Diff for /imach/src/imach.c between versions 1.51 and 1.89

version 1.51, 2002/07/19 12:22:25 version 1.89, 2003/06/24 12:30:52
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.89  2003/06/24 12:30:52  brouard
      (Module): Some bugs corrected for windows. Also, when
   This program computes Healthy Life Expectancies from    mle=-1 a template is output in file "or"mypar.txt with the design
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    of the covariance matrix to be input.
   first survey ("cross") where individuals from different ages are  
   interviewed on their health status or degree of disability (in the    Revision 1.88  2003/06/23 17:54:56  brouard
   case of a health survey which is our main interest) -2- at least a    * 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.
   second wave of interviews ("longitudinal") which measure each change  
   (if any) in individual health status.  Health expectancies are    Revision 1.87  2003/06/18 12:26:01  brouard
   computed from the time spent in each health state according to a    Version 0.96
   model. More health states you consider, more time is necessary to reach the  
   Maximum Likelihood of the parameters involved in the model.  The    Revision 1.86  2003/06/17 20:04:08  brouard
   simplest model is the multinomial logistic model where pij is the    (Module): Change position of html and gnuplot routines and added
   probability to be observed in state j at the second wave    routine fileappend.
   conditional to be observed in state i at the first wave. Therefore  
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    Revision 1.85  2003/06/17 13:12:43  brouard
   'age' is age and 'sex' is a covariate. If you want to have a more    * imach.c (Repository): Check when date of death was earlier that
   complex model than "constant and age", you should modify the program    current date of interview. It may happen when the death was just
   where the markup *Covariates have to be included here again* invites    prior to the death. In this case, dh was negative and likelihood
   you to do it.  More covariates you add, slower the    was wrong (infinity). We still send an "Error" but patch by
   convergence.    assuming that the date of death was just one stepm after the
     interview.
   The advantage of this computer programme, compared to a simple    (Repository): Because some people have very long ID (first column)
   multinomial logistic model, is clear when the delay between waves is not    we changed int to long in num[] and we added a new lvector for
   identical for each individual. Also, if a individual missed an    memory allocation. But we also truncated to 8 characters (left
   intermediate interview, the information is lost, but taken into    truncation)
   account using an interpolation or extrapolation.      (Repository): No more line truncation errors.
   
   hPijx is the probability to be observed in state i at age x+h    Revision 1.84  2003/06/13 21:44:43  brouard
   conditional to the observed state i at age x. The delay 'h' can be    * imach.c (Repository): Replace "freqsummary" at a correct
   split into an exact number (nh*stepm) of unobserved intermediate    place. It differs from routine "prevalence" which may be called
   states. This elementary transition (by month or quarter trimester,    many times. Probs is memory consuming and must be used with
   semester or year) is model as a multinomial logistic.  The hPx    parcimony.
   matrix is simply the matrix product of nh*stepm elementary matrices    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   and the contribution of each individual to the likelihood is simply  
   hPijx.    Revision 1.83  2003/06/10 13:39:11  lievre
     *** empty log message ***
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.82  2003/06/05 15:57:20  brouard
      Add log in  imach.c and  fullversion number is now printed.
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.  */
   This software have been partly granted by Euro-REVES, a concerted action  /*
   from the European Union.     Interpolated Markov Chain
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Short summary of the programme:
   can be accessed at http://euroreves.ined.fr/imach .    
   **********************************************************************/    This program computes Healthy Life Expectancies from
      cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 #include <math.h>    first survey ("cross") where individuals from different ages are
 #include <stdio.h>    interviewed on their health status or degree of disability (in the
 #include <stdlib.h>    case of a health survey which is our main interest) -2- at least a
 #include <unistd.h>    second wave of interviews ("longitudinal") which measure each change
     (if any) in individual health status.  Health expectancies are
 #define MAXLINE 256    computed from the time spent in each health state according to a
 #define GNUPLOTPROGRAM "gnuplot"    model. More health states you consider, more time is necessary to reach the
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    Maximum Likelihood of the parameters involved in the model.  The
 #define FILENAMELENGTH 80    simplest model is the multinomial logistic model where pij is the
 /*#define DEBUG*/    probability to be observed in state j at the second wave
 #define windows    conditional to be observed in state i at the first wave. Therefore
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    'age' is age and 'sex' is a covariate. If you want to have a more
     complex model than "constant and age", you should modify the program
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    where the markup *Covariates have to be included here again* invites
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    you to do it.  More covariates you add, slower the
     convergence.
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    The advantage of this computer programme, compared to a simple
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    multinomial logistic model, is clear when the delay between waves is not
 #define NCOVMAX 8 /* Maximum number of covariates */    identical for each individual. Also, if a individual missed an
 #define MAXN 20000    intermediate interview, the information is lost, but taken into
 #define YEARM 12. /* Number of months per year */    account using an interpolation or extrapolation.  
 #define AGESUP 130  
 #define AGEBASE 40    hPijx is the probability to be observed in state i at age x+h
 #ifdef windows    conditional to the observed state i at age x. The delay 'h' can be
 #define DIRSEPARATOR '\\'    split into an exact number (nh*stepm) of unobserved intermediate
 #define ODIRSEPARATOR '/'    states. This elementary transition (by month, quarter,
 #else    semester or year) is modelled as a multinomial logistic.  The hPx
 #define DIRSEPARATOR '/'    matrix is simply the matrix product of nh*stepm elementary matrices
 #define ODIRSEPARATOR '\\'    and the contribution of each individual to the likelihood is simply
 #endif    hPijx.
   
 char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";    Also this programme outputs the covariance matrix of the parameters but also
 int erreur; /* Error number */    of the life expectancies. It also computes the stable prevalence. 
 int nvar;    
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 int npar=NPARMAX;             Institut national d'études démographiques, Paris.
 int nlstate=2; /* Number of live states */    This software have been partly granted by Euro-REVES, a concerted action
 int ndeath=1; /* Number of dead states */    from the European Union.
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    It is copyrighted identically to a GNU software product, ie programme and
 int popbased=0;    software can be distributed freely for non commercial use. Latest version
     can be accessed at http://euroreves.ined.fr/imach .
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 int jmin, jmax; /* min, max spacing between 2 waves */    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 int mle, weightopt;    
 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 */  /*
 double jmean; /* Mean space between 2 waves */    main
 double **oldm, **newm, **savm; /* Working pointers to matrices */    read parameterfile
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    read datafile
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    concatwav
 FILE *ficlog;    freqsummary
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;    if (mle >= 1)
 FILE *ficresprobmorprev;      mlikeli
 FILE *fichtm; /* Html File */    print results files
 FILE *ficreseij;    if mle==1 
 char filerese[FILENAMELENGTH];       computes hessian
 FILE  *ficresvij;    read end of parameter file: agemin, agemax, bage, fage, estepm
 char fileresv[FILENAMELENGTH];        begin-prev-date,...
 FILE  *ficresvpl;    open gnuplot file
 char fileresvpl[FILENAMELENGTH];    open html file
 char title[MAXLINE];    stable prevalence
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];     for age prevalim()
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    h Pij x
     variance of p varprob
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    forecasting if prevfcast==1 prevforecast call prevalence()
 char filelog[FILENAMELENGTH]; /* Log file */    health expectancies
 char filerest[FILENAMELENGTH];    Variance-covariance of DFLE
 char fileregp[FILENAMELENGTH];    prevalence()
 char popfile[FILENAMELENGTH];     movingaverage()
     varevsij() 
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    if popbased==1 varevsij(,popbased)
     total life expectancies
 #define NR_END 1    Variance of stable prevalence
 #define FREE_ARG char*   end
 #define FTOL 1.0e-10  */
   
 #define NRANSI  
 #define ITMAX 200  
    
 #define TOL 2.0e-4  #include <math.h>
   #include <stdio.h>
 #define CGOLD 0.3819660  #include <stdlib.h>
 #define ZEPS 1.0e-10  #include <unistd.h>
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
   #include <sys/time.h>
 #define GOLD 1.618034  #include <time.h>
 #define GLIMIT 100.0  #include "timeval.h"
 #define TINY 1.0e-20  
   #define MAXLINE 256
 static double maxarg1,maxarg2;  #define GNUPLOTPROGRAM "gnuplot"
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  #define FILENAMELENGTH 132
    /*#define DEBUG*/
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  /*#define windows*/
 #define rint(a) floor(a+0.5)  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   
 int imx;  #define NINTERVMAX 8
 int stepm;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 /* Stepm, step in month: minimum step interpolation*/  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   #define NCOVMAX 8 /* Maximum number of covariates */
 int estepm;  #define MAXN 20000
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  #define YEARM 12. /* Number of months per year */
   #define AGESUP 130
 int m,nb;  #define AGEBASE 40
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  #ifdef unix
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  #define DIRSEPARATOR '/'
 double **pmmij, ***probs, ***mobaverage;  #define ODIRSEPARATOR '\\'
 double dateintmean=0;  #else
   #define DIRSEPARATOR '\\'
 double *weight;  #define ODIRSEPARATOR '/'
 int **s; /* Status */  #endif
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  /* $Id$ */
   /* $State$ */
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */  char version[]="Imach version 0.96a, June 2003, INED-EUROREVES ";
   char fullversion[]="$Revision$ $Date$"; 
 /**************** split *************************/  int erreur; /* Error number */
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  int nvar;
 {  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
    char *s;                             /* pointer */  int npar=NPARMAX;
    int  l1, l2;                         /* length counters */  int nlstate=2; /* Number of live states */
   int ndeath=1; /* Number of dead states */
    l1 = strlen( path );                 /* length of path */  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  int popbased=0;
    s= strrchr( path, DIRSEPARATOR );            /* find last / */  
    if ( s == NULL ) {                   /* no directory, so use current */  int *wav; /* Number of waves for this individuual 0 is possible */
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)  int maxwav; /* Maxim number of waves */
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/  int jmin, jmax; /* min, max spacing between 2 waves */
 #if     defined(__bsd__)                /* get current working directory */  int gipmx, gsw; /* Global variables on the number of contributions 
       extern char       *getwd( );                     to the likelihood and the sum of weights (done by funcone)*/
   int mle, weightopt;
       if ( getwd( dirc ) == NULL ) {  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 #else  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
       extern char       *getcwd( );  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
              * wave mi and wave mi+1 is not an exact multiple of stepm. */
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  double jmean; /* Mean space between 2 waves */
 #endif  double **oldm, **newm, **savm; /* Working pointers to matrices */
          return( GLOCK_ERROR_GETCWD );  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
       }  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
       strcpy( name, path );             /* we've got it */  FILE *ficlog, *ficrespow;
    } else {                             /* strip direcotry from path */  int globpr; /* Global variable for printing or not */
       s++;                              /* after this, the filename */  double fretone; /* Only one call to likelihood */
       l2 = strlen( s );                 /* length of filename */  long ipmx; /* Number of contributions */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  double sw; /* Sum of weights */
       strcpy( name, s );                /* save file name */  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  FILE *ficresilk;
       dirc[l1-l2] = 0;                  /* add zero */  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
    }  FILE *ficresprobmorprev;
    l1 = strlen( dirc );                 /* length of directory */  FILE *fichtm; /* Html File */
 #ifdef windows  FILE *ficreseij;
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  char filerese[FILENAMELENGTH];
 #else  FILE  *ficresvij;
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  char fileresv[FILENAMELENGTH];
 #endif  FILE  *ficresvpl;
    s = strrchr( name, '.' );            /* find last / */  char fileresvpl[FILENAMELENGTH];
    s++;  char title[MAXLINE];
    strcpy(ext,s);                       /* save extension */  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
    l1= strlen( name);  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
    l2= strlen( s)+1;  char tmpout[FILENAMELENGTH]; 
    strncpy( finame, name, l1-l2);  char command[FILENAMELENGTH];
    finame[l1-l2]= 0;  int  outcmd=0;
    return( 0 );                         /* we're done */  
 }  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   char lfileres[FILENAMELENGTH];
   char filelog[FILENAMELENGTH]; /* Log file */
 /******************************************/  char filerest[FILENAMELENGTH];
   char fileregp[FILENAMELENGTH];
 void replace(char *s, char*t)  char popfile[FILENAMELENGTH];
 {  
   int i;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
   int lg=20;  
   i=0;  #define NR_END 1
   lg=strlen(t);  #define FREE_ARG char*
   for(i=0; i<= lg; i++) {  #define FTOL 1.0e-10
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';  #define NRANSI 
   }  #define ITMAX 200 
 }  
   #define TOL 2.0e-4 
 int nbocc(char *s, char occ)  
 {  #define CGOLD 0.3819660 
   int i,j=0;  #define ZEPS 1.0e-10 
   int lg=20;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   i=0;  
   lg=strlen(s);  #define GOLD 1.618034 
   for(i=0; i<= lg; i++) {  #define GLIMIT 100.0 
   if  (s[i] == occ ) j++;  #define TINY 1.0e-20 
   }  
   return j;  static double maxarg1,maxarg2;
 }  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
 void cutv(char *u,char *v, char*t, char occ)    
 {  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   /* cuts string t into u and v where u is ended by char occ excluding it  #define rint(a) floor(a+0.5)
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)  
      gives u="abcedf" and v="ghi2j" */  static double sqrarg;
   int i,lg,j,p=0;  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   i=0;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   for(j=0; j<=strlen(t)-1; j++) {  
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  int imx; 
   }  int stepm;
   /* Stepm, step in month: minimum step interpolation*/
   lg=strlen(t);  
   for(j=0; j<p; j++) {  int estepm;
     (u[j] = t[j]);  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   }  
      u[p]='\0';  int m,nb;
   long *num;
    for(j=0; j<= lg; j++) {  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
     if (j>=(p+1))(v[j-p-1] = t[j]);  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   }  double **pmmij, ***probs;
 }  double dateintmean=0;
   
 /********************** nrerror ********************/  double *weight;
   int **s; /* Status */
 void nrerror(char error_text[])  double *agedc, **covar, idx;
 {  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   exit(1);  double ftolhess; /* Tolerance for computing hessian */
 }  
 /*********************** vector *******************/  /**************** split *************************/
 double *vector(int nl, int nh)  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 {  {
   double *v;    char  *ss;                            /* pointer */
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    int   l1, l2;                         /* length counters */
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;    l1 = strlen(path );                   /* length of path */
 }    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     ss= strrchr( path, DIRSEPARATOR );            /* find last / */
 /************************ free vector ******************/    if ( ss == NULL ) {                   /* no directory, so use current */
 void free_vector(double*v, int nl, int nh)      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 {        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   free((FREE_ARG)(v+nl-NR_END));      /* get current working directory */
 }      /*    extern  char* getcwd ( char *buf , int len);*/
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 /************************ivector *******************************/        return( GLOCK_ERROR_GETCWD );
 int *ivector(long nl,long nh)      }
 {      strcpy( name, path );               /* we've got it */
   int *v;    } else {                              /* strip direcotry from path */
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));      ss++;                               /* after this, the filename */
   if (!v) nrerror("allocation failure in ivector");      l2 = strlen( ss );                  /* length of filename */
   return v-nl+NR_END;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 }      strcpy( name, ss );         /* save file name */
       strncpy( dirc, path, l1 - l2 );     /* now the directory */
 /******************free ivector **************************/      dirc[l1-l2] = 0;                    /* add zero */
 void free_ivector(int *v, long nl, long nh)    }
 {    l1 = strlen( dirc );                  /* length of directory */
   free((FREE_ARG)(v+nl-NR_END));    /*#ifdef windows
 }    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   #else
 /******************* imatrix *******************************/    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
 int **imatrix(long nrl, long nrh, long ncl, long nch)  #endif
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    */
 {    ss = strrchr( name, '.' );            /* find last / */
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    ss++;
   int **m;    strcpy(ext,ss);                       /* save extension */
      l1= strlen( name);
   /* allocate pointers to rows */    l2= strlen(ss)+1;
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    strncpy( finame, name, l1-l2);
   if (!m) nrerror("allocation failure 1 in matrix()");    finame[l1-l2]= 0;
   m += NR_END;    return( 0 );                          /* we're done */
   m -= nrl;  }
    
    
   /* allocate rows and set pointers to them */  /******************************************/
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  void replace_back_to_slash(char *s, char*t)
   m[nrl] += NR_END;  {
   m[nrl] -= ncl;    int i;
      int lg=0;
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    i=0;
      lg=strlen(t);
   /* return pointer to array of pointers to rows */    for(i=0; i<= lg; i++) {
   return m;      (s[i] = t[i]);
 }      if (t[i]== '\\') s[i]='/';
     }
 /****************** free_imatrix *************************/  }
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;  int nbocc(char *s, char occ)
       long nch,ncl,nrh,nrl;  {
      /* free an int matrix allocated by imatrix() */    int i,j=0;
 {    int lg=20;
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    i=0;
   free((FREE_ARG) (m+nrl-NR_END));    lg=strlen(s);
 }    for(i=0; i<= lg; i++) {
     if  (s[i] == occ ) j++;
 /******************* matrix *******************************/    }
 double **matrix(long nrl, long nrh, long ncl, long nch)    return j;
 {  }
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;  void cutv(char *u,char *v, char*t, char occ)
   {
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    /* cuts string t into u and v where u is ended by char occ excluding it
   if (!m) nrerror("allocation failure 1 in matrix()");       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   m += NR_END;       gives u="abcedf" and v="ghi2j" */
   m -= nrl;    int i,lg,j,p=0;
     i=0;
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    for(j=0; j<=strlen(t)-1; j++) {
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   m[nrl] += NR_END;    }
   m[nrl] -= ncl;  
     lg=strlen(t);
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    for(j=0; j<p; j++) {
   return m;      (u[j] = t[j]);
 }    }
        u[p]='\0';
 /*************************free matrix ************************/  
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)     for(j=0; j<= lg; j++) {
 {      if (j>=(p+1))(v[j-p-1] = t[j]);
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    }
   free((FREE_ARG)(m+nrl-NR_END));  }
 }  
   /********************** nrerror ********************/
 /******************* ma3x *******************************/  
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  void nrerror(char error_text[])
 {  {
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    fprintf(stderr,"ERREUR ...\n");
   double ***m;    fprintf(stderr,"%s\n",error_text);
     exit(EXIT_FAILURE);
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  }
   if (!m) nrerror("allocation failure 1 in matrix()");  /*********************** vector *******************/
   m += NR_END;  double *vector(int nl, int nh)
   m -= nrl;  {
     double *v;
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    if (!v) nrerror("allocation failure in vector");
   m[nrl] += NR_END;    return v-nl+NR_END;
   m[nrl] -= ncl;  }
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  /************************ free vector ******************/
   void free_vector(double*v, int nl, int nh)
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  {
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    free((FREE_ARG)(v+nl-NR_END));
   m[nrl][ncl] += NR_END;  }
   m[nrl][ncl] -= nll;  
   for (j=ncl+1; j<=nch; j++)  /************************ivector *******************************/
     m[nrl][j]=m[nrl][j-1]+nlay;  int *ivector(long nl,long nh)
    {
   for (i=nrl+1; i<=nrh; i++) {    int *v;
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     for (j=ncl+1; j<=nch; j++)    if (!v) nrerror("allocation failure in ivector");
       m[i][j]=m[i][j-1]+nlay;    return v-nl+NR_END;
   }  }
   return m;  
 }  /******************free ivector **************************/
   void free_ivector(int *v, long nl, long nh)
 /*************************free ma3x ************************/  {
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    free((FREE_ARG)(v+nl-NR_END));
 {  }
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  /************************lvector *******************************/
   free((FREE_ARG)(m+nrl-NR_END));  long *lvector(long nl,long nh)
 }  {
     long *v;
 /***************** f1dim *************************/    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
 extern int ncom;    if (!v) nrerror("allocation failure in ivector");
 extern double *pcom,*xicom;    return v-nl+NR_END;
 extern double (*nrfunc)(double []);  }
    
 double f1dim(double x)  /******************free lvector **************************/
 {  void free_lvector(long *v, long nl, long nh)
   int j;  {
   double f;    free((FREE_ARG)(v+nl-NR_END));
   double *xt;  }
    
   xt=vector(1,ncom);  /******************* imatrix *******************************/
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  int **imatrix(long nrl, long nrh, long ncl, long nch) 
   f=(*nrfunc)(xt);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   free_vector(xt,1,ncom);  { 
   return f;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
 }    int **m; 
     
 /*****************brent *************************/    /* allocate pointers to rows */ 
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 {    if (!m) nrerror("allocation failure 1 in matrix()"); 
   int iter;    m += NR_END; 
   double a,b,d,etemp;    m -= nrl; 
   double fu,fv,fw,fx;    
   double ftemp;    
   double p,q,r,tol1,tol2,u,v,w,x,xm;    /* allocate rows and set pointers to them */ 
   double e=0.0;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
      if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   a=(ax < cx ? ax : cx);    m[nrl] += NR_END; 
   b=(ax > cx ? ax : cx);    m[nrl] -= ncl; 
   x=w=v=bx;    
   fw=fv=fx=(*f)(x);    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   for (iter=1;iter<=ITMAX;iter++) {    
     xm=0.5*(a+b);    /* return pointer to array of pointers to rows */ 
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    return m; 
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  } 
     printf(".");fflush(stdout);  
     fprintf(ficlog,".");fflush(ficlog);  /****************** free_imatrix *************************/
 #ifdef DEBUG  void free_imatrix(m,nrl,nrh,ncl,nch)
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);        int **m;
     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);        long nch,ncl,nrh,nrl; 
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */       /* free an int matrix allocated by imatrix() */ 
 #endif  { 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       *xmin=x;    free((FREE_ARG) (m+nrl-NR_END)); 
       return fx;  } 
     }  
     ftemp=fu;  /******************* matrix *******************************/
     if (fabs(e) > tol1) {  double **matrix(long nrl, long nrh, long ncl, long nch)
       r=(x-w)*(fx-fv);  {
       q=(x-v)*(fx-fw);    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       p=(x-v)*q-(x-w)*r;    double **m;
       q=2.0*(q-r);  
       if (q > 0.0) p = -p;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       q=fabs(q);    if (!m) nrerror("allocation failure 1 in matrix()");
       etemp=e;    m += NR_END;
       e=d;    m -= nrl;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       else {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         d=p/q;    m[nrl] += NR_END;
         u=x+d;    m[nrl] -= ncl;
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       }    return m;
     } else {    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       d=CGOLD*(e=(x >= xm ? a-x : b-x));     */
     }  }
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  
     fu=(*f)(u);  /*************************free matrix ************************/
     if (fu <= fx) {  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       if (u >= x) a=x; else b=x;  {
       SHFT(v,w,x,u)    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         SHFT(fv,fw,fx,fu)    free((FREE_ARG)(m+nrl-NR_END));
         } else {  }
           if (u < x) a=u; else b=u;  
           if (fu <= fw || w == x) {  /******************* ma3x *******************************/
             v=w;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
             w=u;  {
             fv=fw;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
             fw=fu;    double ***m;
           } else if (fu <= fv || v == x || v == w) {  
             v=u;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
             fv=fu;    if (!m) nrerror("allocation failure 1 in matrix()");
           }    m += NR_END;
         }    m -= nrl;
   }  
   nrerror("Too many iterations in brent");    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   *xmin=x;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   return fx;    m[nrl] += NR_END;
 }    m[nrl] -= ncl;
   
