Diff for /imach/src/imach.c between versions 1.23 and 1.92

version 1.23, 2002/02/22 18:08:30 version 1.92, 2003/06/25 16:30:45
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolate Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.92  2003/06/25 16:30:45  brouard
      (Module): On windows (cygwin) function asctime_r doesn't
   This program computes Healthy Life Expectancies from    exist so I changed back to asctime which exists.
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a  
   first survey ("cross") where individuals from different ages are    Revision 1.91  2003/06/25 15:30:29  brouard
   interviewed on their health status or degree of disability (in the    * imach.c (Repository): Duplicated warning errors corrected.
   case of a health survey which is our main interest) -2- at least a    (Repository): Elapsed time after each iteration is now output. It
   second wave of interviews ("longitudinal") which measure each change    helps to forecast when convergence will be reached. Elapsed time
   (if any) in individual health status.  Health expectancies are    is stamped in powell.  We created a new html file for the graphs
   computed from the time spent in each health state according to a    concerning matrix of covariance. It has extension -cov.htm.
   model. More health states you consider, more time is necessary to reach the  
   Maximum Likelihood of the parameters involved in the model.  The    Revision 1.90  2003/06/24 12:34:15  brouard
   simplest model is the multinomial logistic model where pij is the    (Module): Some bugs corrected for windows. Also, when
   probabibility to be observed in state j at the second wave    mle=-1 a template is output in file "or"mypar.txt with the design
   conditional to be observed in state i at the first wave. Therefore    of the covariance matrix to be input.
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where  
   'age' is age and 'sex' is a covariate. If you want to have a more    Revision 1.89  2003/06/24 12:30:52  brouard
   complex model than "constant and age", you should modify the program    (Module): Some bugs corrected for windows. Also, when
   where the markup *Covariates have to be included here again* invites    mle=-1 a template is output in file "or"mypar.txt with the design
   you to do it.  More covariates you add, slower the    of the covariance matrix to be input.
   convergence.  
     Revision 1.88  2003/06/23 17:54:56  brouard
   The advantage of this computer programme, compared to a simple    * 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.
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.87  2003/06/18 12:26:01  brouard
   intermediate interview, the information is lost, but taken into    Version 0.96
   account using an interpolation or extrapolation.    
     Revision 1.86  2003/06/17 20:04:08  brouard
   hPijx is the probability to be observed in state i at age x+h    (Module): Change position of html and gnuplot routines and added
   conditional to the observed state i at age x. The delay 'h' can be    routine fileappend.
   split into an exact number (nh*stepm) of unobserved intermediate  
   states. This elementary transition (by month or quarter trimester,    Revision 1.85  2003/06/17 13:12:43  brouard
   semester or year) is model as a multinomial logistic.  The hPx    * imach.c (Repository): Check when date of death was earlier that
   matrix is simply the matrix product of nh*stepm elementary matrices    current date of interview. It may happen when the death was just
   and the contribution of each individual to the likelihood is simply    prior to the death. In this case, dh was negative and likelihood
   hPijx.    was wrong (infinity). We still send an "Error" but patch by
     assuming that the date of death was just one stepm after the
   Also this programme outputs the covariance matrix of the parameters but also    interview.
   of the life expectancies. It also computes the prevalence limits.    (Repository): Because some people have very long ID (first column)
      we changed int to long in num[] and we added a new lvector for
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    memory allocation. But we also truncated to 8 characters (left
            Institut national d'études démographiques, Paris.    truncation)
   This software have been partly granted by Euro-REVES, a concerted action    (Repository): No more line truncation errors.
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.84  2003/06/13 21:44:43  brouard
   software can be distributed freely for non commercial use. Latest version    * imach.c (Repository): Replace "freqsummary" at a correct
   can be accessed at http://euroreves.ined.fr/imach .    place. It differs from routine "prevalence" which may be called
   **********************************************************************/    many times. Probs is memory consuming and must be used with
      parcimony.
 #include <math.h>    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 #include <stdio.h>  
 #include <stdlib.h>    Revision 1.83  2003/06/10 13:39:11  lievre
 #include <unistd.h>    *** empty log message ***
   
 #define MAXLINE 256    Revision 1.82  2003/06/05 15:57:20  brouard
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    Add log in  imach.c and  fullversion number is now printed.
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/  */
 #define windows  /*
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */     Interpolated Markov Chain
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Short summary of the programme:
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    This program computes Healthy Life Expectancies from
     cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 #define NINTERVMAX 8    first survey ("cross") where individuals from different ages are
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    interviewed on their health status or degree of disability (in the
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    case of a health survey which is our main interest) -2- at least a
 #define NCOVMAX 8 /* Maximum number of covariates */    second wave of interviews ("longitudinal") which measure each change
 #define MAXN 20000    (if any) in individual health status.  Health expectancies are
 #define YEARM 12. /* Number of months per year */    computed from the time spent in each health state according to a
 #define AGESUP 130    model. More health states you consider, more time is necessary to reach the
 #define AGEBASE 40    Maximum Likelihood of the parameters involved in the model.  The
     simplest model is the multinomial logistic model where pij is the
     probability to be observed in state j at the second wave
 int erreur; /* Error number */    conditional to be observed in state i at the first wave. Therefore
 int nvar;    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    'age' is age and 'sex' is a covariate. If you want to have a more
 int npar=NPARMAX;    complex model than "constant and age", you should modify the program
 int nlstate=2; /* Number of live states */    where the markup *Covariates have to be included here again* invites
 int ndeath=1; /* Number of dead states */    you to do it.  More covariates you add, slower the
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    convergence.
 int popbased=0;  
     The advantage of this computer programme, compared to a simple
 int *wav; /* Number of waves for this individuual 0 is possible */    multinomial logistic model, is clear when the delay between waves is not
 int maxwav; /* Maxim number of waves */    identical for each individual. Also, if a individual missed an
 int jmin, jmax; /* min, max spacing between 2 waves */    intermediate interview, the information is lost, but taken into
 int mle, weightopt;    account using an interpolation or extrapolation.  
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    hPijx is the probability to be observed in state i at age x+h
 double jmean; /* Mean space between 2 waves */    conditional to the observed state i at age x. The delay 'h' can be
 double **oldm, **newm, **savm; /* Working pointers to matrices */    split into an exact number (nh*stepm) of unobserved intermediate
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    states. This elementary transition (by month, quarter,
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    semester or year) is modelled as a multinomial logistic.  The hPx
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;    matrix is simply the matrix product of nh*stepm elementary matrices
 FILE *ficreseij;    and the contribution of each individual to the likelihood is simply
   char filerese[FILENAMELENGTH];    hPijx.
  FILE  *ficresvij;  
   char fileresv[FILENAMELENGTH];    Also this programme outputs the covariance matrix of the parameters but also
  FILE  *ficresvpl;    of the life expectancies. It also computes the stable prevalence. 
   char fileresvpl[FILENAMELENGTH];    
     Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 #define NR_END 1             Institut national d'études démographiques, Paris.
 #define FREE_ARG char*    This software have been partly granted by Euro-REVES, a concerted action
 #define FTOL 1.0e-10    from the European Union.
     It is copyrighted identically to a GNU software product, ie programme and
 #define NRANSI    software can be distributed freely for non commercial use. Latest version
 #define ITMAX 200    can be accessed at http://euroreves.ined.fr/imach .
   
 #define TOL 2.0e-4    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 #define CGOLD 0.3819660    
 #define ZEPS 1.0e-10    **********************************************************************/
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  /*
     main
 #define GOLD 1.618034    read parameterfile
 #define GLIMIT 100.0    read datafile
 #define TINY 1.0e-20    concatwav
     freqsummary
 static double maxarg1,maxarg2;    if (mle >= 1)
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))      mlikeli
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    print results files
      if mle==1 
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))       computes hessian
 #define rint(a) floor(a+0.5)    read end of parameter file: agemin, agemax, bage, fage, estepm
         begin-prev-date,...
 static double sqrarg;    open gnuplot file
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    open html file
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    stable prevalence
      for age prevalim()
 int imx;    h Pij x
 int stepm;    variance of p varprob
 /* Stepm, step in month: minimum step interpolation*/    forecasting if prevfcast==1 prevforecast call prevalence()
     health expectancies
 int m,nb;    Variance-covariance of DFLE
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    prevalence()
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;     movingaverage()
 double **pmmij, ***probs, ***mobaverage;    varevsij() 
 double dateintmean=0;    if popbased==1 varevsij(,popbased)
     total life expectancies
 double *weight;    Variance of stable prevalence
 int **s; /* Status */   end
 double *agedc, **covar, idx;  */
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
   
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */   
   #include <math.h>
 /**************** split *************************/  #include <stdio.h>
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  #include <stdlib.h>
 {  #include <unistd.h>
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */  #include <sys/time.h>
   #include <time.h>
    l1 = strlen( path );                 /* length of path */  #include "timeval.h"
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
 #ifdef windows  #define MAXLINE 256
    s = strrchr( path, '\\' );           /* find last / */  #define GNUPLOTPROGRAM "gnuplot"
 #else  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
    s = strrchr( path, '/' );            /* find last / */  #define FILENAMELENGTH 132
 #endif  /*#define DEBUG*/
    if ( s == NULL ) {                   /* no directory, so use current */  /*#define windows*/
 #if     defined(__bsd__)                /* get current working directory */  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
       extern char       *getwd( );  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
       if ( getwd( dirc ) == NULL ) {  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 #else  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
       extern char       *getcwd( );  
   #define NINTERVMAX 8
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 #endif  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
          return( GLOCK_ERROR_GETCWD );  #define NCOVMAX 8 /* Maximum number of covariates */
       }  #define MAXN 20000
       strcpy( name, path );             /* we've got it */  #define YEARM 12. /* Number of months per year */
    } else {                             /* strip direcotry from path */  #define AGESUP 130
       s++;                              /* after this, the filename */  #define AGEBASE 40
       l2 = strlen( s );                 /* length of filename */  #ifdef unix
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  #define DIRSEPARATOR '/'
       strcpy( name, s );                /* save file name */  #define ODIRSEPARATOR '\\'
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  #else
       dirc[l1-l2] = 0;                  /* add zero */  #define DIRSEPARATOR '\\'
    }  #define ODIRSEPARATOR '/'
    l1 = strlen( dirc );                 /* length of directory */  #endif
 #ifdef windows  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  /* $Id$ */
 #else  /* $State$ */
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  
 #endif  char version[]="Imach version 0.96a, June 2003, INED-EUROREVES ";
    s = strrchr( name, '.' );            /* find last / */  char fullversion[]="$Revision$ $Date$"; 
    s++;  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
    strcpy(ext,s);                       /* save extension */  int nvar;
    l1= strlen( name);  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
    l2= strlen( s)+1;  int npar=NPARMAX;
    strncpy( finame, name, l1-l2);  int nlstate=2; /* Number of live states */
    finame[l1-l2]= 0;  int ndeath=1; /* Number of dead states */
    return( 0 );                         /* we're done */  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 }  int popbased=0;
   
   int *wav; /* Number of waves for this individuual 0 is possible */
 /******************************************/  int maxwav; /* Maxim number of waves */
   int jmin, jmax; /* min, max spacing between 2 waves */
 void replace(char *s, char*t)  int gipmx, gsw; /* Global variables on the number of contributions 
 {                     to the likelihood and the sum of weights (done by funcone)*/
   int i;  int mle, weightopt;
   int lg=20;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   i=0;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   lg=strlen(t);  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   for(i=0; i<= lg; i++) {             * wave mi and wave mi+1 is not an exact multiple of stepm. */
     (s[i] = t[i]);  double jmean; /* Mean space between 2 waves */
     if (t[i]== '\\') s[i]='/';  double **oldm, **newm, **savm; /* Working pointers to matrices */
   }  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 }  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   FILE *ficlog, *ficrespow;
 int nbocc(char *s, char occ)  int globpr; /* Global variable for printing or not */
 {  double fretone; /* Only one call to likelihood */
   int i,j=0;  long ipmx; /* Number of contributions */
   int lg=20;  double sw; /* Sum of weights */
   i=0;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   lg=strlen(s);  FILE *ficresilk;
   for(i=0; i<= lg; i++) {  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   if  (s[i] == occ ) j++;  FILE *ficresprobmorprev;
   }  FILE *fichtm, *fichtmcov; /* Html File */
   return j;  FILE *ficreseij;
 }  char filerese[FILENAMELENGTH];
   FILE  *ficresvij;
 void cutv(char *u,char *v, char*t, char occ)  char fileresv[FILENAMELENGTH];
 {  FILE  *ficresvpl;
   int i,lg,j,p=0;  char fileresvpl[FILENAMELENGTH];
   i=0;  char title[MAXLINE];
   for(j=0; j<=strlen(t)-1; j++) {  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   }  char tmpout[FILENAMELENGTH]; 
   char command[FILENAMELENGTH];
   lg=strlen(t);  int  outcmd=0;
   for(j=0; j<p; j++) {  
     (u[j] = t[j]);  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   }  char lfileres[FILENAMELENGTH];
      u[p]='\0';  char filelog[FILENAMELENGTH]; /* Log file */
   char filerest[FILENAMELENGTH];
    for(j=0; j<= lg; j++) {  char fileregp[FILENAMELENGTH];
     if (j>=(p+1))(v[j-p-1] = t[j]);  char popfile[FILENAMELENGTH];
   }  
 }  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   
 /********************** nrerror ********************/  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   struct timezone tzp;
 void nrerror(char error_text[])  extern int gettimeofday();
 {  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   fprintf(stderr,"ERREUR ...\n");  long time_value;
   fprintf(stderr,"%s\n",error_text);  extern long time();
   exit(1);  char strcurr[80], strfor[80];
 }  
 /*********************** vector *******************/  #define NR_END 1
 double *vector(int nl, int nh)  #define FREE_ARG char*
 {  #define FTOL 1.0e-10
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  #define NRANSI 
   if (!v) nrerror("allocation failure in vector");  #define ITMAX 200 
   return v-nl+NR_END;  
 }  #define TOL 2.0e-4 
   
 /************************ free vector ******************/  #define CGOLD 0.3819660 
 void free_vector(double*v, int nl, int nh)  #define ZEPS 1.0e-10 
 {  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   free((FREE_ARG)(v+nl-NR_END));  
 }  #define GOLD 1.618034 
   #define GLIMIT 100.0 
 /************************ivector *******************************/  #define TINY 1.0e-20 
 int *ivector(long nl,long nh)  
 {  static double maxarg1,maxarg2;
   int *v;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   if (!v) nrerror("allocation failure in ivector");    
   return v-nl+NR_END;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 }  #define rint(a) floor(a+0.5)
   
 /******************free ivector **************************/  static double sqrarg;
 void free_ivector(int *v, long nl, long nh)  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 {  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   free((FREE_ARG)(v+nl-NR_END));  
 }  int imx; 
   int stepm;
 /******************* imatrix *******************************/  /* Stepm, step in month: minimum step interpolation*/
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  int estepm;
 {  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;  int m,nb;
    long *num;
   /* allocate pointers to rows */  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   if (!m) nrerror("allocation failure 1 in matrix()");  double **pmmij, ***probs;
   m += NR_END;  double dateintmean=0;
   m -= nrl;  
    double *weight;
    int **s; /* Status */
   /* allocate rows and set pointers to them */  double *agedc, **covar, idx;
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   m[nrl] -= ncl;  double ftolhess; /* Tolerance for computing hessian */
    
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  /**************** split *************************/
    static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   /* return pointer to array of pointers to rows */  {
   return m;    char  *ss;                            /* pointer */
 }    int   l1, l2;                         /* length counters */
   
 /****************** free_imatrix *************************/    l1 = strlen(path );                   /* length of path */
 void free_imatrix(m,nrl,nrh,ncl,nch)    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
       int **m;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       long nch,ncl,nrh,nrl;    if ( ss == NULL ) {                   /* no directory, so use current */
      /* free an int matrix allocated by imatrix() */      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 {        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   free((FREE_ARG) (m[nrl]+ncl-NR_END));      /* get current working directory */
   free((FREE_ARG) (m+nrl-NR_END));      /*    extern  char* getcwd ( char *buf , int len);*/
 }      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
         return( GLOCK_ERROR_GETCWD );
 /******************* matrix *******************************/      }
 double **matrix(long nrl, long nrh, long ncl, long nch)      strcpy( name, path );               /* we've got it */
 {    } else {                              /* strip direcotry from path */
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;      ss++;                               /* after this, the filename */
   double **m;      l2 = strlen( ss );                  /* length of filename */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));      strcpy( name, ss );         /* save file name */
   if (!m) nrerror("allocation failure 1 in matrix()");      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   m += NR_END;      dirc[l1-l2] = 0;                    /* add zero */
   m -= nrl;    }
     l1 = strlen( dirc );                  /* length of directory */
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    /*#ifdef windows
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   m[nrl] += NR_END;  #else
   m[nrl] -= ncl;    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   #endif
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    */
   return m;    ss = strrchr( name, '.' );            /* find last / */
 }    ss++;
     strcpy(ext,ss);                       /* save extension */
 /*************************free matrix ************************/    l1= strlen( name);
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    l2= strlen(ss)+1;
 {    strncpy( finame, name, l1-l2);
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    finame[l1-l2]= 0;
   free((FREE_ARG)(m+nrl-NR_END));    return( 0 );                          /* we're done */
 }  }
   
