Diff for /imach/src/imach.c between versions 1.47 and 1.90

version 1.47, 2002/06/10 13:12:01 version 1.90, 2003/06/24 12:34:15
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.90  2003/06/24 12:34:15  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 1.89  2003/06/24 12:30:52  brouard
   case of a health survey which is our main interest) -2- at least a    (Module): Some bugs corrected for windows. Also, when
   second wave of interviews ("longitudinal") which measure each change    mle=-1 a template is output in file "or"mypar.txt with the design
   (if any) in individual health status.  Health expectancies are    of the covariance matrix to be input.
   computed from the time spent in each health state according to a  
   model. More health states you consider, more time is necessary to reach the    Revision 1.88  2003/06/23 17:54:56  brouard
   Maximum Likelihood of the parameters involved in the model.  The    * 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.
   simplest model is the multinomial logistic model where pij is the  
   probability to be observed in state j at the second wave    Revision 1.87  2003/06/18 12:26:01  brouard
   conditional to be observed in state i at the first wave. Therefore    Version 0.96
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where  
   'age' is age and 'sex' is a covariate. If you want to have a more    Revision 1.86  2003/06/17 20:04:08  brouard
   complex model than "constant and age", you should modify the program    (Module): Change position of html and gnuplot routines and added
   where the markup *Covariates have to be included here again* invites    routine fileappend.
   you to do it.  More covariates you add, slower the  
   convergence.    Revision 1.85  2003/06/17 13:12:43  brouard
     * imach.c (Repository): Check when date of death was earlier that
   The advantage of this computer programme, compared to a simple    current date of interview. It may happen when the death was just
   multinomial logistic model, is clear when the delay between waves is not    prior to the death. In this case, dh was negative and likelihood
   identical for each individual. Also, if a individual missed an    was wrong (infinity). We still send an "Error" but patch by
   intermediate interview, the information is lost, but taken into    assuming that the date of death was just one stepm after the
   account using an interpolation or extrapolation.      interview.
     (Repository): Because some people have very long ID (first column)
   hPijx is the probability to be observed in state i at age x+h    we changed int to long in num[] and we added a new lvector for
   conditional to the observed state i at age x. The delay 'h' can be    memory allocation. But we also truncated to 8 characters (left
   split into an exact number (nh*stepm) of unobserved intermediate    truncation)
   states. This elementary transition (by month or quarter trimester,    (Repository): No more line truncation errors.
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.84  2003/06/13 21:44:43  brouard
   and the contribution of each individual to the likelihood is simply    * imach.c (Repository): Replace "freqsummary" at a correct
   hPijx.    place. It differs from routine "prevalence" which may be called
     many times. Probs is memory consuming and must be used with
   Also this programme outputs the covariance matrix of the parameters but also    parcimony.
   of the life expectancies. It also computes the prevalence limits.    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Revision 1.83  2003/06/10 13:39:11  lievre
            Institut national d'études démographiques, Paris.    *** empty log message ***
   This software have been partly granted by Euro-REVES, a concerted action  
   from the European Union.    Revision 1.82  2003/06/05 15:57:20  brouard
   It is copyrighted identically to a GNU software product, ie programme and    Add log in  imach.c and  fullversion number is now printed.
   software can be distributed freely for non commercial use. Latest version  
   can be accessed at http://euroreves.ined.fr/imach .  */
   **********************************************************************/  /*
       Interpolated Markov Chain
 #include <math.h>  
 #include <stdio.h>    Short summary of the programme:
 #include <stdlib.h>    
 #include <unistd.h>    This program computes Healthy Life Expectancies from
     cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 #define MAXLINE 256    first survey ("cross") where individuals from different ages are
 #define GNUPLOTPROGRAM "gnuplot"    interviewed on their health status or degree of disability (in the
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    case of a health survey which is our main interest) -2- at least a
 #define FILENAMELENGTH 80    second wave of interviews ("longitudinal") which measure each change
 /*#define DEBUG*/    (if any) in individual health status.  Health expectancies are
 #define windows    computed from the time spent in each health state according to a
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    model. More health states you consider, more time is necessary to reach the
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Maximum Likelihood of the parameters involved in the model.  The
     simplest model is the multinomial logistic model where pij is the
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    probability to be observed in state j at the second wave
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    conditional to be observed in state i at the first wave. Therefore
     the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 #define NINTERVMAX 8    'age' is age and 'sex' is a covariate. If you want to have a more
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    complex model than "constant and age", you should modify the program
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    where the markup *Covariates have to be included here again* invites
 #define NCOVMAX 8 /* Maximum number of covariates */    you to do it.  More covariates you add, slower the
 #define MAXN 20000    convergence.
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    The advantage of this computer programme, compared to a simple
 #define AGEBASE 40    multinomial logistic model, is clear when the delay between waves is not
 #ifdef windows    identical for each individual. Also, if a individual missed an
 #define DIRSEPARATOR '\\'    intermediate interview, the information is lost, but taken into
 #else    account using an interpolation or extrapolation.  
 #define DIRSEPARATOR '/'  
 #endif    hPijx is the probability to be observed in state i at age x+h
     conditional to the observed state i at age x. The delay 'h' can be
 char version[80]="Imach version 0.8g, May 2002, INED-EUROREVES ";    split into an exact number (nh*stepm) of unobserved intermediate
 int erreur; /* Error number */    states. This elementary transition (by month, quarter,
 int nvar;    semester or year) is modelled as a multinomial logistic.  The hPx
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    matrix is simply the matrix product of nh*stepm elementary matrices
 int npar=NPARMAX;    and the contribution of each individual to the likelihood is simply
 int nlstate=2; /* Number of live states */    hPijx.
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Also this programme outputs the covariance matrix of the parameters but also
 int popbased=0;    of the life expectancies. It also computes the stable prevalence. 
     
 int *wav; /* Number of waves for this individuual 0 is possible */    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 int maxwav; /* Maxim number of waves */             Institut national d'études démographiques, Paris.
 int jmin, jmax; /* min, max spacing between 2 waves */    This software have been partly granted by Euro-REVES, a concerted action
 int mle, weightopt;    from the European Union.
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    It is copyrighted identically to a GNU software product, ie programme and
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    software can be distributed freely for non commercial use. Latest version
 double jmean; /* Mean space between 2 waves */    can be accessed at http://euroreves.ined.fr/imach .
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;    
 FILE *fichtm; /* Html File */    **********************************************************************/
 FILE *ficreseij;  /*
 char filerese[FILENAMELENGTH];    main
 FILE  *ficresvij;    read parameterfile
 char fileresv[FILENAMELENGTH];    read datafile
 FILE  *ficresvpl;    concatwav
 char fileresvpl[FILENAMELENGTH];    freqsummary
 char title[MAXLINE];    if (mle >= 1)
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];      mlikeli
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    print results files
     if mle==1 
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];       computes hessian
     read end of parameter file: agemin, agemax, bage, fage, estepm
 char filerest[FILENAMELENGTH];        begin-prev-date,...
 char fileregp[FILENAMELENGTH];    open gnuplot file
 char popfile[FILENAMELENGTH];    open html file
     stable prevalence
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];     for age prevalim()
     h Pij x
 #define NR_END 1    variance of p varprob
 #define FREE_ARG char*    forecasting if prevfcast==1 prevforecast call prevalence()
 #define FTOL 1.0e-10    health expectancies
     Variance-covariance of DFLE
 #define NRANSI    prevalence()
 #define ITMAX 200     movingaverage()
     varevsij() 
 #define TOL 2.0e-4    if popbased==1 varevsij(,popbased)
     total life expectancies
 #define CGOLD 0.3819660    Variance of stable prevalence
 #define ZEPS 1.0e-10   end
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  */
   
 #define GOLD 1.618034  
 #define GLIMIT 100.0  
 #define TINY 1.0e-20   
   #include <math.h>
 static double maxarg1,maxarg2;  #include <stdio.h>
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  #include <stdlib.h>
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  #include <unistd.h>
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))  #include <sys/time.h>
 #define rint(a) floor(a+0.5)  #include <time.h>
   #include "timeval.h"
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  #define MAXLINE 256
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  #define GNUPLOTPROGRAM "gnuplot"
   /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 int imx;  #define FILENAMELENGTH 132
 int stepm;  /*#define DEBUG*/
 /* Stepm, step in month: minimum step interpolation*/  /*#define windows*/
   #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 int estepm;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  
   #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 int m,nb;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  #define NINTERVMAX 8
 double **pmmij, ***probs, ***mobaverage;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 double dateintmean=0;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   #define NCOVMAX 8 /* Maximum number of covariates */
 double *weight;  #define MAXN 20000
 int **s; /* Status */  #define YEARM 12. /* Number of months per year */
 double *agedc, **covar, idx;  #define AGESUP 130
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  #define AGEBASE 40
   #ifdef unix
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  #define DIRSEPARATOR '/'
 double ftolhess; /* Tolerance for computing hessian */  #define ODIRSEPARATOR '\\'
   #else
 /**************** split *************************/  #define DIRSEPARATOR '\\'
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  #define ODIRSEPARATOR '/'
 {  #endif
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */  /* $Id$ */
   /* $State$ */
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  char version[]="Imach version 0.96a, June 2003, INED-EUROREVES ";
    s = strrchr( path,  DIRSEPARATOR );          /* find last / */  char fullversion[]="$Revision$ $Date$"; 
    if ( s == NULL ) {                   /* no directory, so use current */  int erreur; /* Error number */
 #if     defined(__bsd__)                /* get current working directory */  int nvar;
       extern char       *getwd( );  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   int npar=NPARMAX;
       if ( getwd( dirc ) == NULL ) {  int nlstate=2; /* Number of live states */
 #else  int ndeath=1; /* Number of dead states */
       extern char       *getcwd( );  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int popbased=0;
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif  int *wav; /* Number of waves for this individuual 0 is possible */
          return( GLOCK_ERROR_GETCWD );  int maxwav; /* Maxim number of waves */
       }  int jmin, jmax; /* min, max spacing between 2 waves */
       strcpy( name, path );             /* we've got it */  int gipmx, gsw; /* Global variables on the number of contributions 
    } else {                             /* strip direcotry from path */                     to the likelihood and the sum of weights (done by funcone)*/
       s++;                              /* after this, the filename */  int mle, weightopt;
       l2 = strlen( s );                 /* length of filename */  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
       strcpy( name, s );                /* save file name */  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
       strncpy( dirc, path, l1 - l2 );   /* now the directory */             * wave mi and wave mi+1 is not an exact multiple of stepm. */
       dirc[l1-l2] = 0;                  /* add zero */  double jmean; /* Mean space between 2 waves */
    }  double **oldm, **newm, **savm; /* Working pointers to matrices */
    l1 = strlen( dirc );                 /* length of directory */  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 #ifdef windows  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  FILE *ficlog, *ficrespow;
 #else  int globpr; /* Global variable for printing or not */
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  double fretone; /* Only one call to likelihood */
 #endif  long ipmx; /* Number of contributions */
    s = strrchr( name, '.' );            /* find last / */  double sw; /* Sum of weights */
    s++;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
    strcpy(ext,s);                       /* save extension */  FILE *ficresilk;
    l1= strlen( name);  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
    l2= strlen( s)+1;  FILE *ficresprobmorprev;
    strncpy( finame, name, l1-l2);  FILE *fichtm; /* Html File */
    finame[l1-l2]= 0;  FILE *ficreseij;
    return( 0 );                         /* we're done */  char filerese[FILENAMELENGTH];
 }  FILE  *ficresvij;
   char fileresv[FILENAMELENGTH];
   FILE  *ficresvpl;
 /******************************************/  char fileresvpl[FILENAMELENGTH];
   char title[MAXLINE];
 void replace(char *s, char*t)  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 {  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   int i;  char tmpout[FILENAMELENGTH]; 
   int lg=20;  char command[FILENAMELENGTH];
   i=0;  int  outcmd=0;
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
     (s[i] = t[i]);  char lfileres[FILENAMELENGTH];
     if (t[i]== '\\') s[i]='/';  char filelog[FILENAMELENGTH]; /* Log file */
   }  char filerest[FILENAMELENGTH];
 }  char fileregp[FILENAMELENGTH];
   char popfile[FILENAMELENGTH];
 int nbocc(char *s, char occ)  
 {  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];
   int i,j=0;  
   int lg=20;  #define NR_END 1
   i=0;  #define FREE_ARG char*
   lg=strlen(s);  #define FTOL 1.0e-10
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;  #define NRANSI 
   }  #define ITMAX 200 
   return j;  
 }  #define TOL 2.0e-4 
   
 void cutv(char *u,char *v, char*t, char occ)  #define CGOLD 0.3819660 
 {  #define ZEPS 1.0e-10 
   int i,lg,j,p=0;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   i=0;  
   for(j=0; j<=strlen(t)-1; j++) {  #define GOLD 1.618034 
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  #define GLIMIT 100.0 
   }  #define TINY 1.0e-20 
   
   lg=strlen(t);  static double maxarg1,maxarg2;
   for(j=0; j<p; j++) {  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
     (u[j] = t[j]);  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   }    
      u[p]='\0';  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   #define rint(a) floor(a+0.5)
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);  static double sqrarg;
   }  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 }  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   
 /********************** nrerror ********************/  int imx; 
   int stepm;
 void nrerror(char error_text[])  /* Stepm, step in month: minimum step interpolation*/
 {  
   fprintf(stderr,"ERREUR ...\n");  int estepm;
   fprintf(stderr,"%s\n",error_text);  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   exit(1);  
 }  int m,nb;
 /*********************** vector *******************/  long *num;
 double *vector(int nl, int nh)  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 {  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double *v;  double **pmmij, ***probs;
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  double dateintmean=0;
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;  double *weight;
 }  int **s; /* Status */
   double *agedc, **covar, idx;
 /************************ free vector ******************/  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 void free_vector(double*v, int nl, int nh)  
 {  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   free((FREE_ARG)(v+nl-NR_END));  double ftolhess; /* Tolerance for computing hessian */
 }  
   /**************** split *************************/
 /************************ivector *******************************/  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 int *ivector(long nl,long nh)  {
 {    char  *ss;                            /* pointer */
   int *v;    int   l1, l2;                         /* length counters */
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");    l1 = strlen(path );                   /* length of path */
   return v-nl+NR_END;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 }    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     if ( ss == NULL ) {                   /* no directory, so use current */
 /******************free ivector **************************/      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 void free_ivector(int *v, long nl, long nh)        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 {      /* get current working directory */
   free((FREE_ARG)(v+nl-NR_END));      /*    extern  char* getcwd ( char *buf , int len);*/
 }      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
         return( GLOCK_ERROR_GETCWD );
 /******************* imatrix *******************************/      }
 int **imatrix(long nrl, long nrh, long ncl, long nch)      strcpy( name, path );               /* we've got it */
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    } else {                              /* strip direcotry from path */
 {      ss++;                               /* after this, the filename */
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;      l2 = strlen( ss );                  /* length of filename */
   int **m;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
        strcpy( name, ss );         /* save file name */
   /* allocate pointers to rows */      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));      dirc[l1-l2] = 0;                    /* add zero */
   if (!m) nrerror("allocation failure 1 in matrix()");    }
   m += NR_END;    l1 = strlen( dirc );                  /* length of directory */
   m -= nrl;    /*#ifdef windows
      if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
    #else
   /* allocate rows and set pointers to them */    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  #endif
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    */
   m[nrl] += NR_END;    ss = strrchr( name, '.' );            /* find last / */
   m[nrl] -= ncl;    ss++;
      strcpy(ext,ss);                       /* save extension */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    l1= strlen( name);
      l2= strlen(ss)+1;
   /* return pointer to array of pointers to rows */    strncpy( finame, name, l1-l2);
   return m;    finame[l1-l2]= 0;
 }    return( 0 );                          /* we're done */
   }
 /****************** free_imatrix *************************/  
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;  /******************************************/
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */  void replace_back_to_slash(char *s, char*t)
 {  {
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    int i;
   free((FREE_ARG) (m+nrl-NR_END));    int lg=0;
 }    i=0;
     lg=strlen(t);
 /******************* matrix *******************************/    for(i=0; i<= lg; i++) {
 double **matrix(long nrl, long nrh, long ncl, long nch)      (s[i] = t[i]);
 {      if (t[i]== '\\') s[i]='/';
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    }
   double **m;  }
   
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  int nbocc(char *s, char occ)
   if (!m) nrerror("allocation failure 1 in matrix()");  {
   m += NR_END;    int i,j=0;
   m -= nrl;    int lg=20;
     i=0;
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    lg=strlen(s);
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    for(i=0; i<= lg; i++) {
   m[nrl] += NR_END;    if  (s[i] == occ ) j++;
   m[nrl] -= ncl;    }
     return j;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  }
   return m;  
 }  void cutv(char *u,char *v, char*t, char occ)
   {
 /*************************free matrix ************************/    /* cuts string t into u and v where u is ended by char occ excluding it
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
 {       gives u="abcedf" and v="ghi2j" */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    int i,lg,j,p=0;
   free((FREE_ARG)(m+nrl-NR_END));    i=0;
 }    for(j=0; j<=strlen(t)-1; j++) {
       if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 /******************* ma3x *******************************/    }
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  
 {    lg=strlen(t);
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    for(j=0; j<p; j++) {
   double ***m;      (u[j] = t[j]);
     }
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));       u[p]='\0';
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;     for(j=0; j<= lg; j++) {
   m -= nrl;      if (j>=(p+1))(v[j-p-1] = t[j]);
     }
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  }
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  /********************** nrerror ********************/
   m[nrl] -= ncl;  
   void nrerror(char error_text[])
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  {
     fprintf(stderr,"ERREUR ...\n");
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    fprintf(stderr,"%s\n",error_text);
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    exit(EXIT_FAILURE);
   m[nrl][ncl] += NR_END;  }
   m[nrl][ncl] -= nll;  /*********************** vector *******************/
   for (j=ncl+1; j<=nch; j++)  double *vector(int nl, int nh)
     m[nrl][j]=m[nrl][j-1]+nlay;  {
      double *v;
   for (i=nrl+1; i<=nrh; i++) {    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    if (!v) nrerror("allocation failure in vector");
     for (j=ncl+1; j<=nch; j++)    return v-nl+NR_END;
       m[i][j]=m[i][j-1]+nlay;  }
   }  
   return m;  /************************ free vector ******************/
 }  void free_vector(double*v, int nl, int nh)
   {
 /*************************free ma3x ************************/    free((FREE_ARG)(v+nl-NR_END));
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  }
 {  
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  /************************ivector *******************************/
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  int *ivector(long nl,long nh)
   free((FREE_ARG)(m+nrl-NR_END));  {
 }    int *v;
     v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
 /***************** f1dim *************************/    if (!v) nrerror("allocation failure in ivector");
 extern int ncom;    return v-nl+NR_END;
 extern double *pcom,*xicom;  }
 extern double (*nrfunc)(double []);  
    /******************free ivector **************************/
 double f1dim(double x)  void free_ivector(int *v, long nl, long nh)
 {  {
   int j;    free((FREE_ARG)(v+nl-NR_END));
   double f;  }
   double *xt;  
    /************************lvector *******************************/
   xt=vector(1,ncom);  long *lvector(long nl,long nh)
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  {
   f=(*nrfunc)(xt);    long *v;
   free_vector(xt,1,ncom);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   return f;    if (!v) nrerror("allocation failure in ivector");
 }    return v-nl+NR_END;
   }
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  /******************free lvector **************************/
 {  void free_lvector(long *v, long nl, long nh)
   int iter;  {
   double a,b,d,etemp;    free((FREE_ARG)(v+nl-NR_END));
   double fu,fv,fw,fx;  }
   double ftemp;  
   double p,q,r,tol1,tol2,u,v,w,x,xm;  /******************* imatrix *******************************/
   double e=0.0;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
         /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   a=(ax < cx ? ax : cx);  { 
   b=(ax > cx ? ax : cx);    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   x=w=v=bx;    int **m; 
   fw=fv=fx=(*f)(x);    
   for (iter=1;iter<=ITMAX;iter++) {    /* allocate pointers to rows */ 
     xm=0.5*(a+b);    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    if (!m) nrerror("allocation failure 1 in matrix()"); 
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    m += NR_END; 
     printf(".");fflush(stdout);    m -= nrl; 
 #ifdef DEBUG    
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    /* allocate rows and set pointers to them */ 
 #endif    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       *xmin=x;    m[nrl] += NR_END; 
       return fx;    m[nrl] -= ncl; 
     }    
     ftemp=fu;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     if (fabs(e) > tol1) {    
       r=(x-w)*(fx-fv);    /* return pointer to array of pointers to rows */ 
       q=(x-v)*(fx-fw);    return m; 
       p=(x-v)*q-(x-w)*r;  } 
       q=2.0*(q-r);  
       if (q > 0.0) p = -p;  /****************** free_imatrix *************************/
       q=fabs(q);  void free_imatrix(m,nrl,nrh,ncl,nch)
       etemp=e;        int **m;
       e=d;        long nch,ncl,nrh,nrl; 
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))       /* free an int matrix allocated by imatrix() */ 
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  { 
       else {    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
         d=p/q;    free((FREE_ARG) (m+nrl-NR_END)); 
         u=x+d;  } 
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);  /******************* matrix *******************************/
       }  double **matrix(long nrl, long nrh, long ncl, long nch)
     } else {  {
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     }    double **m;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  
     fu=(*f)(u);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (fu <= fx) {    if (!m) nrerror("allocation failure 1 in matrix()");
       if (u >= x) a=x; else b=x;    m += NR_END;
       SHFT(v,w,x,u)    m -= nrl;
         SHFT(fv,fw,fx,fu)  
         } else {    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
           if (u < x) a=u; else b=u;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
           if (fu <= fw || w == x) {    m[nrl] += NR_END;
             v=w;    m[nrl] -= ncl;
             w=u;  
             fv=fw;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
             fw=fu;    return m;
           } else if (fu <= fv || v == x || v == w) {    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
             v=u;     */
             fv=fu;  }
           }  
         }  /*************************free matrix ************************/
   }  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   nrerror("Too many iterations in brent");  {
   *xmin=x;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   return fx;    free((FREE_ARG)(m+nrl-NR_END));
 }  }
   
