Diff for /imach/src/imach.c between versions 1.36 and 1.95

version 1.36, 2002/03/29 15:27:27 version 1.95, 2003/07/08 07:54:34
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.95  2003/07/08 07:54:34  brouard
      * imach.c (Repository):
   This program computes Healthy Life Expectancies from    (Repository): Using imachwizard code to output a more meaningful covariance
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    matrix (cov(a12,c31) instead of numbers.
   first survey ("cross") where individuals from different ages are  
   interviewed on their health status or degree of disability (in the    Revision 1.94  2003/06/27 13:00:02  brouard
   case of a health survey which is our main interest) -2- at least a    Just cleaning
   second wave of interviews ("longitudinal") which measure each change  
   (if any) in individual health status.  Health expectancies are    Revision 1.93  2003/06/25 16:33:55  brouard
   computed from the time spent in each health state according to a    (Module): On windows (cygwin) function asctime_r doesn't
   model. More health states you consider, more time is necessary to reach the    exist so I changed back to asctime which exists.
   Maximum Likelihood of the parameters involved in the model.  The    (Module): Version 0.96b
   simplest model is the multinomial logistic model where pij is the  
   probabibility to be observed in state j at the second wave    Revision 1.92  2003/06/25 16:30:45  brouard
   conditional to be observed in state i at the first wave. Therefore    (Module): On windows (cygwin) function asctime_r doesn't
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    exist so I changed back to asctime which exists.
   'age' is age and 'sex' is a covariate. If you want to have a more  
   complex model than "constant and age", you should modify the program    Revision 1.91  2003/06/25 15:30:29  brouard
   where the markup *Covariates have to be included here again* invites    * imach.c (Repository): Duplicated warning errors corrected.
   you to do it.  More covariates you add, slower the    (Repository): Elapsed time after each iteration is now output. It
   convergence.    helps to forecast when convergence will be reached. Elapsed time
     is stamped in powell.  We created a new html file for the graphs
   The advantage of this computer programme, compared to a simple    concerning matrix of covariance. It has extension -cov.htm.
   multinomial logistic model, is clear when the delay between waves is not  
   identical for each individual. Also, if a individual missed an    Revision 1.90  2003/06/24 12:34:15  brouard
   intermediate interview, the information is lost, but taken into    (Module): Some bugs corrected for windows. Also, when
   account using an interpolation or extrapolation.      mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
   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    Revision 1.89  2003/06/24 12:30:52  brouard
   split into an exact number (nh*stepm) of unobserved intermediate    (Module): Some bugs corrected for windows. Also, when
   states. This elementary transition (by month or quarter trimester,    mle=-1 a template is output in file "or"mypar.txt with the design
   semester or year) is model as a multinomial logistic.  The hPx    of the covariance matrix to be input.
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Revision 1.88  2003/06/23 17:54:56  brouard
   hPijx.    * 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.
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.87  2003/06/18 12:26:01  brouard
   of the life expectancies. It also computes the prevalence limits.    Version 0.96
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Revision 1.86  2003/06/17 20:04:08  brouard
            Institut national d'études démographiques, Paris.    (Module): Change position of html and gnuplot routines and added
   This software have been partly granted by Euro-REVES, a concerted action    routine fileappend.
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.85  2003/06/17 13:12:43  brouard
   software can be distributed freely for non commercial use. Latest version    * imach.c (Repository): Check when date of death was earlier that
   can be accessed at http://euroreves.ined.fr/imach .    current date of interview. It may happen when the death was just
   **********************************************************************/    prior to the death. In this case, dh was negative and likelihood
      was wrong (infinity). We still send an "Error" but patch by
 #include <math.h>    assuming that the date of death was just one stepm after the
 #include <stdio.h>    interview.
 #include <stdlib.h>    (Repository): Because some people have very long ID (first column)
 #include <unistd.h>    we changed int to long in num[] and we added a new lvector for
     memory allocation. But we also truncated to 8 characters (left
 #define MAXLINE 256    truncation)
 #define GNUPLOTPROGRAM "wgnuplot"    (Repository): No more line truncation errors.
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  
 #define FILENAMELENGTH 80    Revision 1.84  2003/06/13 21:44:43  brouard
 /*#define DEBUG*/    * imach.c (Repository): Replace "freqsummary" at a correct
 #define windows    place. It differs from routine "prevalence" which may be called
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    many times. Probs is memory consuming and must be used with
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    parcimony.
     Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Revision 1.83  2003/06/10 13:39:11  lievre
     *** empty log message ***
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.82  2003/06/05 15:57:20  brouard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Add log in  imach.c and  fullversion number is now printed.
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000  */
 #define YEARM 12. /* Number of months per year */  /*
 #define AGESUP 130     Interpolated Markov Chain
 #define AGEBASE 40  
     Short summary of the programme:
     
 int erreur; /* Error number */    This program computes Healthy Life Expectancies from
 int nvar;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    first survey ("cross") where individuals from different ages are
 int npar=NPARMAX;    interviewed on their health status or degree of disability (in the
 int nlstate=2; /* Number of live states */    case of a health survey which is our main interest) -2- at least a
 int ndeath=1; /* Number of dead states */    second wave of interviews ("longitudinal") which measure each change
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    (if any) in individual health status.  Health expectancies are
 int popbased=0;    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
 int *wav; /* Number of waves for this individuual 0 is possible */    Maximum Likelihood of the parameters involved in the model.  The
 int maxwav; /* Maxim number of waves */    simplest model is the multinomial logistic model where pij is the
 int jmin, jmax; /* min, max spacing between 2 waves */    probability to be observed in state j at the second wave
 int mle, weightopt;    conditional to be observed in state i at the first wave. Therefore
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    'age' is age and 'sex' is a covariate. If you want to have a more
 double jmean; /* Mean space between 2 waves */    complex model than "constant and age", you should modify the program
 double **oldm, **newm, **savm; /* Working pointers to matrices */    where the markup *Covariates have to be included here again* invites
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    you to do it.  More covariates you add, slower the
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    convergence.
 FILE *ficgp,*ficresprob,*ficpop;  
 FILE *ficreseij;    The advantage of this computer programme, compared to a simple
   char filerese[FILENAMELENGTH];    multinomial logistic model, is clear when the delay between waves is not
  FILE  *ficresvij;    identical for each individual. Also, if a individual missed an
   char fileresv[FILENAMELENGTH];    intermediate interview, the information is lost, but taken into
  FILE  *ficresvpl;    account using an interpolation or extrapolation.  
   char fileresvpl[FILENAMELENGTH];  
     hPijx is the probability to be observed in state i at age x+h
 #define NR_END 1    conditional to the observed state i at age x. The delay 'h' can be
 #define FREE_ARG char*    split into an exact number (nh*stepm) of unobserved intermediate
 #define FTOL 1.0e-10    states. This elementary transition (by month, quarter,
     semester or year) is modelled as a multinomial logistic.  The hPx
 #define NRANSI    matrix is simply the matrix product of nh*stepm elementary matrices
 #define ITMAX 200    and the contribution of each individual to the likelihood is simply
     hPijx.
 #define TOL 2.0e-4  
     Also this programme outputs the covariance matrix of the parameters but also
 #define CGOLD 0.3819660    of the life expectancies. It also computes the stable prevalence. 
 #define ZEPS 1.0e-10    
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
              Institut national d'études démographiques, Paris.
 #define GOLD 1.618034    This software have been partly granted by Euro-REVES, a concerted action
 #define GLIMIT 100.0    from the European Union.
 #define TINY 1.0e-20    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
 static double maxarg1,maxarg2;    can be accessed at http://euroreves.ined.fr/imach .
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
      or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    
 #define rint(a) floor(a+0.5)    **********************************************************************/
   /*
 static double sqrarg;    main
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    read parameterfile
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    read datafile
     concatwav
 int imx;    freqsummary
 int stepm;    if (mle >= 1)
 /* Stepm, step in month: minimum step interpolation*/      mlikeli
     print results files
 int estepm;    if mle==1 
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/       computes hessian
     read end of parameter file: agemin, agemax, bage, fage, estepm
 int m,nb;        begin-prev-date,...
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    open gnuplot file
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    open html file
 double **pmmij, ***probs, ***mobaverage;    stable prevalence
 double dateintmean=0;     for age prevalim()
     h Pij x
 double *weight;    variance of p varprob
 int **s; /* Status */    forecasting if prevfcast==1 prevforecast call prevalence()
 double *agedc, **covar, idx;    health expectancies
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Variance-covariance of DFLE
     prevalence()
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */     movingaverage()
 double ftolhess; /* Tolerance for computing hessian */    varevsij() 
     if popbased==1 varevsij(,popbased)
 /**************** split *************************/    total life expectancies
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    Variance of stable prevalence
 {   end
    char *s;                             /* pointer */  */
    int  l1, l2;                         /* length counters */  
   
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );   
 #ifdef windows  #include <math.h>
    s = strrchr( path, '\\' );           /* find last / */  #include <stdio.h>
 #else  #include <stdlib.h>
    s = strrchr( path, '/' );            /* find last / */  #include <unistd.h>
 #endif  
    if ( s == NULL ) {                   /* no directory, so use current */  #include <sys/time.h>
 #if     defined(__bsd__)                /* get current working directory */  #include <time.h>
       extern char       *getwd( );  #include "timeval.h"
   
       if ( getwd( dirc ) == NULL ) {  /* #include <libintl.h> */
 #else  /* #define _(String) gettext (String) */
       extern char       *getcwd( );  
   #define MAXLINE 256
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  #define GNUPLOTPROGRAM "gnuplot"
 #endif  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
          return( GLOCK_ERROR_GETCWD );  #define FILENAMELENGTH 132
       }  /*#define DEBUG*/
       strcpy( name, path );             /* we've got it */  /*#define windows*/
    } else {                             /* strip direcotry from path */  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
       s++;                              /* after this, the filename */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
       strcpy( name, s );                /* save file name */  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */  #define NINTERVMAX 8
    }  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
    l1 = strlen( dirc );                 /* length of directory */  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #ifdef windows  #define NCOVMAX 8 /* Maximum number of covariates */
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  #define MAXN 20000
 #else  #define YEARM 12. /* Number of months per year */
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  #define AGESUP 130
 #endif  #define AGEBASE 40
    s = strrchr( name, '.' );            /* find last / */  #ifdef unix
    s++;  #define DIRSEPARATOR '/'
    strcpy(ext,s);                       /* save extension */  #define ODIRSEPARATOR '\\'
    l1= strlen( name);  #else
    l2= strlen( s)+1;  #define DIRSEPARATOR '\\'
    strncpy( finame, name, l1-l2);  #define ODIRSEPARATOR '/'
    finame[l1-l2]= 0;  #endif
    return( 0 );                         /* we're done */  
 }  /* $Id$ */
   /* $State$ */
   
 /******************************************/  char version[]="Imach version 0.96b, June 2003, INED-EUROREVES ";
   char fullversion[]="$Revision$ $Date$"; 
 void replace(char *s, char*t)  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 {  int nvar;
   int i;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   int lg=20;  int npar=NPARMAX;
   i=0;  int nlstate=2; /* Number of live states */
   lg=strlen(t);  int ndeath=1; /* Number of dead states */
   for(i=0; i<= lg; i++) {  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
     (s[i] = t[i]);  int popbased=0;
     if (t[i]== '\\') s[i]='/';  
   }  int *wav; /* Number of waves for this individuual 0 is possible */
 }  int maxwav; /* Maxim number of waves */
   int jmin, jmax; /* min, max spacing between 2 waves */
 int nbocc(char *s, char occ)  int gipmx, gsw; /* Global variables on the number of contributions 
 {                     to the likelihood and the sum of weights (done by funcone)*/
   int i,j=0;  int mle, weightopt;
   int lg=20;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   i=0;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   lg=strlen(s);  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   for(i=0; i<= lg; i++) {             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   if  (s[i] == occ ) j++;  double jmean; /* Mean space between 2 waves */
   }  double **oldm, **newm, **savm; /* Working pointers to matrices */
   return j;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 }  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   FILE *ficlog, *ficrespow;
 void cutv(char *u,char *v, char*t, char occ)  int globpr; /* Global variable for printing or not */
 {  double fretone; /* Only one call to likelihood */
   int i,lg,j,p=0;  long ipmx; /* Number of contributions */
   i=0;  double sw; /* Sum of weights */
   for(j=0; j<=strlen(t)-1; j++) {  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  FILE *ficresilk;
   }  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   FILE *ficresprobmorprev;
   lg=strlen(t);  FILE *fichtm, *fichtmcov; /* Html File */
   for(j=0; j<p; j++) {  FILE *ficreseij;
     (u[j] = t[j]);  char filerese[FILENAMELENGTH];
   }  FILE  *ficresvij;
      u[p]='\0';  char fileresv[FILENAMELENGTH];
   FILE  *ficresvpl;
    for(j=0; j<= lg; j++) {  char fileresvpl[FILENAMELENGTH];
     if (j>=(p+1))(v[j-p-1] = t[j]);  char title[MAXLINE];
   }  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 }  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   char tmpout[FILENAMELENGTH]; 
 /********************** nrerror ********************/  char command[FILENAMELENGTH];
   int  outcmd=0;
 void nrerror(char error_text[])  
 {  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   fprintf(stderr,"ERREUR ...\n");  
   fprintf(stderr,"%s\n",error_text);  char filelog[FILENAMELENGTH]; /* Log file */
   exit(1);  char filerest[FILENAMELENGTH];
 }  char fileregp[FILENAMELENGTH];
 /*********************** vector *******************/  char popfile[FILENAMELENGTH];
 double *vector(int nl, int nh)  
 {  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   if (!v) nrerror("allocation failure in vector");  struct timezone tzp;
   return v-nl+NR_END;  extern int gettimeofday();
 }  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   long time_value;
 /************************ free vector ******************/  extern long time();
 void free_vector(double*v, int nl, int nh)  char strcurr[80], strfor[80];
 {  
   free((FREE_ARG)(v+nl-NR_END));  #define NR_END 1
 }  #define FREE_ARG char*
   #define FTOL 1.0e-10
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)  #define NRANSI 
 {  #define ITMAX 200 
   int *v;  
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  #define TOL 2.0e-4 
   if (!v) nrerror("allocation failure in ivector");  
   return v-nl+NR_END;  #define CGOLD 0.3819660 
 }  #define ZEPS 1.0e-10 
   #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 /******************free ivector **************************/  
 void free_ivector(int *v, long nl, long nh)  #define GOLD 1.618034 
 {  #define GLIMIT 100.0 
   free((FREE_ARG)(v+nl-NR_END));  #define TINY 1.0e-20 
 }  
   static double maxarg1,maxarg2;
 /******************* imatrix *******************************/  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 int **imatrix(long nrl, long nrh, long ncl, long nch)  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    
 {  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  #define rint(a) floor(a+0.5)
   int **m;  
    static double sqrarg;
   /* allocate pointers to rows */  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  int imx; 
   m -= nrl;  int stepm;
    /* Stepm, step in month: minimum step interpolation*/
    
