Diff for /imach/src/imach.c between versions 1.33 and 1.91

version 1.33, 2002/03/12 22:13:38 version 1.91, 2003/06/25 15:30:29
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.91  2003/06/25 15:30:29  brouard
      * imach.c (Repository): Duplicated warning errors corrected.
   This program computes Healthy Life Expectancies from    (Repository): Elapsed time after each iteration is now output. It
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    helps to forecast when convergence will be reached. Elapsed time
   first survey ("cross") where individuals from different ages are    is stamped in powell.  We created a new html file for the graphs
   interviewed on their health status or degree of disability (in the    concerning matrix of covariance. It has extension -cov.htm.
   case of a health survey which is our main interest) -2- at least a  
   second wave of interviews ("longitudinal") which measure each change    Revision 1.90  2003/06/24 12:34:15  brouard
   (if any) in individual health status.  Health expectancies are    (Module): Some bugs corrected for windows. Also, when
   computed from the time spent in each health state according to a    mle=-1 a template is output in file "or"mypar.txt with the design
   model. More health states you consider, more time is necessary to reach the    of the covariance matrix to be input.
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    Revision 1.89  2003/06/24 12:30:52  brouard
   probabibility to be observed in state j at the second wave    (Module): Some bugs corrected for windows. Also, when
   conditional to be observed in state i at the first wave. Therefore    mle=-1 a template is output in file "or"mypar.txt with the design
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    of the covariance matrix to be input.
   'age' is age and 'sex' is a covariate. If you want to have a more  
   complex model than "constant and age", you should modify the program    Revision 1.88  2003/06/23 17:54:56  brouard
   where the markup *Covariates have to be included here again* invites    * 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.
   you to do it.  More covariates you add, slower the  
   convergence.    Revision 1.87  2003/06/18 12:26:01  brouard
     Version 0.96
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Revision 1.86  2003/06/17 20:04:08  brouard
   identical for each individual. Also, if a individual missed an    (Module): Change position of html and gnuplot routines and added
   intermediate interview, the information is lost, but taken into    routine fileappend.
   account using an interpolation or extrapolation.    
     Revision 1.85  2003/06/17 13:12:43  brouard
   hPijx is the probability to be observed in state i at age x+h    * imach.c (Repository): Check when date of death was earlier that
   conditional to the observed state i at age x. The delay 'h' can be    current date of interview. It may happen when the death was just
   split into an exact number (nh*stepm) of unobserved intermediate    prior to the death. In this case, dh was negative and likelihood
   states. This elementary transition (by month or quarter trimester,    was wrong (infinity). We still send an "Error" but patch by
   semester or year) is model as a multinomial logistic.  The hPx    assuming that the date of death was just one stepm after the
   matrix is simply the matrix product of nh*stepm elementary matrices    interview.
   and the contribution of each individual to the likelihood is simply    (Repository): Because some people have very long ID (first column)
   hPijx.    we changed int to long in num[] and we added a new lvector for
     memory allocation. But we also truncated to 8 characters (left
   Also this programme outputs the covariance matrix of the parameters but also    truncation)
   of the life expectancies. It also computes the prevalence limits.    (Repository): No more line truncation errors.
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Revision 1.84  2003/06/13 21:44:43  brouard
            Institut national d'études démographiques, Paris.    * imach.c (Repository): Replace "freqsummary" at a correct
   This software have been partly granted by Euro-REVES, a concerted action    place. It differs from routine "prevalence" which may be called
   from the European Union.    many times. Probs is memory consuming and must be used with
   It is copyrighted identically to a GNU software product, ie programme and    parcimony.
   software can be distributed freely for non commercial use. Latest version    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   can be accessed at http://euroreves.ined.fr/imach .  
   **********************************************************************/    Revision 1.83  2003/06/10 13:39:11  lievre
      *** empty log message ***
 #include <math.h>  
 #include <stdio.h>    Revision 1.82  2003/06/05 15:57:20  brouard
 #include <stdlib.h>    Add log in  imach.c and  fullversion number is now printed.
 #include <unistd.h>  
   */
 #define MAXLINE 256  /*
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"     Interpolated Markov Chain
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Short summary of the programme:
 #define windows    
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    This program computes Healthy Life Expectancies from
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
     first survey ("cross") where individuals from different ages are
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    interviewed on their health status or degree of disability (in the
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    case of a health survey which is our main interest) -2- at least a
     second wave of interviews ("longitudinal") which measure each change
 #define NINTERVMAX 8    (if any) in individual health status.  Health expectancies are
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    computed from the time spent in each health state according to a
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    model. More health states you consider, more time is necessary to reach the
 #define NCOVMAX 8 /* Maximum number of covariates */    Maximum Likelihood of the parameters involved in the model.  The
 #define MAXN 20000    simplest model is the multinomial logistic model where pij is the
 #define YEARM 12. /* Number of months per year */    probability to be observed in state j at the second wave
 #define AGESUP 130    conditional to be observed in state i at the first wave. Therefore
 #define AGEBASE 40    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
     'age' is age and 'sex' is a covariate. If you want to have a more
     complex model than "constant and age", you should modify the program
 int erreur; /* Error number */    where the markup *Covariates have to be included here again* invites
 int nvar;    you to do it.  More covariates you add, slower the
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    convergence.
 int npar=NPARMAX;  
 int nlstate=2; /* Number of live states */    The advantage of this computer programme, compared to a simple
 int ndeath=1; /* Number of dead states */    multinomial logistic model, is clear when the delay between waves is not
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    identical for each individual. Also, if a individual missed an
 int popbased=0;    intermediate interview, the information is lost, but taken into
     account using an interpolation or extrapolation.  
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    hPijx is the probability to be observed in state i at age x+h
 int jmin, jmax; /* min, max spacing between 2 waves */    conditional to the observed state i at age x. The delay 'h' can be
 int mle, weightopt;    split into an exact number (nh*stepm) of unobserved intermediate
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    states. This elementary transition (by month, quarter,
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    semester or year) is modelled as a multinomial logistic.  The hPx
 double jmean; /* Mean space between 2 waves */    matrix is simply the matrix product of nh*stepm elementary matrices
 double **oldm, **newm, **savm; /* Working pointers to matrices */    and the contribution of each individual to the likelihood is simply
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    hPijx.
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  
 FILE *ficgp,*ficresprob,*ficpop;    Also this programme outputs the covariance matrix of the parameters but also
 FILE *ficreseij;    of the life expectancies. It also computes the stable prevalence. 
   char filerese[FILENAMELENGTH];    
  FILE  *ficresvij;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   char fileresv[FILENAMELENGTH];             Institut national d'études démographiques, Paris.
  FILE  *ficresvpl;    This software have been partly granted by Euro-REVES, a concerted action
   char fileresvpl[FILENAMELENGTH];    from the European Union.
     It is copyrighted identically to a GNU software product, ie programme and
 #define NR_END 1    software can be distributed freely for non commercial use. Latest version
 #define FREE_ARG char*    can be accessed at http://euroreves.ined.fr/imach .
 #define FTOL 1.0e-10  
     Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #define NRANSI    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 #define ITMAX 200    
     **********************************************************************/
 #define TOL 2.0e-4  /*
     main
 #define CGOLD 0.3819660    read parameterfile
 #define ZEPS 1.0e-10    read datafile
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    concatwav
     freqsummary
 #define GOLD 1.618034    if (mle >= 1)
 #define GLIMIT 100.0      mlikeli
 #define TINY 1.0e-20    print results files
     if mle==1 
 static double maxarg1,maxarg2;       computes hessian
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    read end of parameter file: agemin, agemax, bage, fage, estepm
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))        begin-prev-date,...
      open gnuplot file
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    open html file
 #define rint(a) floor(a+0.5)    stable prevalence
      for age prevalim()
 static double sqrarg;    h Pij x
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    variance of p varprob
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    forecasting if prevfcast==1 prevforecast call prevalence()
     health expectancies
 int imx;    Variance-covariance of DFLE
 int stepm;    prevalence()
 /* Stepm, step in month: minimum step interpolation*/     movingaverage()
     varevsij() 
 int m,nb;    if popbased==1 varevsij(,popbased)
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    total life expectancies
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Variance of stable prevalence
 double **pmmij, ***probs, ***mobaverage;   end
 double dateintmean=0;  */
   
 double *weight;  
 int **s; /* Status */  
 double *agedc, **covar, idx;   
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  #include <math.h>
   #include <stdio.h>
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  #include <stdlib.h>
 double ftolhess; /* Tolerance for computing hessian */  #include <unistd.h>
   
 /**************** split *************************/  #include <sys/time.h>
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  #include <time.h>
 {  #include "timeval.h"
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */  #define MAXLINE 256
   #define GNUPLOTPROGRAM "gnuplot"
    l1 = strlen( path );                 /* length of path */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  #define FILENAMELENGTH 132
 #ifdef windows  /*#define DEBUG*/
    s = strrchr( path, '\\' );           /* find last / */  /*#define windows*/
 #else  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
    s = strrchr( path, '/' );            /* find last / */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 #endif  
    if ( s == NULL ) {                   /* no directory, so use current */  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 #if     defined(__bsd__)                /* get current working directory */  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
       extern char       *getwd( );  
   #define NINTERVMAX 8
       if ( getwd( dirc ) == NULL ) {  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #else  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
       extern char       *getcwd( );  #define NCOVMAX 8 /* Maximum number of covariates */
   #define MAXN 20000
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  #define YEARM 12. /* Number of months per year */
 #endif  #define AGESUP 130
          return( GLOCK_ERROR_GETCWD );  #define AGEBASE 40
       }  #ifdef unix
       strcpy( name, path );             /* we've got it */  #define DIRSEPARATOR '/'
    } else {                             /* strip direcotry from path */  #define ODIRSEPARATOR '\\'
       s++;                              /* after this, the filename */  #else
       l2 = strlen( s );                 /* length of filename */  #define DIRSEPARATOR '\\'
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  #define ODIRSEPARATOR '/'
       strcpy( name, s );                /* save file name */  #endif
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */  /* $Id$ */
    }  /* $State$ */
    l1 = strlen( dirc );                 /* length of directory */  
 #ifdef windows  char version[]="Imach version 0.96a, June 2003, INED-EUROREVES ";
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  char fullversion[]="$Revision$ $Date$"; 
 #else  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  int nvar;
 #endif  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
    s = strrchr( name, '.' );            /* find last / */  int npar=NPARMAX;
    s++;  int nlstate=2; /* Number of live states */
    strcpy(ext,s);                       /* save extension */  int ndeath=1; /* Number of dead states */
    l1= strlen( name);  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
    l2= strlen( s)+1;  int popbased=0;
    strncpy( finame, name, l1-l2);  
    finame[l1-l2]= 0;  int *wav; /* Number of waves for this individuual 0 is possible */
    return( 0 );                         /* we're done */  int maxwav; /* Maxim number of waves */
 }  int jmin, jmax; /* min, max spacing between 2 waves */
   int gipmx, gsw; /* Global variables on the number of contributions 
                      to the likelihood and the sum of weights (done by funcone)*/
 /******************************************/  int mle, weightopt;
   int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 void replace(char *s, char*t)  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
   int i;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   int lg=20;  double jmean; /* Mean space between 2 waves */
   i=0;  double **oldm, **newm, **savm; /* Working pointers to matrices */
   lg=strlen(t);  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   for(i=0; i<= lg; i++) {  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
     (s[i] = t[i]);  FILE *ficlog, *ficrespow;
     if (t[i]== '\\') s[i]='/';  int globpr; /* Global variable for printing or not */
   }  double fretone; /* Only one call to likelihood */
 }  long ipmx; /* Number of contributions */
   double sw; /* Sum of weights */
 int nbocc(char *s, char occ)  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
 {  FILE *ficresilk;
   int i,j=0;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   int lg=20;  FILE *ficresprobmorprev;
   i=0;  FILE *fichtm, *fichtmcov; /* Html File */
   lg=strlen(s);  FILE *ficreseij;
   for(i=0; i<= lg; i++) {  char filerese[FILENAMELENGTH];
   if  (s[i] == occ ) j++;  FILE  *ficresvij;
   }  char fileresv[FILENAMELENGTH];
   return j;  FILE  *ficresvpl;
 }  char fileresvpl[FILENAMELENGTH];
   char title[MAXLINE];
 void cutv(char *u,char *v, char*t, char occ)  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 {  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   int i,lg,j,p=0;  char tmpout[FILENAMELENGTH]; 
   i=0;  char command[FILENAMELENGTH];
   for(j=0; j<=strlen(t)-1; j++) {  int  outcmd=0;
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   char lfileres[FILENAMELENGTH];
   lg=strlen(t);  char filelog[FILENAMELENGTH]; /* Log file */
   for(j=0; j<p; j++) {  char filerest[FILENAMELENGTH];
     (u[j] = t[j]);  char fileregp[FILENAMELENGTH];
   }  char popfile[FILENAMELENGTH];
      u[p]='\0';  
   char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   }  struct timezone tzp;
 }  extern int gettimeofday();
   struct tm tmg, tm, tmf, *gmtime(), *localtime();
 /********************** nrerror ********************/  long time_value;
   extern long time();
 void nrerror(char error_text[])  char strcurr[80], strfor[80];
 {  
   fprintf(stderr,"ERREUR ...\n");  #define NR_END 1
   fprintf(stderr,"%s\n",error_text);  #define FREE_ARG char*
   exit(1);  #define FTOL 1.0e-10
 }  
 /*********************** vector *******************/  #define NRANSI 
 double *vector(int nl, int nh)  #define ITMAX 200 
 {  
   double *v;  #define TOL 2.0e-4 
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");  #define CGOLD 0.3819660 
   return v-nl+NR_END;  #define ZEPS 1.0e-10 
 }  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   
 /************************ free vector ******************/  #define GOLD 1.618034 
 void free_vector(double*v, int nl, int nh)  #define GLIMIT 100.0 
 {  #define TINY 1.0e-20 
   free((FREE_ARG)(v+nl-NR_END));  
 }  static double maxarg1,maxarg2;
   #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 /************************ivector *******************************/  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 int *ivector(long nl,long nh)    
 {  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   int *v;  #define rint(a) floor(a+0.5)
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");  static double sqrarg;
   return v-nl+NR_END;  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 }  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   
 /******************free ivector **************************/  int imx; 
 void free_ivector(int *v, long nl, long nh)  int stepm;
 {  /* Stepm, step in month: minimum step interpolation*/
   free((FREE_ARG)(v+nl-NR_END));  
 }  int estepm;
   /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 /******************* imatrix *******************************/  
 int **imatrix(long nrl, long nrh, long ncl, long nch)  int m,nb;
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  long *num;
 {  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   int **m;  double **pmmij, ***probs;
    double dateintmean=0;
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  double *weight;
   if (!m) nrerror("allocation failure 1 in matrix()");  int **s; /* Status */
   m += NR_END;  double *agedc, **covar, idx;
   m -= nrl;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
    
    double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   /* allocate rows and set pointers to them */  double ftolhess; /* Tolerance for computing hessian */
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  /**************** split *************************/
   m[nrl] += NR_END;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   m[nrl] -= ncl;  {
      char  *ss;                            /* pointer */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    int   l1, l2;                         /* length counters */
    
   /* return pointer to array of pointers to rows */    l1 = strlen(path );                   /* length of path */
   return m;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 }    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     if ( ss == NULL ) {                   /* no directory, so use current */
 /****************** free_imatrix *************************/      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 void free_imatrix(m,nrl,nrh,ncl,nch)        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       int **m;      /* get current working directory */
       long nch,ncl,nrh,nrl;      /*    extern  char* getcwd ( char *buf , int len);*/
      /* free an int matrix allocated by imatrix() */      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 {        return( GLOCK_ERROR_GETCWD );
   free((FREE_ARG) (m[nrl]+ncl-NR_END));      }
   free((FREE_ARG) (m+nrl-NR_END));      strcpy( name, path );               /* we've got it */
 }    } else {                              /* strip direcotry from path */
       ss++;                               /* after this, the filename */
 /******************* matrix *******************************/      l2 = strlen( ss );                  /* length of filename */
 double **matrix(long nrl, long nrh, long ncl, long nch)      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 {      strcpy( name, ss );         /* save file name */
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   double **m;      dirc[l1-l2] = 0;                    /* add zero */
     }
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    l1 = strlen( dirc );                  /* length of directory */
   if (!m) nrerror("allocation failure 1 in matrix()");    /*#ifdef windows
   m += NR_END;    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   m -= nrl;  #else
     if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #endif
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    */
   m[nrl] += NR_END;    ss = strrchr( name, '.' );            /* find last / */
   m[nrl] -= ncl;    ss++;
     strcpy(ext,ss);                       /* save extension */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    l1= strlen( name);
   return m;    l2= strlen(ss)+1;
 }    strncpy( finame, name, l1-l2);
     finame[l1-l2]= 0;
 /*************************free matrix ************************/    return( 0 );                          /* we're done */
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  }
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));  /******************************************/
 }  
   void replace_back_to_slash(char *s, char*t)
 /******************* ma3x *******************************/  {
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    int i;
 {    int lg=0;
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    i=0;
   double ***m;    lg=strlen(t);
     for(i=0; i<= lg; i++) {
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));      (s[i] = t[i]);
   if (!m) nrerror("allocation failure 1 in matrix()");      if (t[i]== '\\') s[i]='/';
   m += NR_END;    }
   m -= nrl;  }
   