 /****************** mnbrak ***********************/  /******************* ma3x *******************************/
   double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  {
             double (*func)(double))    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
 {    double ***m;
   double ulim,u,r,q, dum;  
   double fu;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
      if (!m) nrerror("allocation failure 1 in matrix()");
   *fa=(*func)(*ax);    m += NR_END;
   *fb=(*func)(*bx);    m -= nrl;
   if (*fb > *fa) {  
     SHFT(dum,*ax,*bx,dum)    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       SHFT(dum,*fb,*fa,dum)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       }    m[nrl] += NR_END;
   *cx=(*bx)+GOLD*(*bx-*ax);    m[nrl] -= ncl;
   *fc=(*func)(*cx);  
   while (*fb > *fc) {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     r=(*bx-*ax)*(*fb-*fc);  
     q=(*bx-*cx)*(*fb-*fa);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    m[nrl][ncl] += NR_END;
     ulim=(*bx)+GLIMIT*(*cx-*bx);    m[nrl][ncl] -= nll;
     if ((*bx-u)*(u-*cx) > 0.0) {    for (j=ncl+1; j<=nch; j++) 
       fu=(*func)(u);      m[nrl][j]=m[nrl][j-1]+nlay;
     } else if ((*cx-u)*(u-ulim) > 0.0) {    
       fu=(*func)(u);    for (i=nrl+1; i<=nrh; i++) {
       if (fu < *fc) {      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))      for (j=ncl+1; j<=nch; j++) 
           SHFT(*fb,*fc,fu,(*func)(u))        m[i][j]=m[i][j-1]+nlay;
           }    }
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    return m; 
       u=ulim;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       fu=(*func)(u);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     } else {    */
       u=(*cx)+GOLD*(*cx-*bx);  }
       fu=(*func)(u);  
     }  /*************************free ma3x ************************/
     SHFT(*ax,*bx,*cx,u)  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       SHFT(*fa,*fb,*fc,fu)  {
       }    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
 }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
 /*************** linmin ************************/  }
   
 int ncom;  /***************** f1dim *************************/
 double *pcom,*xicom;  extern int ncom; 
 double (*nrfunc)(double []);  extern double *pcom,*xicom;
    extern double (*nrfunc)(double []); 
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))   
 {  double f1dim(double x) 
   double brent(double ax, double bx, double cx,  { 
                double (*f)(double), double tol, double *xmin);    int j; 
   double f1dim(double x);    double f;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    double *xt; 
               double *fc, double (*func)(double));   
   int j;    xt=vector(1,ncom); 
   double xx,xmin,bx,ax;    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   double fx,fb,fa;    f=(*nrfunc)(xt); 
      free_vector(xt,1,ncom); 
   ncom=n;    return f; 
   pcom=vector(1,n);  } 
   xicom=vector(1,n);  
   nrfunc=func;  /*****************brent *************************/
   for (j=1;j<=n;j++) {  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     pcom[j]=p[j];  { 
     xicom[j]=xi[j];    int iter; 
   }    double a,b,d,etemp;
   ax=0.0;    double fu,fv,fw,fx;
   xx=1.0;    double ftemp;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    double e=0.0; 
 #ifdef DEBUG   
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    a=(ax < cx ? ax : cx); 
 #endif    b=(ax > cx ? ax : cx); 
   for (j=1;j<=n;j++) {    x=w=v=bx; 
     xi[j] *= xmin;    fw=fv=fx=(*f)(x); 
     p[j] += xi[j];    for (iter=1;iter<=ITMAX;iter++) { 
   }      xm=0.5*(a+b); 
   free_vector(xicom,1,n);      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   free_vector(pcom,1,n);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
 }      printf(".");fflush(stdout);
       fprintf(ficlog,".");fflush(ficlog);
 /*************** powell ************************/  #ifdef DEBUG
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
             double (*func)(double []))      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
 {      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
   void linmin(double p[], double xi[], int n, double *fret,  #endif
               double (*func)(double []));      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   int i,ibig,j;        *xmin=x; 
   double del,t,*pt,*ptt,*xit;        return fx; 
   double fp,fptt;      } 
   double *xits;      ftemp=fu;
   pt=vector(1,n);      if (fabs(e) > tol1) { 
   ptt=vector(1,n);        r=(x-w)*(fx-fv); 
   xit=vector(1,n);        q=(x-v)*(fx-fw); 
   xits=vector(1,n);        p=(x-v)*q-(x-w)*r; 
   *fret=(*func)(p);        q=2.0*(q-r); 
   for (j=1;j<=n;j++) pt[j]=p[j];        if (q > 0.0) p = -p; 
   for (*iter=1;;++(*iter)) {        q=fabs(q); 
     fp=(*fret);        etemp=e; 
     ibig=0;        e=d; 
     del=0.0;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     for (i=1;i<=n;i++)        else { 
       printf(" %d %.12f",i, p[i]);          d=p/q; 
     printf("\n");          u=x+d; 
     for (i=1;i<=n;i++) {          if (u-a < tol2 || b-u < tol2) 
       for (j=1;j<=n;j++) xit[j]=xi[j][i];            d=SIGN(tol1,xm-x); 
       fptt=(*fret);        } 
 #ifdef DEBUG      } else { 
       printf("fret=%lf \n",*fret);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 #endif      } 
       printf("%d",i);fflush(stdout);      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       linmin(p,xit,n,fret,func);      fu=(*f)(u); 
       if (fabs(fptt-(*fret)) > del) {      if (fu <= fx) { 
         del=fabs(fptt-(*fret));        if (u >= x) a=x; else b=x; 
         ibig=i;        SHFT(v,w,x,u) 
       }          SHFT(fv,fw,fx,fu) 
 #ifdef DEBUG          } else { 
       printf("%d %.12e",i,(*fret));            if (u < x) a=u; else b=u; 
       for (j=1;j<=n;j++) {            if (fu <= fw || w == x) { 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);              v=w; 
         printf(" x(%d)=%.12e",j,xit[j]);              w=u; 
       }              fv=fw; 
       for(j=1;j<=n;j++)              fw=fu; 
         printf(" p=%.12e",p[j]);            } else if (fu <= fv || v == x || v == w) { 
       printf("\n");              v=u; 
 #endif              fv=fu; 
     }            } 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {          } 
 #ifdef DEBUG    } 
       int k[2],l;    nrerror("Too many iterations in brent"); 
       k[0]=1;    *xmin=x; 
       k[1]=-1;    return fx; 
       printf("Max: %.12e",(*func)(p));  } 
       for (j=1;j<=n;j++)  
         printf(" %.12e",p[j]);  /****************** mnbrak ***********************/
       printf("\n");  
       for(l=0;l<=1;l++) {  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
         for (j=1;j<=n;j++) {              double (*func)(double)) 
           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]);    double ulim,u,r,q, dum;
         }    double fu; 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));   
       }    *fa=(*func)(*ax); 
 #endif    *fb=(*func)(*bx); 
     if (*fb > *fa) { 
       SHFT(dum,*ax,*bx,dum) 
       free_vector(xit,1,n);        SHFT(dum,*fb,*fa,dum) 
       free_vector(xits,1,n);        } 
       free_vector(ptt,1,n);    *cx=(*bx)+GOLD*(*bx-*ax); 
       free_vector(pt,1,n);    *fc=(*func)(*cx); 
       return;    while (*fb > *fc) { 
     }      r=(*bx-*ax)*(*fb-*fc); 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");      q=(*bx-*cx)*(*fb-*fa); 
     for (j=1;j<=n;j++) {      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
       ptt[j]=2.0*p[j]-pt[j];        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       xit[j]=p[j]-pt[j];      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       pt[j]=p[j];      if ((*bx-u)*(u-*cx) > 0.0) { 
     }        fu=(*func)(u); 
     fptt=(*func)(ptt);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
     if (fptt < fp) {        fu=(*func)(u); 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);        if (fu < *fc) { 
       if (t < 0.0) {          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
         linmin(p,xit,n,fret,func);            SHFT(*fb,*fc,fu,(*func)(u)) 
         for (j=1;j<=n;j++) {            } 
           xi[j][ibig]=xi[j][n];      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
           xi[j][n]=xit[j];        u=ulim; 
         }        fu=(*func)(u); 
 #ifdef DEBUG      } else { 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);        u=(*cx)+GOLD*(*cx-*bx); 
         for(j=1;j<=n;j++)        fu=(*func)(u); 
           printf(" %.12e",xit[j]);      } 
         printf("\n");      SHFT(*ax,*bx,*cx,u) 
 #endif        SHFT(*fa,*fb,*fc,fu) 
       }        } 
     }  } 
   }  
 }  /*************** linmin ************************/
   
 /**** Prevalence limit ****************/  int ncom; 
   double *pcom,*xicom;
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  double (*nrfunc)(double []); 
 {   
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
      matrix by transitions matrix until convergence is reached */  { 
     double brent(double ax, double bx, double cx, 
   int i, ii,j,k;                 double (*f)(double), double tol, double *xmin); 
   double min, max, maxmin, maxmax,sumnew=0.;    double f1dim(double x); 
   double **matprod2();    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   double **out, cov[NCOVMAX], **pmij();                double *fc, double (*func)(double)); 
   double **newm;    int j; 
   double agefin, delaymax=50 ; /* Max number of years to converge */    double xx,xmin,bx,ax; 
     double fx,fb,fa;
   for (ii=1;ii<=nlstate+ndeath;ii++)   
     for (j=1;j<=nlstate+ndeath;j++){    ncom=n; 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    pcom=vector(1,n); 
     }    xicom=vector(1,n); 
     nrfunc=func; 
    cov[1]=1.;    for (j=1;j<=n;j++) { 
        pcom[j]=p[j]; 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */      xicom[j]=xi[j]; 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    } 
     newm=savm;    ax=0.0; 
     /* Covariates have to be included here again */    xx=1.0; 
      cov[2]=agefin;    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
      *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       for (k=1; k<=cptcovn;k++) {  #ifdef DEBUG
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         /*      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]]);*/    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       }  #endif
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    for (j=1;j<=n;j++) { 
       for (k=1; k<=cptcovprod;k++)      xi[j] *= xmin; 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      p[j] += xi[j]; 
     } 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    free_vector(xicom,1,n); 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    free_vector(pcom,1,n); 
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/  } 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  
   /*************** powell ************************/
     savm=oldm;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
     oldm=newm;              double (*func)(double [])) 
     maxmax=0.;  { 
     for(j=1;j<=nlstate;j++){    void linmin(double p[], double xi[], int n, double *fret, 
       min=1.;                double (*func)(double [])); 
       max=0.;    int i,ibig,j; 
       for(i=1; i<=nlstate; i++) {    double del,t,*pt,*ptt,*xit;
         sumnew=0;    double fp,fptt;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    double *xits;
         prlim[i][j]= newm[i][j]/(1-sumnew);    pt=vector(1,n); 
         max=FMAX(max,prlim[i][j]);    ptt=vector(1,n); 
         min=FMIN(min,prlim[i][j]);    xit=vector(1,n); 
       }    xits=vector(1,n); 
       maxmin=max-min;    *fret=(*func)(p); 
       maxmax=FMAX(maxmax,maxmin);    for (j=1;j<=n;j++) pt[j]=p[j]; 
     }    for (*iter=1;;++(*iter)) { 
     if(maxmax < ftolpl){      fp=(*fret); 
       return prlim;      ibig=0; 
     }      del=0.0; 
   }      printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
 }      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);
       fprintf(ficrespow,"%d %.12f",*iter,*fret);
 /*************** transition probabilities ***************/      for (i=1;i<=n;i++) {
         printf(" %d %.12f",i, p[i]);
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )        fprintf(ficlog," %d %.12lf",i, p[i]);
 {        fprintf(ficrespow," %.12lf", p[i]);
   double s1, s2;      }
   /*double t34;*/      printf("\n");
   int i,j,j1, nc, ii, jj;      fprintf(ficlog,"\n");
       fprintf(ficrespow,"\n");
     for(i=1; i<= nlstate; i++){      for (i=1;i<=n;i++) { 
     for(j=1; j<i;j++){        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        fptt=(*fret); 
         /*s2 += param[i][j][nc]*cov[nc];*/  #ifdef DEBUG
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        printf("fret=%lf \n",*fret);
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/        fprintf(ficlog,"fret=%lf \n",*fret);
       }  #endif
       ps[i][j]=s2;        printf("%d",i);fflush(stdout);
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        fprintf(ficlog,"%d",i);fflush(ficlog);
     }        linmin(p,xit,n,fret,func); 
     for(j=i+1; j<=nlstate+ndeath;j++){        if (fabs(fptt-(*fret)) > del) { 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){          del=fabs(fptt-(*fret)); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];          ibig=i; 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/        } 
       }  #ifdef DEBUG
       ps[i][j]=s2;        printf("%d %.12e",i,(*fret));
     }        fprintf(ficlog,"%d %.12e",i,(*fret));
   }        for (j=1;j<=n;j++) {
     /*ps[3][2]=1;*/          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
           printf(" x(%d)=%.12e",j,xit[j]);
   for(i=1; i<= nlstate; i++){          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
      s1=0;        }
     for(j=1; j<i; j++)        for(j=1;j<=n;j++) {
       s1+=exp(ps[i][j]);          printf(" p=%.12e",p[j]);
     for(j=i+1; j<=nlstate+ndeath; j++)          fprintf(ficlog," p=%.12e",p[j]);
       s1+=exp(ps[i][j]);        }
     ps[i][i]=1./(s1+1.);        printf("\n");
     for(j=1; j<i; j++)        fprintf(ficlog,"\n");
       ps[i][j]= exp(ps[i][j])*ps[i][i];  #endif
     for(j=i+1; j<=nlstate+ndeath; j++)      } 
       ps[i][j]= exp(ps[i][j])*ps[i][i];      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  #ifdef DEBUG
   } /* end i */        int k[2],l;
         k[0]=1;
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){        k[1]=-1;
     for(jj=1; jj<= nlstate+ndeath; jj++){        printf("Max: %.12e",(*func)(p));
       ps[ii][jj]=0;        fprintf(ficlog,"Max: %.12e",(*func)(p));
       ps[ii][ii]=1;        for (j=1;j<=n;j++) {
     }          printf(" %.12e",p[j]);
   }          fprintf(ficlog," %.12e",p[j]);
         }
         printf("\n");
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){        fprintf(ficlog,"\n");
     for(jj=1; jj<= nlstate+ndeath; jj++){        for(l=0;l<=1;l++) {
      printf("%lf ",ps[ii][jj]);          for (j=1;j<=n;j++) {
    }            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     printf("\n ");            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]);
     printf("\n ");printf("%lf ",cov[2]);*/          }
 /*          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   for(i=1; i<= npar; i++) printf("%f ",x[i]);          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   goto end;*/        }
     return ps;  #endif
 }  
   
 /**************** Product of 2 matrices ******************/        free_vector(xit,1,n); 
         free_vector(xits,1,n); 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        free_vector(ptt,1,n); 
 {        free_vector(pt,1,n); 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times        return; 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */      } 
   /* in, b, out are matrice of pointers which should have been initialized      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
      before: only the contents of out is modified. The function returns      for (j=1;j<=n;j++) { 
      a pointer to pointers identical to out */        ptt[j]=2.0*p[j]-pt[j]; 
   long i, j, k;        xit[j]=p[j]-pt[j]; 
   for(i=nrl; i<= nrh; i++)        pt[j]=p[j]; 
     for(k=ncolol; k<=ncoloh; k++)      } 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)      fptt=(*func)(ptt); 
         out[i][k] +=in[i][j]*b[j][k];      if (fptt < fp) { 
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   return out;        if (t < 0.0) { 
 }          linmin(p,xit,n,fret,func); 
           for (j=1;j<=n;j++) { 
             xi[j][ibig]=xi[j][n]; 
 /************* Higher Matrix Product ***************/            xi[j][n]=xit[j]; 
           }
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  #ifdef DEBUG
 {          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
      duration (i.e. until          for(j=1;j<=n;j++){
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.            printf(" %.12e",xit[j]);
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step            fprintf(ficlog," %.12e",xit[j]);
      (typically every 2 years instead of every month which is too big).          }
      Model is determined by parameters x and covariates have to be          printf("\n");
      included manually here.          fprintf(ficlog,"\n");
   #endif
      */        }
       } 
   int i, j, d, h, k;    } 
   double **out, cov[NCOVMAX];  } 
   double **newm;  
   /**** Prevalence limit (stable prevalence)  ****************/
   /* Hstepm could be zero and should return the unit matrix */  
   for (i=1;i<=nlstate+ndeath;i++)  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     for (j=1;j<=nlstate+ndeath;j++){  {
       oldm[i][j]=(i==j ? 1.0 : 0.0);    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       po[i][j][0]=(i==j ? 1.0 : 0.0);       matrix by transitions matrix until convergence is reached */
     }  
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    int i, ii,j,k;
   for(h=1; h <=nhstepm; h++){    double min, max, maxmin, maxmax,sumnew=0.;
     for(d=1; d <=hstepm; d++){    double **matprod2();
       newm=savm;    double **out, cov[NCOVMAX], **pmij();
       /* Covariates have to be included here again */    double **newm;
       cov[1]=1.;    double agefin, delaymax=50 ; /* Max number of years to converge */
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    for (ii=1;ii<=nlstate+ndeath;ii++)
       for (k=1; k<=cptcovage;k++)      for (j=1;j<=nlstate+ndeath;j++){
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       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]]];  
      cov[1]=1.;
    
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      newm=savm;
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      /* Covariates have to be included here again */
       savm=oldm;       cov[2]=agefin;
       oldm=newm;    
     }        for (k=1; k<=cptcovn;k++) {
     for(i=1; i<=nlstate+ndeath; i++)          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       for(j=1;j<=nlstate+ndeath;j++) {          /*      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]]);*/
         po[i][j][h]=newm[i][j];        }
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);        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]]];
   } /* end h */  
   return po;        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
 }        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
         /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
 /*************** log-likelihood *************/  
 double func( double *x)      savm=oldm;
 {      oldm=newm;
   int i, ii, j, k, mi, d, kk;      maxmax=0.;
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      for(j=1;j<=nlstate;j++){
   double **out;        min=1.;
   double sw; /* Sum of weights */        max=0.;
   double lli; /* Individual log likelihood */        for(i=1; i<=nlstate; i++) {
   long ipmx;          sumnew=0;
   /*extern weight */          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   /* We are differentiating ll according to initial status */          prlim[i][j]= newm[i][j]/(1-sumnew);
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/          max=FMAX(max,prlim[i][j]);
   /*for(i=1;i<imx;i++)          min=FMIN(min,prlim[i][j]);
     printf(" %d\n",s[4][i]);        }
   */        maxmin=max-min;
   cov[1]=1.;        maxmax=FMAX(maxmax,maxmin);
       }
   for(k=1; k<=nlstate; k++) ll[k]=0.;      if(maxmax < ftolpl){
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        return prlim;
     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++)  }
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);  
       for(d=0; d<dh[mi][i]; d++){  /*************** transition probabilities ***************/ 
         newm=savm;  
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
         for (kk=1; kk<=cptcovage;kk++) {  {
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    double s1, s2;
         }    /*double t34;*/
            int i,j,j1, nc, ii, jj;
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));      for(i=1; i<= nlstate; i++){
         savm=oldm;      for(j=1; j<i;j++){
         oldm=newm;        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];
       } /* end mult */          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
              }
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        ps[i][j]=s2;
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
       ipmx +=1;      }
       sw += weight[i];      for(j=i+1; j<=nlstate+ndeath;j++){
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     } /* end of wave */          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   } /* end of individual */          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
         }
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        ps[i][j]=s2;
   /* 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;      /*ps[3][2]=1;*/
 }  
     for(i=1; i<= nlstate; i++){
        s1=0;
 /*********** Maximum Likelihood Estimation ***************/      for(j=1; j<i; j++)
         s1+=exp(ps[i][j]);
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))      for(j=i+1; j<=nlstate+ndeath; j++)
 {        s1+=exp(ps[i][j]);
   int i,j, iter;      ps[i][i]=1./(s1+1.);
   double **xi,*delti;      for(j=1; j<i; j++)
   double fret;        ps[i][j]= exp(ps[i][j])*ps[i][i];
   xi=matrix(1,npar,1,npar);      for(j=i+1; j<=nlstate+ndeath; j++)
   for (i=1;i<=npar;i++)        ps[i][j]= exp(ps[i][j])*ps[i][i];
     for (j=1;j<=npar;j++)      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       xi[i][j]=(i==j ? 1.0 : 0.0);    } /* end i */
   printf("Powell\n");  
   powell(p,xi,npar,ftol,&iter,&fret,func);    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       for(jj=1; jj<= nlstate+ndeath; jj++){
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));        ps[ii][jj]=0;
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        ps[ii][ii]=1;
       }
 }    }
   