   /* allocate rows and set pointers to them */  int estepm;
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  int m,nb;
   m[nrl] -= ncl;  long *num;
    int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
    double **pmmij, ***probs;
   /* return pointer to array of pointers to rows */  double dateintmean=0;
   return m;  
 }  double *weight;
   int **s; /* Status */
 /****************** free_imatrix *************************/  double *agedc, **covar, idx;
 void free_imatrix(m,nrl,nrh,ncl,nch)  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
       int **m;  
       long nch,ncl,nrh,nrl;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
      /* free an int matrix allocated by imatrix() */  double ftolhess; /* Tolerance for computing hessian */
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  /**************** split *************************/
   free((FREE_ARG) (m+nrl-NR_END));  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 }  {
     char  *ss;                            /* pointer */
 /******************* matrix *******************************/    int   l1, l2;                         /* length counters */
 double **matrix(long nrl, long nrh, long ncl, long nch)  
 {    l1 = strlen(path );                   /* length of path */
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   double **m;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
     if ( ss == NULL ) {                   /* no directory, so use current */
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   if (!m) nrerror("allocation failure 1 in matrix()");        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   m += NR_END;      /* get current working directory */
   m -= nrl;      /*    extern  char* getcwd ( char *buf , int len);*/
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));        return( GLOCK_ERROR_GETCWD );
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");      }
   m[nrl] += NR_END;      strcpy( name, path );               /* we've got it */
   m[nrl] -= ncl;    } else {                              /* strip direcotry from path */
       ss++;                               /* after this, the filename */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;      l2 = strlen( ss );                  /* length of filename */
   return m;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 }      strcpy( name, ss );         /* save file name */
       strncpy( dirc, path, l1 - l2 );     /* now the directory */
 /*************************free matrix ************************/      dirc[l1-l2] = 0;                    /* add zero */
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    }
 {    l1 = strlen( dirc );                  /* length of directory */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    /*#ifdef windows
   free((FREE_ARG)(m+nrl-NR_END));    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
 }  #else
     if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
 /******************* ma3x *******************************/  #endif
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    */
 {    ss = strrchr( name, '.' );            /* find last / */
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    ss++;
   double ***m;    strcpy(ext,ss);                       /* save extension */
     l1= strlen( name);
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    l2= strlen(ss)+1;
   if (!m) nrerror("allocation failure 1 in matrix()");    strncpy( finame, name, l1-l2);
   m += NR_END;    finame[l1-l2]= 0;
   m -= nrl;    return( 0 );                          /* we're done */
   }
   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;  /******************************************/
   m[nrl] -= ncl;  
   void replace_back_to_slash(char *s, char*t)
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  {
     int i;
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    int lg=0;
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    i=0;
   m[nrl][ncl] += NR_END;    lg=strlen(t);
   m[nrl][ncl] -= nll;    for(i=0; i<= lg; i++) {
   for (j=ncl+1; j<=nch; j++)      (s[i] = t[i]);
     m[nrl][j]=m[nrl][j-1]+nlay;      if (t[i]== '\\') s[i]='/';
      }
   for (i=nrl+1; i<=nrh; i++) {  }
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)  int nbocc(char *s, char occ)
       m[i][j]=m[i][j-1]+nlay;  {
   }    int i,j=0;
   return m;    int lg=20;
 }    i=0;
     lg=strlen(s);
 /*************************free ma3x ************************/    for(i=0; i<= lg; i++) {
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    if  (s[i] == occ ) j++;
 {    }
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    return j;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  }
   free((FREE_ARG)(m+nrl-NR_END));  
 }  void cutv(char *u,char *v, char*t, char occ)
   {
 /***************** f1dim *************************/    /* cuts string t into u and v where u is ended by char occ excluding it
 extern int ncom;       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
 extern double *pcom,*xicom;       gives u="abcedf" and v="ghi2j" */
 extern double (*nrfunc)(double []);    int i,lg,j,p=0;
      i=0;
 double f1dim(double x)    for(j=0; j<=strlen(t)-1; j++) {
 {      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   int j;    }
   double f;  
   double *xt;    lg=strlen(t);
      for(j=0; j<p; j++) {
   xt=vector(1,ncom);      (u[j] = t[j]);
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    }
   f=(*nrfunc)(xt);       u[p]='\0';
   free_vector(xt,1,ncom);  
   return f;     for(j=0; j<= lg; j++) {
 }      if (j>=(p+1))(v[j-p-1] = t[j]);
     }
 /*****************brent *************************/  }
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  
 {  /********************** nrerror ********************/
   int iter;  
   double a,b,d,etemp;  void nrerror(char error_text[])
   double fu,fv,fw,fx;  {
   double ftemp;    fprintf(stderr,"ERREUR ...\n");
   double p,q,r,tol1,tol2,u,v,w,x,xm;    fprintf(stderr,"%s\n",error_text);
   double e=0.0;    exit(EXIT_FAILURE);
    }
   a=(ax < cx ? ax : cx);  /*********************** vector *******************/
   b=(ax > cx ? ax : cx);  double *vector(int nl, int nh)
   x=w=v=bx;  {
   fw=fv=fx=(*f)(x);    double *v;
   for (iter=1;iter<=ITMAX;iter++) {    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     xm=0.5*(a+b);    if (!v) nrerror("allocation failure in vector");
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    return v-nl+NR_END;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  }
     printf(".");fflush(stdout);  
 #ifdef DEBUG  /************************ free vector ******************/
     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);  void free_vector(double*v, int nl, int nh)
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  {
 #endif    free((FREE_ARG)(v+nl-NR_END));
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  }
       *xmin=x;  
       return fx;  /************************ivector *******************************/
     }  int *ivector(long nl,long nh)
     ftemp=fu;  {
     if (fabs(e) > tol1) {    int *v;
       r=(x-w)*(fx-fv);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       q=(x-v)*(fx-fw);    if (!v) nrerror("allocation failure in ivector");
       p=(x-v)*q-(x-w)*r;    return v-nl+NR_END;
       q=2.0*(q-r);  }
       if (q > 0.0) p = -p;  
       q=fabs(q);  /******************free ivector **************************/
       etemp=e;  void free_ivector(int *v, long nl, long nh)
       e=d;  {
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    free((FREE_ARG)(v+nl-NR_END));
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  }
       else {  
         d=p/q;  /************************lvector *******************************/
         u=x+d;  long *lvector(long nl,long nh)
         if (u-a < tol2 || b-u < tol2)  {
           d=SIGN(tol1,xm-x);    long *v;
       }    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     } else {    if (!v) nrerror("allocation failure in ivector");
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    return v-nl+NR_END;
     }  }
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  
     fu=(*f)(u);  /******************free lvector **************************/
     if (fu <= fx) {  void free_lvector(long *v, long nl, long nh)
       if (u >= x) a=x; else b=x;  {
       SHFT(v,w,x,u)    free((FREE_ARG)(v+nl-NR_END));
         SHFT(fv,fw,fx,fu)  }
         } else {  
           if (u < x) a=u; else b=u;  /******************* imatrix *******************************/
           if (fu <= fw || w == x) {  int **imatrix(long nrl, long nrh, long ncl, long nch) 
             v=w;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
             w=u;  { 
             fv=fw;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
             fw=fu;    int **m; 
           } else if (fu <= fv || v == x || v == w) {    
             v=u;    /* allocate pointers to rows */ 
             fv=fu;    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
           }    if (!m) nrerror("allocation failure 1 in matrix()"); 
         }    m += NR_END; 
   }    m -= nrl; 
   nrerror("Too many iterations in brent");    
   *xmin=x;    
   return fx;    /* allocate rows and set pointers to them */ 
 }    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
 /****************** mnbrak ***********************/    m[nrl] += NR_END; 
     m[nrl] -= ncl; 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    
             double (*func)(double))    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
 {    
   double ulim,u,r,q, dum;    /* return pointer to array of pointers to rows */ 
   double fu;    return m; 
    } 
   *fa=(*func)(*ax);  
   *fb=(*func)(*bx);  /****************** free_imatrix *************************/
   if (*fb > *fa) {  void free_imatrix(m,nrl,nrh,ncl,nch)
     SHFT(dum,*ax,*bx,dum)        int **m;
       SHFT(dum,*fb,*fa,dum)        long nch,ncl,nrh,nrl; 
       }       /* free an int matrix allocated by imatrix() */ 
   *cx=(*bx)+GOLD*(*bx-*ax);  { 
   *fc=(*func)(*cx);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   while (*fb > *fc) {    free((FREE_ARG) (m+nrl-NR_END)); 
     r=(*bx-*ax)*(*fb-*fc);  } 
     q=(*bx-*cx)*(*fb-*fa);  
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  /******************* matrix *******************************/
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  double **matrix(long nrl, long nrh, long ncl, long nch)
     ulim=(*bx)+GLIMIT*(*cx-*bx);  {
     if ((*bx-u)*(u-*cx) > 0.0) {    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       fu=(*func)(u);    double **m;
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       if (fu < *fc) {    if (!m) nrerror("allocation failure 1 in matrix()");
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    m += NR_END;
           SHFT(*fb,*fc,fu,(*func)(u))    m -= nrl;
           }  
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       u=ulim;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       fu=(*func)(u);    m[nrl] += NR_END;
     } else {    m[nrl] -= ncl;
       u=(*cx)+GOLD*(*cx-*bx);  
       fu=(*func)(u);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     }    return m;
     SHFT(*ax,*bx,*cx,u)    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       SHFT(*fa,*fb,*fc,fu)     */
       }  }
 }  
   /*************************free matrix ************************/
 /*************** linmin ************************/  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   {
 int ncom;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 double *pcom,*xicom;    free((FREE_ARG)(m+nrl-NR_END));
 double (*nrfunc)(double []);  }
    