 /****************** mnbrak ***********************/    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,    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
             double (*func)(double))    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
 {    m[nrl][ncl] += NR_END;
   double ulim,u,r,q, dum;    m[nrl][ncl] -= nll;
   double fu;    for (j=ncl+1; j<=nch; j++) 
        m[nrl][j]=m[nrl][j-1]+nlay;
   *fa=(*func)(*ax);    
   *fb=(*func)(*bx);    for (i=nrl+1; i<=nrh; i++) {
   if (*fb > *fa) {      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     SHFT(dum,*ax,*bx,dum)      for (j=ncl+1; j<=nch; j++) 
       SHFT(dum,*fb,*fa,dum)        m[i][j]=m[i][j-1]+nlay;
       }    }
   *cx=(*bx)+GOLD*(*bx-*ax);    return m; 
   *fc=(*func)(*cx);    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   while (*fb > *fc) {             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     r=(*bx-*ax)*(*fb-*fc);    */
     q=(*bx-*cx)*(*fb-*fa);  }
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  /*************************free ma3x ************************/
     ulim=(*bx)+GLIMIT*(*cx-*bx);  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     if ((*bx-u)*(u-*cx) > 0.0) {  {
       fu=(*func)(u);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     } else if ((*cx-u)*(u-ulim) > 0.0) {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       fu=(*func)(u);    free((FREE_ARG)(m+nrl-NR_END));
       if (fu < *fc) {  }
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))  /***************** f1dim *************************/
           }  extern int ncom; 
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  extern double *pcom,*xicom;
       u=ulim;  extern double (*nrfunc)(double []); 
       fu=(*func)(u);   
     } else {  double f1dim(double x) 
       u=(*cx)+GOLD*(*cx-*bx);  { 
       fu=(*func)(u);    int j; 
     }    double f;
     SHFT(*ax,*bx,*cx,u)    double *xt; 
       SHFT(*fa,*fb,*fc,fu)   
       }    xt=vector(1,ncom); 
 }    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     f=(*nrfunc)(xt); 
 /*************** linmin ************************/    free_vector(xt,1,ncom); 
     return f; 
 int ncom;  } 
 double *pcom,*xicom;  
 double (*nrfunc)(double []);  /*****************brent *************************/
    double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  { 
 {    int iter; 
   double brent(double ax, double bx, double cx,    double a,b,d,etemp;
                double (*f)(double), double tol, double *xmin);    double fu,fv,fw,fx;
   double f1dim(double x);    double ftemp;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    double p,q,r,tol1,tol2,u,v,w,x,xm; 
               double *fc, double (*func)(double));    double e=0.0; 
   int j;   
   double xx,xmin,bx,ax;    a=(ax < cx ? ax : cx); 
   double fx,fb,fa;    b=(ax > cx ? ax : cx); 
      x=w=v=bx; 
   ncom=n;    fw=fv=fx=(*f)(x); 
   pcom=vector(1,n);    for (iter=1;iter<=ITMAX;iter++) { 
   xicom=vector(1,n);      xm=0.5*(a+b); 
   nrfunc=func;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   for (j=1;j<=n;j++) {      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     pcom[j]=p[j];      printf(".");fflush(stdout);
     xicom[j]=xi[j];      fprintf(ficlog,".");fflush(ficlog);
   }  #ifdef DEBUG
   ax=0.0;      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   xx=1.0;      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  #endif
 #ifdef DEBUG      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);        *xmin=x; 
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);        return fx; 
 #endif      } 
   for (j=1;j<=n;j++) {      ftemp=fu;
     xi[j] *= xmin;      if (fabs(e) > tol1) { 
     p[j] += xi[j];        r=(x-w)*(fx-fv); 
   }        q=(x-v)*(fx-fw); 
   free_vector(xicom,1,n);        p=(x-v)*q-(x-w)*r; 
   free_vector(pcom,1,n);        q=2.0*(q-r); 
 }        if (q > 0.0) p = -p; 
         q=fabs(q); 
 /*************** powell ************************/        etemp=e; 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,        e=d; 
             double (*func)(double []))        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
 {          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   void linmin(double p[], double xi[], int n, double *fret,        else { 
               double (*func)(double []));          d=p/q; 
   int i,ibig,j;          u=x+d; 
   double del,t,*pt,*ptt,*xit;          if (u-a < tol2 || b-u < tol2) 
   double fp,fptt;            d=SIGN(tol1,xm-x); 
   double *xits;        } 
   pt=vector(1,n);      } else { 
   ptt=vector(1,n);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   xit=vector(1,n);      } 
   xits=vector(1,n);      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   *fret=(*func)(p);      fu=(*f)(u); 
   for (j=1;j<=n;j++) pt[j]=p[j];      if (fu <= fx) { 
   for (*iter=1;;++(*iter)) {        if (u >= x) a=x; else b=x; 
     fp=(*fret);        SHFT(v,w,x,u) 
     ibig=0;          SHFT(fv,fw,fx,fu) 
     del=0.0;          } else { 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);            if (u < x) a=u; else b=u; 
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);            if (fu <= fw || w == x) { 
     for (i=1;i<=n;i++)              v=w; 
       printf(" %d %.12f",i, p[i]);              w=u; 
     fprintf(ficlog," %d %.12f",i, p[i]);              fv=fw; 
     printf("\n");              fw=fu; 
     fprintf(ficlog,"\n");            } else if (fu <= fv || v == x || v == w) { 
     for (i=1;i<=n;i++) {              v=u; 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];              fv=fu; 
       fptt=(*fret);            } 
 #ifdef DEBUG          } 
       printf("fret=%lf \n",*fret);    } 
       fprintf(ficlog,"fret=%lf \n",*fret);    nrerror("Too many iterations in brent"); 
 #endif    *xmin=x; 
       printf("%d",i);fflush(stdout);    return fx; 
       fprintf(ficlog,"%d",i);fflush(ficlog);  } 
       linmin(p,xit,n,fret,func);  
       if (fabs(fptt-(*fret)) > del) {  /****************** mnbrak ***********************/
         del=fabs(fptt-(*fret));  
         ibig=i;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       }              double (*func)(double)) 
 #ifdef DEBUG  { 
       printf("%d %.12e",i,(*fret));    double ulim,u,r,q, dum;
       fprintf(ficlog,"%d %.12e",i,(*fret));    double fu; 
       for (j=1;j<=n;j++) {   
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    *fa=(*func)(*ax); 
         printf(" x(%d)=%.12e",j,xit[j]);    *fb=(*func)(*bx); 
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);    if (*fb > *fa) { 
       }      SHFT(dum,*ax,*bx,dum) 
       for(j=1;j<=n;j++) {        SHFT(dum,*fb,*fa,dum) 
         printf(" p=%.12e",p[j]);        } 
         fprintf(ficlog," p=%.12e",p[j]);    *cx=(*bx)+GOLD*(*bx-*ax); 
       }    *fc=(*func)(*cx); 
       printf("\n");    while (*fb > *fc) { 
       fprintf(ficlog,"\n");      r=(*bx-*ax)*(*fb-*fc); 
 #endif      q=(*bx-*cx)*(*fb-*fa); 
     }      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 #ifdef DEBUG      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       int k[2],l;      if ((*bx-u)*(u-*cx) > 0.0) { 
       k[0]=1;        fu=(*func)(u); 
       k[1]=-1;      } else if ((*cx-u)*(u-ulim) > 0.0) { 
       printf("Max: %.12e",(*func)(p));        fu=(*func)(u); 
       fprintf(ficlog,"Max: %.12e",(*func)(p));        if (fu < *fc) { 
       for (j=1;j<=n;j++) {          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
         printf(" %.12e",p[j]);            SHFT(*fb,*fc,fu,(*func)(u)) 
         fprintf(ficlog," %.12e",p[j]);            } 
       }      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       printf("\n");        u=ulim; 
       fprintf(ficlog,"\n");        fu=(*func)(u); 
       for(l=0;l<=1;l++) {      } else { 
         for (j=1;j<=n;j++) {        u=(*cx)+GOLD*(*cx-*bx); 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];        fu=(*func)(u); 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);      } 
           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);      SHFT(*ax,*bx,*cx,u) 
         }        SHFT(*fa,*fb,*fc,fu) 
         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)));  } 
       }  
 #endif  /*************** linmin ************************/
   
   int ncom; 
       free_vector(xit,1,n);  double *pcom,*xicom;
       free_vector(xits,1,n);  double (*nrfunc)(double []); 
       free_vector(ptt,1,n);   
       free_vector(pt,1,n);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       return;  { 
     }    double brent(double ax, double bx, double cx, 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");                 double (*f)(double), double tol, double *xmin); 
     for (j=1;j<=n;j++) {    double f1dim(double x); 
       ptt[j]=2.0*p[j]-pt[j];    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       xit[j]=p[j]-pt[j];                double *fc, double (*func)(double)); 
       pt[j]=p[j];    int j; 
     }    double xx,xmin,bx,ax; 
     fptt=(*func)(ptt);    double fx,fb,fa;
     if (fptt < fp) {   
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    ncom=n; 
       if (t < 0.0) {    pcom=vector(1,n); 
         linmin(p,xit,n,fret,func);    xicom=vector(1,n); 
         for (j=1;j<=n;j++) {    nrfunc=func; 
           xi[j][ibig]=xi[j][n];    for (j=1;j<=n;j++) { 
           xi[j][n]=xit[j];      pcom[j]=p[j]; 
         }      xicom[j]=xi[j]; 
 #ifdef DEBUG    } 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    ax=0.0; 
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    xx=1.0; 
         for(j=1;j<=n;j++){    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
           printf(" %.12e",xit[j]);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
           fprintf(ficlog," %.12e",xit[j]);  #ifdef DEBUG
         }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         printf("\n");    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         fprintf(ficlog,"\n");  #endif
 #endif    for (j=1;j<=n;j++) { 
       }      xi[j] *= xmin; 
     }      p[j] += xi[j]; 
   }    } 
 }    free_vector(xicom,1,n); 
     free_vector(pcom,1,n); 
 /**** Prevalence limit ****************/  } 
   
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  /*************** powell ************************/
 {  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit              double (*func)(double [])) 
      matrix by transitions matrix until convergence is reached */  { 
     void linmin(double p[], double xi[], int n, double *fret, 
   int i, ii,j,k;                double (*func)(double [])); 
   double min, max, maxmin, maxmax,sumnew=0.;    int i,ibig,j; 
   double **matprod2();    double del,t,*pt,*ptt,*xit;
   double **out, cov[NCOVMAX], **pmij();    double fp,fptt;
   double **newm;    double *xits;
   double agefin, delaymax=50 ; /* Max number of years to converge */    pt=vector(1,n); 
     ptt=vector(1,n); 
   for (ii=1;ii<=nlstate+ndeath;ii++)    xit=vector(1,n); 
     for (j=1;j<=nlstate+ndeath;j++){    xits=vector(1,n); 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    *fret=(*func)(p); 
     }    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for (*iter=1;;++(*iter)) { 
    cov[1]=1.;      fp=(*fret); 
        ibig=0; 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */      del=0.0; 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
     newm=savm;      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
     /* Covariates have to be included here again */      fprintf(ficrespow,"%d %.12f",*iter,*fret);
      cov[2]=agefin;      for (i=1;i<=n;i++) {
          printf(" %d %.12f",i, p[i]);
       for (k=1; k<=cptcovn;k++) {        fprintf(ficlog," %d %.12lf",i, p[i]);
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        fprintf(ficrespow," %.12lf", p[i]);
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/      }
       }      printf("\n");
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      fprintf(ficlog,"\n");
       for (k=1; k<=cptcovprod;k++)      fprintf(ficrespow,"\n");
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      for (i=1;i<=n;i++) { 
         for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/        fptt=(*fret); 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  #ifdef DEBUG
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/        printf("fret=%lf \n",*fret);
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);        fprintf(ficlog,"fret=%lf \n",*fret);
   #endif
     savm=oldm;        printf("%d",i);fflush(stdout);
     oldm=newm;        fprintf(ficlog,"%d",i);fflush(ficlog);
     maxmax=0.;        linmin(p,xit,n,fret,func); 
     for(j=1;j<=nlstate;j++){        if (fabs(fptt-(*fret)) > del) { 
       min=1.;          del=fabs(fptt-(*fret)); 
       max=0.;          ibig=i; 
       for(i=1; i<=nlstate; i++) {        } 
         sumnew=0;  #ifdef DEBUG
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];        printf("%d %.12e",i,(*fret));
         prlim[i][j]= newm[i][j]/(1-sumnew);        fprintf(ficlog,"%d %.12e",i,(*fret));
         max=FMAX(max,prlim[i][j]);        for (j=1;j<=n;j++) {
         min=FMIN(min,prlim[i][j]);          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       }          printf(" x(%d)=%.12e",j,xit[j]);
       maxmin=max-min;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       maxmax=FMAX(maxmax,maxmin);        }
     }        for(j=1;j<=n;j++) {
     if(maxmax < ftolpl){          printf(" p=%.12e",p[j]);
       return prlim;          fprintf(ficlog," p=%.12e",p[j]);
     }        }
   }        printf("\n");
 }        fprintf(ficlog,"\n");
   #endif
 /*************** transition probabilities ***************/      } 
       if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  #ifdef DEBUG
 {        int k[2],l;
   double s1, s2;        k[0]=1;
   /*double t34;*/        k[1]=-1;
   int i,j,j1, nc, ii, jj;        printf("Max: %.12e",(*func)(p));
         fprintf(ficlog,"Max: %.12e",(*func)(p));
     for(i=1; i<= nlstate; i++){        for (j=1;j<=n;j++) {
     for(j=1; j<i;j++){          printf(" %.12e",p[j]);
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){          fprintf(ficlog," %.12e",p[j]);
         /*s2 += param[i][j][nc]*cov[nc];*/        }
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        printf("\n");
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/        fprintf(ficlog,"\n");
       }        for(l=0;l<=1;l++) {
       ps[i][j]=s2;          for (j=1;j<=n;j++) {
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     }            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     for(j=i+1; j<=nlstate+ndeath;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]);
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){          }
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       }        }
       ps[i][j]=s2;  #endif
     }  
   }  
     /*ps[3][2]=1;*/        free_vector(xit,1,n); 
         free_vector(xits,1,n); 
   for(i=1; i<= nlstate; i++){        free_vector(ptt,1,n); 
      s1=0;        free_vector(pt,1,n); 
     for(j=1; j<i; j++)        return; 
       s1+=exp(ps[i][j]);      } 
     for(j=i+1; j<=nlstate+ndeath; j++)      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       s1+=exp(ps[i][j]);      for (j=1;j<=n;j++) { 
     ps[i][i]=1./(s1+1.);        ptt[j]=2.0*p[j]-pt[j]; 
     for(j=1; j<i; j++)        xit[j]=p[j]-pt[j]; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];        pt[j]=p[j]; 
     for(j=i+1; j<=nlstate+ndeath; j++)      } 
       ps[i][j]= exp(ps[i][j])*ps[i][i];      fptt=(*func)(ptt); 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */      if (fptt < fp) { 
   } /* end i */        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         if (t < 0.0) { 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){          linmin(p,xit,n,fret,func); 
     for(jj=1; jj<= nlstate+ndeath; jj++){          for (j=1;j<=n;j++) { 
       ps[ii][jj]=0;            xi[j][ibig]=xi[j][n]; 
       ps[ii][ii]=1;            xi[j][n]=xit[j]; 
     }          }
   }  #ifdef DEBUG
           printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){          for(j=1;j<=n;j++){
     for(jj=1; jj<= nlstate+ndeath; jj++){            printf(" %.12e",xit[j]);
      printf("%lf ",ps[ii][jj]);            fprintf(ficlog," %.12e",xit[j]);
    }          }
     printf("\n ");          printf("\n");
     }          fprintf(ficlog,"\n");
     printf("\n ");printf("%lf ",cov[2]);*/  #endif
 /*        }
   for(i=1; i<= npar; i++) printf("%f ",x[i]);      } 
   goto end;*/    } 
     return ps;  } 
 }  
   /**** Prevalence limit (stable prevalence)  ****************/
 /**************** Product of 2 matrices ******************/  
   double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  {
 {    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times       matrix by transitions matrix until convergence is reached */
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  
   /* in, b, out are matrice of pointers which should have been initialized    int i, ii,j,k;
      before: only the contents of out is modified. The function returns    double min, max, maxmin, maxmax,sumnew=0.;
      a pointer to pointers identical to out */    double **matprod2();
   long i, j, k;    double **out, cov[NCOVMAX], **pmij();
   for(i=nrl; i<= nrh; i++)    double **newm;
     for(k=ncolol; k<=ncoloh; k++)    double agefin, delaymax=50 ; /* Max number of years to converge */
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  
         out[i][k] +=in[i][j]*b[j][k];    for (ii=1;ii<=nlstate+ndeath;ii++)
       for (j=1;j<=nlstate+ndeath;j++){
   return out;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 }      }
   
      cov[1]=1.;
 /************* Higher Matrix Product ***************/   
    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
 {      newm=savm;
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      /* Covariates have to be included here again */
      duration (i.e. until       cov[2]=agefin;
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step        for (k=1; k<=cptcovn;k++) {
      (typically every 2 years instead of every month which is too big).          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
      Model is determined by parameters x and covariates have to be          /*      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]]);*/
      included manually here.        }
         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]]];
   int i, j, d, h, k;  
   double **out, cov[NCOVMAX];        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   double **newm;        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
         /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   /* Hstepm could be zero and should return the unit matrix */      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   for (i=1;i<=nlstate+ndeath;i++)  
     for (j=1;j<=nlstate+ndeath;j++){      savm=oldm;
       oldm[i][j]=(i==j ? 1.0 : 0.0);      oldm=newm;
       po[i][j][0]=(i==j ? 1.0 : 0.0);      maxmax=0.;
     }      for(j=1;j<=nlstate;j++){
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */        min=1.;
   for(h=1; h <=nhstepm; h++){        max=0.;
     for(d=1; d <=hstepm; d++){        for(i=1; i<=nlstate; i++) {
       newm=savm;          sumnew=0;
       /* Covariates have to be included here again */          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       cov[1]=1.;          prlim[i][j]= newm[i][j]/(1-sumnew);
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;          max=FMAX(max,prlim[i][j]);
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];          min=FMIN(min,prlim[i][j]);
       for (k=1; k<=cptcovage;k++)        }
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        maxmin=max-min;
       for (k=1; k<=cptcovprod;k++)        maxmax=FMAX(maxmax,maxmin);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      }
       if(maxmax < ftolpl){
         return prlim;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      }
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    }
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  }
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  
       savm=oldm;  /*************** transition probabilities ***************/ 
       oldm=newm;  
     }  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     for(i=1; i<=nlstate+ndeath; i++)  {
       for(j=1;j<=nlstate+ndeath;j++) {    double s1, s2;
         po[i][j][h]=newm[i][j];    /*double t34;*/
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    int i,j,j1, nc, ii, jj;
          */  
       }      for(i=1; i<= nlstate; i++){
   } /* end h */      for(j=1; j<i;j++){
   return po;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
 }          /*s2 += param[i][j][nc]*cov[nc];*/
           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
           /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
 /*************** log-likelihood *************/        }
 double func( double *x)        ps[i][j]=s2;
 {        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
   int i, ii, j, k, mi, d, kk;      }
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      for(j=i+1; j<=nlstate+ndeath;j++){
   double **out;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   double sw; /* Sum of weights */          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   double lli; /* Individual log likelihood */          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
   long ipmx;        }
   /*extern weight */        ps[i][j]=s2;
   /* We are differentiating ll according to initial status */      }
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    }
   /*for(i=1;i<imx;i++)      /*ps[3][2]=1;*/
     printf(" %d\n",s[4][i]);  
   */    for(i=1; i<= nlstate; i++){
   cov[1]=1.;       s1=0;
       for(j=1; j<i; j++)
   for(k=1; k<=nlstate; k++) ll[k]=0.;        s1+=exp(ps[i][j]);
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      for(j=i+1; j<=nlstate+ndeath; j++)
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        s1+=exp(ps[i][j]);
     for(mi=1; mi<= wav[i]-1; mi++){      ps[i][i]=1./(s1+1.);
       for (ii=1;ii<=nlstate+ndeath;ii++)      for(j=1; j<i; j++)
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        ps[i][j]= exp(ps[i][j])*ps[i][i];
       for(d=0; d<dh[mi][i]; d++){      for(j=i+1; j<=nlstate+ndeath; j++)
         newm=savm;        ps[i][j]= exp(ps[i][j])*ps[i][i];
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
         for (kk=1; kk<=cptcovage;kk++) {    } /* end i */
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  
         }    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
              for(jj=1; jj<= nlstate+ndeath; jj++){
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        ps[ii][jj]=0;
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        ps[ii][ii]=1;
         savm=oldm;      }
         oldm=newm;    }
          
          
       } /* end mult */    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
            for(jj=1; jj<= nlstate+ndeath; jj++){
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);       printf("%lf ",ps[ii][jj]);
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/     }
       ipmx +=1;      printf("\n ");
       sw += weight[i];      }
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;      printf("\n ");printf("%lf ",cov[2]);*/
     } /* end of wave */  /*
   } /* end of individual */    for(i=1; i<= npar; i++) printf("%f ",x[i]);
     goto end;*/
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];      return ps;
   /* 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;  /**************** Product of 2 matrices ******************/
 }  
   double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   {
 /*********** Maximum Likelihood Estimation ***************/    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
        b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    /* in, b, out are matrice of pointers which should have been initialized 
 {       before: only the contents of out is modified. The function returns
   int i,j, iter;       a pointer to pointers identical to out */
   double **xi,*delti;    long i, j, k;
   double fret;    for(i=nrl; i<= nrh; i++)
   xi=matrix(1,npar,1,npar);      for(k=ncolol; k<=ncoloh; k++)
   for (i=1;i<=npar;i++)        for(j=ncl,out[i][k]=0.; j<=nch; j++)
     for (j=1;j<=npar;j++)          out[i][k] +=in[i][j]*b[j][k];
       xi[i][j]=(i==j ? 1.0 : 0.0);  
   printf("Powell\n");  fprintf(ficlog,"Powell\n");    return out;
   powell(p,xi,npar,ftol,&iter,&fret,func);  }
   