 /******************* ma3x *******************************/  
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  /******************************************/
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  void replace_back_to_slash(char *s, char*t)
   double ***m;  {
     int i;
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    int lg=0;
   if (!m) nrerror("allocation failure 1 in matrix()");    i=0;
   m += NR_END;    lg=strlen(t);
   m -= nrl;    for(i=0; i<= lg; i++) {
       (s[i] = t[i]);
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));      if (t[i]== '\\') s[i]='/';
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    }
   m[nrl] += NR_END;  }
   m[nrl] -= ncl;  
   int nbocc(char *s, char occ)
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  {
     int i,j=0;
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    int lg=20;
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    i=0;
   m[nrl][ncl] += NR_END;    lg=strlen(s);
   m[nrl][ncl] -= nll;    for(i=0; i<= lg; i++) {
   for (j=ncl+1; j<=nch; j++)    if  (s[i] == occ ) j++;
     m[nrl][j]=m[nrl][j-1]+nlay;    }
      return j;
   for (i=nrl+1; i<=nrh; i++) {  }
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)  void cutv(char *u,char *v, char*t, char occ)
       m[i][j]=m[i][j-1]+nlay;  {
   }    /* cuts string t into u and v where u is ended by char occ excluding it
   return m;       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
 }       gives u="abcedf" and v="ghi2j" */
     int i,lg,j,p=0;
 /*************************free ma3x ************************/    i=0;
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    for(j=0; j<=strlen(t)-1; j++) {
 {      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    }
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));    lg=strlen(t);
 }    for(j=0; j<p; j++) {
       (u[j] = t[j]);
 /***************** f1dim *************************/    }
 extern int ncom;       u[p]='\0';
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);     for(j=0; j<= lg; j++) {
        if (j>=(p+1))(v[j-p-1] = t[j]);
 double f1dim(double x)    }
 {  }
   int j;  
   double f;  /********************** nrerror ********************/
   double *xt;  
    void nrerror(char error_text[])
   xt=vector(1,ncom);  {
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    fprintf(stderr,"ERREUR ...\n");
   f=(*nrfunc)(xt);    fprintf(stderr,"%s\n",error_text);
   free_vector(xt,1,ncom);    exit(EXIT_FAILURE);
   return f;  }
 }  /*********************** vector *******************/
   double *vector(int nl, int nh)
 /*****************brent *************************/  {
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    double *v;
 {    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   int iter;    if (!v) nrerror("allocation failure in vector");
   double a,b,d,etemp;    return v-nl+NR_END;
   double fu,fv,fw,fx;  }
   double ftemp;  
   double p,q,r,tol1,tol2,u,v,w,x,xm;  /************************ free vector ******************/
   double e=0.0;  void free_vector(double*v, int nl, int nh)
    {
   a=(ax < cx ? ax : cx);    free((FREE_ARG)(v+nl-NR_END));
   b=(ax > cx ? ax : cx);  }
   x=w=v=bx;  
   fw=fv=fx=(*f)(x);  /************************ivector *******************************/
   for (iter=1;iter<=ITMAX;iter++) {  int *ivector(long nl,long nh)
     xm=0.5*(a+b);  {
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    int *v;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     printf(".");fflush(stdout);    if (!v) nrerror("allocation failure in ivector");
 #ifdef DEBUG    return v-nl+NR_END;
     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)))) { */  
 #endif  /******************free ivector **************************/
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  void free_ivector(int *v, long nl, long nh)
       *xmin=x;  {
       return fx;    free((FREE_ARG)(v+nl-NR_END));
     }  }
     ftemp=fu;  
     if (fabs(e) > tol1) {  /************************lvector *******************************/
       r=(x-w)*(fx-fv);  long *lvector(long nl,long nh)
       q=(x-v)*(fx-fw);  {
       p=(x-v)*q-(x-w)*r;    long *v;
       q=2.0*(q-r);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       if (q > 0.0) p = -p;    if (!v) nrerror("allocation failure in ivector");
       q=fabs(q);    return v-nl+NR_END;
       etemp=e;  }
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  /******************free lvector **************************/
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  void free_lvector(long *v, long nl, long nh)
       else {  {
         d=p/q;    free((FREE_ARG)(v+nl-NR_END));
         u=x+d;  }
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);  /******************* imatrix *******************************/
       }  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     } else {       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  { 
     }    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    int **m; 
     fu=(*f)(u);    
     if (fu <= fx) {    /* allocate pointers to rows */ 
       if (u >= x) a=x; else b=x;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       SHFT(v,w,x,u)    if (!m) nrerror("allocation failure 1 in matrix()"); 
         SHFT(fv,fw,fx,fu)    m += NR_END; 
         } else {    m -= nrl; 
           if (u < x) a=u; else b=u;    
           if (fu <= fw || w == x) {    
             v=w;    /* allocate rows and set pointers to them */ 
             w=u;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
             fv=fw;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
             fw=fu;    m[nrl] += NR_END; 
           } else if (fu <= fv || v == x || v == w) {    m[nrl] -= ncl; 
             v=u;    
             fv=fu;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
           }    
         }    /* return pointer to array of pointers to rows */ 
   }    return m; 
   nrerror("Too many iterations in brent");  } 
   *xmin=x;  
   return fx;  /****************** free_imatrix *************************/
 }  void free_imatrix(m,nrl,nrh,ncl,nch)
         int **m;
 /****************** mnbrak ***********************/        long nch,ncl,nrh,nrl; 
        /* free an int matrix allocated by imatrix() */ 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  { 
             double (*func)(double))    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
 {    free((FREE_ARG) (m+nrl-NR_END)); 
   double ulim,u,r,q, dum;  } 
   double fu;  
    /******************* matrix *******************************/
   *fa=(*func)(*ax);  double **matrix(long nrl, long nrh, long ncl, long nch)
   *fb=(*func)(*bx);  {
   if (*fb > *fa) {    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     SHFT(dum,*ax,*bx,dum)    double **m;
       SHFT(dum,*fb,*fa,dum)  
       }    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   *cx=(*bx)+GOLD*(*bx-*ax);    if (!m) nrerror("allocation failure 1 in matrix()");
   *fc=(*func)(*cx);    m += NR_END;
   while (*fb > *fc) {    m -= nrl;
     r=(*bx-*ax)*(*fb-*fc);  
     q=(*bx-*cx)*(*fb-*fa);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    m[nrl] += NR_END;
     ulim=(*bx)+GLIMIT*(*cx-*bx);    m[nrl] -= ncl;
     if ((*bx-u)*(u-*cx) > 0.0) {  
       fu=(*func)(u);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     } else if ((*cx-u)*(u-ulim) > 0.0) {    return m;
       fu=(*func)(u);    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       if (fu < *fc) {     */
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  }
           SHFT(*fb,*fc,fu,(*func)(u))  
           }  /*************************free matrix ************************/
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       u=ulim;  {
       fu=(*func)(u);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     } else {    free((FREE_ARG)(m+nrl-NR_END));
       u=(*cx)+GOLD*(*cx-*bx);  }
       fu=(*func)(u);  
     }  /******************* ma3x *******************************/
     SHFT(*ax,*bx,*cx,u)  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       SHFT(*fa,*fb,*fc,fu)  {
       }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
 }    double ***m;
   
 /*************** linmin ************************/    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (!m) nrerror("allocation failure 1 in matrix()");
 int ncom;    m += NR_END;
 double *pcom,*xicom;    m -= nrl;
 double (*nrfunc)(double []);  
      m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 {    m[nrl] += NR_END;
   double brent(double ax, double bx, double cx,    m[nrl] -= ncl;
                double (*f)(double), double tol, double *xmin);  
   double f1dim(double x);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  
               double *fc, double (*func)(double));    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   int j;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   double xx,xmin,bx,ax;    m[nrl][ncl] += NR_END;
   double fx,fb,fa;    m[nrl][ncl] -= nll;
      for (j=ncl+1; j<=nch; j++) 
   ncom=n;      m[nrl][j]=m[nrl][j-1]+nlay;
   pcom=vector(1,n);    
   xicom=vector(1,n);    for (i=nrl+1; i<=nrh; i++) {
   nrfunc=func;      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   for (j=1;j<=n;j++) {      for (j=ncl+1; j<=nch; j++) 
     pcom[j]=p[j];        m[i][j]=m[i][j-1]+nlay;
     xicom[j]=xi[j];    }
   }    return m; 
   ax=0.0;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   xx=1.0;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    */
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  }
 #ifdef DEBUG  
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  /*************************free ma3x ************************/
 #endif  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   for (j=1;j<=n;j++) {  {
     xi[j] *= xmin;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     p[j] += xi[j];    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   }    free((FREE_ARG)(m+nrl-NR_END));
   free_vector(xicom,1,n);  }
   free_vector(pcom,1,n);  
 }  /***************** f1dim *************************/
   extern int ncom; 
 /*************** powell ************************/  extern double *pcom,*xicom;
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  extern double (*nrfunc)(double []); 
             double (*func)(double []))   
 {  double f1dim(double x) 
   void linmin(double p[], double xi[], int n, double *fret,  { 
               double (*func)(double []));    int j; 
   int i,ibig,j;    double f;
   double del,t,*pt,*ptt,*xit;    double *xt; 
   double fp,fptt;   
   double *xits;    xt=vector(1,ncom); 
   pt=vector(1,n);    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   ptt=vector(1,n);    f=(*nrfunc)(xt); 
   xit=vector(1,n);    free_vector(xt,1,ncom); 
   xits=vector(1,n);    return f; 
   *fret=(*func)(p);  } 
   for (j=1;j<=n;j++) pt[j]=p[j];  
   for (*iter=1;;++(*iter)) {  /*****************brent *************************/
     fp=(*fret);  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     ibig=0;  { 
     del=0.0;    int iter; 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    double a,b,d,etemp;
     for (i=1;i<=n;i++)    double fu,fv,fw,fx;
       printf(" %d %.12f",i, p[i]);    double ftemp;
     printf("\n");    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     for (i=1;i<=n;i++) {    double e=0.0; 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];   
       fptt=(*fret);    a=(ax < cx ? ax : cx); 
 #ifdef DEBUG    b=(ax > cx ? ax : cx); 
       printf("fret=%lf \n",*fret);    x=w=v=bx; 
 #endif    fw=fv=fx=(*f)(x); 
       printf("%d",i);fflush(stdout);    for (iter=1;iter<=ITMAX;iter++) { 
       linmin(p,xit,n,fret,func);      xm=0.5*(a+b); 
       if (fabs(fptt-(*fret)) > del) {      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
         del=fabs(fptt-(*fret));      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
         ibig=i;      printf(".");fflush(stdout);
       }      fprintf(ficlog,".");fflush(ficlog);
 #ifdef DEBUG  #ifdef DEBUG
       printf("%d %.12e",i,(*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);
       for (j=1;j<=n;j++) {      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
         printf(" x(%d)=%.12e",j,xit[j]);  #endif
       }      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       for(j=1;j<=n;j++)        *xmin=x; 
         printf(" p=%.12e",p[j]);        return fx; 
       printf("\n");      } 
 #endif      ftemp=fu;
     }      if (fabs(e) > tol1) { 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {        r=(x-w)*(fx-fv); 
 #ifdef DEBUG        q=(x-v)*(fx-fw); 
       int k[2],l;        p=(x-v)*q-(x-w)*r; 
       k[0]=1;        q=2.0*(q-r); 
       k[1]=-1;        if (q > 0.0) p = -p; 
       printf("Max: %.12e",(*func)(p));        q=fabs(q); 
       for (j=1;j<=n;j++)        etemp=e; 
         printf(" %.12e",p[j]);        e=d; 
       printf("\n");        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
       for(l=0;l<=1;l++) {          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         for (j=1;j<=n;j++) {        else { 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];          d=p/q; 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);          u=x+d; 
         }          if (u-a < tol2 || b-u < tol2) 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));            d=SIGN(tol1,xm-x); 
       }        } 
 #endif      } else { 
         d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       } 
       free_vector(xit,1,n);      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       free_vector(xits,1,n);      fu=(*f)(u); 
       free_vector(ptt,1,n);      if (fu <= fx) { 
       free_vector(pt,1,n);        if (u >= x) a=x; else b=x; 
       return;        SHFT(v,w,x,u) 
     }          SHFT(fv,fw,fx,fu) 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");          } else { 
     for (j=1;j<=n;j++) {            if (u < x) a=u; else b=u; 
       ptt[j]=2.0*p[j]-pt[j];            if (fu <= fw || w == x) { 
       xit[j]=p[j]-pt[j];              v=w; 
       pt[j]=p[j];              w=u; 
     }              fv=fw; 
     fptt=(*func)(ptt);              fw=fu; 
     if (fptt < fp) {            } else if (fu <= fv || v == x || v == w) { 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);              v=u; 
       if (t < 0.0) {              fv=fu; 
         linmin(p,xit,n,fret,func);            } 
         for (j=1;j<=n;j++) {          } 
           xi[j][ibig]=xi[j][n];    } 
           xi[j][n]=xit[j];    nrerror("Too many iterations in brent"); 
         }    *xmin=x; 
 #ifdef DEBUG    return fx; 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  } 
         for(j=1;j<=n;j++)  
           printf(" %.12e",xit[j]);  /****************** mnbrak ***********************/
         printf("\n");  
 #endif  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       }              double (*func)(double)) 
     }  { 
   }    double ulim,u,r,q, dum;
 }    double fu; 
    
 /**** Prevalence limit ****************/    *fa=(*func)(*ax); 
     *fb=(*func)(*bx); 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    if (*fb > *fa) { 
 {      SHFT(dum,*ax,*bx,dum) 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit        SHFT(dum,*fb,*fa,dum) 
      matrix by transitions matrix until convergence is reached */        } 
     *cx=(*bx)+GOLD*(*bx-*ax); 
   int i, ii,j,k;    *fc=(*func)(*cx); 
   double min, max, maxmin, maxmax,sumnew=0.;    while (*fb > *fc) { 
   double **matprod2();      r=(*bx-*ax)*(*fb-*fc); 
   double **out, cov[NCOVMAX], **pmij();      q=(*bx-*cx)*(*fb-*fa); 
   double **newm;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   double agefin, delaymax=50 ; /* Max number of years to converge */        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       ulim=(*bx)+GLIMIT*(*cx-*bx); 
   for (ii=1;ii<=nlstate+ndeath;ii++)      if ((*bx-u)*(u-*cx) > 0.0) { 
     for (j=1;j<=nlstate+ndeath;j++){        fu=(*func)(u); 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
     }        fu=(*func)(u); 
         if (fu < *fc) { 
    cov[1]=1.;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
              SHFT(*fb,*fc,fu,(*func)(u)) 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */            } 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
     newm=savm;        u=ulim; 
     /* Covariates have to be included here again */        fu=(*func)(u); 
      cov[2]=agefin;      } else { 
          u=(*cx)+GOLD*(*cx-*bx); 
       for (k=1; k<=cptcovn;k++) {        fu=(*func)(u); 
         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]);*/      SHFT(*ax,*bx,*cx,u) 
       }        SHFT(*fa,*fb,*fc,fu) 
       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]]];  /*************** linmin ************************/
   
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  int ncom; 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  double *pcom,*xicom;
   double (*nrfunc)(double []); 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);   
   void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     savm=oldm;  { 
     oldm=newm;    double brent(double ax, double bx, double cx, 
     maxmax=0.;                 double (*f)(double), double tol, double *xmin); 
     for(j=1;j<=nlstate;j++){    double f1dim(double x); 
       min=1.;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       max=0.;                double *fc, double (*func)(double)); 
       for(i=1; i<=nlstate; i++) {    int j; 
         sumnew=0;    double xx,xmin,bx,ax; 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    double fx,fb,fa;
         prlim[i][j]= newm[i][j]/(1-sumnew);   
         max=FMAX(max,prlim[i][j]);    ncom=n; 
         min=FMIN(min,prlim[i][j]);    pcom=vector(1,n); 
       }    xicom=vector(1,n); 
       maxmin=max-min;    nrfunc=func; 
       maxmax=FMAX(maxmax,maxmin);    for (j=1;j<=n;j++) { 
     }      pcom[j]=p[j]; 
     if(maxmax < ftolpl){      xicom[j]=xi[j]; 
       return prlim;    } 
     }    ax=0.0; 
   }    xx=1.0; 
 }    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
 /*************** transition probabilities ***************/  #ifdef DEBUG
     printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 {  #endif
   double s1, s2;    for (j=1;j<=n;j++) { 
   /*double t34;*/      xi[j] *= xmin; 
   int i,j,j1, nc, ii, jj;      p[j] += xi[j]; 
     } 
     for(i=1; i<= nlstate; i++){    free_vector(xicom,1,n); 
     for(j=1; j<i;j++){    free_vector(pcom,1,n); 
       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];  char *asc_diff_time(long time_sec, char ascdiff[])
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  {
       }    long sec_left, days, hours, minutes;
       ps[i][j]=s2;    days = (time_sec) / (60*60*24);
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    sec_left = (time_sec) % (60*60*24);
     }    hours = (sec_left) / (60*60) ;
     for(j=i+1; j<=nlstate+ndeath;j++){    sec_left = (sec_left) %(60*60);
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    minutes = (sec_left) /60;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    sec_left = (sec_left) % (60);
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
       }    return ascdiff;
       ps[i][j]=s2;  }
     }  
   }  /*************** powell ************************/
     /*ps[3][2]=1;*/  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
               double (*func)(double [])) 
   for(i=1; i<= nlstate; i++){  { 
      s1=0;    void linmin(double p[], double xi[], int n, double *fret, 
     for(j=1; j<i; j++)                double (*func)(double [])); 
       s1+=exp(ps[i][j]);    int i,ibig,j; 
     for(j=i+1; j<=nlstate+ndeath; j++)    double del,t,*pt,*ptt,*xit;
       s1+=exp(ps[i][j]);    double fp,fptt;
     ps[i][i]=1./(s1+1.);    double *xits;
     for(j=1; j<i; j++)    int niterf, itmp;
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     for(j=i+1; j<=nlstate+ndeath; j++)    pt=vector(1,n); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    ptt=vector(1,n); 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    xit=vector(1,n); 
   } /* end i */    xits=vector(1,n); 
     *fret=(*func)(p); 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for(jj=1; jj<= nlstate+ndeath; jj++){    for (*iter=1;;++(*iter)) { 
       ps[ii][jj]=0;      fp=(*fret); 
       ps[ii][ii]=1;      ibig=0; 
     }      del=0.0; 
   }      last_time=curr_time;
       (void) gettimeofday(&curr_time,&tzp);
       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);
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){      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);
     for(jj=1; jj<= nlstate+ndeath; jj++){      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
      printf("%lf ",ps[ii][jj]);      for (i=1;i<=n;i++) {
    }        printf(" %d %.12f",i, p[i]);
     printf("\n ");        fprintf(ficlog," %d %.12lf",i, p[i]);
     }        fprintf(ficrespow," %.12lf", p[i]);
     printf("\n ");printf("%lf ",cov[2]);*/      }
 /*      printf("\n");
   for(i=1; i<= npar; i++) printf("%f ",x[i]);      fprintf(ficlog,"\n");
   goto end;*/      fprintf(ficrespow,"\n");fflush(ficrespow);
     return ps;      if(*iter <=3){
 }        tm = *localtime(&curr_time.tv_sec);
         strcpy(strcurr,asctime(&tmf));
 /**************** Product of 2 matrices ******************/  /*       asctime_r(&tm,strcurr); */
         forecast_time=curr_time;
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        itmp = strlen(strcurr);
 {        if(strcurr[itmp-1]=='\n')
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times          strcurr[itmp-1]='\0';
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   /* in, b, out are matrice of pointers which should have been initialized        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
      before: only the contents of out is modified. The function returns        for(niterf=10;niterf<=30;niterf+=10){
      a pointer to pointers identical to out */          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
   long i, j, k;          tmf = *localtime(&forecast_time.tv_sec);
   for(i=nrl; i<= nrh; i++)  /*      asctime_r(&tmf,strfor); */
     for(k=ncolol; k<=ncoloh; k++)          strcpy(strfor,asctime(&tmf));
       for(j=ncl,out[i][k]=0.; j<=nch; j++)          itmp = strlen(strfor);
         out[i][k] +=in[i][j]*b[j][k];          if(strfor[itmp-1]=='\n')
           strfor[itmp-1]='\0';
   return out;          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);
 }          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);
         }
       }
 /************* Higher Matrix Product ***************/      for (i=1;i<=n;i++) { 
         for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )        fptt=(*fret); 
 {  #ifdef DEBUG
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month        printf("fret=%lf \n",*fret);
      duration (i.e. until        fprintf(ficlog,"fret=%lf \n",*fret);
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  #endif
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        printf("%d",i);fflush(stdout);
      (typically every 2 years instead of every month which is too big).        fprintf(ficlog,"%d",i);fflush(ficlog);
      Model is determined by parameters x and covariates have to be        linmin(p,xit,n,fret,func); 
      included manually here.        if (fabs(fptt-(*fret)) > del) { 
           del=fabs(fptt-(*fret)); 
      */          ibig=i; 
         } 
   int i, j, d, h, k;  #ifdef DEBUG
   double **out, cov[NCOVMAX];        printf("%d %.12e",i,(*fret));
   double **newm;        fprintf(ficlog,"%d %.12e",i,(*fret));
         for (j=1;j<=n;j++) {
   /* Hstepm could be zero and should return the unit matrix */          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   for (i=1;i<=nlstate+ndeath;i++)          printf(" x(%d)=%.12e",j,xit[j]);
     for (j=1;j<=nlstate+ndeath;j++){          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       oldm[i][j]=(i==j ? 1.0 : 0.0);        }
       po[i][j][0]=(i==j ? 1.0 : 0.0);        for(j=1;j<=n;j++) {
     }          printf(" p=%.12e",p[j]);
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */          fprintf(ficlog," p=%.12e",p[j]);
   for(h=1; h <=nhstepm; h++){        }
     for(d=1; d <=hstepm; d++){        printf("\n");
       newm=savm;        fprintf(ficlog,"\n");
       /* Covariates have to be included here again */  #endif
       cov[1]=1.;      } 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  #ifdef DEBUG
       for (k=1; k<=cptcovage;k++)        int k[2],l;
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        k[0]=1;
       for (k=1; k<=cptcovprod;k++)        k[1]=-1;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        printf("Max: %.12e",(*func)(p));
         fprintf(ficlog,"Max: %.12e",(*func)(p));
         for (j=1;j<=n;j++) {
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/          printf(" %.12e",p[j]);
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/          fprintf(ficlog," %.12e",p[j]);
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,        }
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        printf("\n");
       savm=oldm;        fprintf(ficlog,"\n");
       oldm=newm;        for(l=0;l<=1;l++) {
     }          for (j=1;j<=n;j++) {
     for(i=1; i<=nlstate+ndeath; i++)            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       for(j=1;j<=nlstate+ndeath;j++) {            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         po[i][j][h]=newm[i][j];            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);          }
          */          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       }          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   } /* end h */        }
   return po;  #endif
 }  
   