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  /******************* ma3x *******************************/
 {  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   double brent(double ax, double bx, double cx,  {
                double (*f)(double), double tol, double *xmin);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   double f1dim(double x);    double ***m;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  
               double *fc, double (*func)(double));    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   int j;    if (!m) nrerror("allocation failure 1 in matrix()");
   double xx,xmin,bx,ax;    m += NR_END;
   double fx,fb,fa;    m -= nrl;
    
   ncom=n;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   pcom=vector(1,n);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   xicom=vector(1,n);    m[nrl] += NR_END;
   nrfunc=func;    m[nrl] -= ncl;
   for (j=1;j<=n;j++) {  
     pcom[j]=p[j];    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     xicom[j]=xi[j];  
   }    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   ax=0.0;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   xx=1.0;    m[nrl][ncl] += NR_END;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    m[nrl][ncl] -= nll;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    for (j=ncl+1; j<=nch; j++) 
 #ifdef DEBUG      m[nrl][j]=m[nrl][j-1]+nlay;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    
 #endif    for (i=nrl+1; i<=nrh; i++) {
   for (j=1;j<=n;j++) {      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     xi[j] *= xmin;      for (j=ncl+1; j<=nch; j++) 
     p[j] += xi[j];        m[i][j]=m[i][j-1]+nlay;
   }    }
   free_vector(xicom,1,n);    return m; 
   free_vector(pcom,1,n);    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
 }             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     */
 /*************** powell ************************/  }
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  
             double (*func)(double []))  /*************************free ma3x ************************/
 {  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   void linmin(double p[], double xi[], int n, double *fret,  {
               double (*func)(double []));    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   int i,ibig,j;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double del,t,*pt,*ptt,*xit;    free((FREE_ARG)(m+nrl-NR_END));
   double fp,fptt;  }
   double *xits;  
   pt=vector(1,n);  /*************** function subdirf ***********/
   ptt=vector(1,n);  char *subdirf(char fileres[])
   xit=vector(1,n);  {
   xits=vector(1,n);    /* Caution optionfilefiname is hidden */
   *fret=(*func)(p);    strcpy(tmpout,optionfilefiname);
   for (j=1;j<=n;j++) pt[j]=p[j];    strcat(tmpout,"/"); /* Add to the right */
   for (*iter=1;;++(*iter)) {    strcat(tmpout,fileres);
     fp=(*fret);    return tmpout;
     ibig=0;  }
     del=0.0;  
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  /*************** function subdirf2 ***********/
     for (i=1;i<=n;i++)  char *subdirf2(char fileres[], char *preop)
       printf(" %d %.12f",i, p[i]);  {
     printf("\n");    
     for (i=1;i<=n;i++) {    /* Caution optionfilefiname is hidden */
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    strcpy(tmpout,optionfilefiname);
       fptt=(*fret);    strcat(tmpout,"/");
 #ifdef DEBUG    strcat(tmpout,preop);
       printf("fret=%lf \n",*fret);    strcat(tmpout,fileres);
 #endif    return tmpout;
       printf("%d",i);fflush(stdout);  }
       linmin(p,xit,n,fret,func);  
       if (fabs(fptt-(*fret)) > del) {  /*************** function subdirf3 ***********/
         del=fabs(fptt-(*fret));  char *subdirf3(char fileres[], char *preop, char *preop2)
         ibig=i;  {
       }    
 #ifdef DEBUG    /* Caution optionfilefiname is hidden */
       printf("%d %.12e",i,(*fret));    strcpy(tmpout,optionfilefiname);
       for (j=1;j<=n;j++) {    strcat(tmpout,"/");
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    strcat(tmpout,preop);
         printf(" x(%d)=%.12e",j,xit[j]);    strcat(tmpout,preop2);
       }    strcat(tmpout,fileres);
       for(j=1;j<=n;j++)    return tmpout;
         printf(" p=%.12e",p[j]);  }
       printf("\n");  
 #endif  /***************** f1dim *************************/
     }  extern int ncom; 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  extern double *pcom,*xicom;
 #ifdef DEBUG  extern double (*nrfunc)(double []); 
       int k[2],l;   
       k[0]=1;  double f1dim(double x) 
       k[1]=-1;  { 
       printf("Max: %.12e",(*func)(p));    int j; 
       for (j=1;j<=n;j++)    double f;
         printf(" %.12e",p[j]);    double *xt; 
       printf("\n");   
       for(l=0;l<=1;l++) {    xt=vector(1,ncom); 
         for (j=1;j<=n;j++) {    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    f=(*nrfunc)(xt); 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    free_vector(xt,1,ncom); 
         }    return f; 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  } 
       }  
 #endif  /*****************brent *************************/
   double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   { 
       free_vector(xit,1,n);    int iter; 
       free_vector(xits,1,n);    double a,b,d,etemp;
       free_vector(ptt,1,n);    double fu,fv,fw,fx;
       free_vector(pt,1,n);    double ftemp;
       return;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     }    double e=0.0; 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");   
     for (j=1;j<=n;j++) {    a=(ax < cx ? ax : cx); 
       ptt[j]=2.0*p[j]-pt[j];    b=(ax > cx ? ax : cx); 
       xit[j]=p[j]-pt[j];    x=w=v=bx; 
       pt[j]=p[j];    fw=fv=fx=(*f)(x); 
     }    for (iter=1;iter<=ITMAX;iter++) { 
     fptt=(*func)(ptt);      xm=0.5*(a+b); 
     if (fptt < fp) {      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       if (t < 0.0) {      printf(".");fflush(stdout);
         linmin(p,xit,n,fret,func);      fprintf(ficlog,".");fflush(ficlog);
         for (j=1;j<=n;j++) {  #ifdef DEBUG
           xi[j][ibig]=xi[j][n];      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);
           xi[j][n]=xit[j];      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
         }      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
 #ifdef DEBUG  #endif
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         for(j=1;j<=n;j++)        *xmin=x; 
           printf(" %.12e",xit[j]);        return fx; 
         printf("\n");      } 
 #endif      ftemp=fu;
       }      if (fabs(e) > tol1) { 
     }        r=(x-w)*(fx-fv); 
   }        q=(x-v)*(fx-fw); 
 }        p=(x-v)*q-(x-w)*r; 
         q=2.0*(q-r); 
 /**** Prevalence limit ****************/        if (q > 0.0) p = -p; 
         q=fabs(q); 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)        etemp=e; 
 {        e=d; 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
      matrix by transitions matrix until convergence is reached */          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         else { 
   int i, ii,j,k;          d=p/q; 
   double min, max, maxmin, maxmax,sumnew=0.;          u=x+d; 
   double **matprod2();          if (u-a < tol2 || b-u < tol2) 
   double **out, cov[NCOVMAX], **pmij();            d=SIGN(tol1,xm-x); 
   double **newm;        } 
   double agefin, delaymax=50 ; /* Max number of years to converge */      } else { 
         d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   for (ii=1;ii<=nlstate+ndeath;ii++)      } 
     for (j=1;j<=nlstate+ndeath;j++){      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      fu=(*f)(u); 
     }      if (fu <= fx) { 
         if (u >= x) a=x; else b=x; 
    cov[1]=1.;        SHFT(v,w,x,u) 
            SHFT(fv,fw,fx,fu) 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */          } else { 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){            if (u < x) a=u; else b=u; 
     newm=savm;            if (fu <= fw || w == x) { 
     /* Covariates have to be included here again */              v=w; 
      cov[2]=agefin;              w=u; 
                fv=fw; 
       for (k=1; k<=cptcovn;k++) {              fw=fu; 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];            } else if (fu <= fv || v == x || v == w) { 
         /*      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]]);*/              v=u; 
       }              fv=fu; 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];            } 
       for (k=1; k<=cptcovprod;k++)          } 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    } 
     nrerror("Too many iterations in brent"); 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    *xmin=x; 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    return fx; 
       /*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);  
   /****************** mnbrak ***********************/
     savm=oldm;  
     oldm=newm;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
     maxmax=0.;              double (*func)(double)) 
     for(j=1;j<=nlstate;j++){  { 
       min=1.;    double ulim,u,r,q, dum;
       max=0.;    double fu; 
       for(i=1; i<=nlstate; i++) {   
         sumnew=0;    *fa=(*func)(*ax); 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    *fb=(*func)(*bx); 
         prlim[i][j]= newm[i][j]/(1-sumnew);    if (*fb > *fa) { 
         max=FMAX(max,prlim[i][j]);      SHFT(dum,*ax,*bx,dum) 
         min=FMIN(min,prlim[i][j]);        SHFT(dum,*fb,*fa,dum) 
       }        } 
       maxmin=max-min;    *cx=(*bx)+GOLD*(*bx-*ax); 
       maxmax=FMAX(maxmax,maxmin);    *fc=(*func)(*cx); 
     }    while (*fb > *fc) { 
     if(maxmax < ftolpl){      r=(*bx-*ax)*(*fb-*fc); 
       return prlim;      q=(*bx-*cx)*(*fb-*fa); 
     }      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   }        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 }      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       if ((*bx-u)*(u-*cx) > 0.0) { 
 /*************** transition probabilities ***************/        fu=(*func)(u); 
       } else if ((*cx-u)*(u-ulim) > 0.0) { 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )        fu=(*func)(u); 
 {        if (fu < *fc) { 
   double s1, s2;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   /*double t34;*/            SHFT(*fb,*fc,fu,(*func)(u)) 
   int i,j,j1, nc, ii, jj;            } 
       } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
     for(i=1; i<= nlstate; i++){        u=ulim; 
     for(j=1; j<i;j++){        fu=(*func)(u); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      } else { 
         /*s2 += param[i][j][nc]*cov[nc];*/        u=(*cx)+GOLD*(*cx-*bx); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        fu=(*func)(u); 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/      } 
       }      SHFT(*ax,*bx,*cx,u) 
       ps[i][j]=s2;        SHFT(*fa,*fb,*fc,fu) 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        } 
     }  } 
     for(j=i+1; j<=nlstate+ndeath;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  /*************** linmin ************************/
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  int ncom; 
       }  double *pcom,*xicom;
       ps[i][j]=s2;  double (*nrfunc)(double []); 
     }   
   }  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     /*ps[3][2]=1;*/  { 
     double brent(double ax, double bx, double cx, 
   for(i=1; i<= nlstate; i++){                 double (*f)(double), double tol, double *xmin); 
      s1=0;    double f1dim(double x); 
     for(j=1; j<i; j++)    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       s1+=exp(ps[i][j]);                double *fc, double (*func)(double)); 
     for(j=i+1; j<=nlstate+ndeath; j++)    int j; 
       s1+=exp(ps[i][j]);    double xx,xmin,bx,ax; 
     ps[i][i]=1./(s1+1.);    double fx,fb,fa;
     for(j=1; j<i; j++)   
       ps[i][j]= exp(ps[i][j])*ps[i][i];    ncom=n; 
     for(j=i+1; j<=nlstate+ndeath; j++)    pcom=vector(1,n); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    xicom=vector(1,n); 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    nrfunc=func; 
   } /* end i */    for (j=1;j<=n;j++) { 
       pcom[j]=p[j]; 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){      xicom[j]=xi[j]; 
     for(jj=1; jj<= nlstate+ndeath; jj++){    } 
       ps[ii][jj]=0;    ax=0.0; 
       ps[ii][ii]=1;    xx=1.0; 
     }    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   }    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   #ifdef DEBUG
     printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     for(jj=1; jj<= nlstate+ndeath; jj++){  #endif
      printf("%lf ",ps[ii][jj]);    for (j=1;j<=n;j++) { 
    }      xi[j] *= xmin; 
     printf("\n ");      p[j] += xi[j]; 
     }    } 
     printf("\n ");printf("%lf ",cov[2]);*/    free_vector(xicom,1,n); 
 /*    free_vector(pcom,1,n); 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  } 
   goto end;*/  
     return ps;  char *asc_diff_time(long time_sec, char ascdiff[])
 }  {
     long sec_left, days, hours, minutes;
 /**************** Product of 2 matrices ******************/    days = (time_sec) / (60*60*24);
     sec_left = (time_sec) % (60*60*24);
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    hours = (sec_left) / (60*60) ;
 {    sec_left = (sec_left) %(60*60);
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    minutes = (sec_left) /60;
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    sec_left = (sec_left) % (60);
   /* in, b, out are matrice of pointers which should have been initialized    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
      before: only the contents of out is modified. The function returns    return ascdiff;
      a pointer to pointers identical to out */  }
   long i, j, k;  
   for(i=nrl; i<= nrh; i++)  /*************** powell ************************/
     for(k=ncolol; k<=ncoloh; k++)  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)              double (*func)(double [])) 
         out[i][k] +=in[i][j]*b[j][k];  { 
     void linmin(double p[], double xi[], int n, double *fret, 
   return out;                double (*func)(double [])); 
 }    int i,ibig,j; 
     double del,t,*pt,*ptt,*xit;
     double fp,fptt;
 /************* Higher Matrix Product ***************/    double *xits;
     int niterf, itmp;
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  
 {    pt=vector(1,n); 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    ptt=vector(1,n); 
      duration (i.e. until    xit=vector(1,n); 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    xits=vector(1,n); 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    *fret=(*func)(p); 
      (typically every 2 years instead of every month which is too big).    for (j=1;j<=n;j++) pt[j]=p[j]; 
      Model is determined by parameters x and covariates have to be    for (*iter=1;;++(*iter)) { 
      included manually here.      fp=(*fret); 
       ibig=0; 
      */      del=0.0; 
       last_time=curr_time;
   int i, j, d, h, k;      (void) gettimeofday(&curr_time,&tzp);
   double **out, cov[NCOVMAX];      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
   double **newm;      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
       fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
   /* Hstepm could be zero and should return the unit matrix */      for (i=1;i<=n;i++) {
   for (i=1;i<=nlstate+ndeath;i++)        printf(" %d %.12f",i, p[i]);
     for (j=1;j<=nlstate+ndeath;j++){        fprintf(ficlog," %d %.12lf",i, p[i]);
       oldm[i][j]=(i==j ? 1.0 : 0.0);        fprintf(ficrespow," %.12lf", p[i]);
       po[i][j][0]=(i==j ? 1.0 : 0.0);      }
     }      printf("\n");
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      fprintf(ficlog,"\n");
   for(h=1; h <=nhstepm; h++){      fprintf(ficrespow,"\n");fflush(ficrespow);
     for(d=1; d <=hstepm; d++){      if(*iter <=3){
       newm=savm;        tm = *localtime(&curr_time.tv_sec);
       /* Covariates have to be included here again */        strcpy(strcurr,asctime(&tmf));
       cov[1]=1.;  /*       asctime_r(&tm,strcurr); */
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        forecast_time=curr_time;
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        itmp = strlen(strcurr);
       for (k=1; k<=cptcovage;k++)        if(strcurr[itmp-1]=='\n')
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          strcurr[itmp-1]='\0';
       for (k=1; k<=cptcovprod;k++)        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         for(niterf=10;niterf<=30;niterf+=10){
           forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/          tmf = *localtime(&forecast_time.tv_sec);
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  /*      asctime_r(&tmf,strfor); */
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,          strcpy(strfor,asctime(&tmf));
                    pmij(pmmij,cov,ncovmodel,x,nlstate));          itmp = strlen(strfor);
       savm=oldm;          if(strfor[itmp-1]=='\n')
       oldm=newm;          strfor[itmp-1]='\0';
     }          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
     for(i=1; i<=nlstate+ndeath; i++)          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
       for(j=1;j<=nlstate+ndeath;j++) {        }
         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 (i=1;i<=n;i++) { 
          */        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       }        fptt=(*fret); 
   } /* end h */  #ifdef DEBUG
   return po;        printf("fret=%lf \n",*fret);
 }        fprintf(ficlog,"fret=%lf \n",*fret);
   #endif
         printf("%d",i);fflush(stdout);
 /*************** log-likelihood *************/        fprintf(ficlog,"%d",i);fflush(ficlog);
 double func( double *x)        linmin(p,xit,n,fret,func); 
 {        if (fabs(fptt-(*fret)) > del) { 
   int i, ii, j, k, mi, d, kk;          del=fabs(fptt-(*fret)); 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];          ibig=i; 
   double **out;        } 
   double sw; /* Sum of weights */  #ifdef DEBUG
   double lli; /* Individual log likelihood */        printf("%d %.12e",i,(*fret));
   long ipmx;        fprintf(ficlog,"%d %.12e",i,(*fret));
   /*extern weight */        for (j=1;j<=n;j++) {
   /* We are differentiating ll according to initial status */          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/          printf(" x(%d)=%.12e",j,xit[j]);
   /*for(i=1;i<imx;i++)          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     printf(" %d\n",s[4][i]);        }
   */        for(j=1;j<=n;j++) {
   cov[1]=1.;          printf(" p=%.12e",p[j]);
           fprintf(ficlog," p=%.12e",p[j]);
   for(k=1; k<=nlstate; k++) ll[k]=0.;        }
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        printf("\n");
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        fprintf(ficlog,"\n");
     for(mi=1; mi<= wav[i]-1; mi++){  #endif
       for (ii=1;ii<=nlstate+ndeath;ii++)      } 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
       for(d=0; d<dh[mi][i]; d++){  #ifdef DEBUG
         newm=savm;        int k[2],l;
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;        k[0]=1;
         for (kk=1; kk<=cptcovage;kk++) {        k[1]=-1;
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        printf("Max: %.12e",(*func)(p));
         }        fprintf(ficlog,"Max: %.12e",(*func)(p));
                for (j=1;j<=n;j++) {
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,          printf(" %.12e",p[j]);
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));          fprintf(ficlog," %.12e",p[j]);
         savm=oldm;        }
         oldm=newm;        printf("\n");
                fprintf(ficlog,"\n");
                for(l=0;l<=1;l++) {
       } /* end mult */          for (j=1;j<=n;j++) {
                  ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       ipmx +=1;          }
       sw += weight[i];          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     } /* end of wave */        }
   } /* end of individual */  #endif
   