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  int nbocc(char *s, char occ)
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  {
   m[nrl] += NR_END;    int i,j=0;
   m[nrl] -= ncl;    int lg=20;
     i=0;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    lg=strlen(s);
     for(i=0; i<= lg; i++) {
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    if  (s[i] == occ ) j++;
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    }
   m[nrl][ncl] += NR_END;    return j;
   m[nrl][ncl] -= nll;  }
   for (j=ncl+1; j<=nch; j++)  
     m[nrl][j]=m[nrl][j-1]+nlay;  void cutv(char *u,char *v, char*t, char occ)
    {
   for (i=nrl+1; i<=nrh; i++) {    /* cuts string t into u and v where u is ended by char occ excluding it
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
     for (j=ncl+1; j<=nch; j++)       gives u="abcedf" and v="ghi2j" */
       m[i][j]=m[i][j-1]+nlay;    int i,lg,j,p=0;
   }    i=0;
   return m;    for(j=0; j<=strlen(t)-1; j++) {
 }      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     }
 /*************************free ma3x ************************/  
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    lg=strlen(t);
 {    for(j=0; j<p; j++) {
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));      (u[j] = t[j]);
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    }
   free((FREE_ARG)(m+nrl-NR_END));       u[p]='\0';
 }  
      for(j=0; j<= lg; j++) {
 /***************** f1dim *************************/      if (j>=(p+1))(v[j-p-1] = t[j]);
 extern int ncom;    }
 extern double *pcom,*xicom;  }
 extern double (*nrfunc)(double []);  
    /********************** nrerror ********************/
 double f1dim(double x)  
 {  void nrerror(char error_text[])
   int j;  {
   double f;    fprintf(stderr,"ERREUR ...\n");
   double *xt;    fprintf(stderr,"%s\n",error_text);
      exit(EXIT_FAILURE);
   xt=vector(1,ncom);  }
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  /*********************** vector *******************/
   f=(*nrfunc)(xt);  double *vector(int nl, int nh)
   free_vector(xt,1,ncom);  {
   return f;    double *v;
 }    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     if (!v) nrerror("allocation failure in vector");
 /*****************brent *************************/    return v-nl+NR_END;
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  }
 {  
   int iter;  /************************ free vector ******************/
   double a,b,d,etemp;  void free_vector(double*v, int nl, int nh)
   double fu,fv,fw,fx;  {
   double ftemp;    free((FREE_ARG)(v+nl-NR_END));
   double p,q,r,tol1,tol2,u,v,w,x,xm;  }
   double e=0.0;  
    /************************ivector *******************************/
   a=(ax < cx ? ax : cx);  int *ivector(long nl,long nh)
   b=(ax > cx ? ax : cx);  {
   x=w=v=bx;    int *v;
   fw=fv=fx=(*f)(x);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
   for (iter=1;iter<=ITMAX;iter++) {    if (!v) nrerror("allocation failure in ivector");
     xm=0.5*(a+b);    return v-nl+NR_END;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  }
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);  /******************free ivector **************************/
 #ifdef DEBUG  void free_ivector(int *v, long nl, long nh)
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  {
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    free((FREE_ARG)(v+nl-NR_END));
 #endif  }
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  
       *xmin=x;  /************************lvector *******************************/
       return fx;  long *lvector(long nl,long nh)
     }  {
     ftemp=fu;    long *v;
     if (fabs(e) > tol1) {    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       r=(x-w)*(fx-fv);    if (!v) nrerror("allocation failure in ivector");
       q=(x-v)*(fx-fw);    return v-nl+NR_END;
       p=(x-v)*q-(x-w)*r;  }
       q=2.0*(q-r);  
       if (q > 0.0) p = -p;  /******************free lvector **************************/
       q=fabs(q);  void free_lvector(long *v, long nl, long nh)
       etemp=e;  {
       e=d;    free((FREE_ARG)(v+nl-NR_END));
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  }
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  
       else {  /******************* imatrix *******************************/
         d=p/q;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
         u=x+d;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
         if (u-a < tol2 || b-u < tol2)  { 
           d=SIGN(tol1,xm-x);    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       }    int **m; 
     } else {    
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    /* allocate pointers to rows */ 
     }    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    if (!m) nrerror("allocation failure 1 in matrix()"); 
     fu=(*f)(u);    m += NR_END; 
     if (fu <= fx) {    m -= nrl; 
       if (u >= x) a=x; else b=x;    
       SHFT(v,w,x,u)    
         SHFT(fv,fw,fx,fu)    /* allocate rows and set pointers to them */ 
         } else {    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
           if (u < x) a=u; else b=u;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
           if (fu <= fw || w == x) {    m[nrl] += NR_END; 
             v=w;    m[nrl] -= ncl; 
             w=u;    
             fv=fw;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
             fw=fu;    
           } else if (fu <= fv || v == x || v == w) {    /* return pointer to array of pointers to rows */ 
             v=u;    return m; 
             fv=fu;  } 
           }  
         }  /****************** free_imatrix *************************/
   }  void free_imatrix(m,nrl,nrh,ncl,nch)
   nrerror("Too many iterations in brent");        int **m;
   *xmin=x;        long nch,ncl,nrh,nrl; 
   return fx;       /* free an int matrix allocated by imatrix() */ 
 }  { 
     free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
 /****************** mnbrak ***********************/    free((FREE_ARG) (m+nrl-NR_END)); 
   } 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  
             double (*func)(double))  /******************* matrix *******************************/
 {  double **matrix(long nrl, long nrh, long ncl, long nch)
   double ulim,u,r,q, dum;  {
   double fu;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
      double **m;
   *fa=(*func)(*ax);  
   *fb=(*func)(*bx);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   if (*fb > *fa) {    if (!m) nrerror("allocation failure 1 in matrix()");
     SHFT(dum,*ax,*bx,dum)    m += NR_END;
       SHFT(dum,*fb,*fa,dum)    m -= nrl;
       }  
   *cx=(*bx)+GOLD*(*bx-*ax);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   *fc=(*func)(*cx);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   while (*fb > *fc) {    m[nrl] += NR_END;
     r=(*bx-*ax)*(*fb-*fc);    m[nrl] -= ncl;
     q=(*bx-*cx)*(*fb-*fa);  
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    return m;
     ulim=(*bx)+GLIMIT*(*cx-*bx);    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
     if ((*bx-u)*(u-*cx) > 0.0) {     */
       fu=(*func)(u);  }
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);  /*************************free matrix ************************/
       if (fu < *fc) {  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  {
           SHFT(*fb,*fc,fu,(*func)(u))    free((FREE_ARG)(m[nrl]+ncl-NR_END));
           }    free((FREE_ARG)(m+nrl-NR_END));
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  }
       u=ulim;  
       fu=(*func)(u);  /******************* ma3x *******************************/
     } else {  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       u=(*cx)+GOLD*(*cx-*bx);  {
       fu=(*func)(u);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     }    double ***m;
     SHFT(*ax,*bx,*cx,u)  
       SHFT(*fa,*fb,*fc,fu)    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       }    if (!m) nrerror("allocation failure 1 in matrix()");
 }    m += NR_END;
     m -= nrl;
 /*************** linmin ************************/  
     m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 int ncom;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 double *pcom,*xicom;    m[nrl] += NR_END;
 double (*nrfunc)(double []);    m[nrl] -= ncl;
    
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 {  
   double brent(double ax, double bx, double cx,    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
                double (*f)(double), double tol, double *xmin);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   double f1dim(double x);    m[nrl][ncl] += NR_END;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    m[nrl][ncl] -= nll;
               double *fc, double (*func)(double));    for (j=ncl+1; j<=nch; j++) 
   int j;      m[nrl][j]=m[nrl][j-1]+nlay;
   double xx,xmin,bx,ax;    
   double fx,fb,fa;    for (i=nrl+1; i<=nrh; i++) {
        m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   ncom=n;      for (j=ncl+1; j<=nch; j++) 
   pcom=vector(1,n);        m[i][j]=m[i][j-1]+nlay;
   xicom=vector(1,n);    }
   nrfunc=func;    return m; 
   for (j=1;j<=n;j++) {    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     pcom[j]=p[j];             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     xicom[j]=xi[j];    */
   }  }
   ax=0.0;  
   xx=1.0;  /*************************free ma3x ************************/
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  {
 #ifdef DEBUG    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 #endif    free((FREE_ARG)(m+nrl-NR_END));
   for (j=1;j<=n;j++) {  }
     xi[j] *= xmin;  
     p[j] += xi[j];  /***************** f1dim *************************/
   }  extern int ncom; 
   free_vector(xicom,1,n);  extern double *pcom,*xicom;
   free_vector(pcom,1,n);  extern double (*nrfunc)(double []); 
 }   
   double f1dim(double x) 
 /*************** powell ************************/  { 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    int j; 
             double (*func)(double []))    double f;
 {    double *xt; 
   void linmin(double p[], double xi[], int n, double *fret,   
               double (*func)(double []));    xt=vector(1,ncom); 
   int i,ibig,j;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   double del,t,*pt,*ptt,*xit;    f=(*nrfunc)(xt); 
   double fp,fptt;    free_vector(xt,1,ncom); 
   double *xits;    return f; 
   pt=vector(1,n);  } 
   ptt=vector(1,n);  
   xit=vector(1,n);  /*****************brent *************************/
   xits=vector(1,n);  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   *fret=(*func)(p);  { 
   for (j=1;j<=n;j++) pt[j]=p[j];    int iter; 
   for (*iter=1;;++(*iter)) {    double a,b,d,etemp;
     fp=(*fret);    double fu,fv,fw,fx;
     ibig=0;    double ftemp;
     del=0.0;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    double e=0.0; 
     for (i=1;i<=n;i++)   
       printf(" %d %.12f",i, p[i]);    a=(ax < cx ? ax : cx); 
     printf("\n");    b=(ax > cx ? ax : cx); 
     for (i=1;i<=n;i++) {    x=w=v=bx; 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    fw=fv=fx=(*f)(x); 
       fptt=(*fret);    for (iter=1;iter<=ITMAX;iter++) { 
 #ifdef DEBUG      xm=0.5*(a+b); 
       printf("fret=%lf \n",*fret);      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
 #endif      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       printf("%d",i);fflush(stdout);      printf(".");fflush(stdout);
       linmin(p,xit,n,fret,func);      fprintf(ficlog,".");fflush(ficlog);
       if (fabs(fptt-(*fret)) > del) {  #ifdef DEBUG
         del=fabs(fptt-(*fret));      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
         ibig=i;      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       }      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
 #ifdef DEBUG  #endif
       printf("%d %.12e",i,(*fret));      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       for (j=1;j<=n;j++) {        *xmin=x; 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);        return fx; 
         printf(" x(%d)=%.12e",j,xit[j]);      } 
       }      ftemp=fu;
       for(j=1;j<=n;j++)      if (fabs(e) > tol1) { 
         printf(" p=%.12e",p[j]);        r=(x-w)*(fx-fv); 
       printf("\n");        q=(x-v)*(fx-fw); 
 #endif        p=(x-v)*q-(x-w)*r; 
     }        q=2.0*(q-r); 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {        if (q > 0.0) p = -p; 
 #ifdef DEBUG        q=fabs(q); 
       int k[2],l;        etemp=e; 
       k[0]=1;        e=d; 
       k[1]=-1;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
       printf("Max: %.12e",(*func)(p));          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       for (j=1;j<=n;j++)        else { 
         printf(" %.12e",p[j]);          d=p/q; 
       printf("\n");          u=x+d; 
       for(l=0;l<=1;l++) {          if (u-a < tol2 || b-u < tol2) 
         for (j=1;j<=n;j++) {            d=SIGN(tol1,xm-x); 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];        } 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);      } else { 
         }        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));      } 
       }      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
 #endif      fu=(*f)(u); 
       if (fu <= fx) { 
         if (u >= x) a=x; else b=x; 
       free_vector(xit,1,n);        SHFT(v,w,x,u) 
       free_vector(xits,1,n);          SHFT(fv,fw,fx,fu) 
       free_vector(ptt,1,n);          } else { 
       free_vector(pt,1,n);            if (u < x) a=u; else b=u; 
       return;            if (fu <= fw || w == x) { 
     }              v=w; 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");              w=u; 
     for (j=1;j<=n;j++) {              fv=fw; 
       ptt[j]=2.0*p[j]-pt[j];              fw=fu; 
       xit[j]=p[j]-pt[j];            } else if (fu <= fv || v == x || v == w) { 
       pt[j]=p[j];              v=u; 
     }              fv=fu; 
     fptt=(*func)(ptt);            } 
     if (fptt < fp) {          } 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    } 
       if (t < 0.0) {    nrerror("Too many iterations in brent"); 
         linmin(p,xit,n,fret,func);    *xmin=x; 
         for (j=1;j<=n;j++) {    return fx; 
           xi[j][ibig]=xi[j][n];  } 
           xi[j][n]=xit[j];  
         }  /****************** mnbrak ***********************/
 #ifdef DEBUG  
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
         for(j=1;j<=n;j++)              double (*func)(double)) 
           printf(" %.12e",xit[j]);  { 
         printf("\n");    double ulim,u,r,q, dum;
 #endif    double fu; 
       }   
     }    *fa=(*func)(*ax); 
   }    *fb=(*func)(*bx); 
 }    if (*fb > *fa) { 
       SHFT(dum,*ax,*bx,dum) 
 /**** Prevalence limit ****************/        SHFT(dum,*fb,*fa,dum) 
         } 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    *cx=(*bx)+GOLD*(*bx-*ax); 
 {    *fc=(*func)(*cx); 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    while (*fb > *fc) { 
      matrix by transitions matrix until convergence is reached */      r=(*bx-*ax)*(*fb-*fc); 
       q=(*bx-*cx)*(*fb-*fa); 
   int i, ii,j,k;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   double min, max, maxmin, maxmax,sumnew=0.;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   double **matprod2();      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   double **out, cov[NCOVMAX], **pmij();      if ((*bx-u)*(u-*cx) > 0.0) { 
   double **newm;        fu=(*func)(u); 
   double agefin, delaymax=50 ; /* Max number of years to converge */      } else if ((*cx-u)*(u-ulim) > 0.0) { 
         fu=(*func)(u); 
   for (ii=1;ii<=nlstate+ndeath;ii++)        if (fu < *fc) { 
     for (j=1;j<=nlstate+ndeath;j++){          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);            SHFT(*fb,*fc,fu,(*func)(u)) 
     }            } 
       } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
    cov[1]=1.;        u=ulim; 
          fu=(*func)(u); 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */      } else { 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        u=(*cx)+GOLD*(*cx-*bx); 
     newm=savm;        fu=(*func)(u); 
     /* Covariates have to be included here again */      } 
      cov[2]=agefin;      SHFT(*ax,*bx,*cx,u) 
          SHFT(*fa,*fb,*fc,fu) 
       for (k=1; k<=cptcovn;k++) {        } 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  } 
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  
       }  /*************** linmin ************************/
       for (k=1; k<=cptcovage;k++)  
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  int ncom; 
       for (k=1; k<=cptcovprod;k++)  double *pcom,*xicom;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  double (*nrfunc)(double []); 
    
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  { 
     double brent(double ax, double bx, double cx, 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);                 double (*f)(double), double tol, double *xmin); 
     double f1dim(double x); 
     savm=oldm;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     oldm=newm;                double *fc, double (*func)(double)); 
     maxmax=0.;    int j; 
     for(j=1;j<=nlstate;j++){    double xx,xmin,bx,ax; 
       min=1.;    double fx,fb,fa;
       max=0.;   
       for(i=1; i<=nlstate; i++) {    ncom=n; 
         sumnew=0;    pcom=vector(1,n); 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    xicom=vector(1,n); 
         prlim[i][j]= newm[i][j]/(1-sumnew);    nrfunc=func; 
         max=FMAX(max,prlim[i][j]);    for (j=1;j<=n;j++) { 
         min=FMIN(min,prlim[i][j]);      pcom[j]=p[j]; 
       }      xicom[j]=xi[j]; 
       maxmin=max-min;    } 
       maxmax=FMAX(maxmax,maxmin);    ax=0.0; 
     }    xx=1.0; 
     if(maxmax < ftolpl){    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       return prlim;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     }  #ifdef DEBUG
   }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 }    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   #endif
 /*************** transition probabilities ***************/    for (j=1;j<=n;j++) { 
       xi[j] *= xmin; 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )      p[j] += xi[j]; 
 {    } 
   double s1, s2;    free_vector(xicom,1,n); 
   /*double t34;*/    free_vector(pcom,1,n); 
   int i,j,j1, nc, ii, jj;  } 
   
     for(i=1; i<= nlstate; i++){  char *asc_diff_time(long time_sec, char ascdiff[])
     for(j=1; j<i;j++){  {
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    long sec_left, days, hours, minutes;
         /*s2 += param[i][j][nc]*cov[nc];*/    days = (time_sec) / (60*60*24);
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    sec_left = (time_sec) % (60*60*24);
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    hours = (sec_left) / (60*60) ;
       }    sec_left = (sec_left) %(60*60);
       ps[i][j]=s2;    minutes = (sec_left) /60;
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    sec_left = (sec_left) % (60);
     }    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
     for(j=i+1; j<=nlstate+ndeath;j++){    return ascdiff;
       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];  
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  /*************** powell ************************/
       }  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       ps[i][j]=s2;              double (*func)(double [])) 
     }  { 
   }    void linmin(double p[], double xi[], int n, double *fret, 
     /*ps[3][2]=1;*/                double (*func)(double [])); 
     int i,ibig,j; 
   for(i=1; i<= nlstate; i++){    double del,t,*pt,*ptt,*xit;
      s1=0;    double fp,fptt;
     for(j=1; j<i; j++)    double *xits;
       s1+=exp(ps[i][j]);    int niterf, itmp;
     for(j=i+1; j<=nlstate+ndeath; j++)  
       s1+=exp(ps[i][j]);    pt=vector(1,n); 
     ps[i][i]=1./(s1+1.);    ptt=vector(1,n); 
     for(j=1; j<i; j++)    xit=vector(1,n); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    xits=vector(1,n); 
     for(j=i+1; j<=nlstate+ndeath; j++)    *fret=(*func)(p); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    for (j=1;j<=n;j++) pt[j]=p[j]; 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    for (*iter=1;;++(*iter)) { 
   } /* end i */      fp=(*fret); 
       ibig=0; 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      del=0.0; 
     for(jj=1; jj<= nlstate+ndeath; jj++){      last_time=curr_time;
       ps[ii][jj]=0;      (void) gettimeofday(&curr_time,&tzp);
       ps[ii][ii]=1;      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
     }      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
   }      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
       for (i=1;i<=n;i++) {
         printf(" %d %.12f",i, p[i]);
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        fprintf(ficlog," %d %.12lf",i, p[i]);
     for(jj=1; jj<= nlstate+ndeath; jj++){        fprintf(ficrespow," %.12lf", p[i]);
      printf("%lf ",ps[ii][jj]);      }
    }      printf("\n");
     printf("\n ");      fprintf(ficlog,"\n");
     }      fprintf(ficrespow,"\n");fflush(ficrespow);
     printf("\n ");printf("%lf ",cov[2]);*/      if(*iter <=3){
 /*        tm = *localtime(&curr_time.tv_sec);
   for(i=1; i<= npar; i++) printf("%f ",x[i]);        asctime_r(&tm,strcurr);
   goto end;*/        forecast_time=curr_time;
     return ps;        itmp = strlen(strcurr);
 }        if(strcurr[itmp-1]=='\n')
           strcurr[itmp-1]='\0';
 /**************** Product of 2 matrices ******************/        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        for(niterf=10;niterf<=30;niterf+=10){
 {          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times          tmf = *localtime(&forecast_time.tv_sec);
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */          asctime_r(&tmf,strfor);
   /* in, b, out are matrice of pointers which should have been initialized  /*      strcpy(strfor,asctime(&tmf)); */
      before: only the contents of out is modified. The function returns          itmp = strlen(strfor);
      a pointer to pointers identical to out */          if(strfor[itmp-1]=='\n')
   long i, j, k;          strfor[itmp-1]='\0';
   for(i=nrl; i<= nrh; i++)          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
     for(k=ncolol; k<=ncoloh; k++)          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        }
         out[i][k] +=in[i][j]*b[j][k];      }
       for (i=1;i<=n;i++) { 
   return out;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
 }        fptt=(*fret); 
   #ifdef DEBUG
         printf("fret=%lf \n",*fret);
 /************* Higher Matrix Product ***************/        fprintf(ficlog,"fret=%lf \n",*fret);
   #endif
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )        printf("%d",i);fflush(stdout);
 {        fprintf(ficlog,"%d",i);fflush(ficlog);
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month        linmin(p,xit,n,fret,func); 
      duration (i.e. until        if (fabs(fptt-(*fret)) > del) { 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.          del=fabs(fptt-(*fret)); 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step          ibig=i; 
      (typically every 2 years instead of every month which is too big).        } 
      Model is determined by parameters x and covariates have to be  #ifdef DEBUG
      included manually here.        printf("%d %.12e",i,(*fret));
         fprintf(ficlog,"%d %.12e",i,(*fret));
      */        for (j=1;j<=n;j++) {
           xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   int i, j, d, h, k;          printf(" x(%d)=%.12e",j,xit[j]);
   double **out, cov[NCOVMAX];          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   double **newm;        }
         for(j=1;j<=n;j++) {
   /* Hstepm could be zero and should return the unit matrix */          printf(" p=%.12e",p[j]);
   for (i=1;i<=nlstate+ndeath;i++)          fprintf(ficlog," p=%.12e",p[j]);
     for (j=1;j<=nlstate+ndeath;j++){        }
       oldm[i][j]=(i==j ? 1.0 : 0.0);        printf("\n");
       po[i][j][0]=(i==j ? 1.0 : 0.0);        fprintf(ficlog,"\n");
     }  #endif
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      } 
   for(h=1; h <=nhstepm; h++){      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     for(d=1; d <=hstepm; d++){  #ifdef DEBUG
       newm=savm;        int k[2],l;
       /* Covariates have to be included here again */        k[0]=1;
       cov[1]=1.;        k[1]=-1;
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        printf("Max: %.12e",(*func)(p));
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        fprintf(ficlog,"Max: %.12e",(*func)(p));
       for (k=1; k<=cptcovage;k++)        for (j=1;j<=n;j++) {
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          printf(" %.12e",p[j]);
       for (k=1; k<=cptcovprod;k++)          fprintf(ficlog," %.12e",p[j]);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        }
         printf("\n");
         fprintf(ficlog,"\n");
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        for(l=0;l<=1;l++) {
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/          for (j=1;j<=n;j++) {
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
                    pmij(pmmij,cov,ncovmodel,x,nlstate));            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       savm=oldm;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       oldm=newm;          }
     }          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     for(i=1; i<=nlstate+ndeath; i++)          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       for(j=1;j<=nlstate+ndeath;j++) {        }
         po[i][j][h]=newm[i][j];  #endif
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);  
          */  
       }        free_vector(xit,1,n); 
   } /* end h */        free_vector(xits,1,n); 
   return po;        free_vector(ptt,1,n); 
 }        free_vector(pt,1,n); 
         return; 
       } 
 /*************** log-likelihood *************/      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
 double func( double *x)      for (j=1;j<=n;j++) { 
 {        ptt[j]=2.0*p[j]-pt[j]; 
   int i, ii, j, k, mi, d, kk;        xit[j]=p[j]-pt[j]; 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        pt[j]=p[j]; 
   double **out;      } 
   double sw; /* Sum of weights */      fptt=(*func)(ptt); 
   double lli; /* Individual log likelihood */      if (fptt < fp) { 
   long ipmx;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   /*extern weight */        if (t < 0.0) { 
   /* We are differentiating ll according to initial status */          linmin(p,xit,n,fret,func); 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/          for (j=1;j<=n;j++) { 
   /*for(i=1;i<imx;i++)            xi[j][ibig]=xi[j][n]; 
     printf(" %d\n",s[4][i]);            xi[j][n]=xit[j]; 
   */          }
   cov[1]=1.;  #ifdef DEBUG
           printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   for(k=1; k<=nlstate; k++) ll[k]=0.;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){          for(j=1;j<=n;j++){
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];            printf(" %.12e",xit[j]);
     for(mi=1; mi<= wav[i]-1; mi++){            fprintf(ficlog," %.12e",xit[j]);
       for (ii=1;ii<=nlstate+ndeath;ii++)          }
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);          printf("\n");
       for(d=0; d<dh[mi][i]; d++){          fprintf(ficlog,"\n");
         newm=savm;  #endif
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;        }
         for (kk=1; kk<=cptcovage;kk++) {      } 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    } 
         }  } 
          