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  
   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));  /************* Higher Matrix Product ***************/
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));  
   double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
 }  {
     /* Computes the transition matrix starting at age 'age' over 
 /**** Computes Hessian and covariance matrix ***/       'nhstepm*hstepm*stepm' months (i.e. until
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
 {       nhstepm*hstepm matrices. 
   double  **a,**y,*x,pd;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   double **hess;       (typically every 2 years instead of every month which is too big 
   int i, j,jk;       for the memory).
   int *indx;       Model is determined by parameters x and covariates have to be 
        included manually here. 
   double hessii(double p[], double delta, int theta, double delti[]);  
   double hessij(double p[], double delti[], int i, int j);       */
   void lubksb(double **a, int npar, int *indx, double b[]) ;  
   void ludcmp(double **a, int npar, int *indx, double *d) ;    int i, j, d, h, k;
     double **out, cov[NCOVMAX];
   hess=matrix(1,npar,1,npar);    double **newm;
   
   printf("\nCalculation of the hessian matrix. Wait...\n");    /* Hstepm could be zero and should return the unit matrix */
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");    for (i=1;i<=nlstate+ndeath;i++)
   for (i=1;i<=npar;i++){      for (j=1;j<=nlstate+ndeath;j++){
     printf("%d",i);fflush(stdout);        oldm[i][j]=(i==j ? 1.0 : 0.0);
     fprintf(ficlog,"%d",i);fflush(ficlog);        po[i][j][0]=(i==j ? 1.0 : 0.0);
     hess[i][i]=hessii(p,ftolhess,i,delti);      }
     /*printf(" %f ",p[i]);*/    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     /*printf(" %lf ",hess[i][i]);*/    for(h=1; h <=nhstepm; h++){
   }      for(d=1; d <=hstepm; d++){
          newm=savm;
   for (i=1;i<=npar;i++) {        /* Covariates have to be included here again */
     for (j=1;j<=npar;j++)  {        cov[1]=1.;
       if (j>i) {        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         printf(".%d%d",i,j);fflush(stdout);        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);        for (k=1; k<=cptcovage;k++)
         hess[i][j]=hessij(p,delti,i,j);          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         hess[j][i]=hess[i][j];            for (k=1; k<=cptcovprod;k++)
         /*printf(" %lf ",hess[i][j]);*/          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       }  
     }  
   }        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   printf("\n");        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   fprintf(ficlog,"\n");        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                      pmij(pmmij,cov,ncovmodel,x,nlstate));
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        savm=oldm;
   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");        oldm=newm;
        }
   a=matrix(1,npar,1,npar);      for(i=1; i<=nlstate+ndeath; i++)
   y=matrix(1,npar,1,npar);        for(j=1;j<=nlstate+ndeath;j++) {
   x=vector(1,npar);          po[i][j][h]=newm[i][j];
   indx=ivector(1,npar);          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
   for (i=1;i<=npar;i++)           */
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        }
   ludcmp(a,npar,indx,&pd);    } /* end h */
     return po;
   for (j=1;j<=npar;j++) {  }
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;  
     lubksb(a,npar,indx,x);  /*************** log-likelihood *************/
     for (i=1;i<=npar;i++){  double func( double *x)
       matcov[i][j]=x[i];  {
     }    int i, ii, j, k, mi, d, kk;
   }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     double **out;
   printf("\n#Hessian matrix#\n");    double sw; /* Sum of weights */
   fprintf(ficlog,"\n#Hessian matrix#\n");    double lli; /* Individual log likelihood */
   for (i=1;i<=npar;i++) {    int s1, s2;
     for (j=1;j<=npar;j++) {    double bbh, survp;
       printf("%.3e ",hess[i][j]);    long ipmx;
       fprintf(ficlog,"%.3e ",hess[i][j]);    /*extern weight */
     }    /* We are differentiating ll according to initial status */
     printf("\n");    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     fprintf(ficlog,"\n");    /*for(i=1;i<imx;i++) 
   }      printf(" %d\n",s[4][i]);
     */
   /* Recompute Inverse */    cov[1]=1.;
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    for(k=1; k<=nlstate; k++) ll[k]=0.;
   ludcmp(a,npar,indx,&pd);  
     if(mle==1){
   /*  printf("\n#Hessian matrix recomputed#\n");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   for (j=1;j<=npar;j++) {        for(mi=1; mi<= wav[i]-1; mi++){
     for (i=1;i<=npar;i++) x[i]=0;          for (ii=1;ii<=nlstate+ndeath;ii++)
     x[j]=1;            for (j=1;j<=nlstate+ndeath;j++){
     lubksb(a,npar,indx,x);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for (i=1;i<=npar;i++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       y[i][j]=x[i];            }
       printf("%.3e ",y[i][j]);          for(d=0; d<dh[mi][i]; d++){
       fprintf(ficlog,"%.3e ",y[i][j]);            newm=savm;
     }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     printf("\n");            for (kk=1; kk<=cptcovage;kk++) {
     fprintf(ficlog,"\n");              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   }            }
   */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   free_matrix(a,1,npar,1,npar);            savm=oldm;
   free_matrix(y,1,npar,1,npar);            oldm=newm;
   free_vector(x,1,npar);          } /* end mult */
   free_ivector(indx,1,npar);        
   free_matrix(hess,1,npar,1,npar);          /*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 
 }           * (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
 /*************** hessian matrix ****************/           * we keep into memory the bias bh[mi][i] and also the previous matrix product
 double hessii( double x[], double delta, int theta, double delti[])           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
 {           * probability in order to take into account the bias as a fraction of the way
   int i;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   int l=1, lmax=20;           * -stepm/2 to stepm/2 .
   double k1,k2;           * For stepm=1 the results are the same as for previous versions of Imach.
   double p2[NPARMAX+1];           * For stepm > 1 the results are less biased than in previous versions. 
   double res;           */
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;          s1=s[mw[mi][i]][i];
   double fx;          s2=s[mw[mi+1][i]][i];
   int k=0,kmax=10;          bbh=(double)bh[mi][i]/(double)stepm; 
   double l1;          /* bias is positive if real duration
            * is higher than the multiple of stepm and negative otherwise.
   fx=func(x);           */
   for (i=1;i<=npar;i++) p2[i]=x[i];          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   for(l=0 ; l <=lmax; l++){          if( s2 > nlstate){ 
     l1=pow(10,l);            /* i.e. if s2 is a death state and if the date of death is known then the contribution
     delts=delt;               to the likelihood is the probability to die between last step unit time and current 
     for(k=1 ; k <kmax; k=k+1){               step unit time, which is also the differences between probability to die before dh 
       delt = delta*(l1*k);               and probability to die before dh-stepm . 
       p2[theta]=x[theta] +delt;               In version up to 0.92 likelihood was computed
       k1=func(p2)-fx;          as if date of death was unknown. Death was treated as any other
       p2[theta]=x[theta]-delt;          health state: the date of the interview describes the actual state
       k2=func(p2)-fx;          and not the date of a change in health state. The former idea was
       /*res= (k1-2.0*fx+k2)/delt/delt; */          to consider that at each interview the state was recorded
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          (healthy, disable or death) and IMaCh was corrected; but when we
                introduced the exact date of death then we should have modified
 #ifdef DEBUG          the contribution of an exact death to the likelihood. This new
       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);          contribution is smaller and very dependent of the step unit
       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);          stepm. It is no more the probability to die between last interview
 #endif          and month of death but the probability to survive from last
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          interview up to one month before death multiplied by the
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          probability to die within a month. Thanks to Chris
         k=kmax;          Jackson for correcting this bug.  Former versions increased
       }          mortality artificially. The bad side is that we add another loop
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          which slows down the processing. The difference can be up to 10%
         k=kmax; l=lmax*10.;          lower mortality.
       }            */
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){            lli=log(out[s1][s2] - savm[s1][s2]);
         delts=delt;          }else{
       }            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     }            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
   }          } 
   delti[theta]=delts;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   return res;          /*if(lli ==000.0)*/
            /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
 }          ipmx +=1;
           sw += weight[i];
 double hessij( double x[], double delti[], int thetai,int thetaj)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 {        } /* end of wave */
   int i;      } /* end of individual */
   int l=1, l1, lmax=20;    }  else if(mle==2){
   double k1,k2,k3,k4,res,fx;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double p2[NPARMAX+1];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int k;        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
   fx=func(x);            for (j=1;j<=nlstate+ndeath;j++){
   for (k=1; k<=2; k++) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for (i=1;i<=npar;i++) p2[i]=x[i];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     p2[thetai]=x[thetai]+delti[thetai]/k;            }
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          for(d=0; d<=dh[mi][i]; d++){
     k1=func(p2)-fx;            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     p2[thetai]=x[thetai]+delti[thetai]/k;            for (kk=1; kk<=cptcovage;kk++) {
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     k2=func(p2)-fx;            }
              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     p2[thetai]=x[thetai]-delti[thetai]/k;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;            savm=oldm;
     k3=func(p2)-fx;            oldm=newm;
            } /* end mult */
     p2[thetai]=x[thetai]-delti[thetai]/k;        
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     k4=func(p2)-fx;          /* But now since version 0.9 we anticipate for bias and large stepm.
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */           * If stepm is larger than one month (smallest stepm) and if the exact delay 
 #ifdef DEBUG           * (in months) between two waves is not a multiple of stepm, we rounded to 
     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);           * the nearest (and in case of equal distance, to the lowest) interval but now
     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);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
 #endif           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   }           * probability in order to take into account the bias as a fraction of the way
   return res;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
 }           * -stepm/2 to stepm/2 .
            * For stepm=1 the results are the same as for previous versions of Imach.
 /************** Inverse of matrix **************/           * For stepm > 1 the results are less biased than in previous versions. 
 void ludcmp(double **a, int n, int *indx, double *d)           */
 {          s1=s[mw[mi][i]][i];
   int i,imax,j,k;          s2=s[mw[mi+1][i]][i];
   double big,dum,sum,temp;          bbh=(double)bh[mi][i]/(double)stepm; 
   double *vv;          /* bias is positive if real duration
             * is higher than the multiple of stepm and negative otherwise.
   vv=vector(1,n);           */
   *d=1.0;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   for (i=1;i<=n;i++) {          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     big=0.0;          /*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 */
     for (j=1;j<=n;j++)          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       if ((temp=fabs(a[i][j])) > big) big=temp;          /*if(lli ==000.0)*/
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          /*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); */
     vv[i]=1.0/big;          ipmx +=1;
   }          sw += weight[i];
   for (j=1;j<=n;j++) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for (i=1;i<j;i++) {        } /* end of wave */
       sum=a[i][j];      } /* end of individual */
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    }  else if(mle==3){  /* exponential inter-extrapolation */
       a[i][j]=sum;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     big=0.0;        for(mi=1; mi<= wav[i]-1; mi++){
     for (i=j;i<=n;i++) {          for (ii=1;ii<=nlstate+ndeath;ii++)
       sum=a[i][j];            for (j=1;j<=nlstate+ndeath;j++){
       for (k=1;k<j;k++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         sum -= a[i][k]*a[k][j];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       a[i][j]=sum;            }
       if ( (dum=vv[i]*fabs(sum)) >= big) {          for(d=0; d<dh[mi][i]; d++){
         big=dum;            newm=savm;
         imax=i;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       }            for (kk=1; kk<=cptcovage;kk++) {
     }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     if (j != imax) {            }
       for (k=1;k<=n;k++) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         dum=a[imax][k];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         a[imax][k]=a[j][k];            savm=oldm;
         a[j][k]=dum;            oldm=newm;
       }          } /* end mult */
       *d = -(*d);        
       vv[imax]=vv[j];          /*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.
     indx[j]=imax;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     if (a[j][j] == 0.0) a[j][j]=TINY;           * (in months) between two waves is not a multiple of stepm, we rounded to 
     if (j != n) {           * the nearest (and in case of equal distance, to the lowest) interval but now
       dum=1.0/(a[j][j]);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       for (i=j+1;i<=n;i++) a[i][j] *= dum;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     }           * probability in order to take into account the bias as a fraction of the way
   }           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   free_vector(vv,1,n);  /* Doesn't work */           * -stepm/2 to stepm/2 .
 ;           * 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. 
            */
 void lubksb(double **a, int n, int *indx, double b[])          s1=s[mw[mi][i]][i];
 {          s2=s[mw[mi+1][i]][i];
   int i,ii=0,ip,j;          bbh=(double)bh[mi][i]/(double)stepm; 
   double sum;          /* bias is positive if real duration
             * is higher than the multiple of stepm and negative otherwise.
   for (i=1;i<=n;i++) {           */
     ip=indx[i];          /* lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); */ /* linear interpolation */
     sum=b[ip];          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 */
     b[ip]=b[i];          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     if (ii)          /*if(lli ==000.0)*/
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
     else if (sum) ii=i;          ipmx +=1;
     b[i]=sum;          sw += weight[i];
   }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   for (i=n;i>=1;i--) {        } /* end of wave */
     sum=b[i];      } /* end of individual */
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    }else if (mle==4){  /* ml=4 no inter-extrapolation */
     b[i]=sum/a[i][i];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 }        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
 /************ Frequencies ********************/            for (j=1;j<=nlstate+ndeath;j++){
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 {  /* Some frequencies */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
              }
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          for(d=0; d<dh[mi][i]; d++){
   int first;            newm=savm;
   double ***freq; /* Frequencies */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double *pp;            for (kk=1; kk<=cptcovage;kk++) {
   double pos, k2, dateintsum=0,k2cpt=0;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   FILE *ficresp;            }
   char fileresp[FILENAMELENGTH];          
              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   pp=vector(1,nlstate);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            savm=oldm;
   strcpy(fileresp,"p");            oldm=newm;
   strcat(fileresp,fileres);          } /* end mult */
   if((ficresp=fopen(fileresp,"w"))==NULL) {        
     printf("Problem with prevalence resultfile: %s\n", fileresp);          s1=s[mw[mi][i]][i];
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);          s2=s[mw[mi+1][i]][i];
     exit(0);          if( s2 > nlstate){ 
   }            lli=log(out[s1][s2] - savm[s1][s2]);
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          }else{
   j1=0;            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
            }
   j=cptcoveff;          ipmx +=1;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   first=1;  /*      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 */
   for(k1=1; k1<=j;k1++){      } /* end of individual */
     for(i1=1; i1<=ncodemax[k1];i1++){    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       j1++;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         scanf("%d", i);*/        for(mi=1; mi<= wav[i]-1; mi++){
       for (i=-1; i<=nlstate+ndeath; i++)            for (ii=1;ii<=nlstate+ndeath;ii++)
         for (jk=-1; jk<=nlstate+ndeath; jk++)              for (j=1;j<=nlstate+ndeath;j++){
           for(m=agemin; m <= agemax+3; m++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             freq[i][jk][m]=0;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                  }
       dateintsum=0;          for(d=0; d<dh[mi][i]; d++){
       k2cpt=0;            newm=savm;
       for (i=1; i<=imx; i++) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         bool=1;            for (kk=1; kk<=cptcovage;kk++) {
         if  (cptcovn>0) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           for (z1=1; z1<=cptcoveff; z1++)            }
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          
               bool=0;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         if (bool==1) {            savm=oldm;
           for(m=firstpass; m<=lastpass; m++){            oldm=newm;
             k2=anint[m][i]+(mint[m][i]/12.);          } /* end mult */
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        
               if(agev[m][i]==0) agev[m][i]=agemax+1;          s1=s[mw[mi][i]][i];
               if(agev[m][i]==1) agev[m][i]=agemax+2;          s2=s[mw[mi+1][i]][i];
               if (m<lastpass) {          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          ipmx +=1;
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          sw += weight[i];
               }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                        /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {        } /* end of wave */
                 dateintsum=dateintsum+k2;      } /* end of individual */
                 k2cpt++;    } /* End of if */
               }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
             }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
           }    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         }    return -l;
       }  }
          
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  /*************** log-likelihood *************/
   double funcone( double *x)
       if  (cptcovn>0) {  {
         fprintf(ficresp, "\n#********** Variable ");    /* Same as likeli but slower because of a lot of printf and if */
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    int i, ii, j, k, mi, d, kk;
         fprintf(ficresp, "**********\n#");    double l, ll[NLSTATEMAX], cov[NCOVMAX];
       }    double **out;
       for(i=1; i<=nlstate;i++)    double lli; /* Individual log likelihood */
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    double llt;
       fprintf(ficresp, "\n");    int s1, s2;
          double bbh, survp;
       for(i=(int)agemin; i <= (int)agemax+3; i++){    /*extern weight */
         if(i==(int)agemax+3){    /* We are differentiating ll according to initial status */
           fprintf(ficlog,"Total");    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
         }else{    /*for(i=1;i<imx;i++) 
           if(first==1){      printf(" %d\n",s[4][i]);
             first=0;    */
             printf("See log file for details...\n");    cov[1]=1.;
           }  
           fprintf(ficlog,"Age %d", i);    for(k=1; k<=nlstate; k++) ll[k]=0.;
         }  
         for(jk=1; jk <=nlstate ; jk++){    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
             pp[jk] += freq[jk][m][i];      for(mi=1; mi<= wav[i]-1; mi++){
         }        for (ii=1;ii<=nlstate+ndeath;ii++)
         for(jk=1; jk <=nlstate ; jk++){          for (j=1;j<=nlstate+ndeath;j++){
           for(m=-1, pos=0; m <=0 ; m++)            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             pos += freq[jk][m][i];            savm[ii][j]=(ii==j ? 1.0 : 0.0);
           if(pp[jk]>=1.e-10){          }
             if(first==1){        for(d=0; d<dh[mi][i]; d++){
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          newm=savm;
             }          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          for (kk=1; kk<=cptcovage;kk++) {
           }else{            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             if(first==1)          }
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           }          savm=oldm;
         }          oldm=newm;
         } /* end mult */
         for(jk=1; jk <=nlstate ; jk++){        
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        s1=s[mw[mi][i]][i];
             pp[jk] += freq[jk][m][i];        s2=s[mw[mi+1][i]][i];
         }        bbh=(double)bh[mi][i]/(double)stepm; 
         /* bias is positive if real duration
         for(jk=1,pos=0; jk <=nlstate ; jk++)         * is higher than the multiple of stepm and negative otherwise.
           pos += pp[jk];         */
         for(jk=1; jk <=nlstate ; jk++){        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           if(pos>=1.e-5){          lli=log(out[s1][s2] - savm[s1][s2]);
             if(first==1)        } else if (mle==1){
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        } else if(mle==2){
           }else{          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
             if(first==1)        } else if(mle==3){  /* exponential inter-extrapolation */
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          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 */
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        } else if (mle==4){  /* mle=4 no inter-extrapolation */
           }          lli=log(out[s1][s2]); /* Original formula */
           if( i <= (int) agemax){        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
             if(pos>=1.e-5){          lli=log(out[s1][s2]); /* Original formula */
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        } /* End of if */
               probs[i][jk][j1]= pp[jk]/pos;        ipmx +=1;
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/        sw += weight[i];
             }        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             else  /*       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]); */
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        if(globpr){
           }          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
         }   %10.6f %10.6f %10.6f ", \
                          num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
         for(jk=-1; jk <=nlstate+ndeath; jk++)                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
           for(m=-1; m <=nlstate+ndeath; m++)          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
             if(freq[jk][m][i] !=0 ) {            llt +=ll[k]*gipmx/gsw;
             if(first==1)            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          }
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);          fprintf(ficresilk," %10.6f\n", -llt);
             }        }
         if(i <= (int) agemax)      } /* end of wave */
           fprintf(ficresp,"\n");    } /* end of individual */
         if(first==1)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
           printf("Others in log...\n");    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         fprintf(ficlog,"\n");    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       }    if(globpr==0){ /* First time we count the contributions and weights */
     }      gipmx=ipmx;
   }      gsw=sw;
   dateintmean=dateintsum/k2cpt;    }
      return -l;
   fclose(ficresp);  }
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  
   free_vector(pp,1,nlstate);  char *subdirf(char fileres[])
    {
   /* End of Freq */    
 }    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/"); /* Add to the right */
 /************ Prevalence ********************/    strcat(tmpout,fileres);
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)    return tmpout;
 {  /* Some frequencies */  }
    
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  char *subdirf2(char fileres[], char *preop)
   double ***freq; /* Frequencies */  {
   double *pp;    
   double pos, k2;    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
   pp=vector(1,nlstate);    strcat(tmpout,preop);
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    strcat(tmpout,fileres);
      return tmpout;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  }
   j1=0;  char *subdirf3(char fileres[], char *preop, char *preop2)
    {
   j=cptcoveff;    
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    strcpy(tmpout,optionfilefiname);
      strcat(tmpout,"/");
   for(k1=1; k1<=j;k1++){    strcat(tmpout,preop);
     for(i1=1; i1<=ncodemax[k1];i1++){    strcat(tmpout,preop2);
       j1++;    strcat(tmpout,fileres);
          return tmpout;
       for (i=-1; i<=nlstate+ndeath; i++)    }
         for (jk=-1; jk<=nlstate+ndeath; jk++)    
           for(m=agemin; m <= agemax+3; m++)  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
             freq[i][jk][m]=0;  {
          /* This routine should help understanding what is done with 
       for (i=1; i<=imx; i++) {       the selection of individuals/waves and
         bool=1;       to check the exact contribution to the likelihood.
         if  (cptcovn>0) {       Plotting could be done.
           for (z1=1; z1<=cptcoveff; z1++)     */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    int k;
               bool=0;  
         }    if(*globpri !=0){ /* Just counts and sums, no printings */
         if (bool==1) {      strcpy(fileresilk,"ilk"); 
           for(m=firstpass; m<=lastpass; m++){      strcat(fileresilk,fileres);
             k2=anint[m][i]+(mint[m][i]/12.);      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        printf("Problem with resultfile: %s\n", fileresilk);
               if(agev[m][i]==0) agev[m][i]=agemax+1;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
               if(agev[m][i]==1) agev[m][i]=agemax+2;      }
               if (m<lastpass) {      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
                 if (calagedate>0)      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
                 else      for(k=1; k<=nlstate; k++) 
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
               }    }
             }  
           }    *fretone=(*funcone)(p);
         }    if(*globpri !=0){
       }      fclose(ficresilk);
       for(i=(int)agemin; i <= (int)agemax+3; i++){      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
         for(jk=1; jk <=nlstate ; jk++){      fflush(fichtm); 
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    } 
             pp[jk] += freq[jk][m][i];    return;
         }  }
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=-1, pos=0; m <=0 ; m++)  
             pos += freq[jk][m][i];  /*********** Maximum Likelihood Estimation ***************/
         }  
          void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
         for(jk=1; jk <=nlstate ; jk++){  {
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    int i,j, iter;
             pp[jk] += freq[jk][m][i];    double **xi;
         }    double fret;
            double fretone; /* Only one call to likelihood */
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    char filerespow[FILENAMELENGTH];
            xi=matrix(1,npar,1,npar);
         for(jk=1; jk <=nlstate ; jk++){        for (i=1;i<=npar;i++)
           if( i <= (int) agemax){      for (j=1;j<=npar;j++)
             if(pos>=1.e-5){        xi[i][j]=(i==j ? 1.0 : 0.0);
               probs[i][jk][j1]= pp[jk]/pos;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
             }    strcpy(filerespow,"pow"); 
           }    strcat(filerespow,fileres);
         }/* end jk */    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       }/* end i */      printf("Problem with resultfile: %s\n", filerespow);
     } /* end i1 */      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   } /* end k1 */    }
     fprintf(ficrespow,"# Powell\n# iter -2*LL");
      for (i=1;i<=nlstate;i++)
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      for(j=1;j<=nlstate+ndeath;j++)
   free_vector(pp,1,nlstate);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
      fprintf(ficrespow,"\n");
 }  /* End of Freq */  
     powell(p,xi,npar,ftol,&iter,&fret,func);
 /************* Waves Concatenation ***************/  
     fclose(ficrespow);
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
 {    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
      Death is a valid wave (if date is known).  
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  }
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  
      and mw[mi+1][i]. dh depends on stepm.  /**** Computes Hessian and covariance matrix ***/
      */  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   {
   int i, mi, m;    double  **a,**y,*x,pd;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    double **hess;
      double sum=0., jmean=0.;*/    int i, j,jk;
   int first;    int *indx;
   int j, k=0,jk, ju, jl;  
   double sum=0.;    double hessii(double p[], double delta, int theta, double delti[]);
   first=0;    double hessij(double p[], double delti[], int i, int j);
   jmin=1e+5;    void lubksb(double **a, int npar, int *indx, double b[]) ;
   jmax=-1;    void ludcmp(double **a, int npar, int *indx, double *d) ;
   jmean=0.;  
   for(i=1; i<=imx; i++){    hess=matrix(1,npar,1,npar);
     mi=0;  
     m=firstpass;    printf("\nCalculation of the hessian matrix. Wait...\n");
     while(s[m][i] <= nlstate){    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
       if(s[m][i]>=1)    for (i=1;i<=npar;i++){
         mw[++mi][i]=m;      printf("%d",i);fflush(stdout);
       if(m >=lastpass)      fprintf(ficlog,"%d",i);fflush(ficlog);
         break;      hess[i][i]=hessii(p,ftolhess,i,delti);
       else      /*printf(" %f ",p[i]);*/
         m++;      /*printf(" %lf ",hess[i][i]);*/
     }/* end while */    }
     if (s[m][i] > nlstate){    
       mi++;     /* Death is another wave */    for (i=1;i<=npar;i++) {
       /* if(mi==0)  never been interviewed correctly before death */      for (j=1;j<=npar;j++)  {
          /* Only death is a correct wave */        if (j>i) { 
       mw[mi][i]=m;          printf(".%d%d",i,j);fflush(stdout);
     }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
           hess[i][j]=hessij(p,delti,i,j);
     wav[i]=mi;          hess[j][i]=hess[i][j];    
     if(mi==0){          /*printf(" %lf ",hess[i][j]);*/
       if(first==0){        }
         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);      }
         first=1;    }
       }    printf("\n");
       if(first==1){    fprintf(ficlog,"\n");
         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);  
       }    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     } /* end mi==0 */    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   }    
     a=matrix(1,npar,1,npar);
   for(i=1; i<=imx; i++){    y=matrix(1,npar,1,npar);
     for(mi=1; mi<wav[i];mi++){    x=vector(1,npar);
       if (stepm <=0)    indx=ivector(1,npar);
         dh[mi][i]=1;    for (i=1;i<=npar;i++)
       else{      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
         if (s[mw[mi+1][i]][i] > nlstate) {    ludcmp(a,npar,indx,&pd);
           if (agedc[i] < 2*AGESUP) {  
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    for (j=1;j<=npar;j++) {
           if(j==0) j=1;  /* Survives at least one month after exam */      for (i=1;i<=npar;i++) x[i]=0;
           k=k+1;      x[j]=1;
           if (j >= jmax) jmax=j;      lubksb(a,npar,indx,x);
           if (j <= jmin) jmin=j;      for (i=1;i<=npar;i++){ 
           sum=sum+j;        matcov[i][j]=x[i];
           /*if (j<0) printf("j=%d num=%d \n",j,i); */      }
           }    }
         }  
         else{    printf("\n#Hessian matrix#\n");
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    fprintf(ficlog,"\n#Hessian matrix#\n");
           k=k+1;    for (i=1;i<=npar;i++) { 
           if (j >= jmax) jmax=j;      for (j=1;j<=npar;j++) { 
           else if (j <= jmin)jmin=j;        printf("%.3e ",hess[i][j]);
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        fprintf(ficlog,"%.3e ",hess[i][j]);
           sum=sum+j;      }
         }      printf("\n");
         jk= j/stepm;      fprintf(ficlog,"\n");
         jl= j -jk*stepm;    }
         ju= j -(jk+1)*stepm;  
         if(jl <= -ju)    /* Recompute Inverse */
           dh[mi][i]=jk;    for (i=1;i<=npar;i++)
         else      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
           dh[mi][i]=jk+1;    ludcmp(a,npar,indx,&pd);
         if(dh[mi][i]==0)  
           dh[mi][i]=1; /* At least one step */    /*  printf("\n#Hessian matrix recomputed#\n");
       }  
     }    for (j=1;j<=npar;j++) {
   }      for (i=1;i<=npar;i++) x[i]=0;
   jmean=sum/k;      x[j]=1;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);      lubksb(a,npar,indx,x);
   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);      for (i=1;i<=npar;i++){ 
  }        y[i][j]=x[i];
         printf("%.3e ",y[i][j]);
 /*********** Tricode ****************************/        fprintf(ficlog,"%.3e ",y[i][j]);
 void tricode(int *Tvar, int **nbcode, int imx)      }
 {      printf("\n");
   int Ndum[20],ij=1, k, j, i;      fprintf(ficlog,"\n");
   int cptcode=0;    }
   cptcoveff=0;    */
    