 /**** Computes Hessian and covariance matrix ***/  
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
 {      for(jj=1; jj<= nlstate+ndeath; jj++){
   double  **a,**y,*x,pd;       printf("%lf ",ps[ii][jj]);
   double **hess;     }
   int i, j,jk;      printf("\n ");
   int *indx;      }
       printf("\n ");printf("%lf ",cov[2]);*/
   double hessii(double p[], double delta, int theta, double delti[]);  /*
   double hessij(double p[], double delti[], int i, int j);    for(i=1; i<= npar; i++) printf("%f ",x[i]);
   void lubksb(double **a, int npar, int *indx, double b[]) ;    goto end;*/
   void ludcmp(double **a, int npar, int *indx, double *d) ;      return ps;
   }
   hess=matrix(1,npar,1,npar);  
   /**************** Product of 2 matrices ******************/
   printf("\nCalculation of the hessian matrix. Wait...\n");  
   for (i=1;i<=npar;i++){  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
     printf("%d",i);fflush(stdout);  {
     hess[i][i]=hessii(p,ftolhess,i,delti);    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
     /*printf(" %f ",p[i]);*/       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     /*printf(" %lf ",hess[i][i]);*/    /* in, b, out are matrice of pointers which should have been initialized 
   }       before: only the contents of out is modified. The function returns
         a pointer to pointers identical to out */
   for (i=1;i<=npar;i++) {    long i, j, k;
     for (j=1;j<=npar;j++)  {    for(i=nrl; i<= nrh; i++)
       if (j>i) {      for(k=ncolol; k<=ncoloh; k++)
         printf(".%d%d",i,j);fflush(stdout);        for(j=ncl,out[i][k]=0.; j<=nch; j++)
         hess[i][j]=hessij(p,delti,i,j);          out[i][k] +=in[i][j]*b[j][k];
         hess[j][i]=hess[i][j];      
         /*printf(" %lf ",hess[i][j]);*/    return out;
       }  }
     }  
   }  
   printf("\n");  /************* Higher Matrix Product ***************/
   
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
    {
   a=matrix(1,npar,1,npar);    /* Computes the transition matrix starting at age 'age' over 
   y=matrix(1,npar,1,npar);       'nhstepm*hstepm*stepm' months (i.e. until
   x=vector(1,npar);       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   indx=ivector(1,npar);       nhstepm*hstepm matrices. 
   for (i=1;i<=npar;i++)       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];       (typically every 2 years instead of every month which is too big 
   ludcmp(a,npar,indx,&pd);       for the memory).
        Model is determined by parameters x and covariates have to be 
   for (j=1;j<=npar;j++) {       included manually here. 
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;       */
     lubksb(a,npar,indx,x);  
     for (i=1;i<=npar;i++){    int i, j, d, h, k;
       matcov[i][j]=x[i];    double **out, cov[NCOVMAX];
     }    double **newm;
   }  
     /* Hstepm could be zero and should return the unit matrix */
   printf("\n#Hessian matrix#\n");    for (i=1;i<=nlstate+ndeath;i++)
   for (i=1;i<=npar;i++) {      for (j=1;j<=nlstate+ndeath;j++){
     for (j=1;j<=npar;j++) {        oldm[i][j]=(i==j ? 1.0 : 0.0);
       printf("%.3e ",hess[i][j]);        po[i][j][0]=(i==j ? 1.0 : 0.0);
     }      }
     printf("\n");    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   }    for(h=1; h <=nhstepm; h++){
       for(d=1; d <=hstepm; d++){
   /* Recompute Inverse */        newm=savm;
   for (i=1;i<=npar;i++)        /* Covariates have to be included here again */
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        cov[1]=1.;
   ludcmp(a,npar,indx,&pd);        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
         for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   /*  printf("\n#Hessian matrix recomputed#\n");        for (k=1; k<=cptcovage;k++)
           cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   for (j=1;j<=npar;j++) {        for (k=1; k<=cptcovprod;k++)
     for (i=1;i<=npar;i++) x[i]=0;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     x[j]=1;  
     lubksb(a,npar,indx,x);  
     for (i=1;i<=npar;i++){        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       y[i][j]=x[i];        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
       printf("%.3e ",y[i][j]);        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
     }                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     printf("\n");        savm=oldm;
   }        oldm=newm;
   */      }
       for(i=1; i<=nlstate+ndeath; i++)
   free_matrix(a,1,npar,1,npar);        for(j=1;j<=nlstate+ndeath;j++) {
   free_matrix(y,1,npar,1,npar);          po[i][j][h]=newm[i][j];
   free_vector(x,1,npar);          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
   free_ivector(indx,1,npar);           */
   free_matrix(hess,1,npar,1,npar);        }
     } /* end h */
     return po;
 }  }
   
 /*************** hessian matrix ****************/  
 double hessii( double x[], double delta, int theta, double delti[])  /*************** log-likelihood *************/
 {  double func( double *x)
   int i;  {
   int l=1, lmax=20;    int i, ii, j, k, mi, d, kk;
   double k1,k2;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   double p2[NPARMAX+1];    double **out;
   double res;    double sw; /* Sum of weights */
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    double lli; /* Individual log likelihood */
   double fx;    int s1, s2;
   int k=0,kmax=10;    double bbh, survp;
   double l1;    long ipmx;
     /*extern weight */
   fx=func(x);    /* We are differentiating ll according to initial status */
   for (i=1;i<=npar;i++) p2[i]=x[i];    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   for(l=0 ; l <=lmax; l++){    /*for(i=1;i<imx;i++) 
     l1=pow(10,l);      printf(" %d\n",s[4][i]);
     delts=delt;    */
     for(k=1 ; k <kmax; k=k+1){    cov[1]=1.;
       delt = delta*(l1*k);  
       p2[theta]=x[theta] +delt;    for(k=1; k<=nlstate; k++) ll[k]=0.;
       k1=func(p2)-fx;  
       p2[theta]=x[theta]-delt;    if(mle==1){
       k2=func(p2)-fx;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       /*res= (k1-2.0*fx+k2)/delt/delt; */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        for(mi=1; mi<= wav[i]-1; mi++){
                for (ii=1;ii<=nlstate+ndeath;ii++)
 #ifdef DEBUG            for (j=1;j<=nlstate+ndeath;j++){
       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);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 #endif              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */            }
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){          for(d=0; d<dh[mi][i]; d++){
         k=kmax;            newm=savm;
       }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */            for (kk=1; kk<=cptcovage;kk++) {
         k=kmax; l=lmax*10.;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       }            }
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         delts=delt;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       }            savm=oldm;
     }            oldm=newm;
   }          } /* end mult */
   delti[theta]=delts;        
   return res;          /*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 
 double hessij( double x[], double delti[], int thetai,int thetaj)           * the nearest (and in case of equal distance, to the lowest) interval but now
 {           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   int i;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   int l=1, l1, lmax=20;           * probability in order to take into account the bias as a fraction of the way
   double k1,k2,k3,k4,res,fx;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   double p2[NPARMAX+1];           * -stepm/2 to stepm/2 .
   int k;           * 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. 
   fx=func(x);           */
   for (k=1; k<=2; k++) {          s1=s[mw[mi][i]][i];
     for (i=1;i<=npar;i++) p2[i]=x[i];          s2=s[mw[mi+1][i]][i];
     p2[thetai]=x[thetai]+delti[thetai]/k;          bbh=(double)bh[mi][i]/(double)stepm; 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          /* bias is positive if real duration
     k1=func(p2)-fx;           * is higher than the multiple of stepm and negative otherwise.
             */
     p2[thetai]=x[thetai]+delti[thetai]/k;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          if( s2 > nlstate){ 
     k2=func(p2)-fx;            /* i.e. if s2 is a death state and if the date of death is known then the contribution
                 to the likelihood is the probability to die between last step unit time and current 
     p2[thetai]=x[thetai]-delti[thetai]/k;               step unit time, which is also the differences between probability to die before dh 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;               and probability to die before dh-stepm . 
     k3=func(p2)-fx;               In version up to 0.92 likelihood was computed
            as if date of death was unknown. Death was treated as any other
     p2[thetai]=x[thetai]-delti[thetai]/k;          health state: the date of the interview describes the actual state
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          and not the date of a change in health state. The former idea was
     k4=func(p2)-fx;          to consider that at each interview the state was recorded
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          (healthy, disable or death) and IMaCh was corrected; but when we
 #ifdef DEBUG          introduced the exact date of death then we should have modified
     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 contribution of an exact death to the likelihood. This new
 #endif          contribution is smaller and very dependent of the step unit
   }          stepm. It is no more the probability to die between last interview
   return res;          and month of death but the probability to survive from last
 }          interview up to one month before death multiplied by the
           probability to die within a month. Thanks to Chris
 /************** Inverse of matrix **************/          Jackson for correcting this bug.  Former versions increased
 void ludcmp(double **a, int n, int *indx, double *d)          mortality artificially. The bad side is that we add another loop
 {          which slows down the processing. The difference can be up to 10%
   int i,imax,j,k;          lower mortality.
   double big,dum,sum,temp;            */
   double *vv;            lli=log(out[s1][s2] - savm[s1][s2]);
            }else{
   vv=vector(1,n);            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   *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++) {          } 
     big=0.0;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
     for (j=1;j<=n;j++)          /*if(lli ==000.0)*/
       if ((temp=fabs(a[i][j])) > big) big=temp;          /*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); */
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          ipmx +=1;
     vv[i]=1.0/big;          sw += weight[i];
   }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   for (j=1;j<=n;j++) {        } /* end of wave */
     for (i=1;i<j;i++) {      } /* end of individual */
       sum=a[i][j];    }  else if(mle==2){
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       a[i][j]=sum;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     }        for(mi=1; mi<= wav[i]-1; mi++){
     big=0.0;          for (ii=1;ii<=nlstate+ndeath;ii++)
     for (i=j;i<=n;i++) {            for (j=1;j<=nlstate+ndeath;j++){
       sum=a[i][j];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for (k=1;k<j;k++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         sum -= a[i][k]*a[k][j];            }
       a[i][j]=sum;          for(d=0; d<=dh[mi][i]; d++){
       if ( (dum=vv[i]*fabs(sum)) >= big) {            newm=savm;
         big=dum;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         imax=i;            for (kk=1; kk<=cptcovage;kk++) {
       }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     }            }
     if (j != imax) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for (k=1;k<=n;k++) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         dum=a[imax][k];            savm=oldm;
         a[imax][k]=a[j][k];            oldm=newm;
         a[j][k]=dum;          } /* end mult */
       }        
       *d = -(*d);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       vv[imax]=vv[j];          /* 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 
     indx[j]=imax;           * (in months) between two waves is not a multiple of stepm, we rounded to 
     if (a[j][j] == 0.0) a[j][j]=TINY;           * the nearest (and in case of equal distance, to the lowest) interval but now
     if (j != n) {           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       dum=1.0/(a[j][j]);           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
       for (i=j+1;i<=n;i++) a[i][j] *= dum;           * 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
   }           * -stepm/2 to stepm/2 .
   free_vector(vv,1,n);  /* Doesn't work */           * For stepm=1 the results are the same as for previous versions of Imach.
 ;           * For stepm > 1 the results are less biased than in previous versions. 
 }           */
           s1=s[mw[mi][i]][i];
 void lubksb(double **a, int n, int *indx, double b[])          s2=s[mw[mi+1][i]][i];
 {          bbh=(double)bh[mi][i]/(double)stepm; 
   int i,ii=0,ip,j;          /* bias is positive if real duration
   double sum;           * is higher than the multiple of stepm and negative otherwise.
             */
   for (i=1;i<=n;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 */
     ip=indx[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]));*/
     sum=b[ip];          /*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 */
     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==3){  /* exponential 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++){
   double ***freq; /* Frequencies */            newm=savm;
   double *pp;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double pos, k2, dateintsum=0,k2cpt=0;            for (kk=1; kk<=cptcovage;kk++) {
   FILE *ficresp;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   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);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
     exit(0);          /* 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 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);           * (in months) between two waves is not a multiple of stepm, we rounded to 
   j1=0;           * the nearest (and in case of equal distance, to the lowest) interval but now
             * we keep into memory the bias bh[mi][i] and also the previous matrix product
   j=cptcoveff;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   if (cptcovn<1) {j=1;ncodemax[1]=1;}           * 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
   for(k1=1; k1<=j;k1++){           * -stepm/2 to stepm/2 .
     for(i1=1; i1<=ncodemax[k1];i1++){           * For stepm=1 the results are the same as for previous versions of Imach.
       j1++;           * For stepm > 1 the results are less biased than in previous versions. 
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);           */
         scanf("%d", i);*/          s1=s[mw[mi][i]][i];
       for (i=-1; i<=nlstate+ndeath; i++)            s2=s[mw[mi+1][i]][i];
         for (jk=-1; jk<=nlstate+ndeath; jk++)            bbh=(double)bh[mi][i]/(double)stepm; 
           for(m=agemin; m <= agemax+3; m++)          /* bias is positive if real duration
             freq[i][jk][m]=0;           * is higher than the multiple of stepm and negative otherwise.
                 */
       dateintsum=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 */
       k2cpt=0;          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
       for (i=1; i<=imx; i++) {          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         bool=1;          /*if(lli ==000.0)*/
         if  (cptcovn>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); */
           for (z1=1; z1<=cptcoveff; z1++)          ipmx +=1;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          sw += weight[i];
               bool=0;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         }        } /* end of wave */
         if (bool==1) {      } /* end of individual */
           for(m=firstpass; m<=lastpass; m++){    }else if (mle==4){  /* ml=4 no inter-extrapolation */
             k2=anint[m][i]+(mint[m][i]/12.);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
               if(agev[m][i]==0) agev[m][i]=agemax+1;        for(mi=1; mi<= wav[i]-1; mi++){
               if(agev[m][i]==1) agev[m][i]=agemax+2;          for (ii=1;ii<=nlstate+ndeath;ii++)
               if (m<lastpass) {            for (j=1;j<=nlstate+ndeath;j++){
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
               }            }
                        for(d=0; d<dh[mi][i]; d++){
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {            newm=savm;
                 dateintsum=dateintsum+k2;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                 k2cpt++;            for (kk=1; kk<=cptcovage;kk++) {
               }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }            }
           }          
         }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                    savm=oldm;
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);            oldm=newm;
           } /* end mult */
       if  (cptcovn>0) {        
         fprintf(ficresp, "\n#********** Variable ");          s1=s[mw[mi][i]][i];
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          s2=s[mw[mi+1][i]][i];
         fprintf(ficresp, "**********\n#");          if( s2 > nlstate){ 
       }            lli=log(out[s1][s2] - savm[s1][s2]);
       for(i=1; i<=nlstate;i++)          }else{
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       fprintf(ficresp, "\n");          }
                ipmx +=1;
       for(i=(int)agemin; i <= (int)agemax+3; i++){          sw += weight[i];
         if(i==(int)agemax+3)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           printf("Total");  /*      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]); */
         else        } /* end of wave */
           printf("Age %d", i);      } /* end of individual */
         for(jk=1; jk <=nlstate ; jk++){    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             pp[jk] += freq[jk][m][i];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         }        for(mi=1; mi<= wav[i]-1; mi++){
         for(jk=1; jk <=nlstate ; jk++){          for (ii=1;ii<=nlstate+ndeath;ii++)
           for(m=-1, pos=0; m <=0 ; m++)            for (j=1;j<=nlstate+ndeath;j++){
             pos += freq[jk][m][i];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           if(pp[jk]>=1.e-10)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);            }
           else          for(d=0; d<dh[mi][i]; d++){
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);            newm=savm;
         }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
         for(jk=1; jk <=nlstate ; jk++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)            }
             pp[jk] += freq[jk][m][i];          
         }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         for(jk=1,pos=0; jk <=nlstate ; jk++)            savm=oldm;
           pos += pp[jk];            oldm=newm;
         for(jk=1; jk <=nlstate ; jk++){          } /* end mult */
           if(pos>=1.e-5)        
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);          s1=s[mw[mi][i]][i];
           else          s2=s[mw[mi+1][i]][i];
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           if( i <= (int) agemax){          ipmx +=1;
             if(pos>=1.e-5){          sw += weight[i];
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
               probs[i][jk][j1]= pp[jk]/pos;          /*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]);*/
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/        } /* end of wave */
             }      } /* end of individual */
             else    } /* End of if */
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    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;
         for(jk=-1; jk <=nlstate+ndeath; jk++)  }
           for(m=-1; m <=nlstate+ndeath; m++)  
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  /*************** log-likelihood *************/
         if(i <= (int) agemax)  double funcone( double *x)
           fprintf(ficresp,"\n");  {
         printf("\n");    /* Same as likeli but slower because of a lot of printf and if */
       }    int i, ii, j, k, mi, d, kk;
     }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   }    double **out;
   dateintmean=dateintsum/k2cpt;    double lli; /* Individual log likelihood */
      double llt;
   fclose(ficresp);    int s1, s2;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    double bbh, survp;
   free_vector(pp,1,nlstate);    /*extern weight */
      /* We are differentiating ll according to initial status */
   /* End of Freq */    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 }    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
 /************ Prevalence ********************/    */
 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)    cov[1]=1.;
 {  /* Some frequencies */  
      for(k=1; k<=nlstate; k++) ll[k]=0.;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  
   double ***freq; /* Frequencies */    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double *pp;      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double pos, k2;      for(mi=1; mi<= wav[i]-1; mi++){
         for (ii=1;ii<=nlstate+ndeath;ii++)
   pp=vector(1,nlstate);          for (j=1;j<=nlstate+ndeath;j++){
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          }
   j1=0;        for(d=0; d<dh[mi][i]; d++){
            newm=savm;
   j=cptcoveff;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          for (kk=1; kk<=cptcovage;kk++) {
              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   for(k1=1; k1<=j;k1++){          }
     for(i1=1; i1<=ncodemax[k1];i1++){          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       j1++;                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                savm=oldm;
       for (i=-1; i<=nlstate+ndeath; i++)            oldm=newm;
         for (jk=-1; jk<=nlstate+ndeath; jk++)          } /* end mult */
           for(m=agemin; m <= agemax+3; m++)        
             freq[i][jk][m]=0;        s1=s[mw[mi][i]][i];
              s2=s[mw[mi+1][i]][i];
       for (i=1; i<=imx; i++) {        bbh=(double)bh[mi][i]/(double)stepm; 
         bool=1;        /* bias is positive if real duration
         if  (cptcovn>0) {         * is higher than the multiple of stepm and negative otherwise.
           for (z1=1; z1<=cptcoveff; z1++)         */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        if( s2 > nlstate && (mle <5) ){  /* Jackson */
               bool=0;          lli=log(out[s1][s2] - savm[s1][s2]);
         }        } else if (mle==1){
         if (bool==1) {          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           for(m=firstpass; m<=lastpass; m++){        } else if(mle==2){
             k2=anint[m][i]+(mint[m][i]/12.);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        } else if(mle==3){  /* exponential inter-extrapolation */
               if(agev[m][i]==0) agev[m][i]=agemax+1;          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
               if(agev[m][i]==1) agev[m][i]=agemax+2;        } else if (mle==4){  /* mle=4 no inter-extrapolation */
               if (m<lastpass) {          lli=log(out[s1][s2]); /* Original formula */
                 if (calagedate>0)        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          lli=log(out[s1][s2]); /* Original formula */
                 else        } /* End of if */
                   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(globpr){
         }          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
       }   %10.6f %10.6f %10.6f ", \
       for(i=(int)agemin; i <= (int)agemax+3; i++){                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
         for(jk=1; jk <=nlstate ; jk++){                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
             pp[jk] += freq[jk][m][i];            llt +=ll[k]*gipmx/gsw;
         }            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
         for(jk=1; jk <=nlstate ; jk++){          }
           for(m=-1, pos=0; m <=0 ; m++)          fprintf(ficresilk," %10.6f\n", -llt);
             pos += freq[jk][m][i];        }
         }      } /* end of wave */
            } /* end of individual */
         for(jk=1; jk <=nlstate ; jk++){    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
             pp[jk] += freq[jk][m][i];    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;
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      gsw=sw;
            }
         for(jk=1; jk <=nlstate ; jk++){        return -l;
           if( i <= (int) agemax){  }
             if(pos>=1.e-5){  
               probs[i][jk][j1]= pp[jk]/pos;  char *subdirf(char fileres[])
             }  {
           }    
         }    strcpy(tmpout,optionfilefiname);
            strcat(tmpout,"/"); /* Add to the right */
       }    strcat(tmpout,fileres);
     }    return tmpout;
   }  }
   