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  /**** Prevalence limit (stable prevalence)  ****************/
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  
         savm=oldm;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
         oldm=newm;  {
            /* Computes the prevalence limit in each live state at age x by left multiplying the unit
               matrix by transitions matrix until convergence is reached */
       } /* end mult */  
          int i, ii,j,k;
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    double min, max, maxmin, maxmax,sumnew=0.;
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    double **matprod2();
       ipmx +=1;    double **out, cov[NCOVMAX], **pmij();
       sw += weight[i];    double **newm;
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    double agefin, delaymax=50 ; /* Max number of years to converge */
     } /* end of wave */  
   } /* end of individual */    for (ii=1;ii<=nlstate+ndeath;ii++)
       for (j=1;j<=nlstate+ndeath;j++){
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      }
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  
   return -l;     cov[1]=1.;
 }   
    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
 /*********** Maximum Likelihood Estimation ***************/      newm=savm;
       /* Covariates have to be included here again */
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))       cov[2]=agefin;
 {    
   int i,j, iter;        for (k=1; k<=cptcovn;k++) {
   double **xi,*delti;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   double fret;          /*      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]]);*/
   xi=matrix(1,npar,1,npar);        }
   for (i=1;i<=npar;i++)        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     for (j=1;j<=npar;j++)        for (k=1; k<=cptcovprod;k++)
       xi[i][j]=(i==j ? 1.0 : 0.0);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   printf("Powell\n");  
   powell(p,xi,npar,ftol,&iter,&fret,func);        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   
 }      savm=oldm;
       oldm=newm;
 /**** Computes Hessian and covariance matrix ***/      maxmax=0.;
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      for(j=1;j<=nlstate;j++){
 {        min=1.;
   double  **a,**y,*x,pd;        max=0.;
   double **hess;        for(i=1; i<=nlstate; i++) {
   int i, j,jk;          sumnew=0;
   int *indx;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
           prlim[i][j]= newm[i][j]/(1-sumnew);
   double hessii(double p[], double delta, int theta, double delti[]);          max=FMAX(max,prlim[i][j]);
   double hessij(double p[], double delti[], int i, int j);          min=FMIN(min,prlim[i][j]);
   void lubksb(double **a, int npar, int *indx, double b[]) ;        }
   void ludcmp(double **a, int npar, int *indx, double *d) ;        maxmin=max-min;
         maxmax=FMAX(maxmax,maxmin);
   hess=matrix(1,npar,1,npar);      }
       if(maxmax < ftolpl){
   printf("\nCalculation of the hessian matrix. Wait...\n");        return prlim;
   for (i=1;i<=npar;i++){      }
     printf("%d",i);fflush(stdout);    }
     hess[i][i]=hessii(p,ftolhess,i,delti);  }
     /*printf(" %f ",p[i]);*/  
     /*printf(" %lf ",hess[i][i]);*/  /*************** transition probabilities ***************/ 
   }  
    double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   for (i=1;i<=npar;i++) {  {
     for (j=1;j<=npar;j++)  {    double s1, s2;
       if (j>i) {    /*double t34;*/
         printf(".%d%d",i,j);fflush(stdout);    int i,j,j1, nc, ii, jj;
         hess[i][j]=hessij(p,delti,i,j);  
         hess[j][i]=hess[i][j];          for(i=1; i<= nlstate; i++){
         /*printf(" %lf ",hess[i][j]);*/      for(j=1; j<i;j++){
       }        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     }          /*s2 += param[i][j][nc]*cov[nc];*/
   }          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   printf("\n");          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
         }
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        ps[i][j]=s2;
          /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
   a=matrix(1,npar,1,npar);      }
   y=matrix(1,npar,1,npar);      for(j=i+1; j<=nlstate+ndeath;j++){
   x=vector(1,npar);        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   indx=ivector(1,npar);          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   for (i=1;i<=npar;i++)          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        }
   ludcmp(a,npar,indx,&pd);        ps[i][j]=s2;
       }
   for (j=1;j<=npar;j++) {    }
     for (i=1;i<=npar;i++) x[i]=0;      /*ps[3][2]=1;*/
     x[j]=1;  
     lubksb(a,npar,indx,x);    for(i=1; i<= nlstate; i++){
     for (i=1;i<=npar;i++){       s1=0;
       matcov[i][j]=x[i];      for(j=1; j<i; j++)
     }        s1+=exp(ps[i][j]);
   }      for(j=i+1; j<=nlstate+ndeath; j++)
         s1+=exp(ps[i][j]);
   printf("\n#Hessian matrix#\n");      ps[i][i]=1./(s1+1.);
   for (i=1;i<=npar;i++) {      for(j=1; j<i; j++)
     for (j=1;j<=npar;j++) {        ps[i][j]= exp(ps[i][j])*ps[i][i];
       printf("%.3e ",hess[i][j]);      for(j=i+1; j<=nlstate+ndeath; j++)
     }        ps[i][j]= exp(ps[i][j])*ps[i][i];
     printf("\n");      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   }    } /* end i */
   
   /* Recompute Inverse */    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
   for (i=1;i<=npar;i++)      for(jj=1; jj<= nlstate+ndeath; jj++){
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        ps[ii][jj]=0;
   ludcmp(a,npar,indx,&pd);        ps[ii][ii]=1;
       }
   /*  printf("\n#Hessian matrix recomputed#\n");    }
   
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
     x[j]=1;      for(jj=1; jj<= nlstate+ndeath; jj++){
     lubksb(a,npar,indx,x);       printf("%lf ",ps[ii][jj]);
     for (i=1;i<=npar;i++){     }
       y[i][j]=x[i];      printf("\n ");
       printf("%.3e ",y[i][j]);      }
     }      printf("\n ");printf("%lf ",cov[2]);*/
     printf("\n");  /*
   }    for(i=1; i<= npar; i++) printf("%f ",x[i]);
   */    goto end;*/
       return ps;
   free_matrix(a,1,npar,1,npar);  }
   free_matrix(y,1,npar,1,npar);  
   free_vector(x,1,npar);  /**************** Product of 2 matrices ******************/
   free_ivector(indx,1,npar);  
   free_matrix(hess,1,npar,1,npar);  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   {
     /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
 }       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     /* in, b, out are matrice of pointers which should have been initialized 
 /*************** hessian matrix ****************/       before: only the contents of out is modified. The function returns
 double hessii( double x[], double delta, int theta, double delti[])       a pointer to pointers identical to out */
 {    long i, j, k;
   int i;    for(i=nrl; i<= nrh; i++)
   int l=1, lmax=20;      for(k=ncolol; k<=ncoloh; k++)
   double k1,k2;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
   double p2[NPARMAX+1];          out[i][k] +=in[i][j]*b[j][k];
   double res;  
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    return out;
   double fx;  }
   int k=0,kmax=10;  
   double l1;  
   /************* Higher Matrix Product ***************/
   fx=func(x);  
   for (i=1;i<=npar;i++) p2[i]=x[i];  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   for(l=0 ; l <=lmax; l++){  {
     l1=pow(10,l);    /* Computes the transition matrix starting at age 'age' over 
     delts=delt;       'nhstepm*hstepm*stepm' months (i.e. until
     for(k=1 ; k <kmax; k=k+1){       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
       delt = delta*(l1*k);       nhstepm*hstepm matrices. 
       p2[theta]=x[theta] +delt;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
       k1=func(p2)-fx;       (typically every 2 years instead of every month which is too big 
       p2[theta]=x[theta]-delt;       for the memory).
       k2=func(p2)-fx;       Model is determined by parameters x and covariates have to be 
       /*res= (k1-2.0*fx+k2)/delt/delt; */       included manually here. 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */  
             */
 #ifdef DEBUG  
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);    int i, j, d, h, k;
 #endif    double **out, cov[NCOVMAX];
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    double **newm;
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  
         k=kmax;    /* Hstepm could be zero and should return the unit matrix */
       }    for (i=1;i<=nlstate+ndeath;i++)
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */      for (j=1;j<=nlstate+ndeath;j++){
         k=kmax; l=lmax*10.;        oldm[i][j]=(i==j ? 1.0 : 0.0);
       }        po[i][j][0]=(i==j ? 1.0 : 0.0);
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      }
         delts=delt;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       }    for(h=1; h <=nhstepm; h++){
     }      for(d=1; d <=hstepm; d++){
   }        newm=savm;
   delti[theta]=delts;        /* Covariates have to be included here again */
   return res;        cov[1]=1.;
          cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
 }        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         for (k=1; k<=cptcovage;k++)
 double hessij( double x[], double delti[], int thetai,int thetaj)          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
 {        for (k=1; k<=cptcovprod;k++)
   int i;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   int l=1, l1, lmax=20;  
   double k1,k2,k3,k4,res,fx;  
   double p2[NPARMAX+1];        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   int k;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
   fx=func(x);                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   for (k=1; k<=2; k++) {        savm=oldm;
     for (i=1;i<=npar;i++) p2[i]=x[i];        oldm=newm;
     p2[thetai]=x[thetai]+delti[thetai]/k;      }
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      for(i=1; i<=nlstate+ndeath; i++)
     k1=func(p2)-fx;        for(j=1;j<=nlstate+ndeath;j++) {
            po[i][j][h]=newm[i][j];
     p2[thetai]=x[thetai]+delti[thetai]/k;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;           */
     k2=func(p2)-fx;        }
      } /* end h */
     p2[thetai]=x[thetai]-delti[thetai]/k;    return po;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  }
     k3=func(p2)-fx;  
    