   for (k=0; k<19; k++) Ndum[k]=0;    free_matrix(a,1,npar,1,npar);
   for (k=1; k<=7; k++) ncodemax[k]=0;    free_matrix(y,1,npar,1,npar);
     free_vector(x,1,npar);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    free_ivector(indx,1,npar);
     for (i=1; i<=imx; i++) {    free_matrix(hess,1,npar,1,npar);
       ij=(int)(covar[Tvar[j]][i]);  
       Ndum[ij]++;  
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  }
       if (ij > cptcode) cptcode=ij;  
     }  /*************** hessian matrix ****************/
   double hessii( double x[], double delta, int theta, double delti[])
     for (i=0; i<=cptcode; i++) {  {
       if(Ndum[i]!=0) ncodemax[j]++;    int i;
     }    int l=1, lmax=20;
     ij=1;    double k1,k2;
     double p2[NPARMAX+1];
     double res;
     for (i=1; i<=ncodemax[j]; i++) {    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
       for (k=0; k<=19; k++) {    double fx;
         if (Ndum[k] != 0) {    int k=0,kmax=10;
           nbcode[Tvar[j]][ij]=k;    double l1;
            
           ij++;    fx=func(x);
         }    for (i=1;i<=npar;i++) p2[i]=x[i];
         if (ij > ncodemax[j]) break;    for(l=0 ; l <=lmax; l++){
       }        l1=pow(10,l);
     }      delts=delt;
   }        for(k=1 ; k <kmax; k=k+1){
         delt = delta*(l1*k);
  for (k=0; k<19; k++) Ndum[k]=0;        p2[theta]=x[theta] +delt;
         k1=func(p2)-fx;
  for (i=1; i<=ncovmodel-2; i++) {        p2[theta]=x[theta]-delt;
    ij=Tvar[i];        k2=func(p2)-fx;
    Ndum[ij]++;        /*res= (k1-2.0*fx+k2)/delt/delt; */
  }        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         
  ij=1;  #ifdef DEBUG
  for (i=1; i<=10; i++) {        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
    if((Ndum[i]!=0) && (i<=ncovcol)){        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);
      Tvaraff[ij]=i;  #endif
      ij++;        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
    }        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
  }          k=kmax;
          }
  cptcoveff=ij-1;        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
 }          k=kmax; l=lmax*10.;
         }
 /*********** Health Expectancies ****************/        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           delts=delt;
 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 )        }
       }
 {    }
   /* Health expectancies */    delti[theta]=delts;
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;    return res; 
   double age, agelim, hf;    
   double ***p3mat,***varhe;  }
   double **dnewm,**doldm;  
   double *xp;  double hessij( double x[], double delti[], int thetai,int thetaj)
   double **gp, **gm;  {
   double ***gradg, ***trgradg;    int i;
   int theta;    int l=1, l1, lmax=20;
     double k1,k2,k3,k4,res,fx;
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);    double p2[NPARMAX+1];
   xp=vector(1,npar);    int k;
   dnewm=matrix(1,nlstate*2,1,npar);  
   doldm=matrix(1,nlstate*2,1,nlstate*2);    fx=func(x);
      for (k=1; k<=2; k++) {
   fprintf(ficreseij,"# Health expectancies\n");      for (i=1;i<=npar;i++) p2[i]=x[i];
   fprintf(ficreseij,"# Age");      p2[thetai]=x[thetai]+delti[thetai]/k;
   for(i=1; i<=nlstate;i++)      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     for(j=1; j<=nlstate;j++)      k1=func(p2)-fx;
       fprintf(ficreseij," %1d-%1d (SE)",i,j);    
   fprintf(ficreseij,"\n");      p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   if(estepm < stepm){      k2=func(p2)-fx;
     printf ("Problem %d lower than %d\n",estepm, stepm);    
   }      p2[thetai]=x[thetai]-delti[thetai]/k;
   else  hstepm=estepm;        p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   /* We compute the life expectancy from trapezoids spaced every estepm months      k3=func(p2)-fx;
    * This is mainly to measure the difference between two models: for example    
    * if stepm=24 months pijx are given only every 2 years and by summing them      p2[thetai]=x[thetai]-delti[thetai]/k;
    * we are calculating an estimate of the Life Expectancy assuming a linear      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
    * progression inbetween and thus overestimating or underestimating according      k4=func(p2)-fx;
    * to the curvature of the survival function. If, for the same date, we      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
    * estimate the model with stepm=1 month, we can keep estepm to 24 months  #ifdef DEBUG
    * to compare the new estimate of Life expectancy with the same linear      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);
    * hypothesis. A more precise result, taking into account a more precise      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);
    * curvature will be obtained if estepm is as small as stepm. */  #endif
     }
   /* For example we decided to compute the life expectancy with the smallest unit */    return res;
   /* 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  
      nstepm is the number of stepm from age to agelin.  /************** Inverse of matrix **************/
      Look at hpijx to understand the reason of that which relies in memory size  void ludcmp(double **a, int n, int *indx, double *d) 
      and note for a fixed period like estepm months */  { 
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    int i,imax,j,k; 
      survival function given by stepm (the optimization length). Unfortunately it    double big,dum,sum,temp; 
      means that if the survival funtion is printed only each two years of age and if    double *vv; 
      you sum them up and add 1 year (area under the trapezoids) you won't get the same   
      results. So we changed our mind and took the option of the best precision.    vv=vector(1,n); 
   */    *d=1.0; 
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    for (i=1;i<=n;i++) { 
       big=0.0; 
   agelim=AGESUP;      for (j=1;j<=n;j++) 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        if ((temp=fabs(a[i][j])) > big) big=temp; 
     /* nhstepm age range expressed in number of stepm */      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     nstepm=(int) rint((agelim-age)*YEARM/stepm);      vv[i]=1.0/big; 
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    } 
     /* if (stepm >= YEARM) hstepm=1;*/    for (j=1;j<=n;j++) { 
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      for (i=1;i<j;i++) { 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        sum=a[i][j]; 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     gp=matrix(0,nhstepm,1,nlstate*2);        a[i][j]=sum; 
     gm=matrix(0,nhstepm,1,nlstate*2);      } 
       big=0.0; 
     /* Computed by stepm unit matrices, product of hstepm matrices, stored      for (i=j;i<=n;i++) { 
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        sum=a[i][j]; 
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);          for (k=1;k<j;k++) 
            sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           big=dum; 
     /* Computing Variances of health expectancies */          imax=i; 
         } 
      for(theta=1; theta <=npar; theta++){      } 
       for(i=1; i<=npar; i++){      if (j != imax) { 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        for (k=1;k<=n;k++) { 
       }          dum=a[imax][k]; 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            a[imax][k]=a[j][k]; 
            a[j][k]=dum; 
       cptj=0;        } 
       for(j=1; j<= nlstate; j++){        *d = -(*d); 
         for(i=1; i<=nlstate; i++){        vv[imax]=vv[j]; 
           cptj=cptj+1;      } 
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){      indx[j]=imax; 
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;      if (a[j][j] == 0.0) a[j][j]=TINY; 
           }      if (j != n) { 
         }        dum=1.0/(a[j][j]); 
       }        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
            } 
          } 
       for(i=1; i<=npar; i++)    free_vector(vv,1,n);  /* Doesn't work */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  ;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    } 
        
       cptj=0;  void lubksb(double **a, int n, int *indx, double b[]) 
       for(j=1; j<= nlstate; j++){  { 
         for(i=1;i<=nlstate;i++){    int i,ii=0,ip,j; 
           cptj=cptj+1;    double sum; 
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){   
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    for (i=1;i<=n;i++) { 
           }      ip=indx[i]; 
         }      sum=b[ip]; 
       }      b[ip]=b[i]; 
       for(j=1; j<= nlstate*2; j++)      if (ii) 
         for(h=0; h<=nhstepm-1; h++){        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      else if (sum) ii=i; 
         }      b[i]=sum; 
      }    } 
        for (i=n;i>=1;i--) { 
 /* End theta */      sum=b[i]; 
       for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);      b[i]=sum/a[i][i]; 
     } 
      for(h=0; h<=nhstepm-1; h++)  } 
       for(j=1; j<=nlstate*2;j++)  
         for(theta=1; theta <=npar; theta++)  /************ Frequencies ********************/
           trgradg[h][j][theta]=gradg[h][theta][j];  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint)
        {  /* Some frequencies */
     
      for(i=1;i<=nlstate*2;i++)    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
       for(j=1;j<=nlstate*2;j++)    int first;
         varhe[i][j][(int)age] =0.;    double ***freq; /* Frequencies */
     double *pp, **prop;
      printf("%d|",(int)age);fflush(stdout);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);    FILE *ficresp;
      for(h=0;h<=nhstepm-1;h++){    char fileresp[FILENAMELENGTH];
       for(k=0;k<=nhstepm-1;k++){    
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);    pp=vector(1,nlstate);
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);    prop=matrix(1,nlstate,iagemin,iagemax+3);
         for(i=1;i<=nlstate*2;i++)    strcpy(fileresp,"p");
           for(j=1;j<=nlstate*2;j++)    strcat(fileresp,fileres);
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;    if((ficresp=fopen(fileresp,"w"))==NULL) {
       }      printf("Problem with prevalence resultfile: %s\n", fileresp);
     }      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     /* Computing expectancies */      exit(0);
     for(i=1; i<=nlstate;i++)    }
       for(j=1; j<=nlstate;j++)    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    j1=0;
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;    
              j=cptcoveff;
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   
         }    first=1;
   
     fprintf(ficreseij,"%3.0f",age );    for(k1=1; k1<=j;k1++){
     cptj=0;      for(i1=1; i1<=ncodemax[k1];i1++){
     for(i=1; i<=nlstate;i++)        j1++;
       for(j=1; j<=nlstate;j++){        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
         cptj++;          scanf("%d", i);*/
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );        for (i=-1; i<=nlstate+ndeath; i++)  
       }          for (jk=-1; jk<=nlstate+ndeath; jk++)  
     fprintf(ficreseij,"\n");            for(m=iagemin; m <= iagemax+3; m++)
                  freq[i][jk][m]=0;
     free_matrix(gm,0,nhstepm,1,nlstate*2);  
     free_matrix(gp,0,nhstepm,1,nlstate*2);      for (i=1; i<=nlstate; i++)  
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);        for(m=iagemin; m <= iagemax+3; m++)
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);          prop[i][m]=0;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        
   }        dateintsum=0;
   printf("\n");        k2cpt=0;
   fprintf(ficlog,"\n");        for (i=1; i<=imx; i++) {
           bool=1;
   free_vector(xp,1,npar);          if  (cptcovn>0) {
   free_matrix(dnewm,1,nlstate*2,1,npar);            for (z1=1; z1<=cptcoveff; z1++) 
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);                bool=0;
 }          }
           if (bool==1){
 /************ Variance ******************/            for(m=firstpass; m<=lastpass; m++){
 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)              k2=anint[m][i]+(mint[m][i]/12.);
 {              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
   /* Variance of health expectancies */                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   /* double **newm;*/                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   double **dnewm,**doldm;                if (m<lastpass) {
   double **dnewmp,**doldmp;                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   int i, j, nhstepm, hstepm, h, nstepm ;                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
   int k, cptcode;                }
   double *xp;                
   double **gp, **gm;  /* for var eij */                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   double ***gradg, ***trgradg; /*for var eij */                  dateintsum=dateintsum+k2;
   double **gradgp, **trgradgp; /* for var p point j */                  k2cpt++;
   double *gpp, *gmp; /* for var p point j */                }
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */                /*}*/
   double ***p3mat;            }
   double age,agelim, hf;          }
   int theta;        }
   char digit[4];         
   char digitp[16];        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   
   char fileresprobmorprev[FILENAMELENGTH];        if  (cptcovn>0) {
           fprintf(ficresp, "\n#********** Variable "); 
   if(popbased==1)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     strcpy(digitp,"-populbased-");          fprintf(ficresp, "**********\n#");
   else        }
     strcpy(digitp,"-stablbased-");        for(i=1; i<=nlstate;i++) 
           fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   strcpy(fileresprobmorprev,"prmorprev");        fprintf(ficresp, "\n");
   sprintf(digit,"%-d",ij);        
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/        for(i=iagemin; i <= iagemax+3; i++){
   strcat(fileresprobmorprev,digit); /* Tvar to be done */          if(i==iagemax+3){
   strcat(fileresprobmorprev,digitp); /* Popbased or not */            fprintf(ficlog,"Total");
   strcat(fileresprobmorprev,fileres);          }else{
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {            if(first==1){
     printf("Problem with resultfile: %s\n", fileresprobmorprev);              first=0;
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);              printf("See log file for details...\n");
   }            }
   printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);            fprintf(ficlog,"Age %d", i);
   fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);          }
   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");          for(jk=1; jk <=nlstate ; jk++){
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){              pp[jk] += freq[jk][m][i]; 
     fprintf(ficresprobmorprev," p.%-d SE",j);          }
     for(i=1; i<=nlstate;i++)          for(jk=1; jk <=nlstate ; jk++){
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);            for(m=-1, pos=0; m <=0 ; m++)
   }                pos += freq[jk][m][i];
   fprintf(ficresprobmorprev,"\n");            if(pp[jk]>=1.e-10){
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {              if(first==1){
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);              }
     exit(0);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   }            }else{
   else{              if(first==1)
     fprintf(ficgp,"\n# Routine varevsij");                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   }              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {            }
     printf("Problem with html file: %s\n", optionfilehtm);          }
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);  
     exit(0);          for(jk=1; jk <=nlstate ; jk++){
   }            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   else{              pp[jk] += freq[jk][m][i];
     fprintf(fichtm,"\n<li><h4> Computing step probabilities of dying and weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");          }       
   }          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);            pos += pp[jk];
             posprop += prop[jk][i];
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");          }
   fprintf(ficresvij,"# Age");          for(jk=1; jk <=nlstate ; jk++){
   for(i=1; i<=nlstate;i++)            if(pos>=1.e-5){
     for(j=1; j<=nlstate;j++)              if(first==1)
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   fprintf(ficresvij,"\n");              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
             }else{
   xp=vector(1,npar);              if(first==1)
   dnewm=matrix(1,nlstate,1,npar);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   doldm=matrix(1,nlstate,1,nlstate);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);            }
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);            if( i <= iagemax){
               if(pos>=1.e-5){
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   gpp=vector(nlstate+1,nlstate+ndeath);                /*probs[i][jk][j1]= pp[jk]/pos;*/
   gmp=vector(nlstate+1,nlstate+ndeath);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/              }
                else
   if(estepm < stepm){                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     printf ("Problem %d lower than %d\n",estepm, stepm);            }
   }          }
   else  hstepm=estepm;            
   /* For example we decided to compute the life expectancy with the smallest unit */          for(jk=-1; jk <=nlstate+ndeath; jk++)
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.            for(m=-1; m <=nlstate+ndeath; m++)
      nhstepm is the number of hstepm from age to agelim              if(freq[jk][m][i] !=0 ) {
      nstepm is the number of stepm from age to agelin.              if(first==1)
      Look at hpijx to understand the reason of that which relies in memory size                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
      and note for a fixed period like k years */                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the              }
      survival function given by stepm (the optimization length). Unfortunately it          if(i <= iagemax)
      means that if the survival funtion is printed only each two years of age and if            fprintf(ficresp,"\n");
      you sum them up and add 1 year (area under the trapezoids) you won't get the same          if(first==1)
      results. So we changed our mind and took the option of the best precision.            printf("Others in log...\n");
   */          fprintf(ficlog,"\n");
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        }
   agelim = AGESUP;      }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    }
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    dateintmean=dateintsum/k2cpt; 
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */   
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fclose(ficresp);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
     gp=matrix(0,nhstepm,1,nlstate);    free_vector(pp,1,nlstate);
     gm=matrix(0,nhstepm,1,nlstate);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     /* End of Freq */
   }
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient */  /************ Prevalence ********************/
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  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)
       }  {  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);       in each health status at the date of interview (if between dateprev1 and dateprev2).
        We still use firstpass and lastpass as another selection.
       if (popbased==1) {    */
         for(i=1; i<=nlstate;i++)   
           prlim[i][i]=probs[(int)age][i][ij];    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
       }    double ***freq; /* Frequencies */
      double *pp, **prop;
       for(j=1; j<= nlstate; j++){    double pos,posprop; 
         for(h=0; h<=nhstepm; h++){    double  y2; /* in fractional years */
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    int iagemin, iagemax;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];  
         }    iagemin= (int) agemin;
       }    iagemax= (int) agemax;
       /* This for computing forces of mortality (h=1)as a weighted average */    /*pp=vector(1,nlstate);*/
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){    prop=matrix(1,nlstate,iagemin,iagemax+3); 
         for(i=1; i<= nlstate; i++)    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
           gpp[j] += prlim[i][i]*p3mat[i][j][1];    j1=0;
       }        
       /* end force of mortality */    j=cptcoveff;
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
       for(i=1; i<=npar; i++) /* Computes gradient */    
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    for(k1=1; k1<=j;k1++){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        for(i1=1; i1<=ncodemax[k1];i1++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        j1++;
          
       if (popbased==1) {        for (i=1; i<=nlstate; i++)  
         for(i=1; i<=nlstate;i++)          for(m=iagemin; m <= iagemax+3; m++)
           prlim[i][i]=probs[(int)age][i][ij];            prop[i][m]=0.0;
       }       
         for (i=1; i<=imx; i++) { /* Each individual */
       for(j=1; j<= nlstate; j++){          bool=1;
         for(h=0; h<=nhstepm; h++){          if  (cptcovn>0) {
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)            for (z1=1; z1<=cptcoveff; z1++) 
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
         }                bool=0;
       }          } 
       /* This for computing force of mortality (h=1)as a weighted average */          if (bool==1) { 
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
         for(i=1; i<= nlstate; i++)              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
           gmp[j] += prlim[i][i]*p3mat[i][j][1];              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
       }                    if(agev[m][i]==0) agev[m][i]=iagemax+1;
       /* end force of mortality */                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 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); 
       for(j=1; j<= nlstate; j++) /* vareij */                if (s[m][i]>0 && s[m][i]<=nlstate) { 
         for(h=0; h<=nhstepm; h++){                  /*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]]);*/
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
         }                  prop[s[m][i]][iagemax+3] += weight[i]; 
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */                } 
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];              }
       }            } /* end selection of waves */
           }
     } /* End theta */        }
         for(i=iagemin; i <= iagemax+3; i++){  
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */          
           for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
     for(h=0; h<=nhstepm; h++) /* veij */            posprop += prop[jk][i]; 
       for(j=1; j<=nlstate;j++)          } 
         for(theta=1; theta <=npar; theta++)  
           trgradg[h][j][theta]=gradg[h][theta][j];          for(jk=1; jk <=nlstate ; jk++){     
             if( i <=  iagemax){ 
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */              if(posprop>=1.e-5){ 
       for(theta=1; theta <=npar; theta++)                probs[i][jk][j1]= prop[jk][i]/posprop;
         trgradgp[j][theta]=gradgp[theta][j];              } 
             } 
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */          }/* end jk */ 
     for(i=1;i<=nlstate;i++)        }/* end i */ 
       for(j=1;j<=nlstate;j++)      } /* end i1 */
         vareij[i][j][(int)age] =0.;    } /* end k1 */
     