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */        free_vector(xit,1,n); 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        free_vector(xits,1,n); 
   return -l;        free_vector(ptt,1,n); 
 }        free_vector(pt,1,n); 
         return; 
       } 
 /*********** Maximum Likelihood Estimation ***************/      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       for (j=1;j<=n;j++) { 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        ptt[j]=2.0*p[j]-pt[j]; 
 {        xit[j]=p[j]-pt[j]; 
   int i,j, iter;        pt[j]=p[j]; 
   double **xi,*delti;      } 
   double fret;      fptt=(*func)(ptt); 
   xi=matrix(1,npar,1,npar);      if (fptt < fp) { 
   for (i=1;i<=npar;i++)        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     for (j=1;j<=npar;j++)        if (t < 0.0) { 
       xi[i][j]=(i==j ? 1.0 : 0.0);          linmin(p,xit,n,fret,func); 
   printf("Powell\n");          for (j=1;j<=n;j++) { 
   powell(p,xi,npar,ftol,&iter,&fret,func);            xi[j][ibig]=xi[j][n]; 
             xi[j][n]=xit[j]; 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));          }
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));  #ifdef DEBUG
           printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 }          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           for(j=1;j<=n;j++){
 /**** Computes Hessian and covariance matrix ***/            printf(" %.12e",xit[j]);
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))            fprintf(ficlog," %.12e",xit[j]);
 {          }
   double  **a,**y,*x,pd;          printf("\n");
   double **hess;          fprintf(ficlog,"\n");
   int i, j,jk;  #endif
   int *indx;        }
       } 
   double hessii(double p[], double delta, int theta, double delti[]);    } 
   double hessij(double p[], double delti[], int i, int j);  } 
   void lubksb(double **a, int npar, int *indx, double b[]) ;  
   void ludcmp(double **a, int npar, int *indx, double *d) ;  /**** Prevalence limit (stable prevalence)  ****************/
   
   hess=matrix(1,npar,1,npar);  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   {
   printf("\nCalculation of the hessian matrix. Wait...\n");    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   for (i=1;i<=npar;i++){       matrix by transitions matrix until convergence is reached */
     printf("%d",i);fflush(stdout);  
     hess[i][i]=hessii(p,ftolhess,i,delti);    int i, ii,j,k;
     /*printf(" %f ",p[i]);*/    double min, max, maxmin, maxmax,sumnew=0.;
     /*printf(" %lf ",hess[i][i]);*/    double **matprod2();
   }    double **out, cov[NCOVMAX], **pmij();
      double **newm;
   for (i=1;i<=npar;i++) {    double agefin, delaymax=50 ; /* Max number of years to converge */
     for (j=1;j<=npar;j++)  {  
       if (j>i) {    for (ii=1;ii<=nlstate+ndeath;ii++)
         printf(".%d%d",i,j);fflush(stdout);      for (j=1;j<=nlstate+ndeath;j++){
         hess[i][j]=hessij(p,delti,i,j);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         hess[j][i]=hess[i][j];          }
         /*printf(" %lf ",hess[i][j]);*/  
       }     cov[1]=1.;
     }   
   }   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   printf("\n");    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       newm=savm;
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");      /* Covariates have to be included here again */
         cov[2]=agefin;
   a=matrix(1,npar,1,npar);    
   y=matrix(1,npar,1,npar);        for (k=1; k<=cptcovn;k++) {
   x=vector(1,npar);          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   indx=ivector(1,npar);          /*      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]]);*/
   for (i=1;i<=npar;i++)        }
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   ludcmp(a,npar,indx,&pd);        for (k=1; k<=cptcovprod;k++)
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   for (j=1;j<=npar;j++) {  
     for (i=1;i<=npar;i++) x[i]=0;        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     x[j]=1;        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     lubksb(a,npar,indx,x);        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     for (i=1;i<=npar;i++){      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
       matcov[i][j]=x[i];  
     }      savm=oldm;
   }      oldm=newm;
       maxmax=0.;
   printf("\n#Hessian matrix#\n");      for(j=1;j<=nlstate;j++){
   for (i=1;i<=npar;i++) {        min=1.;
     for (j=1;j<=npar;j++) {        max=0.;
       printf("%.3e ",hess[i][j]);        for(i=1; i<=nlstate; i++) {
     }          sumnew=0;
     printf("\n");          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   }          prlim[i][j]= newm[i][j]/(1-sumnew);
           max=FMAX(max,prlim[i][j]);
   /* Recompute Inverse */          min=FMIN(min,prlim[i][j]);
   for (i=1;i<=npar;i++)        }
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        maxmin=max-min;
   ludcmp(a,npar,indx,&pd);        maxmax=FMAX(maxmax,maxmin);
       }
   /*  printf("\n#Hessian matrix recomputed#\n");      if(maxmax < ftolpl){
         return prlim;
   for (j=1;j<=npar;j++) {      }
     for (i=1;i<=npar;i++) x[i]=0;    }
     x[j]=1;  }
     lubksb(a,npar,indx,x);  
     for (i=1;i<=npar;i++){  /*************** transition probabilities ***************/ 
       y[i][j]=x[i];  
       printf("%.3e ",y[i][j]);  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     }  {
     printf("\n");    double s1, s2;
   }    /*double t34;*/
   */    int i,j,j1, nc, ii, jj;
   
   free_matrix(a,1,npar,1,npar);      for(i=1; i<= nlstate; i++){
   free_matrix(y,1,npar,1,npar);      for(j=1; j<i;j++){
   free_vector(x,1,npar);        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   free_ivector(indx,1,npar);          /*s2 += param[i][j][nc]*cov[nc];*/
   free_matrix(hess,1,npar,1,npar);          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
           /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
         }
 }        ps[i][j]=s2;
         /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
 /*************** hessian matrix ****************/      }
 double hessii( double x[], double delta, int theta, double delti[])      for(j=i+1; j<=nlstate+ndeath;j++){
 {        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   int i;          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   int l=1, lmax=20;          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
   double k1,k2;        }
   double p2[NPARMAX+1];        ps[i][j]=s2;
   double res;      }
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    }
   double fx;      /*ps[3][2]=1;*/
   int k=0,kmax=10;  
   double l1;    for(i=1; i<= nlstate; i++){
        s1=0;
   fx=func(x);      for(j=1; j<i; j++)
   for (i=1;i<=npar;i++) p2[i]=x[i];        s1+=exp(ps[i][j]);
   for(l=0 ; l <=lmax; l++){      for(j=i+1; j<=nlstate+ndeath; j++)
     l1=pow(10,l);        s1+=exp(ps[i][j]);
     delts=delt;      ps[i][i]=1./(s1+1.);
     for(k=1 ; k <kmax; k=k+1){      for(j=1; j<i; j++)
       delt = delta*(l1*k);        ps[i][j]= exp(ps[i][j])*ps[i][i];
       p2[theta]=x[theta] +delt;      for(j=i+1; j<=nlstate+ndeath; j++)
       k1=func(p2)-fx;        ps[i][j]= exp(ps[i][j])*ps[i][i];
       p2[theta]=x[theta]-delt;      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       k2=func(p2)-fx;    } /* end i */
       /*res= (k1-2.0*fx+k2)/delt/delt; */  
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
            for(jj=1; jj<= nlstate+ndeath; jj++){
 #ifdef DEBUG        ps[ii][jj]=0;
       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);        ps[ii][ii]=1;
 #endif      }
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    }
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  
         k=kmax;  
       }    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */      for(jj=1; jj<= nlstate+ndeath; jj++){
         k=kmax; l=lmax*10.;       printf("%lf ",ps[ii][jj]);
       }     }
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      printf("\n ");
         delts=delt;      }
       }      printf("\n ");printf("%lf ",cov[2]);*/
     }  /*
   }    for(i=1; i<= npar; i++) printf("%f ",x[i]);
   delti[theta]=delts;    goto end;*/
   return res;      return ps;
    }
 }  
   /**************** Product of 2 matrices ******************/
 double hessij( double x[], double delti[], int thetai,int thetaj)  
 {  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   int i;  {
   int l=1, l1, lmax=20;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   double k1,k2,k3,k4,res,fx;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   double p2[NPARMAX+1];    /* in, b, out are matrice of pointers which should have been initialized 
   int k;       before: only the contents of out is modified. The function returns
        a pointer to pointers identical to out */
   fx=func(x);    long i, j, k;
   for (k=1; k<=2; k++) {    for(i=nrl; i<= nrh; i++)
     for (i=1;i<=npar;i++) p2[i]=x[i];      for(k=ncolol; k<=ncoloh; k++)
     p2[thetai]=x[thetai]+delti[thetai]/k;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          out[i][k] +=in[i][j]*b[j][k];
     k1=func(p2)-fx;  
      return out;
     p2[thetai]=x[thetai]+delti[thetai]/k;  }
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k2=func(p2)-fx;  
    /************* Higher Matrix Product ***************/
     p2[thetai]=x[thetai]-delti[thetai]/k;  
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     k3=func(p2)-fx;  {
      /* Computes the transition matrix starting at age 'age' over 
     p2[thetai]=x[thetai]-delti[thetai]/k;       'nhstepm*hstepm*stepm' months (i.e. until
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
     k4=func(p2)-fx;       nhstepm*hstepm matrices. 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
 #ifdef DEBUG       (typically every 2 years instead of every month which is too big 
     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 the memory).
 #endif       Model is determined by parameters x and covariates have to be 
   }       included manually here. 
   return res;  
 }       */
   