         free_vector(xit,1,n); 
 /*************** log-likelihood *************/        free_vector(xits,1,n); 
 double func( double *x)        free_vector(ptt,1,n); 
 {        free_vector(pt,1,n); 
   int i, ii, j, k, mi, d, kk;        return; 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      } 
   double **out;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   double sw; /* Sum of weights */      for (j=1;j<=n;j++) { 
   double lli; /* Individual log likelihood */        ptt[j]=2.0*p[j]-pt[j]; 
   long ipmx;        xit[j]=p[j]-pt[j]; 
   /*extern weight */        pt[j]=p[j]; 
   /* We are differentiating ll according to initial status */      } 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      fptt=(*func)(ptt); 
   /*for(i=1;i<imx;i++)      if (fptt < fp) { 
     printf(" %d\n",s[4][i]);        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   */        if (t < 0.0) { 
   cov[1]=1.;          linmin(p,xit,n,fret,func); 
           for (j=1;j<=n;j++) { 
   for(k=1; k<=nlstate; k++) ll[k]=0.;            xi[j][ibig]=xi[j][n]; 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){            xi[j][n]=xit[j]; 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];          }
     for(mi=1; mi<= wav[i]-1; mi++){  #ifdef DEBUG
       for (ii=1;ii<=nlstate+ndeath;ii++)          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       for(d=0; d<dh[mi][i]; d++){          for(j=1;j<=n;j++){
         newm=savm;            printf(" %.12e",xit[j]);
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;            fprintf(ficlog," %.12e",xit[j]);
         for (kk=1; kk<=cptcovage;kk++) {          }
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];          printf("\n");
         }          fprintf(ficlog,"\n");
          #endif
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        }
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      } 
         savm=oldm;    } 
         oldm=newm;  } 
          
          /**** Prevalence limit (stable prevalence)  ****************/
       } /* end mult */  
        double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  {
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       ipmx +=1;       matrix by transitions matrix until convergence is reached */
       sw += weight[i];  
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    int i, ii,j,k;
     } /* end of wave */    double min, max, maxmin, maxmax,sumnew=0.;
   } /* end of individual */    double **matprod2();
     double **out, cov[NCOVMAX], **pmij();
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    double **newm;
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    double agefin, delaymax=50 ; /* Max number of years to converge */
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  
   return -l;    for (ii=1;ii<=nlstate+ndeath;ii++)
 }      for (j=1;j<=nlstate+ndeath;j++){
         oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       }
 /*********** Maximum Likelihood Estimation ***************/  
      cov[1]=1.;
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))   
 {   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   int i,j, iter;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   double **xi,*delti;      newm=savm;
   double fret;      /* Covariates have to be included here again */
   xi=matrix(1,npar,1,npar);       cov[2]=agefin;
   for (i=1;i<=npar;i++)    
     for (j=1;j<=npar;j++)        for (k=1; k<=cptcovn;k++) {
       xi[i][j]=(i==j ? 1.0 : 0.0);          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   printf("Powell\n");          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
   powell(p,xi,npar,ftol,&iter,&fret,func);        }
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        for (k=1; k<=cptcovprod;k++)
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
 }        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
 /**** Computes Hessian and covariance matrix ***/        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
 {  
   double  **a,**y,*x,pd;      savm=oldm;
   double **hess;      oldm=newm;
   int i, j,jk;      maxmax=0.;
   int *indx;      for(j=1;j<=nlstate;j++){
         min=1.;
   double hessii(double p[], double delta, int theta, double delti[]);        max=0.;
   double hessij(double p[], double delti[], int i, int j);        for(i=1; i<=nlstate; i++) {
   void lubksb(double **a, int npar, int *indx, double b[]) ;          sumnew=0;
   void ludcmp(double **a, int npar, int *indx, double *d) ;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
           prlim[i][j]= newm[i][j]/(1-sumnew);
   hess=matrix(1,npar,1,npar);          max=FMAX(max,prlim[i][j]);
           min=FMIN(min,prlim[i][j]);
   printf("\nCalculation of the hessian matrix. Wait...\n");        }
   for (i=1;i<=npar;i++){        maxmin=max-min;
     printf("%d",i);fflush(stdout);        maxmax=FMAX(maxmax,maxmin);
     hess[i][i]=hessii(p,ftolhess,i,delti);      }
     /*printf(" %f ",p[i]);*/      if(maxmax < ftolpl){
     /*printf(" %lf ",hess[i][i]);*/        return prlim;
   }      }
      }
   for (i=1;i<=npar;i++) {  }
     for (j=1;j<=npar;j++)  {  
       if (j>i) {  /*************** transition probabilities ***************/ 
         printf(".%d%d",i,j);fflush(stdout);  
         hess[i][j]=hessij(p,delti,i,j);  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
         hess[j][i]=hess[i][j];      {
         /*printf(" %lf ",hess[i][j]);*/    double s1, s2;
       }    /*double t34;*/
     }    int i,j,j1, nc, ii, jj;
   }  
   printf("\n");      for(i=1; i<= nlstate; i++){
       for(j=1; j<i;j++){
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
            /*s2 += param[i][j][nc]*cov[nc];*/
   a=matrix(1,npar,1,npar);          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   y=matrix(1,npar,1,npar);          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
   x=vector(1,npar);        }
   indx=ivector(1,npar);        ps[i][j]=s2;
   for (i=1;i<=npar;i++)        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];      }
   ludcmp(a,npar,indx,&pd);      for(j=i+1; j<=nlstate+ndeath;j++){
         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   for (j=1;j<=npar;j++) {          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     for (i=1;i<=npar;i++) x[i]=0;          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
     x[j]=1;        }
     lubksb(a,npar,indx,x);        ps[i][j]=s2;
     for (i=1;i<=npar;i++){      }
       matcov[i][j]=x[i];    }
     }      /*ps[3][2]=1;*/
   }  
     for(i=1; i<= nlstate; i++){
   printf("\n#Hessian matrix#\n");       s1=0;
   for (i=1;i<=npar;i++) {      for(j=1; j<i; j++)
     for (j=1;j<=npar;j++) {        s1+=exp(ps[i][j]);
       printf("%.3e ",hess[i][j]);      for(j=i+1; j<=nlstate+ndeath; j++)
     }        s1+=exp(ps[i][j]);
     printf("\n");      ps[i][i]=1./(s1+1.);
   }      for(j=1; j<i; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];
   /* Recompute Inverse */      for(j=i+1; j<=nlstate+ndeath; j++)
   for (i=1;i<=npar;i++)        ps[i][j]= exp(ps[i][j])*ps[i][i];
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   ludcmp(a,npar,indx,&pd);    } /* end i */
   
   /*  printf("\n#Hessian matrix recomputed#\n");    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       for(jj=1; jj<= nlstate+ndeath; jj++){
   for (j=1;j<=npar;j++) {        ps[ii][jj]=0;
     for (i=1;i<=npar;i++) x[i]=0;        ps[ii][ii]=1;
     x[j]=1;      }
     lubksb(a,npar,indx,x);    }
     for (i=1;i<=npar;i++){  
       y[i][j]=x[i];  
       printf("%.3e ",y[i][j]);    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
     }      for(jj=1; jj<= nlstate+ndeath; jj++){
     printf("\n");       printf("%lf ",ps[ii][jj]);
   }     }
   */      printf("\n ");
       }
   free_matrix(a,1,npar,1,npar);      printf("\n ");printf("%lf ",cov[2]);*/
   free_matrix(y,1,npar,1,npar);  /*
   free_vector(x,1,npar);    for(i=1; i<= npar; i++) printf("%f ",x[i]);
   free_ivector(indx,1,npar);    goto end;*/
   free_matrix(hess,1,npar,1,npar);      return ps;
   }
   
 }  /**************** Product of 2 matrices ******************/
   
 /*************** hessian matrix ****************/  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
 double hessii( double x[], double delta, int theta, double delti[])  {
 {    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   int i;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   int l=1, lmax=20;    /* in, b, out are matrice of pointers which should have been initialized 
   double k1,k2;       before: only the contents of out is modified. The function returns
   double p2[NPARMAX+1];       a pointer to pointers identical to out */
   double res;    long i, j, k;
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    for(i=nrl; i<= nrh; i++)
   double fx;      for(k=ncolol; k<=ncoloh; k++)
   int k=0,kmax=10;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
   double l1;          out[i][k] +=in[i][j]*b[j][k];
   