     for(h=0;h<=nhstepm;h++){    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
       for(k=0;k<=nhstepm;k++){    /*free_vector(pp,1,nlstate);*/
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);  }  /* End of prevalence */
         for(i=1;i<=nlstate;i++)  
           for(j=1;j<=nlstate;j++)  /************* Waves Concatenation ***************/
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;  
       }  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
     }  {
     /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     /* pptj */       Death is a valid wave (if date is known).
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
     for(j=nlstate+1;j<=nlstate+ndeath;j++)       and mw[mi+1][i]. dh depends on stepm.
       for(i=nlstate+1;i<=nlstate+ndeath;i++)       */
         varppt[j][i]=doldmp[j][i];  
     /* end ppptj */    int i, mi, m;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);      /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);       double sum=0., jmean=0.;*/
      int first;
     if (popbased==1) {    int j, k=0,jk, ju, jl;
       for(i=1; i<=nlstate;i++)    double sum=0.;
         prlim[i][i]=probs[(int)age][i][ij];    first=0;
     }    jmin=1e+5;
        jmax=-1;
     /* This for computing force of mortality (h=1)as a weighted average */    jmean=0.;
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){    for(i=1; i<=imx; i++){
       for(i=1; i<= nlstate; i++)      mi=0;
         gmp[j] += prlim[i][i]*p3mat[i][j][1];      m=firstpass;
     }          while(s[m][i] <= nlstate){
     /* end force of mortality */        if(s[m][i]>=1)
           mw[++mi][i]=m;
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);        if(m >=lastpass)
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){          break;
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));        else
       for(i=1; i<=nlstate;i++){          m++;
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);      }/* end while */
       }      if (s[m][i] > nlstate){
     }        mi++;     /* Death is another wave */
     fprintf(ficresprobmorprev,"\n");        /* if(mi==0)  never been interviewed correctly before death */
            /* Only death is a correct wave */
     fprintf(ficresvij,"%.0f ",age );        mw[mi][i]=m;
     for(i=1; i<=nlstate;i++)      }
       for(j=1; j<=nlstate;j++){  
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);      wav[i]=mi;
       }      if(mi==0){
     fprintf(ficresvij,"\n");        if(first==0){
     free_matrix(gp,0,nhstepm,1,nlstate);          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
     free_matrix(gm,0,nhstepm,1,nlstate);          first=1;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        }
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);        if(first==1){
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
   } /* End age */        }
   free_vector(gpp,nlstate+1,nlstate+ndeath);      } /* end mi==0 */
   free_vector(gmp,nlstate+1,nlstate+ndeath);    } /* End individuals */
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);  
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/    for(i=1; i<=imx; i++){
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");      for(mi=1; mi<wav[i];mi++){
   /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */        if (stepm <=0)
   fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");          dh[mi][i]=1;
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);        else{
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);            if (agedc[i] < 2*AGESUP) {
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);              if(j==0) j=1;  /* Survives at least one month after exam */
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);              else if(j<0){
                 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]);
   free_vector(xp,1,npar);                j=1; /* Careful Patch */
   free_matrix(doldm,1,nlstate,1,nlstate);                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);
   free_matrix(dnewm,1,nlstate,1,npar);                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]);
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);                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);
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);              }
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);              k=k+1;
   fclose(ficresprobmorprev);              if (j >= jmax) jmax=j;
   fclose(ficgp);              if (j <= jmin) jmin=j;
   fclose(fichtm);              sum=sum+j;
               /*if (j<0) printf("j=%d num=%d \n",j,i);*/
 }              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             }
 /************ Variance of prevlim ******************/          }
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)          else{
 {            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   /* Variance of prevalence limit */            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            k=k+1;
   double **newm;            if (j >= jmax) jmax=j;
   double **dnewm,**doldm;            else if (j <= jmin)jmin=j;
   int i, j, nhstepm, hstepm;            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   int k, cptcode;            /*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]);*/
   double *xp;            if(j<0){
   double *gp, *gm;              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]);
   double **gradg, **trgradg;              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]);
   double age,agelim;            }
   int theta;            sum=sum+j;
              }
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");          jk= j/stepm;
   fprintf(ficresvpl,"# Age");          jl= j -jk*stepm;
   for(i=1; i<=nlstate;i++)          ju= j -(jk+1)*stepm;
       fprintf(ficresvpl," %1d-%1d",i,i);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
   fprintf(ficresvpl,"\n");            if(jl==0){
               dh[mi][i]=jk;
   xp=vector(1,npar);              bh[mi][i]=0;
   dnewm=matrix(1,nlstate,1,npar);            }else{ /* We want a negative bias in order to only have interpolation ie
   doldm=matrix(1,nlstate,1,nlstate);                    * at the price of an extra matrix product in likelihood */
                dh[mi][i]=jk+1;
   hstepm=1*YEARM; /* Every year of age */              bh[mi][i]=ju;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            }
   agelim = AGESUP;          }else{
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            if(jl <= -ju){
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */              dh[mi][i]=jk;
     if (stepm >= YEARM) hstepm=1;              bh[mi][i]=jl;       /* bias is positive if real duration
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */                                   * is higher than the multiple of stepm and negative otherwise.
     gradg=matrix(1,npar,1,nlstate);                                   */
     gp=vector(1,nlstate);            }
     gm=vector(1,nlstate);            else{
               dh[mi][i]=jk+1;
     for(theta=1; theta <=npar; theta++){              bh[mi][i]=ju;
       for(i=1; i<=npar; i++){ /* Computes gradient */            }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            if(dh[mi][i]==0){
       }              dh[mi][i]=1; /* At least one step */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              bh[mi][i]=ju; /* At least one step */
       for(i=1;i<=nlstate;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);*/
         gp[i] = prlim[i][i];            }
              } /* end if mle */
       for(i=1; i<=npar; i++) /* Computes gradient */        }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      } /* end wave */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    }
       for(i=1;i<=nlstate;i++)    jmean=sum/k;
         gm[i] = prlim[i][i];    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
     fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
       for(i=1;i<=nlstate;i++)   }
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];  
     } /* End theta */  /*********** Tricode ****************************/
   void tricode(int *Tvar, int **nbcode, int imx)
     trgradg =matrix(1,nlstate,1,npar);  {
     
     for(j=1; j<=nlstate;j++)    int Ndum[20],ij=1, k, j, i, maxncov=19;
       for(theta=1; theta <=npar; theta++)    int cptcode=0;
         trgradg[j][theta]=gradg[theta][j];    cptcoveff=0; 
    
     for(i=1;i<=nlstate;i++)    for (k=0; k<maxncov; k++) Ndum[k]=0;
       varpl[i][(int)age] =0.;    for (k=1; k<=7; k++) ncodemax[k]=0;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);  
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
     for(i=1;i<=nlstate;i++)      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */                                 modality*/ 
         ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
     fprintf(ficresvpl,"%.0f ",age );        Ndum[ij]++; /*store the modality */
     for(i=1; i<=nlstate;i++)        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
     fprintf(ficresvpl,"\n");                                         Tvar[j]. If V=sex and male is 0 and 
     free_vector(gp,1,nlstate);                                         female is 1, then  cptcode=1.*/
     free_vector(gm,1,nlstate);      }
     free_matrix(gradg,1,npar,1,nlstate);  
     free_matrix(trgradg,1,nlstate,1,npar);      for (i=0; i<=cptcode; i++) {
   } /* End age */        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
       }
   free_vector(xp,1,npar);  
   free_matrix(doldm,1,nlstate,1,npar);      ij=1; 
   free_matrix(dnewm,1,nlstate,1,nlstate);      for (i=1; i<=ncodemax[j]; i++) {
         for (k=0; k<= maxncov; k++) {
 }          if (Ndum[k] != 0) {
             nbcode[Tvar[j]][ij]=k; 
 /************ Variance of one-step probabilities  ******************/            /* 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; */
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)            
 {            ij++;
   int i, j=0,  i1, k1, l1, t, tj;          }
   int k2, l2, j1,  z1;          if (ij > ncodemax[j]) break; 
   int k=0,l, cptcode;        }  
   int first=1, first1;      } 
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;    }  
   double **dnewm,**doldm;  
   double *xp;   for (k=0; k< maxncov; k++) Ndum[k]=0;
   double *gp, *gm;  
   double **gradg, **trgradg;   for (i=1; i<=ncovmodel-2; i++) { 
   double **mu;     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
   double age,agelim, cov[NCOVMAX];     ij=Tvar[i];
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */     Ndum[ij]++;
   int theta;   }
   char fileresprob[FILENAMELENGTH];  
   char fileresprobcov[FILENAMELENGTH];   ij=1;
   char fileresprobcor[FILENAMELENGTH];   for (i=1; i<= maxncov; i++) {
      if((Ndum[i]!=0) && (i<=ncovcol)){
   double ***varpij;       Tvaraff[ij]=i; /*For printing */
        ij++;
   strcpy(fileresprob,"prob");     }
   strcat(fileresprob,fileres);   }
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {   
     printf("Problem with resultfile: %s\n", fileresprob);   cptcoveff=ij-1; /*Number of simple covariates*/
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);  }
   }  
   strcpy(fileresprobcov,"probcov");  /*********** Health Expectancies ****************/
   strcat(fileresprobcov,fileres);  
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {  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("Problem with resultfile: %s\n", fileresprobcov);  
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);  {
   }    /* Health expectancies */
   strcpy(fileresprobcor,"probcor");    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
   strcat(fileresprobcor,fileres);    double age, agelim, hf;
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {    double ***p3mat,***varhe;
     printf("Problem with resultfile: %s\n", fileresprobcor);    double **dnewm,**doldm;
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);    double *xp;
   }    double **gp, **gm;
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    double ***gradg, ***trgradg;
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    int theta;
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);  
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);    xp=vector(1,npar);
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);    dnewm=matrix(1,nlstate*nlstate,1,npar);
      doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");    
   fprintf(ficresprob,"# Age");    fprintf(ficreseij,"# Health expectancies\n");
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");    fprintf(ficreseij,"# Age");
   fprintf(ficresprobcov,"# Age");    for(i=1; i<=nlstate;i++)
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");      for(j=1; j<=nlstate;j++)
   fprintf(ficresprobcov,"# Age");        fprintf(ficreseij," %1d-%1d (SE)",i,j);
     fprintf(ficreseij,"\n");
   
   for(i=1; i<=nlstate;i++)    if(estepm < stepm){
     for(j=1; j<=(nlstate+ndeath);j++){      printf ("Problem %d lower than %d\n",estepm, stepm);
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);    }
       fprintf(ficresprobcov," p%1d-%1d ",i,j);    else  hstepm=estepm;   
       fprintf(ficresprobcor," p%1d-%1d ",i,j);    /* We compute the life expectancy from trapezoids spaced every estepm months
     }       * This is mainly to measure the difference between two models: for example
   fprintf(ficresprob,"\n");     * if stepm=24 months pijx are given only every 2 years and by summing them
   fprintf(ficresprobcov,"\n");     * we are calculating an estimate of the Life Expectancy assuming a linear 
   fprintf(ficresprobcor,"\n");     * progression in between and thus overestimating or underestimating according
   xp=vector(1,npar);     * to the curvature of the survival function. If, for the same date, we 
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));     * to compare the new estimate of Life expectancy with the same linear 
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);     * hypothesis. A more precise result, taking into account a more precise
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);     * curvature will be obtained if estepm is as small as stepm. */
   first=1;  
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {    /* For example we decided to compute the life expectancy with the smallest unit */
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);       nhstepm is the number of hstepm from age to agelim 
     exit(0);       nstepm is the number of stepm from age to agelin. 
   }       Look at hpijx to understand the reason of that which relies in memory size
   else{       and note for a fixed period like estepm months */
     fprintf(ficgp,"\n# Routine varprob");    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   }       survival function given by stepm (the optimization length). Unfortunately it
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {       means that if the survival funtion is printed only each two years of age and if
     printf("Problem with html file: %s\n", optionfilehtm);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);       results. So we changed our mind and took the option of the best precision.
     exit(0);    */
   }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   else{  
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");    agelim=AGESUP;
     fprintf(fichtm,"\n");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       /* nhstepm age range expressed in number of stepm */
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
     fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");      /* if (stepm >= YEARM) hstepm=1;*/
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   }      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
        gp=matrix(0,nhstepm,1,nlstate*nlstate);
   cov[1]=1;      gm=matrix(0,nhstepm,1,nlstate*nlstate);
   tj=cptcoveff;  
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   j1=0;         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   for(t=1; t<=tj;t++){      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
     for(i1=1; i1<=ncodemax[t];i1++){   
       j1++;  
            hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       if  (cptcovn>0) {  
         fprintf(ficresprob, "\n#********** Variable ");      /* Computing Variances of health expectancies */
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
         fprintf(ficresprob, "**********\n#");       for(theta=1; theta <=npar; theta++){
         fprintf(ficresprobcov, "\n#********** Variable ");        for(i=1; i<=npar; i++){ 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         fprintf(ficresprobcov, "**********\n#");        }
                hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         fprintf(ficgp, "\n#********** Variable ");    
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        cptj=0;
         fprintf(ficgp, "**********\n#");        for(j=1; j<= nlstate; j++){
                  for(i=1; i<=nlstate; i++){
                    cptj=cptj+1;
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");            }
                  }
         fprintf(ficresprobcor, "\n#********** Variable ");            }
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);       
         fprintf(ficgp, "**********\n#");           
       }        for(i=1; i<=npar; i++) 
                xp[i] = x[i] - (i==theta ?delti[theta]:0);
       for (age=bage; age<=fage; age ++){        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         cov[2]=age;        
         for (k=1; k<=cptcovn;k++) {        cptj=0;
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];        for(j=1; j<= nlstate; j++){
         }          for(i=1;i<=nlstate;i++){
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];            cptj=cptj+1;
         for (k=1; k<=cptcovprod;k++)            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  
                      gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));            }
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);          }
         gp=vector(1,(nlstate)*(nlstate+ndeath));        }
         gm=vector(1,(nlstate)*(nlstate+ndeath));        for(j=1; j<= nlstate*nlstate; j++)
              for(h=0; h<=nhstepm-1; h++){
         for(theta=1; theta <=npar; theta++){            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           for(i=1; i<=npar; i++)          }
             xp[i] = x[i] + (i==theta ?delti[theta]:0);       } 
               
           pmij(pmmij,cov,ncovmodel,xp,nlstate);  /* End theta */
            
           k=0;       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
           for(i=1; i<= (nlstate); i++){  
             for(j=1; j<=(nlstate+ndeath);j++){       for(h=0; h<=nhstepm-1; h++)
               k=k+1;        for(j=1; j<=nlstate*nlstate;j++)
               gp[k]=pmmij[i][j];          for(theta=1; theta <=npar; theta++)
             }            trgradg[h][j][theta]=gradg[h][theta][j];
           }       
            
           for(i=1; i<=npar; i++)       for(i=1;i<=nlstate*nlstate;i++)
             xp[i] = x[i] - (i==theta ?delti[theta]:0);        for(j=1;j<=nlstate*nlstate;j++)
              varhe[i][j][(int)age] =0.;
           pmij(pmmij,cov,ncovmodel,xp,nlstate);  
           k=0;       printf("%d|",(int)age);fflush(stdout);
           for(i=1; i<=(nlstate); i++){       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
             for(j=1; j<=(nlstate+ndeath);j++){       for(h=0;h<=nhstepm-1;h++){
               k=k+1;        for(k=0;k<=nhstepm-1;k++){
               gm[k]=pmmij[i][j];          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
             }          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
           }          for(i=1;i<=nlstate*nlstate;i++)
                  for(j=1;j<=nlstate*nlstate;j++)
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];          }
         }      }
       /* Computing expectancies */
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)      for(i=1; i<=nlstate;i++)
           for(theta=1; theta <=npar; theta++)        for(j=1; j<=nlstate;j++)
             trgradg[j][theta]=gradg[theta][j];          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
                    eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
         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);  /* 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]);*/
          
         pmij(pmmij,cov,ncovmodel,x,nlstate);          }
          
         k=0;      fprintf(ficreseij,"%3.0f",age );
         for(i=1; i<=(nlstate); i++){      cptj=0;
           for(j=1; j<=(nlstate+ndeath);j++){      for(i=1; i<=nlstate;i++)
             k=k+1;        for(j=1; j<=nlstate;j++){
             mu[k][(int) age]=pmmij[i][j];          cptj++;
           }          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
         }        }
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)      fprintf(ficreseij,"\n");
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)     
             varpij[i][j][(int)age] = doldm[i][j];      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
       free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
         /*printf("\n%d ",(int)age);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    }
      }*/    printf("\n");
     fprintf(ficlog,"\n");
         fprintf(ficresprob,"\n%d ",(int)age);  
         fprintf(ficresprobcov,"\n%d ",(int)age);    free_vector(xp,1,npar);
         fprintf(ficresprobcor,"\n%d ",(int)age);    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
           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]);  /************ Variance ******************/
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);  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)
         }  {
         i=0;    /* Variance of health expectancies */
         for (k=1; k<=(nlstate);k++){    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
           for (l=1; l<=(nlstate+ndeath);l++){    /* double **newm;*/
             i=i++;    double **dnewm,**doldm;
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);    double **dnewmp,**doldmp;
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);    int i, j, nhstepm, hstepm, h, nstepm ;
             for (j=1; j<=i;j++){    int k, cptcode;
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);    double *xp;
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));    double **gp, **gm;  /* for var eij */
             }    double ***gradg, ***trgradg; /*for var eij */
           }    double **gradgp, **trgradgp; /* for var p point j */
         }/* end of loop for state */    double *gpp, *gmp; /* for var p point j */
       } /* end of loop for age */    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     double ***p3mat;
       /* Confidence intervalle of pij  */    double age,agelim, hf;
       /*    double ***mobaverage;
       fprintf(ficgp,"\nset noparametric;unset label");    int theta;
       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");    char digit[4];
       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");    char digitp[25];
       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);    char fileresprobmorprev[FILENAMELENGTH];
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);  
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);    if(popbased==1){
       */      if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/      else strcpy(digitp,"-populbased-nomobil-");
       first1=1;    }
       for (k2=1; k2<=(nlstate);k2++){    else 
         for (l2=1; l2<=(nlstate+ndeath);l2++){      strcpy(digitp,"-stablbased-");
           if(l2==k2) continue;  
           j=(k2-1)*(nlstate+ndeath)+l2;    if (mobilav!=0) {
           for (k1=1; k1<=(nlstate);k1++){      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
             for (l1=1; l1<=(nlstate+ndeath);l1++){      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
               if(l1==k1) continue;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
               i=(k1-1)*(nlstate+ndeath)+l1;        printf(" Error in movingaverage mobilav=%d\n",mobilav);
               if(i<=j) continue;      }
               for (age=bage; age<=fage; age ++){    }
                 if ((int)age %5==0){  
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;    strcpy(fileresprobmorprev,"prmorprev"); 
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;    sprintf(digit,"%-d",ij);
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
                   mu1=mu[i][(int) age]/stepm*YEARM ;    strcat(fileresprobmorprev,digit); /* Tvar to be done */
                   mu2=mu[j][(int) age]/stepm*YEARM;    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
                   c12=cv12/sqrt(v1*v2);    strcat(fileresprobmorprev,fileres);
                   /* Computing eigen value of matrix of covariance */    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
                   lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;      printf("Problem with resultfile: %s\n", fileresprobmorprev);
                   lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
                   /* Eigen vectors */    }
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
                   /*v21=sqrt(1.-v11*v11); *//* error */    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
                   v21=(lc1-v1)/cv12*v11;    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);
                   v12=-v21;    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
                   v22=v11;    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
                   tnalp=v21/v11;      fprintf(ficresprobmorprev," p.%-d SE",j);
                   if(first1==1){      for(i=1; i<=nlstate;i++)
                     first1=0;        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
                     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);    }  
                   }    fprintf(ficresprobmorprev,"\n");
                   fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);    fprintf(ficgp,"\n# Routine varevsij");
                   /*printf(fignu*/    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");
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
                   /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */  /*   } */
                   if(first==1){    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                     first=0;  
                     fprintf(ficgp,"\nset parametric;unset label");    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
                     fprintf(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(ficresvij,"# Age");
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");    for(i=1; i<=nlstate;i++)
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2,optionfilefiname, j1,k1,l1,k2,l2);      for(j=1; j<=nlstate;j++)
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k1,l1,k2,l2);        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k1,l1,k2,l2);    fprintf(ficresvij,"\n");
                     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);    xp=vector(1,npar);
                     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",\    dnewm=matrix(1,nlstate,1,npar);
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\    doldm=matrix(1,nlstate,1,nlstate);
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
                   }else{    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                     first=0;  
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);    gpp=vector(nlstate+1,nlstate+ndeath);
                     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",\    gmp=vector(nlstate+1,nlstate+ndeath);
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
                             mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));    
                   }/* if first */    if(estepm < stepm){
                 } /* age mod 5 */      printf ("Problem %d lower than %d\n",estepm, stepm);
               } /* end loop age */    }
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k1,l1,k2,l2);    else  hstepm=estepm;   
               first=1;    /* For example we decided to compute the life expectancy with the smallest unit */
             } /*l12 */    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           } /* k12 */       nhstepm is the number of hstepm from age to agelim 
         } /*l1 */       nstepm is the number of stepm from age to agelin. 
       }/* k1 */       Look at hpijx to understand the reason of that which relies in memory size
     } /* loop covariates */       and note for a fixed period like k years */
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));       survival function given by stepm (the optimization length). Unfortunately it
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));       means that if the survival funtion is printed every two years of age and if
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);       results. So we changed our mind and took the option of the best precision.
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    */
   }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   free_vector(xp,1,npar);    agelim = AGESUP;
   fclose(ficresprob);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   fclose(ficresprobcov);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   fclose(ficresprobcor);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   fclose(ficgp);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fclose(fichtm);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
 }      gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   
 /******************* Printing html file ***********/  
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \      for(theta=1; theta <=npar; theta++){
                   int lastpass, int stepm, int weightopt, char model[],\        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\          xp[i] = x[i] + (i==theta ?delti[theta]:0);
                   int popforecast, int estepm ,\        }
                   double jprev1, double mprev1,double anprev1, \        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
                   double jprev2, double mprev2,double anprev2){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   int jj1, k1, i1, cpt;  
   /*char optionfilehtm[FILENAMELENGTH];*/        if (popbased==1) {
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {          if(mobilav ==0){
     printf("Problem with %s \n",optionfilehtm), exit(0);            for(i=1; i<=nlstate;i++)
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);              prlim[i][i]=probs[(int)age][i][ij];
   }          }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n              prlim[i][i]=mobaverage[(int)age][i][ij];
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n          }
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n        }
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n    
  - Life expectancies by age and initial health status (estepm=%2d months):        for(j=1; j<= nlstate; j++){
    <a href=\"e%s\">e%s</a> <br>\n</li>", \          for(h=0; h<=nhstepm; h++){
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");          }
         }
  m=cptcoveff;        /* This for computing probability of death (h=1 means
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}           computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
  jj1=0;        */
  for(k1=1; k1<=m;k1++){        for(j=nlstate+1;j<=nlstate+ndeath;j++){
    for(i1=1; i1<=ncodemax[k1];i1++){          for(i=1,gpp[j]=0.; i<= nlstate; i++)
      jj1++;            gpp[j] += prlim[i][i]*p3mat[i][j][1];
      if (cptcovn > 0) {        }    
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        /* end probability of death */
        for (cpt=1; cpt<=cptcoveff;cpt++)  
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");          xp[i] = x[i] - (i==theta ?delti[theta]:0);
      }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
      /* Pij */        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>   
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);            if (popbased==1) {
      /* Quasi-incidences */          if(mobilav ==0){
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>            for(i=1; i<=nlstate;i++)
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);              prlim[i][i]=probs[(int)age][i][ij];
        /* Stable prevalence in each health state */          }else{ /* mobilav */ 
        for(cpt=1; cpt<nlstate;cpt++){            for(i=1; i<=nlstate;i++)
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>              prlim[i][i]=mobaverage[(int)age][i][ij];
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          }
        }        }
      for(cpt=1; cpt<=nlstate;cpt++) {  
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>        for(j=1; j<= nlstate; j++){
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          for(h=0; h<=nhstepm; h++){
      }            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
      fprintf(fichtm,"\n<br>- Total life expectancy by age and              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
 health expectancies in states (1) and (2): e%s%d.png<br>          }
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        }
    } /* end i1 */        /* This for computing probability of death (h=1 means
  }/* End k1 */           computed over hstepm matrices product = hstepm*stepm months) 
  fprintf(fichtm,"</ul>");           as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n          for(i=1,gmp[j]=0.; i<= nlstate; i++)
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n           gmp[j] += prlim[i][i]*p3mat[i][j][1];
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n        }    
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n        /* end probability of death */
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n  
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n        for(j=1; j<= nlstate; j++) /* vareij */
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n          for(h=0; h<=nhstepm; h++){
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
  if(popforecast==1) fprintf(fichtm,"\n  
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         <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);      } /* End theta */
 fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");  
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
  m=cptcoveff;  
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}      for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
  jj1=0;          for(theta=1; theta <=npar; theta++)
  for(k1=1; k1<=m;k1++){            trgradg[h][j][theta]=gradg[h][theta][j];
    for(i1=1; i1<=ncodemax[k1];i1++){  
      jj1++;      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
      if (cptcovn > 0) {        for(theta=1; theta <=npar; theta++)
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");          trgradgp[j][theta]=gradgp[theta][j];
        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\">");      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
      }      for(i=1;i<=nlstate;i++)
      for(cpt=1; cpt<=nlstate;cpt++) {        for(j=1;j<=nlstate;j++)
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident          vareij[i][j][(int)age] =0.;
 interval) in state (%d): v%s%d%d.png <br>  
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        for(h=0;h<=nhstepm;h++){
      }        for(k=0;k<=nhstepm;k++){
    } /* end i1 */          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
  }/* End k1 */          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
  fprintf(fichtm,"</ul>");          for(i=1;i<=nlstate;i++)
 fclose(fichtm);            for(j=1;j<=nlstate;j++)
 }              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
 /******************* Gnuplot file **************/      }
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){    
       /* pptj */
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   int ng;      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {      for(j=nlstate+1;j<=nlstate+ndeath;j++)
     printf("Problem with file %s",optionfilegnuplot);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);          varppt[j][i]=doldmp[j][i];
   }      /* end ppptj */
       /*  x centered again */
 #ifdef windows      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
     fprintf(ficgp,"cd \"%s\" \n",pathc);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
 #endif   
 m=pow(2,cptcoveff);      if (popbased==1) {
          if(mobilav ==0){
  /* 1eme*/          for(i=1; i<=nlstate;i++)
   for (cpt=1; cpt<= nlstate ; cpt ++) {            prlim[i][i]=probs[(int)age][i][ij];
    for (k1=1; k1<= m ; k1 ++) {        }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
 #ifdef windows            prlim[i][i]=mobaverage[(int)age][i][ij];
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        }
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);      }
 #endif               
 #ifdef unix      /* This for computing probability of death (h=1 means
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);         as a weighted average of prlim.
 #endif      */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
 for (i=1; i<= nlstate ; i ++) {        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   else fprintf(ficgp," \%%*lf (\%%*lf)");      }    
 }      /* end probability of death */
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);  
     for (i=1; i<= nlstate ; i ++) {      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
 }        for(i=1; i<=nlstate;i++){
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
      for (i=1; i<= nlstate ; i ++) {        }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      } 
   else fprintf(ficgp," \%%*lf (\%%*lf)");      fprintf(ficresprobmorprev,"\n");
 }    
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      fprintf(ficresvij,"%.0f ",age );
 #ifdef unix      for(i=1; i<=nlstate;i++)
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");        for(j=1; j<=nlstate;j++){
 #endif          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
    }        }
   }      fprintf(ficresvij,"\n");
   /*2 eme*/      free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
   for (k1=1; k1<= m ; k1 ++) {      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        } /* End age */
     for (i=1; i<= nlstate+1 ; i ++) {    free_vector(gpp,nlstate+1,nlstate+ndeath);
       k=2*i;    free_vector(gmp,nlstate+1,nlstate+ndeath);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
       for (j=1; j<= nlstate+1 ; j ++) {    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
   else fprintf(ficgp," \%%*lf (\%%*lf)");    /* 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)\";");
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
       for (j=1; j<= nlstate+1 ; j ++) {    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
         else fprintf(ficgp," \%%*lf (\%%*lf)");    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
 }      fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
       fprintf(ficgp,"\" t\"\" w l 0,");    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
       for (j=1; j<= nlstate+1 ; j ++) {  */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
   else fprintf(ficgp," \%%*lf (\%%*lf)");    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
 }    
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    free_vector(xp,1,npar);
       else fprintf(ficgp,"\" t\"\" w l 0,");    free_matrix(doldm,1,nlstate,1,nlstate);
     }    free_matrix(dnewm,1,nlstate,1,npar);
   }    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
   /*3eme*/    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   for (k1=1; k1<= m ; k1 ++) {    fclose(ficresprobmorprev);
     for (cpt=1; cpt<= nlstate ; cpt ++) {    fflush(ficgp);
       k=2+nlstate*(2*cpt-2);    fflush(fichtm); 
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);  }  /* end varevsij */
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);  
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);  /************ Variance of prevlim ******************/
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);  {
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    /* Variance of prevalence limit */
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    double **newm;
     double **dnewm,**doldm;
 */    int i, j, nhstepm, hstepm;
       for (i=1; i< nlstate ; i ++) {    int k, cptcode;
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);    double *xp;
     double *gp, *gm;
       }    double **gradg, **trgradg;
     }    double age,agelim;
   }    int theta;
       