    char *subdirf2(char fileres[], char *preop)
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  {
   free_vector(pp,1,nlstate);    
      strcpy(tmpout,optionfilefiname);
 }  /* End of Freq */    strcat(tmpout,"/");
     strcat(tmpout,preop);
 /************* Waves Concatenation ***************/    strcat(tmpout,fileres);
     return tmpout;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  }
 {  char *subdirf3(char fileres[], char *preop, char *preop2)
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  {
      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    strcpy(tmpout,optionfilefiname);
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    strcat(tmpout,"/");
      and mw[mi+1][i]. dh depends on stepm.    strcat(tmpout,preop);
      */    strcat(tmpout,preop2);
     strcat(tmpout,fileres);
   int i, mi, m;    return tmpout;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  }
      double sum=0., jmean=0.;*/  
   void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   int j, k=0,jk, ju, jl;  {
   double sum=0.;    /* This routine should help understanding what is done with 
   jmin=1e+5;       the selection of individuals/waves and
   jmax=-1;       to check the exact contribution to the likelihood.
   jmean=0.;       Plotting could be done.
   for(i=1; i<=imx; i++){     */
     mi=0;    int k;
     m=firstpass;  
     while(s[m][i] <= nlstate){    if(*globpri !=0){ /* Just counts and sums, no printings */
       if(s[m][i]>=1)      strcpy(fileresilk,"ilk"); 
         mw[++mi][i]=m;      strcat(fileresilk,fileres);
       if(m >=lastpass)      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         break;        printf("Problem with resultfile: %s\n", fileresilk);
       else        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
         m++;      }
     }/* end while */      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 (s[m][i] > nlstate){      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       mi++;     /* Death is another wave */      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       /* if(mi==0)  never been interviewed correctly before death */      for(k=1; k<=nlstate; k++) 
          /* Only death is a correct wave */        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       mw[mi][i]=m;      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     }    }
   
     wav[i]=mi;    *fretone=(*funcone)(p);
     if(mi==0)    if(*globpri !=0){
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);      fclose(ficresilk);
   }      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       fflush(fichtm); 
   for(i=1; i<=imx; i++){    } 
     for(mi=1; mi<wav[i];mi++){    return;
       if (stepm <=0)  }
         dh[mi][i]=1;  
       else{  
         if (s[mw[mi+1][i]][i] > nlstate) {  /*********** Maximum Likelihood Estimation ***************/
           if (agedc[i] < 2*AGESUP) {  
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
           if(j==0) j=1;  /* Survives at least one month after exam */  {
           k=k+1;    int i,j, iter;
           if (j >= jmax) jmax=j;    double **xi;
           if (j <= jmin) jmin=j;    double fret;
           sum=sum+j;    double fretone; /* Only one call to likelihood */
           /*if (j<0) printf("j=%d num=%d \n",j,i); */    char filerespow[FILENAMELENGTH];
           }    xi=matrix(1,npar,1,npar);
         }    for (i=1;i<=npar;i++)
         else{      for (j=1;j<=npar;j++)
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));        xi[i][j]=(i==j ? 1.0 : 0.0);
           k=k+1;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
           if (j >= jmax) jmax=j;    strcpy(filerespow,"pow"); 
           else if (j <= jmin)jmin=j;    strcat(filerespow,fileres);
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    if((ficrespow=fopen(filerespow,"w"))==NULL) {
           sum=sum+j;      printf("Problem with resultfile: %s\n", filerespow);
         }      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
         jk= j/stepm;    }
         jl= j -jk*stepm;    fprintf(ficrespow,"# Powell\n# iter -2*LL");
         ju= j -(jk+1)*stepm;    for (i=1;i<=nlstate;i++)
         if(jl <= -ju)      for(j=1;j<=nlstate+ndeath;j++)
           dh[mi][i]=jk;        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
         else    fprintf(ficrespow,"\n");
           dh[mi][i]=jk+1;  
         if(dh[mi][i]==0)    powell(p,xi,npar,ftol,&iter,&fret,func);
           dh[mi][i]=1; /* At least one step */  
       }    fclose(ficrespow);
     }    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));
   jmean=sum/k;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);  
  }  }
 /*********** Tricode ****************************/  
 void tricode(int *Tvar, int **nbcode, int imx)  /**** Computes Hessian and covariance matrix ***/
 {  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   int Ndum[20],ij=1, k, j, i;  {
   int cptcode=0;    double  **a,**y,*x,pd;
   cptcoveff=0;    double **hess;
      int i, j,jk;
   for (k=0; k<19; k++) Ndum[k]=0;    int *indx;
   for (k=1; k<=7; k++) ncodemax[k]=0;  
     double hessii(double p[], double delta, int theta, double delti[]);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    double hessij(double p[], double delti[], int i, int j);
     for (i=1; i<=imx; i++) {    void lubksb(double **a, int npar, int *indx, double b[]) ;
       ij=(int)(covar[Tvar[j]][i]);    void ludcmp(double **a, int npar, int *indx, double *d) ;
       Ndum[ij]++;  
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    hess=matrix(1,npar,1,npar);
       if (ij > cptcode) cptcode=ij;  
     }    printf("\nCalculation of the hessian matrix. Wait...\n");
     fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     for (i=0; i<=cptcode; i++) {    for (i=1;i<=npar;i++){
       if(Ndum[i]!=0) ncodemax[j]++;      printf("%d",i);fflush(stdout);
     }      fprintf(ficlog,"%d",i);fflush(ficlog);
     ij=1;      hess[i][i]=hessii(p,ftolhess,i,delti);
       /*printf(" %f ",p[i]);*/
       /*printf(" %lf ",hess[i][i]);*/
     for (i=1; i<=ncodemax[j]; i++) {    }
       for (k=0; k<=19; k++) {    
         if (Ndum[k] != 0) {    for (i=1;i<=npar;i++) {
           nbcode[Tvar[j]][ij]=k;      for (j=1;j<=npar;j++)  {
                  if (j>i) { 
           ij++;          printf(".%d%d",i,j);fflush(stdout);
         }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
         if (ij > ncodemax[j]) break;          hess[i][j]=hessij(p,delti,i,j);
       }            hess[j][i]=hess[i][j];    
     }          /*printf(" %lf ",hess[i][j]);*/
   }          }
       }
  for (k=0; k<19; k++) Ndum[k]=0;    }
     printf("\n");
  for (i=1; i<=ncovmodel-2; i++) {    fprintf(ficlog,"\n");
       ij=Tvar[i];  
       Ndum[ij]++;    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     }    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     
  ij=1;    a=matrix(1,npar,1,npar);
  for (i=1; i<=10; i++) {    y=matrix(1,npar,1,npar);
    if((Ndum[i]!=0) && (i<=ncovcol)){    x=vector(1,npar);
      Tvaraff[ij]=i;    indx=ivector(1,npar);
      ij++;    for (i=1;i<=npar;i++)
    }      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
  }    ludcmp(a,npar,indx,&pd);
    
     cptcoveff=ij-1;    for (j=1;j<=npar;j++) {
 }      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
 /*********** Health Expectancies ****************/      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
 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 )        matcov[i][j]=x[i];
       }
 {    }
   /* Health expectancies */  
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;    printf("\n#Hessian matrix#\n");
   double age, agelim, hf;    fprintf(ficlog,"\n#Hessian matrix#\n");
   double ***p3mat,***varhe;    for (i=1;i<=npar;i++) { 
   double **dnewm,**doldm;      for (j=1;j<=npar;j++) { 
   double *xp;        printf("%.3e ",hess[i][j]);
   double **gp, **gm;        fprintf(ficlog,"%.3e ",hess[i][j]);
   double ***gradg, ***trgradg;      }
   int theta;      printf("\n");
       fprintf(ficlog,"\n");
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);    }
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate*2,1,npar);    /* Recompute Inverse */
   doldm=matrix(1,nlstate*2,1,nlstate*2);    for (i=1;i<=npar;i++)
        for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   fprintf(ficreseij,"# Health expectancies\n");    ludcmp(a,npar,indx,&pd);
   fprintf(ficreseij,"# Age");  
   for(i=1; i<=nlstate;i++)    /*  printf("\n#Hessian matrix recomputed#\n");
     for(j=1; j<=nlstate;j++)  
       fprintf(ficreseij," %1d-%1d (SE)",i,j);    for (j=1;j<=npar;j++) {
   fprintf(ficreseij,"\n");      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
   if(estepm < stepm){      lubksb(a,npar,indx,x);
     printf ("Problem %d lower than %d\n",estepm, stepm);      for (i=1;i<=npar;i++){ 
   }        y[i][j]=x[i];
   else  hstepm=estepm;          printf("%.3e ",y[i][j]);
   /* We compute the life expectancy from trapezoids spaced every estepm months        fprintf(ficlog,"%.3e ",y[i][j]);
    * 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      printf("\n");
    * we are calculating an estimate of the Life Expectancy assuming a linear      fprintf(ficlog,"\n");
    * progression inbetween and thus overestimating or underestimating according    }
    * to the curvature of the survival function. If, for the same date, we    */
    * estimate the model with stepm=1 month, we can keep estepm to 24 months  
    * to compare the new estimate of Life expectancy with the same linear    free_matrix(a,1,npar,1,npar);
    * hypothesis. A more precise result, taking into account a more precise    free_matrix(y,1,npar,1,npar);
    * curvature will be obtained if estepm is as small as stepm. */    free_vector(x,1,npar);
     free_ivector(indx,1,npar);
   /* For example we decided to compute the life expectancy with the smallest unit */    free_matrix(hess,1,npar,1,npar);
   /* 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.  }
      Look at hpijx to understand the reason of that which relies in memory size  
      and note for a fixed period like estepm months */  /*************** hessian matrix ****************/
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the  double hessii( double x[], double delta, int theta, double delti[])
      survival function given by stepm (the optimization length). Unfortunately it  {
      means that if the survival funtion is printed only each two years of age and if    int i;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    int l=1, lmax=20;
      results. So we changed our mind and took the option of the best precision.    double k1,k2;
   */    double p2[NPARMAX+1];
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    double res;
     double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   agelim=AGESUP;    double fx;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    int k=0,kmax=10;
     /* nhstepm age range expressed in number of stepm */    double l1;
     nstepm=(int) rint((agelim-age)*YEARM/stepm);  
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    fx=func(x);
     /* if (stepm >= YEARM) hstepm=1;*/    for (i=1;i<=npar;i++) p2[i]=x[i];
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    for(l=0 ; l <=lmax; l++){
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      l1=pow(10,l);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);      delts=delt;
     gp=matrix(0,nhstepm,1,nlstate*2);      for(k=1 ; k <kmax; k=k+1){
     gm=matrix(0,nhstepm,1,nlstate*2);        delt = delta*(l1*k);
         p2[theta]=x[theta] +delt;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored        k1=func(p2)-fx;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        p2[theta]=x[theta]-delt;
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);          k2=func(p2)-fx;
          /*res= (k1-2.0*fx+k2)/delt/delt; */
         res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        
   #ifdef DEBUG
     /* Computing Variances of health expectancies */        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
      for(theta=1; theta <=npar; theta++){  #endif
       for(i=1; i<=npar; i++){        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
       }          k=kmax;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          }
          else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       cptj=0;          k=kmax; l=lmax*10.;
       for(j=1; j<= nlstate; j++){        }
         for(i=1; i<=nlstate; i++){        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           cptj=cptj+1;          delts=delt;
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){        }
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;      }
           }    }
         }    delti[theta]=delts;
       }    return res; 
          
        }
       for(i=1; i<=npar; i++)  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  double hessij( double x[], double delti[], int thetai,int thetaj)
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    {
          int i;
       cptj=0;    int l=1, l1, lmax=20;
       for(j=1; j<= nlstate; j++){    double k1,k2,k3,k4,res,fx;
         for(i=1;i<=nlstate;i++){    double p2[NPARMAX+1];
           cptj=cptj+1;    int k;
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){  
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    fx=func(x);
           }    for (k=1; k<=2; k++) {
         }      for (i=1;i<=npar;i++) p2[i]=x[i];
       }      p2[thetai]=x[thetai]+delti[thetai]/k;
       for(j=1; j<= nlstate*2; j++)      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         for(h=0; h<=nhstepm-1; h++){      k1=func(p2)-fx;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    
         }      p2[thetai]=x[thetai]+delti[thetai]/k;
      }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
          k2=func(p2)-fx;
 /* End theta */    
       p2[thetai]=x[thetai]-delti[thetai]/k;
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k3=func(p2)-fx;
      for(h=0; h<=nhstepm-1; h++)    
       for(j=1; j<=nlstate*2;j++)      p2[thetai]=x[thetai]-delti[thetai]/k;
         for(theta=1; theta <=npar; theta++)      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
           trgradg[h][j][theta]=gradg[h][theta][j];      k4=func(p2)-fx;
            res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   #ifdef DEBUG
      for(i=1;i<=nlstate*2;i++)      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       for(j=1;j<=nlstate*2;j++)      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);
         varhe[i][j][(int)age] =0.;  #endif
     }
      printf("%d|",(int)age);fflush(stdout);    return res;
      for(h=0;h<=nhstepm-1;h++){  }
       for(k=0;k<=nhstepm-1;k++){  
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);  /************** Inverse of matrix **************/
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);  void ludcmp(double **a, int n, int *indx, double *d) 
         for(i=1;i<=nlstate*2;i++)  { 
           for(j=1;j<=nlstate*2;j++)    int i,imax,j,k; 
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;    double big,dum,sum,temp; 
       }    double *vv; 
     }   
     /* Computing expectancies */    vv=vector(1,n); 
     for(i=1; i<=nlstate;i++)    *d=1.0; 
       for(j=1; j<=nlstate;j++)    for (i=1;i<=n;i++) { 
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){      big=0.0; 
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;      for (j=1;j<=n;j++) 
                  if ((temp=fabs(a[i][j])) > big) big=temp; 
 /* 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 (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
       vv[i]=1.0/big; 
         }    } 
     for (j=1;j<=n;j++) { 
     fprintf(ficreseij,"%3.0f",age );      for (i=1;i<j;i++) { 
     cptj=0;        sum=a[i][j]; 
     for(i=1; i<=nlstate;i++)        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
       for(j=1; j<=nlstate;j++){        a[i][j]=sum; 
         cptj++;      } 
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );      big=0.0; 
       }      for (i=j;i<=n;i++) { 
     fprintf(ficreseij,"\n");        sum=a[i][j]; 
            for (k=1;k<j;k++) 
     free_matrix(gm,0,nhstepm,1,nlstate*2);          sum -= a[i][k]*a[k][j]; 
     free_matrix(gp,0,nhstepm,1,nlstate*2);        a[i][j]=sum; 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);          big=dum; 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          imax=i; 
   }        } 
   printf("\n");      } 
       if (j != imax) { 
   free_vector(xp,1,npar);        for (k=1;k<=n;k++) { 
   free_matrix(dnewm,1,nlstate*2,1,npar);          dum=a[imax][k]; 
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);          a[imax][k]=a[j][k]; 
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);          a[j][k]=dum; 
 }        } 
         *d = -(*d); 
 /************ Variance ******************/        vv[imax]=vv[j]; 
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)      } 
 {      indx[j]=imax; 
   /* Variance of health expectancies */      if (a[j][j] == 0.0) a[j][j]=TINY; 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      if (j != n) { 
   double **newm;        dum=1.0/(a[j][j]); 
   double **dnewm,**doldm;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   int i, j, nhstepm, hstepm, h, nstepm ;      } 
   int k, cptcode;    } 
   double *xp;    free_vector(vv,1,n);  /* Doesn't work */
   double **gp, **gm;  ;
   double ***gradg, ***trgradg;  } 
   double ***p3mat;  
   double age,agelim, hf;  void lubksb(double **a, int n, int *indx, double b[]) 
   int theta;  { 
     int i,ii=0,ip,j; 
   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");    double sum; 
   fprintf(ficresvij,"# Age");   
   for(i=1; i<=nlstate;i++)    for (i=1;i<=n;i++) { 
     for(j=1; j<=nlstate;j++)      ip=indx[i]; 
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      sum=b[ip]; 
   fprintf(ficresvij,"\n");      b[ip]=b[i]; 
       if (ii) 
   xp=vector(1,npar);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   dnewm=matrix(1,nlstate,1,npar);      else if (sum) ii=i; 
   doldm=matrix(1,nlstate,1,nlstate);      b[i]=sum; 
      } 
   if(estepm < stepm){    for (i=n;i>=1;i--) { 
     printf ("Problem %d lower than %d\n",estepm, stepm);      sum=b[i]; 
   }      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   else  hstepm=estepm;        b[i]=sum/a[i][i]; 
   /* For example we decided to compute the life expectancy with the smallest unit */    } 
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.  } 
      nhstepm is the number of hstepm from age to agelim  
      nstepm is the number of stepm from age to agelin.  /************ Frequencies ********************/
      Look at hpijx to understand the reason of that which relies in memory size  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)
      and note for a fixed period like k years */  {  /* Some frequencies */
   /* 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    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
      means that if the survival funtion is printed only each two years of age and if    int first;
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    double ***freq; /* Frequencies */
      results. So we changed our mind and took the option of the best precision.    double *pp, **prop;
   */    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    FILE *ficresp;
   agelim = AGESUP;    char fileresp[FILENAMELENGTH];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    pp=vector(1,nlstate);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    prop=matrix(1,nlstate,iagemin,iagemax+3);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    strcpy(fileresp,"p");
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    strcat(fileresp,fileres);
     gp=matrix(0,nhstepm,1,nlstate);    if((ficresp=fopen(fileresp,"w"))==NULL) {
     gm=matrix(0,nhstepm,1,nlstate);      printf("Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     for(theta=1; theta <=npar; theta++){      exit(0);
       for(i=1; i<=npar; i++){ /* Computes gradient */    }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
       }    j1=0;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    j=cptcoveff;
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
       if (popbased==1) {  
         for(i=1; i<=nlstate;i++)    first=1;
           prlim[i][i]=probs[(int)age][i][ij];  
       }    for(k1=1; k1<=j;k1++){
        for(i1=1; i1<=ncodemax[k1];i1++){
       for(j=1; j<= nlstate; j++){        j1++;
         for(h=0; h<=nhstepm; h++){        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          scanf("%d", i);*/
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        for (i=-1; i<=nlstate+ndeath; i++)  
         }          for (jk=-1; jk<=nlstate+ndeath; jk++)  
       }            for(m=iagemin; m <= iagemax+3; m++)
                  freq[i][jk][m]=0;
       for(i=1; i<=npar; i++) /* Computes gradient */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      for (i=1; i<=nlstate; i++)  
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          for(m=iagemin; m <= iagemax+3; m++)
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          prop[i][m]=0;
          
       if (popbased==1) {        dateintsum=0;
         for(i=1; i<=nlstate;i++)        k2cpt=0;
           prlim[i][i]=probs[(int)age][i][ij];        for (i=1; i<=imx; i++) {
       }          bool=1;
           if  (cptcovn>0) {
       for(j=1; j<= nlstate; j++){            for (z1=1; z1<=cptcoveff; z1++) 
         for(h=0; h<=nhstepm; h++){              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)                bool=0;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          }
         }          if (bool==1){
       }            for(m=firstpass; m<=lastpass; m++){
               k2=anint[m][i]+(mint[m][i]/12.);
       for(j=1; j<= nlstate; j++)              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
         for(h=0; h<=nhstepm; h++){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];                if(agev[m][i]==1) agev[m][i]=iagemax+2;
         }                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     } /* End theta */                if (m<lastpass) {
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
                 }
     for(h=0; h<=nhstepm; h++)                
       for(j=1; j<=nlstate;j++)                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
         for(theta=1; theta <=npar; theta++)                  dateintsum=dateintsum+k2;
           trgradg[h][j][theta]=gradg[h][theta][j];                  k2cpt++;
                 }
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */                /*}*/
     for(i=1;i<=nlstate;i++)            }
       for(j=1;j<=nlstate;j++)          }
         vareij[i][j][(int)age] =0.;        }
          