     p2[thetai]=x[thetai]-delti[thetai]/k;  /*************** log-likelihood *************/
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  double func( double *x)
     k4=func(p2)-fx;  {
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    int i, ii, j, k, mi, d, kk;
 #ifdef DEBUG    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     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);    double **out;
 #endif    double sw; /* Sum of weights */
   }    double lli; /* Individual log likelihood */
   return res;    int s1, s2;
 }    double bbh, survp;
     long ipmx;
 /************** Inverse of matrix **************/    /*extern weight */
 void ludcmp(double **a, int n, int *indx, double *d)    /* We are differentiating ll according to initial status */
 {    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   int i,imax,j,k;    /*for(i=1;i<imx;i++) 
   double big,dum,sum,temp;      printf(" %d\n",s[4][i]);
   double *vv;    */
      cov[1]=1.;
   vv=vector(1,n);  
   *d=1.0;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   for (i=1;i<=n;i++) {  
     big=0.0;    if(mle==1){
     for (j=1;j<=n;j++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       if ((temp=fabs(a[i][j])) > big) big=temp;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        for(mi=1; mi<= wav[i]-1; mi++){
     vv[i]=1.0/big;          for (ii=1;ii<=nlstate+ndeath;ii++)
   }            for (j=1;j<=nlstate+ndeath;j++){
   for (j=1;j<=n;j++) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for (i=1;i<j;i++) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       sum=a[i][j];            }
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];          for(d=0; d<dh[mi][i]; d++){
       a[i][j]=sum;            newm=savm;
     }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     big=0.0;            for (kk=1; kk<=cptcovage;kk++) {
     for (i=j;i<=n;i++) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       sum=a[i][j];            }
       for (k=1;k<j;k++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         sum -= a[i][k]*a[k][j];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       a[i][j]=sum;            savm=oldm;
       if ( (dum=vv[i]*fabs(sum)) >= big) {            oldm=newm;
         big=dum;          } /* end mult */
         imax=i;        
       }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     }          /* But now since version 0.9 we anticipate for bias and large stepm.
     if (j != imax) {           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       for (k=1;k<=n;k++) {           * (in months) between two waves is not a multiple of stepm, we rounded to 
         dum=a[imax][k];           * the nearest (and in case of equal distance, to the lowest) interval but now
         a[imax][k]=a[j][k];           * we keep into memory the bias bh[mi][i] and also the previous matrix product
         a[j][k]=dum;           * (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
       *d = -(*d);           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
       vv[imax]=vv[j];           * -stepm/2 to stepm/2 .
     }           * For stepm=1 the results are the same as for previous versions of Imach.
     indx[j]=imax;           * For stepm > 1 the results are less biased than in previous versions. 
     if (a[j][j] == 0.0) a[j][j]=TINY;           */
     if (j != n) {          s1=s[mw[mi][i]][i];
       dum=1.0/(a[j][j]);          s2=s[mw[mi+1][i]][i];
       for (i=j+1;i<=n;i++) a[i][j] *= dum;          bbh=(double)bh[mi][i]/(double)stepm; 
     }          /* bias is positive if real duration
   }           * is higher than the multiple of stepm and negative otherwise.
   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]));*/
 }          if( s2 > nlstate){ 
             /* i.e. if s2 is a death state and if the date of death is known then the contribution
 void lubksb(double **a, int n, int *indx, double b[])               to the likelihood is the probability to die between last step unit time and current 
 {               step unit time, which is also the differences between probability to die before dh 
   int i,ii=0,ip,j;               and probability to die before dh-stepm . 
   double sum;               In version up to 0.92 likelihood was computed
            as if date of death was unknown. Death was treated as any other
   for (i=1;i<=n;i++) {          health state: the date of the interview describes the actual state
     ip=indx[i];          and not the date of a change in health state. The former idea was
     sum=b[ip];          to consider that at each interview the state was recorded
     b[ip]=b[i];          (healthy, disable or death) and IMaCh was corrected; but when we
     if (ii)          introduced the exact date of death then we should have modified
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          the contribution of an exact death to the likelihood. This new
     else if (sum) ii=i;          contribution is smaller and very dependent of the step unit
     b[i]=sum;          stepm. It is no more the probability to die between last interview
   }          and month of death but the probability to survive from last
   for (i=n;i>=1;i--) {          interview up to one month before death multiplied by the
     sum=b[i];          probability to die within a month. Thanks to Chris
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          Jackson for correcting this bug.  Former versions increased
     b[i]=sum/a[i][i];          mortality artificially. The bad side is that we add another loop
   }          which slows down the processing. The difference can be up to 10%
 }          lower mortality.
             */
 /************ Frequencies ********************/            lli=log(out[s1][s2] - savm[s1][s2]);
 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)          }else{
 {  /* Some frequencies */            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 */
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          } 
   double ***freq; /* Frequencies */          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   double *pp;          /*if(lli ==000.0)*/
   double pos, k2, dateintsum=0,k2cpt=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); */
   FILE *ficresp;          ipmx +=1;
   char fileresp[FILENAMELENGTH];          sw += weight[i];
            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   pp=vector(1,nlstate);        } /* end of wave */
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);      } /* end of individual */
   strcpy(fileresp,"p");    }  else if(mle==2){
   strcat(fileresp,fileres);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   if((ficresp=fopen(fileresp,"w"))==NULL) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     printf("Problem with prevalence resultfile: %s\n", fileresp);        for(mi=1; mi<= wav[i]-1; mi++){
     exit(0);          for (ii=1;ii<=nlstate+ndeath;ii++)
   }            for (j=1;j<=nlstate+ndeath;j++){
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   j1=0;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
   j=cptcoveff;          for(d=0; d<=dh[mi][i]; d++){
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   for(k1=1; k1<=j;k1++){            for (kk=1; kk<=cptcovage;kk++) {
    for(i1=1; i1<=ncodemax[k1];i1++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
        j1++;            }
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
          scanf("%d", i);*/                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         for (i=-1; i<=nlstate+ndeath; i++)              savm=oldm;
          for (jk=-1; jk<=nlstate+ndeath; jk++)              oldm=newm;
            for(m=agemin; m <= agemax+3; m++)          } /* end mult */
              freq[i][jk][m]=0;        
           /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         dateintsum=0;          /* But now since version 0.9 we anticipate for bias and large stepm.
         k2cpt=0;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
        for (i=1; i<=imx; i++) {           * (in months) between two waves is not a multiple of stepm, we rounded to 
          bool=1;           * the nearest (and in case of equal distance, to the lowest) interval but now
          if  (cptcovn>0) {           * we keep into memory the bias bh[mi][i] and also the previous matrix product
            for (z1=1; z1<=cptcoveff; z1++)           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])           * probability in order to take into account the bias as a fraction of the way
                bool=0;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
          }           * -stepm/2 to stepm/2 .
          if (bool==1) {           * For stepm=1 the results are the same as for previous versions of Imach.
            for(m=firstpass; m<=lastpass; m++){           * For stepm > 1 the results are less biased than in previous versions. 
              k2=anint[m][i]+(mint[m][i]/12.);           */
              if ((k2>=dateprev1) && (k2<=dateprev2)) {          s1=s[mw[mi][i]][i];
                if(agev[m][i]==0) agev[m][i]=agemax+1;          s2=s[mw[mi+1][i]][i];
                if(agev[m][i]==1) agev[m][i]=agemax+2;          bbh=(double)bh[mi][i]/(double)stepm; 
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          /* bias is positive if real duration
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];           * is higher than the multiple of stepm and negative otherwise.
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {           */
                  dateintsum=dateintsum+k2;          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 */
                  k2cpt++;          /* 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)*/
            }          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
          }          ipmx +=1;
        }          sw += weight[i];
                  ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
        fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        } /* end of wave */
       } /* end of individual */
         if  (cptcovn>0) {    }  else if(mle==3){  /* exponential inter-extrapolation */
          fprintf(ficresp, "\n#********** Variable ");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
        fprintf(ficresp, "**********\n#");        for(mi=1; mi<= wav[i]-1; mi++){
         }          for (ii=1;ii<=nlstate+ndeath;ii++)
        for(i=1; i<=nlstate;i++)            for (j=1;j<=nlstate+ndeath;j++){
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
        fprintf(ficresp, "\n");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                    }
   for(i=(int)agemin; i <= (int)agemax+3; i++){          for(d=0; d<dh[mi][i]; d++){
     if(i==(int)agemax+3)            newm=savm;
       printf("Total");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     else            for (kk=1; kk<=cptcovage;kk++) {
       printf("Age %d", i);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for(jk=1; jk <=nlstate ; jk++){            }
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         pp[jk] += freq[jk][m][i];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     }            savm=oldm;
     for(jk=1; jk <=nlstate ; jk++){            oldm=newm;
       for(m=-1, pos=0; m <=0 ; m++)          } /* end mult */
         pos += freq[jk][m][i];        
       if(pp[jk]>=1.e-10)          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          /* But now since version 0.9 we anticipate for bias and large stepm.
       else           * If stepm is larger than one month (smallest stepm) and if the exact delay 
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);           * (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
            * we keep into memory the bias bh[mi][i] and also the previous matrix product
      for(jk=1; jk <=nlstate ; jk++){           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)           * probability in order to take into account the bias as a fraction of the way
         pp[jk] += freq[jk][m][i];           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
      }           * -stepm/2 to stepm/2 .
            * For stepm=1 the results are the same as for previous versions of Imach.
     for(jk=1,pos=0; jk <=nlstate ; jk++)           * For stepm > 1 the results are less biased than in previous versions. 
       pos += pp[jk];           */
     for(jk=1; jk <=nlstate ; jk++){          s1=s[mw[mi][i]][i];
       if(pos>=1.e-5)          s2=s[mw[mi+1][i]][i];
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          bbh=(double)bh[mi][i]/(double)stepm; 
       else          /* bias is positive if real duration
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);           * is higher than the multiple of stepm and negative otherwise.
       if( i <= (int) agemax){           */
         if(pos>=1.e-5){          /* 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 */
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          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 */
           probs[i][jk][j1]= pp[jk]/pos;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/          /*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); */
       else          ipmx +=1;
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          sw += weight[i];
       }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }        } /* end of wave */
     for(jk=-1; jk <=nlstate+ndeath; jk++)      } /* end of individual */
       for(m=-1; m <=nlstate+ndeath; m++)    }else if (mle==4){  /* ml=4 no inter-extrapolation */
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     if(i <= (int) agemax)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       fprintf(ficresp,"\n");        for(mi=1; mi<= wav[i]-1; mi++){
     printf("\n");          for (ii=1;ii<=nlstate+ndeath;ii++)
     }            for (j=1;j<=nlstate+ndeath;j++){
     }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
  }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   dateintmean=dateintsum/k2cpt;            }
            for(d=0; d<dh[mi][i]; d++){
   fclose(ficresp);            newm=savm;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   free_vector(pp,1,nlstate);            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   /* End of Freq */            }
 }          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 /************ Prevalence ********************/                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 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=oldm;
 {  /* Some frequencies */            oldm=newm;
            } /* end mult */
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;        
   double ***freq; /* Frequencies */          s1=s[mw[mi][i]][i];
   double *pp;          s2=s[mw[mi+1][i]][i];
   double pos, k2;          if( s2 > nlstate){ 
             lli=log(out[s1][s2] - savm[s1][s2]);
   pp=vector(1,nlstate);          }else{
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
            }
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          ipmx +=1;
   j1=0;          sw += weight[i];
            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   j=cptcoveff;  /*      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 (cptcovn<1) {j=1;ncodemax[1]=1;}        } /* end of wave */
        } /* end of individual */
  for(k1=1; k1<=j;k1++){    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
     for(i1=1; i1<=ncodemax[k1];i1++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       j1++;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          for(mi=1; mi<= wav[i]-1; mi++){
       for (i=-1; i<=nlstate+ndeath; i++)            for (ii=1;ii<=nlstate+ndeath;ii++)
         for (jk=-1; jk<=nlstate+ndeath; jk++)              for (j=1;j<=nlstate+ndeath;j++){
           for(m=agemin; m <= agemax+3; m++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             freq[i][jk][m]=0;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                  }
       for (i=1; i<=imx; i++) {          for(d=0; d<dh[mi][i]; d++){
         bool=1;            newm=savm;
         if  (cptcovn>0) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for (z1=1; z1<=cptcoveff; z1++)            for (kk=1; kk<=cptcovage;kk++) {
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
               bool=0;            }
         }          
         if (bool==1) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           for(m=firstpass; m<=lastpass; m++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             k2=anint[m][i]+(mint[m][i]/12.);            savm=oldm;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {            oldm=newm;
               if(agev[m][i]==0) agev[m][i]=agemax+1;          } /* end mult */
               if(agev[m][i]==1) agev[m][i]=agemax+2;        
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          s1=s[mw[mi][i]][i];
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */          s2=s[mw[mi+1][i]][i];
             }          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           }          ipmx +=1;
         }          sw += weight[i];
       }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         for(i=(int)agemin; i <= (int)agemax+3; i++){          /*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(jk=1; jk <=nlstate ; jk++){        } /* end of wave */
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      } /* end of individual */
               pp[jk] += freq[jk][m][i];    } /* End of if */
           }    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, pos=0; m <=0 ; m++)    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
             pos += freq[jk][m][i];    return -l;
         }  }
          
          for(jk=1; jk <=nlstate ; jk++){  /*************** log-likelihood *************/
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  double funcone( double *x)
              pp[jk] += freq[jk][m][i];  {
          }    /* Same as likeli but slower because of a lot of printf and if */
              int i, ii, j, k, mi, d, kk;
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     double **out;
          for(jk=1; jk <=nlstate ; jk++){              double lli; /* Individual log likelihood */
            if( i <= (int) agemax){    double llt;
              if(pos>=1.e-5){    int s1, s2;
                probs[i][jk][j1]= pp[jk]/pos;    double bbh, survp;
              }    /*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]);
     }    */
   }    cov[1]=1.;
    
      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++)
 /************* Waves Concatenation ***************/          for (j=1;j<=nlstate+ndeath;j++){
             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)            savm[ii][j]=(ii==j ? 1.0 : 0.0);
 {          }
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.        for(d=0; d<dh[mi][i]; d++){
      Death is a valid wave (if date is known).          newm=savm;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          for (kk=1; kk<=cptcovage;kk++) {
      and mw[mi+1][i]. dh depends on stepm.            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
      */          }
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int i, mi, m;                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;          savm=oldm;
      double sum=0., jmean=0.;*/          oldm=newm;
         } /* end mult */
   int j, k=0,jk, ju, jl;        
   double sum=0.;        s1=s[mw[mi][i]][i];
   jmin=1e+5;        s2=s[mw[mi+1][i]][i];
   jmax=-1;        bbh=(double)bh[mi][i]/(double)stepm; 
   jmean=0.;        /* bias is positive if real duration
   for(i=1; i<=imx; i++){         * is higher than the multiple of stepm and negative otherwise.
     mi=0;         */
     m=firstpass;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
     while(s[m][i] <= nlstate){          lli=log(out[s1][s2] - savm[s1][s2]);
       if(s[m][i]>=1)        } else if (mle==1){
         mw[++mi][i]=m;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       if(m >=lastpass)        } else if(mle==2){
         break;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
       else        } else if(mle==3){  /* exponential inter-extrapolation */
         m++;          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
     }/* end while */        } else if (mle==4){  /* mle=4 no inter-extrapolation */
     if (s[m][i] > nlstate){          lli=log(out[s1][s2]); /* Original formula */
       mi++;     /* Death is another wave */        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
       /* if(mi==0)  never been interviewed correctly before death */          lli=log(out[s1][s2]); /* Original formula */
          /* Only death is a correct wave */        } /* End of if */
       mw[mi][i]=m;        ipmx +=1;
     }        sw += weight[i];
         ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     wav[i]=mi;  /*       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(mi==0)        if(globpr){
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
   }   %10.6f %10.6f %10.6f ", \
                   num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   for(i=1; i<=imx; i++){                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
     for(mi=1; mi<wav[i];mi++){          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
       if (stepm <=0)            llt +=ll[k]*gipmx/gsw;
         dh[mi][i]=1;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
       else{          }
         if (s[mw[mi+1][i]][i] > nlstate) {          fprintf(ficresilk," %10.6f\n", -llt);
           if (agedc[i] < 2*AGESUP) {        }
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);      } /* end of wave */
           if(j==0) j=1;  /* Survives at least one month after exam */    } /* end of individual */
           k=k+1;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
           if (j >= jmax) jmax=j;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
           if (j <= jmin) jmin=j;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
           sum=sum+j;    if(globpr==0){ /* First time we count the contributions and weights */
           /*if (j<0) printf("j=%d num=%d \n",j,i); */      gipmx=ipmx;
           }      gsw=sw;
         }    }
         else{    return -l;
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));  }
           k=k+1;  
           if (j >= jmax) jmax=j;  char *subdirf(char fileres[])
           else if (j <= jmin)jmin=j;  {
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    /* Caution optionfilefiname is hidden */
           sum=sum+j;    strcpy(tmpout,optionfilefiname);
         }    strcat(tmpout,"/"); /* Add to the right */
         jk= j/stepm;    strcat(tmpout,fileres);
         jl= j -jk*stepm;    return tmpout;
         ju= j -(jk+1)*stepm;  }
         if(jl <= -ju)  
           dh[mi][i]=jk;  char *subdirf2(char fileres[], char *preop)
         else  {
           dh[mi][i]=jk+1;    
         if(dh[mi][i]==0)    strcpy(tmpout,optionfilefiname);
           dh[mi][i]=1; /* At least one step */    strcat(tmpout,"/");
       }    strcat(tmpout,preop);
     }    strcat(tmpout,fileres);
   }    return tmpout;
   jmean=sum/k;  }
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);  char *subdirf3(char fileres[], char *preop, char *preop2)
  }  {
 /*********** Tricode ****************************/    
 void tricode(int *Tvar, int **nbcode, int imx)    strcpy(tmpout,optionfilefiname);
 {    strcat(tmpout,"/");
   int Ndum[20],ij=1, k, j, i;    strcat(tmpout,preop);
   int cptcode=0;    strcat(tmpout,preop2);
   cptcoveff=0;    strcat(tmpout,fileres);
      return tmpout;
   for (k=0; k<19; k++) Ndum[k]=0;  }
   for (k=1; k<=7; k++) ncodemax[k]=0;  
   void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  {
     for (i=1; i<=imx; i++) {    /* This routine should help understanding what is done with 
       ij=(int)(covar[Tvar[j]][i]);       the selection of individuals/waves and
       Ndum[ij]++;       to check the exact contribution to the likelihood.
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/       Plotting could be done.
       if (ij > cptcode) cptcode=ij;     */
     }    int k;
   
     for (i=0; i<=cptcode; i++) {    if(*globpri !=0){ /* Just counts and sums, no printings */
       if(Ndum[i]!=0) ncodemax[j]++;      strcpy(fileresilk,"ilk"); 
     }      strcat(fileresilk,fileres);
     ij=1;      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", fileresilk);
         fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     for (i=1; i<=ncodemax[j]; i++) {      }
       for (k=0; k<=19; k++) {      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");
         if (Ndum[k] != 0) {      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
           nbcode[Tvar[j]][ij]=k;      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
           ij++;      for(k=1; k<=nlstate; k++) 
         }        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
         if (ij > ncodemax[j]) break;      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
       }      }
     }  
   }      *fretone=(*funcone)(p);
     if(*globpri !=0){
  for (k=0; k<19; k++) Ndum[k]=0;      fclose(ficresilk);
       fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
  for (i=1; i<=ncovmodel-2; i++) {      fflush(fichtm); 
       ij=Tvar[i];    } 
       Ndum[ij]++;    return;
     }  }
   
  ij=1;  
  for (i=1; i<=10; i++) {  /*********** Maximum Likelihood Estimation ***************/
    if((Ndum[i]!=0) && (i<=ncov)){  
      Tvaraff[ij]=i;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
      ij++;  {
    }    int i,j, iter;
  }    double **xi;
      double fret;
     cptcoveff=ij-1;    double fretone; /* Only one call to likelihood */
 }    char filerespow[FILENAMELENGTH];
     xi=matrix(1,npar,1,npar);
 /*********** Health Expectancies ****************/    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++)
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)        xi[i][j]=(i==j ? 1.0 : 0.0);
 {    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   /* Health expectancies */    strcpy(filerespow,"pow"); 
   int i, j, nhstepm, hstepm, h, nstepm, k;    strcat(filerespow,fileres);
   double age, agelim,hf;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   double ***p3mat;      printf("Problem with resultfile: %s\n", filerespow);
        fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   fprintf(ficreseij,"# Health expectancies\n");    }
   fprintf(ficreseij,"# Age");    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   for(i=1; i<=nlstate;i++)    for (i=1;i<=nlstate;i++)
     for(j=1; j<=nlstate;j++)      for(j=1;j<=nlstate+ndeath;j++)
       fprintf(ficreseij," %1d-%1d",i,j);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   fprintf(ficreseij,"\n");    fprintf(ficrespow,"\n");
   
   k=1;             /* For example stepm=6 months */    powell(p,xi,npar,ftol,&iter,&fret,func);
   hstepm=k*YEARM; /* (a) Every k years of age (in months), for example every k=2 years 24 m */  
   hstepm=stepm;   /* or (b) We decided to compute the life expectancy with the smallest unit */    fclose(ficrespow);
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
      nhstepm is the number of hstepm from age to agelim    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
      nstepm is the number of stepm from age to agelin.    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
      Look at hpijx to understand the reason of that which relies in memory size  
      and note for a fixed period like k years */  }
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the  
      survival function given by stepm (the optimization length). Unfortunately it  /**** Computes Hessian and covariance matrix ***/
      means that if the survival funtion is printed only each two years of age and if  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
      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.    double  **a,**y,*x,pd;
   */    double **hess;
   hstepm=hstepm/stepm; /* Typically in stepm units, if k= 2 years, = 2/6 months = 4 */    int i, j,jk;
     int *indx;
   agelim=AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    double hessii(double p[], double delta, int theta, double delti[]);
     /* nhstepm age range expressed in number of stepm */    double hessij(double p[], double delti[], int i, int j);
     nstepm=(int) rint((agelim-age)*YEARM/stepm);    void lubksb(double **a, int npar, int *indx, double b[]) ;
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    void ludcmp(double **a, int npar, int *indx, double *d) ;
     /* if (stepm >= YEARM) hstepm=1;*/  
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    hess=matrix(1,npar,1,npar);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    printf("\nCalculation of the hessian matrix. Wait...\n");
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      for (i=1;i<=npar;i++){
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      printf("%d",i);fflush(stdout);
     for(i=1; i<=nlstate;i++)      fprintf(ficlog,"%d",i);fflush(ficlog);
       for(j=1; j<=nlstate;j++)      hess[i][i]=hessii(p,ftolhess,i,delti);
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){      /*printf(" %f ",p[i]);*/
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;      /*printf(" %lf ",hess[i][i]);*/
           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/    }
         }    
     fprintf(ficreseij,"%3.0f",age );    for (i=1;i<=npar;i++) {
     for(i=1; i<=nlstate;i++)      for (j=1;j<=npar;j++)  {
       for(j=1; j<=nlstate;j++){        if (j>i) { 
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);          printf(".%d%d",i,j);fflush(stdout);
       }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     fprintf(ficreseij,"\n");          hess[i][j]=hessij(p,delti,i,j);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          hess[j][i]=hess[i][j];    
   }          /*printf(" %lf ",hess[i][j]);*/
 }        }
       }
 /************ 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)    printf("\n");
 {    fprintf(ficlog,"\n");
   /* Variance of health expectancies */  
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   double **newm;    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   double **dnewm,**doldm;    
   int i, j, nhstepm, hstepm, h;    a=matrix(1,npar,1,npar);
   int k, cptcode;    y=matrix(1,npar,1,npar);
   double *xp;    x=vector(1,npar);
   double **gp, **gm;    indx=ivector(1,npar);
   double ***gradg, ***trgradg;    for (i=1;i<=npar;i++)
   double ***p3mat;      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   double age,agelim;    ludcmp(a,npar,indx,&pd);
   int theta;  
     for (j=1;j<=npar;j++) {
    fprintf(ficresvij,"# Covariances of life expectancies\n");      for (i=1;i<=npar;i++) x[i]=0;
   fprintf(ficresvij,"# Age");      x[j]=1;
   for(i=1; i<=nlstate;i++)      lubksb(a,npar,indx,x);
     for(j=1; j<=nlstate;j++)      for (i=1;i<=npar;i++){ 
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        matcov[i][j]=x[i];
   fprintf(ficresvij,"\n");      }
     }
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);    printf("\n#Hessian matrix#\n");
   doldm=matrix(1,nlstate,1,nlstate);    fprintf(ficlog,"\n#Hessian matrix#\n");
      for (i=1;i<=npar;i++) { 
   hstepm=1*YEARM; /* Every year of age */      for (j=1;j<=npar;j++) { 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        printf("%.3e ",hess[i][j]);
   agelim = AGESUP;        fprintf(ficlog,"%.3e ",hess[i][j]);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      printf("\n");
     if (stepm >= YEARM) hstepm=1;      fprintf(ficlog,"\n");
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    /* Recompute Inverse */
     gp=matrix(0,nhstepm,1,nlstate);    for (i=1;i<=npar;i++)
     gm=matrix(0,nhstepm,1,nlstate);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     ludcmp(a,npar,indx,&pd);
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient */    /*  printf("\n#Hessian matrix recomputed#\n");
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
       }    for (j=1;j<=npar;j++) {
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        for (i=1;i<=npar;i++) x[i]=0;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      x[j]=1;
       lubksb(a,npar,indx,x);
       if (popbased==1) {      for (i=1;i<=npar;i++){ 
         for(i=1; i<=nlstate;i++)        y[i][j]=x[i];
           prlim[i][i]=probs[(int)age][i][ij];        printf("%.3e ",y[i][j]);
       }        fprintf(ficlog,"%.3e ",y[i][j]);
        }
       for(j=1; j<= nlstate; j++){      printf("\n");
         for(h=0; h<=nhstepm; h++){      fprintf(ficlog,"\n");
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    }
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    */
         }  
       }    free_matrix(a,1,npar,1,npar);
        free_matrix(y,1,npar,1,npar);
       for(i=1; i<=npar; i++) /* Computes gradient */    free_vector(x,1,npar);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    free_ivector(indx,1,npar);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      free_matrix(hess,1,npar,1,npar);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
    