   /* CV preval stat */    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
     for (k1=1; k1<= m ; k1 ++) {    fprintf(ficresvpl,"# Age");
     for (cpt=1; cpt<nlstate ; cpt ++) {    for(i=1; i<=nlstate;i++)
       k=3;        fprintf(ficresvpl," %1d-%1d",i,i);
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    fprintf(ficresvpl,"\n");
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);  
     xp=vector(1,npar);
       for (i=1; i< nlstate ; i ++)    dnewm=matrix(1,nlstate,1,npar);
         fprintf(ficgp,"+$%d",k+i+1);    doldm=matrix(1,nlstate,1,nlstate);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    
          hstepm=1*YEARM; /* Every year of age */
       l=3+(nlstate+ndeath)*cpt;    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    agelim = AGESUP;
       for (i=1; i< nlstate ; i ++) {    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         l=3+(nlstate+ndeath)*cpt;      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         fprintf(ficgp,"+$%d",l+i+1);      if (stepm >= YEARM) hstepm=1;
       }      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);        gradg=matrix(1,npar,1,nlstate);
     }      gp=vector(1,nlstate);
   }        gm=vector(1,nlstate);
    
   /* proba elementaires */      for(theta=1; theta <=npar; theta++){
    for(i=1,jk=1; i <=nlstate; i++){        for(i=1; i<=npar; i++){ /* Computes gradient */
     for(k=1; k <=(nlstate+ndeath); k++){          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       if (k != i) {        }
         for(j=1; j <=ncovmodel; j++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);        for(i=1;i<=nlstate;i++)
           jk++;          gp[i] = prlim[i][i];
           fprintf(ficgp,"\n");      
         }        for(i=1; i<=npar; i++) /* Computes gradient */
       }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    }        for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/  
      for(jk=1; jk <=m; jk++) {        for(i=1;i<=nlstate;i++)
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
        if (ng==2)      } /* End theta */
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");  
        else      trgradg =matrix(1,nlstate,1,npar);
          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);      for(j=1; j<=nlstate;j++)
        i=1;        for(theta=1; theta <=npar; theta++)
        for(k2=1; k2<=nlstate; k2++) {          trgradg[j][theta]=gradg[theta][j];
          k3=i;  
          for(k=1; k<=(nlstate+ndeath); k++) {      for(i=1;i<=nlstate;i++)
            if (k != k2){        varpl[i][(int)age] =0.;
              if(ng==2)      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
              else      for(i=1;i<=nlstate;i++)
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
              ij=1;  
              for(j=3; j <=ncovmodel; j++) {      fprintf(ficresvpl,"%.0f ",age );
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      for(i=1; i<=nlstate;i++)
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
                  ij++;      fprintf(ficresvpl,"\n");
                }      free_vector(gp,1,nlstate);
                else      free_vector(gm,1,nlstate);
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      free_matrix(gradg,1,npar,1,nlstate);
              }      free_matrix(trgradg,1,nlstate,1,npar);
              fprintf(ficgp,")/(1");    } /* End age */
                
              for(k1=1; k1 <=nlstate; k1++){      free_vector(xp,1,npar);
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    free_matrix(doldm,1,nlstate,1,npar);
                ij=1;    free_matrix(dnewm,1,nlstate,1,nlstate);
                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++;  /************ Variance of one-step probabilities  ******************/
                  }  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
                  else  {
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    int i, j=0,  i1, k1, l1, t, tj;
                }    int k2, l2, j1,  z1;
                fprintf(ficgp,")");    int k=0,l, cptcode;
              }    int first=1, first1;
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    double **dnewm,**doldm;
              i=i+ncovmodel;    double *xp;
            }    double *gp, *gm;
          } /* end k */    double **gradg, **trgradg;
        } /* end k2 */    double **mu;
      } /* end jk */    double age,agelim, cov[NCOVMAX];
    } /* end ng */    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
    fclose(ficgp);    int theta;
 }  /* end gnuplot */    char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
 /*************** Moving average **************/  
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    double ***varpij;
   
   int i, cpt, cptcod;    strcpy(fileresprob,"prob"); 
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    strcat(fileresprob,fileres);
       for (i=1; i<=nlstate;i++)    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)      printf("Problem with resultfile: %s\n", fileresprob);
           mobaverage[(int)agedeb][i][cptcod]=0.;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
        }
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){    strcpy(fileresprobcov,"probcov"); 
       for (i=1; i<=nlstate;i++){    strcat(fileresprobcov,fileres);
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
           for (cpt=0;cpt<=4;cpt++){      printf("Problem with resultfile: %s\n", fileresprobcov);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
           }    }
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;    strcpy(fileresprobcor,"probcor"); 
         }    strcat(fileresprobcor,fileres);
       }    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
     }      printf("Problem with resultfile: %s\n", fileresprobcor);
          fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
 }    }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
 /************** Forecasting ******************/    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
      printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   int *popage;    
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   double *popeffectif,*popcount;    fprintf(ficresprob,"# Age");
   double ***p3mat;    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   char fileresf[FILENAMELENGTH];    fprintf(ficresprobcov,"# Age");
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
  agelim=AGESUP;    fprintf(ficresprobcov,"# Age");
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;  
   
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    for(i=1; i<=nlstate;i++)
        for(j=1; j<=(nlstate+ndeath);j++){
          fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   strcpy(fileresf,"f");        fprintf(ficresprobcov," p%1d-%1d ",i,j);
   strcat(fileresf,fileres);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
   if((ficresf=fopen(fileresf,"w"))==NULL) {      }  
     printf("Problem with forecast resultfile: %s\n", fileresf);   /* fprintf(ficresprob,"\n");
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);    fprintf(ficresprobcov,"\n");
   }    fprintf(ficresprobcor,"\n");
   printf("Computing forecasting: result on file '%s' \n", fileresf);   */
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);   xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
   if (mobilav==1) {    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    first=1;
     movingaverage(agedeb, fage, ageminpar, mobaverage);    fprintf(ficgp,"\n# Routine varprob");
   }    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   if (stepm<=12) stepsize=1;    fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");
      fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
   agelim=AGESUP;    fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");
    
   hstepm=1;    cov[1]=1;
   hstepm=hstepm/stepm;    tj=cptcoveff;
   yp1=modf(dateintmean,&yp);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   anprojmean=yp;    j1=0;
   yp2=modf((yp1*12),&yp);    for(t=1; t<=tj;t++){
   mprojmean=yp;      for(i1=1; i1<=ncodemax[t];i1++){ 
   yp1=modf((yp2*30.5),&yp);        j1++;
   jprojmean=yp;        if  (cptcovn>0) {
   if(jprojmean==0) jprojmean=1;          fprintf(ficresprob, "\n#********** Variable "); 
   if(mprojmean==0) jprojmean=1;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficresprob, "**********\n#\n");
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);          fprintf(ficresprobcov, "\n#********** Variable "); 
            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   for(cptcov=1;cptcov<=i2;cptcov++){          fprintf(ficresprobcov, "**********\n#\n");
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          
       k=k+1;          fprintf(ficgp, "\n#********** Variable "); 
       fprintf(ficresf,"\n#******");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       for(j=1;j<=cptcoveff;j++) {          fprintf(ficgp, "**********\n#\n");
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          
       }          
       fprintf(ficresf,"******\n");          fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
       fprintf(ficresf,"# StartingAge FinalAge");          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
                
                fprintf(ficresprobcor, "\n#********** Variable ");    
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         fprintf(ficresf,"\n");          fprintf(ficresprobcor, "**********\n#");    
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);          }
         
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        for (age=bage; age<=fage; age ++){ 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          cov[2]=age;
           nhstepm = nhstepm/hstepm;          for (k=1; k<=cptcovn;k++) {
                      cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
           oldm=oldms;savm=savms;          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            for (k=1; k<=cptcovprod;k++)
                    cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           for (h=0; h<=nhstepm; h++){          
             if (h==(int) (calagedate+YEARM*cpt)) {          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
             }          gp=vector(1,(nlstate)*(nlstate+ndeath));
             for(j=1; j<=nlstate+ndeath;j++) {          gm=vector(1,(nlstate)*(nlstate+ndeath));
               kk1=0.;kk2=0;      
               for(i=1; i<=nlstate;i++) {                        for(theta=1; theta <=npar; theta++){
                 if (mobilav==1)            for(i=1; i<=npar; i++)
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
                 else {            
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];            pmij(pmmij,cov,ncovmodel,xp,nlstate);
                 }            
                            k=0;
               }            for(i=1; i<= (nlstate); i++){
               if (h==(int)(calagedate+12*cpt)){              for(j=1; j<=(nlstate+ndeath);j++){
                 fprintf(ficresf," %.3f", kk1);                k=k+1;
                                        gp[k]=pmmij[i][j];
               }              }
             }            }
           }            
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for(i=1; i<=npar; i++)
         }              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       }      
     }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   }            k=0;
                    for(i=1; i<=(nlstate); i++){
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
   fclose(ficresf);                gm[k]=pmmij[i][j];
 }              }
 /************** Forecasting ******************/            }
 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){       
              for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
   int *popage;          }
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  
   double *popeffectif,*popcount;          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
   double ***p3mat,***tabpop,***tabpopprev;            for(theta=1; theta <=npar; theta++)
   char filerespop[FILENAMELENGTH];              trgradg[j][theta]=gradg[theta][j];
           
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   agelim=AGESUP;          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
            free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
    
            pmij(pmmij,cov,ncovmodel,x,nlstate);
   strcpy(filerespop,"pop");          
   strcat(filerespop,fileres);          k=0;
   if((ficrespop=fopen(filerespop,"w"))==NULL) {          for(i=1; i<=(nlstate); i++){
     printf("Problem with forecast resultfile: %s\n", filerespop);            for(j=1; j<=(nlstate+ndeath);j++){
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);              k=k+1;
   }              mu[k][(int) age]=pmmij[i][j];
   printf("Computing forecasting: result on file '%s' \n", filerespop);            }
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);          }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   if (cptcoveff==0) ncodemax[cptcoveff]=1;            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   if (mobilav==1) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          /*printf("\n%d ",(int)age);
     movingaverage(agedeb, fage, ageminpar, mobaverage);            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]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   stepsize=(int) (stepm+YEARM-1)/YEARM;            }*/
   if (stepm<=12) stepsize=1;  
            fprintf(ficresprob,"\n%d ",(int)age);
   agelim=AGESUP;          fprintf(ficresprobcov,"\n%d ",(int)age);
            fprintf(ficresprobcor,"\n%d ",(int)age);
   hstepm=1;  
   hstepm=hstepm/stepm;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
              fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
   if (popforecast==1) {          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     if((ficpop=fopen(popfile,"r"))==NULL) {            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
       printf("Problem with population file : %s\n",popfile);exit(0);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);          }
     }          i=0;
     popage=ivector(0,AGESUP);          for (k=1; k<=(nlstate);k++){
     popeffectif=vector(0,AGESUP);            for (l=1; l<=(nlstate+ndeath);l++){ 
     popcount=vector(0,AGESUP);              i=i++;
                  fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
     i=1;                fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;              for (j=1; j<=i;j++){
                    fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
     imx=i;                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];              }
   }            }
           }/* end of loop for state */
   for(cptcov=1;cptcov<=i2;cptcov++){        } /* end of loop for age */
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
       k=k+1;        /* Confidence intervalle of pij  */
       fprintf(ficrespop,"\n#******");        /*
       for(j=1;j<=cptcoveff;j++) {          fprintf(ficgp,"\nset noparametric;unset label");
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
       }          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
       fprintf(ficrespop,"******\n");          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
       fprintf(ficrespop,"# Age");          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
       if (popforecast==1)  fprintf(ficrespop," [Population]");          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
              */
       for (cpt=0; cpt<=0;cpt++) {  
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
                first1=1;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        for (k2=1; k2<=(nlstate);k2++){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
           nhstepm = nhstepm/hstepm;            if(l2==k2) continue;
                      j=(k2-1)*(nlstate+ndeath)+l2;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for (k1=1; k1<=(nlstate);k1++){
           oldm=oldms;savm=savms;              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                  if(l1==k1) continue;
                        i=(k1-1)*(nlstate+ndeath)+l1;
           for (h=0; h<=nhstepm; h++){                if(i<=j) continue;
             if (h==(int) (calagedate+YEARM*cpt)) {                for (age=bage; age<=fage; age ++){ 
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);                  if ((int)age %5==0){
             }                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
             for(j=1; j<=nlstate+ndeath;j++) {                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
               kk1=0.;kk2=0;                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
               for(i=1; i<=nlstate;i++) {                                  mu1=mu[i][(int) age]/stepm*YEARM ;
                 if (mobilav==1)                    mu2=mu[j][(int) age]/stepm*YEARM;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];                    c12=cv12/sqrt(v1*v2);
                 else {                    /* Computing eigen value of matrix of covariance */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];                    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.;
               }                    /* Eigen vectors */
               if (h==(int)(calagedate+12*cpt)){                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;                    /*v21=sqrt(1.-v11*v11); *//* error */
                   /*fprintf(ficrespop," %.3f", kk1);                    v21=(lc1-v1)/cv12*v11;
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/                    v12=-v21;
               }                    v22=v11;
             }                    tnalp=v21/v11;
             for(i=1; i<=nlstate;i++){                    if(first1==1){
               kk1=0.;                      first1=0;
                 for(j=1; j<=nlstate;j++){                      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);
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];                    }
                 }                    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);
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];                    /*printf(fignu*/
             }                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)                    if(first==1){
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);                      first=0;
           }                      fprintf(ficgp,"\nset parametric;unset label");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
         }                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
       }                      fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
     :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   /******/  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);                        fprintf(fichtm,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
           nhstepm = nhstepm/hstepm;                      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);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                      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",\
           oldm=oldms;savm=savms;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                                mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
           for (h=0; h<=nhstepm; h++){                    }else{
             if (h==(int) (calagedate+YEARM*cpt)) {                      first=0;
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
             }                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
             for(j=1; j<=nlstate+ndeath;j++) {                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
               kk1=0.;kk2=0;                      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(i=1; i<=nlstate;i++) {                                            mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                                  mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
               }                    }/* if first */
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);                  } /* age mod 5 */
             }                } /* end loop age */
           }                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                first=1;
         }              } /*l12 */
       }            } /* k12 */
    }          } /*l1 */
   }        }/* k1 */
        } /* loop covariates */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   if (popforecast==1) {    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_ivector(popage,0,AGESUP);    free_vector(xp,1,npar);
     free_vector(popeffectif,0,AGESUP);    fclose(ficresprob);
     free_vector(popcount,0,AGESUP);    fclose(ficresprobcov);
   }    fclose(ficresprobcor);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /*  fclose(ficgp);*/
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  }
   fclose(ficrespop);  
 }  
   /******************* Printing html file ***********/
 /***********************************************/  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
 /**************** Main Program *****************/                    int lastpass, int stepm, int weightopt, char model[],\
 /***********************************************/                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
 int main(int argc, char *argv[])                    double jprev1, double mprev1,double anprev1, \
 {                    double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    /*char optionfilehtm[FILENAMELENGTH];*/
   double agedeb, agefin,hf;  /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    { */
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;  /*     printf("Problem with %s \n",optionfilehtm), exit(0); */
   /*     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
   double fret;  /*   } */
   double **xi,tmp,delta;  
      fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
   double dum; /* Dummy variable */   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n \
   double ***p3mat;   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n \
   int *indx;   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n \
   char line[MAXLINE], linepar[MAXLINE];   - Life expectancies by age and initial health status (estepm=%2d months): \
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];     <a href=\"%s\">%s</a> <br>\n</li>", \
   int firstobs=1, lastobs=10;             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
   int sdeb, sfin; /* Status at beginning and end */             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
   int c,  h , cpt,l;             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
   int ju,jl, mi;             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;  
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   int mobilav=0,popforecast=0;  
   int hstepm, nhstepm;   m=cptcoveff;
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
   double bage, fage, age, agelim, agebase;   jj1=0;
   double ftolpl=FTOL;   for(k1=1; k1<=m;k1++){
   double **prlim;     for(i1=1; i1<=ncodemax[k1];i1++){
   double *severity;       jj1++;
   double ***param; /* Matrix of parameters */       if (cptcovn > 0) {
   double  *p;         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   double **matcov; /* Matrix of covariance */         for (cpt=1; cpt<=cptcoveff;cpt++) 
   double ***delti3; /* Scale */           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   double *delti; /* Scale */         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   double ***eij, ***vareij;       }
   double **varpl; /* Variances of prevalence limits by age */       /* Pij */
   double *epj, vepp;       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> \
   double kk1, kk2;  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;       /* Quasi-incidences */
         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> \
   char *alph[]={"a","a","b","c","d","e"}, str[4];  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Stable prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
   char z[1]="c", occ;           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
 #include <sys/time.h>  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
 #include <time.h>         }
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];       for(cpt=1; cpt<=nlstate;cpt++) {
            fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
   /* long total_usecs;  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
   struct timeval start_time, end_time;       }
         fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */  health expectancies in states (1) and (2): %s%d.png<br>\
   getcwd(pathcd, size);  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
   printf("\n%s",version);   }/* End k1 */
   if(argc <=1){   fprintf(fichtm,"</ul>");
     printf("\nEnter the parameter file name: ");  
     scanf("%s",pathtot);  
   }   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
   else{   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
     strcpy(pathtot,argv[1]);   - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
   }   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
   /*cygwin_split_path(pathtot,path,optionfile);   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n\
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n\
   /* cutv(path,optionfile,pathtot,'\\');*/   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
            rfileres,rfileres,\
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
   chdir(path);           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
   replace(pathc,path);           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
            subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
 /*-------- arguments in the command line --------*/           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /* Log file */  /*  if(popforecast==1) fprintf(fichtm,"\n */
   strcat(filelog, optionfilefiname);  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   strcat(filelog,".log");    /* */  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   if((ficlog=fopen(filelog,"w"))==NULL)    {  /*      <br>",fileres,fileres,fileres,fileres); */
     printf("Problem with logfile %s\n",filelog);  /*  else  */
     goto end;  /*    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>");
   fprintf(ficlog,"Log filename:%s\n",filelog);  
   fprintf(ficlog,"\n%s",version);   m=cptcoveff;
   fprintf(ficlog,"\nEnter the parameter file name: ");   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);  
   fflush(ficlog);   jj1=0;
    for(k1=1; k1<=m;k1++){
   /* */     for(i1=1; i1<=ncodemax[k1];i1++){
   strcpy(fileres,"r");       jj1++;
   strcat(fileres, optionfilefiname);       if (cptcovn > 0) {
   strcat(fileres,".txt");    /* Other files have txt extension */         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
   /*---------arguments file --------*/           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   if((ficpar=fopen(optionfile,"r"))==NULL)    {       }
     printf("Problem with optionfile %s\n",optionfile);       for(cpt=1; cpt<=nlstate;cpt++) {
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);         fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
     goto end;  interval) in state (%d): %s%d%d.png <br>\
   }  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"vr"),cpt,jj1,subdirf2(optionfilefiname,"vr"),cpt,jj1);  
        }
   strcpy(filereso,"o");     } /* end i1 */
   strcat(filereso,fileres);   }/* End k1 */
   if((ficparo=fopen(filereso,"w"))==NULL) {   fprintf(fichtm,"</ul>");
     printf("Problem with Output resultfile: %s\n", filereso);   fflush(fichtm);
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);  }
     goto end;  
   }  /******************* Gnuplot file **************/
   void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){    char dirfileres[132],optfileres[132];
     ungetc(c,ficpar);    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     fgets(line, MAXLINE, ficpar);    int ng;
     puts(line);  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
     fputs(line,ficparo);  /*     printf("Problem with file %s",optionfilegnuplot); */
   }  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   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);    /*#ifdef windows */
   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(ficgp,"cd \"%s\" \n",pathc);
   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);      /*#endif */
 while((c=getc(ficpar))=='#' && c!= EOF){    m=pow(2,cptcoveff);
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    strcpy(dirfileres,optionfilefiname);
     puts(line);    strcpy(optfileres,"vpl");
     fputs(line,ficparo);   /* 1eme*/
   }    for (cpt=1; cpt<= nlstate ; cpt ++) {
   ungetc(c,ficpar);     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);
   covar=matrix(0,NCOVMAX,1,n);       fprintf(ficgp,"set xlabel \"Age\" \n\
   cptcovn=0;  set ylabel \"Probability\" \n\
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;  set ter png small\n\
   set size 0.65,0.65\n\
   ncovmodel=2+cptcovn;  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  
         for (i=1; i<= nlstate ; i ++) {
   /* Read guess parameters */         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   /* Reads comments: lines beginning with '#' */         else fprintf(ficgp," \%%*lf (\%%*lf)");
   while((c=getc(ficpar))=='#' && c!= EOF){       }
     ungetc(c,ficpar);       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);
     fgets(line, MAXLINE, ficpar);       for (i=1; i<= nlstate ; i ++) {
     puts(line);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     fputs(line,ficparo);         else fprintf(ficgp," \%%*lf (\%%*lf)");
   }       } 
   ungetc(c,ficpar);       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
         for (i=1; i<= nlstate ; i ++) {
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     for(i=1; i <=nlstate; i++)         else fprintf(ficgp," \%%*lf (\%%*lf)");
     for(j=1; j <=nlstate+ndeath-1; j++){       }  
       fscanf(ficpar,"%1d%1d",&i1,&j1);       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
       fprintf(ficparo,"%1d%1d",i1,j1);     }
       if(mle==1)    }
         printf("%1d%1d",i,j);    /*2 eme*/
       fprintf(ficlog,"%1d%1d",i,j);    
       for(k=1; k<=ncovmodel;k++){    for (k1=1; k1<= m ; k1 ++) { 
         fscanf(ficpar," %lf",&param[i][j][k]);      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
         if(mle==1){      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
           printf(" %lf",param[i][j][k]);      
           fprintf(ficlog," %lf",param[i][j][k]);      for (i=1; i<= nlstate+1 ; i ++) {
         }        k=2*i;
         else        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
           fprintf(ficlog," %lf",param[i][j][k]);        for (j=1; j<= nlstate+1 ; j ++) {
         fprintf(ficparo," %lf",param[i][j][k]);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       }          else fprintf(ficgp," \%%*lf (\%%*lf)");
       fscanf(ficpar,"\n");        }   
       if(mle==1)        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         printf("\n");        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
       fprintf(ficlog,"\n");        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       fprintf(ficparo,"\n");        for (j=1; j<= nlstate+1 ; j ++) {
     }          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
            else fprintf(ficgp," \%%*lf (\%%*lf)");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;        }   
         fprintf(ficgp,"\" t\"\" w l 0,");
   p=param[1][1];        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
          for (j=1; j<= nlstate+1 ; j ++) {
   /* Reads comments: lines beginning with '#' */          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   while((c=getc(ficpar))=='#' && c!= EOF){          else fprintf(ficgp," \%%*lf (\%%*lf)");
     ungetc(c,ficpar);        }   
     fgets(line, MAXLINE, ficpar);        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
     puts(line);        else fprintf(ficgp,"\" t\"\" w l 0,");
     fputs(line,ficparo);      }
   }    }
   ungetc(c,ficpar);    
     /*3eme*/
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    for (k1=1; k1<= m ; k1 ++) { 
   for(i=1; i <=nlstate; i++){      for (cpt=1; cpt<= nlstate ; cpt ++) {
     for(j=1; j <=nlstate+ndeath-1; j++){        k=2+nlstate*(2*cpt-2);
       fscanf(ficpar,"%1d%1d",&i1,&j1);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
       printf("%1d%1d",i,j);        fprintf(ficgp,"set ter png small\n\
       fprintf(ficparo,"%1d%1d",i1,j1);  set size 0.65,0.65\n\
       for(k=1; k<=ncovmodel;k++){  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         fscanf(ficpar,"%le",&delti3[i][j][k]);        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
         printf(" %le",delti3[i][j][k]);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
         fprintf(ficparo," %le",delti3[i][j][k]);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
       }          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
       fscanf(ficpar,"\n");          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
       printf("\n");          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
       fprintf(ficparo,"\n");          
     }        */
   }        for (i=1; i< nlstate ; i ++) {
   delti=delti3[1][1];          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);
            
