# Age");    
           for(i=1; i<=nlstate;i++)    strcpy(filerespop,"pop"); 
             for(j=1; j<=nlstate+ndeath;j++)    strcat(filerespop,fileres);
               fprintf(ficrespij," %1d-%1d",i,j);    if((ficrespop=fopen(filerespop,"w"))==NULL) {
           fprintf(ficrespij,"\n");      printf("Problem with forecast resultfile: %s\n", filerespop);
            for (h=0; h<=nhstepm; h++){      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    }
             for(i=1; i<=nlstate;i++)    printf("Computing forecasting: result on file '%s' \n", filerespop);
               for(j=1; j<=nlstate+ndeath;j++)    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);  
             fprintf(ficrespij,"\n");    if (cptcoveff==0) ncodemax[cptcoveff]=1;
              }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    if (mobilav!=0) {
           fprintf(ficrespij,"\n");      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);
       }
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);    }
   
   fclose(ficrespij);    stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
   /*---------- Forecasting ------------------*/    agelim=AGESUP;
   if((stepm == 1) && (strcmp(model,".")==0)){    
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    hstepm=1;
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    hstepm=hstepm/stepm; 
   }    
   else{    if (popforecast==1) {
     erreur=108;      if((ficpop=fopen(popfile,"r"))==NULL) {
     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);        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);
   /*---------- Health expectancies and variances ------------*/      popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
   strcpy(filerest,"t");      
   strcat(filerest,fileres);      i=1;   
   if((ficrest=fopen(filerest,"w"))==NULL) {      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;     
   }      imx=i;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
   strcpy(filerese,"e");    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
   strcat(filerese,fileres);     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   if((ficreseij=fopen(filerese,"w"))==NULL) {        k=k+1;
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        fprintf(ficrespop,"\n#******");
   }        for(j=1;j<=cptcoveff;j++) {
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
  strcpy(fileresv,"v");        fprintf(ficrespop,"******\n");
   strcat(fileresv,fileres);        fprintf(ficrespop,"# Age");
   if((ficresvij=fopen(fileresv,"w"))==NULL) {        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);        if (popforecast==1)  fprintf(ficrespop," [Population]");
   }        
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);        for (cpt=0; cpt<=0;cpt++) { 
   calagedate=-1;          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
   k=0;            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
   for(cptcov=1;cptcov<=i1;cptcov++){            nhstepm = nhstepm/hstepm; 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            
       k=k+1;            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficrest,"\n#****** ");            oldm=oldms;savm=savms;
       for(j=1;j<=cptcoveff;j++)            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          
       fprintf(ficrest,"******\n");            for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
       fprintf(ficreseij,"\n#****** ");                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
       for(j=1;j<=cptcoveff;j++)              } 
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              for(j=1; j<=nlstate+ndeath;j++) {
       fprintf(ficreseij,"******\n");                kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
       fprintf(ficresvij,"\n#****** ");                  if (mobilav==1) 
       for(j=1;j<=cptcoveff;j++)                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                  else {
       fprintf(ficresvij,"******\n");                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                }
       oldm=oldms;savm=savms;                if (h==(int)(calagedatem+12*cpt)){
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);                    tabpop[(int)(agedeb)][j][cptcod]=kk1;
                      /*fprintf(ficrespop," %.3f", kk1);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
       oldm=oldms;savm=savms;                }
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);              }
                  for(i=1; i<=nlstate;i++){
                 kk1=0.;
                    for(j=1; j<=nlstate;j++){
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);                  }
       fprintf(ficrest,"\n");                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
       epj=vector(1,nlstate+1);  
       for(age=bage; age <=fage ;age++){              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
         if (popbased==1) {            }
           for(i=1; i<=nlstate;i++)            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             prlim[i][i]=probs[(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++) {        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
             epj[j] += prlim[i][i]*eij[i][j][(int)age];          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
           }            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
           epj[nlstate+1] +=epj[j];            nhstepm = nhstepm/hstepm; 
         }            
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         for(i=1, vepp=0.;i <=nlstate;i++)            oldm=oldms;savm=savms;
           for(j=1;j <=nlstate;j++)            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             vepp += vareij[i][j][(int)age];            for (h=0; h<=nhstepm; h++){
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));              if (h==(int) (calagedatem+YEARM*cpt)) {
         for(j=1;j <=nlstate;j++){                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));              } 
         }              for(j=1; j<=nlstate+ndeath;j++) {
         fprintf(ficrest,"\n");                kk1=0.;kk2=0;
       }                for(i=1; i<=nlstate;i++) {              
     }                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
   }                }
 free_matrix(mint,1,maxwav,1,n);                if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);              }
     free_vector(weight,1,n);            }
   fclose(ficreseij);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fclose(ficresvij);          }
   fclose(ficrest);        }
   fclose(ficpar);     } 
   free_vector(epj,1,nlstate+1);    }
     