 /************** Inverse of matrix **************/    int i, j, d, h, k;
 void ludcmp(double **a, int n, int *indx, double *d)    double **out, cov[NCOVMAX];
 {    double **newm;
   int i,imax,j,k;  
   double big,dum,sum,temp;    /* Hstepm could be zero and should return the unit matrix */
   double *vv;    for (i=1;i<=nlstate+ndeath;i++)
        for (j=1;j<=nlstate+ndeath;j++){
   vv=vector(1,n);        oldm[i][j]=(i==j ? 1.0 : 0.0);
   *d=1.0;        po[i][j][0]=(i==j ? 1.0 : 0.0);
   for (i=1;i<=n;i++) {      }
     big=0.0;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for (j=1;j<=n;j++)    for(h=1; h <=nhstepm; h++){
       if ((temp=fabs(a[i][j])) > big) big=temp;      for(d=1; d <=hstepm; d++){
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        newm=savm;
     vv[i]=1.0/big;        /* Covariates have to be included here again */
   }        cov[1]=1.;
   for (j=1;j<=n;j++) {        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     for (i=1;i<j;i++) {        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       sum=a[i][j];        for (k=1; k<=cptcovage;k++)
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       a[i][j]=sum;        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]]];
     big=0.0;  
     for (i=j;i<=n;i++) {  
       sum=a[i][j];        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       for (k=1;k<j;k++)        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         sum -= a[i][k]*a[k][j];        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
       a[i][j]=sum;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
       if ( (dum=vv[i]*fabs(sum)) >= big) {        savm=oldm;
         big=dum;        oldm=newm;
         imax=i;      }
       }      for(i=1; i<=nlstate+ndeath; i++)
     }        for(j=1;j<=nlstate+ndeath;j++) {
     if (j != imax) {          po[i][j][h]=newm[i][j];
       for (k=1;k<=n;k++) {          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
         dum=a[imax][k];           */
         a[imax][k]=a[j][k];        }
         a[j][k]=dum;    } /* end h */
       }    return po;
       *d = -(*d);  }
       vv[imax]=vv[j];  
     }  
     indx[j]=imax;  /*************** log-likelihood *************/
     if (a[j][j] == 0.0) a[j][j]=TINY;  double func( double *x)
     if (j != n) {  {
       dum=1.0/(a[j][j]);    int i, ii, j, k, mi, d, kk;
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     }    double **out;
   }    double sw; /* Sum of weights */
   free_vector(vv,1,n);  /* Doesn't work */    double lli; /* Individual log likelihood */
 ;    int s1, s2;
 }    double bbh, survp;
     long ipmx;
 void lubksb(double **a, int n, int *indx, double b[])    /*extern weight */
 {    /* We are differentiating ll according to initial status */
   int i,ii=0,ip,j;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   double sum;    /*for(i=1;i<imx;i++) 
        printf(" %d\n",s[4][i]);
   for (i=1;i<=n;i++) {    */
     ip=indx[i];    cov[1]=1.;
     sum=b[ip];  
     b[ip]=b[i];    for(k=1; k<=nlstate; k++) ll[k]=0.;
     if (ii)  
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    if(mle==1){
     else if (sum) ii=i;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     b[i]=sum;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   }        for(mi=1; mi<= wav[i]-1; mi++){
   for (i=n;i>=1;i--) {          for (ii=1;ii<=nlstate+ndeath;ii++)
     sum=b[i];            for (j=1;j<=nlstate+ndeath;j++){
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     b[i]=sum/a[i][i];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   }            }
 }          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
 /************ Frequencies ********************/            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 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)            for (kk=1; kk<=cptcovage;kk++) {
 {  /* Some frequencies */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
              }
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double ***freq; /* Frequencies */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double *pp;            savm=oldm;
   double pos, k2, dateintsum=0,k2cpt=0;            oldm=newm;
   FILE *ficresp;          } /* end mult */
   char fileresp[FILENAMELENGTH];        
            /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   pp=vector(1,nlstate);          /* But now since version 0.9 we anticipate for bias and large stepm.
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   strcpy(fileresp,"p");           * (in months) between two waves is not a multiple of stepm, we rounded to 
   strcat(fileresp,fileres);           * the nearest (and in case of equal distance, to the lowest) interval but now
   if((ficresp=fopen(fileresp,"w"))==NULL) {           * we keep into memory the bias bh[mi][i] and also the previous matrix product
     printf("Problem with prevalence resultfile: %s\n", fileresp);           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     exit(0);           * 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
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);           * -stepm/2 to stepm/2 .
   j1=0;           * 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. 
   j=cptcoveff;           */
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          s1=s[mw[mi][i]][i];
            s2=s[mw[mi+1][i]][i];
   for(k1=1; k1<=j;k1++){          bbh=(double)bh[mi][i]/(double)stepm; 
     for(i1=1; i1<=ncodemax[k1];i1++){          /* bias is positive if real duration
       j1++;           * is higher than the multiple of stepm and negative otherwise.
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);           */
         scanf("%d", i);*/          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
       for (i=-1; i<=nlstate+ndeath; i++)            if( s2 > nlstate){ 
         for (jk=-1; jk<=nlstate+ndeath; jk++)              /* i.e. if s2 is a death state and if the date of death is known then the contribution
           for(m=agemin; m <= agemax+3; m++)               to the likelihood is the probability to die between last step unit time and current 
             freq[i][jk][m]=0;               step unit time, which is also the differences between probability to die before dh 
                     and probability to die before dh-stepm . 
       dateintsum=0;               In version up to 0.92 likelihood was computed
       k2cpt=0;          as if date of death was unknown. Death was treated as any other
       for (i=1; i<=imx; i++) {          health state: the date of the interview describes the actual state
         bool=1;          and not the date of a change in health state. The former idea was
         if  (cptcovn>0) {          to consider that at each interview the state was recorded
           for (z1=1; z1<=cptcoveff; z1++)          (healthy, disable or death) and IMaCh was corrected; but when we
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          introduced the exact date of death then we should have modified
               bool=0;          the contribution of an exact death to the likelihood. This new
         }          contribution is smaller and very dependent of the step unit
         if (bool==1) {          stepm. It is no more the probability to die between last interview
           for(m=firstpass; m<=lastpass; m++){          and month of death but the probability to survive from last
             k2=anint[m][i]+(mint[m][i]/12.);          interview up to one month before death multiplied by the
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          probability to die within a month. Thanks to Chris
               if(agev[m][i]==0) agev[m][i]=agemax+1;          Jackson for correcting this bug.  Former versions increased
               if(agev[m][i]==1) agev[m][i]=agemax+2;          mortality artificially. The bad side is that we add another loop
               if (m<lastpass) {          which slows down the processing. The difference can be up to 10%
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          lower mortality.
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];            */
               }            lli=log(out[s1][s2] - savm[s1][s2]);
                        }else{
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
                 dateintsum=dateintsum+k2;            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
                 k2cpt++;          } 
               }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
             }          /*if(lli ==000.0)*/
           }          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
         }          ipmx +=1;
       }          sw += weight[i];
                  ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        } /* end of wave */
       } /* end of individual */
       if  (cptcovn>0) {    }  else if(mle==2){
         fprintf(ficresp, "\n#********** Variable ");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         fprintf(ficresp, "**********\n#");        for(mi=1; mi<= wav[i]-1; mi++){
       }          for (ii=1;ii<=nlstate+ndeath;ii++)
       for(i=1; i<=nlstate;i++)            for (j=1;j<=nlstate+ndeath;j++){
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       fprintf(ficresp, "\n");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                  }
       for(i=(int)agemin; i <= (int)agemax+3; i++){          for(d=0; d<=dh[mi][i]; d++){
         if(i==(int)agemax+3)            newm=savm;
           printf("Total");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         else            for (kk=1; kk<=cptcovage;kk++) {
           printf("Age %d", i);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         for(jk=1; jk <=nlstate ; jk++){            }
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             pp[jk] += freq[jk][m][i];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         }            savm=oldm;
         for(jk=1; jk <=nlstate ; jk++){            oldm=newm;
           for(m=-1, pos=0; m <=0 ; m++)          } /* end mult */
             pos += freq[jk][m][i];        
           if(pp[jk]>=1.e-10)          s1=s[mw[mi][i]][i];
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          s2=s[mw[mi+1][i]][i];
           else          bbh=(double)bh[mi][i]/(double)stepm; 
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          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 */
         }          ipmx +=1;
           sw += weight[i];
         for(jk=1; jk <=nlstate ; jk++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        } /* end of wave */
             pp[jk] += freq[jk][m][i];      } /* end of individual */
         }    }  else if(mle==3){  /* exponential inter-extrapolation */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for(jk=1,pos=0; jk <=nlstate ; jk++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           pos += pp[jk];        for(mi=1; mi<= wav[i]-1; mi++){
         for(jk=1; jk <=nlstate ; jk++){          for (ii=1;ii<=nlstate+ndeath;ii++)
           if(pos>=1.e-5)            for (j=1;j<=nlstate+ndeath;j++){
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           else              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);            }
           if( i <= (int) agemax){          for(d=0; d<dh[mi][i]; d++){
             if(pos>=1.e-5){            newm=savm;
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
               probs[i][jk][j1]= pp[jk]/pos;            for (kk=1; kk<=cptcovage;kk++) {
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }            }
             else            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           }            savm=oldm;
         }            oldm=newm;
                  } /* end mult */
         for(jk=-1; jk <=nlstate+ndeath; jk++)        
           for(m=-1; m <=nlstate+ndeath; m++)          s1=s[mw[mi][i]][i];
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);          s2=s[mw[mi+1][i]][i];
         if(i <= (int) agemax)          bbh=(double)bh[mi][i]/(double)stepm; 
           fprintf(ficresp,"\n");          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 */
         printf("\n");          ipmx +=1;
       }          sw += weight[i];
     }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   }        } /* end of wave */
   dateintmean=dateintsum/k2cpt;      } /* end of individual */
      }else if (mle==4){  /* ml=4 no inter-extrapolation */
   fclose(ficresp);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   free_vector(pp,1,nlstate);        for(mi=1; mi<= wav[i]-1; mi++){
            for (ii=1;ii<=nlstate+ndeath;ii++)
   /* End of Freq */            for (j=1;j<=nlstate+ndeath;j++){
 }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
 /************ 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)          for(d=0; d<dh[mi][i]; d++){
 {  /* Some frequencies */            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;            for (kk=1; kk<=cptcovage;kk++) {
   double ***freq; /* Frequencies */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double *pp;            }
   double pos, k2;          
             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;
              oldm=newm;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          } /* end mult */
   j1=0;        
            s1=s[mw[mi][i]][i];
   j=cptcoveff;          s2=s[mw[mi+1][i]][i];
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          if( s2 > nlstate){ 
              lli=log(out[s1][s2] - savm[s1][s2]);
  for(k1=1; k1<=j;k1++){          }else{
     for(i1=1; i1<=ncodemax[k1];i1++){            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       j1++;          }
            ipmx +=1;
       for (i=-1; i<=nlstate+ndeath; i++)            sw += weight[i];
         for (jk=-1; jk<=nlstate+ndeath; jk++)            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           for(m=agemin; m <= agemax+3; m++)  /*      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]); */
             freq[i][jk][m]=0;        } /* end of wave */
            } /* end of individual */
       for (i=1; i<=imx; i++) {    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
         bool=1;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         if  (cptcovn>0) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           for (z1=1; z1<=cptcoveff; z1++)        for(mi=1; mi<= wav[i]-1; mi++){
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          for (ii=1;ii<=nlstate+ndeath;ii++)
               bool=0;            for (j=1;j<=nlstate+ndeath;j++){
         }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         if (bool==1) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           for(m=firstpass; m<=lastpass; m++){            }
             k2=anint[m][i]+(mint[m][i]/12.);          for(d=0; d<dh[mi][i]; d++){
             if ((k2>=dateprev1) && (k2<=dateprev2)) {            newm=savm;
               if(agev[m][i]==0) agev[m][i]=agemax+1;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
               if(agev[m][i]==1) agev[m][i]=agemax+2;            for (kk=1; kk<=cptcovage;kk++) {
               if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */            }
             }          
           }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       }            savm=oldm;
         for(i=(int)agemin; i <= (int)agemax+3; i++){            oldm=newm;
           for(jk=1; jk <=nlstate ; jk++){          } /* end mult */
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        
               pp[jk] += freq[jk][m][i];          s1=s[mw[mi][i]][i];
           }          s2=s[mw[mi+1][i]][i];
           for(jk=1; jk <=nlstate ; jk++){          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
             for(m=-1, pos=0; m <=0 ; m++)          ipmx +=1;
             pos += freq[jk][m][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]);*/
          for(jk=1; jk <=nlstate ; jk++){        } /* end of wave */
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      } /* end of individual */
              pp[jk] += freq[jk][m][i];    } /* End of if */
          }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
              /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    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 ; jk++){            }
            if( i <= (int) agemax){  
              if(pos>=1.e-5){  /*************** log-likelihood *************/
                probs[i][jk][j1]= pp[jk]/pos;  double funcone( double *x)
              }  {
            }    /* Same as likeli but slower because of a lot of printf and if */
          }    int i, ii, j, k, mi, d, kk;
              double l, ll[NLSTATEMAX], cov[NCOVMAX];
         }    double **out;
     }    double lli; /* Individual log likelihood */
   }    double llt;
      int s1, s2;
      double bbh, survp;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    /*extern weight */
   free_vector(pp,1,nlstate);    /* We are differentiating ll according to initial status */
      /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 }  /* End of Freq */    /*for(i=1;i<imx;i++) 
       printf(" %d\n",s[4][i]);
 /************* Waves Concatenation ***************/    */
     cov[1]=1.;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  
 {    for(k=1; k<=nlstate; k++) ll[k]=0.;
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  
      Death is a valid wave (if date is known).    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]      for(mi=1; mi<= wav[i]-1; mi++){
      and mw[mi+1][i]. dh depends on stepm.        for (ii=1;ii<=nlstate+ndeath;ii++)
      */          for (j=1;j<=nlstate+ndeath;j++){
             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int i, mi, m;            savm[ii][j]=(ii==j ? 1.0 : 0.0);
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;          }
      double sum=0., jmean=0.;*/        for(d=0; d<dh[mi][i]; d++){
           newm=savm;
   int j, k=0,jk, ju, jl;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double sum=0.;          for (kk=1; kk<=cptcovage;kk++) {
   jmin=1e+5;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   jmax=-1;          }
   jmean=0.;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   for(i=1; i<=imx; i++){                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     mi=0;          savm=oldm;
     m=firstpass;          oldm=newm;
     while(s[m][i] <= nlstate){        } /* end mult */
       if(s[m][i]>=1)        
         mw[++mi][i]=m;        s1=s[mw[mi][i]][i];
       if(m >=lastpass)        s2=s[mw[mi+1][i]][i];
         break;        bbh=(double)bh[mi][i]/(double)stepm; 
       else        /* bias is positive if real duration
         m++;         * is higher than the multiple of stepm and negative otherwise.
     }/* end while */         */
     if (s[m][i] > nlstate){        if( s2 > nlstate && (mle <5) ){  /* Jackson */
       mi++;     /* Death is another wave */          lli=log(out[s1][s2] - savm[s1][s2]);
       /* if(mi==0)  never been interviewed correctly before death */        } else if (mle==1){
          /* Only death is a correct wave */          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       mw[mi][i]=m;        } else if(mle==2){
     }          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
         } else if(mle==3){  /* exponential inter-extrapolation */
     wav[i]=mi;          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(mi==0)        } else if (mle==4){  /* mle=4 no inter-extrapolation */
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          lli=log(out[s1][s2]); /* Original formula */
   }        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
           lli=log(out[s1][s2]); /* Original formula */
   for(i=1; i<=imx; i++){        } /* End of if */
     for(mi=1; mi<wav[i];mi++){        ipmx +=1;
       if (stepm <=0)        sw += weight[i];
         dh[mi][i]=1;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       else{  /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         if (s[mw[mi+1][i]][i] > nlstate) {        if(globpr){
           if (agedc[i] < 2*AGESUP) {          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);   %10.6f %10.6f %10.6f ", \
           if(j==0) j=1;  /* Survives at least one month after exam */                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
           k=k+1;                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
           if (j >= jmax) jmax=j;          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
           if (j <= jmin) jmin=j;            llt +=ll[k]*gipmx/gsw;
           sum=sum+j;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           /*if (j<0) printf("j=%d num=%d \n",j,i); */          }
           }          fprintf(ficresilk," %10.6f\n", -llt);
         }        }
         else{      } /* end of wave */
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    } /* end of individual */
           k=k+1;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
           if (j >= jmax) jmax=j;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
           else if (j <= jmin)jmin=j;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    if(globpr==0){ /* First time we count the contributions and weights */
           sum=sum+j;      gipmx=ipmx;
         }      gsw=sw;
         jk= j/stepm;    }
         jl= j -jk*stepm;    return -l;
         ju= j -(jk+1)*stepm;  }
         if(jl <= -ju)  
           dh[mi][i]=jk;  
         else  /*************** function likelione ***********/
           dh[mi][i]=jk+1;  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
         if(dh[mi][i]==0)  {
           dh[mi][i]=1; /* At least one step */    /* This routine should help understanding what is done with 
       }       the selection of individuals/waves and
     }       to check the exact contribution to the likelihood.
   }       Plotting could be done.
   jmean=sum/k;     */
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);    int k;
  }  
 /*********** Tricode ****************************/    if(*globpri !=0){ /* Just counts and sums, no printings */
 void tricode(int *Tvar, int **nbcode, int imx)      strcpy(fileresilk,"ilk"); 
 {      strcat(fileresilk,fileres);
   int Ndum[20],ij=1, k, j, i;      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   int cptcode=0;        printf("Problem with resultfile: %s\n", fileresilk);
   cptcoveff=0;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
        }
   for (k=0; k<19; k++) Ndum[k]=0;      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");
   for (k=1; k<=7; k++) ncodemax[k]=0;      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {      for(k=1; k<=nlstate; k++) 
     for (i=1; i<=imx; i++) {        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
       ij=(int)(covar[Tvar[j]][i]);      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
       Ndum[ij]++;    }
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  
       if (ij > cptcode) cptcode=ij;    *fretone=(*funcone)(p);
     }    if(*globpri !=0){
       fclose(ficresilk);
     for (i=0; i<=cptcode; i++) {      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       if(Ndum[i]!=0) ncodemax[j]++;      fflush(fichtm); 
     }    } 
     ij=1;    return;
   }
   