   /* Reads comments: lines beginning with '#' */        } 
   while((c=getc(ficpar))=='#' && c!= EOF){      }
     ungetc(c,ficpar);    }
     fgets(line, MAXLINE, ficpar);    
     puts(line);    /* CV preval stable (period) */
     fputs(line,ficparo);    for (k1=1; k1<= m ; k1 ++) { 
   }      for (cpt=1; cpt<=nlstate ; cpt ++) {
   ungetc(c,ficpar);        k=3;
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
   matcov=matrix(1,npar,1,npar);        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   for(i=1; i <=npar; i++){  set ter png small\nset size 0.65,0.65\n\
     fscanf(ficpar,"%s",&str);  unset log y\n\
     if(mle==1)  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
       printf("%s",str);        
     fprintf(ficlog,"%s",str);        for (i=1; i< nlstate ; i ++)
     fprintf(ficparo,"%s",str);          fprintf(ficgp,"+$%d",k+i+1);
     for(j=1; j <=i; j++){        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
       fscanf(ficpar," %le",&matcov[i][j]);        
       if(mle==1){        l=3+(nlstate+ndeath)*cpt;
         printf(" %.5le",matcov[i][j]);        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         fprintf(ficlog," %.5le",matcov[i][j]);        for (i=1; i< nlstate ; i ++) {
       }          l=3+(nlstate+ndeath)*cpt;
       else          fprintf(ficgp,"+$%d",l+i+1);
         fprintf(ficlog," %.5le",matcov[i][j]);        }
       fprintf(ficparo," %.5le",matcov[i][j]);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
     }      } 
     fscanf(ficpar,"\n");    }  
     if(mle==1)    
       printf("\n");    /* proba elementaires */
     fprintf(ficlog,"\n");    for(i=1,jk=1; i <=nlstate; i++){
     fprintf(ficparo,"\n");      for(k=1; k <=(nlstate+ndeath); k++){
   }        if (k != i) {
   for(i=1; i <=npar; i++)          for(j=1; j <=ncovmodel; j++){
     for(j=i+1;j<=npar;j++)            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
       matcov[i][j]=matcov[j][i];            jk++; 
                fprintf(ficgp,"\n");
   if(mle==1)          }
     printf("\n");        }
   fprintf(ficlog,"\n");      }
      }
   
     /*-------- Rewriting paramater file ----------*/     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
      strcpy(rfileres,"r");    /* "Rparameterfile */       for(jk=1; jk <=m; jk++) {
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
      strcat(rfileres,".");    /* */         if (ng==2)
      strcat(rfileres,optionfilext);    /* Other files have txt extension */           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
     if((ficres =fopen(rfileres,"w"))==NULL) {         else
       printf("Problem writing new parameter file: %s\n", fileres);goto end;           fprintf(ficgp,"\nset title \"Probability\"\n");
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
     }         i=1;
     fprintf(ficres,"#%s\n",version);         for(k2=1; k2<=nlstate; k2++) {
               k3=i;
     /*-------- data file ----------*/           for(k=1; k<=(nlstate+ndeath); k++) {
     if((fic=fopen(datafile,"r"))==NULL)    {             if (k != k2){
       printf("Problem with datafile: %s\n", datafile);goto end;               if(ng==2)
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;                 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);
     n= lastobs;               ij=1;
     severity = vector(1,maxwav);               for(j=3; j <=ncovmodel; j++) {
     outcome=imatrix(1,maxwav+1,1,n);                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
     num=ivector(1,n);                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
     moisnais=vector(1,n);                   ij++;
     annais=vector(1,n);                 }
     moisdc=vector(1,n);                 else
     andc=vector(1,n);                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
     agedc=vector(1,n);               }
     cod=ivector(1,n);               fprintf(ficgp,")/(1");
     weight=vector(1,n);               
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */               for(k1=1; k1 <=nlstate; k1++){   
     mint=matrix(1,maxwav,1,n);                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
     anint=matrix(1,maxwav,1,n);                 ij=1;
     s=imatrix(1,maxwav+1,1,n);                 for(j=3; j <=ncovmodel; j++){
     adl=imatrix(1,maxwav+1,1,n);                       if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
     tab=ivector(1,NCOVMAX);                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
     ncodemax=ivector(1,8);                     ij++;
                    }
     i=1;                   else
     while (fgets(line, MAXLINE, fic) != NULL)    {                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
       if ((i >= firstobs) && (i <=lastobs)) {                 }
                         fprintf(ficgp,")");
         for (j=maxwav;j>=1;j--){               }
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
           strcpy(line,stra);               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);               i=i+ncovmodel;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);             }
         }           } /* end k */
                 } /* end k2 */
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);       } /* end jk */
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);     } /* end ng */
      fflush(ficgp); 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);  }  /* end gnuplot */
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);  
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);  /*************** Moving average **************/
         for (j=ncovcol;j>=1;j--){  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }    int i, cpt, cptcod;
         num[i]=atol(stra);    int modcovmax =1;
            int mobilavrange, mob;
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    double age;
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/  
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
         i=i+1;                             a covariate has 2 modalities */
       }    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
     }  
     /* printf("ii=%d", ij);    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
        scanf("%d",i);*/      if(mobilav==1) mobilavrange=5; /* default */
   imx=i-1; /* Number of individuals */      else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
   /* for (i=1; i<=imx; i++){        for (i=1; i<=nlstate;i++)
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;          for (cptcod=1;cptcod<=modcovmax;cptcod++)
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;      /* 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
    /*  for (i=1; i<=imx; i++){         we use a 5 terms etc. until the borders are no more concerned. 
      if (s[4][i]==9)  s[4][i]=-1;      */ 
      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]));}*/      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++){
   /* Calculation of the number of parameter from char model*/            for (cptcod=1;cptcod<=modcovmax;cptcod++){
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
   Tprod=ivector(1,15);                for (cpt=1;cpt<=(mob-1)/2;cpt++){
   Tvaraff=ivector(1,15);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
   Tvard=imatrix(1,15,1,2);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
   Tage=ivector(1,15);                      }
                  mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
   if (strlen(model) >1){            }
     j=0, j1=0, k1=1, k2=1;          }
     j=nbocc(model,'+');        }/* end age */
     j1=nbocc(model,'*');      }/* end mob */
     cptcovn=j+1;    }else return -1;
     cptcovprod=j1;    return 0;
      }/* End movingaverage */
     strcpy(modelsav,model);  
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){  
       printf("Error. Non available option model=%s ",model);  /************** Forecasting ******************/
       fprintf(ficlog,"Error. Non available option model=%s ",model);  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){
       goto end;    /* proj1, year, month, day of starting projection 
     }       agemin, agemax range of age
           dateprev1 dateprev2 range of dates during which prevalence is computed
     for(i=(j+1); i>=1;i--){       anproj2 year of en of projection (same day and month as proj1).
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */    */
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    int *popage;
       /*scanf("%d",i);*/    double agec; /* generic age */
       if (strchr(strb,'*')) {  /* Model includes a product */    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/    double *popeffectif,*popcount;
         if (strcmp(strc,"age")==0) { /* Vn*age */    double ***p3mat;
           cptcovprod--;    double ***mobaverage;
           cutv(strb,stre,strd,'V');    char fileresf[FILENAMELENGTH];
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/  
           cptcovage++;    agelim=AGESUP;
             Tage[cptcovage]=i;    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
             /*printf("stre=%s ", stre);*/   
         }    strcpy(fileresf,"f"); 
         else if (strcmp(strd,"age")==0) { /* or age*Vn */    strcat(fileresf,fileres);
           cptcovprod--;    if((ficresf=fopen(fileresf,"w"))==NULL) {
           cutv(strb,stre,strc,'V');      printf("Problem with forecast resultfile: %s\n", fileresf);
           Tvar[i]=atoi(stre);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
           cptcovage++;    }
           Tage[cptcovage]=i;    printf("Computing forecasting: result on file '%s' \n", fileresf);
         }    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
         else {  /* Age is not in the model */  
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/    if (cptcoveff==0) ncodemax[cptcoveff]=1;
           Tvar[i]=ncovcol+k1;  
           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */    if (mobilav!=0) {
           Tprod[k1]=i;      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           Tvard[k1][1]=atoi(strc); /* m*/      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
           Tvard[k1][2]=atoi(stre); /* n */        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           Tvar[cptcovn+k2]=Tvard[k1][1];        printf(" Error in movingaverage mobilav=%d\n",mobilav);
           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++;    stepsize=(int) (stepm+YEARM-1)/YEARM;
           k2=k2+2;    if (stepm<=12) stepsize=1;
         }    if(estepm < stepm){
       }      printf ("Problem %d lower than %d\n",estepm, stepm);
       else { /* no more sum */    }
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    else  hstepm=estepm;   
        /*  scanf("%d",i);*/  
       cutv(strd,strc,strb,'V');    hstepm=hstepm/stepm; 
       Tvar[i]=atoi(strc);    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
       }                                 fractional in yp1 */
       strcpy(modelsav,stra);      anprojmean=yp;
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    yp2=modf((yp1*12),&yp);
         scanf("%d",i);*/    mprojmean=yp;
     } /* end of loop + */    yp1=modf((yp2*30.5),&yp);
   } /* end model */    jprojmean=yp;
      if(jprojmean==0) jprojmean=1;
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    if(mprojmean==0) jprojmean=1;
   printf("cptcovprod=%d ", cptcovprod);  
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);    i1=cptcoveff;
   scanf("%d ",i);*/    if (cptcovn < 1){i1=1;}
     fclose(fic);    
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     /*  if(mle==1){*/    
     if (weightopt != 1) { /* Maximisation without weights*/    fprintf(ficresf,"#****** Routine prevforecast **\n");
       for(i=1;i<=n;i++) weight[i]=1.0;  
     }  /*            if (h==(int)(YEARM*yearp)){ */
     /*-calculation of age at interview from date of interview and age at death -*/    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
     agev=matrix(1,maxwav,1,imx);      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
     for (i=1; i<=imx; i++) {        fprintf(ficresf,"\n#******");
       for(m=2; (m<= maxwav); m++) {        for(j=1;j<=cptcoveff;j++) {
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){          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]]);
          anint[m][i]=9999;        }
          s[m][i]=-1;        fprintf(ficresf,"******\n");
        }        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;        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 (i=1; i<=imx; i++)  {        }
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
       for(m=1; (m<= maxwav); m++){          fprintf(ficresf,"\n");
         if(s[m][i] >0){          fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
           if (s[m][i] >= nlstate+1) {  
             if(agedc[i]>0)          for (agec=fage; agec>=(ageminpar-1); agec--){ 
               if(moisdc[i]!=99 && andc[i]!=9999)            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
                 agev[m][i]=agedc[i];            nhstepm = nhstepm/hstepm; 
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
            else {            oldm=oldms;savm=savms;
               if (andc[i]!=9999){            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
               printf("Warning negative age at death: %d line:%d\n",num[i],i);          
               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);            for (h=0; h<=nhstepm; h++){
               agev[m][i]=-1;              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]]);
           else if(s[m][i] !=9){ /* Should no more exist */                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);              } 
             if(mint[m][i]==99 || anint[m][i]==9999)              for(j=1; j<=nlstate+ndeath;j++) {
               agev[m][i]=1;                ppij=0.;
             else if(agev[m][i] <agemin){                for(i=1; i<=nlstate;i++) {
               agemin=agev[m][i];                  if (mobilav==1) 
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
             }                  else {
             else if(agev[m][i] >agemax){                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
               agemax=agev[m][i];                  }
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/                  if (h*hstepm/YEARM*stepm== yearp) {
             }                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
             /*agev[m][i]=anint[m][i]-annais[i];*/                  }
             /*   agev[m][i] = age[i]+2*m;*/                } /* end i */
           }                if (h*hstepm/YEARM*stepm==yearp) {
           else { /* =9 */                  fprintf(ficresf," %.3f", ppij);
             agev[m][i]=1;                }
             s[m][i]=-1;              }/* end j */
           }            } /* end h */
         }            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         else /*= 0 Unknown */          } /* end agec */
           agev[m][i]=1;        } /* end yearp */
       }      } /* end cptcod */
        } /* end  cptcov */
     }         
     for (i=1; i<=imx; i++)  {    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(m=1; (m<= maxwav); m++){  
         if (s[m][i] > (nlstate+ndeath)) {    fclose(ficresf);
           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;  /************** 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;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    double calagedatem, agelim, kk1, kk2;
  fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     free_vector(severity,1,maxwav);    double ***mobaverage;
     free_imatrix(outcome,1,maxwav+1,1,n);    char filerespop[FILENAMELENGTH];
     free_vector(moisnais,1,n);  
     free_vector(annais,1,n);    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     /* free_matrix(mint,1,maxwav,1,n);    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        free_matrix(anint,1,maxwav,1,n);*/    agelim=AGESUP;
     free_vector(moisdc,1,n);    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     free_vector(andc,1,n);    
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
        