   fx=func(x);    return out;
   for (i=1;i<=npar;i++) p2[i]=x[i];  }
   for(l=0 ; l <=lmax; l++){  
     l1=pow(10,l);  
     delts=delt;  /************* Higher Matrix Product ***************/
     for(k=1 ; k <kmax; k=k+1){  
       delt = delta*(l1*k);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
       p2[theta]=x[theta] +delt;  {
       k1=func(p2)-fx;    /* Computes the transition matrix starting at age 'age' over 
       p2[theta]=x[theta]-delt;       'nhstepm*hstepm*stepm' months (i.e. until
       k2=func(p2)-fx;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
       /*res= (k1-2.0*fx+k2)/delt/delt; */       nhstepm*hstepm matrices. 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
             (typically every 2 years instead of every month which is too big 
 #ifdef DEBUG       for the memory).
       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);       Model is determined by parameters x and covariates have to be 
 #endif       included manually here. 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */  
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){       */
         k=kmax;  
       }    int i, j, d, h, k;
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    double **out, cov[NCOVMAX];
         k=kmax; l=lmax*10.;    double **newm;
       }  
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    /* Hstepm could be zero and should return the unit matrix */
         delts=delt;    for (i=1;i<=nlstate+ndeath;i++)
       }      for (j=1;j<=nlstate+ndeath;j++){
     }        oldm[i][j]=(i==j ? 1.0 : 0.0);
   }        po[i][j][0]=(i==j ? 1.0 : 0.0);
   delti[theta]=delts;      }
   return res;    /* 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;
 double hessij( double x[], double delti[], int thetai,int thetaj)        /* Covariates have to be included here again */
 {        cov[1]=1.;
   int i;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   int l=1, l1, lmax=20;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   double k1,k2,k3,k4,res,fx;        for (k=1; k<=cptcovage;k++)
   double p2[NPARMAX+1];          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   int k;        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]]];
   fx=func(x);  
   for (k=1; k<=2; k++) {  
     for (i=1;i<=npar;i++) p2[i]=x[i];        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
     p2[thetai]=x[thetai]+delti[thetai]/k;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
     k1=func(p2)-fx;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
          savm=oldm;
     p2[thetai]=x[thetai]+delti[thetai]/k;        oldm=newm;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      }
     k2=func(p2)-fx;      for(i=1; i<=nlstate+ndeath; i++)
          for(j=1;j<=nlstate+ndeath;j++) {
     p2[thetai]=x[thetai]-delti[thetai]/k;          po[i][j][h]=newm[i][j];
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
     k3=func(p2)-fx;           */
          }
     p2[thetai]=x[thetai]-delti[thetai]/k;    } /* end h */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    return po;
     k4=func(p2)-fx;  }
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  
 #ifdef DEBUG  
     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);  /*************** log-likelihood *************/
 #endif  double func( double *x)
   }  {
   return res;    int i, ii, j, k, mi, d, kk;
 }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     double **out;
 /************** Inverse of matrix **************/    double sw; /* Sum of weights */
 void ludcmp(double **a, int n, int *indx, double *d)    double lli; /* Individual log likelihood */
 {    int s1, s2;
   int i,imax,j,k;    double bbh, survp;
   double big,dum,sum,temp;    long ipmx;
   double *vv;    /*extern weight */
      /* We are differentiating ll according to initial status */
   vv=vector(1,n);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   *d=1.0;    /*for(i=1;i<imx;i++) 
   for (i=1;i<=n;i++) {      printf(" %d\n",s[4][i]);
     big=0.0;    */
     for (j=1;j<=n;j++)    cov[1]=1.;
       if ((temp=fabs(a[i][j])) > big) big=temp;  
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    for(k=1; k<=nlstate; k++) ll[k]=0.;
     vv[i]=1.0/big;  
   }    if(mle==1){
   for (j=1;j<=n;j++) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for (i=1;i<j;i++) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       sum=a[i][j];        for(mi=1; mi<= wav[i]-1; mi++){
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];          for (ii=1;ii<=nlstate+ndeath;ii++)
       a[i][j]=sum;            for (j=1;j<=nlstate+ndeath;j++){
     }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     big=0.0;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     for (i=j;i<=n;i++) {            }
       sum=a[i][j];          for(d=0; d<dh[mi][i]; d++){
       for (k=1;k<j;k++)            newm=savm;
         sum -= a[i][k]*a[k][j];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       a[i][j]=sum;            for (kk=1; kk<=cptcovage;kk++) {
       if ( (dum=vv[i]*fabs(sum)) >= big) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         big=dum;            }
         imax=i;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     }            savm=oldm;
     if (j != imax) {            oldm=newm;
       for (k=1;k<=n;k++) {          } /* end mult */
         dum=a[imax][k];        
         a[imax][k]=a[j][k];          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         a[j][k]=dum;          /* But now since version 0.9 we anticipate for bias and large stepm.
       }           * If stepm is larger than one month (smallest stepm) and if the exact delay 
       *d = -(*d);           * (in months) between two waves is not a multiple of stepm, we rounded to 
       vv[imax]=vv[j];           * 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
     indx[j]=imax;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     if (a[j][j] == 0.0) a[j][j]=TINY;           * probability in order to take into account the bias as a fraction of the way
     if (j != n) {           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
       dum=1.0/(a[j][j]);           * -stepm/2 to stepm/2 .
       for (i=j+1;i<=n;i++) a[i][j] *= dum;           * For stepm=1 the results are the same as for previous versions of Imach.
     }           * For stepm > 1 the results are less biased than in previous versions. 
   }           */
   free_vector(vv,1,n);  /* Doesn't work */          s1=s[mw[mi][i]][i];
 ;          s2=s[mw[mi+1][i]][i];
 }          bbh=(double)bh[mi][i]/(double)stepm; 
           /* bias is positive if real duration
 void lubksb(double **a, int n, int *indx, double b[])           * is higher than the multiple of stepm and negative otherwise.
 {           */
   int i,ii=0,ip,j;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   double sum;          if( s2 > nlstate){ 
              /* i.e. if s2 is a death state and if the date of death is known then the contribution
   for (i=1;i<=n;i++) {               to the likelihood is the probability to die between last step unit time and current 
     ip=indx[i];               step unit time, which is also the differences between probability to die before dh 
     sum=b[ip];               and probability to die before dh-stepm . 
     b[ip]=b[i];               In version up to 0.92 likelihood was computed
     if (ii)          as if date of death was unknown. Death was treated as any other
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          health state: the date of the interview describes the actual state
     else if (sum) ii=i;          and not the date of a change in health state. The former idea was
     b[i]=sum;          to consider that at each interview the state was recorded
   }          (healthy, disable or death) and IMaCh was corrected; but when we
   for (i=n;i>=1;i--) {          introduced the exact date of death then we should have modified
     sum=b[i];          the contribution of an exact death to the likelihood. This new
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          contribution is smaller and very dependent of the step unit
     b[i]=sum/a[i][i];          stepm. It is no more the probability to die between last interview
   }          and month of death but the probability to survive from last
 }          interview up to one month before death multiplied by the
           probability to die within a month. Thanks to Chris
 /************ Frequencies ********************/          Jackson for correcting this bug.  Former versions increased
 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)          mortality artificially. The bad side is that we add another loop
 {  /* Some frequencies */          which slows down the processing. The difference can be up to 10%
            lower mortality.
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;            */
   double ***freq; /* Frequencies */            lli=log(out[s1][s2] - savm[s1][s2]);
   double *pp;          }else{
   double pos, k2, dateintsum=0,k2cpt=0;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   FILE *ficresp;            /*  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 */
   char fileresp[FILENAMELENGTH];          } 
           /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   pp=vector(1,nlstate);          /*if(lli ==000.0)*/
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          /*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); */
   strcpy(fileresp,"p");          ipmx +=1;
   strcat(fileresp,fileres);          sw += weight[i];
   if((ficresp=fopen(fileresp,"w"))==NULL) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     printf("Problem with prevalence resultfile: %s\n", fileresp);        } /* end of wave */
     exit(0);      } /* end of individual */
   }    }  else if(mle==2){
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   j1=0;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
   j=cptcoveff;          for (ii=1;ii<=nlstate+ndeath;ii++)
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   for(k1=1; k1<=j;k1++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
    for(i1=1; i1<=ncodemax[k1];i1++){            }
        j1++;          for(d=0; d<=dh[mi][i]; d++){
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);            newm=savm;
          scanf("%d", i);*/            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         for (i=-1; i<=nlstate+ndeath; i++)              for (kk=1; kk<=cptcovage;kk++) {
          for (jk=-1; jk<=nlstate+ndeath; jk++)                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
            for(m=agemin; m <= agemax+3; m++)            }
              freq[i][jk][m]=0;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         dateintsum=0;            savm=oldm;
         k2cpt=0;            oldm=newm;
        for (i=1; i<=imx; i++) {          } /* end mult */
          bool=1;        
          if  (cptcovn>0) {          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
            for (z1=1; z1<=cptcoveff; z1++)          /* But now since version 0.9 we anticipate for bias and large stepm.
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])           * If stepm is larger than one month (smallest stepm) and if the exact delay 
                bool=0;           * (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
          if (bool==1) {           * we keep into memory the bias bh[mi][i] and also the previous matrix product
            for(m=firstpass; m<=lastpass; m++){           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
              k2=anint[m][i]+(mint[m][i]/12.);           * probability in order to take into account the bias as a fraction of the way
              if ((k2>=dateprev1) && (k2<=dateprev2)) {           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
                if(agev[m][i]==0) agev[m][i]=agemax+1;           * -stepm/2 to stepm/2 .
                if(agev[m][i]==1) agev[m][i]=agemax+2;           * For stepm=1 the results are the same as for previous versions of Imach.
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];           * For stepm > 1 the results are less biased than in previous versions. 
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];           */
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {          s1=s[mw[mi][i]][i];
                  dateintsum=dateintsum+k2;          s2=s[mw[mi+1][i]][i];
                  k2cpt++;          bbh=(double)bh[mi][i]/(double)stepm; 
                }          /* bias is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
              }           */
            }          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
          }          /* 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 */
         if  (cptcovn>0) {          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
          fprintf(ficresp, "\n#********** Variable ");          /*if(lli ==000.0)*/
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          /*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); */
        fprintf(ficresp, "**********\n#");          ipmx +=1;
         }          sw += weight[i];
        for(i=1; i<=nlstate;i++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        } /* end of wave */
        fprintf(ficresp, "\n");      } /* end of individual */
            }  else if(mle==3){  /* exponential inter-extrapolation */
   for(i=(int)agemin; i <= (int)agemax+3; i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     if(i==(int)agemax+3)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       printf("Total");        for(mi=1; mi<= wav[i]-1; mi++){
     else          for (ii=1;ii<=nlstate+ndeath;ii++)
       printf("Age %d", i);            for (j=1;j<=nlstate+ndeath;j++){
     for(jk=1; jk <=nlstate ; jk++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         pp[jk] += freq[jk][m][i];            }
     }          for(d=0; d<dh[mi][i]; d++){
     for(jk=1; jk <=nlstate ; jk++){            newm=savm;
       for(m=-1, pos=0; m <=0 ; m++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         pos += freq[jk][m][i];            for (kk=1; kk<=cptcovage;kk++) {
       if(pp[jk]>=1.e-10)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);            }
       else            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     }            savm=oldm;
             oldm=newm;
      for(jk=1; jk <=nlstate ; jk++){          } /* end mult */
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        
         pp[jk] += freq[jk][m][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 stepm is larger than one month (smallest stepm) and if the exact delay 
     for(jk=1,pos=0; jk <=nlstate ; jk++)           * (in months) between two waves is not a multiple of stepm, we rounded to 
       pos += pp[jk];           * the nearest (and in case of equal distance, to the lowest) interval but now
     for(jk=1; jk <=nlstate ; jk++){           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       if(pos>=1.e-5)           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);           * probability in order to take into account the bias as a fraction of the way
       else           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);           * -stepm/2 to stepm/2 .
       if( i <= (int) agemax){           * For stepm=1 the results are the same as for previous versions of Imach.
         if(pos>=1.e-5){           * For stepm > 1 the results are less biased than in previous versions. 
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);           */
           probs[i][jk][j1]= pp[jk]/pos;          s1=s[mw[mi][i]][i];
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/          s2=s[mw[mi+1][i]][i];
         }          bbh=(double)bh[mi][i]/(double)stepm; 
       else          /* bias is positive if real duration
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);           * is higher than the multiple of stepm and negative otherwise.
       }           */
     }          /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
     for(jk=-1; jk <=nlstate+ndeath; jk++)          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 */
       for(m=-1; m <=nlstate+ndeath; m++)          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          /*if(lli ==000.0)*/
     if(i <= (int) agemax)          /*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); */
       fprintf(ficresp,"\n");          ipmx +=1;
     printf("\n");          sw += weight[i];
     }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }        } /* end of wave */
  }      } /* end of individual */
   dateintmean=dateintsum/k2cpt;    }else if (mle==4){  /* ml=4 no inter-extrapolation */
        for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   fclose(ficresp);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        for(mi=1; mi<= wav[i]-1; mi++){
   free_vector(pp,1,nlstate);          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
   /* End of Freq */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
 /************ Prevalence ********************/          for(d=0; d<dh[mi][i]; d++){
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)            newm=savm;
 {  /* Some frequencies */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
              for (kk=1; kk<=cptcovage;kk++) {
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double ***freq; /* Frequencies */            }
   double *pp;          
   double pos, k2;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   pp=vector(1,nlstate);            savm=oldm;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            oldm=newm;
            } /* end mult */
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        
   j1=0;          s1=s[mw[mi][i]][i];
            s2=s[mw[mi+1][i]][i];
   j=cptcoveff;          if( s2 > nlstate){ 
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            lli=log(out[s1][s2] - savm[s1][s2]);
            }else{
  for(k1=1; k1<=j;k1++){            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     for(i1=1; i1<=ncodemax[k1];i1++){          }
       j1++;          ipmx +=1;
            sw += weight[i];
       for (i=-1; i<=nlstate+ndeath; i++)            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         for (jk=-1; jk<=nlstate+ndeath; jk++)    /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
           for(m=agemin; m <= agemax+3; m++)        } /* end of wave */
             freq[i][jk][m]=0;      } /* end of individual */
          }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       for (i=1; i<=imx; i++) {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         bool=1;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         if  (cptcovn>0) {        for(mi=1; mi<= wav[i]-1; mi++){
           for (z1=1; z1<=cptcoveff; z1++)          for (ii=1;ii<=nlstate+ndeath;ii++)
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])            for (j=1;j<=nlstate+ndeath;j++){
               bool=0;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         if (bool==1) {            }
           for(m=firstpass; m<=lastpass; m++){          for(d=0; d<dh[mi][i]; d++){
             k2=anint[m][i]+(mint[m][i]/12.);            newm=savm;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
               if(agev[m][i]==0) agev[m][i]=agemax+1;            for (kk=1; kk<=cptcovage;kk++) {
               if(agev[m][i]==1) agev[m][i]=agemax+2;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];            }
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];            
             }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         }            savm=oldm;
       }            oldm=newm;
                } /* end mult */
         for(i=(int)agemin; i <= (int)agemax+3; i++){        
           for(jk=1; jk <=nlstate ; jk++){          s1=s[mw[mi][i]][i];
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          s2=s[mw[mi+1][i]][i];
               pp[jk] += freq[jk][m][i];          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           }          ipmx +=1;
           for(jk=1; jk <=nlstate ; jk++){          sw += weight[i];
             for(m=-1, pos=0; m <=0 ; m++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             pos += freq[jk][m][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]);*/
         }        } /* end of wave */
              } /* end of individual */
          for(jk=1; jk <=nlstate ; jk++){    } /* End of if */
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
              pp[jk] += freq[jk][m][i];    /* 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;
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];  }
   
          for(jk=1; jk <=nlstate ; jk++){            /*************** log-likelihood *************/
            if( i <= (int) agemax){  double funcone( double *x)
              if(pos>=1.e-5){  {
                probs[i][jk][j1]= pp[jk]/pos;    /* Same as likeli but slower because of a lot of printf and if */
              }    int i, ii, j, k, mi, d, kk;
            }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
          }    double **out;
              double lli; /* Individual log likelihood */
         }    double llt;
     }    int s1, s2;
   }    double bbh, survp;
      /*extern weight */
      /* We are differentiating ll according to initial status */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   free_vector(pp,1,nlstate);    /*for(i=1;i<imx;i++) 
        printf(" %d\n",s[4][i]);
 }  /* End of Freq */    */
     cov[1]=1.;
 /************* Waves Concatenation ***************/  
     for(k=1; k<=nlstate; k++) ll[k]=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)  
 {    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
      Death is a valid wave (if date is known).      for(mi=1; mi<= wav[i]-1; mi++){
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i        for (ii=1;ii<=nlstate+ndeath;ii++)
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          for (j=1;j<=nlstate+ndeath;j++){
      and mw[mi+1][i]. dh depends on stepm.            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      */            savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }
   int i, mi, m;        for(d=0; d<dh[mi][i]; d++){
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;          newm=savm;
      double sum=0., jmean=0.;*/          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for (kk=1; kk<=cptcovage;kk++) {
   int j, k=0,jk, ju, jl;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double sum=0.;          }
   jmin=1e+5;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   jmax=-1;                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   jmean=0.;          savm=oldm;
   for(i=1; i<=imx; i++){          oldm=newm;
     mi=0;        } /* end mult */
     m=firstpass;        
     while(s[m][i] <= nlstate){        s1=s[mw[mi][i]][i];
       if(s[m][i]>=1)        s2=s[mw[mi+1][i]][i];
         mw[++mi][i]=m;        bbh=(double)bh[mi][i]/(double)stepm; 
       if(m >=lastpass)        /* bias is positive if real duration
         break;         * is higher than the multiple of stepm and negative otherwise.
       else         */
         m++;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
     }/* end while */          lli=log(out[s1][s2] - savm[s1][s2]);
     if (s[m][i] > nlstate){        } else if (mle==1){
       mi++;     /* Death is another wave */          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       /* if(mi==0)  never been interviewed correctly before death */        } else if(mle==2){
          /* Only death is a correct wave */          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 */
       mw[mi][i]=m;        } else if(mle==3){  /* exponential inter-extrapolation */
     }          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
         } else if (mle==4){  /* mle=4 no inter-extrapolation */
     wav[i]=mi;          lli=log(out[s1][s2]); /* Original formula */
     if(mi==0)        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          lli=log(out[s1][s2]); /* Original formula */
   }        } /* End of if */
         ipmx +=1;
   for(i=1; i<=imx; i++){        sw += weight[i];
     for(mi=1; mi<wav[i];mi++){        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       if (stepm <=0)  /*       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]); */
         dh[mi][i]=1;        if(globpr){
       else{          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
         if (s[mw[mi+1][i]][i] > nlstate) {   %10.6f %10.6f %10.6f ", \
           if (agedc[i] < 2*AGESUP) {                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
           if(j==0) j=1;  /* Survives at least one month after exam */          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
           k=k+1;            llt +=ll[k]*gipmx/gsw;
           if (j >= jmax) jmax=j;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           if (j <= jmin) jmin=j;          }
           sum=sum+j;          fprintf(ficresilk," %10.6f\n", -llt);
           /* if (j<10) printf("j=%d num=%d ",j,i); */        }
           }      } /* end of wave */
         }    } /* end of individual */
         else{    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
           k=k+1;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
           if (j >= jmax) jmax=j;    if(globpr==0){ /* First time we count the contributions and weights */
           else if (j <= jmin)jmin=j;      gipmx=ipmx;
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */      gsw=sw;
           sum=sum+j;    }
         }    return -l;
         jk= j/stepm;  }
         jl= j -jk*stepm;  
         ju= j -(jk+1)*stepm;  char *subdirf(char fileres[])
         if(jl <= -ju)  {
           dh[mi][i]=jk;    /* Caution optionfilefiname is hidden */
         else    strcpy(tmpout,optionfilefiname);
           dh[mi][i]=jk+1;    strcat(tmpout,"/"); /* Add to the right */
         if(dh[mi][i]==0)    strcat(tmpout,fileres);
           dh[mi][i]=1; /* At least one step */    return tmpout;
       }  }
     }  
   }  char *subdirf2(char fileres[], char *preop)
   jmean=sum/k;  {
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    
  }    strcpy(tmpout,optionfilefiname);
 /*********** Tricode ****************************/    strcat(tmpout,"/");
 void tricode(int *Tvar, int **nbcode, int imx)    strcat(tmpout,preop);
 {    strcat(tmpout,fileres);
   int Ndum[20],ij=1, k, j, i;    return tmpout;
   int cptcode=0;  }
   cptcoveff=0;  char *subdirf3(char fileres[], char *preop, char *preop2)
    {
   for (k=0; k<19; k++) Ndum[k]=0;    
   for (k=1; k<=7; k++) ncodemax[k]=0;    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    strcat(tmpout,preop);
     for (i=1; i<=imx; i++) {    strcat(tmpout,preop2);
       ij=(int)(covar[Tvar[j]][i]);    strcat(tmpout,fileres);
       Ndum[ij]++;    return tmpout;
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  }
       if (ij > cptcode) cptcode=ij;  
     }  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   {
     for (i=0; i<=cptcode; i++) {    /* This routine should help understanding what is done with 
       if(Ndum[i]!=0) ncodemax[j]++;       the selection of individuals/waves and
     }       to check the exact contribution to the likelihood.
     ij=1;       Plotting could be done.
      */
     int k;
     for (i=1; i<=ncodemax[j]; i++) {  
       for (k=0; k<=19; k++) {    if(*globpri !=0){ /* Just counts and sums, no printings */
         if (Ndum[k] != 0) {      strcpy(fileresilk,"ilk"); 
           nbcode[Tvar[j]][ij]=k;      strcat(fileresilk,fileres);
           ij++;      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         }        printf("Problem with resultfile: %s\n", fileresilk);
         if (ij > ncodemax[j]) break;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }        }
     }      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
   }        fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
  for (k=0; k<19; k++) Ndum[k]=0;      for(k=1; k<=nlstate; k++) 
         fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
  for (i=1; i<=ncovmodel-2; i++) {      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
       ij=Tvar[i];    }
       Ndum[ij]++;  
     }    *fretone=(*funcone)(p);
     if(*globpri !=0){
  ij=1;      fclose(ficresilk);
  for (i=1; i<=10; i++) {      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
    if((Ndum[i]!=0) && (i<=ncov)){      fflush(fichtm); 
      Tvaraff[ij]=i;    } 
      ij++;    return;
    }  }
  }  
    
     cptcoveff=ij-1;  /*********** Maximum Likelihood Estimation ***************/
 }  
   void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
 /*********** Health Expectancies ****************/  {
     int i,j, iter;
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)    double **xi;
 {    double fret;
   /* Health expectancies */    double fretone; /* Only one call to likelihood */
   int i, j, nhstepm, hstepm, h;    char filerespow[FILENAMELENGTH];
   double age, agelim,hf;    xi=matrix(1,npar,1,npar);
   double ***p3mat;    for (i=1;i<=npar;i++)
        for (j=1;j<=npar;j++)
   fprintf(ficreseij,"# Health expectancies\n");        xi[i][j]=(i==j ? 1.0 : 0.0);
   fprintf(ficreseij,"# Age");    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   for(i=1; i<=nlstate;i++)    strcpy(filerespow,"pow"); 
     for(j=1; j<=nlstate;j++)    strcat(filerespow,fileres);
       fprintf(ficreseij," %1d-%1d",i,j);    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   fprintf(ficreseij,"\n");      printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   hstepm=1*YEARM; /*  Every j years of age (in month) */    }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     for (i=1;i<=nlstate;i++)
   agelim=AGESUP;      for(j=1;j<=nlstate+ndeath;j++)
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     /* nhstepm age range expressed in number of stepm */    fprintf(ficrespow,"\n");
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);  
     /* Typically if 20 years = 20*12/6=40 stepm */    powell(p,xi,npar,ftol,&iter,&fret,func);
     if (stepm >= YEARM) hstepm=1;  
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */    fclose(ficrespow);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);    
   }
   