       if (popbased==1) {  }
         for(i=1; i<=nlstate;i++)  
           prlim[i][i]=probs[(int)age][i][ij];  /*************** hessian matrix ****************/
       }  double hessii( double x[], double delta, int theta, double delti[])
   {
       for(j=1; j<= nlstate; j++){    int i;
         for(h=0; h<=nhstepm; h++){    int l=1, lmax=20;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    double k1,k2;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    double p2[NPARMAX+1];
         }    double res;
       }    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     double fx;
       for(j=1; j<= nlstate; j++)    int k=0,kmax=10;
         for(h=0; h<=nhstepm; h++){    double l1;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  
         }    fx=func(x);
     } /* End theta */    for (i=1;i<=npar;i++) p2[i]=x[i];
     for(l=0 ; l <=lmax; l++){
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);      l1=pow(10,l);
       delts=delt;
     for(h=0; h<=nhstepm; h++)      for(k=1 ; k <kmax; k=k+1){
       for(j=1; j<=nlstate;j++)        delt = delta*(l1*k);
         for(theta=1; theta <=npar; theta++)        p2[theta]=x[theta] +delt;
           trgradg[h][j][theta]=gradg[h][theta][j];        k1=func(p2)-fx;
         p2[theta]=x[theta]-delt;
     for(i=1;i<=nlstate;i++)        k2=func(p2)-fx;
       for(j=1;j<=nlstate;j++)        /*res= (k1-2.0*fx+k2)/delt/delt; */
         vareij[i][j][(int)age] =0.;        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     for(h=0;h<=nhstepm;h++){        
       for(k=0;k<=nhstepm;k++){  #ifdef DEBUG
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);        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);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         for(i=1;i<=nlstate;i++)  #endif
           for(j=1;j<=nlstate;j++)        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
             vareij[i][j][(int)age] += doldm[i][j];        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
       }          k=kmax;
     }        }
     h=1;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     if (stepm >= YEARM) h=stepm/YEARM;          k=kmax; l=lmax*10.;
     fprintf(ficresvij,"%.0f ",age );        }
     for(i=1; i<=nlstate;i++)        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       for(j=1; j<=nlstate;j++){          delts=delt;
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);        }
       }      }
     fprintf(ficresvij,"\n");    }
     free_matrix(gp,0,nhstepm,1,nlstate);    delti[theta]=delts;
     free_matrix(gm,0,nhstepm,1,nlstate);    return res; 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);  }
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   } /* End age */  double hessij( double x[], double delti[], int thetai,int thetaj)
    {
   free_vector(xp,1,npar);    int i;
   free_matrix(doldm,1,nlstate,1,npar);    int l=1, l1, lmax=20;
   free_matrix(dnewm,1,nlstate,1,nlstate);    double k1,k2,k3,k4,res,fx;
     double p2[NPARMAX+1];
 }    int k;
   
 /************ Variance of prevlim ******************/    fx=func(x);
 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 (k=1; k<=2; k++) {
 {      for (i=1;i<=npar;i++) p2[i]=x[i];
   /* Variance of prevalence limit */      p2[thetai]=x[thetai]+delti[thetai]/k;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   double **newm;      k1=func(p2)-fx;
   double **dnewm,**doldm;    
   int i, j, nhstepm, hstepm;      p2[thetai]=x[thetai]+delti[thetai]/k;
   int k, cptcode;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   double *xp;      k2=func(p2)-fx;
   double *gp, *gm;    
   double **gradg, **trgradg;      p2[thetai]=x[thetai]-delti[thetai]/k;
   double age,agelim;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   int theta;      k3=func(p2)-fx;
        
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");      p2[thetai]=x[thetai]-delti[thetai]/k;
   fprintf(ficresvpl,"# Age");      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   for(i=1; i<=nlstate;i++)      k4=func(p2)-fx;
       fprintf(ficresvpl," %1d-%1d",i,i);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   fprintf(ficresvpl,"\n");  #ifdef DEBUG
       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   xp=vector(1,npar);      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   dnewm=matrix(1,nlstate,1,npar);  #endif
   doldm=matrix(1,nlstate,1,nlstate);    }
      return res;
   hstepm=1*YEARM; /* Every year of age */  }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */  
   agelim = AGESUP;  /************** Inverse of matrix **************/
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  void ludcmp(double **a, int n, int *indx, double *d) 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  { 
     if (stepm >= YEARM) hstepm=1;    int i,imax,j,k; 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    double big,dum,sum,temp; 
     gradg=matrix(1,npar,1,nlstate);    double *vv; 
     gp=vector(1,nlstate);   
     gm=vector(1,nlstate);    vv=vector(1,n); 
     *d=1.0; 
     for(theta=1; theta <=npar; theta++){    for (i=1;i<=n;i++) { 
       for(i=1; i<=npar; i++){ /* Computes gradient */      big=0.0; 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      for (j=1;j<=n;j++) 
       }        if ((temp=fabs(a[i][j])) > big) big=temp; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       for(i=1;i<=nlstate;i++)      vv[i]=1.0/big; 
         gp[i] = prlim[i][i];    } 
        for (j=1;j<=n;j++) { 
       for(i=1; i<=npar; i++) /* Computes gradient */      for (i=1;i<j;i++) { 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        sum=a[i][j]; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
       for(i=1;i<=nlstate;i++)        a[i][j]=sum; 
         gm[i] = prlim[i][i];      } 
       big=0.0; 
       for(i=1;i<=nlstate;i++)      for (i=j;i<=n;i++) { 
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        sum=a[i][j]; 
     } /* End theta */        for (k=1;k<j;k++) 
           sum -= a[i][k]*a[k][j]; 
     trgradg =matrix(1,nlstate,1,npar);        a[i][j]=sum; 
         if ( (dum=vv[i]*fabs(sum)) >= big) { 
     for(j=1; j<=nlstate;j++)          big=dum; 
       for(theta=1; theta <=npar; theta++)          imax=i; 
         trgradg[j][theta]=gradg[theta][j];        } 
       } 
     for(i=1;i<=nlstate;i++)      if (j != imax) { 
       varpl[i][(int)age] =0.;        for (k=1;k<=n;k++) { 
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          dum=a[imax][k]; 
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          a[imax][k]=a[j][k]; 
     for(i=1;i<=nlstate;i++)          a[j][k]=dum; 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */        } 
         *d = -(*d); 
     fprintf(ficresvpl,"%.0f ",age );        vv[imax]=vv[j]; 
     for(i=1; i<=nlstate;i++)      } 
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));      indx[j]=imax; 
     fprintf(ficresvpl,"\n");      if (a[j][j] == 0.0) a[j][j]=TINY; 
     free_vector(gp,1,nlstate);      if (j != n) { 
     free_vector(gm,1,nlstate);        dum=1.0/(a[j][j]); 
     free_matrix(gradg,1,npar,1,nlstate);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     free_matrix(trgradg,1,nlstate,1,npar);      } 
   } /* End age */    } 
     free_vector(vv,1,n);  /* Doesn't work */
   free_vector(xp,1,npar);  ;
   free_matrix(doldm,1,nlstate,1,npar);  } 
   free_matrix(dnewm,1,nlstate,1,nlstate);  
   void lubksb(double **a, int n, int *indx, double b[]) 
 }  { 
     int i,ii=0,ip,j; 
 /************ Variance of one-step probabilities  ******************/    double sum; 
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)   
 {    for (i=1;i<=n;i++) { 
   int i, j;      ip=indx[i]; 
   int k=0, cptcode;      sum=b[ip]; 
   double **dnewm,**doldm;      b[ip]=b[i]; 
   double *xp;      if (ii) 
   double *gp, *gm;        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   double **gradg, **trgradg;      else if (sum) ii=i; 
   double age,agelim, cov[NCOVMAX];      b[i]=sum; 
   int theta;    } 
   char fileresprob[FILENAMELENGTH];    for (i=n;i>=1;i--) { 
       sum=b[i]; 
   strcpy(fileresprob,"prob");      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   strcat(fileresprob,fileres);      b[i]=sum/a[i][i]; 
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    } 
     printf("Problem with resultfile: %s\n", fileresprob);  } 
   }  
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);  /************ Frequencies ********************/
    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 */
   xp=vector(1,npar);    
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    int first;
      double ***freq; /* Frequencies */
   cov[1]=1;    double *pp, **prop;
   for (age=bage; age<=fage; age ++){    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     cov[2]=age;    FILE *ficresp;
     gradg=matrix(1,npar,1,9);    char fileresp[FILENAMELENGTH];
     trgradg=matrix(1,9,1,npar);    
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    pp=vector(1,nlstate);
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    prop=matrix(1,nlstate,iagemin,iagemax+3);
        strcpy(fileresp,"p");
     for(theta=1; theta <=npar; theta++){    strcat(fileresp,fileres);
       for(i=1; i<=npar; i++)    if((ficresp=fopen(fileresp,"w"))==NULL) {
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      printf("Problem with prevalence resultfile: %s\n", fileresp);
            fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       pmij(pmmij,cov,ncovmodel,xp,nlstate);      exit(0);
        }
       k=0;    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
       for(i=1; i<= (nlstate+ndeath); i++){    j1=0;
         for(j=1; j<=(nlstate+ndeath);j++){    
            k=k+1;    j=cptcoveff;
           gp[k]=pmmij[i][j];    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         }  
       }    first=1;
   
       for(i=1; i<=npar; i++)    for(k1=1; k1<=j;k1++){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      for(i1=1; i1<=ncodemax[k1];i1++){
            j1++;
         /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       pmij(pmmij,cov,ncovmodel,xp,nlstate);          scanf("%d", i);*/
       k=0;        for (i=-1; i<=nlstate+ndeath; i++)  
       for(i=1; i<=(nlstate+ndeath); i++){          for (jk=-1; jk<=nlstate+ndeath; jk++)  
         for(j=1; j<=(nlstate+ndeath);j++){            for(m=iagemin; m <= iagemax+3; m++)
           k=k+1;              freq[i][jk][m]=0;
           gm[k]=pmmij[i][j];  
         }      for (i=1; i<=nlstate; i++)  
       }        for(m=iagemin; m <= iagemax+3; m++)
                prop[i][m]=0;
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)        
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];          dateintsum=0;
     }        k2cpt=0;
         for (i=1; i<=imx; i++) {
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)          bool=1;
       for(theta=1; theta <=npar; theta++)          if  (cptcovn>0) {
       trgradg[j][theta]=gradg[theta][j];            for (z1=1; z1<=cptcoveff; z1++) 
                if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);                bool=0;
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);          }
           if (bool==1){
      pmij(pmmij,cov,ncovmodel,x,nlstate);            for(m=firstpass; m<=lastpass; m++){
               k2=anint[m][i]+(mint[m][i]/12.);
      k=0;              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
      for(i=1; i<=(nlstate+ndeath); i++){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
        for(j=1; j<=(nlstate+ndeath);j++){                if(agev[m][i]==1) agev[m][i]=iagemax+2;
          k=k+1;                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
          gm[k]=pmmij[i][j];                if (m<lastpass) {
         }                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
      }                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
                      }
      /*printf("\n%d ",(int)age);                
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                          dateintsum=dateintsum+k2;
                   k2cpt++;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));                }
      }*/                /*}*/
             }
   fprintf(ficresprob,"\n%d ",(int)age);          }
         }
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){         
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  
   }        if  (cptcovn>0) {
           fprintf(ficresp, "\n#********** Variable "); 
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));          fprintf(ficresp, "**********\n#");
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        }
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        for(i=1; i<=nlstate;i++) 
 }          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
  free_vector(xp,1,npar);        fprintf(ficresp, "\n");
 fclose(ficresprob);        
         for(i=iagemin; i <= iagemax+3; i++){
 }          if(i==iagemax+3){
             fprintf(ficlog,"Total");
 /******************* Printing html file ***********/          }else{
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, int lastpass, int stepm, int weightopt, char model[],int imx,int jmin, int jmax, double jmeanint,char optionfile[],char optionfilehtm[],char rfileres[] ){            if(first==1){
   int jj1, k1, i1, cpt;              first=0;
   FILE *fichtm;              printf("See log file for details...\n");
   /*char optionfilehtm[FILENAMELENGTH];*/            }
             fprintf(ficlog,"Age %d", i);
   strcpy(optionfilehtm,optionfile);          }
   strcat(optionfilehtm,".htm");          for(jk=1; jk <=nlstate ; jk++){
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     printf("Problem with %s \n",optionfilehtm), exit(0);              pp[jk] += freq[jk][m][i]; 
   }          }
           for(jk=1; jk <=nlstate ; jk++){
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.71e </font> <hr size=\"2\" color=\"#EC5E5E\">            for(m=-1, pos=0; m <=0 ; m++)
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>              pos += freq[jk][m][i];
             if(pp[jk]>=1.e-10){
 Total number of observations=%d <br>              if(first==1){
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 <hr  size=\"2\" color=\"#EC5E5E\">              }
 <li>Outputs files<br><br>\n              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n            }else{
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>              if(first==1)
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>            }
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>          }
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>  
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>          for(jk=1; jk <=nlstate ; jk++){
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
         - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>              pp[jk] += freq[jk][m][i];
         - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>          }       
         <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
              pos += pp[jk];
 fprintf(fichtm," <li>Graphs</li><p>");            posprop += prop[jk][i];
           }
  m=cptcoveff;          for(jk=1; jk <=nlstate ; jk++){
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}            if(pos>=1.e-5){
               if(first==1)
  jj1=0;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
  for(k1=1; k1<=m;k1++){              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
    for(i1=1; i1<=ncodemax[k1];i1++){            }else{
        jj1++;              if(first==1)
        if (cptcovn > 0) {                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
          for (cpt=1; cpt<=cptcoveff;cpt++)            }
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);            if( i <= iagemax){
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");              if(pos>=1.e-5){
        }                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>                /*probs[i][jk][j1]= pp[jk]/pos;*/
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);                    /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
        for(cpt=1; cpt<nlstate;cpt++){              }
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>              else
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
        }            }
     for(cpt=1; cpt<=nlstate;cpt++) {          }
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident          
 interval) in state (%d): v%s%d%d.gif <br>          for(jk=-1; jk <=nlstate+ndeath; jk++)
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);              for(m=-1; m <=nlstate+ndeath; m++)
      }              if(freq[jk][m][i] !=0 ) {
      for(cpt=1; cpt<=nlstate;cpt++) {              if(first==1)
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
      }              }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and          if(i <= iagemax)
 health expectancies in states (1) and (2): e%s%d.gif<br>            fprintf(ficresp,"\n");
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          if(first==1)
 fprintf(fichtm,"\n</body>");            printf("Others in log...\n");
    }          fprintf(ficlog,"\n");
    }        }
 fclose(fichtm);      }
 }    }
     dateintmean=dateintsum/k2cpt; 
 /******************* Gnuplot file **************/   
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double agemin, double agemaxpar, double fage , char pathc[], double p[]){    fclose(ficresp);
     free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;    free_vector(pp,1,nlstate);
     free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   strcpy(optionfilegnuplot,optionfilefiname);    /* End of Freq */
   strcat(optionfilegnuplot,".plt");  }
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {  
     printf("Problem with file %s",optionfilegnuplot);  /************ 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)
   {  
 #ifdef windows    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     fprintf(ficgp,"cd \"%s\" \n",pathc);       in each health status at the date of interview (if between dateprev1 and dateprev2).
 #endif       We still use firstpass and lastpass as another selection.
 m=pow(2,cptcoveff);    */
     