     for(h=0;h<=nhstepm;h++){        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       for(k=0;k<=nhstepm;k++){  
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);        if  (cptcovn>0) {
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          fprintf(ficresp, "\n#********** Variable "); 
         for(i=1;i<=nlstate;i++)          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           for(j=1;j<=nlstate;j++)          fprintf(ficresp, "**********\n#");
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;        }
       }        for(i=1; i<=nlstate;i++) 
     }          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         fprintf(ficresp, "\n");
     fprintf(ficresvij,"%.0f ",age );        
     for(i=1; i<=nlstate;i++)        for(i=iagemin; i <= iagemax+3; i++){
       for(j=1; j<=nlstate;j++){          if(i==iagemax+3){
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);            fprintf(ficlog,"Total");
       }          }else{
     fprintf(ficresvij,"\n");            if(first==1){
     free_matrix(gp,0,nhstepm,1,nlstate);              first=0;
     free_matrix(gm,0,nhstepm,1,nlstate);              printf("See log file for details...\n");
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);            }
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);            fprintf(ficlog,"Age %d", i);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          }
   } /* End age */          for(jk=1; jk <=nlstate ; jk++){
              for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   free_vector(xp,1,npar);              pp[jk] += freq[jk][m][i]; 
   free_matrix(doldm,1,nlstate,1,npar);          }
   free_matrix(dnewm,1,nlstate,1,nlstate);          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pos=0; m <=0 ; m++)
 }              pos += freq[jk][m][i];
             if(pp[jk]>=1.e-10){
 /************ Variance of prevlim ******************/              if(first==1){
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 {              }
   /* Variance of prevalence limit */              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            }else{
   double **newm;              if(first==1)
   double **dnewm,**doldm;                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   int i, j, nhstepm, hstepm;              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   int k, cptcode;            }
   double *xp;          }
   double *gp, *gm;  
   double **gradg, **trgradg;          for(jk=1; jk <=nlstate ; jk++){
   double age,agelim;            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   int theta;              pp[jk] += freq[jk][m][i];
              }       
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   fprintf(ficresvpl,"# Age");            pos += pp[jk];
   for(i=1; i<=nlstate;i++)            posprop += prop[jk][i];
       fprintf(ficresvpl," %1d-%1d",i,i);          }
   fprintf(ficresvpl,"\n");          for(jk=1; jk <=nlstate ; jk++){
             if(pos>=1.e-5){
   xp=vector(1,npar);              if(first==1)
   dnewm=matrix(1,nlstate,1,npar);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   doldm=matrix(1,nlstate,1,nlstate);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
              }else{
   hstepm=1*YEARM; /* Every year of age */              if(first==1)
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   agelim = AGESUP;              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            if( i <= iagemax){
     if (stepm >= YEARM) hstepm=1;              if(pos>=1.e-5){
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
     gradg=matrix(1,npar,1,nlstate);                /*probs[i][jk][j1]= pp[jk]/pos;*/
     gp=vector(1,nlstate);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     gm=vector(1,nlstate);              }
               else
     for(theta=1; theta <=npar; theta++){                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
       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(jk=-1; jk <=nlstate+ndeath; jk++)
       for(i=1;i<=nlstate;i++)            for(m=-1; m <=nlstate+ndeath; m++)
         gp[i] = prlim[i][i];              if(freq[jk][m][i] !=0 ) {
                  if(first==1)
       for(i=1; i<=npar; i++) /* Computes gradient */                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              }
       for(i=1;i<=nlstate;i++)          if(i <= iagemax)
         gm[i] = prlim[i][i];            fprintf(ficresp,"\n");
           if(first==1)
       for(i=1;i<=nlstate;i++)            printf("Others in log...\n");
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          fprintf(ficlog,"\n");
     } /* End theta */        }
       }
     trgradg =matrix(1,nlstate,1,npar);    }
     dateintmean=dateintsum/k2cpt; 
     for(j=1; j<=nlstate;j++)   
       for(theta=1; theta <=npar; theta++)    fclose(ficresp);
         trgradg[j][theta]=gradg[theta][j];    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
     free_vector(pp,1,nlstate);
     for(i=1;i<=nlstate;i++)    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
       varpl[i][(int)age] =0.;    /* End of Freq */
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);  }
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);  
     for(i=1;i<=nlstate;i++)  /************ Prevalence ********************/
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */  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)
   {  
     fprintf(ficresvpl,"%.0f ",age );    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     for(i=1; i<=nlstate;i++)       in each health status at the date of interview (if between dateprev1 and dateprev2).
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));       We still use firstpass and lastpass as another selection.
     fprintf(ficresvpl,"\n");    */
     free_vector(gp,1,nlstate);   
     free_vector(gm,1,nlstate);    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     free_matrix(gradg,1,npar,1,nlstate);    double ***freq; /* Frequencies */
     free_matrix(trgradg,1,nlstate,1,npar);    double *pp, **prop;
   } /* End age */    double pos,posprop; 
     double  y2; /* in fractional years */
   free_vector(xp,1,npar);    int iagemin, iagemax;
   free_matrix(doldm,1,nlstate,1,npar);  
   free_matrix(dnewm,1,nlstate,1,nlstate);    iagemin= (int) agemin;
     iagemax= (int) agemax;
 }    /*pp=vector(1,nlstate);*/
     prop=matrix(1,nlstate,iagemin,iagemax+3); 
 /************ Variance of one-step probabilities  ******************/    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)    j1=0;
 {    
   int i, j,  i1, k1, l1;    j=cptcoveff;
   int k2, l2, j1,  z1;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   int k=0,l, cptcode;    
   int first=1;    for(k1=1; k1<=j;k1++){
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;      for(i1=1; i1<=ncodemax[k1];i1++){
   double **dnewm,**doldm;        j1++;
   double *xp;        
   double *gp, *gm;        for (i=1; i<=nlstate; i++)  
   double **gradg, **trgradg;          for(m=iagemin; m <= iagemax+3; m++)
   double **mu;            prop[i][m]=0.0;
   double age,agelim, cov[NCOVMAX];       
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */        for (i=1; i<=imx; i++) { /* Each individual */
   int theta;          bool=1;
   char fileresprob[FILENAMELENGTH];          if  (cptcovn>0) {
   char fileresprobcov[FILENAMELENGTH];            for (z1=1; z1<=cptcoveff; z1++) 
   char fileresprobcor[FILENAMELENGTH];              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                 bool=0;
   double ***varpij;          } 
           if (bool==1) { 
   strcpy(fileresprob,"prob");            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   strcat(fileresprob,fileres);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
     printf("Problem with resultfile: %s\n", fileresprob);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   strcpy(fileresprobcov,"probcov");                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); 
   strcat(fileresprobcov,fileres);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {                  /*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]]);*/
     printf("Problem with resultfile: %s\n", fileresprobcov);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   }                  prop[s[m][i]][iagemax+3] += weight[i]; 
   strcpy(fileresprobcor,"probcor");                } 
   strcat(fileresprobcor,fileres);              }
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {            } /* end selection of waves */
     printf("Problem with resultfile: %s\n", fileresprobcor);          }
   }        }
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);        for(i=iagemin; i <= iagemax+3; i++){  
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);          
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
              posprop += prop[jk][i]; 
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");          } 
   fprintf(ficresprob,"# Age");  
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");          for(jk=1; jk <=nlstate ; jk++){     
   fprintf(ficresprobcov,"# Age");            if( i <=  iagemax){ 
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");              if(posprop>=1.e-5){ 
   fprintf(ficresprobcov,"# Age");                probs[i][jk][j1]= prop[jk][i]/posprop;
               } 
             } 
   for(i=1; i<=nlstate;i++)          }/* end jk */ 
     for(j=1; j<=(nlstate+ndeath);j++){        }/* end i */ 
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);      } /* end i1 */
       fprintf(ficresprobcov," p%1d-%1d ",i,j);    } /* end k1 */
       fprintf(ficresprobcor," p%1d-%1d ",i,j);    
     }      /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   fprintf(ficresprob,"\n");    /*free_vector(pp,1,nlstate);*/
   fprintf(ficresprobcov,"\n");    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   fprintf(ficresprobcor,"\n");  }  /* End of prevalence */
   xp=vector(1,npar);  
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);  /************* Waves Concatenation ***************/
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));  
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);  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)
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);  {
   first=1;    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {       Death is a valid wave (if date is known).
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
     exit(0);       dh[m][i] or 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.
   else{       */
     fprintf(ficgp,"\n# Routine varprob");  
   }    int i, mi, m;
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
     printf("Problem with html file: %s\n", optionfilehtm);       double sum=0., jmean=0.;*/
     exit(0);    int first;
   }    int j, k=0,jk, ju, jl;
   else{    double sum=0.;
     fprintf(fichtm,"\n<H2> Computing matrix of variance-covariance of step probabilities</h2>\n");    first=0;
     fprintf(fichtm,"\n<br> We have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");    jmin=1e+5;
     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");    jmax=-1;
     jmean=0.;
   }    for(i=1; i<=imx; i++){
   cov[1]=1;      mi=0;
   j=cptcoveff;      m=firstpass;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      while(s[m][i] <= nlstate){
   j1=0;        if(s[m][i]>=1)
   for(k1=1; k1<=1;k1++){          mw[++mi][i]=m;
     for(i1=1; i1<=ncodemax[k1];i1++){        if(m >=lastpass)
     j1++;          break;
         else
     if  (cptcovn>0) {          m++;
       fprintf(ficresprob, "\n#********** Variable ");      }/* end while */
       fprintf(ficresprobcov, "\n#********** Variable ");      if (s[m][i] > nlstate){
       fprintf(ficgp, "\n#********** Variable ");        mi++;     /* Death is another wave */
       fprintf(fichtm, "\n<h4>********** Variable</h4>\n ");        /* if(mi==0)  never been interviewed correctly before death */
       fprintf(ficresprobcor, "\n#********** Variable ");           /* Only death is a correct wave */
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        mw[mi][i]=m;
       fprintf(ficresprob, "**********\n#");      }
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
       fprintf(ficresprobcov, "**********\n#");      wav[i]=mi;
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      if(mi==0){
       fprintf(ficgp, "**********\n#");        if(first==0){
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
       fprintf(ficgp, "**********\n#");          first=1;
       for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        }
       fprintf(fichtm, "**********\n#");        if(first==1){
     }          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
            }
       for (age=bage; age<=fage; age ++){      } /* end mi==0 */
         cov[2]=age;    } /* End individuals */
         for (k=1; k<=cptcovn;k++) {  
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];    for(i=1; i<=imx; i++){
         }      for(mi=1; mi<wav[i];mi++){
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        if (stepm <=0)
         for (k=1; k<=cptcovprod;k++)          dh[mi][i]=1;
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        else{
                  if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));            if (agedc[i] < 2*AGESUP) {
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
         gp=vector(1,(nlstate)*(nlstate+ndeath));              if(j==0) j=1;  /* Survives at least one month after exam */
         gm=vector(1,(nlstate)*(nlstate+ndeath));              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]);
         for(theta=1; theta <=npar; theta++){                j=1; /* Careful Patch */
           for(i=1; i<=npar; i++)                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);
             xp[i] = x[i] + (i==theta ?delti[theta]: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]);
                          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);
           pmij(pmmij,cov,ncovmodel,xp,nlstate);              }
                        k=k+1;
           k=0;              if (j >= jmax) jmax=j;
           for(i=1; i<= (nlstate); i++){              if (j <= jmin) jmin=j;
             for(j=1; j<=(nlstate+ndeath);j++){              sum=sum+j;
               k=k+1;              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
               gp[k]=pmmij[i][j];              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             }            }
           }          }
                    else{
           for(i=1; i<=npar; i++)            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
             xp[i] = x[i] - (i==theta ?delti[theta]:0);            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
                k=k+1;
           pmij(pmmij,cov,ncovmodel,xp,nlstate);            if (j >= jmax) jmax=j;
           k=0;            else if (j <= jmin)jmin=j;
           for(i=1; i<=(nlstate); i++){            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             for(j=1; j<=(nlstate+ndeath);j++){            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
               k=k+1;            if(j<0){
               gm[k]=pmmij[i][j];              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             }              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
           }            }
                  sum=sum+j;
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)          }
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];            jk= j/stepm;
         }          jl= j -jk*stepm;
           ju= j -(jk+1)*stepm;
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
           for(theta=1; theta <=npar; theta++)            if(jl==0){
             trgradg[j][theta]=gradg[theta][j];              dh[mi][i]=jk;
                      bh[mi][i]=0;
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);            }else{ /* We want a negative bias in order to only have interpolation ie
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);                    * at the price of an extra matrix product in likelihood */
                      dh[mi][i]=jk+1;
         pmij(pmmij,cov,ncovmodel,x,nlstate);              bh[mi][i]=ju;
                    }
         k=0;          }else{
         for(i=1; i<=(nlstate); i++){            if(jl <= -ju){
           for(j=1; j<=(nlstate+ndeath);j++){              dh[mi][i]=jk;
             k=k+1;              bh[mi][i]=jl;       /* bias is positive if real duration
             mu[k][(int) age]=pmmij[i][j];                                   * is higher than the multiple of stepm and negative otherwise.
           }                                   */
         }            }
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)            else{
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)              dh[mi][i]=jk+1;
             varpij[i][j][(int)age] = doldm[i][j];              bh[mi][i]=ju;
             }
         /*printf("\n%d ",(int)age);            if(dh[mi][i]==0){
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){              dh[mi][i]=1; /* At least one step */
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));              bh[mi][i]=ju; /* At least one step */
      }*/              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
             }
         fprintf(ficresprob,"\n%d ",(int)age);          } /* end if mle */
         fprintf(ficresprobcov,"\n%d ",(int)age);        }
         fprintf(ficresprobcor,"\n%d ",(int)age);      } /* end wave */
     }
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)    jmean=sum/k;
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);   }
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);  
         }  /*********** Tricode ****************************/
         i=0;  void tricode(int *Tvar, int **nbcode, int imx)
         for (k=1; k<=(nlstate);k++){  {
           for (l=1; l<=(nlstate+ndeath);l++){    
             i=i++;    int Ndum[20],ij=1, k, j, i, maxncov=19;
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);    int cptcode=0;
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);    cptcoveff=0; 
             for (j=1; j<=i;j++){   
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);    for (k=0; k<maxncov; k++) Ndum[k]=0;
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));    for (k=1; k<=7; k++) ncodemax[k]=0;
             }  
           }    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
         }/* end of loop for state */      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
       } /* end of loop for age */                                 modality*/ 
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
       for (k1=1; k1<=(nlstate);k1++){        Ndum[ij]++; /*store the modality */
         for (l1=1; l1<=(nlstate+ndeath);l1++){        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
           if(l1==k1) continue;        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
           i=(k1-1)*(nlstate+ndeath)+l1;                                         Tvar[j]. If V=sex and male is 0 and 
           for (k2=1; k2<=(nlstate);k2++){                                         female is 1, then  cptcode=1.*/
             for (l2=1; l2<=(nlstate+ndeath);l2++){      }
               if(l2==k2) continue;  
               j=(k2-1)*(nlstate+ndeath)+l2;      for (i=0; i<=cptcode; i++) {
               if(j<=i) continue;        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 */
               for (age=bage; age<=fage; age ++){      }
                 if ((int)age %5==0){  
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;      ij=1; 
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;      for (i=1; i<=ncodemax[j]; i++) {
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;        for (k=0; k<= maxncov; k++) {
                   mu1=mu[i][(int) age]/stepm*YEARM ;          if (Ndum[k] != 0) {
                   mu2=mu[j][(int) age]/stepm*YEARM;            nbcode[Tvar[j]][ij]=k; 
                   /* Computing eigen value of matrix of covariance */            /* 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; */
                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));            
                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));            ij++;
                   printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);          }
                   /* Eigen vectors */          if (ij > ncodemax[j]) break; 
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));        }  
                   v21=sqrt(1.-v11*v11);      } 
                   v12=-v21;    }  
                   v22=v11;  
                   /*printf(fignu*/   for (k=0; k< maxncov; k++) Ndum[k]=0;
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */  
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */   for (i=1; i<=ncovmodel-2; i++) { 
                   if(first==1){     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
                     first=0;     ij=Tvar[i];
                     fprintf(ficgp,"\nset parametric;set nolabel");     Ndum[ij]++;
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);   }
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");  
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%1d%1d-%1d%1d.png\">varpijgr%s%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1);   ij=1;
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%1d%1d-%1d%1d.png\">, ",optionfilefiname,k2,l2,k1,l1);   for (i=1; i<= maxncov; i++) {
                     fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\"",optionfilefiname,k2,l2,k1,l1);     if((Ndum[i]!=0) && (i<=ncovcol)){
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);       Tvaraff[ij]=i; /*For printing */
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);       ij++;
                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\     }
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \   }
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);   
                   }else{   cptcoveff=ij-1; /*Number of simple covariates*/
                     first=0;  }
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);  
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);  /*********** Health Expectancies ****************/
                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\  
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \  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 )
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);  
                   }/* if first */  {
                 } /* age mod 5 */    /* Health expectancies */
               } /* end loop age */    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
               fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\";replot;",optionfilefiname,k2,l2,k1,l1);    double age, agelim, hf;
               first=1;    double ***p3mat,***varhe;
             } /*l12 */    double **dnewm,**doldm;
           } /* k12 */    double *xp;
         } /*l1 */    double **gp, **gm;
       }/* k1 */    double ***gradg, ***trgradg;
     } /* loop covariates */    int theta;
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);  
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    xp=vector(1,npar);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);    dnewm=matrix(1,nlstate*nlstate,1,npar);
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    
   }    fprintf(ficreseij,"# Health expectancies\n");
   free_vector(xp,1,npar);    fprintf(ficreseij,"# Age");
   fclose(ficresprob);    for(i=1; i<=nlstate;i++)
   fclose(ficresprobcov);      for(j=1; j<=nlstate;j++)
   fclose(ficresprobcor);        fprintf(ficreseij," %1d-%1d (SE)",i,j);
   fclose(ficgp);    fprintf(ficreseij,"\n");
   fclose(fichtm);  
 }    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
 /******************* Printing html file ***********/    else  hstepm=estepm;   
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \    /* We compute the life expectancy from trapezoids spaced every estepm months
                   int lastpass, int stepm, int weightopt, char model[],\     * This is mainly to measure the difference between two models: for example
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\     * if stepm=24 months pijx are given only every 2 years and by summing them
                   int popforecast, int estepm ,\     * we are calculating an estimate of the Life Expectancy assuming a linear 
                   double jprev1, double mprev1,double anprev1, \     * progression in between and thus overestimating or underestimating according
                   double jprev2, double mprev2,double anprev2){     * to the curvature of the survival function. If, for the same date, we 
   int jj1, k1, i1, cpt;     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   /*char optionfilehtm[FILENAMELENGTH];*/     * to compare the new estimate of Life expectancy with the same linear 
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {     * hypothesis. A more precise result, taking into account a more precise
     printf("Problem with %s \n",optionfilehtm), exit(0);     * curvature will be obtained if estepm is as small as stepm. */
   }  
     /* For example we decided to compute the life expectancy with the smallest unit */
    fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
  - 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       nhstepm is the number of hstepm from age to agelim 
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n       nstepm is the number of stepm from age to agelin. 
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n       Look at hpijx to understand the reason of that which relies in memory size
  - Life expectancies by age and initial health status (estepm=%2d months):       and note for a fixed period like estepm months */
    <a href=\"e%s\">e%s</a> <br>\n</li>", \    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);       survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
  fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n       results. So we changed our mind and took the option of the best precision.
  - 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    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
  - 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    agelim=AGESUP;
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
  - 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);      /* nhstepm age range expressed in number of stepm */
       nstepm=(int) rint((agelim-age)*YEARM/stepm); 
  if(popforecast==1) fprintf(fichtm,"\n      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n      /* if (stepm >= YEARM) hstepm=1;*/
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         <br>",fileres,fileres,fileres,fileres);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  else      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
    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);      gp=matrix(0,nhstepm,1,nlstate*nlstate);
 fprintf(fichtm," <li>Graphs</li><p>");      gm=matrix(0,nhstepm,1,nlstate*nlstate);
   
  m=cptcoveff;      /* Computed by stepm unit matrices, product of hstepm matrices, stored
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
  jj1=0;   
  for(k1=1; k1<=m;k1++){  
    for(i1=1; i1<=ncodemax[k1];i1++){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
      jj1++;  
      if (cptcovn > 0) {      /* Computing Variances of health expectancies */
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");  
        for (cpt=1; cpt<=cptcoveff;cpt++)       for(theta=1; theta <=npar; theta++){
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);        for(i=1; i<=npar; i++){ 
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
      }        }
      /* Pij */        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, 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);            cptj=0;
      /* Quasi-incidences */        for(j=1; j<= nlstate; j++){
      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);            cptj=cptj+1;
        /* Stable prevalence in each health state */            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
        for(cpt=1; cpt<nlstate;cpt++){              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>            }
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          }
        }        }
     for(cpt=1; cpt<=nlstate;cpt++) {       
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident       
 interval) in state (%d): v%s%d%d.png <br>        for(i=1; i<=npar; i++) 
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            xp[i] = x[i] - (i==theta ?delti[theta]:0);
      }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
      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>        cptj=0;
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        for(j=1; j<= nlstate; j++){
      }          for(i=1;i<=nlstate;i++){
      fprintf(fichtm,"\n<br>- Total life expectancy by age and            cptj=cptj+1;
 health expectancies in states (1) and (2): e%s%d.png<br>            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);  
    }              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
  }            }
 fclose(fichtm);          }
 }        }
         for(j=1; j<= nlstate*nlstate; j++)
 /******************* Gnuplot file **************/          for(h=0; h<=nhstepm-1; h++){
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;       } 
   int ng;     
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {  /* End theta */
     printf("Problem with file %s",optionfilegnuplot);  
   }       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   
 #ifdef windows       for(h=0; h<=nhstepm-1; h++)
     fprintf(ficgp,"cd \"%s\" \n",pathc);        for(j=1; j<=nlstate*nlstate;j++)
 #endif          for(theta=1; theta <=npar; theta++)
 m=pow(2,cptcoveff);            trgradg[h][j][theta]=gradg[h][theta][j];
         