     for(i=1; i<=nlstate;i++)  /**** Computes Hessian and covariance matrix ***/
       for(j=1; j<=nlstate;j++)  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){  {
           eij[i][j][(int)age] +=p3mat[i][j][h];    double  **a,**y,*x,pd;
         }    double **hess;
        int i, j,jk;
     hf=1;    int *indx;
     if (stepm >= YEARM) hf=stepm/YEARM;  
     fprintf(ficreseij,"%.0f",age );    double hessii(double p[], double delta, int theta, double delti[]);
     for(i=1; i<=nlstate;i++)    double hessij(double p[], double delti[], int i, int j);
       for(j=1; j<=nlstate;j++){    void lubksb(double **a, int npar, int *indx, double b[]) ;
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);    void ludcmp(double **a, int npar, int *indx, double *d) ;
       }  
     fprintf(ficreseij,"\n");    hess=matrix(1,npar,1,npar);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   }    printf("\nCalculation of the hessian matrix. Wait...\n");
 }    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     for (i=1;i<=npar;i++){
 /************ Variance ******************/      printf("%d",i);fflush(stdout);
 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)      fprintf(ficlog,"%d",i);fflush(ficlog);
 {      hess[i][i]=hessii(p,ftolhess,i,delti);
   /* Variance of health expectancies */      /*printf(" %f ",p[i]);*/
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      /*printf(" %lf ",hess[i][i]);*/
   double **newm;    }
   double **dnewm,**doldm;    
   int i, j, nhstepm, hstepm, h;    for (i=1;i<=npar;i++) {
   int k, cptcode;      for (j=1;j<=npar;j++)  {
   double *xp;        if (j>i) { 
   double **gp, **gm;          printf(".%d%d",i,j);fflush(stdout);
   double ***gradg, ***trgradg;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   double ***p3mat;          hess[i][j]=hessij(p,delti,i,j);
   double age,agelim;          hess[j][i]=hess[i][j];    
   int theta;          /*printf(" %lf ",hess[i][j]);*/
         }
    fprintf(ficresvij,"# Covariances of life expectancies\n");      }
   fprintf(ficresvij,"# Age");    }
   for(i=1; i<=nlstate;i++)    printf("\n");
     for(j=1; j<=nlstate;j++)    fprintf(ficlog,"\n");
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);  
   fprintf(ficresvij,"\n");    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   xp=vector(1,npar);    
   dnewm=matrix(1,nlstate,1,npar);    a=matrix(1,npar,1,npar);
   doldm=matrix(1,nlstate,1,nlstate);    y=matrix(1,npar,1,npar);
      x=vector(1,npar);
   hstepm=1*YEARM; /* Every year of age */    indx=ivector(1,npar);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    for (i=1;i<=npar;i++)
   agelim = AGESUP;      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    ludcmp(a,npar,indx,&pd);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  
     if (stepm >= YEARM) hstepm=1;    for (j=1;j<=npar;j++) {
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      for (i=1;i<=npar;i++) x[i]=0;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      x[j]=1;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      lubksb(a,npar,indx,x);
     gp=matrix(0,nhstepm,1,nlstate);      for (i=1;i<=npar;i++){ 
     gm=matrix(0,nhstepm,1,nlstate);        matcov[i][j]=x[i];
       }
     for(theta=1; theta <=npar; theta++){    }
       for(i=1; i<=npar; i++){ /* Computes gradient */  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    printf("\n#Hessian matrix#\n");
       }    fprintf(ficlog,"\n#Hessian matrix#\n");
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      for (i=1;i<=npar;i++) { 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      for (j=1;j<=npar;j++) { 
         printf("%.3e ",hess[i][j]);
       if (popbased==1) {        fprintf(ficlog,"%.3e ",hess[i][j]);
         for(i=1; i<=nlstate;i++)      }
           prlim[i][i]=probs[(int)age][i][ij];      printf("\n");
       }      fprintf(ficlog,"\n");
          }
       for(j=1; j<= nlstate; j++){  
         for(h=0; h<=nhstepm; h++){    /* Recompute Inverse */
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    for (i=1;i<=npar;i++)
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
         }    ludcmp(a,npar,indx,&pd);
       }  
        /*  printf("\n#Hessian matrix recomputed#\n");
       for(i=1; i<=npar; i++) /* Computes gradient */  
         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, gm[h][j]=0.;i<=nlstate;i++)    }
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    */
         }  
       }    free_matrix(a,1,npar,1,npar);
     free_matrix(y,1,npar,1,npar);
       for(j=1; j<= nlstate; j++)    free_vector(x,1,npar);
         for(h=0; h<=nhstepm; h++){    free_ivector(indx,1,npar);
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    free_matrix(hess,1,npar,1,npar);
         }  
     } /* End theta */  
   }
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);  
   /*************** hessian matrix ****************/
     for(h=0; h<=nhstepm; h++)  double hessii( double x[], double delta, int theta, double delti[])
       for(j=1; j<=nlstate;j++)  {
         for(theta=1; theta <=npar; theta++)    int i;
           trgradg[h][j][theta]=gradg[h][theta][j];    int l=1, lmax=20;
     double k1,k2;
     for(i=1;i<=nlstate;i++)    double p2[NPARMAX+1];
       for(j=1;j<=nlstate;j++)    double res;
         vareij[i][j][(int)age] =0.;    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     for(h=0;h<=nhstepm;h++){    double fx;
       for(k=0;k<=nhstepm;k++){    int k=0,kmax=10;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    double l1;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);  
         for(i=1;i<=nlstate;i++)    fx=func(x);
           for(j=1;j<=nlstate;j++)    for (i=1;i<=npar;i++) p2[i]=x[i];
             vareij[i][j][(int)age] += doldm[i][j];    for(l=0 ; l <=lmax; l++){
       }      l1=pow(10,l);
     }      delts=delt;
     h=1;      for(k=1 ; k <kmax; k=k+1){
     if (stepm >= YEARM) h=stepm/YEARM;        delt = delta*(l1*k);
     fprintf(ficresvij,"%.0f ",age );        p2[theta]=x[theta] +delt;
     for(i=1; i<=nlstate;i++)        k1=func(p2)-fx;
       for(j=1; j<=nlstate;j++){        p2[theta]=x[theta]-delt;
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);        k2=func(p2)-fx;
       }        /*res= (k1-2.0*fx+k2)/delt/delt; */
     fprintf(ficresvij,"\n");        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     free_matrix(gp,0,nhstepm,1,nlstate);        
     free_matrix(gm,0,nhstepm,1,nlstate);  #ifdef DEBUG
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        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);
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);        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);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  #endif
   } /* End age */        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
          if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   free_vector(xp,1,npar);          k=kmax;
   free_matrix(doldm,1,nlstate,1,npar);        }
   free_matrix(dnewm,1,nlstate,1,nlstate);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           k=kmax; l=lmax*10.;
 }        }
         else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
 /************ Variance of prevlim ******************/          delts=delt;
 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)        }
 {      }
   /* Variance of prevalence limit */    }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    delti[theta]=delts;
   double **newm;    return res; 
   double **dnewm,**doldm;    
   int i, j, nhstepm, hstepm;  }
   int k, cptcode;  
   double *xp;  double hessij( double x[], double delti[], int thetai,int thetaj)
   double *gp, *gm;  {
   double **gradg, **trgradg;    int i;
   double age,agelim;    int l=1, l1, lmax=20;
   int theta;    double k1,k2,k3,k4,res,fx;
        double p2[NPARMAX+1];
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    int k;
   fprintf(ficresvpl,"# Age");  
   for(i=1; i<=nlstate;i++)    fx=func(x);
       fprintf(ficresvpl," %1d-%1d",i,i);    for (k=1; k<=2; k++) {
   fprintf(ficresvpl,"\n");      for (i=1;i<=npar;i++) p2[i]=x[i];
       p2[thetai]=x[thetai]+delti[thetai]/k;
   xp=vector(1,npar);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   dnewm=matrix(1,nlstate,1,npar);      k1=func(p2)-fx;
   doldm=matrix(1,nlstate,1,nlstate);    
        p2[thetai]=x[thetai]+delti[thetai]/k;
   hstepm=1*YEARM; /* Every year of age */      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      k2=func(p2)-fx;
   agelim = AGESUP;    
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      p2[thetai]=x[thetai]-delti[thetai]/k;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     if (stepm >= YEARM) hstepm=1;      k3=func(p2)-fx;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    
     gradg=matrix(1,npar,1,nlstate);      p2[thetai]=x[thetai]-delti[thetai]/k;
     gp=vector(1,nlstate);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     gm=vector(1,nlstate);      k4=func(p2)-fx;
       res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
     for(theta=1; theta <=npar; theta++){  #ifdef DEBUG
       for(i=1; i<=npar; i++){ /* Computes gradient */      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[i] = x[i] + (i==theta ?delti[theta]:0);      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);
       }  #endif
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    }
       for(i=1;i<=nlstate;i++)    return res;
         gp[i] = prlim[i][i];  }
      
       for(i=1; i<=npar; i++) /* Computes gradient */  /************** Inverse of matrix **************/
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  void ludcmp(double **a, int n, int *indx, double *d) 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  { 
       for(i=1;i<=nlstate;i++)    int i,imax,j,k; 
         gm[i] = prlim[i][i];    double big,dum,sum,temp; 
     double *vv; 
       for(i=1;i<=nlstate;i++)   
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    vv=vector(1,n); 
     } /* End theta */    *d=1.0; 
     for (i=1;i<=n;i++) { 
     trgradg =matrix(1,nlstate,1,npar);      big=0.0; 
       for (j=1;j<=n;j++) 
     for(j=1; j<=nlstate;j++)        if ((temp=fabs(a[i][j])) > big) big=temp; 
       for(theta=1; theta <=npar; theta++)      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
         trgradg[j][theta]=gradg[theta][j];      vv[i]=1.0/big; 
     } 
     for(i=1;i<=nlstate;i++)    for (j=1;j<=n;j++) { 
       varpl[i][(int)age] =0.;      for (i=1;i<j;i++) { 
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);        sum=a[i][j]; 
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     for(i=1;i<=nlstate;i++)        a[i][j]=sum; 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */      } 
       big=0.0; 
     fprintf(ficresvpl,"%.0f ",age );      for (i=j;i<=n;i++) { 
     for(i=1; i<=nlstate;i++)        sum=a[i][j]; 
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        for (k=1;k<j;k++) 
     fprintf(ficresvpl,"\n");          sum -= a[i][k]*a[k][j]; 
     free_vector(gp,1,nlstate);        a[i][j]=sum; 
     free_vector(gm,1,nlstate);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
     free_matrix(gradg,1,npar,1,nlstate);          big=dum; 
     free_matrix(trgradg,1,nlstate,1,npar);          imax=i; 
   } /* End age */        } 
       } 
   free_vector(xp,1,npar);      if (j != imax) { 
   free_matrix(doldm,1,nlstate,1,npar);        for (k=1;k<=n;k++) { 
   free_matrix(dnewm,1,nlstate,1,nlstate);          dum=a[imax][k]; 
           a[imax][k]=a[j][k]; 
 }          a[j][k]=dum; 
         } 
 /************ Variance of one-step probabilities  ******************/        *d = -(*d); 
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)        vv[imax]=vv[j]; 
 {      } 
   int i, j;      indx[j]=imax; 
   int k=0, cptcode;      if (a[j][j] == 0.0) a[j][j]=TINY; 
   double **dnewm,**doldm;      if (j != n) { 
   double *xp;        dum=1.0/(a[j][j]); 
   double *gp, *gm;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   double **gradg, **trgradg;      } 
   double age,agelim, cov[NCOVMAX];    } 
   int theta;    free_vector(vv,1,n);  /* Doesn't work */
   char fileresprob[FILENAMELENGTH];  ;
   } 
   strcpy(fileresprob,"prob");  
   strcat(fileresprob,fileres);  void lubksb(double **a, int n, int *indx, double b[]) 
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {  { 
     printf("Problem with resultfile: %s\n", fileresprob);    int i,ii=0,ip,j; 
   }    double sum; 
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);   
      for (i=1;i<=n;i++) { 
       ip=indx[i]; 
   xp=vector(1,npar);      sum=b[ip]; 
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      b[ip]=b[i]; 
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));      if (ii) 
          for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   cov[1]=1;      else if (sum) ii=i; 
   for (age=bage; age<=fage; age ++){      b[i]=sum; 
     cov[2]=age;    } 
     gradg=matrix(1,npar,1,9);    for (i=n;i>=1;i--) { 
     trgradg=matrix(1,9,1,npar);      sum=b[i]; 
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      b[i]=sum/a[i][i]; 
        } 
     for(theta=1; theta <=npar; theta++){  } 
       for(i=1; i<=npar; i++)  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  /************ 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)
       pmij(pmmij,cov,ncovmodel,xp,nlstate);  {  /* Some frequencies */
        
       k=0;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
       for(i=1; i<= (nlstate+ndeath); i++){    int first;
         for(j=1; j<=(nlstate+ndeath);j++){    double ***freq; /* Frequencies */
            k=k+1;    double *pp, **prop;
           gp[k]=pmmij[i][j];    double pos,posprop, k2, dateintsum=0,k2cpt=0;
         }    FILE *ficresp;
       }    char fileresp[FILENAMELENGTH];
     
       for(i=1; i<=npar; i++)    pp=vector(1,nlstate);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    prop=matrix(1,nlstate,iagemin,iagemax+3);
        strcpy(fileresp,"p");
     strcat(fileresp,fileres);
       pmij(pmmij,cov,ncovmodel,xp,nlstate);    if((ficresp=fopen(fileresp,"w"))==NULL) {
       k=0;      printf("Problem with prevalence resultfile: %s\n", fileresp);
       for(i=1; i<=(nlstate+ndeath); i++){      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
         for(j=1; j<=(nlstate+ndeath);j++){      exit(0);
           k=k+1;    }
           gm[k]=pmmij[i][j];    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
         }    j1=0;
       }    
          j=cptcoveff;
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    if (cptcovn<1) {j=1;ncodemax[1]=1;}
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];    
     }    first=1;
   
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    for(k1=1; k1<=j;k1++){
       for(theta=1; theta <=npar; theta++)      for(i1=1; i1<=ncodemax[k1];i1++){
       trgradg[j][theta]=gradg[theta][j];        j1++;
          /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);          scanf("%d", i);*/
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);        for (i=-1; i<=nlstate+ndeath; i++)  
           for (jk=-1; jk<=nlstate+ndeath; jk++)  
      pmij(pmmij,cov,ncovmodel,x,nlstate);            for(m=iagemin; m <= iagemax+3; m++)
               freq[i][jk][m]=0;
      k=0;  
      for(i=1; i<=(nlstate+ndeath); i++){      for (i=1; i<=nlstate; i++)  
        for(j=1; j<=(nlstate+ndeath);j++){        for(m=iagemin; m <= iagemax+3; m++)
          k=k+1;          prop[i][m]=0;
          gm[k]=pmmij[i][j];        
         }        dateintsum=0;
      }        k2cpt=0;
              for (i=1; i<=imx; i++) {
      /*printf("\n%d ",(int)age);          bool=1;
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){          if  (cptcovn>0) {
                    for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));                bool=0;
      }*/          }
           if (bool==1){
   fprintf(ficresprob,"\n%d ",(int)age);            for(m=firstpass; m<=lastpass; m++){
               k2=anint[m][i]+(mint[m][i]/12.);
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   }                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
                 if (m<lastpass) {
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);                }
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);                
 }                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
  free_vector(xp,1,npar);                  dateintsum=dateintsum+k2;
 fclose(ficresprob);                  k2cpt++;
  exit(0);                }
 }                /*}*/
             }
 /***********************************************/          }
 /**************** Main Program *****************/        }
 /***********************************************/         
         /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
 int main(int argc, char *argv[])  
 {        if  (cptcovn>0) {
           fprintf(ficresp, "\n#********** Variable "); 
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   double agedeb, agefin,hf;          fprintf(ficresp, "**********\n#");
   double agemin=1.e20, agemax=-1.e20;        }
         for(i=1; i<=nlstate;i++) 
   double fret;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   double **xi,tmp,delta;        fprintf(ficresp, "\n");
         
   double dum; /* Dummy variable */        for(i=iagemin; i <= iagemax+3; i++){
   double ***p3mat;          if(i==iagemax+3){
   int *indx;            fprintf(ficlog,"Total");
   char line[MAXLINE], linepar[MAXLINE];          }else{
   char title[MAXLINE];            if(first==1){
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];              first=0;
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];              printf("See log file for details...\n");
              }
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];            fprintf(ficlog,"Age %d", i);
           }
   char filerest[FILENAMELENGTH];          for(jk=1; jk <=nlstate ; jk++){
   char fileregp[FILENAMELENGTH];            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   char popfile[FILENAMELENGTH];              pp[jk] += freq[jk][m][i]; 
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];          }
   int firstobs=1, lastobs=10;          for(jk=1; jk <=nlstate ; jk++){
   int sdeb, sfin; /* Status at beginning and end */            for(m=-1, pos=0; m <=0 ; m++)
   int c,  h , cpt,l;              pos += freq[jk][m][i];
   int ju,jl, mi;            if(pp[jk]>=1.e-10){
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;              if(first==1){
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   int mobilav=0,popforecast=0;              }
   int hstepm, nhstepm;              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   int *popage;/*boolprev=0 if date and zero if wave*/            }else{
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;              if(first==1)
                 printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   double bage, fage, age, agelim, agebase;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   double ftolpl=FTOL;            }
   double **prlim;          }
   double *severity;  
   double ***param; /* Matrix of parameters */          for(jk=1; jk <=nlstate ; jk++){
   double  *p;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   double **matcov; /* Matrix of covariance */              pp[jk] += freq[jk][m][i];
   double ***delti3; /* Scale */          }       
   double *delti; /* Scale */          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   double ***eij, ***vareij;            pos += pp[jk];
   double **varpl; /* Variances of prevalence limits by age */            posprop += prop[jk][i];
   double *epj, vepp;          }
   double kk1, kk2;          for(jk=1; jk <=nlstate ; jk++){
   double *popeffectif,*popcount;            if(pos>=1.e-5){
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;              if(first==1)
   double yp,yp1,yp2;                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
               fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";            }else{
   char *alph[]={"a","a","b","c","d","e"}, str[4];              if(first==1)
                 printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   char z[1]="c", occ;            }
 #include <sys/time.h>            if( i <= iagemax){
 #include <time.h>              if(pos>=1.e-5){
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                  /*probs[i][jk][j1]= pp[jk]/pos;*/
   /* long total_usecs;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   struct timeval start_time, end_time;              }
                else
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
             }
           }
   printf("\n%s",version);          
   if(argc <=1){          for(jk=-1; jk <=nlstate+ndeath; jk++)
     printf("\nEnter the parameter file name: ");            for(m=-1; m <=nlstate+ndeath; m++)
     scanf("%s",pathtot);              if(freq[jk][m][i] !=0 ) {
   }              if(first==1)
   else{                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     strcpy(pathtot,argv[1]);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   }              }
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/          if(i <= iagemax)
   /*cygwin_split_path(pathtot,path,optionfile);            fprintf(ficresp,"\n");
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/          if(first==1)
   /* cutv(path,optionfile,pathtot,'\\');*/            printf("Others in log...\n");
           fprintf(ficlog,"\n");
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);        }
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);      }
   chdir(path);    }
   replace(pathc,path);    dateintmean=dateintsum/k2cpt; 
    