   /*------- Variance limit prevalence------*/      if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
   strcpy(fileresvpl,"vpl");    if (popforecast==1) {
   strcat(fileresvpl,fileres);      free_ivector(popage,0,AGESUP);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      free_vector(popeffectif,0,AGESUP);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);      free_vector(popcount,0,AGESUP);
     exit(0);    }
   }    free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   k=0;  } /* End of popforecast */
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  int fileappend(FILE *fichier, char *optionfich)
       k=k+1;  {
       fprintf(ficresvpl,"\n#****** ");    if((fichier=fopen(optionfich,"a"))==NULL) {
       for(j=1;j<=cptcoveff;j++)      printf("Problem with file: %s\n", optionfich);
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      fprintf(ficlog,"Problem with file: %s\n", optionfich);
       fprintf(ficresvpl,"******\n");      return (0);
          }
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    fflush(fichier);
       oldm=oldms;savm=savms;    return (1);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  }
     }  void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
  }  {
   
   fclose(ficresvpl);    char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
   /*---------- End : free ----------------*/    int numlinepar;
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  
      printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    for(i=1; i <=nlstate; i++){
        jj=0;
        for(j=1; j <=nlstate+ndeath; j++){
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);        if(j==i) continue;
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);        jj++;
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);        /*ca[0]= k+'a'-1;ca[1]='\0';*/
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);        printf("%1d%1d",i,j);
          fprintf(ficparo,"%1d%1d",i,j);
   free_matrix(matcov,1,npar,1,npar);        for(k=1; k<=ncovmodel;k++){
   free_vector(delti,1,npar);          /*        printf(" %lf",param[i][j][k]); */
   free_matrix(agev,1,maxwav,1,imx);          /*        fprintf(ficparo," %lf",param[i][j][k]); */
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);          printf(" 0.");
           fprintf(ficparo," 0.");
   fprintf(fichtm,"\n</body>");        }
   fclose(fichtm);        printf("\n");
   fclose(ficgp);        fprintf(ficparo,"\n");
        }
     }
   if(erreur >0)    printf("# Scales (for hessian or gradient estimation)\n");
     printf("End of Imach with error or warning %d\n",erreur);    fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
   else   printf("End of Imach\n");    npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    for(i=1; i <=nlstate; i++){
        jj=0;
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/      for(j=1; j <=nlstate+ndeath; j++){
   /*printf("Total time was %d uSec.\n", total_usecs);*/        if(j==i) continue;
   /*------ End -----------*/        jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
  end:        fflush(stdout);
 #ifdef windows        for(k=1; k<=ncovmodel;k++){
   /* chdir(pathcd);*/          /*      printf(" %le",delti3[i][j][k]); */
 #endif          /*      fprintf(ficparo," %le",delti3[i][j][k]); */
  /*system("wgnuplot graph.plt");*/          printf(" 0.");
  /*system("../gp37mgw/wgnuplot graph.plt");*/          fprintf(ficparo," 0.");
  /*system("cd ../gp37mgw");*/        }
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/        numlinepar++;
  strcpy(plotcmd,GNUPLOTPROGRAM);        printf("\n");
  strcat(plotcmd," ");        fprintf(ficparo,"\n");
  strcat(plotcmd,optionfilegnuplot);      }
  system(plotcmd);    }
     printf("# Covariance matrix\n");
 #ifdef windows  /* # 121 Var(a12)\n\ */
   while (z[0] != 'q') {  /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* chdir(path); */  /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");  /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
     scanf("%s",z);  /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
     if (z[0] == 'c') system("./imach");  /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
     else if (z[0] == 'e') system(optionfilehtm);  /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
     else if (z[0] == 'g') system(plotcmd);  /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     else if (z[0] == 'q') exit(0);    fflush(stdout);
   }    fprintf(ficparo,"# Covariance matrix\n");
 #endif    /* # 121 Var(a12)\n\ */
 }    /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     }
   