     wav=ivector(1,imx);    
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    strcpy(filerespop,"pop"); 
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    strcat(filerespop,fileres);
        if((ficrespop=fopen(filerespop,"w"))==NULL) {
     /* Concatenates waves */      printf("Problem with forecast resultfile: %s\n", filerespop);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
       Tcode=ivector(1,100);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);  
       ncodemax[1]=1;    if (cptcoveff==0) ncodemax[cptcoveff]=1;
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);  
          if (mobilav!=0) {
    codtab=imatrix(1,100,1,10);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    h=0;      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
    m=pow(2,cptcoveff);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
          printf(" Error in movingaverage mobilav=%d\n",mobilav);
    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++){    stepsize=(int) (stepm+YEARM-1)/YEARM;
            h++;    if (stepm<=12) stepsize=1;
            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]);*/    agelim=AGESUP;
          }    
        }    hstepm=1;
      }    hstepm=hstepm/stepm; 
    }    
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);    if (popforecast==1) {
       codtab[1][2]=1;codtab[2][2]=2; */      if((ficpop=fopen(popfile,"r"))==NULL) {
    /* for(i=1; i <=m ;i++){        printf("Problem with population file : %s\n",popfile);exit(0);
       for(k=1; k <=cptcovn; k++){        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);      } 
       }      popage=ivector(0,AGESUP);
       printf("\n");      popeffectif=vector(0,AGESUP);
       }      popcount=vector(0,AGESUP);
       scanf("%d",i);*/      
          i=1;   
    /* Calculates basic frequencies. Computes observed prevalence at single age      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
        and prints on file fileres'p'. */     
       imx=i;
          for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
        }
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        k=k+1;
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        fprintf(ficrespop,"\n#******");
              for(j=1;j<=cptcoveff;j++) {
     /* For Powell, parameters are in a vector p[] starting at p[1]          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
        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) */        fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
     if(mle==1){        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        if (popforecast==1)  fprintf(ficrespop," [Population]");
     }        
            for (cpt=0; cpt<=0;cpt++) { 
     /*--------- results files --------------*/          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);          
            for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
    jk=1;            nhstepm = nhstepm/hstepm; 
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");            
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");            oldm=oldms;savm=savms;
    for(i=1,jk=1; i <=nlstate; i++){            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
      for(k=1; k <=(nlstate+ndeath); k++){          
        if (k != i)            for (h=0; h<=nhstepm; h++){
          {              if (h==(int) (calagedatem+YEARM*cpt)) {
            printf("%d%d ",i,k);                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
            fprintf(ficlog,"%d%d ",i,k);              } 
            fprintf(ficres,"%1d%1d ",i,k);              for(j=1; j<=nlstate+ndeath;j++) {
            for(j=1; j <=ncovmodel; j++){                kk1=0.;kk2=0;
              printf("%f ",p[jk]);                for(i=1; i<=nlstate;i++) {              
              fprintf(ficlog,"%f ",p[jk]);                  if (mobilav==1) 
              fprintf(ficres,"%f ",p[jk]);                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
              jk++;                  else {
            }                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
            printf("\n");                  }
            fprintf(ficlog,"\n");                }
            fprintf(ficres,"\n");                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]);*/
    if(mle==1){                }
      /* Computing hessian and covariance matrix */              }
      ftolhess=ftol; /* Usually correct */              for(i=1; i<=nlstate;i++){
      hesscov(matcov, p, npar, delti, ftolhess, func);                kk1=0.;
    }                  for(j=1; j<=nlstate;j++){
    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
    printf("# Scales (for hessian or gradient estimation)\n");                  }
    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
    for(i=1,jk=1; i <=nlstate; i++){              }
      for(j=1; j <=nlstate+ndeath; j++){  
        if (j!=i) {              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
          fprintf(ficres,"%1d%1d",i,j);                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
          printf("%1d%1d",i,j);            }
          fprintf(ficlog,"%1d%1d",i,j);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
          for(k=1; k<=ncovmodel;k++){          }
            printf(" %.5e",delti[jk]);        }
            fprintf(ficlog," %.5e",delti[jk]);   
            fprintf(ficres," %.5e",delti[jk]);    /******/
            jk++;  
          }        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
          printf("\n");          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
          fprintf(ficlog,"\n");          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
          fprintf(ficres,"\n");            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
        }            nhstepm = nhstepm/hstepm; 
      }            
    }            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                oldm=oldms;savm=savms;
    k=1;            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
    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");            for (h=0; h<=nhstepm; h++){
    if(mle==1)              if (h==(int) (calagedatem+YEARM*cpt)) {
      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(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
    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;i<=npar;i++){              for(j=1; j<=nlstate+ndeath;j++) {
      /*  if (k>nlstate) k=1;                kk1=0.;kk2=0;
          i1=(i-1)/(ncovmodel*nlstate)+1;                for(i=1; i<=nlstate;i++) {              
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
          printf("%s%d%d",alph[k],i1,tab[i]);*/                }
      fprintf(ficres,"%3d",i);                if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
      if(mle==1)              }
        printf("%3d",i);            }
      fprintf(ficlog,"%3d",i);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      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]);   
      }    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      fprintf(ficres,"\n");  
      if(mle==1)    if (popforecast==1) {
        printf("\n");      free_ivector(popage,0,AGESUP);
      fprintf(ficlog,"\n");      free_vector(popeffectif,0,AGESUP);
      k++;      free_vector(popcount,0,AGESUP);
    }    }
        free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    while((c=getc(ficpar))=='#' && c!= EOF){    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
      ungetc(c,ficpar);    fclose(ficrespop);
      fgets(line, MAXLINE, ficpar);  } /* End of popforecast */
      puts(line);  
      fputs(line,ficparo);  int fileappend(FILE *fichier, char *optionfich)
    }  {
    ungetc(c,ficpar);    if((fichier=fopen(optionfich,"a"))==NULL) {
    estepm=0;      printf("Problem with file: %s\n", optionfich);
    fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);      fprintf(ficlog,"Problem with file: %s\n", optionfich);
    if (estepm==0 || estepm < stepm) estepm=stepm;      return (0);
    if (fage <= 2) {    }
      bage = ageminpar;    fflush(fichier);
      fage = agemaxpar;    return (1);
    }  }
      void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
    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);    char ca[32], cb[32], cc[32];
        int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
    while((c=getc(ficpar))=='#' && c!= EOF){    int numlinepar;
      ungetc(c,ficpar);  
      fgets(line, MAXLINE, ficpar);    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
      puts(line);    fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
      fputs(line,ficparo);    for(i=1; i <=nlstate; i++){
    }      jj=0;
    ungetc(c,ficpar);      for(j=1; j <=nlstate+ndeath; j++){
          if(j==i) continue;
    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);        jj++;
    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        /*ca[0]= k+'a'-1;ca[1]='\0';*/
    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        printf("%1d%1d",i,j);
            fprintf(ficparo,"%1d%1d",i,j);
    while((c=getc(ficpar))=='#' && c!= EOF){        for(k=1; k<=ncovmodel;k++){
      ungetc(c,ficpar);          /*        printf(" %lf",param[i][j][k]); */
      fgets(line, MAXLINE, ficpar);          /*        fprintf(ficparo," %lf",param[i][j][k]); */
      puts(line);          printf(" 0.");
      fputs(line,ficparo);          fprintf(ficparo," 0.");
    }        }
    ungetc(c,ficpar);        printf("\n");
          fprintf(ficparo,"\n");
       }
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    }
    dateprev2=anprev2+mprev2/12.+jprev2/365.;    printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
   fscanf(ficpar,"pop_based=%d\n",&popbased);    npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
   fprintf(ficparo,"pop_based=%d\n",popbased);      for(i=1; i <=nlstate; i++){
   fprintf(ficres,"pop_based=%d\n",popbased);        jj=0;
        for(j=1; j <=nlstate+ndeath; j++){
   while((c=getc(ficpar))=='#' && c!= EOF){        if(j==i) continue;
     ungetc(c,ficpar);        jj++;
     fgets(line, MAXLINE, ficpar);        fprintf(ficparo,"%1d%1d",i,j);
     puts(line);        printf("%1d%1d",i,j);
     fputs(line,ficparo);        fflush(stdout);
   }        for(k=1; k<=ncovmodel;k++){
   ungetc(c,ficpar);          /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);          printf(" 0.");
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);          fprintf(ficparo," 0.");
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);        }
         numlinepar++;
         printf("\n");
 while((c=getc(ficpar))=='#' && c!= EOF){        fprintf(ficparo,"\n");
     ungetc(c,ficpar);      }
     fgets(line, MAXLINE, ficpar);    }
     puts(line);    printf("# Covariance matrix\n");
     fputs(line,ficparo);  /* # 121 Var(a12)\n\ */
   }  /* # 122 Cov(b12,a12) Var(b12)\n\ */
   ungetc(c,ficpar);  /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);  /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);  /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);  /* # 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" */
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
 /*------------ gnuplot -------------*/    /* # 121 Var(a12)\n\ */
   strcpy(optionfilegnuplot,optionfilefiname);    /* # 122 Cov(b12,a12) Var(b12)\n\ */
   strcat(optionfilegnuplot,".gp");    /* #   ...\n\ */
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     printf("Problem with file %s",optionfilegnuplot);    
   }    for(itimes=1;itimes<=2;itimes++){
   fclose(ficgp);      jj=0;
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);      for(i=1; i <=nlstate; i++){
 /*--------- index.htm --------*/        for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
   strcpy(optionfilehtm,optionfile);          for(k=1; k<=ncovmodel;k++){
   strcat(optionfilehtm,".htm");            jj++;
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {            ca[0]= k+'a'-1;ca[1]='\0';
     printf("Problem with %s \n",optionfilehtm), exit(0);            if(itimes==1){
   }              printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n            }else{
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n              printf("%1d%1d%d",i,j,k);
 \n              fprintf(ficparo,"%1d%1d%d",i,j,k);
 Total number of observations=%d <br>\n              /*  printf(" %.5le",matcov[i][j]); */
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n            }
 <hr  size=\"2\" color=\"#EC5E5E\">            ll=0;
  <ul><li><h4>Parameter files</h4>\n            for(li=1;li <=nlstate; li++){
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n              for(lj=1;lj <=nlstate+ndeath; lj++){
  - Log file of the run: <a href=\"%s\">%s</a><br>\n                if(lj==li) continue;
  - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);                for(lk=1;lk<=ncovmodel;lk++){
   fclose(fichtm);                  ll++;
                   if(ll<=jj){
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);                    cb[0]= lk +'a'-1;cb[1]='\0';
                      if(ll<jj){
 /*------------ free_vector  -------------*/                      if(itimes==1){
  chdir(path);                        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);
  free_ivector(wav,1,imx);                      }else{
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);                        printf(" 0.");
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);                          fprintf(ficparo," 0.");
  free_ivector(num,1,n);                      }
  free_vector(agedc,1,n);                    }else{
  /*free_matrix(covar,1,NCOVMAX,1,n);*/                      if(itimes==1){
  fclose(ficparo);                        printf(" Var(%s%1d%1d)",ca,i,j);
  fclose(ficres);                        fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
   /*--------------- Prevalence limit --------------*/                        fprintf(ficparo," 0.");
                        }
   strcpy(filerespl,"pl");                    }
   strcat(filerespl,fileres);                  }
   if((ficrespl=fopen(filerespl,"w"))==NULL) {                } /* end lk */
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;              } /* end lj */
     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;            } /* end li */
   }            printf("\n");
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);            fprintf(ficparo,"\n");
   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);            numlinepar++;
   fprintf(ficrespl,"#Prevalence limit\n");          } /* end k*/
   fprintf(ficrespl,"#Age ");        } /*end j */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      } /* end i */
   fprintf(ficrespl,"\n");    }
    
   prlim=matrix(1,nlstate,1,nlstate);  } /* end of prwizard */
   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 */  /**************** Main Program *****************/
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  /***********************************************/
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
   k=0;  int main(int argc, char *argv[])
   agebase=ageminpar;  {
   agelim=agemaxpar;    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
   ftolpl=1.e-10;    int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
   i1=cptcoveff;    int jj, imk;
   if (cptcovn < 1){i1=1;}    int numlinepar=0; /* Current linenumber of parameter file */
     /*  FILE *fichtm; *//* Html File */
   for(cptcov=1;cptcov<=i1;cptcov++){    /* FILE *ficgp;*/ /*Gnuplot File */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    double agedeb, agefin,hf;
         k=k+1;    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/  
         fprintf(ficrespl,"\n#******");    double fret;
         printf("\n#******");    double **xi,tmp,delta;
         fprintf(ficlog,"\n#******");  
         for(j=1;j<=cptcoveff;j++) {    double dum; /* Dummy variable */
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double ***p3mat;
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double ***mobaverage;
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    int *indx;
         }    char line[MAXLINE], linepar[MAXLINE];
         fprintf(ficrespl,"******\n");    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
         printf("******\n");    char pathr[MAXLINE]; 
         fprintf(ficlog,"******\n");    int firstobs=1, lastobs=10;
            int sdeb, sfin; /* Status at beginning and end */
         for (age=agebase; age<=agelim; age++){    int c,  h , cpt,l;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    int ju,jl, mi;
           fprintf(ficrespl,"%.0f",age );    int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
           for(i=1; i<=nlstate;i++)    int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
           fprintf(ficrespl," %.5f", prlim[i][i]);    int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
           fprintf(ficrespl,"\n");    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;
   fclose(ficrespl);  
     double bage, fage, age, agelim, agebase;
   /*------------- h Pij x at various ages ------------*/    double ftolpl=FTOL;
      double **prlim;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    double *severity;
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    double ***param; /* Matrix of parameters */
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    double  *p;
     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;    double **matcov; /* Matrix of covariance */
   }    double ***delti3; /* Scale */
   printf("Computing pij: result on file '%s' \n", filerespij);    double *delti; /* Scale */
   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);    double ***eij, ***vareij;
      double **varpl; /* Variances of prevalence limits by age */
   stepsize=(int) (stepm+YEARM-1)/YEARM;    double *epj, vepp;
   /*if (stepm<=24) stepsize=2;*/    double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   agelim=AGESUP;  
   hstepm=stepsize*YEARM; /* Every year of age */    char *alph[]={"a","a","b","c","d","e"}, str[4];
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */  
   
   /* hstepm=1;   aff par mois*/    char z[1]="c", occ;
   
   k=0;    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
   for(cptcov=1;cptcov<=i1;cptcov++){    char strstart[80], *strt, strtend[80];
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    char *stratrunc;
       k=k+1;    int lstra;
         fprintf(ficrespij,"\n#****** ");  
         for(j=1;j<=cptcoveff;j++)    long total_usecs;
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    struct timeval start_time, end_time, curr_time;
         fprintf(ficrespij,"******\n");    struct timezone tzp;
            extern int gettimeofday();
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    struct tm tmg, tm, *gmtime(), *localtime();
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    long time_value;
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    extern long time();
    
           /*      nhstepm=nhstepm*YEARM; aff par mois*/    /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    tm = *localtime(&start_time.tv_sec);
           oldm=oldms;savm=savms;    tmg = *gmtime(&start_time.tv_sec);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      strcpy(strstart,asctime(&tm));
           fprintf(ficrespij,"# Age");  
           for(i=1; i<=nlstate;i++)  /*  printf("Localtime (at start)=%s",strstart); */
             for(j=1; j<=nlstate+ndeath;j++)  /*  tp.tv_sec = tp.tv_sec +86400; */
               fprintf(ficrespij," %1d-%1d",i,j);  /*  tm = *localtime(&start_time.tv_sec); */
           fprintf(ficrespij,"\n");  /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
            for (h=0; h<=nhstepm; h++){  /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  /*   tmg.tm_hour=tmg.tm_hour + 1; */
             for(i=1; i<=nlstate;i++)  /*   tp.tv_sec = mktime(&tmg); */
               for(j=1; j<=nlstate+ndeath;j++)  /*   strt=asctime(&tmg); */
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);  /*   printf("Time(after) =%s",strstart);  */
             fprintf(ficrespij,"\n");  /*  (void) time (&time_value);
              }  *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  *  tm = *localtime(&time_value);
           fprintf(ficrespij,"\n");  *  strstart=asctime(&tm);
         }  *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
     }  */
   }  
     getcwd(pathcd, size);
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);  
     printf("\n%s\n%s",version,fullversion);
   fclose(ficrespij);    if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
   /*---------- Forecasting ------------------*/    }
   if((stepm == 1) && (strcmp(model,".")==0)){    else{
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);      strcpy(pathtot,argv[1]);
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    }
   }    /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
   else{    /*cygwin_split_path(pathtot,path,optionfile);
     erreur=108;      printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     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);    /* cutv(path,optionfile,pathtot,'\\');*/
     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);  
   }    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);
   /*---------- Health expectancies and variances ------------*/    strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
   strcpy(filerest,"t");    if((outcmd=system(command)) != 0){
   strcat(filerest,fileres);      printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
   if((ficrest=fopen(filerest,"w"))==NULL) {      /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;      /* fclose(ficlog); */
     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;  /*     exit(1); */
   }    }
   printf("Computing Total LEs with variances: file '%s' \n", filerest);  /*   if((imk=mkdir(optionfilefiname))<0){ */
   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);  /*     perror("mkdir"); */
   /*   } */
   
   strcpy(filerese,"e");    /*-------- arguments in the command line --------*/
   strcat(filerese,fileres);  
   if((ficreseij=fopen(filerese,"w"))==NULL) {    /* Log file */
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    strcat(filelog, optionfilefiname);
     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    strcat(filelog,".log");    /* */
   }    if((ficlog=fopen(filelog,"w"))==NULL)    {
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      printf("Problem with logfile %s\n",filelog);
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);      goto end;
     }
   strcpy(fileresv,"v");    fprintf(ficlog,"Log filename:%s\n",filelog);
   strcat(fileresv,fileres);    fprintf(ficlog,"\n%s\n%s",version,fullversion);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    fprintf(ficlog,"\nEnter the parameter file name: ");
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    fprintf(ficlog,"pathtot=%s\n\
     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);   path=%s \n\
   }   optionfile=%s\n\
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);   optionfilext=%s\n\
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);   optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   calagedate=-1;  
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    printf("Localtime (at start):%s",strstart);
     fprintf(ficlog,"Localtime (at start): %s",strstart);
   k=0;    fflush(ficlog);
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    /* */
       k=k+1;    strcpy(fileres,"r");
       fprintf(ficrest,"\n#****** ");    strcat(fileres, optionfilefiname);
       for(j=1;j<=cptcoveff;j++)    strcat(fileres,".txt");    /* Other files have txt extension */
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficrest,"******\n");    /*---------arguments file --------*/
   
       fprintf(ficreseij,"\n#****** ");    if((ficpar=fopen(optionfile,"r"))==NULL)    {
       for(j=1;j<=cptcoveff;j++)      printf("Problem with optionfile %s\n",optionfile);
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fprintf(ficreseij,"******\n");      fflush(ficlog);
       goto end;
       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");  
     strcpy(filereso,"o");
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    strcat(filereso,fileres);
       oldm=oldms;savm=savms;    if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);        printf("Problem with Output resultfile: %s\n", filereso);
        fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);      fflush(ficlog);
       oldm=oldms;savm=savms;      goto end;
       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0);    }
       if(popbased==1){  
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);    /* Reads comments: lines beginning with '#' */
        }    numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
        ungetc(c,ficpar);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      fgets(line, MAXLINE, ficpar);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      numlinepar++;
       fprintf(ficrest,"\n");      puts(line);
       fputs(line,ficparo);
       epj=vector(1,nlstate+1);      fputs(line,ficlog);
       for(age=bage; age <=fage ;age++){    }
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    ungetc(c,ficpar);
         if (popbased==1) {  
           for(i=1; i<=nlstate;i++)    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);
             prlim[i][i]=probs[(int)age][i][k];    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(ficrest," %4.0f",age);    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);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    fflush(ficlog);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    while((c=getc(ficpar))=='#' && c!= EOF){
             epj[j] += prlim[i][i]*eij[i][j][(int)age];      ungetc(c,ficpar);
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/      fgets(line, MAXLINE, ficpar);
           }      numlinepar++;
           epj[nlstate+1] +=epj[j];      puts(line);
         }      fputs(line,ficparo);
       fputs(line,ficlog);
         for(i=1, vepp=0.;i <=nlstate;i++)    }
           for(j=1;j <=nlstate;j++)    ungetc(c,ficpar);
             vepp += vareij[i][j][(int)age];  
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));     
         for(j=1;j <=nlstate;j++){    covar=matrix(0,NCOVMAX,1,n); 
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
         }    if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
         fprintf(ficrest,"\n");  
       }    ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     }    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
   }   
 free_matrix(mint,1,maxwav,1,n);    if(mle==-1){ /* Print a wizard for help writing covariance matrix */
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
     free_vector(weight,1,n);      printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
   fclose(ficreseij);      fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
   fclose(ficresvij);      fclose (ficparo);
   fclose(ficrest);      fclose (ficlog);
   fclose(ficpar);      exit(0);
   free_vector(epj,1,nlstate+1);    }
      /* Read guess parameters */
   /*------- Variance limit prevalence------*/      /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
   strcpy(fileresvpl,"vpl");      ungetc(c,ficpar);
   strcat(fileresvpl,fileres);      fgets(line, MAXLINE, ficpar);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {      numlinepar++;
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);      puts(line);
     exit(0);      fputs(line,ficparo);
   }      fputs(line,ficlog);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    }
     ungetc(c,ficpar);
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){    param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    for(i=1; i <=nlstate; i++){
       k=k+1;      j=0;
       fprintf(ficresvpl,"\n#****** ");      for(jj=1; jj <=nlstate+ndeath; jj++){
       for(j=1;j<=cptcoveff;j++)        if(jj==i) continue;
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        j++;
       fprintf(ficresvpl,"******\n");        fscanf(ficpar,"%1d%1d",&i1,&j1);
              if ((i1 != i) && (j1 != j)){
       varpl=matrix(1,nlstate,(int) bage, (int) fage);          printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
       oldm=oldms;savm=savms;          exit(1);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        }
     }        fprintf(ficparo,"%1d%1d",i1,j1);
  }        if(mle==1)
           printf("%1d%1d",i,j);
   fclose(ficresvpl);        fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
   /*---------- End : free ----------------*/          fscanf(ficpar," %lf",&param[i][j][k]);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);          if(mle==1){
              printf(" %lf",param[i][j][k]);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);            fprintf(ficlog," %lf",param[i][j][k]);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);          }
            else
              fprintf(ficlog," %lf",param[i][j][k]);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);          fprintf(ficparo," %lf",param[i][j][k]);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);        }
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);        fscanf(ficpar,"\n");
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);        numlinepar++;
          if(mle==1)
   free_matrix(matcov,1,npar,1,npar);          printf("\n");
   free_vector(delti,1,npar);        fprintf(ficlog,"\n");
   free_matrix(agev,1,maxwav,1,imx);        fprintf(ficparo,"\n");
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      }
     }  
   fprintf(fichtm,"\n</body>");    fflush(ficlog);
   fclose(fichtm);  
   fclose(ficgp);    npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
    
     p=param[1][1];
   if(erreur >0){    
     printf("End of Imach with error or warning %d\n",erreur);    /* Reads comments: lines beginning with '#' */
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);    while((c=getc(ficpar))=='#' && c!= EOF){
   }else{      ungetc(c,ficpar);
    printf("End of Imach\n");      fgets(line, MAXLINE, ficpar);
    fprintf(ficlog,"End of Imach\n");      numlinepar++;
   }      puts(line);
   printf("See log file on %s\n",filelog);      fputs(line,ficparo);
   fclose(ficlog);      fputs(line,ficlog);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    }
      ungetc(c,ficpar);
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/  
   /*printf("Total time was %d uSec.\n", total_usecs);*/    delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
   /*------ End -----------*/    /* 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++){
  end:        fscanf(ficpar,"%1d%1d",&i1,&j1);
 #ifdef windows        if ((i1-i)*(j1-j)!=0){
   /* chdir(pathcd);*/          printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
 #endif          exit(1);
  /*system("wgnuplot graph.plt");*/        }
  /*system("../gp37mgw/wgnuplot graph.plt");*/        printf("%1d%1d",i,j);
  /*system("cd ../gp37mgw");*/        fprintf(ficparo,"%1d%1d",i1,j1);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/        fprintf(ficlog,"%1d%1d",i1,j1);
  strcpy(plotcmd,GNUPLOTPROGRAM);        for(k=1; k<=ncovmodel;k++){
  strcat(plotcmd," ");          fscanf(ficpar,"%le",&delti3[i][j][k]);
  strcat(plotcmd,optionfilegnuplot);          printf(" %le",delti3[i][j][k]);
  system(plotcmd);          fprintf(ficparo," %le",delti3[i][j][k]);
           fprintf(ficlog," %le",delti3[i][j][k]);
 #ifdef windows        }
   while (z[0] != 'q') {        fscanf(ficpar,"\n");
     /* chdir(path); */        numlinepar++;
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");        printf("\n");
     scanf("%s",z);        fprintf(ficparo,"\n");
     if (z[0] == 'c') system("./imach");        fprintf(ficlog,"\n");
     else if (z[0] == 'e') system(optionfilehtm);      }
     else if (z[0] == 'g') system(plotcmd);    }
     else if (z[0] == 'q') exit(0);    fflush(ficlog);
   }  
 #endif    delti=delti3[1][1];
 }  
   
     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);
       if(mle==1)
         printf("%s",str);
       fprintf(ficlog,"%s",str);
       fprintf(ficparo,"%s",str);
       for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
           printf(" %.5le",matcov[i][j]);
         }
         fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       numlinepar++;
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
     for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];
      
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
   
     fflush(ficlog);
   
     /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         lstra=strlen(stra);
         if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
           stratrunc = &(stra[lstra-9]);
           num[i]=atol(stratrunc);
         }
         else
           num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt,\
             model,fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     /*fclose(fichtm);*/
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     strcpy(lfileres,fileres);
     strcat(lfileres,"/");
     strcat(lfileres,optionfilefiname);
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);
     printf("\n");
     globpr=1; /* to print the contributions */
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);
     printf("\n");
     if(mle>=1){ /* Could be 1 or 2 */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
       
     /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
     jk=1;
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) 
           {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
       }
     }
     if(mle!=0){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);
             jk++;
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle==1)
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     for(i=1,k=1;i<=npar;i++){
       /*  if (k>nlstate) k=1;
           i1=(i-1)/(ncovmodel*nlstate)+1; 
           fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);
           printf("%s%d%d",alph[k],i1,tab[i]);
       */
       fprintf(ficres,"%3d",i);
       if(mle==1)
         printf("%3d",i);
       fprintf(ficlog,"%3d",i);
       for(j=1; j<=i;j++){
         fprintf(ficres," %.5e",matcov[i][j]);
         if(mle==1)
           printf(" %.5e",matcov[i][j]);
         fprintf(ficlog," %.5e",matcov[i][j]);
       }
       fprintf(ficres,"\n");
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       k++;
     }
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   
     replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     /*  chdir(path); */
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_lvector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
   /*      }  */
   /*      else{ */
   /*        erreur=108; */
   /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*      } */
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     fflush(fichtm);
     fflush(ficgp);
     
   
     if(erreur >0){
       printf("End of Imach with error or warning %d\n",erreur);
       fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);
     }else{
      printf("End of Imach\n");
      fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     fclose(ficlog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Localtime at start %s\nLocaltime at end   %s",strstart, strtend); 
     fprintf(ficlog,"Localtime at start %s\nLocal time at end   %s",strstart, strtend); 
     /*  printf("Total time used %d Sec\n", asc_time(end_time.tv_sec -start_time.tv_sec);*/
   
     printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
     fprintf(ficlog,"Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
     fclose(fichtm);
     fclose(ficgp);
     /*------ End -----------*/
   
     end:
   #ifdef windows
     /* chdir(pathcd);*/
   #endif 
     chdir(path);
    /*system("wgnuplot graph.plt");*/
    /*system("../gp37mgw/wgnuplot graph.plt");*/
    /*system("cd ../gp37mgw");*/
    /* system("..\\gp37mgw\\wgnuplot graph.plt");*/
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     system(plotcmd);
     printf(" Wait...");
   
    /*#ifdef windows*/
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");
       scanf("%s",z);
       if (z[0] == 'c') system("./imach");
       else if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     /*#endif */
   }
   
   
   

Removed from v.1.51  
changed lines
  Added in v.1.89


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