     for (i=1; i<=ncodemax[j]; i++) {  
       for (k=0; k<=19; k++) {  /*********** Maximum Likelihood Estimation ***************/
         if (Ndum[k] != 0) {  
           nbcode[Tvar[j]][ij]=k;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
           /*     printf("nbcodeaaaaaaaaaaa=%d Tvar[j]=%d ij=%d j=%d",nbcode[Tvar[j]][ij],Tvar[j],ij,j);*/  {
           ij++;    int i,j, iter;
         }    double **xi;
         if (ij > ncodemax[j]) break;    double fret;
       }      double fretone; /* Only one call to likelihood */
     }    char filerespow[FILENAMELENGTH];
   }      xi=matrix(1,npar,1,npar);
     for (i=1;i<=npar;i++)
  for (k=0; k<19; k++) Ndum[k]=0;      for (j=1;j<=npar;j++)
         xi[i][j]=(i==j ? 1.0 : 0.0);
  for (i=1; i<=ncovmodel-2; i++) {    printf("Powell\n");  fprintf(ficlog,"Powell\n");
       ij=Tvar[i];    strcpy(filerespow,"pow"); 
       Ndum[ij]++;    strcat(filerespow,fileres);
     }    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
  ij=1;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
  for (i=1; i<=10; i++) {    }
    if((Ndum[i]!=0) && (i<=ncovcol)){    fprintf(ficrespow,"# Powell\n# iter -2*LL");
      Tvaraff[ij]=i;    for (i=1;i<=nlstate;i++)
      ij++;      for(j=1;j<=nlstate+ndeath;j++)
    }        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
  }    fprintf(ficrespow,"\n");
    
     cptcoveff=ij-1;    powell(p,xi,npar,ftol,&iter,&fret,func);
 }  
     fclose(ficrespow);
 /*********** Health Expectancies ****************/    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));
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm)    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
 {  
   /* Health expectancies */  }
   int i, j, nhstepm, hstepm, h, nstepm;  
   double age, agelim, hf;  /**** Computes Hessian and covariance matrix ***/
   double ***p3mat;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
    {
   fprintf(ficreseij,"# Health expectancies\n");    double  **a,**y,*x,pd;
   fprintf(ficreseij,"# Age");    double **hess;
   for(i=1; i<=nlstate;i++)    int i, j,jk;
     for(j=1; j<=nlstate;j++)    int *indx;
       fprintf(ficreseij," %1d-%1d",i,j);  
   fprintf(ficreseij,"\n");    double hessii(double p[], double delta, int theta, double delti[]);
     double hessij(double p[], double delti[], int i, int j);
   if(estepm < stepm){    void lubksb(double **a, int npar, int *indx, double b[]) ;
     printf ("Problem %d lower than %d\n",estepm, stepm);    void ludcmp(double **a, int npar, int *indx, double *d) ;
   }  
   else  hstepm=estepm;      hess=matrix(1,npar,1,npar);
   /* We compute the life expectancy from trapezoids spaced every estepm months  
    * This is mainly to measure the difference between two models: for example    printf("\nCalculation of the hessian matrix. Wait...\n");
    * if stepm=24 months pijx are given only every 2 years and by summing them    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
    * we are calculating an estimate of the Life Expectancy assuming a linear    for (i=1;i<=npar;i++){
    * progression inbetween and thus overestimating or underestimating according      printf("%d",i);fflush(stdout);
    * to the curvature of the survival function. If, for the same date, we      fprintf(ficlog,"%d",i);fflush(ficlog);
    * estimate the model with stepm=1 month, we can keep estepm to 24 months      hess[i][i]=hessii(p,ftolhess,i,delti);
    * to compare the new estimate of Life expectancy with the same linear      /*printf(" %f ",p[i]);*/
    * hypothesis. A more precise result, taking into account a more precise      /*printf(" %lf ",hess[i][i]);*/
    * curvature will be obtained if estepm is as small as stepm. */    }
     
   /* For example we decided to compute the life expectancy with the smallest unit */    for (i=1;i<=npar;i++) {
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.      for (j=1;j<=npar;j++)  {
      nhstepm is the number of hstepm from age to agelim        if (j>i) { 
      nstepm is the number of stepm from age to agelin.          printf(".%d%d",i,j);fflush(stdout);
      Look at hpijx to understand the reason of that which relies in memory size          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
      and note for a fixed period like estepm months */          hess[i][j]=hessij(p,delti,i,j);
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the          hess[j][i]=hess[i][j];    
      survival function given by stepm (the optimization length). Unfortunately it          /*printf(" %lf ",hess[i][j]);*/
      means that if the survival funtion is printed only each two years of age and if        }
      you sum them up and add 1 year (area under the trapezoids) you won't get the same      }
      results. So we changed our mind and took the option of the best precision.    }
   */    printf("\n");
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    fprintf(ficlog,"\n");
   