  /* 1eme*/  
   for (cpt=1; cpt<= nlstate ; cpt ++) {       for(i=1;i<=nlstate*nlstate;i++)
    for (k1=1; k1<= m ; k1 ++) {        for(j=1;j<=nlstate*nlstate;j++)
           varhe[i][j][(int)age] =0.;
 #ifdef windows  
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);       printf("%d|",(int)age);fflush(stdout);
      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);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
 #endif       for(h=0;h<=nhstepm-1;h++){
 #ifdef unix        for(k=0;k<=nhstepm-1;k++){
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
 #endif          for(i=1;i<=nlstate*nlstate;i++)
             for(j=1;j<=nlstate*nlstate;j++)
 for (i=1; i<= nlstate ; i ++) {              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        }
   else fprintf(ficgp," \%%*lf (\%%*lf)");      }
 }      /* Computing expectancies */
     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++)
     for (i=1; i<= nlstate ; i ++) {        for(j=1; j<=nlstate;j++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
 }            
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
      for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          }
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }        fprintf(ficreseij,"%3.0f",age );
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      cptj=0;
 #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          cptj++;
    }          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   }        }
   /*2 eme*/      fprintf(ficreseij,"\n");
      
   for (k1=1; k1<= m ; k1 ++) {      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
          free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     for (i=1; i<= nlstate+1 ; i ++) {      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       k=2*i;    }
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    printf("\n");
       for (j=1; j<= nlstate+1 ; j ++) {    fprintf(ficlog,"\n");
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");    free_vector(xp,1,npar);
 }      free_matrix(dnewm,1,nlstate*nlstate,1,npar);
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);  }
       for (j=1; j<= nlstate+1 ; j ++) {  
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  /************ Variance ******************/
         else fprintf(ficgp," \%%*lf (\%%*lf)");  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)
 }    {
       fprintf(ficgp,"\" t\"\" w l 0,");    /* Variance of health expectancies */
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
       for (j=1; j<= nlstate+1 ; j ++) {    /* double **newm;*/
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    double **dnewm,**doldm;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double **dnewmp,**doldmp;
 }      int i, j, nhstepm, hstepm, h, nstepm ;
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    int k, cptcode;
       else fprintf(ficgp,"\" t\"\" w l 0,");    double *xp;
     }    double **gp, **gm;  /* for var eij */
   }    double ***gradg, ***trgradg; /*for var eij */
      double **gradgp, **trgradgp; /* for var p point j */
   /*3eme*/    double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   for (k1=1; k1<= m ; k1 ++) {    double ***p3mat;
     for (cpt=1; cpt<= nlstate ; cpt ++) {    double age,agelim, hf;
       k=2+nlstate*(2*cpt-2);    double ***mobaverage;
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    int theta;
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);    char digit[4];
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);    char digitp[25];
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");  
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);    char fileresprobmorprev[FILENAMELENGTH];
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);  
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");    if(popbased==1){
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);      if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
 */      else strcpy(digitp,"-populbased-nomobil-");
       for (i=1; i< nlstate ; i ++) {    }
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);    else 
       strcpy(digitp,"-stablbased-");
       }  
     }    if (mobilav!=0) {
   }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   /* CV preval stat */        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
     for (k1=1; k1<= m ; k1 ++) {        printf(" Error in movingaverage mobilav=%d\n",mobilav);
     for (cpt=1; cpt<nlstate ; cpt ++) {      }
       k=3;    }
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);  
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);    strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
       for (i=1; i< nlstate ; i ++)    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
         fprintf(ficgp,"+$%d",k+i+1);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
          strcat(fileresprobmorprev,fileres);
       l=3+(nlstate+ndeath)*cpt;    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       for (i=1; i< nlstate ; i ++) {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
         l=3+(nlstate+ndeath)*cpt;    }
         fprintf(ficgp,"+$%d",l+i+1);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       }    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
     }    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   }      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
        fprintf(ficresprobmorprev," p.%-d SE",j);
   /* proba elementaires */      for(i=1; i<=nlstate;i++)
    for(i=1,jk=1; i <=nlstate; i++){        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     for(k=1; k <=(nlstate+ndeath); k++){    }  
       if (k != i) {    fprintf(ficresprobmorprev,"\n");
         for(j=1; j <=ncovmodel; j++){    fprintf(ficgp,"\n# Routine varevsij");
            fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
           jk++;  /*   } */
           fprintf(ficgp,"\n");    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         }  
       }    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
     }    fprintf(ficresvij,"# Age");
    }    for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
      for(jk=1; jk <=m; jk++) {    fprintf(ficresvij,"\n");
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);  
        if (ng==2)    xp=vector(1,npar);
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");    dnewm=matrix(1,nlstate,1,npar);
        else    doldm=matrix(1,nlstate,1,nlstate);
          fprintf(ficgp,"\nset title \"Probability\"\n");    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
        i=1;  
        for(k2=1; k2<=nlstate; k2++) {    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
          k3=i;    gpp=vector(nlstate+1,nlstate+ndeath);
          for(k=1; k<=(nlstate+ndeath); k++) {    gmp=vector(nlstate+1,nlstate+ndeath);
            if (k != k2){    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
              if(ng==2)    
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);    if(estepm < stepm){
              else      printf ("Problem %d lower than %d\n",estepm, stepm);
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    }
              ij=1;    else  hstepm=estepm;   
              for(j=3; j <=ncovmodel; j++) {    /* For example we decided to compute the life expectancy with the smallest unit */
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);       nhstepm is the number of hstepm from age to agelim 
                  ij++;       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 k years */
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    /* 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
              fprintf(ficgp,")/(1");       means that if the survival funtion is printed every two years of age and if
                     you sum them up and add 1 year (area under the trapezoids) you won't get the same 
              for(k1=1; k1 <=nlstate; k1++){         results. So we changed our mind and took the option of the best precision.
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    */
                ij=1;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
                for(j=3; j <=ncovmodel; j++){    agelim = AGESUP;
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
                    ij++;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                  }      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                  else      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      gp=matrix(0,nhstepm,1,nlstate);
                }      gm=matrix(0,nhstepm,1,nlstate);
                fprintf(ficgp,")");  
              }  
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);      for(theta=1; theta <=npar; theta++){
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
              i=i+ncovmodel;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
            }        }
          }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
        }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
      }  
    }        if (popbased==1) {
    fclose(ficgp);          if(mobilav ==0){
 }  /* end gnuplot */            for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
 /*************** Moving average **************/            for(i=1; i<=nlstate;i++)
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){              prlim[i][i]=mobaverage[(int)age][i][ij];
           }
   int i, cpt, cptcod;        }
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    
       for (i=1; i<=nlstate;i++)        for(j=1; j<= nlstate; j++){
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          for(h=0; h<=nhstepm; h++){
           mobaverage[(int)agedeb][i][cptcod]=0.;            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
                  gp[h][j] += prlim[i][i]*p3mat[i][j][h];
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){          }
       for (i=1; i<=nlstate;i++){        }
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        /* This for computing probability of death (h=1 means
           for (cpt=0;cpt<=4;cpt++){           computed over hstepm matrices product = hstepm*stepm months) 
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];           as a weighted average of prlim.
           }        */
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
         }          for(i=1,gpp[j]=0.; i<= nlstate; i++)
       }            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     }        }    
            /* end probability of death */
 }  
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
 /************** Forecasting ******************/        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 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){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        if (popbased==1) {
   int *popage;          if(mobilav ==0){
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;            for(i=1; i<=nlstate;i++)
   double *popeffectif,*popcount;              prlim[i][i]=probs[(int)age][i][ij];
   double ***p3mat;          }else{ /* mobilav */ 
   char fileresf[FILENAMELENGTH];            for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
  agelim=AGESUP;          }
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;        }
   
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        for(j=1; j<= nlstate; j++){
            for(h=0; h<=nhstepm; h++){
              for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   strcpy(fileresf,"f");              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   strcat(fileresf,fileres);          }
   if((ficresf=fopen(fileresf,"w"))==NULL) {        }
     printf("Problem with forecast resultfile: %s\n", fileresf);        /* This for computing probability of death (h=1 means
   }           computed over hstepm matrices product = hstepm*stepm months) 
   printf("Computing forecasting: result on file '%s' \n", fileresf);           as a weighted average of prlim.
         */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
   if (mobilav==1) {           gmp[j] += prlim[i][i]*p3mat[i][j][1];
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        }    
     movingaverage(agedeb, fage, ageminpar, mobaverage);        /* end probability of death */
   }  
         for(j=1; j<= nlstate; j++) /* vareij */
   stepsize=(int) (stepm+YEARM-1)/YEARM;          for(h=0; h<=nhstepm; h++){
   if (stepm<=12) stepsize=1;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
            }
   agelim=AGESUP;  
          for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   hstepm=1;          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   hstepm=hstepm/stepm;        }
   yp1=modf(dateintmean,&yp);  
   anprojmean=yp;      } /* End theta */
   yp2=modf((yp1*12),&yp);  
   mprojmean=yp;      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   yp1=modf((yp2*30.5),&yp);  
   jprojmean=yp;      for(h=0; h<=nhstepm; h++) /* veij */
   if(jprojmean==0) jprojmean=1;        for(j=1; j<=nlstate;j++)
   if(mprojmean==0) jprojmean=1;          for(theta=1; theta <=npar; theta++)
              trgradg[h][j][theta]=gradg[h][theta][j];
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);  
        for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   for(cptcov=1;cptcov<=i2;cptcov++){        for(theta=1; theta <=npar; theta++)
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          trgradgp[j][theta]=gradgp[theta][j];
       k=k+1;    
       fprintf(ficresf,"\n#******");  
       for(j=1;j<=cptcoveff;j++) {      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for(i=1;i<=nlstate;i++)
       }        for(j=1;j<=nlstate;j++)
       fprintf(ficresf,"******\n");          vareij[i][j][(int)age] =0.;
       fprintf(ficresf,"# StartingAge FinalAge");  
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);      for(h=0;h<=nhstepm;h++){
              for(k=0;k<=nhstepm;k++){
                matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
         fprintf(ficresf,"\n");          for(i=1;i<=nlstate;i++)
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);              for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        }
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      }
           nhstepm = nhstepm/hstepm;    
                /* pptj */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
           oldm=oldms;savm=savms;      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        for(j=nlstate+1;j<=nlstate+ndeath;j++)
                for(i=nlstate+1;i<=nlstate+ndeath;i++)
           for (h=0; h<=nhstepm; h++){          varppt[j][i]=doldmp[j][i];
             if (h==(int) (calagedate+YEARM*cpt)) {      /* end ppptj */
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);      /*  x centered again */
             }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
             for(j=1; j<=nlstate+ndeath;j++) {      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
               kk1=0.;kk2=0;   
               for(i=1; i<=nlstate;i++) {                    if (popbased==1) {
                 if (mobilav==1)        if(mobilav ==0){
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];          for(i=1; i<=nlstate;i++)
                 else {            prlim[i][i]=probs[(int)age][i][ij];
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        }else{ /* mobilav */ 
                 }          for(i=1; i<=nlstate;i++)
                            prlim[i][i]=mobaverage[(int)age][i][ij];
               }        }
               if (h==(int)(calagedate+12*cpt)){      }
                 fprintf(ficresf," %.3f", kk1);               
                              /* This for computing probability of death (h=1 means
               }         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
             }         as a weighted average of prlim.
           }      */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
         }        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
       }          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
     }      }    
   }      /* end probability of death */
          
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   fclose(ficresf);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
 }        for(i=1; i<=nlstate;i++){
 /************** Forecasting ******************/          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
 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;      fprintf(ficresprobmorprev,"\n");
   int *popage;  
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      fprintf(ficresvij,"%.0f ",age );
   double *popeffectif,*popcount;      for(i=1; i<=nlstate;i++)
   double ***p3mat,***tabpop,***tabpopprev;        for(j=1; j<=nlstate;j++){
   char filerespop[FILENAMELENGTH];          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      fprintf(ficresvij,"\n");
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      free_matrix(gp,0,nhstepm,1,nlstate);
   agelim=AGESUP;      free_matrix(gm,0,nhstepm,1,nlstate);
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
        free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      } /* End age */
      free_vector(gpp,nlstate+1,nlstate+ndeath);
   strcpy(filerespop,"pop");    free_vector(gmp,nlstate+1,nlstate+ndeath);
   strcat(filerespop,fileres);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     printf("Problem with forecast resultfile: %s\n", filerespop);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
   }    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
   printf("Computing forecasting: result on file '%s' \n", filerespop);    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   if (cptcoveff==0) ncodemax[cptcoveff]=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,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   if (mobilav==1) {    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
     movingaverage(agedeb, fage, ageminpar, mobaverage);    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(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   stepsize=(int) (stepm+YEARM-1)/YEARM;    /*  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 (stepm<=12) stepsize=1;  */
    /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
   agelim=AGESUP;    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
    
   hstepm=1;    free_vector(xp,1,npar);
   hstepm=hstepm/stepm;    free_matrix(doldm,1,nlstate,1,nlstate);
      free_matrix(dnewm,1,nlstate,1,npar);
   if (popforecast==1) {    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if((ficpop=fopen(popfile,"r"))==NULL) {    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
       printf("Problem with population file : %s\n",popfile);exit(0);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     }    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     popage=ivector(0,AGESUP);    fclose(ficresprobmorprev);
     popeffectif=vector(0,AGESUP);    fflush(ficgp);
     popcount=vector(0,AGESUP);    fflush(fichtm); 
      }  /* end varevsij */
     i=1;    
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;  /************ 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)
     imx=i;  {
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    /* Variance of prevalence limit */
   }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     double **newm;
   for(cptcov=1;cptcov<=i2;cptcov++){    double **dnewm,**doldm;
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    int i, j, nhstepm, hstepm;
       k=k+1;    int k, cptcode;
       fprintf(ficrespop,"\n#******");    double *xp;
       for(j=1;j<=cptcoveff;j++) {    double *gp, *gm;
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double **gradg, **trgradg;
       }    double age,agelim;
       fprintf(ficrespop,"******\n");    int theta;
       fprintf(ficrespop,"# Age");     
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
       if (popforecast==1)  fprintf(ficrespop," [Population]");    fprintf(ficresvpl,"# Age");
          for(i=1; i<=nlstate;i++)
       for (cpt=0; cpt<=0;cpt++) {        fprintf(ficresvpl," %1d-%1d",i,i);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      fprintf(ficresvpl,"\n");
          
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    xp=vector(1,npar);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    dnewm=matrix(1,nlstate,1,npar);
           nhstepm = nhstepm/hstepm;    doldm=matrix(1,nlstate,1,nlstate);
              
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    hstepm=1*YEARM; /* Every year of age */
           oldm=oldms;savm=savms;    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      agelim = AGESUP;
            for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
           for (h=0; h<=nhstepm; h++){      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             if (h==(int) (calagedate+YEARM*cpt)) {      if (stepm >= YEARM) hstepm=1;
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
             }      gradg=matrix(1,npar,1,nlstate);
             for(j=1; j<=nlstate+ndeath;j++) {      gp=vector(1,nlstate);
               kk1=0.;kk2=0;      gm=vector(1,nlstate);
               for(i=1; i<=nlstate;i++) {                
                 if (mobilav==1)      for(theta=1; theta <=npar; theta++){
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        for(i=1; i<=npar; i++){ /* Computes gradient */
                 else {          xp[i] = x[i] + (i==theta ?delti[theta]:0);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];        }
                 }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
               }        for(i=1;i<=nlstate;i++)
               if (h==(int)(calagedate+12*cpt)){          gp[i] = prlim[i][i];
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;      
                   /*fprintf(ficrespop," %.3f", kk1);        for(i=1; i<=npar; i++) /* Computes gradient */
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/          xp[i] = x[i] - (i==theta ?delti[theta]:0);
               }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
             }        for(i=1;i<=nlstate;i++)
             for(i=1; i<=nlstate;i++){          gm[i] = prlim[i][i];
               kk1=0.;  
                 for(j=1; j<=nlstate;j++){        for(i=1;i<=nlstate;i++)
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
                 }      } /* End theta */
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];  
             }      trgradg =matrix(1,nlstate,1,npar);
   
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)      for(j=1; j<=nlstate;j++)
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);        for(theta=1; theta <=npar; theta++)
           }          trgradg[j][theta]=gradg[theta][j];
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
         }      for(i=1;i<=nlstate;i++)
       }        varpl[i][(int)age] =0.;
        matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   /******/      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      fprintf(ficresvpl,"%.0f ",age );
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      for(i=1; i<=nlstate;i++)
           nhstepm = nhstepm/hstepm;        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
                fprintf(ficresvpl,"\n");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      free_vector(gp,1,nlstate);
           oldm=oldms;savm=savms;      free_vector(gm,1,nlstate);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        free_matrix(gradg,1,npar,1,nlstate);
           for (h=0; h<=nhstepm; h++){      free_matrix(trgradg,1,nlstate,1,npar);
             if (h==(int) (calagedate+YEARM*cpt)) {    } /* End age */
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  
             }    free_vector(xp,1,npar);
             for(j=1; j<=nlstate+ndeath;j++) {    free_matrix(doldm,1,nlstate,1,npar);
               kk1=0.;kk2=0;    free_matrix(dnewm,1,nlstate,1,nlstate);
               for(i=1; i<=nlstate;i++) {                
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];      }
               }  
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);  /************ 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)
           }  {
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int i, j=0,  i1, k1, l1, t, tj;
         }    int k2, l2, j1,  z1;
       }    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;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    double *xp;
     double *gp, *gm;
   if (popforecast==1) {    double **gradg, **trgradg;
     free_ivector(popage,0,AGESUP);    double **mu;
     free_vector(popeffectif,0,AGESUP);    double age,agelim, cov[NCOVMAX];
     free_vector(popcount,0,AGESUP);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   }    int theta;
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    char fileresprob[FILENAMELENGTH];
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    char fileresprobcov[FILENAMELENGTH];
   fclose(ficrespop);    char fileresprobcor[FILENAMELENGTH];
 }  
     double ***varpij;
 /***********************************************/  
 /**************** Main Program *****************/    strcpy(fileresprob,"prob"); 
 /***********************************************/    strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
 int main(int argc, char *argv[])      printf("Problem with resultfile: %s\n", fileresprob);
 {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    strcpy(fileresprobcov,"probcov"); 
   double agedeb, agefin,hf;    strcat(fileresprobcov,fileres);
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
   double fret;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   double **xi,tmp,delta;    }
     strcpy(fileresprobcor,"probcor"); 
   double dum; /* Dummy variable */    strcat(fileresprobcor,fileres);
   double ***p3mat;    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   int *indx;      printf("Problem with resultfile: %s\n", fileresprobcor);
   char line[MAXLINE], linepar[MAXLINE];      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    }
   int firstobs=1, lastobs=10;    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   int sdeb, sfin; /* Status at beginning and end */    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   int c,  h , cpt,l;    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   int ju,jl, mi;    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   int mobilav=0,popforecast=0;    
   int hstepm, nhstepm;    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;    fprintf(ficresprob,"# Age");
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   double bage, fage, age, agelim, agebase;    fprintf(ficresprobcov,"# Age");
   double ftolpl=FTOL;    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   double **prlim;    fprintf(ficresprobcov,"# Age");
   double *severity;  
   double ***param; /* Matrix of parameters */  
   double  *p;    for(i=1; i<=nlstate;i++)
   double **matcov; /* Matrix of covariance */      for(j=1; j<=(nlstate+ndeath);j++){
   double ***delti3; /* Scale */        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   double *delti; /* Scale */        fprintf(ficresprobcov," p%1d-%1d ",i,j);
   double ***eij, ***vareij;        fprintf(ficresprobcor," p%1d-%1d ",i,j);
   double **varpl; /* Variances of prevalence limits by age */      }  
   double *epj, vepp;   /* fprintf(ficresprob,"\n");
   double kk1, kk2;    fprintf(ficresprobcov,"\n");
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    fprintf(ficresprobcor,"\n");
     */
    xp=vector(1,npar);
   char *alph[]={"a","a","b","c","d","e"}, str[4];    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
   char z[1]="c", occ;    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
 #include <sys/time.h>    first=1;
 #include <time.h>    fprintf(ficgp,"\n# Routine varprob");
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
      fprintf(fichtm,"\n");
   /* long total_usecs;  
   struct timeval start_time, end_time;    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");
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    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");
   getcwd(pathcd, size);  
     cov[1]=1;
   printf("\n%s",version);    tj=cptcoveff;
   if(argc <=1){    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     printf("\nEnter the parameter file name: ");    j1=0;
     scanf("%s",pathtot);    for(t=1; t<=tj;t++){
   }      for(i1=1; i1<=ncodemax[t];i1++){ 
   else{        j1++;
     strcpy(pathtot,argv[1]);        if  (cptcovn>0) {
   }          fprintf(ficresprob, "\n#********** Variable "); 
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   /*cygwin_split_path(pathtot,path,optionfile);          fprintf(ficresprob, "**********\n#\n");
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/          fprintf(ficresprobcov, "\n#********** Variable "); 
   /* cutv(path,optionfile,pathtot,'\\');*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcov, "**********\n#\n");
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);          
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);          fprintf(ficgp, "\n#********** Variable "); 
   chdir(path);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   replace(pathc,path);          fprintf(ficgp, "**********\n#\n");
           