  /* 1eme*/    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   for (cpt=1; cpt<= nlstate ; cpt ++) {    double ***freq; /* Frequencies */
    for (k1=1; k1<= m ; k1 ++) {    double *pp, **prop;
     double pos,posprop; 
 #ifdef windows    double  y2; /* in fractional years */
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);    int iagemin, iagemax;
 #endif  
 #ifdef unix    iagemin= (int) agemin;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);    iagemax= (int) agemax;
 #endif    /*pp=vector(1,nlstate);*/
     prop=matrix(1,nlstate,iagemin,iagemax+3); 
 for (i=1; i<= nlstate ; i ++) {    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    j1=0;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    
 }    j=cptcoveff;
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     for (i=1; i<= nlstate ; i ++) {    
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    for(k1=1; k1<=j;k1++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for(i1=1; i1<=ncodemax[k1];i1++){
 }        j1++;
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);        
      for (i=1; i<= nlstate ; i ++) {        for (i=1; i<=nlstate; i++)  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          for(m=iagemin; m <= iagemax+3; m++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");            prop[i][m]=0.0;
 }         
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));        for (i=1; i<=imx; i++) { /* Each individual */
 #ifdef unix          bool=1;
 fprintf(ficgp,"\nset ter gif small size 400,300");          if  (cptcovn>0) {
 #endif            for (z1=1; z1<=cptcoveff; z1++) 
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
    }                bool=0;
   }          } 
   /*2 eme*/          if (bool==1) { 
             for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   for (k1=1; k1<= m ; k1 ++) {              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                    if(agev[m][i]==0) agev[m][i]=iagemax+1;
     for (i=1; i<= nlstate+1 ; i ++) {                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       k=2*i;                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); 
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
       for (j=1; j<= nlstate+1 ; j ++) {                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   else fprintf(ficgp," \%%*lf (\%%*lf)");                  prop[s[m][i]][iagemax+3] += weight[i]; 
 }                  } 
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");              }
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);            } /* end selection of waves */
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);          }
       for (j=1; j<= nlstate+1 ; j ++) {        }
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        for(i=iagemin; i <= iagemax+3; i++){  
         else fprintf(ficgp," \%%*lf (\%%*lf)");          
 }            for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
       fprintf(ficgp,"\" t\"\" w l 0,");            posprop += prop[jk][i]; 
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);          } 
       for (j=1; j<= nlstate+1 ; j ++) {  
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          for(jk=1; jk <=nlstate ; jk++){     
   else fprintf(ficgp," \%%*lf (\%%*lf)");            if( i <=  iagemax){ 
 }                if(posprop>=1.e-5){ 
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");                probs[i][jk][j1]= prop[jk][i]/posprop;
       else fprintf(ficgp,"\" t\"\" w l 0,");              } 
     }            } 
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);          }/* end jk */ 
   }        }/* end i */ 
        } /* end i1 */
   /*3eme*/    } /* end k1 */
     
   for (k1=1; k1<= m ; k1 ++) {    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {    /*free_vector(pp,1,nlstate);*/
       k=2+nlstate*(cpt-1);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);  }  /* End of prevalence */
       for (i=1; i< nlstate ; i ++) {  
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);  /************* Waves Concatenation ***************/
       }  
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  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)
     }  {
     }    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
         Death is a valid wave (if date is known).
   /* CV preval stat */       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     for (k1=1; k1<= m ; k1 ++) {       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
     for (cpt=1; cpt<nlstate ; cpt ++) {       and mw[mi+1][i]. dh depends on stepm.
       k=3;       */
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemaxpar,fileres,k1,k+cpt+1,k+1);  
     int i, mi, m;
       for (i=1; i< nlstate ; i ++)    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
         fprintf(ficgp,"+$%d",k+i+1);       double sum=0., jmean=0.;*/
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    int first;
          int j, k=0,jk, ju, jl;
       l=3+(nlstate+ndeath)*cpt;    double sum=0.;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    first=0;
       for (i=1; i< nlstate ; i ++) {    jmin=1e+5;
         l=3+(nlstate+ndeath)*cpt;    jmax=-1;
         fprintf(ficgp,"+$%d",l+i+1);    jmean=0.;
       }    for(i=1; i<=imx; i++){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);        mi=0;
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      m=firstpass;
     }      while(s[m][i] <= nlstate){
   }          if(s[m][i]>=1)
            mw[++mi][i]=m;
   /* proba elementaires */        if(m >=lastpass)
    for(i=1,jk=1; i <=nlstate; i++){          break;
     for(k=1; k <=(nlstate+ndeath); k++){        else
       if (k != i) {          m++;
         for(j=1; j <=ncovmodel; j++){      }/* end while */
              if (s[m][i] > nlstate){
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);        mi++;     /* Death is another wave */
           jk++;        /* if(mi==0)  never been interviewed correctly before death */
           fprintf(ficgp,"\n");           /* Only death is a correct wave */
         }        mw[mi][i]=m;
       }      }
     }  
     }      wav[i]=mi;
       if(mi==0){
     for(jk=1; jk <=m; jk++) {        nbwarn++;
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemaxpar);        if(first==0){
    i=1;          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
    for(k2=1; k2<=nlstate; k2++) {          first=1;
      k3=i;        }
      for(k=1; k<=(nlstate+ndeath); k++) {        if(first==1){
        if (k != k2){          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);        }
 ij=1;      } /* end mi==0 */
         for(j=3; j <=ncovmodel; j++) {    } /* End individuals */
           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]]]);    for(i=1; i<=imx; i++){
             ij++;      for(mi=1; mi<wav[i];mi++){
           }        if (stepm <=0)
           else          dh[mi][i]=1;
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        else{
         }          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
           fprintf(ficgp,")/(1");            if (agedc[i] < 2*AGESUP) {
                      j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
         for(k1=1; k1 <=nlstate; k1++){                if(j==0) j=1;  /* Survives at least one month after exam */
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);              else if(j<0){
 ij=1;                nberr++;
           for(j=3; j <=ncovmodel; j++){                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                j=1; /* Temporary Dangerous patch */
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-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);
             ij++;                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
           }                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
           else              }
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              k=k+1;
           }              if (j >= jmax) jmax=j;
           fprintf(ficgp,")");              if (j <= jmin) jmin=j;
         }              sum=sum+j;
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
         i=i+ncovmodel;            }
        }          }
      }          else{
    }            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
    }            k=k+1;
                if (j >= jmax) jmax=j;
   fclose(ficgp);            else if (j <= jmin)jmin=j;
 }  /* end gnuplot */            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
             if(j<0){
 /*************** Moving average **************/              nberr++;
 void movingaverage(double agedeb, double fage,double agemin, double ***mobaverage){              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]);
   int i, cpt, cptcod;            }
     for (agedeb=agemin; agedeb<=fage; agedeb++)            sum=sum+j;
       for (i=1; i<=nlstate;i++)          }
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          jk= j/stepm;
           mobaverage[(int)agedeb][i][cptcod]=0.;          jl= j -jk*stepm;
              ju= j -(jk+1)*stepm;
     for (agedeb=agemin+4; agedeb<=fage; agedeb++){          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
       for (i=1; i<=nlstate;i++){            if(jl==0){
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){              dh[mi][i]=jk;
           for (cpt=0;cpt<=4;cpt++){              bh[mi][i]=0;
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];            }else{ /* We want a negative bias in order to only have interpolation ie
           }                    * at the price of an extra matrix product in likelihood */
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;              dh[mi][i]=jk+1;
         }              bh[mi][i]=ju;
       }            }
     }          }else{
                if(jl <= -ju){
 }              dh[mi][i]=jk;
               bh[mi][i]=jl;       /* bias is positive if real duration
                                    * is higher than the multiple of stepm and negative otherwise.
 /************** Forecasting ******************/                                   */
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){            }
              else{
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;              dh[mi][i]=jk+1;
   int *popage;              bh[mi][i]=ju;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;            }
   double *popeffectif,*popcount;            if(dh[mi][i]==0){
   double ***p3mat;              dh[mi][i]=1; /* At least one step */
   char fileresf[FILENAMELENGTH];              bh[mi][i]=ju; /* At least one step */
               /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
  agelim=AGESUP;            }
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;          } /* end if mle */
         }
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      } /* end wave */
      }
      jmean=sum/k;
   strcpy(fileresf,"f");    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   strcat(fileresf,fileres);    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   if((ficresf=fopen(fileresf,"w"))==NULL) {   }
     printf("Problem with forecast resultfile: %s\n", fileresf);  
   }  /*********** Tricode ****************************/
   printf("Computing forecasting: result on file '%s' \n", fileresf);  void tricode(int *Tvar, int **nbcode, int imx)
   {
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    
     int Ndum[20],ij=1, k, j, i, maxncov=19;
   if (mobilav==1) {    int cptcode=0;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    cptcoveff=0; 
     movingaverage(agedeb, fage, agemin, mobaverage);   
   }    for (k=0; k<maxncov; k++) Ndum[k]=0;
     for (k=1; k<=7; k++) ncodemax[k]=0;
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   if (stepm<=12) stepsize=1;    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
        for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
   agelim=AGESUP;                                 modality*/ 
          ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
   hstepm=1;        Ndum[ij]++; /*store the modality */
   hstepm=hstepm/stepm;        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   yp1=modf(dateintmean,&yp);        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
   anprojmean=yp;                                         Tvar[j]. If V=sex and male is 0 and 
   yp2=modf((yp1*12),&yp);                                         female is 1, then  cptcode=1.*/
   mprojmean=yp;      }
   yp1=modf((yp2*30.5),&yp);  
   jprojmean=yp;      for (i=0; i<=cptcode; i++) {
   if(jprojmean==0) jprojmean=1;        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 */
   if(mprojmean==0) jprojmean=1;      }
    
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);      ij=1; 
        for (i=1; i<=ncodemax[j]; i++) {
   for(cptcov=1;cptcov<=i2;cptcov++){        for (k=0; k<= maxncov; k++) {
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          if (Ndum[k] != 0) {
       k=k+1;            nbcode[Tvar[j]][ij]=k; 
       fprintf(ficresf,"\n#******");            /* 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; */
       for(j=1;j<=cptcoveff;j++) {            
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            ij++;
       }          }
       fprintf(ficresf,"******\n");          if (ij > ncodemax[j]) break; 
       fprintf(ficresf,"# StartingAge FinalAge");        }  
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);      } 
          }  
        
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {   for (k=0; k< maxncov; k++) Ndum[k]=0;
         fprintf(ficresf,"\n");  
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);     for (i=1; i<=ncovmodel-2; i++) { 
      /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){     ij=Tvar[i];
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);     Ndum[ij]++;
           nhstepm = nhstepm/hstepm;   }
            
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   ij=1;
           oldm=oldms;savm=savms;   for (i=1; i<= maxncov; i++) {
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);       if((Ndum[i]!=0) && (i<=ncovcol)){
               Tvaraff[ij]=i; /*For printing */
           for (h=0; h<=nhstepm; h++){       ij++;
             if (h==(int) (calagedate+YEARM*cpt)) {     }
               fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);   }
             }   
             for(j=1; j<=nlstate+ndeath;j++) {   cptcoveff=ij-1; /*Number of simple covariates*/
               kk1=0.;kk2=0;  }
               for(i=1; i<=nlstate;i++) {                
                 if (mobilav==1)  /*********** Health Expectancies ****************/
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  
                 else {  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 )
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];  
                 }  {
                    /* Health expectancies */
               }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
               if (h==(int)(calagedate+12*cpt)){    double age, agelim, hf;
                 fprintf(ficresf," %.3f", kk1);    double ***p3mat,***varhe;
                            double **dnewm,**doldm;
               }    double *xp;
             }    double **gp, **gm;
           }    double ***gradg, ***trgradg;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int theta;
         }  
       }    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     }    xp=vector(1,npar);
   }    dnewm=matrix(1,nlstate*nlstate,1,npar);
            doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    
     fprintf(ficreseij,"# Health expectancies\n");
   fclose(ficresf);    fprintf(ficreseij,"# Age");
 }    for(i=1; i<=nlstate;i++)
 /************** Forecasting ******************/      for(j=1; j<=nlstate;j++)
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double agemin, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){        fprintf(ficreseij," %1d-%1d (SE)",i,j);
      fprintf(ficreseij,"\n");
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;  
   int *popage;    if(estepm < stepm){
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      printf ("Problem %d lower than %d\n",estepm, stepm);
   double *popeffectif,*popcount;    }
   double ***p3mat,***tabpop,***tabpopprev;    else  hstepm=estepm;   
   char filerespop[FILENAMELENGTH];    /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     * if stepm=24 months pijx are given only every 2 years and by summing them
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     * we are calculating an estimate of the Life Expectancy assuming a linear 
   agelim=AGESUP;     * progression in between and thus overestimating or underestimating according
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;     * 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
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);     * to compare the new estimate of Life expectancy with the same linear 
       * hypothesis. A more precise result, taking into account a more precise
       * curvature will be obtained if estepm is as small as stepm. */
   strcpy(filerespop,"pop");  
   strcat(filerespop,fileres);    /* For example we decided to compute the life expectancy with the smallest unit */
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     printf("Problem with forecast resultfile: %s\n", filerespop);       nhstepm is the number of hstepm from age to agelim 
   }       nstepm is the number of stepm from age to agelin. 
   printf("Computing forecasting: result on file '%s' \n", filerespop);       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like estepm months */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
   if (mobilav==1) {       means that if the survival funtion is printed only each two years of age and if
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     movingaverage(agedeb, fage, agemin, mobaverage);       results. So we changed our mind and took the option of the best precision.
   }    */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   if (stepm<=12) stepsize=1;    agelim=AGESUP;
      for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   agelim=AGESUP;      /* nhstepm age range expressed in number of stepm */
        nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   hstepm=1;      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   hstepm=hstepm/stepm;      /* if (stepm >= YEARM) hstepm=1;*/
        nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   if (popforecast==1) {      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     if((ficpop=fopen(popfile,"r"))==NULL) {      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
       printf("Problem with population file : %s\n",popfile);exit(0);      gp=matrix(0,nhstepm,1,nlstate*nlstate);
     }      gm=matrix(0,nhstepm,1,nlstate*nlstate);
     popage=ivector(0,AGESUP);  
     popeffectif=vector(0,AGESUP);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
     popcount=vector(0,AGESUP);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
          hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
     i=1;     
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;  
          hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     imx=i;  
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];      /* Computing Variances of health expectancies */
   }  
        for(theta=1; theta <=npar; theta++){
   for(cptcov=1;cptcov<=i2;cptcov++){        for(i=1; i<=npar; i++){ 
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       k=k+1;        }
       fprintf(ficrespop,"\n#******");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       for(j=1;j<=cptcoveff;j++) {    
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        cptj=0;
       }        for(j=1; j<= nlstate; j++){
       fprintf(ficrespop,"******\n");          for(i=1; i<=nlstate; i++){
       fprintf(ficrespop,"# Age");            cptj=cptj+1;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
       if (popforecast==1)  fprintf(ficrespop," [Population]");              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
                  }
       for (cpt=0; cpt<=0;cpt++) {          }
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          }
               
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){       
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        for(i=1; i<=npar; i++) 
           nhstepm = nhstepm/hstepm;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
                  hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        
           oldm=oldms;savm=savms;        cptj=0;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          for(j=1; j<= nlstate; j++){
                  for(i=1;i<=nlstate;i++){
           for (h=0; h<=nhstepm; h++){            cptj=cptj+1;
             if (h==(int) (calagedate+YEARM*cpt)) {            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  
             }              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
             for(j=1; j<=nlstate+ndeath;j++) {            }
               kk1=0.;kk2=0;          }
               for(i=1; i<=nlstate;i++) {                      }
                 if (mobilav==1)        for(j=1; j<= nlstate*nlstate; j++)
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];          for(h=0; h<=nhstepm-1; h++){
                 else {            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          }
                 }       } 
               }     
               if (h==(int)(calagedate+12*cpt)){  /* End theta */
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;  
                   /*fprintf(ficrespop," %.3f", kk1);       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/  
               }       for(h=0; h<=nhstepm-1; h++)
             }        for(j=1; j<=nlstate*nlstate;j++)
             for(i=1; i<=nlstate;i++){          for(theta=1; theta <=npar; theta++)
               kk1=0.;            trgradg[h][j][theta]=gradg[h][theta][j];
                 for(j=1; j<=nlstate;j++){       
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];  
                 }       for(i=1;i<=nlstate*nlstate;i++)
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];        for(j=1;j<=nlstate*nlstate;j++)
             }          varhe[i][j][(int)age] =0.;
   
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)       printf("%d|",(int)age);fflush(stdout);
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
           }       for(h=0;h<=nhstepm-1;h++){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(k=0;k<=nhstepm-1;k++){
         }          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
       }          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
            for(i=1;i<=nlstate*nlstate;i++)
   /******/            for(j=1;j<=nlstate*nlstate;j++)
               varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {        }
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);        }
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(agemin-((int)calagedate %12)/12.); agedeb--){      /* Computing expectancies */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      for(i=1; i<=nlstate;i++)
           nhstepm = nhstepm/hstepm;        for(j=1; j<=nlstate;j++)
                    for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
           oldm=oldms;savm=savms;            
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    /* 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 (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {          }
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  
             }      fprintf(ficreseij,"%3.0f",age );
             for(j=1; j<=nlstate+ndeath;j++) {      cptj=0;
               kk1=0.;kk2=0;      for(i=1; i<=nlstate;i++)
               for(i=1; i<=nlstate;i++) {                      for(j=1; j<=nlstate;j++){
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];              cptj++;
               }          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);        }
             }      fprintf(ficreseij,"\n");
           }     
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
         }      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
       }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
    }      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      }
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    printf("\n");
     fprintf(ficlog,"\n");
   if (popforecast==1) {  
     free_ivector(popage,0,AGESUP);    free_vector(xp,1,npar);
     free_vector(popeffectif,0,AGESUP);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     free_vector(popcount,0,AGESUP);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   }    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  }
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
   fclose(ficrespop);  /************ Variance ******************/
 }  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
   {
 /***********************************************/    /* Variance of health expectancies */
 /**************** Main Program *****************/    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
 /***********************************************/    /* double **newm;*/
     double **dnewm,**doldm;
 int main(int argc, char *argv[])    double **dnewmp,**doldmp;
 {    int i, j, nhstepm, hstepm, h, nstepm ;
     int k, cptcode;
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    double *xp;
   double agedeb, agefin,hf;    double **gp, **gm;  /* for var eij */
   double agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
   double fret;    double *gpp, *gmp; /* for var p point j */
   double **xi,tmp,delta;    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     double ***p3mat;
   double dum; /* Dummy variable */    double age,agelim, hf;
   double ***p3mat;    double ***mobaverage;
   int *indx;    int theta;
   char line[MAXLINE], linepar[MAXLINE];    char digit[4];
   char title[MAXLINE];    char digitp[25];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    char fileresprobmorprev[FILENAMELENGTH];
    
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    if(popbased==1){
       if(mobilav!=0)
   char filerest[FILENAMELENGTH];        strcpy(digitp,"-populbased-mobilav-");
   char fileregp[FILENAMELENGTH];      else strcpy(digitp,"-populbased-nomobil-");
   char popfile[FILENAMELENGTH];    }
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    else 
   int firstobs=1, lastobs=10;      strcpy(digitp,"-stablbased-");
   int sdeb, sfin; /* Status at beginning and end */  
   int c,  h , cpt,l;    if (mobilav!=0) {
   int ju,jl, mi;      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   int mobilav=0,popforecast=0;        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   int hstepm, nhstepm;      }
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;    }
   
   double bage, fage, age, agelim, agebase;    strcpy(fileresprobmorprev,"prmorprev"); 
   double ftolpl=FTOL;    sprintf(digit,"%-d",ij);
   double **prlim;    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   double *severity;    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   double ***param; /* Matrix of parameters */    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   double  *p;    strcat(fileresprobmorprev,fileres);
   double **matcov; /* Matrix of covariance */    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   double ***delti3; /* Scale */      printf("Problem with resultfile: %s\n", fileresprobmorprev);
   double *delti; /* Scale */      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   double ***eij, ***vareij;    }
   double **varpl; /* Variances of prevalence limits by age */    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   double *epj, vepp;    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   double kk1, kk2;    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);
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
   char version[80]="Imach version 0.71e, March 2002, INED-EUROREVES ";      for(i=1; i<=nlstate;i++)
   char *alph[]={"a","a","b","c","d","e"}, str[4];        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
     fprintf(ficresprobmorprev,"\n");
   char z[1]="c", occ;    fprintf(ficgp,"\n# Routine varevsij");
 #include <sys/time.h>    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");
 #include <time.h>    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  /*   } */
      varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   /* long total_usecs;  
   struct timeval start_time, end_time;    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");
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   printf("\n%s",version);    fprintf(ficresvij,"\n");
   if(argc <=1){  
     printf("\nEnter the parameter file name: ");    xp=vector(1,npar);
     scanf("%s",pathtot);    dnewm=matrix(1,nlstate,1,npar);
   }    doldm=matrix(1,nlstate,1,nlstate);
   else{    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     strcpy(pathtot,argv[1]);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   }  
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   /*cygwin_split_path(pathtot,path,optionfile);    gpp=vector(nlstate+1,nlstate+ndeath);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    gmp=vector(nlstate+1,nlstate+ndeath);
   /* cutv(path,optionfile,pathtot,'\\');*/    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    if(estepm < stepm){
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);      printf ("Problem %d lower than %d\n",estepm, stepm);
   chdir(path);    }
   replace(pathc,path);    else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
 /*-------- arguments in the command line --------*/    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        nhstepm is the number of hstepm from age to agelim 
   strcpy(fileres,"r");       nstepm is the number of stepm from age to agelin. 
   strcat(fileres, optionfilefiname);       Look at hpijx to understand the reason of that which relies in memory size
   strcat(fileres,".txt");    /* Other files have txt extension */       and note for a fixed period like k years */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   /*---------arguments file --------*/       survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed every two years of age and if
   if((ficpar=fopen(optionfile,"r"))==NULL)    {       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     printf("Problem with optionfile %s\n",optionfile);       results. So we changed our mind and took the option of the best precision.
     goto end;    */
   }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
   strcpy(filereso,"o");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   strcat(filereso,fileres);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   if((ficparo=fopen(filereso,"w"))==NULL) {      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
   /* Reads comments: lines beginning with '#' */      gm=matrix(0,nhstepm,1,nlstate);
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);      for(theta=1; theta <=npar; theta++){
     puts(line);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
     fputs(line,ficparo);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   }        }
   ungetc(c,ficpar);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);  
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);        if (popbased==1) {
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);          if(mobilav ==0){
 while((c=getc(ficpar))=='#' && c!= EOF){            for(i=1; i<=nlstate;i++)
     ungetc(c,ficpar);              prlim[i][i]=probs[(int)age][i][ij];
     fgets(line, MAXLINE, ficpar);          }else{ /* mobilav */ 
     puts(line);            for(i=1; i<=nlstate;i++)
     fputs(line,ficparo);              prlim[i][i]=mobaverage[(int)age][i][ij];
   }          }
   ungetc(c,ficpar);        }
      