   agelim=AGESUP;    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     /* nhstepm age range expressed in number of stepm */    
     nstepm=(int) rint((agelim-age)*YEARM/stepm);    a=matrix(1,npar,1,npar);
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    y=matrix(1,npar,1,npar);
     /* if (stepm >= YEARM) hstepm=1;*/    x=vector(1,npar);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    indx=ivector(1,npar);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for (i=1;i<=npar;i++)
     /* Computed by stepm unit matrices, product of hstepm matrices, stored      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    ludcmp(a,npar,indx,&pd);
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);    
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    for (j=1;j<=npar;j++) {
     for(i=1; i<=nlstate;i++)      for (i=1;i<=npar;i++) x[i]=0;
       for(j=1; j<=nlstate;j++)      x[j]=1;
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){      lubksb(a,npar,indx,x);
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;      for (i=1;i<=npar;i++){ 
           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/        matcov[i][j]=x[i];
         }      }
     fprintf(ficreseij,"%3.0f",age );    }
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){    printf("\n#Hessian matrix#\n");
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);    fprintf(ficlog,"\n#Hessian matrix#\n");
       }    for (i=1;i<=npar;i++) { 
     fprintf(ficreseij,"\n");      for (j=1;j<=npar;j++) { 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        printf("%.3e ",hess[i][j]);
   }        fprintf(ficlog,"%.3e ",hess[i][j]);
 }      }
       printf("\n");
 /************ Variance ******************/      fprintf(ficlog,"\n");
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)    }
 {  
   /* Variance of health expectancies */    /* Recompute Inverse */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    for (i=1;i<=npar;i++)
   double **newm;      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   double **dnewm,**doldm;    ludcmp(a,npar,indx,&pd);
   int i, j, nhstepm, hstepm, h, nstepm ;  
   int k, cptcode;    /*  printf("\n#Hessian matrix recomputed#\n");
   double *xp;  
   double **gp, **gm;    for (j=1;j<=npar;j++) {
   double ***gradg, ***trgradg;      for (i=1;i<=npar;i++) x[i]=0;
   double ***p3mat;      x[j]=1;
   double age,agelim, hf;      lubksb(a,npar,indx,x);
   int theta;      for (i=1;i<=npar;i++){ 
         y[i][j]=x[i];
    fprintf(ficresvij,"# Covariances of life expectancies\n");        printf("%.3e ",y[i][j]);
   fprintf(ficresvij,"# Age");        fprintf(ficlog,"%.3e ",y[i][j]);
   for(i=1; i<=nlstate;i++)      }
     for(j=1; j<=nlstate;j++)      printf("\n");
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      fprintf(ficlog,"\n");
   fprintf(ficresvij,"\n");    }
     */
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);    free_matrix(a,1,npar,1,npar);
   doldm=matrix(1,nlstate,1,nlstate);    free_matrix(y,1,npar,1,npar);
      free_vector(x,1,npar);
   if(estepm < stepm){    free_ivector(indx,1,npar);
     printf ("Problem %d lower than %d\n",estepm, stepm);    free_matrix(hess,1,npar,1,npar);
   }  
   else  hstepm=estepm;    
   /* 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  /*************** hessian matrix ****************/
      nstepm is the number of stepm from age to agelin.  double hessii( double x[], double delta, int theta, double delti[])
      Look at hpijx to understand the reason of that which relies in memory size  {
      and note for a fixed period like k years */    int i;
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    int l=1, lmax=20;
      survival function given by stepm (the optimization length). Unfortunately it    double k1,k2;
      means that if the survival funtion is printed only each two years of age and if    double p2[NPARMAX+1];
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    double res;
      results. So we changed our mind and took the option of the best precision.    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   */    double fx;
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    int k=0,kmax=10;
   agelim = AGESUP;    double l1;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */  
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    fx=func(x);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    for (i=1;i<=npar;i++) p2[i]=x[i];
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for(l=0 ; l <=lmax; l++){
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      l1=pow(10,l);
     gp=matrix(0,nhstepm,1,nlstate);      delts=delt;
     gm=matrix(0,nhstepm,1,nlstate);      for(k=1 ; k <kmax; k=k+1){
         delt = delta*(l1*k);
     for(theta=1; theta <=npar; theta++){        p2[theta]=x[theta] +delt;
       for(i=1; i<=npar; i++){ /* Computes gradient */        k1=func(p2)-fx;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        p2[theta]=x[theta]-delt;
       }        k2=func(p2)-fx;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          /*res= (k1-2.0*fx+k2)/delt/delt; */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         
       if (popbased==1) {  #ifdef DEBUG
         for(i=1; i<=nlstate;i++)        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
           prlim[i][i]=probs[(int)age][i][ij];        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       }  #endif
          /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
       for(j=1; j<= nlstate; j++){        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         for(h=0; h<=nhstepm; h++){          k=kmax;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)        }
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
         }          k=kmax; l=lmax*10.;
       }        }
            else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       for(i=1; i<=npar; i++) /* Computes gradient */          delts=delt;
         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);    }
      delti[theta]=delts;
       if (popbased==1) {    return res; 
         for(i=1; i<=nlstate;i++)    
           prlim[i][i]=probs[(int)age][i][ij];  }
       }  
   double hessij( double x[], double delti[], int thetai,int thetaj)
       for(j=1; j<= nlstate; j++){  {
         for(h=0; h<=nhstepm; h++){    int i;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    int l=1, l1, lmax=20;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    double k1,k2,k3,k4,res,fx;
         }    double p2[NPARMAX+1];
       }    int k;
   
       for(j=1; j<= nlstate; j++)    fx=func(x);
         for(h=0; h<=nhstepm; h++){    for (k=1; k<=2; k++) {
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      for (i=1;i<=npar;i++) p2[i]=x[i];
         }      p2[thetai]=x[thetai]+delti[thetai]/k;
     } /* End theta */      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k1=func(p2)-fx;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    
       p2[thetai]=x[thetai]+delti[thetai]/k;
     for(h=0; h<=nhstepm; h++)      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       for(j=1; j<=nlstate;j++)      k2=func(p2)-fx;
         for(theta=1; theta <=npar; theta++)    
           trgradg[h][j][theta]=gradg[h][theta][j];      p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      k3=func(p2)-fx;
     for(i=1;i<=nlstate;i++)    
       for(j=1;j<=nlstate;j++)      p2[thetai]=x[thetai]-delti[thetai]/k;
         vareij[i][j][(int)age] =0.;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       k4=func(p2)-fx;
     for(h=0;h<=nhstepm;h++){      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
       for(k=0;k<=nhstepm;k++){  #ifdef DEBUG
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      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);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      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);
         for(i=1;i<=nlstate;i++)  #endif
           for(j=1;j<=nlstate;j++)    }
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;    return res;
       }  }
     }  
   /************** Inverse of matrix **************/
     fprintf(ficresvij,"%.0f ",age );  void ludcmp(double **a, int n, int *indx, double *d) 
     for(i=1; i<=nlstate;i++)  { 
       for(j=1; j<=nlstate;j++){    int i,imax,j,k; 
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);    double big,dum,sum,temp; 
       }    double *vv; 
     fprintf(ficresvij,"\n");   
     free_matrix(gp,0,nhstepm,1,nlstate);    vv=vector(1,n); 
     free_matrix(gm,0,nhstepm,1,nlstate);    *d=1.0; 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    for (i=1;i<=n;i++) { 
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);      big=0.0; 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for (j=1;j<=n;j++) 
   } /* End age */        if ((temp=fabs(a[i][j])) > big) big=temp; 
        if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   free_vector(xp,1,npar);      vv[i]=1.0/big; 
   free_matrix(doldm,1,nlstate,1,npar);    } 
   free_matrix(dnewm,1,nlstate,1,nlstate);    for (j=1;j<=n;j++) { 
       for (i=1;i<j;i++) { 
 }        sum=a[i][j]; 
         for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
 /************ Variance of prevlim ******************/        a[i][j]=sum; 
 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)      } 
 {      big=0.0; 
   /* Variance of prevalence limit */      for (i=j;i<=n;i++) { 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        sum=a[i][j]; 
   double **newm;        for (k=1;k<j;k++) 
   double **dnewm,**doldm;          sum -= a[i][k]*a[k][j]; 
   int i, j, nhstepm, hstepm;        a[i][j]=sum; 
   int k, cptcode;        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   double *xp;          big=dum; 
   double *gp, *gm;          imax=i; 
   double **gradg, **trgradg;        } 
   double age,agelim;      } 
   int theta;      if (j != imax) { 
            for (k=1;k<=n;k++) { 
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");          dum=a[imax][k]; 
   fprintf(ficresvpl,"# Age");          a[imax][k]=a[j][k]; 
   for(i=1; i<=nlstate;i++)          a[j][k]=dum; 
       fprintf(ficresvpl," %1d-%1d",i,i);        } 
   fprintf(ficresvpl,"\n");        *d = -(*d); 
         vv[imax]=vv[j]; 
   xp=vector(1,npar);      } 
   dnewm=matrix(1,nlstate,1,npar);      indx[j]=imax; 
   doldm=matrix(1,nlstate,1,nlstate);      if (a[j][j] == 0.0) a[j][j]=TINY; 
        if (j != n) { 
   hstepm=1*YEARM; /* Every year of age */        dum=1.0/(a[j][j]); 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   agelim = AGESUP;      } 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    } 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    free_vector(vv,1,n);  /* Doesn't work */
     if (stepm >= YEARM) hstepm=1;  ;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  } 
     gradg=matrix(1,npar,1,nlstate);  
     gp=vector(1,nlstate);  void lubksb(double **a, int n, int *indx, double b[]) 
     gm=vector(1,nlstate);  { 
     int i,ii=0,ip,j; 
     for(theta=1; theta <=npar; theta++){    double sum; 
       for(i=1; i<=npar; i++){ /* Computes gradient */   
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    for (i=1;i<=n;i++) { 
       }      ip=indx[i]; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      sum=b[ip]; 
       for(i=1;i<=nlstate;i++)      b[ip]=b[i]; 
         gp[i] = prlim[i][i];      if (ii) 
            for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
       for(i=1; i<=npar; i++) /* Computes gradient */      else if (sum) ii=i; 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      b[i]=sum; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    } 
       for(i=1;i<=nlstate;i++)    for (i=n;i>=1;i--) { 
         gm[i] = prlim[i][i];      sum=b[i]; 
       for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       for(i=1;i<=nlstate;i++)      b[i]=sum/a[i][i]; 
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    } 
     } /* End theta */  } 
   
     trgradg =matrix(1,nlstate,1,npar);  /************ Frequencies ********************/
   void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint)
     for(j=1; j<=nlstate;j++)  {  /* Some frequencies */
       for(theta=1; theta <=npar; theta++)    
         trgradg[j][theta]=gradg[theta][j];    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     int first;
     for(i=1;i<=nlstate;i++)    double ***freq; /* Frequencies */
       varpl[i][(int)age] =0.;    double *pp, **prop;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    FILE *ficresp;
     for(i=1;i<=nlstate;i++)    char fileresp[FILENAMELENGTH];
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    
     pp=vector(1,nlstate);
     fprintf(ficresvpl,"%.0f ",age );    prop=matrix(1,nlstate,iagemin,iagemax+3);
     for(i=1; i<=nlstate;i++)    strcpy(fileresp,"p");
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    strcat(fileresp,fileres);
     fprintf(ficresvpl,"\n");    if((ficresp=fopen(fileresp,"w"))==NULL) {
     free_vector(gp,1,nlstate);      printf("Problem with prevalence resultfile: %s\n", fileresp);
     free_vector(gm,1,nlstate);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
     free_matrix(gradg,1,npar,1,nlstate);      exit(0);
     free_matrix(trgradg,1,nlstate,1,npar);    }
   } /* End age */    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
     j1=0;
   free_vector(xp,1,npar);    
   free_matrix(doldm,1,nlstate,1,npar);    j=cptcoveff;
   free_matrix(dnewm,1,nlstate,1,nlstate);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   
 }    first=1;
   
 /************ Variance of one-step probabilities  ******************/    for(k1=1; k1<=j;k1++){
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)      for(i1=1; i1<=ncodemax[k1];i1++){
 {        j1++;
   int i, j;        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   int k=0, cptcode;          scanf("%d", i);*/
   double **dnewm,**doldm;        for (i=-1; i<=nlstate+ndeath; i++)  
   double *xp;          for (jk=-1; jk<=nlstate+ndeath; jk++)  
   double *gp, *gm;            for(m=iagemin; m <= iagemax+3; m++)
   double **gradg, **trgradg;              freq[i][jk][m]=0;
   double age,agelim, cov[NCOVMAX];  
   int theta;      for (i=1; i<=nlstate; i++)  
   char fileresprob[FILENAMELENGTH];        for(m=iagemin; m <= iagemax+3; m++)
           prop[i][m]=0;
   strcpy(fileresprob,"prob");        
   strcat(fileresprob,fileres);        dateintsum=0;
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {        k2cpt=0;
     printf("Problem with resultfile: %s\n", fileresprob);        for (i=1; i<=imx; i++) {
   }          bool=1;
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);          if  (cptcovn>0) {
              for (z1=1; z1<=cptcoveff; z1++) 
               if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   xp=vector(1,npar);                bool=0;
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          }
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));          if (bool==1){
              for(m=firstpass; m<=lastpass; m++){
   cov[1]=1;              k2=anint[m][i]+(mint[m][i]/12.);
   for (age=bage; age<=fage; age ++){              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     cov[2]=age;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     gradg=matrix(1,npar,1,9);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     trgradg=matrix(1,9,1,npar);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));                if (m<lastpass) {
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                      freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
     for(theta=1; theta <=npar; theta++){                }
       for(i=1; i<=npar; i++)                
         xp[i] = x[i] + (i==theta ?delti[theta]:0);                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                        dateintsum=dateintsum+k2;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);                  k2cpt++;
                    }
       k=0;                /*}*/
       for(i=1; i<= (nlstate+ndeath); i++){            }
         for(j=1; j<=(nlstate+ndeath);j++){          }
            k=k+1;        }
           gp[k]=pmmij[i][j];         
         }        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       }  
         if  (cptcovn>0) {
       for(i=1; i<=npar; i++)          fprintf(ficresp, "\n#********** Variable "); 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
              fprintf(ficresp, "**********\n#");
         }
       pmij(pmmij,cov,ncovmodel,xp,nlstate);        for(i=1; i<=nlstate;i++) 
       k=0;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
       for(i=1; i<=(nlstate+ndeath); i++){        fprintf(ficresp, "\n");
         for(j=1; j<=(nlstate+ndeath);j++){        
           k=k+1;        for(i=iagemin; i <= iagemax+3; i++){
           gm[k]=pmmij[i][j];          if(i==iagemax+3){
         }            fprintf(ficlog,"Total");
       }          }else{
                  if(first==1){
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)              first=0;
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];                printf("See log file for details...\n");
     }            }
             fprintf(ficlog,"Age %d", i);
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)          }
       for(theta=1; theta <=npar; theta++)          for(jk=1; jk <=nlstate ; jk++){
       trgradg[j][theta]=gradg[theta][j];            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
                pp[jk] += freq[jk][m][i]; 
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);          }
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pos=0; m <=0 ; m++)
      pmij(pmmij,cov,ncovmodel,x,nlstate);              pos += freq[jk][m][i];
             if(pp[jk]>=1.e-10){
      k=0;              if(first==1){
      for(i=1; i<=(nlstate+ndeath); i++){              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
        for(j=1; j<=(nlstate+ndeath);j++){              }
          k=k+1;              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
          gm[k]=pmmij[i][j];            }else{
         }              if(first==1)
      }                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                    fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
      /*printf("\n%d ",(int)age);            }
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){          }
          