   } /* end of prwizard */
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int jj, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE]; 
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   
     char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char strstart[80], *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
     struct timeval start_time, end_time, curr_time;
     struct timezone tzp;
     extern int gettimeofday();
     struct tm tmg, tm, *gmtime(), *localtime();
     long time_value;
     extern long time();
    
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: ");
     fprintf(ficlog,"pathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Localtime (at start):%s",strstart);
     fprintf(ficlog,"Localtime (at start): %s",strstart);
     fflush(ficlog);
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
    
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     /* Read guess parameters */
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++){
       j=0;
       for(jj=1; jj <=nlstate+ndeath; jj++){
         if(jj==i) continue;
         j++;
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1 != i) && (j1 != j)){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);
         }
         fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)
           printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);
           if(mle==1){
             printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);
           }
           else
             fprintf(ficlog," %lf",param[i][j][k]);
           fprintf(ficparo," %lf",param[i][j][k]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     }  
     fflush(ficlog);
   
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1-i)*(j1-j)!=0){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);
         }
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         fprintf(ficlog,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);
           fprintf(ficlog," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
         fprintf(ficlog,"\n");
       }
     }
     fflush(ficlog);
   
     delti=delti3[1][1];
   
   
     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);
       if(mle==1)
         printf("%s",str);
       fprintf(ficlog,"%s",str);
       fprintf(ficparo,"%s",str);
       for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
           printf(" %.5le",matcov[i][j]);
         }
         fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       numlinepar++;
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
     for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];
      
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
   
     fflush(ficlog);
   
     /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         lstra=strlen(stra);
         if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
           stratrunc = &(stra[lstra-9]);
           num[i]=atol(stratrunc);
         }
         else
           num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt,\
             model,fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     /*fclose(fichtm);*/
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     strcpy(lfileres,fileres);
     strcat(lfileres,"/");
     strcat(lfileres,optionfilefiname);
     
     /*  replace(pathc,path);*/
   
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);
     printf("\n");
     globpr=1; /* to print the contributions */
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);
     printf("\n");
     if(mle>=1){ /* Could be 1 or 2 */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
       
     /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
     jk=1;
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) 
           {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
       }
     }
     if(mle!=0){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);
             jk++;
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle==1)
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
           i1=(i-1)/(ncovmodel*nlstate)+1; 
           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
           printf("%s%d%d",alph[k],i1,tab[i]);
       */
       fprintf(ficres,"%3d",i);
       if(mle==1)
         printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   
     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, path,p);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     /*  chdir(path); */
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_lvector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
   /*      }  */
   /*      else{ */
   /*        erreur=108; */
   /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*      } */
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     fflush(fichtm);
     fflush(ficgp);
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Localtime at start %s\nLocaltime at end   %s",strstart, strtend); 
     fprintf(ficlog,"Localtime at start %s\nLocal time at end   %s",strstart, strtend); 
     /*  printf("Total time used %d Sec\n", asc_time(end_time.tv_sec -start_time.tv_sec);*/
   
     printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
     fprintf(ficlog,"Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
     fclose(fichtm);
     fclose(ficgp);
     /*------ End -----------*/
   
     end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
     chdir(path);
    /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     system(plotcmd);
     printf(" Wait...");
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   
   

Removed from v.1.47  
changed lines
  Added in v.1.88


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