            for(j=1; j<= nlstate; j++){
   covar=matrix(0,NCOVMAX,1,n);          for(h=0; h<=nhstepm; h++){
   cptcovn=0;            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
   ncovmodel=2+cptcovn;        }
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */        /* This for computing probability of death (h=1 means
             computed over hstepm matrices product = hstepm*stepm months) 
   /* Read guess parameters */           as a weighted average of prlim.
   /* Reads comments: lines beginning with '#' */        */
   while((c=getc(ficpar))=='#' && c!= EOF){        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     ungetc(c,ficpar);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
     fgets(line, MAXLINE, ficpar);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     puts(line);        }    
     fputs(line,ficparo);        /* end probability of death */
   }  
   ungetc(c,ficpar);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
            xp[i] = x[i] - (i==theta ?delti[theta]:0);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     for(i=1; i <=nlstate; i++)        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     for(j=1; j <=nlstate+ndeath-1; j++){   
       fscanf(ficpar,"%1d%1d",&i1,&j1);        if (popbased==1) {
       fprintf(ficparo,"%1d%1d",i1,j1);          if(mobilav ==0){
       printf("%1d%1d",i,j);            for(i=1; i<=nlstate;i++)
       for(k=1; k<=ncovmodel;k++){              prlim[i][i]=probs[(int)age][i][ij];
         fscanf(ficpar," %lf",&param[i][j][k]);          }else{ /* mobilav */ 
         printf(" %lf",param[i][j][k]);            for(i=1; i<=nlstate;i++)
         fprintf(ficparo," %lf",param[i][j][k]);              prlim[i][i]=mobaverage[(int)age][i][ij];
       }          }
       fscanf(ficpar,"\n");        }
       printf("\n");  
       fprintf(ficparo,"\n");        for(j=1; j<= nlstate; j++){
     }          for(h=0; h<=nhstepm; h++){
              for(i=1, gm[h][j]=0.;i<=nlstate;i++)
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
   p=param[1][1];        }
          /* This for computing probability of death (h=1 means
   /* Reads comments: lines beginning with '#' */           computed over hstepm matrices product = hstepm*stepm months) 
   while((c=getc(ficpar))=='#' && c!= EOF){           as a weighted average of prlim.
     ungetc(c,ficpar);        */
     fgets(line, MAXLINE, ficpar);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     puts(line);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
     fputs(line,ficparo);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
   }        }    
   ungetc(c,ficpar);        /* end probability of death */
   
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        for(j=1; j<= nlstate; j++) /* vareij */
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */          for(h=0; h<=nhstepm; h++){
   for(i=1; i <=nlstate; i++){            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     for(j=1; j <=nlstate+ndeath-1; j++){          }
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       printf("%1d%1d",i,j);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
       fprintf(ficparo,"%1d%1d",i1,j1);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
       for(k=1; k<=ncovmodel;k++){        }
         fscanf(ficpar,"%le",&delti3[i][j][k]);  
         printf(" %le",delti3[i][j][k]);      } /* End theta */
         fprintf(ficparo," %le",delti3[i][j][k]);  
       }      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
       fscanf(ficpar,"\n");  
       printf("\n");      for(h=0; h<=nhstepm; h++) /* veij */
       fprintf(ficparo,"\n");        for(j=1; j<=nlstate;j++)
     }          for(theta=1; theta <=npar; theta++)
   }            trgradg[h][j][theta]=gradg[h][theta][j];
   delti=delti3[1][1];  
        for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   /* Reads comments: lines beginning with '#' */        for(theta=1; theta <=npar; theta++)
   while((c=getc(ficpar))=='#' && c!= EOF){          trgradgp[j][theta]=gradgp[theta][j];
     ungetc(c,ficpar);    
     fgets(line, MAXLINE, ficpar);  
     puts(line);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     fputs(line,ficparo);      for(i=1;i<=nlstate;i++)
   }        for(j=1;j<=nlstate;j++)
   ungetc(c,ficpar);          vareij[i][j][(int)age] =0.;
    
   matcov=matrix(1,npar,1,npar);      for(h=0;h<=nhstepm;h++){
   for(i=1; i <=npar; i++){        for(k=0;k<=nhstepm;k++){
     fscanf(ficpar,"%s",&str);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
     printf("%s",str);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
     fprintf(ficparo,"%s",str);          for(i=1;i<=nlstate;i++)
     for(j=1; j <=i; j++){            for(j=1;j<=nlstate;j++)
       fscanf(ficpar," %le",&matcov[i][j]);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       printf(" %.5le",matcov[i][j]);        }
       fprintf(ficparo," %.5le",matcov[i][j]);      }
     }    
     fscanf(ficpar,"\n");      /* pptj */
     printf("\n");      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
     fprintf(ficparo,"\n");      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   }      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   for(i=1; i <=npar; i++)        for(i=nlstate+1;i<=nlstate+ndeath;i++)
     for(j=i+1;j<=npar;j++)          varppt[j][i]=doldmp[j][i];
       matcov[i][j]=matcov[j][i];      /* end ppptj */
          /*  x centered again */
   printf("\n");      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
     /*-------- Rewriting paramater file ----------*/      if (popbased==1) {
      strcpy(rfileres,"r");    /* "Rparameterfile */        if(mobilav ==0){
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/          for(i=1; i<=nlstate;i++)
      strcat(rfileres,".");    /* */            prlim[i][i]=probs[(int)age][i][ij];
      strcat(rfileres,optionfilext);    /* Other files have txt extension */        }else{ /* mobilav */ 
     if((ficres =fopen(rfileres,"w"))==NULL) {          for(i=1; i<=nlstate;i++)
       printf("Problem writing new parameter file: %s\n", fileres);goto end;            prlim[i][i]=mobaverage[(int)age][i][ij];
     }        }
     fprintf(ficres,"#%s\n",version);      }
                   
     /*-------- data file ----------*/      /* This for computing probability of death (h=1 means
     if((fic=fopen(datafile,"r"))==NULL)    {         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
       printf("Problem with datafile: %s\n", datafile);goto end;         as a weighted average of prlim.
     }      */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
     n= lastobs;        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
     severity = vector(1,maxwav);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
     outcome=imatrix(1,maxwav+1,1,n);      }    
     num=ivector(1,n);      /* end probability of death */
     moisnais=vector(1,n);  
     annais=vector(1,n);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
     moisdc=vector(1,n);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     andc=vector(1,n);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     agedc=vector(1,n);        for(i=1; i<=nlstate;i++){
     cod=ivector(1,n);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     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);      fprintf(ficresprobmorprev,"\n");
     anint=matrix(1,maxwav,1,n);  
     s=imatrix(1,maxwav+1,1,n);      fprintf(ficresvij,"%.0f ",age );
     adl=imatrix(1,maxwav+1,1,n);          for(i=1; i<=nlstate;i++)
     tab=ivector(1,NCOVMAX);        for(j=1; j<=nlstate;j++){
     ncodemax=ivector(1,8);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
     i=1;      fprintf(ficresvij,"\n");
     while (fgets(line, MAXLINE, fic) != NULL)    {      free_matrix(gp,0,nhstepm,1,nlstate);
       if ((i >= firstobs) && (i <=lastobs)) {      free_matrix(gm,0,nhstepm,1,nlstate);
              free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
         for (j=maxwav;j>=1;j--){      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           strcpy(line,stra);    } /* End age */
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    free_vector(gpp,nlstate+1,nlstate+ndeath);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    free_vector(gmp,nlstate+1,nlstate+ndeath);
         }    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
            free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);  /*   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); */
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
         for (j=ncov;j>=1;j--){    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
         }    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
         num[i]=atol(stra);    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);
         /*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;}*/  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
         i=i+1;  
       }    free_vector(xp,1,npar);
     }    free_matrix(doldm,1,nlstate,1,nlstate);
     /* printf("ii=%d", ij);    free_matrix(dnewm,1,nlstate,1,npar);
        scanf("%d",i);*/    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   imx=i-1; /* Number of individuals */    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   /* for (i=1; i<=imx; i++){    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    fclose(ficresprobmorprev);
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    fflush(ficgp);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;    fflush(fichtm); 
     }  }  /* end varevsij */
   
     for (i=1; i<=imx; i++)  /************ Variance of prevlim ******************/
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/  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)
   {
   /* Calculation of the number of parameter from char model*/    /* Variance of prevalence limit */
   Tvar=ivector(1,15);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   Tprod=ivector(1,15);    double **newm;
   Tvaraff=ivector(1,15);    double **dnewm,**doldm;
   Tvard=imatrix(1,15,1,2);    int i, j, nhstepm, hstepm;
   Tage=ivector(1,15);          int k, cptcode;
        double *xp;
   if (strlen(model) >1){    double *gp, *gm;
     j=0, j1=0, k1=1, k2=1;    double **gradg, **trgradg;
     j=nbocc(model,'+');    double age,agelim;
     j1=nbocc(model,'*');    int theta;
     cptcovn=j+1;     
     cptcovprod=j1;    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
        fprintf(ficresvpl,"# Age");
        for(i=1; i<=nlstate;i++)
     strcpy(modelsav,model);        fprintf(ficresvpl," %1d-%1d",i,i);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    fprintf(ficresvpl,"\n");
       printf("Error. Non available option model=%s ",model);  
       goto end;    xp=vector(1,npar);
     }    dnewm=matrix(1,nlstate,1,npar);
        doldm=matrix(1,nlstate,1,nlstate);
     for(i=(j+1); i>=1;i--){    
       cutv(stra,strb,modelsav,'+');    hstepm=1*YEARM; /* Every year of age */
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    agelim = AGESUP;
       /*scanf("%d",i);*/    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       if (strchr(strb,'*')) {      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         cutv(strd,strc,strb,'*');      if (stepm >= YEARM) hstepm=1;
         if (strcmp(strc,"age")==0) {      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
           cptcovprod--;      gradg=matrix(1,npar,1,nlstate);
           cutv(strb,stre,strd,'V');      gp=vector(1,nlstate);
           Tvar[i]=atoi(stre);      gm=vector(1,nlstate);
           cptcovage++;  
             Tage[cptcovage]=i;      for(theta=1; theta <=npar; theta++){
             /*printf("stre=%s ", stre);*/        for(i=1; i<=npar; i++){ /* Computes gradient */
         }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         else if (strcmp(strd,"age")==0) {        }
           cptcovprod--;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           cutv(strb,stre,strc,'V');        for(i=1;i<=nlstate;i++)
           Tvar[i]=atoi(stre);          gp[i] = prlim[i][i];
           cptcovage++;      
           Tage[cptcovage]=i;        for(i=1; i<=npar; i++) /* Computes gradient */
         }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         else {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           cutv(strb,stre,strc,'V');        for(i=1;i<=nlstate;i++)
           Tvar[i]=ncov+k1;          gm[i] = prlim[i][i];
           cutv(strb,strc,strd,'V');  
           Tprod[k1]=i;        for(i=1;i<=nlstate;i++)
           Tvard[k1][1]=atoi(strc);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
           Tvard[k1][2]=atoi(stre);      } /* End theta */
           Tvar[cptcovn+k2]=Tvard[k1][1];  
           Tvar[cptcovn+k2+1]=Tvard[k1][2];      trgradg =matrix(1,nlstate,1,npar);
           for (k=1; k<=lastobs;k++)  
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];      for(j=1; j<=nlstate;j++)
           k1++;        for(theta=1; theta <=npar; theta++)
           k2=k2+2;          trgradg[j][theta]=gradg[theta][j];
         }  
       }      for(i=1;i<=nlstate;i++)
       else {        varpl[i][(int)age] =0.;
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
        /*  scanf("%d",i);*/      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       cutv(strd,strc,strb,'V');      for(i=1;i<=nlstate;i++)
       Tvar[i]=atoi(strc);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
       }  
       strcpy(modelsav,stra);        fprintf(ficresvpl,"%.0f ",age );
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);      for(i=1; i<=nlstate;i++)
         scanf("%d",i);*/        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);
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);      free_matrix(gradg,1,npar,1,nlstate);
   printf("cptcovprod=%d ", cptcovprod);      free_matrix(trgradg,1,nlstate,1,npar);
   scanf("%d ",i);*/    } /* End age */
     fclose(fic);  
     free_vector(xp,1,npar);
     /*  if(mle==1){*/    free_matrix(doldm,1,nlstate,1,npar);
     if (weightopt != 1) { /* Maximisation without weights*/    free_matrix(dnewm,1,nlstate,1,nlstate);
       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);  /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
    for (i=1; i<=imx; i++)  {
      for(m=2; (m<= maxwav); m++)    int i, j=0,  i1, k1, l1, t, tj;
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    int k2, l2, j1,  z1;
          anint[m][i]=9999;    int k=0,l, cptcode;
          s[m][i]=-1;    int first=1, first1;
        }    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
        double **dnewm,**doldm;
     for (i=1; i<=imx; i++)  {    double *xp;
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    double *gp, *gm;
       for(m=1; (m<= maxwav); m++){    double **gradg, **trgradg;
         if(s[m][i] >0){    double **mu;
           if (s[m][i] == nlstate+1) {    double age,agelim, cov[NCOVMAX];
             if(agedc[i]>0)    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
               if(moisdc[i]!=99 && andc[i]!=9999)    int theta;
               agev[m][i]=agedc[i];    char fileresprob[FILENAMELENGTH];
             else {    char fileresprobcov[FILENAMELENGTH];
               if (andc[i]!=9999){    char fileresprobcor[FILENAMELENGTH];
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  
               agev[m][i]=-1;    double ***varpij;
               }  
             }    strcpy(fileresprob,"prob"); 
           }    strcat(fileresprob,fileres);
           else if(s[m][i] !=9){ /* Should no more exist */    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);      printf("Problem with resultfile: %s\n", fileresprob);
             if(mint[m][i]==99 || anint[m][i]==9999)      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
               agev[m][i]=1;    }
             else if(agev[m][i] <agemin){    strcpy(fileresprobcov,"probcov"); 
               agemin=agev[m][i];    strcat(fileresprobcov,fileres);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
             }      printf("Problem with resultfile: %s\n", fileresprobcov);
             else if(agev[m][i] >agemax){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
               agemax=agev[m][i];    }
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    strcpy(fileresprobcor,"probcor"); 
             }    strcat(fileresprobcor,fileres);
             /*agev[m][i]=anint[m][i]-annais[i];*/    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
             /*   agev[m][i] = age[i]+2*m;*/      printf("Problem with resultfile: %s\n", fileresprobcor);
           }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
           else { /* =9 */    }
             agev[m][i]=1;    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
             s[m][i]=-1;    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
           }    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
         }    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
         else /*= 0 Unknown */    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
           agev[m][i]=1;    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
       }    
        fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     }    fprintf(ficresprob,"# Age");
     for (i=1; i<=imx; i++)  {    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
       for(m=1; (m<= maxwav); m++){    fprintf(ficresprobcov,"# Age");
         if (s[m][i] > (nlstate+ndeath)) {    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
           printf("Error: Wrong value in nlstate or ndeath\n");      fprintf(ficresprobcov,"# Age");
           goto end;  
         }  
       }    for(i=1; i<=nlstate;i++)
     }      for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);        fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
     free_vector(severity,1,maxwav);      }  
     free_imatrix(outcome,1,maxwav+1,1,n);   /* fprintf(ficresprob,"\n");
     free_vector(moisnais,1,n);    fprintf(ficresprobcov,"\n");
     free_vector(annais,1,n);    fprintf(ficresprobcor,"\n");
     /* free_matrix(mint,1,maxwav,1,n);   */
        free_matrix(anint,1,maxwav,1,n);*/   xp=vector(1,npar);
     free_vector(moisdc,1,n);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(andc,1,n);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
        varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     wav=ivector(1,imx);    first=1;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    fprintf(ficgp,"\n# Routine varprob");
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
        fprintf(fichtm,"\n");
     /* Concatenates waves */  
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Computing matrix of variance-covariance of step probabilities</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Computing matrix of variance-covariance of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
       Tcode=ivector(1,100);    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);  and drawn. It helps understanding how is the covariance between two incidences.\
       ncodemax[1]=1;   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
        It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
    codtab=imatrix(1,100,1,10);  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
    h=0;  standard deviations wide on each axis. <br>\
    m=pow(2,cptcoveff);   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
     and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
    for(k=1;k<=cptcoveff; k++){  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
      for(i=1; i <=(m/pow(2,k));i++){  
        for(j=1; j <= ncodemax[k]; j++){    cov[1]=1;
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    tj=cptcoveff;
            h++;    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
            if (h>m) h=1;codtab[h][k]=j;    j1=0;
          }    for(t=1; t<=tj;t++){
        }      for(i1=1; i1<=ncodemax[t];i1++){ 
      }        j1++;
    }        if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
    /*for(i=1; i <=m ;i++){          fprintf(ficresprob, "**********\n#\n");
      for(k=1; k <=cptcovn; k++){          fprintf(ficresprobcov, "\n#********** Variable "); 
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
      }          fprintf(ficresprobcov, "**********\n#\n");
      printf("\n");          
    }          fprintf(ficgp, "\n#********** Variable "); 
    scanf("%d",i);*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
              fprintf(ficgp, "**********\n#\n");
    /* Calculates basic frequencies. Computes observed prevalence at single age          
        and prints on file fileres'p'. */          
           fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
              for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
              fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fprintf(ficresprobcor, "\n#********** Variable ");    
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fprintf(ficresprobcor, "**********\n#");    
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        }
              