 /*-------- arguments in the command line --------*/          
           fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   strcpy(fileres,"r");          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   strcat(fileres, optionfilefiname);          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
   strcat(fileres,".txt");    /* Other files have txt extension */          
           fprintf(ficresprobcor, "\n#********** Variable ");    
   /*---------arguments file --------*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        }
     printf("Problem with optionfile %s\n",optionfile);        
     goto end;        for (age=bage; age<=fage; age ++){ 
   }          cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
   strcpy(filereso,"o");            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
   strcat(filereso,fileres);          }
   if((ficparo=fopen(filereso,"w"))==NULL) {          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     printf("Problem with Output resultfile: %s\n", filereso);goto end;          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]]];
           
   /* Reads comments: lines beginning with '#' */          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   while((c=getc(ficpar))=='#' && c!= EOF){          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     ungetc(c,ficpar);          gp=vector(1,(nlstate)*(nlstate+ndeath));
     fgets(line, MAXLINE, ficpar);          gm=vector(1,(nlstate)*(nlstate+ndeath));
     puts(line);      
     fputs(line,ficparo);          for(theta=1; theta <=npar; theta++){
   }            for(i=1; i<=npar; i++)
   ungetc(c,ficpar);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   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);            k=0;
 while((c=getc(ficpar))=='#' && c!= EOF){            for(i=1; i<= (nlstate); i++){
     ungetc(c,ficpar);              for(j=1; j<=(nlstate+ndeath);j++){
     fgets(line, MAXLINE, ficpar);                k=k+1;
     puts(line);                gp[k]=pmmij[i][j];
     fputs(line,ficparo);              }
   }            }
   ungetc(c,ficpar);            
              for(i=1; i<=npar; i++)
                  xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
   covar=matrix(0,NCOVMAX,1,n);      
   cptcovn=0;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;            k=0;
             for(i=1; i<=(nlstate); i++){
   ncovmodel=2+cptcovn;              for(j=1; j<=(nlstate+ndeath);j++){
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */                k=k+1;
                  gm[k]=pmmij[i][j];
   /* Read guess parameters */              }
   /* Reads comments: lines beginning with '#' */            }
   while((c=getc(ficpar))=='#' && c!= EOF){       
     ungetc(c,ficpar);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     fgets(line, MAXLINE, ficpar);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
     puts(line);          }
     fputs(line,ficparo);  
   }          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
   ungetc(c,ficpar);            for(theta=1; theta <=npar; theta++)
                trgradg[j][theta]=gradg[theta][j];
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          
     for(i=1; i <=nlstate; i++)          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
     for(j=1; j <=nlstate+ndeath-1; j++){          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
       fscanf(ficpar,"%1d%1d",&i1,&j1);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
       fprintf(ficparo,"%1d%1d",i1,j1);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
       printf("%1d%1d",i,j);          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       for(k=1; k<=ncovmodel;k++){          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
         fscanf(ficpar," %lf",&param[i][j][k]);  
         printf(" %lf",param[i][j][k]);          pmij(pmmij,cov,ncovmodel,x,nlstate);
         fprintf(ficparo," %lf",param[i][j][k]);          
       }          k=0;
       fscanf(ficpar,"\n");          for(i=1; i<=(nlstate); i++){
       printf("\n");            for(j=1; j<=(nlstate+ndeath);j++){
       fprintf(ficparo,"\n");              k=k+1;
     }              mu[k][(int) age]=pmmij[i][j];
              }
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;          }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
   p=param[1][1];            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
                varpij[i][j][(int)age] = doldm[i][j];
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){          /*printf("\n%d ",(int)age);
     ungetc(c,ficpar);            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     fgets(line, MAXLINE, ficpar);            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     puts(line);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     fputs(line,ficparo);            }*/
   }  
   ungetc(c,ficpar);          fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          fprintf(ficresprobcor,"\n%d ",(int)age);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */  
   for(i=1; i <=nlstate; i++){          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
     for(j=1; j <=nlstate+ndeath-1; j++){            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
       fscanf(ficpar,"%1d%1d",&i1,&j1);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
       printf("%1d%1d",i,j);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
       fprintf(ficparo,"%1d%1d",i1,j1);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
       for(k=1; k<=ncovmodel;k++){          }
         fscanf(ficpar,"%le",&delti3[i][j][k]);          i=0;
         printf(" %le",delti3[i][j][k]);          for (k=1; k<=(nlstate);k++){
         fprintf(ficparo," %le",delti3[i][j][k]);            for (l=1; l<=(nlstate+ndeath);l++){ 
       }              i=i++;
       fscanf(ficpar,"\n");              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
       printf("\n");              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
       fprintf(ficparo,"\n");              for (j=1; j<=i;j++){
     }                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
   }                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
   delti=delti3[1][1];              }
              }
   /* Reads comments: lines beginning with '#' */          }/* end of loop for state */
   while((c=getc(ficpar))=='#' && c!= EOF){        } /* end of loop for age */
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);        /* Confidence intervalle of pij  */
     puts(line);        /*
     fputs(line,ficparo);          fprintf(ficgp,"\nset noparametric;unset label");
   }          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
   ungetc(c,ficpar);          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
            fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
   matcov=matrix(1,npar,1,npar);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
   for(i=1; i <=npar; i++){          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
     fscanf(ficpar,"%s",&str);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
     printf("%s",str);        */
     fprintf(ficparo,"%s",str);  
     for(j=1; j <=i; j++){        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
       fscanf(ficpar," %le",&matcov[i][j]);        first1=1;
       printf(" %.5le",matcov[i][j]);        for (k2=1; k2<=(nlstate);k2++){
       fprintf(ficparo," %.5le",matcov[i][j]);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
     }            if(l2==k2) continue;
     fscanf(ficpar,"\n");            j=(k2-1)*(nlstate+ndeath)+l2;
     printf("\n");            for (k1=1; k1<=(nlstate);k1++){
     fprintf(ficparo,"\n");              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
   }                if(l1==k1) continue;
   for(i=1; i <=npar; i++)                i=(k1-1)*(nlstate+ndeath)+l1;
     for(j=i+1;j<=npar;j++)                if(i<=j) continue;
       matcov[i][j]=matcov[j][i];                for (age=bage; age<=fage; age ++){ 
                      if ((int)age %5==0){
   printf("\n");                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
     /*-------- Rewriting paramater file ----------*/                    mu1=mu[i][(int) age]/stepm*YEARM ;
      strcpy(rfileres,"r");    /* "Rparameterfile */                    mu2=mu[j][(int) age]/stepm*YEARM;
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/                    c12=cv12/sqrt(v1*v2);
      strcat(rfileres,".");    /* */                    /* Computing eigen value of matrix of covariance */
      strcat(rfileres,optionfilext);    /* Other files have txt extension */                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     if((ficres =fopen(rfileres,"w"))==NULL) {                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       printf("Problem writing new parameter file: %s\n", fileres);goto end;                    /* Eigen vectors */
     }                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
     fprintf(ficres,"#%s\n",version);                    /*v21=sqrt(1.-v11*v11); *//* error */
                        v21=(lc1-v1)/cv12*v11;
     /*-------- data file ----------*/                    v12=-v21;
     if((fic=fopen(datafile,"r"))==NULL)    {                    v22=v11;
       printf("Problem with datafile: %s\n", datafile);goto end;                    tnalp=v21/v11;
     }                    if(first1==1){
                       first1=0;
     n= lastobs;                      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);
     severity = vector(1,maxwav);                    }
     outcome=imatrix(1,maxwav+1,1,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);
     num=ivector(1,n);                    /*printf(fignu*/
     moisnais=vector(1,n);                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
     annais=vector(1,n);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
     moisdc=vector(1,n);                    if(first==1){
     andc=vector(1,n);                      first=0;
     agedc=vector(1,n);                      fprintf(ficgp,"\nset parametric;unset label");
     cod=ivector(1,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);
     weight=vector(1,n);                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */                      fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
     mint=matrix(1,maxwav,1,n);   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
     anint=matrix(1,maxwav,1,n);  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
     s=imatrix(1,maxwav+1,1,n);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
     adl=imatrix(1,maxwav+1,1,n);                                  subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     tab=ivector(1,NCOVMAX);                      fprintf(fichtm,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     ncodemax=ivector(1,8);                      fprintf(fichtm,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     i=1;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     while (fgets(line, MAXLINE, fic) != NULL)    {                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
       if ((i >= firstobs) && (i <=lastobs)) {                      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",\
                                      mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
         for (j=maxwav;j>=1;j--){                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);                    }else{
           strcpy(line,stra);                      first=0;
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                      fprintf(fichtm," %d (%.3f),",(int) age, c12);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
         }                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                              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",\
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);                  } /* age mod 5 */
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);                } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);                first=1;
         for (j=ncovcol;j>=1;j--){              } /*l12 */
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);            } /* k12 */
         }          } /*l1 */
         num[i]=atol(stra);        }/* k1 */
              } /* loop covariates */
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){    }
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
         i=i+1;    free_vector(xp,1,npar);
       }    fclose(ficresprob);
     }    fclose(ficresprobcov);
     /* printf("ii=%d", ij);    fclose(ficresprobcor);
        scanf("%d",i);*/    /*  fclose(ficgp);*/
   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;  /******************* Printing html file ***********/
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;                    int lastpass, int stepm, int weightopt, char model[],\
     }*/                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
    /*  for (i=1; i<=imx; i++){                    int popforecast, int estepm ,\
      if (s[4][i]==9)  s[4][i]=-1;                    double jprev1, double mprev1,double anprev1, \
      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]));}*/                    double jprev2, double mprev2,double anprev2){
      int jj1, k1, i1, cpt;
      /*char optionfilehtm[FILENAMELENGTH];*/
   /* Calculation of the number of parameter from char model*/  /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    { */
   Tvar=ivector(1,15);  /*     printf("Problem with %s \n",optionfilehtm), exit(0); */
   Tprod=ivector(1,15);  /*     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
   Tvaraff=ivector(1,15);  /*   } */
   Tvard=imatrix(1,15,1,2);  
   Tage=ivector(1,15);           fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
       - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n \
   if (strlen(model) >1){   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n \
     j=0, j1=0, k1=1, k2=1;   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n \
     j=nbocc(model,'+');   - Life expectancies by age and initial health status (estepm=%2d months): \
     j1=nbocc(model,'*');     <a href=\"%s\">%s</a> <br>\n</li>", \
     cptcovn=j+1;             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
     cptcovprod=j1;             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
                 subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
     strcpy(modelsav,model);             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){  
       printf("Error. Non available option model=%s ",model);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
       goto end;  
     }   m=cptcoveff;
       if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     for(i=(j+1); i>=1;i--){  
       cutv(stra,strb,modelsav,'+');   jj1=0;
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);   for(k1=1; k1<=m;k1++){
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/     for(i1=1; i1<=ncodemax[k1];i1++){
       /*scanf("%d",i);*/       jj1++;
       if (strchr(strb,'*')) {       if (cptcovn > 0) {
         cutv(strd,strc,strb,'*');         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
         if (strcmp(strc,"age")==0) {         for (cpt=1; cpt<=cptcoveff;cpt++) 
           cptcovprod--;           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
           cutv(strb,stre,strd,'V');         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
           Tvar[i]=atoi(stre);       }
           cptcovage++;       /* Pij */
             Tage[cptcovage]=i;       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
             /*printf("stre=%s ", stre);*/  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
         }       /* Quasi-incidences */
         else if (strcmp(strd,"age")==0) {       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
           cptcovprod--;   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
           cutv(strb,stre,strc,'V');  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
           Tvar[i]=atoi(stre);         /* Stable prevalence in each health state */
           cptcovage++;         for(cpt=1; cpt<nlstate;cpt++){
           Tage[cptcovage]=i;           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
         }  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
         else {         }
           cutv(strb,stre,strc,'V');       for(cpt=1; cpt<=nlstate;cpt++) {
           Tvar[i]=ncovcol+k1;          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
           cutv(strb,strc,strd,'V');  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
           Tprod[k1]=i;       }
           Tvard[k1][1]=atoi(strc);       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
           Tvard[k1][2]=atoi(stre);  health expectancies in states (1) and (2): %s%d.png<br>\
           Tvar[cptcovn+k2]=Tvard[k1][1];  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
           Tvar[cptcovn+k2+1]=Tvard[k1][2];     } /* end i1 */
           for (k=1; k<=lastobs;k++)   }/* End k1 */
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];   fprintf(fichtm,"</ul>");
           k1++;  
           k2=k2+2;  
         }   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
       }   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
       else {   - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
        /*  scanf("%d",i);*/   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
       cutv(strd,strc,strb,'V');   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n\
       Tvar[i]=atoi(strc);   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n\
       }   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
       strcpy(modelsav,stra);             rfileres,rfileres,\
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
         scanf("%d",i);*/           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
     }           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
 }           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
             subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   printf("cptcovprod=%d ", cptcovprod);  
   scanf("%d ",i);*/  /*  if(popforecast==1) fprintf(fichtm,"\n */
     fclose(fic);  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
     /*  if(mle==1){*/  /*      <br>",fileres,fileres,fileres,fileres); */
     if (weightopt != 1) { /* Maximisation without weights*/  /*  else  */
       for(i=1;i<=n;i++) weight[i]=1.0;  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
     }  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
     /*-calculation of age at interview from date of interview and age at death -*/  
     agev=matrix(1,maxwav,1,imx);   m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     for (i=1; i<=imx; i++) {  
       for(m=2; (m<= maxwav); m++) {   jj1=0;
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){   for(k1=1; k1<=m;k1++){
          anint[m][i]=9999;     for(i1=1; i1<=ncodemax[k1];i1++){
          s[m][i]=-1;       jj1++;
        }       if (cptcovn > 0) {
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
       }         for (cpt=1; cpt<=cptcoveff;cpt++) 
     }           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     for (i=1; i<=imx; i++)  {       }
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);       for(cpt=1; cpt<=nlstate;cpt++) {
       for(m=1; (m<= maxwav); m++){         fprintf(fichtm,"<br>- Observed and period prevalence (with confident\
         if(s[m][i] >0){  interval) in state (%d): %s%d%d.png <br>\
           if (s[m][i] >= nlstate+1) {  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
             if(agedc[i]>0)       }
               if(moisdc[i]!=99 && andc[i]!=9999)     } /* end i1 */
                 agev[m][i]=agedc[i];   }/* End k1 */
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/   fprintf(fichtm,"</ul>");
            else {   fflush(fichtm);
               if (andc[i]!=9999){  }
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  
               agev[m][i]=-1;  /******************* Gnuplot file **************/
               }  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
             }  
           }    char dirfileres[132],optfileres[132];
           else if(s[m][i] !=9){ /* Should no more exist */    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    int ng;
             if(mint[m][i]==99 || anint[m][i]==9999)  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
               agev[m][i]=1;  /*     printf("Problem with file %s",optionfilegnuplot); */
             else if(agev[m][i] <agemin){  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
               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);*/  
             }    /*#ifdef windows */
             else if(agev[m][i] >agemax){    fprintf(ficgp,"cd \"%s\" \n",pathc);
               agemax=agev[m][i];      /*#endif */
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    m=pow(2,cptcoveff);
             }  
             /*agev[m][i]=anint[m][i]-annais[i];*/    strcpy(dirfileres,optionfilefiname);
             /*   agev[m][i] = age[i]+2*m;*/    strcpy(optfileres,"vpl");
           }   /* 1eme*/
           else { /* =9 */    for (cpt=1; cpt<= nlstate ; cpt ++) {
             agev[m][i]=1;     for (k1=1; k1<= m ; k1 ++) {
             s[m][i]=-1;       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
           }       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
         }       fprintf(ficgp,"set xlabel \"Age\" \n\
         else /*= 0 Unknown */  set ylabel \"Probability\" \n\
           agev[m][i]=1;  set ter png small\n\
       }  set size 0.65,0.65\n\
      plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
     }  
     for (i=1; i<=imx; i++)  {       for (i=1; i<= nlstate ; i ++) {
       for(m=1; (m<= maxwav); m++){         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
         if (s[m][i] > (nlstate+ndeath)) {         else fprintf(ficgp," \%%*lf (\%%*lf)");
           printf("Error: Wrong value in nlstate or ndeath\n");         }
           goto end;       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
         }       for (i=1; i<= nlstate ; i ++) {
       }         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     }         else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
     free_vector(severity,1,maxwav);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     free_imatrix(outcome,1,maxwav+1,1,n);         else fprintf(ficgp," \%%*lf (\%%*lf)");
     free_vector(moisnais,1,n);       }  
     free_vector(annais,1,n);       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
     /* free_matrix(mint,1,maxwav,1,n);     }
        free_matrix(anint,1,maxwav,1,n);*/    }
     free_vector(moisdc,1,n);    /*2 eme*/
     free_vector(andc,1,n);    
     for (k1=1; k1<= m ; k1 ++) { 
          fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
     wav=ivector(1,imx);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      
     mw=imatrix(1,lastpass-firstpass+1,1,imx);      for (i=1; i<= nlstate+1 ; i ++) {
            k=2*i;
     /* Concatenates waves */        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);        for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
       Tcode=ivector(1,100);        }   
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
       ncodemax[1]=1;        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);        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 ++) {
    codtab=imatrix(1,100,1,10);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
    h=0;          else fprintf(ficgp," \%%*lf (\%%*lf)");
    m=pow(2,cptcoveff);        }   
          fprintf(ficgp,"\" t\"\" w l 0,");
    for(k=1;k<=cptcoveff; k++){        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
      for(i=1; i <=(m/pow(2,k));i++){        for (j=1; j<= nlstate+1 ; j ++) {
        for(j=1; j <= ncodemax[k]; j++){          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){          else fprintf(ficgp," \%%*lf (\%%*lf)");
            h++;        }   
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/        else fprintf(ficgp,"\" t\"\" w l 0,");
          }      }
        }    }
      }    
    }    /*3eme*/
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);    
       codtab[1][2]=1;codtab[2][2]=2; */    for (k1=1; k1<= m ; k1 ++) { 
    /* for(i=1; i <=m ;i++){      for (cpt=1; cpt<= nlstate ; cpt ++) {
       for(k=1; k <=cptcovn; k++){        k=2+nlstate*(2*cpt-2);
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
       }        fprintf(ficgp,"set ter png small\n\
       printf("\n");  set size 0.65,0.65\n\
       }  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
       scanf("%d",i);*/        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
              for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
    /* Calculates basic frequencies. Computes observed prevalence at single age          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
        and prints on file fileres'p'. */          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
              fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
              