 /*-------- arguments in the command line --------*/    fclose(ficresp);
     free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
   strcpy(fileres,"r");    free_vector(pp,1,nlstate);
   strcat(fileres, optionfilefiname);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   strcat(fileres,".txt");    /* Other files have txt extension */    /* End of Freq */
   }
   /*---------arguments file --------*/  
   /************ Prevalence ********************/
   if((ficpar=fopen(optionfile,"r"))==NULL)    {  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)
     printf("Problem with optionfile %s\n",optionfile);  {  
     goto end;    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   }       in each health status at the date of interview (if between dateprev1 and dateprev2).
        We still use firstpass and lastpass as another selection.
   strcpy(filereso,"o");    */
   strcat(filereso,fileres);   
   if((ficparo=fopen(filereso,"w"))==NULL) {    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    double ***freq; /* Frequencies */
   }    double *pp, **prop;
     double pos,posprop; 
   /* Reads comments: lines beginning with '#' */    double  y2; /* in fractional years */
   while((c=getc(ficpar))=='#' && c!= EOF){    int iagemin, iagemax;
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    iagemin= (int) agemin;
     puts(line);    iagemax= (int) agemax;
     fputs(line,ficparo);    /*pp=vector(1,nlstate);*/
   }    prop=matrix(1,nlstate,iagemin,iagemax+3); 
   ungetc(c,ficpar);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     j1=0;
   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);    j=cptcoveff;
   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 (cptcovn<1) {j=1;ncodemax[1]=1;}
 while((c=getc(ficpar))=='#' && c!= EOF){    
     ungetc(c,ficpar);    for(k1=1; k1<=j;k1++){
     fgets(line, MAXLINE, ficpar);      for(i1=1; i1<=ncodemax[k1];i1++){
     puts(line);        j1++;
     fputs(line,ficparo);        
   }        for (i=1; i<=nlstate; i++)  
   ungetc(c,ficpar);          for(m=iagemin; m <= iagemax+3; m++)
              prop[i][m]=0.0;
           
   covar=matrix(0,NCOVMAX,1,n);        for (i=1; i<=imx; i++) { /* Each individual */
   cptcovn=0;          bool=1;
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;          if  (cptcovn>0) {
             for (z1=1; z1<=cptcoveff; z1++) 
   ncovmodel=2+cptcovn;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */                bool=0;
            } 
   /* Read guess parameters */          if (bool==1) { 
   /* Reads comments: lines beginning with '#' */            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   while((c=getc(ficpar))=='#' && c!= EOF){              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     ungetc(c,ficpar);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
     fgets(line, MAXLINE, ficpar);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     puts(line);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     fputs(line,ficparo);                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
   }                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   ungetc(c,ficpar);                  /*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]]);*/
                    prop[s[m][i]][(int)agev[m][i]] += weight[i];
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);                  prop[s[m][i]][iagemax+3] += weight[i]; 
     for(i=1; i <=nlstate; i++)                } 
     for(j=1; j <=nlstate+ndeath-1; j++){              }
       fscanf(ficpar,"%1d%1d",&i1,&j1);            } /* end selection of waves */
       fprintf(ficparo,"%1d%1d",i1,j1);          }
       printf("%1d%1d",i,j);        }
       for(k=1; k<=ncovmodel;k++){        for(i=iagemin; i <= iagemax+3; i++){  
         fscanf(ficpar," %lf",&param[i][j][k]);          
         printf(" %lf",param[i][j][k]);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
         fprintf(ficparo," %lf",param[i][j][k]);            posprop += prop[jk][i]; 
       }          } 
       fscanf(ficpar,"\n");  
       printf("\n");          for(jk=1; jk <=nlstate ; jk++){     
       fprintf(ficparo,"\n");            if( i <=  iagemax){ 
     }              if(posprop>=1.e-5){ 
                  probs[i][jk][j1]= prop[jk][i]/posprop;
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;              } 
             } 
   p=param[1][1];          }/* end jk */ 
          }/* end i */ 
   /* Reads comments: lines beginning with '#' */      } /* end i1 */
   while((c=getc(ficpar))=='#' && c!= EOF){    } /* end k1 */
     ungetc(c,ficpar);    
     fgets(line, MAXLINE, ficpar);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     puts(line);    /*free_vector(pp,1,nlstate);*/
     fputs(line,ficparo);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   }  }  /* End of prevalence */
   ungetc(c,ficpar);  
   /************* Waves Concatenation ***************/
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */  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)
   for(i=1; i <=nlstate; i++){  {
     for(j=1; j <=nlstate+ndeath-1; j++){    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
       fscanf(ficpar,"%1d%1d",&i1,&j1);       Death is a valid wave (if date is known).
       printf("%1d%1d",i,j);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
       fprintf(ficparo,"%1d%1d",i1,j1);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
       for(k=1; k<=ncovmodel;k++){       and mw[mi+1][i]. dh depends on stepm.
         fscanf(ficpar,"%le",&delti3[i][j][k]);       */
         printf(" %le",delti3[i][j][k]);  
         fprintf(ficparo," %le",delti3[i][j][k]);    int i, mi, m;
       }    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
       fscanf(ficpar,"\n");       double sum=0., jmean=0.;*/
       printf("\n");    int first;
       fprintf(ficparo,"\n");    int j, k=0,jk, ju, jl;
     }    double sum=0.;
   }    first=0;
   delti=delti3[1][1];    jmin=1e+5;
      jmax=-1;
   /* Reads comments: lines beginning with '#' */    jmean=0.;
   while((c=getc(ficpar))=='#' && c!= EOF){    for(i=1; i<=imx; i++){
     ungetc(c,ficpar);      mi=0;
     fgets(line, MAXLINE, ficpar);      m=firstpass;
     puts(line);      while(s[m][i] <= nlstate){
     fputs(line,ficparo);        if(s[m][i]>=1)
   }          mw[++mi][i]=m;
   ungetc(c,ficpar);        if(m >=lastpass)
            break;
   matcov=matrix(1,npar,1,npar);        else
   for(i=1; i <=npar; i++){          m++;
     fscanf(ficpar,"%s",&str);      }/* end while */
     printf("%s",str);      if (s[m][i] > nlstate){
     fprintf(ficparo,"%s",str);        mi++;     /* Death is another wave */
     for(j=1; j <=i; j++){        /* if(mi==0)  never been interviewed correctly before death */
       fscanf(ficpar," %le",&matcov[i][j]);           /* Only death is a correct wave */
       printf(" %.5le",matcov[i][j]);        mw[mi][i]=m;
       fprintf(ficparo," %.5le",matcov[i][j]);      }
     }  
     fscanf(ficpar,"\n");      wav[i]=mi;
     printf("\n");      if(mi==0){
     fprintf(ficparo,"\n");        nbwarn++;
   }        if(first==0){
   for(i=1; i <=npar; i++)          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
     for(j=i+1;j<=npar;j++)          first=1;
       matcov[i][j]=matcov[j][i];        }
            if(first==1){
   printf("\n");          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
         }
       } /* end mi==0 */
     /*-------- data file ----------*/    } /* End individuals */
     if((ficres =fopen(fileres,"w"))==NULL) {  
       printf("Problem with resultfile: %s\n", fileres);goto end;    for(i=1; i<=imx; i++){
     }      for(mi=1; mi<wav[i];mi++){
     fprintf(ficres,"#%s\n",version);        if (stepm <=0)
              dh[mi][i]=1;
     if((fic=fopen(datafile,"r"))==NULL)    {        else{
       printf("Problem with datafile: %s\n", datafile);goto end;          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
     }            if (agedc[i] < 2*AGESUP) {
               j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     n= lastobs;              if(j==0) j=1;  /* Survives at least one month after exam */
     severity = vector(1,maxwav);              else if(j<0){
     outcome=imatrix(1,maxwav+1,1,n);                nberr++;
     num=ivector(1,n);                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]);
     moisnais=vector(1,n);                j=1; /* Temporary Dangerous patch */
     annais=vector(1,n);                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);
     moisdc=vector(1,n);                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]);
     andc=vector(1,n);                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);
     agedc=vector(1,n);              }
     cod=ivector(1,n);              k=k+1;
     weight=vector(1,n);              if (j >= jmax) jmax=j;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */              if (j <= jmin) jmin=j;
     mint=matrix(1,maxwav,1,n);              sum=sum+j;
     anint=matrix(1,maxwav,1,n);              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
     s=imatrix(1,maxwav+1,1,n);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     adl=imatrix(1,maxwav+1,1,n);                }
     tab=ivector(1,NCOVMAX);          }
     ncodemax=ivector(1,8);          else{
             j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     i=1;            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     while (fgets(line, MAXLINE, fic) != NULL)    {            k=k+1;
       if ((i >= firstobs) && (i <=lastobs)) {            if (j >= jmax) jmax=j;
                    else if (j <= jmin)jmin=j;
         for (j=maxwav;j>=1;j--){            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);            /*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]);*/
           strcpy(line,stra);            if(j<0){
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);              nberr++;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);              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]);
                    }
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);            sum=sum+j;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);          }
           jk= j/stepm;
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);          jl= j -jk*stepm;
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);          ju= j -(jk+1)*stepm;
           if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);            if(jl==0){
         for (j=ncov;j>=1;j--){              dh[mi][i]=jk;
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);              bh[mi][i]=0;
         }            }else{ /* We want a negative bias in order to only have interpolation ie
         num[i]=atol(stra);                    * at the price of an extra matrix product in likelihood */
                      dh[mi][i]=jk+1;
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){              bh[mi][i]=ju;
           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;}*/            }
           }else{
         i=i+1;            if(jl <= -ju){
       }              dh[mi][i]=jk;
     }              bh[mi][i]=jl;       /* bias is positive if real duration
     /* printf("ii=%d", ij);                                   * is higher than the multiple of stepm and negative otherwise.
        scanf("%d",i);*/                                   */
   imx=i-1; /* Number of individuals */            }
             else{
   /* for (i=1; i<=imx; i++){              dh[mi][i]=jk+1;
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;              bh[mi][i]=ju;
     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;            if(dh[mi][i]==0){
     }              dh[mi][i]=1; /* At least one step */
               bh[mi][i]=ju; /* At least one step */
     for (i=1; i<=imx; i++)              /*  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);*/
     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]));*/            }
           } /* end if mle */
   /* Calculation of the number of parameter from char model*/        }
   Tvar=ivector(1,15);      } /* end wave */
   Tprod=ivector(1,15);    }
   Tvaraff=ivector(1,15);    jmean=sum/k;
   Tvard=imatrix(1,15,1,2);    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   Tage=ivector(1,15);          fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
       }
   if (strlen(model) >1){  
     j=0, j1=0, k1=1, k2=1;  /*********** Tricode ****************************/
     j=nbocc(model,'+');  void tricode(int *Tvar, int **nbcode, int imx)
     j1=nbocc(model,'*');  {
     cptcovn=j+1;    
     cptcovprod=j1;    int Ndum[20],ij=1, k, j, i, maxncov=19;
        int cptcode=0;
        cptcoveff=0; 
     strcpy(modelsav,model);   
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    for (k=0; k<maxncov; k++) Ndum[k]=0;
       printf("Error. Non available option model=%s ",model);    for (k=1; k<=7; k++) ncodemax[k]=0;
       goto end;  
     }    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
          for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
     for(i=(j+1); i>=1;i--){                                 modality*/ 
       cutv(stra,strb,modelsav,'+');        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);        Ndum[ij]++; /*store the modality */
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
       /*scanf("%d",i);*/        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
       if (strchr(strb,'*')) {                                         Tvar[j]. If V=sex and male is 0 and 
         cutv(strd,strc,strb,'*');                                         female is 1, then  cptcode=1.*/
         if (strcmp(strc,"age")==0) {      }
           cptcovprod--;  
           cutv(strb,stre,strd,'V');      for (i=0; i<=cptcode; i++) {
           Tvar[i]=atoi(stre);        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 */
           cptcovage++;      }
             Tage[cptcovage]=i;  
             /*printf("stre=%s ", stre);*/      ij=1; 
         }      for (i=1; i<=ncodemax[j]; i++) {
         else if (strcmp(strd,"age")==0) {        for (k=0; k<= maxncov; k++) {
           cptcovprod--;          if (Ndum[k] != 0) {
           cutv(strb,stre,strc,'V');            nbcode[Tvar[j]][ij]=k; 
           Tvar[i]=atoi(stre);            /* 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; */
           cptcovage++;            
           Tage[cptcovage]=i;            ij++;
         }          }
         else {          if (ij > ncodemax[j]) break; 
           cutv(strb,stre,strc,'V');        }  
           Tvar[i]=ncov+k1;      } 
           cutv(strb,strc,strd,'V');    }  
           Tprod[k1]=i;  
           Tvard[k1][1]=atoi(strc);   for (k=0; k< maxncov; k++) Ndum[k]=0;
           Tvard[k1][2]=atoi(stre);  
           Tvar[cptcovn+k2]=Tvard[k1][1];   for (i=1; i<=ncovmodel-2; i++) { 
           Tvar[cptcovn+k2+1]=Tvard[k1][2];     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
           for (k=1; k<=lastobs;k++)     ij=Tvar[i];
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];     Ndum[ij]++;
           k1++;   }
           k2=k2+2;  
         }   ij=1;
       }   for (i=1; i<= maxncov; i++) {
       else {     if((Ndum[i]!=0) && (i<=ncovcol)){
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/       Tvaraff[ij]=i; /*For printing */
        /*  scanf("%d",i);*/       ij++;
       cutv(strd,strc,strb,'V');     }
       Tvar[i]=atoi(strc);   }
       }   
       strcpy(modelsav,stra);     cptcoveff=ij-1; /*Number of simple covariates*/
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);  }
         scanf("%d",i);*/  
     }  /*********** Health Expectancies ****************/
 }  
    void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);  
   printf("cptcovprod=%d ", cptcovprod);  {
   scanf("%d ",i);*/    /* Health expectancies */
     fclose(fic);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     double age, agelim, hf;
     /*  if(mle==1){*/    double ***p3mat,***varhe;
     if (weightopt != 1) { /* Maximisation without weights*/    double **dnewm,**doldm;
       for(i=1;i<=n;i++) weight[i]=1.0;    double *xp;
     }    double **gp, **gm;
     /*-calculation of age at interview from date of interview and age at death -*/    double ***gradg, ***trgradg;
     agev=matrix(1,maxwav,1,imx);    int theta;
   
    for (i=1; i<=imx; i++)    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
      for(m=2; (m<= maxwav); m++)    xp=vector(1,npar);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    dnewm=matrix(1,nlstate*nlstate,1,npar);
          anint[m][i]=9999;    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
          s[m][i]=-1;    
        }    fprintf(ficreseij,"# Health expectancies\n");
        fprintf(ficreseij,"# Age");
     for (i=1; i<=imx; i++)  {    for(i=1; i<=nlstate;i++)
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      for(j=1; j<=nlstate;j++)
       for(m=1; (m<= maxwav); m++){        fprintf(ficreseij," %1d-%1d (SE)",i,j);
         if(s[m][i] >0){    fprintf(ficreseij,"\n");
           if (s[m][i] == nlstate+1) {  
             if(agedc[i]>0)    if(estepm < stepm){
               if(moisdc[i]!=99 && andc[i]!=9999)      printf ("Problem %d lower than %d\n",estepm, stepm);
               agev[m][i]=agedc[i];    }
             else {    else  hstepm=estepm;   
               if (andc[i]!=9999){    /* We compute the life expectancy from trapezoids spaced every estepm months
               printf("Warning negative age at death: %d line:%d\n",num[i],i);     * This is mainly to measure the difference between two models: for example
               agev[m][i]=-1;     * if stepm=24 months pijx are given only every 2 years and by summing them
               }     * we are calculating an estimate of the Life Expectancy assuming a linear 
             }     * progression in between and thus overestimating or underestimating according
           }     * to the curvature of the survival function. If, for the same date, we 
           else if(s[m][i] !=9){ /* Should no more exist */     * estimate the model with stepm=1 month, we can keep estepm to 24 months
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);     * to compare the new estimate of Life expectancy with the same linear 
             if(mint[m][i]==99 || anint[m][i]==9999)     * hypothesis. A more precise result, taking into account a more precise
               agev[m][i]=1;     * curvature will be obtained if estepm is as small as stepm. */
             else if(agev[m][i] <agemin){  
               agemin=agev[m][i];    /* For example we decided to compute the life expectancy with the smallest unit */
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    /* 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 
             else if(agev[m][i] >agemax){       nstepm is the number of stepm from age to agelin. 
               agemax=agev[m][i];       Look at hpijx to understand the reason of that which relies in memory size
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/       and note for a fixed period like estepm months */
             }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
             /*agev[m][i]=anint[m][i]-annais[i];*/       survival function given by stepm (the optimization length). Unfortunately it
             /*   agev[m][i] = age[i]+2*m;*/       means that if the survival funtion is printed only each two years of age and if
           }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           else { /* =9 */       results. So we changed our mind and took the option of the best precision.
             agev[m][i]=1;    */
             s[m][i]=-1;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
           }  
         }    agelim=AGESUP;
         else /*= 0 Unknown */    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
           agev[m][i]=1;      /* nhstepm age range expressed in number of stepm */
       }      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
          /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     }      /* if (stepm >= YEARM) hstepm=1;*/
     for (i=1; i<=imx; i++)  {      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       for(m=1; (m<= maxwav); m++){      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         if (s[m][i] > (nlstate+ndeath)) {      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
           printf("Error: Wrong value in nlstate or ndeath\n");        gp=matrix(0,nhstepm,1,nlstate*nlstate);
           goto end;      gm=matrix(0,nhstepm,1,nlstate*nlstate);
         }  
       }      /* Computed by stepm unit matrices, product of hstepm matrices, stored
     }         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);   
   