     /* For Powell, parameters are in a vector p[] starting at p[1]        for (age=bage; age<=fage; age ++){ 
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */          cov[2]=age;
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */          for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     if(mle==1){          }
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     }          for (k=1; k<=cptcovprod;k++)
                cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     /*--------- results files --------------*/          
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, weightopt,model);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
            trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           gp=vector(1,(nlstate)*(nlstate+ndeath));
    jk=1;          gm=vector(1,(nlstate)*(nlstate+ndeath));
    fprintf(ficres,"# Parameters\n");      
    printf("# Parameters\n");          for(theta=1; theta <=npar; theta++){
    for(i=1,jk=1; i <=nlstate; i++){            for(i=1; i<=npar; i++)
      for(k=1; k <=(nlstate+ndeath); k++){              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
        if (k != i)            
          {            pmij(pmmij,cov,ncovmodel,xp,nlstate);
            printf("%d%d ",i,k);            
            fprintf(ficres,"%1d%1d ",i,k);            k=0;
            for(j=1; j <=ncovmodel; j++){            for(i=1; i<= (nlstate); i++){
              printf("%f ",p[jk]);              for(j=1; j<=(nlstate+ndeath);j++){
              fprintf(ficres,"%f ",p[jk]);                k=k+1;
              jk++;                gp[k]=pmmij[i][j];
            }              }
            printf("\n");            }
            fprintf(ficres,"\n");            
          }            for(i=1; i<=npar; i++)
      }              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
    }      
  if(mle==1){            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     /* Computing hessian and covariance matrix */            k=0;
     ftolhess=ftol; /* Usually correct */            for(i=1; i<=(nlstate); i++){
     hesscov(matcov, p, npar, delti, ftolhess, func);              for(j=1; j<=(nlstate+ndeath);j++){
  }                k=k+1;
     fprintf(ficres,"# Scales\n");                gm[k]=pmmij[i][j];
     printf("# Scales\n");              }
      for(i=1,jk=1; i <=nlstate; i++){            }
       for(j=1; j <=nlstate+ndeath; j++){       
         if (j!=i) {            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
           fprintf(ficres,"%1d%1d",i,j);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           printf("%1d%1d",i,j);          }
           for(k=1; k<=ncovmodel;k++){  
             printf(" %.5e",delti[jk]);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             fprintf(ficres," %.5e",delti[jk]);            for(theta=1; theta <=npar; theta++)
             jk++;              trgradg[j][theta]=gradg[theta][j];
           }          
           printf("\n");          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           fprintf(ficres,"\n");          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
         }          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
       }          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
      }          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
              free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     k=1;  
     fprintf(ficres,"# Covariance\n");          pmij(pmmij,cov,ncovmodel,x,nlstate);
     printf("# Covariance\n");          
     for(i=1;i<=npar;i++){          k=0;
       /*  if (k>nlstate) k=1;          for(i=1; i<=(nlstate); i++){
       i1=(i-1)/(ncovmodel*nlstate)+1;            for(j=1; j<=(nlstate+ndeath);j++){
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);              k=k+1;
       printf("%s%d%d",alph[k],i1,tab[i]);*/              mu[k][(int) age]=pmmij[i][j];
       fprintf(ficres,"%3d",i);            }
       printf("%3d",i);          }
       for(j=1; j<=i;j++){          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
         fprintf(ficres," %.5e",matcov[i][j]);            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
         printf(" %.5e",matcov[i][j]);              varpij[i][j][(int)age] = doldm[i][j];
       }  
       fprintf(ficres,"\n");          /*printf("\n%d ",(int)age);
       printf("\n");            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
       k++;            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]));
                }*/
     while((c=getc(ficpar))=='#' && c!= EOF){  
       ungetc(c,ficpar);          fprintf(ficresprob,"\n%d ",(int)age);
       fgets(line, MAXLINE, ficpar);          fprintf(ficresprobcov,"\n%d ",(int)age);
       puts(line);          fprintf(ficresprobcor,"\n%d ",(int)age);
       fputs(line,ficparo);  
     }          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]));
            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemaxpar, &bage, &fage);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
                fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
     if (fage <= 2) {          }
       bage = agemin;          i=0;
       fage = agemaxpar;          for (k=1; k<=(nlstate);k++){
     }            for (l=1; l<=(nlstate+ndeath);l++){ 
                  i=i++;
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemaxpar,bage,fage);              for (j=1; j<=i;j++){
                  fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
     while((c=getc(ficpar))=='#' && c!= EOF){                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
     ungetc(c,ficpar);              }
     fgets(line, MAXLINE, ficpar);            }
     puts(line);          }/* end of loop for state */
     fputs(line,ficparo);        } /* end of loop for age */
   }  
   ungetc(c,ficpar);        /* Confidence intervalle of pij  */
          /*
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);          fprintf(ficgp,"\nset noparametric;unset label");
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
   while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
     ungetc(c,ficpar);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
     fgets(line, MAXLINE, ficpar);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
     puts(line);        */
     fputs(line,ficparo);  
   }        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
   ungetc(c,ficpar);        first1=1;
          for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
    dateprev1=anprev1+mprev1/12.+jprev1/365.;            if(l2==k2) continue;
    dateprev2=anprev2+mprev2/12.+jprev2/365.;            j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
   fscanf(ficpar,"pop_based=%d\n",&popbased);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
   fprintf(ficparo,"pop_based=%d\n",popbased);                  if(l1==k1) continue;
   fprintf(ficres,"pop_based=%d\n",popbased);                  i=(k1-1)*(nlstate+ndeath)+l1;
                  if(i<=j) continue;
   while((c=getc(ficpar))=='#' && c!= EOF){                for (age=bage; age<=fage; age ++){ 
     ungetc(c,ficpar);                  if ((int)age %5==0){
     fgets(line, MAXLINE, ficpar);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
     puts(line);                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
     fputs(line,ficparo);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
   }                    mu1=mu[i][(int) age]/stepm*YEARM ;
   ungetc(c,ficpar);                    mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
   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);                    /* Computing eigen value of matrix of covariance */
 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);                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
 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);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
 while((c=getc(ficpar))=='#' && c!= EOF){                    /*v21=sqrt(1.-v11*v11); *//* error */
     ungetc(c,ficpar);                    v21=(lc1-v1)/cv12*v11;
     fgets(line, MAXLINE, ficpar);                    v12=-v21;
     puts(line);                    v22=v11;
     fputs(line,ficparo);                    tnalp=v21/v11;
   }                    if(first1==1){
   ungetc(c,ficpar);                      first1=0;
                       printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
   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(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,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);                    /*printf(fignu*/
                     /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
 /*------------ gnuplot -------------*/                      first=0;
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, agemin,agemaxpar,fage, pathc,p);                      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);
 /*------------ free_vector  -------------*/                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
  chdir(path);                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
     :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
  free_ivector(wav,1,imx);  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);                                subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
  free_ivector(num,1,n);                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
  free_vector(agedc,1,n);                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
  fclose(ficparo);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
  fclose(ficres);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
 /*--------- index.htm --------*/                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres);                    }else{
                       first=0;
                        fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
   /*--------------- Prevalence limit --------------*/                      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);
   strcpy(filerespl,"pl");                      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",\
   strcat(filerespl,fileres);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   if((ficrespl=fopen(filerespl,"w"))==NULL) {                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;                    }/* if first */
   }                  } /* age mod 5 */
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);                } /* end loop age */
   fprintf(ficrespl,"#Prevalence limit\n");                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   fprintf(ficrespl,"#Age ");                first=1;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);              } /*l12 */
   fprintf(ficrespl,"\n");            } /* k12 */
            } /*l1 */
   prlim=matrix(1,nlstate,1,nlstate);        }/* k1 */
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      } /* loop covariates */
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    }
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    free_vector(xp,1,npar);
   k=0;    fclose(ficresprob);
   agebase=agemin;    fclose(ficresprobcov);
   agelim=agemaxpar;    fclose(ficresprobcor);
   ftolpl=1.e-10;    fflush(ficgp);
   i1=cptcoveff;    fflush(fichtmcov);
   if (cptcovn < 1){i1=1;}  }
   
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  /******************* Printing html file ***********/
         k=k+1;  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/                    int lastpass, int stepm, int weightopt, char model[],\
         fprintf(ficrespl,"\n#******");                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
         for(j=1;j<=cptcoveff;j++)                    int popforecast, int estepm ,\
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    double jprev1, double mprev1,double anprev1, \
         fprintf(ficrespl,"******\n");                    double jprev2, double mprev2,double anprev2){
            int jj1, k1, i1, cpt;
         for (age=agebase; age<=agelim; age++){    /*char optionfilehtm[FILENAMELENGTH];*/
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    { */
           fprintf(ficrespl,"%.0f",age );  /*     printf("Problem with %s \n",optionfilehtm), exit(0); */
           for(i=1; i<=nlstate;i++)  /*     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
           fprintf(ficrespl," %.5f", prlim[i][i]);  /*   } */
           fprintf(ficrespl,"\n");  
         }     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
       }   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n \
     }   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n \
   fclose(ficrespl);   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n \
    - Life expectancies by age and initial health status (estepm=%2d months): \
   /*------------- h Pij x at various ages ------------*/     <a href=\"%s\">%s</a> <br>\n</li>", \
               jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
   if((ficrespij=fopen(filerespij,"w"))==NULL) {             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   }  
   printf("Computing pij: result on file '%s' \n", filerespij);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
    
   stepsize=(int) (stepm+YEARM-1)/YEARM;   m=cptcoveff;
   /*if (stepm<=24) stepsize=2;*/   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
   agelim=AGESUP;   jj1=0;
   hstepm=stepsize*YEARM; /* Every year of age */   for(k1=1; k1<=m;k1++){
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */     for(i1=1; i1<=ncodemax[k1];i1++){
         jj1++;
   k=0;       if (cptcovn > 0) {
   for(cptcov=1;cptcov<=i1;cptcov++){         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){         for (cpt=1; cpt<=cptcoveff;cpt++) 
       k=k+1;           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
         fprintf(ficrespij,"\n#****** ");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
         for(j=1;j<=cptcoveff;j++)       }
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       /* Pij */
         fprintf(ficrespij,"******\n");       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
          <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */       /* Quasi-incidences */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
           oldm=oldms;savm=savms;         /* Stable prevalence in each health state */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);           for(cpt=1; cpt<nlstate;cpt++){
           fprintf(ficrespij,"# Age");           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
           for(i=1; i<=nlstate;i++)  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
             for(j=1; j<=nlstate+ndeath;j++)         }
               fprintf(ficrespij," %1d-%1d",i,j);       for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(ficrespij,"\n");          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
           for (h=0; h<=nhstepm; h++){  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );       }
             for(i=1; i<=nlstate;i++)       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
               for(j=1; j<=nlstate+ndeath;j++)  health expectancies in states (1) and (2): %s%d.png<br>\
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
             fprintf(ficrespij,"\n");     } /* end i1 */
           }   }/* End k1 */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   fprintf(fichtm,"</ul>");
           fprintf(ficrespij,"\n");  
         }  
     }   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
   }   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
    - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
   fclose(ficrespij);   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n\
    - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n\
    - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
   /*---------- Forecasting ------------------*/           rfileres,rfileres,\
   if((stepm == 1) && (strcmp(model,".")==0)){           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
     free_matrix(mint,1,maxwav,1,n);           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);           subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
     free_vector(weight,1,n);}           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   else{  
     erreur=108;  /*  if(popforecast==1) fprintf(fichtm,"\n */
     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);  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   }  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
    /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*---------- Health expectancies and variances ------------*/  /*    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>");
   strcpy(filerest,"t");  
   strcat(filerest,fileres);   m=cptcoveff;
   if((ficrest=fopen(filerest,"w"))==NULL) {   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;  
   }   jj1=0;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);   for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
   strcpy(filerese,"e");       if (cptcovn > 0) {
   strcat(filerese,fileres);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   if((ficreseij=fopen(filerese,"w"))==NULL) {         for (cpt=1; cpt<=cptcoveff;cpt++) 
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   }         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);       }
        for(cpt=1; cpt<=nlstate;cpt++) {
  strcpy(fileresv,"v");         fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
   strcat(fileresv,fileres);  interval) in state (%d): %s%d%d.png <br>\
   if((ficresvij=fopen(fileresv,"w"))==NULL) {  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);       }
   }     } /* end i1 */
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);   }/* End k1 */
    fprintf(fichtm,"</ul>");
   k=0;   fflush(fichtm);
   for(cptcov=1;cptcov<=i1;cptcov++){  }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;  /******************* Gnuplot file **************/
       fprintf(ficrest,"\n#****** ");  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    char dirfileres[132],optfileres[132];
       fprintf(ficrest,"******\n");    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
       fprintf(ficreseij,"\n#****** ");  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
       for(j=1;j<=cptcoveff;j++)  /*     printf("Problem with file %s",optionfilegnuplot); */
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
       fprintf(ficreseij,"******\n");  /*   } */
   
       fprintf(ficresvij,"\n#****** ");    /*#ifdef windows */
       for(j=1;j<=cptcoveff;j++)    fprintf(ficgp,"cd \"%s\" \n",pathc);
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);      /*#endif */
       fprintf(ficresvij,"******\n");    m=pow(2,cptcoveff);
   
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    strcpy(dirfileres,optionfilefiname);
       oldm=oldms;savm=savms;    strcpy(optfileres,"vpl");
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);     /* 1eme*/
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    for (cpt=1; cpt<= nlstate ; cpt ++) {
       oldm=oldms;savm=savms;     for (k1=1; k1<= m ; k1 ++) {
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
           fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
    set ylabel \"Probability\" \n\
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");  set ter png small\n\
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);  set size 0.65,0.65\n\
       fprintf(ficrest,"\n");  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
       epj=vector(1,nlstate+1);       for (i=1; i<= nlstate ; i ++) {
       for(age=bage; age <=fage ;age++){         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);         else fprintf(ficgp," \%%*lf (\%%*lf)");
         if (popbased==1) {       }
           for(i=1; i<=nlstate;i++)       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);
             prlim[i][i]=probs[(int)age][i][k];       for (i=1; i<= nlstate ; i ++) {
         }         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
                 else fprintf(ficgp," \%%*lf (\%%*lf)");
         fprintf(ficrest," %4.0f",age);       } 
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
           for(i=1, epj[j]=0.;i <=nlstate;i++) {       for (i=1; i<= nlstate ; i ++) {
             epj[j] += prlim[i][i]*eij[i][j][(int)age];         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
           }         else fprintf(ficgp," \%%*lf (\%%*lf)");
           epj[nlstate+1] +=epj[j];       }  
         }       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
         for(i=1, vepp=0.;i <=nlstate;i++)     }
           for(j=1;j <=nlstate;j++)    }
             vepp += vareij[i][j][(int)age];    /*2 eme*/
         fprintf(ficrest," %7.2f (%7.2f)", epj[nlstate+1],sqrt(vepp));    
         for(j=1;j <=nlstate;j++){    for (k1=1; k1<= m ; k1 ++) { 
           fprintf(ficrest," %7.2f (%7.2f)", epj[j],sqrt(vareij[j][j][(int)age]));      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
         }      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
         fprintf(ficrest,"\n");      
       }      for (i=1; i<= nlstate+1 ; i ++) {
     }        k=2*i;
   }        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
   fclose(ficreseij);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   fclose(ficresvij);          else fprintf(ficgp," \%%*lf (\%%*lf)");
   fclose(ficrest);        }   
   fclose(ficpar);        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
   free_vector(epj,1,nlstate+1);        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
          fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
   /*------- Variance limit prevalence------*/          for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   strcpy(fileresvpl,"vpl");          else fprintf(ficgp," \%%*lf (\%%*lf)");
   strcat(fileresvpl,fileres);        }   
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {        fprintf(ficgp,"\" t\"\" w l 0,");
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
     exit(0);        for (j=1; j<= nlstate+1 ; j ++) {
   }          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);          else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
   k=0;        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
   for(cptcov=1;cptcov<=i1;cptcov++){        else fprintf(ficgp,"\" t\"\" w l 0,");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      }
       k=k+1;    }
       fprintf(ficresvpl,"\n#****** ");    
       for(j=1;j<=cptcoveff;j++)    /*3eme*/
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    
       fprintf(ficresvpl,"******\n");    for (k1=1; k1<= m ; k1 ++) { 
            for (cpt=1; cpt<= nlstate ; cpt ++) {
       varpl=matrix(1,nlstate,(int) bage, (int) fage);        k=2+nlstate*(2*cpt-2);
       oldm=oldms;savm=savms;        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        fprintf(ficgp,"set ter png small\n\
     }  set size 0.65,0.65\n\
  }  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   fclose(ficresvpl);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   /*---------- End : free ----------------*/          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
            fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);          
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        */
          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);
   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(matcov,1,npar,1,npar);    /* CV preval stable (period) */
   free_vector(delti,1,npar);    for (k1=1; k1<= m ; k1 ++) { 
   free_matrix(agev,1,maxwav,1,imx);      for (cpt=1; cpt<=nlstate ; cpt ++) {
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);        k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
   if(erreur >0)        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
     printf("End of Imach with error %d\n",erreur);  set ter png small\nset size 0.65,0.65\n\
   else   printf("End of Imach\n");  unset log y\n\
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
          
   /* 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 (i=1; i< nlstate ; i ++)
   /*printf("Total time was %d uSec.\n", total_usecs);*/          fprintf(ficgp,"+$%d",k+i+1);
   /*------ End -----------*/        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
  end:        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
 #ifdef windows        for (i=1; i< nlstate ; i ++) {
   /* chdir(pathcd);*/          l=3+(nlstate+ndeath)*cpt;
 #endif          fprintf(ficgp,"+$%d",l+i+1);
  /*system("wgnuplot graph.plt");*/        }
  /*system("../gp37mgw/wgnuplot graph.plt");*/        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
  /*system("cd ../gp37mgw");*/      } 
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    }  
  strcpy(plotcmd,GNUPLOTPROGRAM);    
  strcat(plotcmd," ");    /* proba elementaires */
  strcat(plotcmd,optionfilegnuplot);    for(i=1,jk=1; i <=nlstate; i++){
  system(plotcmd);      for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
 #ifdef windows          for(j=1; j <=ncovmodel; j++){
   while (z[0] != 'q') {            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
     chdir(path);            jk++; 
     printf("\nType e to edit output files, c to start again, and q for exiting: ");            fprintf(ficgp,"\n");
     scanf("%s",z);          }
     if (z[0] == 'c') system("./imach");        }
     else if (z[0] == 'e') {      }
       chdir(path);     }
       system(optionfilehtm);  
     }     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
     else if (z[0] == 'q') exit(0);       for(jk=1; jk <=m; jk++) {
   }         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
 #endif         if (ng==2)
 }           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     }
   
   } /* end of prwizard */
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int jj, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE]; 
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   
     char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char strstart[80], *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     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); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     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);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     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){
           nberr++;
           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){
           nberr++;
           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){
                   nbwarn++;
                   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)) {
           nberr++;
           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); /* Main html file */
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %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",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     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);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     strcpy(lfileres,fileres);
     strcat(lfileres,"/");
     strcat(lfileres,optionfilefiname);
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);
     printf("\n");
     globpr=1; /* to print the contributions */
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);
     printf("\n");
     if(mle>=1){ /* Could be 1 or 2 */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
       
     /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
     jk=1;
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) 
           {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
       }
     }
     if(mle!=0){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);
             jk++;
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle==1)
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
           i1=(i-1)/(ncovmodel*nlstate)+1; 
           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
           printf("%s%d%d",alph[k],i1,tab[i]);
       */
       fprintf(ficres,"%3d",i);
       if(mle==1)
         printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   
     replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     /*  chdir(path); */
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_lvector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
   /*      }  */
   /*      else{ */
   /*        erreur=108; */
   /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*      } */
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  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\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  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(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
     chdir(path);
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     if((outcmd=system(plotcmd)) != 0){
       printf(" Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.33  
changed lines
  Added in v.1.91


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