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        */
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        for (i=1; i< nlstate ; i ++) {
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          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);
     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) */    /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
     if(mle==1){      for (cpt=1; cpt<=nlstate ; cpt ++) {
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        k=3;
     }        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
            fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
     /*--------- results files --------------*/  set ter png small\nset size 0.65,0.65\n\
     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);  unset log y\n\
    plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
    jk=1;        for (i=1; i< nlstate ; i ++)
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");          fprintf(ficgp,"+$%d",k+i+1);
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
    for(i=1,jk=1; i <=nlstate; i++){        
      for(k=1; k <=(nlstate+ndeath); k++){        l=3+(nlstate+ndeath)*cpt;
        if (k != i)        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
          {        for (i=1; i< nlstate ; i ++) {
            printf("%d%d ",i,k);          l=3+(nlstate+ndeath)*cpt;
            fprintf(ficres,"%1d%1d ",i,k);          fprintf(ficgp,"+$%d",l+i+1);
            for(j=1; j <=ncovmodel; j++){        }
              printf("%f ",p[jk]);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
              fprintf(ficres,"%f ",p[jk]);      } 
              jk++;    }  
            }    
            printf("\n");    /* proba elementaires */
            fprintf(ficres,"\n");    for(i=1,jk=1; i <=nlstate; i++){
          }      for(k=1; k <=(nlstate+ndeath); k++){
      }        if (k != i) {
    }          for(j=1; j <=ncovmodel; j++){
  if(mle==1){            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
     /* Computing hessian and covariance matrix */            jk++; 
     ftolhess=ftol; /* Usually correct */            fprintf(ficgp,"\n");
     hesscov(matcov, p, npar, delti, ftolhess, func);          }
  }        }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");      }
     printf("# Scales (for hessian or gradient estimation)\n");     }
      for(i=1,jk=1; i <=nlstate; i++){  
       for(j=1; j <=nlstate+ndeath; j++){     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
         if (j!=i) {       for(jk=1; jk <=m; jk++) {
           fprintf(ficres,"%1d%1d",i,j);         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
           printf("%1d%1d",i,j);         if (ng==2)
           for(k=1; k<=ncovmodel;k++){           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
             printf(" %.5e",delti[jk]);         else
             fprintf(ficres," %.5e",delti[jk]);           fprintf(ficgp,"\nset title \"Probability\"\n");
             jk++;         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
           }         i=1;
           printf("\n");         for(k2=1; k2<=nlstate; k2++) {
           fprintf(ficres,"\n");           k3=i;
         }           for(k=1; k<=(nlstate+ndeath); k++) {
       }             if (k != k2){
      }               if(ng==2)
                     fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
     k=1;               else
     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");                 fprintf(ficgp," exp(p%d+p%d*x",i,i+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");               ij=1;
     for(i=1;i<=npar;i++){               for(j=3; j <=ncovmodel; j++) {
       /*  if (k>nlstate) k=1;                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
       i1=(i-1)/(ncovmodel*nlstate)+1;                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);                   ij++;
       printf("%s%d%d",alph[k],i1,tab[i]);*/                 }
       fprintf(ficres,"%3d",i);                 else
       printf("%3d",i);                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
       for(j=1; j<=i;j++){               }
         fprintf(ficres," %.5e",matcov[i][j]);               fprintf(ficgp,")/(1");
         printf(" %.5e",matcov[i][j]);               
       }               for(k1=1; k1 <=nlstate; k1++){   
       fprintf(ficres,"\n");                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
       printf("\n");                 ij=1;
       k++;                 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]]]);
     while((c=getc(ficpar))=='#' && c!= EOF){                     ij++;
       ungetc(c,ficpar);                   }
       fgets(line, MAXLINE, ficpar);                   else
       puts(line);                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
       fputs(line,ficparo);                 }
     }                 fprintf(ficgp,")");
     ungetc(c,ficpar);               }
     estepm=0;               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
     if (estepm==0 || estepm < stepm) estepm=stepm;               i=i+ncovmodel;
     if (fage <= 2) {             }
       bage = ageminpar;           } /* end k */
       fage = agemaxpar;         } /* end k2 */
     }       } /* end jk */
         } /* end ng */
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");     fflush(ficgp); 
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);  }  /* end gnuplot */
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);  
    
     while((c=getc(ficpar))=='#' && c!= EOF){  /*************** Moving average **************/
     ungetc(c,ficpar);  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
     fgets(line, MAXLINE, ficpar);  
     puts(line);    int i, cpt, cptcod;
     fputs(line,ficparo);    int modcovmax =1;
   }    int mobilavrange, mob;
   ungetc(c,ficpar);    double age;
    
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                             a covariate has 2 modalities */
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
        
   while((c=getc(ficpar))=='#' && c!= EOF){    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
     ungetc(c,ficpar);      if(mobilav==1) mobilavrange=5; /* default */
     fgets(line, MAXLINE, ficpar);      else mobilavrange=mobilav;
     puts(line);      for (age=bage; age<=fage; age++)
     fputs(line,ficparo);        for (i=1; i<=nlstate;i++)
   }          for (cptcod=1;cptcod<=modcovmax;cptcod++)
   ungetc(c,ficpar);            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
        /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
    dateprev1=anprev1+mprev1/12.+jprev1/365.;         we use a 5 terms etc. until the borders are no more concerned. 
    dateprev2=anprev2+mprev2/12.+jprev2/365.;      */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
   fscanf(ficpar,"pop_based=%d\n",&popbased);        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
   fprintf(ficparo,"pop_based=%d\n",popbased);            for (i=1; i<=nlstate;i++){
   fprintf(ficres,"pop_based=%d\n",popbased);              for (cptcod=1;cptcod<=modcovmax;cptcod++){
                mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
   while((c=getc(ficpar))=='#' && c!= EOF){                for (cpt=1;cpt<=(mob-1)/2;cpt++){
     ungetc(c,ficpar);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
     fgets(line, MAXLINE, ficpar);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
     puts(line);                }
     fputs(line,ficparo);              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
   }            }
   ungetc(c,ficpar);          }
         }/* end age */
   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);      }/* end mob */
 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);    }else return -1;
 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);    return 0;
   }/* End movingaverage */
   
 while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  /************** Forecasting ******************/
     fgets(line, MAXLINE, ficpar);  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){
     puts(line);    /* proj1, year, month, day of starting projection 
     fputs(line,ficparo);       agemin, agemax range of age
   }       dateprev1 dateprev2 range of dates during which prevalence is computed
   ungetc(c,ficpar);       anproj2 year of en of projection (same day and month as proj1).
     */
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    int *popage;
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);    double *popeffectif,*popcount;
     double ***p3mat;
 /*------------ gnuplot -------------*/    double ***mobaverage;
   strcpy(optionfilegnuplot,optionfilefiname);    char fileresf[FILENAMELENGTH];
   strcat(optionfilegnuplot,".gp");  
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    agelim=AGESUP;
     printf("Problem with file %s",optionfilegnuplot);    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   }   
   fclose(ficgp);    strcpy(fileresf,"f"); 
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);    strcat(fileresf,fileres);
 /*--------- index.htm --------*/    if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
   strcpy(optionfilehtm,optionfile);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
   strcat(optionfilehtm,".htm");    }
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    printf("Computing forecasting: result on file '%s' \n", fileresf);
     printf("Problem with %s \n",optionfilehtm), exit(0);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   }  
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n  
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n    if (mobilav!=0) {
 \n      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
 Total number of observations=%d <br>\n      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
 <hr  size=\"2\" color=\"#EC5E5E\">        printf(" Error in movingaverage mobilav=%d\n",mobilav);
  <ul><li>Parameter files<br>\n      }
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n    }
  - Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);  
   fclose(fichtm);    stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);    if(estepm < stepm){
        printf ("Problem %d lower than %d\n",estepm, stepm);
 /*------------ free_vector  -------------*/    }
  chdir(path);    else  hstepm=estepm;   
    
  free_ivector(wav,1,imx);    hstepm=hstepm/stepm; 
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);                                   fractional in yp1 */
  free_ivector(num,1,n);    anprojmean=yp;
  free_vector(agedc,1,n);    yp2=modf((yp1*12),&yp);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/    mprojmean=yp;
  fclose(ficparo);    yp1=modf((yp2*30.5),&yp);
  fclose(ficres);    jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   /*--------------- Prevalence limit --------------*/  
      i1=cptcoveff;
   strcpy(filerespl,"pl");    if (cptcovn < 1){i1=1;}
   strcat(filerespl,fileres);    
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    
   }    fprintf(ficresf,"#****** Routine prevforecast **\n");
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);  
   fprintf(ficrespl,"#Prevalence limit\n");  /*            if (h==(int)(YEARM*yearp)){ */
   fprintf(ficrespl,"#Age ");    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   fprintf(ficrespl,"\n");        k=k+1;
          fprintf(ficresf,"\n#******");
   prlim=matrix(1,nlstate,1,nlstate);        for(j=1;j<=cptcoveff;j++) {
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          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]]);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        }
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        fprintf(ficresf,"******\n");
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        for(j=1; j<=nlstate+ndeath;j++){ 
   k=0;          for(i=1; i<=nlstate;i++)              
   agebase=ageminpar;            fprintf(ficresf," p%d%d",i,j);
   agelim=agemaxpar;          fprintf(ficresf," p.%d",j);
   ftolpl=1.e-10;        }
   i1=cptcoveff;        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
   if (cptcovn < 1){i1=1;}          fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          for (agec=fage; agec>=(ageminpar-1); agec--){ 
         k=k+1;            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/            nhstepm = nhstepm/hstepm; 
         fprintf(ficrespl,"\n#******");            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         for(j=1;j<=cptcoveff;j++)            oldm=oldms;savm=savms;
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
         fprintf(ficrespl,"******\n");          
                    for (h=0; h<=nhstepm; h++){
         for (age=agebase; age<=agelim; age++){              if (h*hstepm/YEARM*stepm ==yearp) {
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                fprintf(ficresf,"\n");
           fprintf(ficrespl,"%.0f",age );                for(j=1;j<=cptcoveff;j++) 
           for(i=1; i<=nlstate;i++)                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespl," %.5f", prlim[i][i]);                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
           fprintf(ficrespl,"\n");              } 
         }              for(j=1; j<=nlstate+ndeath;j++) {
       }                ppij=0.;
     }                for(i=1; i<=nlstate;i++) {
   fclose(ficrespl);                  if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
   /*------------- h Pij x at various ages ------------*/                  else {
                      ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);                  }
   if((ficrespij=fopen(filerespij,"w"))==NULL) {                  if (h*hstepm/YEARM*stepm== yearp) {
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
   }                  }
   printf("Computing pij: result on file '%s' \n", filerespij);                } /* end i */
                  if (h*hstepm/YEARM*stepm==yearp) {
   stepsize=(int) (stepm+YEARM-1)/YEARM;                  fprintf(ficresf," %.3f", ppij);
   /*if (stepm<=24) stepsize=2;*/                }
               }/* end j */
   agelim=AGESUP;            } /* end h */
   hstepm=stepsize*YEARM; /* Every year of age */            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */          } /* end agec */
          } /* end yearp */
   k=0;      } /* end cptcod */
   for(cptcov=1;cptcov<=i1;cptcov++){    } /* end  cptcov */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){         
       k=k+1;    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         fprintf(ficrespij,"\n#****** ");  
         for(j=1;j<=cptcoveff;j++)    fclose(ficresf);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  }
         fprintf(ficrespij,"******\n");  
          /************** Forecasting *****not tested NB*************/
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */  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){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int *popage;
           oldm=oldms;savm=savms;    double calagedatem, agelim, kk1, kk2;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      double *popeffectif,*popcount;
           fprintf(ficrespij,"# Age");    double ***p3mat,***tabpop,***tabpopprev;
           for(i=1; i<=nlstate;i++)    double ***mobaverage;
             for(j=1; j<=nlstate+ndeath;j++)    char filerespop[FILENAMELENGTH];
               fprintf(ficrespij," %1d-%1d",i,j);  
           fprintf(ficrespij,"\n");    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
            for (h=0; h<=nhstepm; h++){    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    agelim=AGESUP;
             for(i=1; i<=nlstate;i++)    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
               for(j=1; j<=nlstate+ndeath;j++)    
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
             fprintf(ficrespij,"\n");    
              }    
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    strcpy(filerespop,"pop"); 
           fprintf(ficrespij,"\n");    strcat(filerespop,fileres);
         }    if((ficrespop=fopen(filerespop,"w"))==NULL) {
     }      printf("Problem with forecast resultfile: %s\n", filerespop);
   }      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);    printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   fclose(ficrespij);  
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
   /*---------- Forecasting ------------------*/    if (mobilav!=0) {
   if((stepm == 1) && (strcmp(model,".")==0)){      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   }        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   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);  
   }    stepsize=(int) (stepm+YEARM-1)/YEARM;
      if (stepm<=12) stepsize=1;
     
   /*---------- Health expectancies and variances ------------*/    agelim=AGESUP;
     
   strcpy(filerest,"t");    hstepm=1;
   strcat(filerest,fileres);    hstepm=hstepm/stepm; 
   if((ficrest=fopen(filerest,"w"))==NULL) {    
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    if (popforecast==1) {
   }      if((ficpop=fopen(popfile,"r"))==NULL) {
   printf("Computing Total LEs with variances: file '%s' \n", filerest);        printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
   strcpy(filerese,"e");      popage=ivector(0,AGESUP);
   strcat(filerese,fileres);      popeffectif=vector(0,AGESUP);
   if((ficreseij=fopen(filerese,"w"))==NULL) {      popcount=vector(0,AGESUP);
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      
   }      i=1;   
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
  strcpy(fileresv,"v");      imx=i;
   strcat(fileresv,fileres);      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    }
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  
   }    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   calagedate=-1;        k=k+1;
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
   k=0;          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
   for(cptcov=1;cptcov<=i1;cptcov++){        }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        fprintf(ficrespop,"******\n");
       k=k+1;        fprintf(ficrespop,"# Age");
       fprintf(ficrest,"\n#****** ");        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
       for(j=1;j<=cptcoveff;j++)        if (popforecast==1)  fprintf(ficrespop," [Population]");
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        
       fprintf(ficrest,"******\n");        for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
       fprintf(ficreseij,"\n#****** ");          
       for(j=1;j<=cptcoveff;j++)          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
       fprintf(ficreseij,"******\n");            nhstepm = nhstepm/hstepm; 
             
       fprintf(ficresvij,"\n#****** ");            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       for(j=1;j<=cptcoveff;j++)            oldm=oldms;savm=savms;
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
       fprintf(ficresvij,"******\n");          
             for (h=0; h<=nhstepm; h++){
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);              if (h==(int) (calagedatem+YEARM*cpt)) {
       oldm=oldms;savm=savms;                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);                } 
                for(j=1; j<=nlstate+ndeath;j++) {
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);                kk1=0.;kk2=0;
       oldm=oldms;savm=savms;                for(i=1; i<=nlstate;i++) {              
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);                  if (mobilav==1) 
                        kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                      kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");                  }
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);                }
       fprintf(ficrest,"\n");                if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
       epj=vector(1,nlstate+1);                    /*fprintf(ficrespop," %.3f", kk1);
       for(age=bage; age <=fage ;age++){                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                }
         if (popbased==1) {              }
           for(i=1; i<=nlstate;i++)              for(i=1; i<=nlstate;i++){
             prlim[i][i]=probs[(int)age][i][k];                kk1=0.;
         }                  for(j=1; j<=nlstate;j++){
                            kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
         fprintf(ficrest," %4.0f",age);                  }
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
           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]);*/              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
           }                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
           epj[nlstate+1] +=epj[j];            }
         }            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         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++){        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
         }          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
         fprintf(ficrest,"\n");            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
       }            nhstepm = nhstepm/hstepm; 
     }            
   }            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 free_matrix(mint,1,maxwav,1,n);            oldm=oldms;savm=savms;
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
     free_vector(weight,1,n);            for (h=0; h<=nhstepm; h++){
   fclose(ficreseij);              if (h==(int) (calagedatem+YEARM*cpt)) {
   fclose(ficresvij);                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
   fclose(ficrest);              } 
   fclose(ficpar);              for(j=1; j<=nlstate+ndeath;j++) {
   free_vector(epj,1,nlstate+1);                kk1=0.;kk2=0;
                  for(i=1; i<=nlstate;i++) {              
   /*------- Variance limit prevalence------*/                    kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
   strcpy(fileresvpl,"vpl");                if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
   strcat(fileresvpl,fileres);              }
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {            }
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     exit(0);          }
   }        }
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);     } 
     }
   k=0;   
   for(cptcov=1;cptcov<=i1;cptcov++){    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;    if (popforecast==1) {
       fprintf(ficresvpl,"\n#****** ");      free_ivector(popage,0,AGESUP);
       for(j=1;j<=cptcoveff;j++)      free_vector(popeffectif,0,AGESUP);
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      free_vector(popcount,0,AGESUP);
       fprintf(ficresvpl,"******\n");    }
          free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       oldm=oldms;savm=savms;    fclose(ficrespop);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  } /* End of popforecast */
     }  
  }  int fileappend(FILE *fichier, char *optionfich)
   {
   fclose(ficresvpl);    if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
   /*---------- End : free ----------------*/      fprintf(ficlog,"Problem with file: %s\n", optionfich);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);      return (0);
      }
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    fflush(fichier);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    return (1);
    }
    void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   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);    char ca[32], cb[32], cc[32];
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
      int numlinepar;
   free_matrix(matcov,1,npar,1,npar);  
   free_vector(delti,1,npar);    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
   free_matrix(agev,1,maxwav,1,imx);    fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    for(i=1; i <=nlstate; i++){
       jj=0;
   fprintf(fichtm,"\n</body>");      for(j=1; j <=nlstate+ndeath; j++){
   fclose(fichtm);        if(j==i) continue;
   fclose(ficgp);        jj++;
          /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
   if(erreur >0)        fprintf(ficparo,"%1d%1d",i,j);
     printf("End of Imach with error or warning %d\n",erreur);        for(k=1; k<=ncovmodel;k++){
   else   printf("End of Imach\n");          /*        printf(" %lf",param[i][j][k]); */
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */          /*        fprintf(ficparo," %lf",param[i][j][k]); */
            printf(" 0.");
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/          fprintf(ficparo," 0.");
   /*printf("Total time was %d uSec.\n", total_usecs);*/        }
   /*------ End -----------*/        printf("\n");
         fprintf(ficparo,"\n");
       }
  end:    }
 #ifdef windows    printf("# Scales (for hessian or gradient estimation)\n");
   /* chdir(pathcd);*/    fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
 #endif    npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
  /*system("wgnuplot graph.plt");*/    for(i=1; i <=nlstate; i++){
  /*system("../gp37mgw/wgnuplot graph.plt");*/      jj=0;
  /*system("cd ../gp37mgw");*/      for(j=1; j <=nlstate+ndeath; j++){
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/        if(j==i) continue;
  strcpy(plotcmd,GNUPLOTPROGRAM);        jj++;
  strcat(plotcmd," ");        fprintf(ficparo,"%1d%1d",i,j);
  strcat(plotcmd,optionfilegnuplot);        printf("%1d%1d",i,j);
  system(plotcmd);        fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
 #ifdef windows          /*      printf(" %le",delti3[i][j][k]); */
   while (z[0] != 'q') {          /*      fprintf(ficparo," %le",delti3[i][j][k]); */
     /* chdir(path); */          printf(" 0.");
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");          fprintf(ficparo," 0.");
     scanf("%s",z);        }
     if (z[0] == 'c') system("./imach");        numlinepar++;
     else if (z[0] == 'e') system(optionfilehtm);        printf("\n");
     else if (z[0] == 'g') system(plotcmd);        fprintf(ficparo,"\n");
     else if (z[0] == 'q') exit(0);      }
   }    }
 #endif    printf("# Covariance matrix\n");
 }  /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     }
   
   } /* end of prwizard */
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int jj, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE]; 
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   
     char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char strstart[80], *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
     struct timeval start_time, end_time, curr_time;
     struct timezone tzp;
     extern int gettimeofday();
     struct tm tmg, tm, *gmtime(), *localtime();
     long time_value;
     extern long time();
    
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: ");
     fprintf(ficlog,"pathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Localtime (at start):%s",strstart);
     fprintf(ficlog,"Localtime (at start): %s",strstart);
     fflush(ficlog);
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
    
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     /* Read guess parameters */
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++){
       j=0;
       for(jj=1; jj <=nlstate+ndeath; jj++){
         if(jj==i) continue;
         j++;
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1 != i) && (j1 != j)){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);
         }
         fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)
           printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);
           if(mle==1){
             printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);
           }
           else
             fprintf(ficlog," %lf",param[i][j][k]);
           fprintf(ficparo," %lf",param[i][j][k]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     }  
     fflush(ficlog);
   
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1-i)*(j1-j)!=0){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);
         }
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         fprintf(ficlog,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);
           fprintf(ficlog," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
         fprintf(ficlog,"\n");
       }
     }
     fflush(ficlog);
   
     delti=delti3[1][1];
   
   
     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);
       if(mle==1)
         printf("%s",str);
       fprintf(ficlog,"%s",str);
       fprintf(ficparo,"%s",str);
       for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
           printf(" %.5le",matcov[i][j]);
         }
         fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       numlinepar++;
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
     for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];
      
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
   
     fflush(ficlog);
   
     /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         lstra=strlen(stra);
         if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
           stratrunc = &(stra[lstra-9]);
           num[i]=atol(stratrunc);
         }
         else
           num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname);
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt,\
             model,fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     /*fclose(fichtm);*/
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     strcpy(lfileres,fileres);
     strcat(lfileres,"/");
     strcat(lfileres,optionfilefiname);
     
     /* 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.1.47  
changed lines
  Added in v.1.90


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