     free_vector(severity,1,maxwav);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     free_imatrix(outcome,1,maxwav+1,1,n);  
     free_vector(moisnais,1,n);      /* Computing Variances of health expectancies */
     free_vector(annais,1,n);  
     /* free_matrix(mint,1,maxwav,1,n);       for(theta=1; theta <=npar; theta++){
        free_matrix(anint,1,maxwav,1,n);*/        for(i=1; i<=npar; i++){ 
     free_vector(moisdc,1,n);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     free_vector(andc,1,n);        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
        
     wav=ivector(1,imx);        cptj=0;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);        for(j=1; j<= nlstate; j++){
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          for(i=1; i<=nlstate; i++){
                cptj=cptj+1;
     /* Concatenates waves */            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
             }
           }
       Tcode=ivector(1,100);        }
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);       
       ncodemax[1]=1;       
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);        for(i=1; i<=npar; i++) 
                xp[i] = x[i] - (i==theta ?delti[theta]:0);
    codtab=imatrix(1,100,1,10);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
    h=0;        
    m=pow(2,cptcoveff);        cptj=0;
          for(j=1; j<= nlstate; j++){
    for(k=1;k<=cptcoveff; k++){          for(i=1;i<=nlstate;i++){
      for(i=1; i <=(m/pow(2,k));i++){            cptj=cptj+1;
        for(j=1; j <= ncodemax[k]; j++){            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){  
            h++;              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
            if (h>m) h=1;codtab[h][k]=j;            }
          }          }
        }        }
      }        for(j=1; j<= nlstate*nlstate; j++)
    }          for(h=0; h<=nhstepm-1; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
    /*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);  /* End theta */
      }  
      printf("\n");       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
    }  
    scanf("%d",i);*/       for(h=0; h<=nhstepm-1; h++)
            for(j=1; j<=nlstate*nlstate;j++)
    /* Calculates basic frequencies. Computes observed prevalence at single age          for(theta=1; theta <=npar; theta++)
        and prints on file fileres'p'. */            trgradg[h][j][theta]=gradg[h][theta][j];
        
      
           for(i=1;i<=nlstate*nlstate;i++)
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for(j=1;j<=nlstate*nlstate;j++)
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          varhe[i][j][(int)age] =0.;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       printf("%d|",(int)age);fflush(stdout);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
             for(h=0;h<=nhstepm-1;h++){
     /* For Powell, parameters are in a vector p[] starting at p[1]        for(k=0;k<=nhstepm-1;k++){
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
           for(i=1;i<=nlstate*nlstate;i++)
     if(mle==1){            for(j=1;j<=nlstate*nlstate;j++)
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
     }        }
          }
     /*--------- results files --------------*/      /* Computing expectancies */
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);      for(i=1; i<=nlstate;i++)
          for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
    jk=1;            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
    fprintf(ficres,"# Parameters\n");            
    printf("# Parameters\n");  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
    for(i=1,jk=1; i <=nlstate; i++){  
      for(k=1; k <=(nlstate+ndeath); k++){          }
        if (k != i)  
          {      fprintf(ficreseij,"%3.0f",age );
            printf("%d%d ",i,k);      cptj=0;
            fprintf(ficres,"%1d%1d ",i,k);      for(i=1; i<=nlstate;i++)
            for(j=1; j <=ncovmodel; j++){        for(j=1; j<=nlstate;j++){
              printf("%f ",p[jk]);          cptj++;
              fprintf(ficres,"%f ",p[jk]);          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
              jk++;        }
            }      fprintf(ficreseij,"\n");
            printf("\n");     
            fprintf(ficres,"\n");      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);
  if(mle==1){      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     /* Computing hessian and covariance matrix */    }
     ftolhess=ftol; /* Usually correct */    printf("\n");
     hesscov(matcov, p, npar, delti, ftolhess, func);    fprintf(ficlog,"\n");
  }  
     fprintf(ficres,"# Scales\n");    free_vector(xp,1,npar);
     printf("# Scales\n");    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
      for(i=1,jk=1; i <=nlstate; i++){    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
       for(j=1; j <=nlstate+ndeath; j++){    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
         if (j!=i) {  }
           fprintf(ficres,"%1d%1d",i,j);  
           printf("%1d%1d",i,j);  /************ Variance ******************/
           for(k=1; k<=ncovmodel;k++){  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
             printf(" %.5e",delti[jk]);  {
             fprintf(ficres," %.5e",delti[jk]);    /* Variance of health expectancies */
             jk++;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
           }    /* double **newm;*/
           printf("\n");    double **dnewm,**doldm;
           fprintf(ficres,"\n");    double **dnewmp,**doldmp;
         }    int i, j, nhstepm, hstepm, h, nstepm ;
       }    int k, cptcode;
      }    double *xp;
        double **gp, **gm;  /* for var eij */
     k=1;    double ***gradg, ***trgradg; /*for var eij */
     fprintf(ficres,"# Covariance\n");    double **gradgp, **trgradgp; /* for var p point j */
     printf("# Covariance\n");    double *gpp, *gmp; /* for var p point j */
     for(i=1;i<=npar;i++){    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
       /*  if (k>nlstate) k=1;    double ***p3mat;
       i1=(i-1)/(ncovmodel*nlstate)+1;    double age,agelim, hf;
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);    double ***mobaverage;
       printf("%s%d%d",alph[k],i1,tab[i]);*/    int theta;
       fprintf(ficres,"%3d",i);    char digit[4];
       printf("%3d",i);    char digitp[25];
       for(j=1; j<=i;j++){  
         fprintf(ficres," %.5e",matcov[i][j]);    char fileresprobmorprev[FILENAMELENGTH];
         printf(" %.5e",matcov[i][j]);  
       }    if(popbased==1){
       fprintf(ficres,"\n");      if(mobilav!=0)
       printf("\n");        strcpy(digitp,"-populbased-mobilav-");
       k++;      else strcpy(digitp,"-populbased-nomobil-");
     }    }
        else 
     while((c=getc(ficpar))=='#' && c!= EOF){      strcpy(digitp,"-stablbased-");
       ungetc(c,ficpar);  
       fgets(line, MAXLINE, ficpar);    if (mobilav!=0) {
       puts(line);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       fputs(line,ficparo);      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
     }        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     ungetc(c,ficpar);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
        }
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    }
      
     if (fage <= 2) {    strcpy(fileresprobmorprev,"prmorprev"); 
       bage = agemin;    sprintf(digit,"%-d",ij);
       fage = agemax;    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     }    strcat(fileresprobmorprev,digit); /* Tvar to be done */
        strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");    strcat(fileresprobmorprev,fileres);
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     while((c=getc(ficpar))=='#' && c!= EOF){    }
     ungetc(c,ficpar);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     fgets(line, MAXLINE, ficpar);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     puts(line);    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);
     fputs(line,ficparo);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   }    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   ungetc(c,ficpar);      fprintf(ficresprobmorprev," p.%-d SE",j);
        for(i=1; i<=nlstate;i++)
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mob_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);    }  
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);    fprintf(ficresprobmorprev,"\n");
          fprintf(ficgp,"\n# Routine varevsij");
   while((c=getc(ficpar))=='#' && c!= EOF){    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");
     ungetc(c,ficpar);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
     fgets(line, MAXLINE, ficpar);  /*   } */
     puts(line);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     fputs(line,ficparo);  
   }    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");
   ungetc(c,ficpar);    fprintf(ficresvij,"# Age");
      for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
    dateprev1=anprev1+mprev1/12.+jprev1/365.;        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    fprintf(ficresvij,"\n");
   
   fscanf(ficpar,"pop_based=%d\n",&popbased);    xp=vector(1,npar);
    fprintf(ficparo,"pop_based=%d\n",popbased);      dnewm=matrix(1,nlstate,1,npar);
    fprintf(ficres,"pop_based=%d\n",popbased);      doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   while((c=getc(ficpar))=='#' && c!= EOF){    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     puts(line);    gpp=vector(nlstate+1,nlstate+ndeath);
     fputs(line,ficparo);    gmp=vector(nlstate+1,nlstate+ndeath);
   }    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   ungetc(c,ficpar);    
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);    if(estepm < stepm){
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);      printf ("Problem %d lower than %d\n",estepm, stepm);
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);    }
     else  hstepm=estepm;   
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);    /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           nhstepm is the number of hstepm from age to agelim 
     /*------------ gnuplot -------------*/       nstepm is the number of stepm from age to agelin. 
     /*chdir(pathcd);*/       Look at hpijx to understand the reason of that which relies in memory size
     strcpy(optionfilegnuplot,optionfilefiname);       and note for a fixed period like k years */
     strcat(optionfilegnuplot,".plt");    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {       survival function given by stepm (the optimization length). Unfortunately it
       printf("Problem with file %s",optionfilegnuplot);goto end;       means that if the survival funtion is printed every two years of age and if
     }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
 #ifdef windows       results. So we changed our mind and took the option of the best precision.
     fprintf(ficgp,"cd \"%s\" \n",pathc);    */
 #endif    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
 m=pow(2,cptcoveff);    agelim = AGESUP;
      for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
  /* 1eme*/      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   for (cpt=1; cpt<= nlstate ; cpt ++) {      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
    for (k1=1; k1<= m ; k1 ++) {      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
 #ifdef windows      gp=matrix(0,nhstepm,1,nlstate);
     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);      gm=matrix(0,nhstepm,1,nlstate);
 #endif  
 #ifdef unix  
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);      for(theta=1; theta <=npar; theta++){
 #endif        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
 for (i=1; i<= nlstate ; i ++) {        }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   else fprintf(ficgp," \%%*lf (\%%*lf)");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 }  
     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 (popbased==1) {
     for (i=1; i<= nlstate ; i ++) {          if(mobilav ==0){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            for(i=1; i<=nlstate;i++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");              prlim[i][i]=probs[(int)age][i][ij];
 }          }else{ /* mobilav */ 
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);            for(i=1; i<=nlstate;i++)
      for (i=1; i<= nlstate ; i ++) {              prlim[i][i]=mobaverage[(int)age][i][ij];
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          }
   else fprintf(ficgp," \%%*lf (\%%*lf)");        }
 }      
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));        for(j=1; j<= nlstate; j++){
 #ifdef unix          for(h=0; h<=nhstepm; h++){
 fprintf(ficgp,"\nset ter gif small size 400,300");            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
 #endif              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          }
    }        }
   }        /* This for computing probability of death (h=1 means
   /*2 eme*/           computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
   for (k1=1; k1<= m ; k1 ++) {        */
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
              for(i=1,gpp[j]=0.; i<= nlstate; i++)
     for (i=1; i<= nlstate+1 ; i ++) {            gpp[j] += prlim[i][i]*p3mat[i][j][1];
       k=2*i;        }    
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);        /* end probability of death */
       for (j=1; j<= nlstate+1 ; j ++) {  
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   else fprintf(ficgp," \%%*lf (\%%*lf)");          xp[i] = x[i] - (i==theta ?delti[theta]:0);
 }          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);   
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);        if (popbased==1) {
       for (j=1; j<= nlstate+1 ; j ++) {          if(mobilav ==0){
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            for(i=1; i<=nlstate;i++)
         else fprintf(ficgp," \%%*lf (\%%*lf)");              prlim[i][i]=probs[(int)age][i][ij];
 }            }else{ /* mobilav */ 
       fprintf(ficgp,"\" t\"\" w l 0,");            for(i=1; i<=nlstate;i++)
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);              prlim[i][i]=mobaverage[(int)age][i][ij];
       for (j=1; j<= nlstate+1 ; j ++) {          }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        }
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }          for(j=1; j<= nlstate; j++){
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");          for(h=0; h<=nhstepm; h++){
       else fprintf(ficgp,"\" t\"\" w l 0,");            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
     }              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);          }
   }        }
          /* This for computing probability of death (h=1 means
   /*3eme*/           computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
   for (k1=1; k1<= m ; k1 ++) {        */
     for (cpt=1; cpt<= nlstate ; cpt ++) {        for(j=nlstate+1;j<=nlstate+ndeath;j++){
       k=2+nlstate*(cpt-1);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
       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);        /* end probability of death */
       }  
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        for(j=1; j<= nlstate; j++) /* vareij */
     }          for(h=0; h<=nhstepm; h++){
   }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
            }
   /* CV preval stat */  
   for (k1=1; k1<= m ; k1 ++) {        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
     for (cpt=1; cpt<nlstate ; cpt ++) {          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
       k=3;        }
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);  
       for (i=1; i< nlstate ; i ++)      } /* End theta */
         fprintf(ficgp,"+$%d",k+i+1);  
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
        
       l=3+(nlstate+ndeath)*cpt;      for(h=0; h<=nhstepm; h++) /* veij */
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        for(j=1; j<=nlstate;j++)
       for (i=1; i< nlstate ; i ++) {          for(theta=1; theta <=npar; theta++)
         l=3+(nlstate+ndeath)*cpt;            trgradg[h][j][theta]=gradg[h][theta][j];
         fprintf(ficgp,"+$%d",l+i+1);  
       }      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);          for(theta=1; theta <=npar; theta++)
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          trgradgp[j][theta]=gradgp[theta][j];
     }    
   }    
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   /* proba elementaires */      for(i=1;i<=nlstate;i++)
    for(i=1,jk=1; i <=nlstate; i++){        for(j=1;j<=nlstate;j++)
     for(k=1; k <=(nlstate+ndeath); k++){          vareij[i][j][(int)age] =0.;
       if (k != i) {  
         for(j=1; j <=ncovmodel; j++){      for(h=0;h<=nhstepm;h++){
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/        for(k=0;k<=nhstepm;k++){
           /*fprintf(ficgp,"%s",alph[1]);*/          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           jk++;          for(i=1;i<=nlstate;i++)
           fprintf(ficgp,"\n");            for(j=1;j<=nlstate;j++)
         }              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       }        }
     }      }
     }    
       /* pptj */
   for(jk=1; jk <=m; jk++) {      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
    i=1;      for(j=nlstate+1;j<=nlstate+ndeath;j++)
    for(k2=1; k2<=nlstate; k2++) {        for(i=nlstate+1;i<=nlstate+ndeath;i++)
      k3=i;          varppt[j][i]=doldmp[j][i];
      for(k=1; k<=(nlstate+ndeath); k++) {      /* end ppptj */
        if (k != k2){      /*  x centered again */
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
 ij=1;      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
         for(j=3; j <=ncovmodel; j++) {   
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      if (popbased==1) {
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        if(mobilav ==0){
             ij++;          for(i=1; i<=nlstate;i++)
           }            prlim[i][i]=probs[(int)age][i][ij];
           else        }else{ /* mobilav */ 
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);          for(i=1; i<=nlstate;i++)
         }            prlim[i][i]=mobaverage[(int)age][i][ij];
           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);      /* This for computing probability of death (h=1 means
 ij=1;         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
           for(j=3; j <=ncovmodel; j++){         as a weighted average of prlim.
           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]]]);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
             ij++;        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           }          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
           else      }    
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      /* end probability of death */
           }  
           fprintf(ficgp,")");      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
         }      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");        for(i=1; i<=nlstate;i++){
         i=i+ncovmodel;          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
        }        }
      }      } 
    }      fprintf(ficresprobmorprev,"\n");
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);  
   }      fprintf(ficresvij,"%.0f ",age );
          for(i=1; i<=nlstate;i++)
   fclose(ficgp);        for(j=1; j<=nlstate;j++){
   /* end gnuplot */          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
            }
 chdir(path);      fprintf(ficresvij,"\n");
          free_matrix(gp,0,nhstepm,1,nlstate);
     free_ivector(wav,1,imx);      free_matrix(gm,0,nhstepm,1,nlstate);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);        free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     free_ivector(num,1,n);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_vector(agedc,1,n);    } /* End age */
     /*free_matrix(covar,1,NCOVMAX,1,n);*/    free_vector(gpp,nlstate+1,nlstate+ndeath);
     fclose(ficparo);    free_vector(gmp,nlstate+1,nlstate+ndeath);
     fclose(ficres);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     /*  }*/    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
        fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
    /*________fin mle=1_________*/    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
        fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
    /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
     /* No more information from the sample is required now */  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /* Reads comments: lines beginning with '#' */    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
     ungetc(c,ficpar);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     fgets(line, MAXLINE, ficpar);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     puts(line);    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);
     fputs(line,ficparo);    /*  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);
   }  */
   ungetc(c,ficpar);  /*   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);
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);  
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);    free_vector(xp,1,npar);
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    free_matrix(doldm,1,nlstate,1,nlstate);
 /*--------- index.htm --------*/    free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   strcpy(optionfilehtm,optionfile);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   strcat(optionfilehtm,".htm");    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     printf("Problem with %s \n",optionfilehtm);goto end;    fclose(ficresprobmorprev);
   }    fflush(ficgp);
     fflush(fichtm); 
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">  }  /* end varevsij */
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>  
 Total number of observations=%d <br>  /************ Variance of prevlim ******************/
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
 <hr  size=\"2\" color=\"#EC5E5E\">  {
 <li>Outputs files<br><br>\n    /* Variance of prevalence limit */
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>    double **newm;
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>    double **dnewm,**doldm;
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>    int i, j, nhstepm, hstepm;
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    int k, cptcode;
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>    double *xp;
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>    double *gp, *gm;
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    double **gradg, **trgradg;
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>    double age,agelim;
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>    int theta;
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);     
     fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
  fprintf(fichtm," <li>Graphs</li><p>");    fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
  m=cptcoveff;        fprintf(ficresvpl," %1d-%1d",i,i);
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    fprintf(ficresvpl,"\n");
   
  j1=0;    xp=vector(1,npar);
  for(k1=1; k1<=m;k1++){    dnewm=matrix(1,nlstate,1,npar);
    for(i1=1; i1<=ncodemax[k1];i1++){    doldm=matrix(1,nlstate,1,nlstate);
        j1++;    
        if (cptcovn > 0) {    hstepm=1*YEARM; /* Every year of age */
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
          for (cpt=1; cpt<=cptcoveff;cpt++)    agelim = AGESUP;
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
        }      if (stepm >= YEARM) hstepm=1;
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);          gradg=matrix(1,npar,1,nlstate);
        for(cpt=1; cpt<nlstate;cpt++){      gp=vector(1,nlstate);
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>      gm=vector(1,nlstate);
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);  
        }      for(theta=1; theta <=npar; theta++){
     for(cpt=1; cpt<=nlstate;cpt++) {        for(i=1; i<=npar; i++){ /* Computes gradient */
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident          xp[i] = x[i] + (i==theta ?delti[theta]:0);
 interval) in state (%d): v%s%d%d.gif <br>        }
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
      }        for(i=1;i<=nlstate;i++)
      for(cpt=1; cpt<=nlstate;cpt++) {          gp[i] = prlim[i][i];
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>      
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);        for(i=1; i<=npar; i++) /* Computes gradient */
      }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
      fprintf(fichtm,"\n<br>- Total life expectancy by age and        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
 health expectancies in states (1) and (2): e%s%d.gif<br>        for(i=1;i<=nlstate;i++)
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);          gm[i] = prlim[i][i];
 fprintf(fichtm,"\n</body>");  
    }        for(i=1;i<=nlstate;i++)
  }          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
 fclose(fichtm);      } /* End theta */
   
   /*--------------- Prevalence limit --------------*/      trgradg =matrix(1,nlstate,1,npar);
    
   strcpy(filerespl,"pl");      for(j=1; j<=nlstate;j++)
   strcat(filerespl,fileres);        for(theta=1; theta <=npar; theta++)
   if((ficrespl=fopen(filerespl,"w"))==NULL) {          trgradg[j][theta]=gradg[theta][j];
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;  
   }      for(i=1;i<=nlstate;i++)
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);        varpl[i][(int)age] =0.;
   fprintf(ficrespl,"#Prevalence limit\n");      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   fprintf(ficrespl,"#Age ");      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      for(i=1;i<=nlstate;i++)
   fprintf(ficrespl,"\n");        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
    
   prlim=matrix(1,nlstate,1,nlstate);      fprintf(ficresvpl,"%.0f ",age );
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      for(i=1; i<=nlstate;i++)
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      fprintf(ficresvpl,"\n");
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      free_vector(gp,1,nlstate);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      free_vector(gm,1,nlstate);
   k=0;      free_matrix(gradg,1,npar,1,nlstate);
   agebase=agemin;      free_matrix(trgradg,1,nlstate,1,npar);
   agelim=agemax;    } /* End age */
   ftolpl=1.e-10;  
   i1=cptcoveff;    free_vector(xp,1,npar);
   if (cptcovn < 1){i1=1;}    free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   for(cptcov=1;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]);*/  /************ Variance of one-step probabilities  ******************/
         fprintf(ficrespl,"\n#******");  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
         for(j=1;j<=cptcoveff;j++)  {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    int i, j=0,  i1, k1, l1, t, tj;
         fprintf(ficrespl,"******\n");    int k2, l2, j1,  z1;
            int k=0,l, cptcode;
         for (age=agebase; age<=agelim; age++){    int first=1, first1;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
           fprintf(ficrespl,"%.0f",age );    double **dnewm,**doldm;
           for(i=1; i<=nlstate;i++)    double *xp;
           fprintf(ficrespl," %.5f", prlim[i][i]);    double *gp, *gm;
           fprintf(ficrespl,"\n");    double **gradg, **trgradg;
         }    double **mu;
       }    double age,agelim, cov[NCOVMAX];
     }    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   fclose(ficrespl);    int theta;
     char fileresprob[FILENAMELENGTH];
   /*------------- h Pij x at various ages ------------*/    char fileresprobcov[FILENAMELENGTH];
      char fileresprobcor[FILENAMELENGTH];
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    double ***varpij;
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;  
   }    strcpy(fileresprob,"prob"); 
   printf("Computing pij: result on file '%s' \n", filerespij);    strcat(fileresprob,fileres);
      if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   stepsize=(int) (stepm+YEARM-1)/YEARM;      printf("Problem with resultfile: %s\n", fileresprob);
   /*if (stepm<=24) stepsize=2;*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
   agelim=AGESUP;    strcpy(fileresprobcov,"probcov"); 
   hstepm=stepsize*YEARM; /* Every year of age */    strcat(fileresprobcov,fileres);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprobcov);
   k=0;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   for(cptcov=1;cptcov<=i1;cptcov++){    }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    strcpy(fileresprobcor,"probcor"); 
       k=k+1;    strcat(fileresprobcor,fileres);
         fprintf(ficrespij,"\n#****** ");    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
         for(j=1;j<=cptcoveff;j++)      printf("Problem with resultfile: %s\n", fileresprobcor);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
         fprintf(ficrespij,"******\n");    }
            printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
           oldm=oldms;savm=savms;    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      
           fprintf(ficrespij,"# Age");    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
           for(i=1; i<=nlstate;i++)    fprintf(ficresprob,"# Age");
             for(j=1; j<=nlstate+ndeath;j++)    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
               fprintf(ficrespij," %1d-%1d",i,j);    fprintf(ficresprobcov,"# Age");
           fprintf(ficrespij,"\n");    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
           for (h=0; h<=nhstepm; h++){    fprintf(ficresprobcov,"# Age");
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  
             for(i=1; i<=nlstate;i++)  
               for(j=1; j<=nlstate+ndeath;j++)    for(i=1; i<=nlstate;i++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);      for(j=1; j<=(nlstate+ndeath);j++){
             fprintf(ficrespij,"\n");        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
           }        fprintf(ficresprobcov," p%1d-%1d ",i,j);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
           fprintf(ficrespij,"\n");      }  
         }   /* fprintf(ficresprob,"\n");
     }    fprintf(ficresprobcov,"\n");
   }    fprintf(ficresprobcor,"\n");
    */
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/   xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   fclose(ficrespij);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
   if(stepm == 1) {    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
   /*---------- Forecasting ------------------*/    first=1;
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
   /*printf("calage= %f", calagedate);*/    fprintf(fichtm,"\n");
    
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    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);
   strcpy(fileresf,"f");    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   strcat(fileresf,fileres);  and drawn. It helps understanding how is the covariance between two incidences.\
   if((ficresf=fopen(fileresf,"w"))==NULL) {   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;    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 \
   printf("Computing forecasting: result on file '%s' \n", fileresf);  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
   free_matrix(mint,1,maxwav,1,n);   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
   free_matrix(anint,1,maxwav,1,n);   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   free_matrix(agev,1,maxwav,1,imx);  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   /* Mobile average */  
     cov[1]=1;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   if (mobilav==1) {    j1=0;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    for(t=1; t<=tj;t++){
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)      for(i1=1; i1<=ncodemax[t];i1++){ 
       for (i=1; i<=nlstate;i++)        j1++;
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)        if  (cptcovn>0) {
           mobaverage[(int)agedeb][i][cptcod]=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 (agedeb=bage+4; agedeb<=fage; agedeb++){          fprintf(ficresprob, "**********\n#\n");
       for (i=1; i<=nlstate;i++){          fprintf(ficresprobcov, "\n#********** Variable "); 
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           for (cpt=0;cpt<=4;cpt++){          fprintf(ficresprobcov, "**********\n#\n");
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];          
           }          fprintf(ficgp, "\n#********** Variable "); 
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         }          fprintf(ficgp, "**********\n#\n");
       }          
     }            
   }          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]]);
   stepsize=(int) (stepm+YEARM-1)/YEARM;          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
   if (stepm<=12) stepsize=1;          
           fprintf(ficresprobcor, "\n#********** Variable ");    
   agelim=AGESUP;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   /*hstepm=stepsize*YEARM; *//* Every year of age */          fprintf(ficresprobcor, "**********\n#");    
   hstepm=1;        }
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */        
   yp1=modf(dateintmean,&yp);        for (age=bage; age<=fage; age ++){ 
   anprojmean=yp;          cov[2]=age;
   yp2=modf((yp1*12),&yp);          for (k=1; k<=cptcovn;k++) {
   mprojmean=yp;            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
   yp1=modf((yp2*30.5),&yp);          }
   jprojmean=yp;          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   if(jprojmean==0) jprojmean=1;          for (k=1; k<=cptcovprod;k++)
   if(mprojmean==0) jprojmean=1;            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   if (popforecast==1) {          gp=vector(1,(nlstate)*(nlstate+ndeath));
     if((ficpop=fopen(popfile,"r"))==NULL)    {          gm=vector(1,(nlstate)*(nlstate+ndeath));
       printf("Problem with population file : %s\n",popfile);goto end;      
     }          for(theta=1; theta <=npar; theta++){
     popage=ivector(0,AGESUP);            for(i=1; i<=npar; i++)
     popeffectif=vector(0,AGESUP);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
     popcount=vector(0,AGESUP);            
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
     i=1;              
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)            k=0;
       {            for(i=1; i<= (nlstate); i++){
         i=i+1;              for(j=1; j<=(nlstate+ndeath);j++){
       }                k=k+1;
     imx=i;                gp[k]=pmmij[i][j];
                  }
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];            }
   }            
             for(i=1; i<=npar; i++)
   for(cptcov=1;cptcov<=i1;cptcov++){              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      
       k=k+1;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       fprintf(ficresf,"\n#******");            k=0;
       for(j=1;j<=cptcoveff;j++) {            for(i=1; i<=(nlstate); i++){
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              for(j=1; j<=(nlstate+ndeath);j++){
       }                k=k+1;
       fprintf(ficresf,"******\n");                gm[k]=pmmij[i][j];
       fprintf(ficresf,"# StartingAge FinalAge");              }
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);            }
       if (popforecast==1)  fprintf(ficresf," [Population]");       
                for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
       for (cpt=0; cpt<4;cpt++) {              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
         fprintf(ficresf,"\n");          }
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);    
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(bage-((int)calagedate %12)/12.); agedeb--){ /* If stepm=6 months */            for(theta=1; theta <=npar; theta++)
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);              trgradg[j][theta]=gradg[theta][j];
         nhstepm = nhstepm/hstepm;          
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         oldm=oldms;savm=savms;          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
                  free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         for (h=0; h<=nhstepm; h++){  
           if (h==(int) (calagedate+YEARM*cpt)) {          pmij(pmmij,cov,ncovmodel,x,nlstate);
             fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);          
           }          k=0;
           for(j=1; j<=nlstate+ndeath;j++) {          for(i=1; i<=(nlstate); i++){
             kk1=0.;kk2=0;            for(j=1; j<=(nlstate+ndeath);j++){
             for(i=1; i<=nlstate;i++) {                      k=k+1;
               if (mobilav==1)              mu[k][(int) age]=pmmij[i][j];
                 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];          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
                 /* fprintf(ficresf," p3=%.3f p=%.3f ", p3mat[i][j][h], probs[(int)(agedeb)+1][i][cptcod]);*/            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               }              varpij[i][j][(int)age] = doldm[i][j];
   
               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];          /*printf("\n%d ",(int)age);
             }            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
                      printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             if (h==(int)(calagedate+12*cpt)){            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
               fprintf(ficresf," %.3f", kk1);            }*/
                
               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);          fprintf(ficresprob,"\n%d ",(int)age);
             }          fprintf(ficresprobcov,"\n%d ",(int)age);
           }          fprintf(ficresprobcor,"\n%d ",(int)age);
         }  
         /*      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);*/          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
       }            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
       }          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     }            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
   }            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
   /*  if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          }
   if (popforecast==1) {          i=0;
     free_ivector(popage,0,AGESUP);          for (k=1; k<=(nlstate);k++){
     free_vector(popeffectif,0,AGESUP);            for (l=1; l<=(nlstate+ndeath);l++){ 
     free_vector(popcount,0,AGESUP);              i=i++;
   }              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
   free_imatrix(s,1,maxwav+1,1,n);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
   free_vector(weight,1,n);*/              for (j=1; j<=i;j++){
   fclose(ficresf);                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
   }/* End forecasting */                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
   else{              }
     erreur=108;            }
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);          }/* end of loop for state */
   }        } /* end of loop for age */
   
   /*---------- Health expectancies and variances ------------*/        /* Confidence intervalle of pij  */
         /*
   strcpy(filerest,"t");          fprintf(ficgp,"\nset noparametric;unset label");
   strcat(filerest,fileres);          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   if((ficrest=fopen(filerest,"w"))==NULL) {          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
   }          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
   printf("Computing Total LEs with variances: file '%s' \n", filerest);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   strcpy(filerese,"e");  
   strcat(filerese,fileres);        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
   if((ficreseij=fopen(filerese,"w"))==NULL) {        first1=1;
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);        for (k2=1; k2<=(nlstate);k2++){
   }          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);            if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
  strcpy(fileresv,"v");            for (k1=1; k1<=(nlstate);k1++){
   strcat(fileresv,fileres);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
   if((ficresvij=fopen(fileresv,"w"))==NULL) {                if(l1==k1) continue;
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);                i=(k1-1)*(nlstate+ndeath)+l1;
   }                if(i<=j) continue;
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);                for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
   k=0;                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   for(cptcov=1;cptcov<=i1;cptcov++){                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
       k=k+1;                    mu1=mu[i][(int) age]/stepm*YEARM ;
       fprintf(ficrest,"\n#****** ");                    mu2=mu[j][(int) age]/stepm*YEARM;
       for(j=1;j<=cptcoveff;j++)                    c12=cv12/sqrt(v1*v2);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    /* Computing eigen value of matrix of covariance */
       fprintf(ficrest,"******\n");                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       fprintf(ficreseij,"\n#****** ");                    /* Eigen vectors */
       for(j=1;j<=cptcoveff;j++)                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);                    /*v21=sqrt(1.-v11*v11); *//* error */
       fprintf(ficreseij,"******\n");                    v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
       fprintf(ficresvij,"\n#****** ");                    v22=v11;
       for(j=1;j<=cptcoveff;j++)                    tnalp=v21/v11;
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);                    if(first1==1){
       fprintf(ficresvij,"******\n");                      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);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                    }
       oldm=oldms;savm=savms;                    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);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);                      /*printf(fignu*/
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
       oldm=oldms;savm=savms;                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);                    if(first==1){
                            first=0;
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");                      fprintf(ficgp,"\nset parametric;unset label");
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
       fprintf(ficrest,"\n");                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                              fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
       hf=1;   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
       if (stepm >= YEARM) hf=stepm/YEARM;  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
       epj=vector(1,nlstate+1);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
       for(age=bage; age <=fage ;age++){                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
         if (popbased==1) {                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
           for(i=1; i<=nlstate;i++)                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
             prlim[i][i]=probs[(int)age][i][k];                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
         }                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                              fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
         fprintf(ficrest," %.0f",age);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
           for(i=1, epj[j]=0.;i <=nlstate;i++) {                    }else{
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];                      first=0;
           }                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
           epj[nlstate+1] +=epj[j];                      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);
         for(i=1, vepp=0.;i <=nlstate;i++)                      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",\
           for(j=1;j <=nlstate;j++)                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
             vepp += vareij[i][j][(int)age];                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));                    }/* if first */
         for(j=1;j <=nlstate;j++){                  } /* age mod 5 */
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));                } /* end loop age */
         }                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
         fprintf(ficrest,"\n");                first=1;
       }              } /*l12 */
     }            } /* k12 */
   }          } /*l1 */
                }/* k1 */
              } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
  fclose(ficreseij);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
  fclose(ficresvij);    free_vector(xp,1,npar);
   fclose(ficrest);    fclose(ficresprob);
   fclose(ficpar);    fclose(ficresprobcov);
   free_vector(epj,1,nlstate+1);    fclose(ficresprobcor);
   /*  scanf("%d ",i); */    fflush(ficgp);
     fflush(fichtmcov);
   /*------- Variance limit prevalence------*/    }
   
 strcpy(fileresvpl,"vpl");  
   strcat(fileresvpl,fileres);  /******************* Printing html file ***********/
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);                    int lastpass, int stepm, int weightopt, char model[],\
     exit(0);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
   }                    int popforecast, int estepm ,\
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);                    double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
  k=0;    int jj1, k1, i1, cpt;
  for(cptcov=1;cptcov<=i1;cptcov++){    /*char optionfilehtm[FILENAMELENGTH];*/
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    { */
      k=k+1;  /*     printf("Problem with %s \n",optionfilehtm), exit(0); */
      fprintf(ficresvpl,"\n#****** ");  /*     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
      for(j=1;j<=cptcoveff;j++)  /*   } */
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
      fprintf(ficresvpl,"******\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 \
      varpl=matrix(1,nlstate,(int) bage, (int) fage);   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n \
      oldm=oldms;savm=savms;   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n \
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);   - Life expectancies by age and initial health status (estepm=%2d months): \
    }     <a href=\"%s\">%s</a> <br>\n</li>", \
  }             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
              stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
   fclose(ficresvpl);             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   /*---------- End : free ----------------*/  
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
    
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);   m=cptcoveff;
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
    
     jj1=0;
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);   for(k1=1; k1<=m;k1++){
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);     for(i1=1; i1<=ncodemax[k1];i1++){
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);       jj1++;
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);       if (cptcovn > 0) {
           fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   free_matrix(matcov,1,npar,1,npar);         for (cpt=1; cpt<=cptcoveff;cpt++) 
   free_vector(delti,1,npar);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
           fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);       }
        /* Pij */
   if(erreur >0)       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
     printf("End of Imach with error %d\n",erreur);  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
   else   printf("End of Imach\n");       /* Quasi-incidences */
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
     before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
   /* 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);*/  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
   /*printf("Total time was %d uSec.\n", total_usecs);*/         /* Stable prevalence in each health state */
   /*------ End -----------*/         for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
  end:         }
 #ifdef windows       for(cpt=1; cpt<=nlstate;cpt++) {
   /* chdir(pathcd);*/          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
 #endif  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
  /*system("wgnuplot graph.plt");*/       }
  /*system("../gp37mgw/wgnuplot graph.plt");*/       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
  /*system("cd ../gp37mgw");*/  health expectancies in states (1) and (2): %s%d.png<br>\
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
  strcpy(plotcmd,GNUPLOTPROGRAM);     } /* end i1 */
  strcat(plotcmd," ");   }/* End k1 */
  strcat(plotcmd,optionfilegnuplot);   fprintf(fichtm,"</ul>");
  system(plotcmd);  
   
 #ifdef windows   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
   while (z[0] != 'q') {   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
     chdir(path);   - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
     printf("\nType e to edit output files, c to start again, and q for exiting: ");   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
     scanf("%s",z);   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
     if (z[0] == 'c') system("./imach");   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n\
     else if (z[0] == 'e') {   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n\
       chdir(path);   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
       system(optionfilehtm);           rfileres,rfileres,\
     }           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
     else if (z[0] == 'q') exit(0);           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
   }           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
 #endif           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
 }           subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
   interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
           
         } 
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     }
   
   } /* end of prwizard */
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int jj, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE]; 
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   
     char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char strstart[80], *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
     /*   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.1.23  
changed lines
  Added in v.1.92


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