           for(jk=1; jk <=nlstate ; jk++){
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
      }*/              pp[jk] += freq[jk][m][i];
           }       
   fprintf(ficresprob,"\n%d ",(int)age);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
             pos += pp[jk];
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){            posprop += prop[jk][i];
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);          }
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);          for(jk=1; jk <=nlstate ; jk++){
   }            if(pos>=1.e-5){
               if(first==1)
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            }else{
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);              if(first==1)
 }                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
  free_vector(xp,1,npar);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 fclose(ficresprob);            }
             if( i <= iagemax){
 }              if(pos>=1.e-5){
                 fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
 /******************* Printing html file ***********/                /*probs[i][jk][j1]= pp[jk]/pos;*/
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
  int lastpass, int stepm, int weightopt, char model[],\              }
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \              else
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
  char version[], int popforecast, int estepm ){            }
   int jj1, k1, i1, cpt;          }
   FILE *fichtm;          
   /*char optionfilehtm[FILENAMELENGTH];*/          for(jk=-1; jk <=nlstate+ndeath; jk++)
             for(m=-1; m <=nlstate+ndeath; m++)
   strcpy(optionfilehtm,optionfile);              if(freq[jk][m][i] !=0 ) {
   strcat(optionfilehtm,".htm");              if(first==1)
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     printf("Problem with %s \n",optionfilehtm), exit(0);                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   }              }
           if(i <= iagemax)
  fprintf(fichtm,"<body> <font size=\"2\">Imach, Version %s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n            fprintf(ficresp,"\n");
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n          if(first==1)
 \n            printf("Others in log...\n");
 Total number of observations=%d <br>\n          fprintf(ficlog,"\n");
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n        }
 <hr  size=\"2\" color=\"#EC5E5E\">      }
  <ul><li>Outputs files<br>\n    }
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n    dateintmean=dateintsum/k2cpt; 
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n   
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    fclose(ficresp);
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n    free_vector(pp,1,nlstate);
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,estepm);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     /* End of Freq */
  fprintf(fichtm,"\n  }
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n  
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n  /************ Prevalence ********************/
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n  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)
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);  {  
     /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
  if(popforecast==1) fprintf(fichtm,"\n       in each health status at the date of interview (if between dateprev1 and dateprev2).
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n       We still use firstpass and lastpass as another selection.
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n    */
         <br>",fileres,fileres,fileres,fileres);   
  else    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
    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);    double ***freq; /* Frequencies */
 fprintf(fichtm," <li>Graphs</li><p>");    double *pp, **prop;
     double pos,posprop; 
  m=cptcoveff;    double  y2; /* in fractional years */
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    int iagemin, iagemax;
   
  jj1=0;    iagemin= (int) agemin;
  for(k1=1; k1<=m;k1++){    iagemax= (int) agemax;
    for(i1=1; i1<=ncodemax[k1];i1++){    /*pp=vector(1,nlstate);*/
        jj1++;    prop=matrix(1,nlstate,iagemin,iagemax+3); 
        if (cptcovn > 0) {    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    j1=0;
          for (cpt=1; cpt<=cptcoveff;cpt++)    
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    j=cptcoveff;
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    if (cptcovn<1) {j=1;ncodemax[1]=1;}
        }    
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    for(k1=1; k1<=j;k1++){
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          for(i1=1; i1<=ncodemax[k1];i1++){
        for(cpt=1; cpt<nlstate;cpt++){        j1++;
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>        
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        for (i=1; i<=nlstate; i++)  
        }          for(m=iagemin; m <= iagemax+3; m++)
     for(cpt=1; cpt<=nlstate;cpt++) {            prop[i][m]=0.0;
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident       
 interval) in state (%d): v%s%d%d.gif <br>        for (i=1; i<=imx; i++) { /* Each individual */
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            bool=1;
      }          if  (cptcovn>0) {
      for(cpt=1; cpt<=nlstate;cpt++) {            for (z1=1; z1<=cptcoveff; z1++) 
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);                bool=0;
      }          } 
      fprintf(fichtm,"\n<br>- Total life expectancy by age and          if (bool==1) { 
 health expectancies in states (1) and (2): e%s%d.gif<br>            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
 fprintf(fichtm,"\n</body>");              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
    }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
    }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
 fclose(fichtm);                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
 }                if (s[m][i]>0 && s[m][i]<=nlstate) { 
                   /*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]]);*/
 /******************* Gnuplot file **************/                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){                  prop[s[m][i]][iagemax+3] += weight[i]; 
                 } 
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;              }
             } /* end selection of waves */
   strcpy(optionfilegnuplot,optionfilefiname);          }
   strcat(optionfilegnuplot,".gp.txt");        }
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {        for(i=iagemin; i <= iagemax+3; i++){  
     printf("Problem with file %s",optionfilegnuplot);          
   }          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
             posprop += prop[jk][i]; 
 #ifdef windows          } 
     fprintf(ficgp,"cd \"%s\" \n",pathc);  
 #endif          for(jk=1; jk <=nlstate ; jk++){     
 m=pow(2,cptcoveff);            if( i <=  iagemax){ 
                if(posprop>=1.e-5){ 
  /* 1eme*/                probs[i][jk][j1]= prop[jk][i]/posprop;
   for (cpt=1; cpt<= nlstate ; cpt ++) {              } 
    for (k1=1; k1<= m ; k1 ++) {            } 
           }/* end jk */ 
 #ifdef windows        }/* end i */ 
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);      } /* end i1 */
 #endif    } /* end k1 */
 #ifdef unix    
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
 #endif    /*free_vector(pp,1,nlstate);*/
     free_matrix(prop,1,nlstate, iagemin,iagemax+3);
 for (i=1; i<= nlstate ; i ++) {  }  /* End of prevalence */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");  /************* Waves Concatenation ***************/
 }  
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
     for (i=1; i<= nlstate ; i ++) {  {
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   else fprintf(ficgp," \%%*lf (\%%*lf)");       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
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
      for (i=1; i<= nlstate ; i ++) {       and mw[mi+1][i]. dh depends on stepm.
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");       */
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      int i, mi, m;
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
 #ifdef unix       double sum=0., jmean=0.;*/
 fprintf(ficgp,"\nset ter gif small size 400,300");    int first;
 #endif    int j, k=0,jk, ju, jl;
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    double sum=0.;
    }    first=0;
   }    jmin=1e+5;
   /*2 eme*/    jmax=-1;
     jmean=0.;
   for (k1=1; k1<= m ; k1 ++) {    for(i=1; i<=imx; i++){
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);      mi=0;
          m=firstpass;
     for (i=1; i<= nlstate+1 ; i ++) {      while(s[m][i] <= nlstate){
       k=2*i;        if(s[m][i]>=1)
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);          mw[++mi][i]=m;
       for (j=1; j<= nlstate+1 ; j ++) {        if(m >=lastpass)
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          break;
   else fprintf(ficgp," \%%*lf (\%%*lf)");        else
 }            m++;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");      }/* end while */
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);      if (s[m][i] > nlstate){
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);        mi++;     /* Death is another wave */
       for (j=1; j<= nlstate+1 ; j ++) {        /* if(mi==0)  never been interviewed correctly before death */
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");           /* Only death is a correct wave */
         else fprintf(ficgp," \%%*lf (\%%*lf)");        mw[mi][i]=m;
 }        }
       fprintf(ficgp,"\" t\"\" w l 0,");  
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      wav[i]=mi;
       for (j=1; j<= nlstate+1 ; j ++) {      if(mi==0){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        nbwarn++;
   else fprintf(ficgp," \%%*lf (\%%*lf)");        if(first==0){
 }            printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");          first=1;
       else fprintf(ficgp,"\" t\"\" w l 0,");        }
     }        if(first==1){
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
   }        }
        } /* end mi==0 */
   /*3eme*/    } /* End individuals */
   
   for (k1=1; k1<= m ; k1 ++) {    for(i=1; i<=imx; i++){
     for (cpt=1; cpt<= nlstate ; cpt ++) {      for(mi=1; mi<wav[i];mi++){
       k=2+nlstate*(cpt-1);        if (stepm <=0)
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);          dh[mi][i]=1;
       for (i=1; i< nlstate ; i ++) {        else{
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
       }            if (agedc[i] < 2*AGESUP) {
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     }              if(j==0) j=1;  /* Survives at least one month after exam */
     }              else if(j<0){
                  nberr++;
   /* CV preval stat */                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 (k1=1; k1<= m ; k1 ++) {                j=1; /* Temporary Dangerous patch */
     for (cpt=1; cpt<nlstate ; cpt ++) {                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);
       k=3;                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
               }
       for (i=1; i< nlstate ; i ++)              k=k+1;
         fprintf(ficgp,"+$%d",k+i+1);              if (j >= jmax) jmax=j;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);              if (j <= jmin) jmin=j;
                    sum=sum+j;
       l=3+(nlstate+ndeath)*cpt;              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       for (i=1; i< nlstate ; i ++) {            }
         l=3+(nlstate+ndeath)*cpt;          }
         fprintf(ficgp,"+$%d",l+i+1);          else{
       }            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);              /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            k=k+1;
     }            if (j >= jmax) jmax=j;
   }              else if (j <= jmin)jmin=j;
              /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   /* proba elementaires */            /*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]);*/
    for(i=1,jk=1; i <=nlstate; i++){            if(j<0){
     for(k=1; k <=(nlstate+ndeath); k++){              nberr++;
       if (k != i) {              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]);
         for(j=1; j <=ncovmodel; j++){              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]);
                    }
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);            sum=sum+j;
           jk++;          }
           fprintf(ficgp,"\n");          jk= j/stepm;
         }          jl= j -jk*stepm;
       }          ju= j -(jk+1)*stepm;
     }          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
     }            if(jl==0){
               dh[mi][i]=jk;
     for(jk=1; jk <=m; jk++) {              bh[mi][i]=0;
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);            }else{ /* We want a negative bias in order to only have interpolation ie
    i=1;                    * at the price of an extra matrix product in likelihood */
    for(k2=1; k2<=nlstate; k2++) {              dh[mi][i]=jk+1;
      k3=i;              bh[mi][i]=ju;
      for(k=1; k<=(nlstate+ndeath); k++) {            }
        if (k != k2){          }else{
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);            if(jl <= -ju){
 ij=1;              dh[mi][i]=jk;
         for(j=3; j <=ncovmodel; j++) {              bh[mi][i]=jl;       /* bias is positive if real duration
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                                   * is higher than the multiple of stepm and negative otherwise.
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                                   */
             ij++;            }
           }            else{
           else              dh[mi][i]=jk+1;
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              bh[mi][i]=ju;
         }            }
           fprintf(ficgp,")/(1");            if(dh[mi][i]==0){
                      dh[mi][i]=1; /* At least one step */
         for(k1=1; k1 <=nlstate; k1++){                bh[mi][i]=ju; /* At least one step */
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);              /*  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);*/
 ij=1;            }
           for(j=3; j <=ncovmodel; j++){          } /* end if mle */
           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]]]);      } /* end wave */
             ij++;    }
           }    jmean=sum/k;
           else    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
           }   }
           fprintf(ficgp,")");  
         }  /*********** Tricode ****************************/
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);  void tricode(int *Tvar, int **nbcode, int imx)
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");  {
         i=i+ncovmodel;    
        }    int Ndum[20],ij=1, k, j, i, maxncov=19;
      }    int cptcode=0;
    }    cptcoveff=0; 
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);   
    }    for (k=0; k<maxncov; k++) Ndum[k]=0;
        for (k=1; k<=7; k++) ncodemax[k]=0;
   fclose(ficgp);  
 }  /* end gnuplot */    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
       for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                  modality*/ 
 /*************** Moving average **************/        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){        Ndum[ij]++; /*store the modality */
         /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   int i, cpt, cptcod;        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)                                         Tvar[j]. If V=sex and male is 0 and 
       for (i=1; i<=nlstate;i++)                                         female is 1, then  cptcode=1.*/
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)      }
           mobaverage[(int)agedeb][i][cptcod]=0.;  
          for (i=0; i<=cptcode; i++) {
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){        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 (i=1; i<=nlstate;i++){      }
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
           for (cpt=0;cpt<=4;cpt++){      ij=1; 
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];      for (i=1; i<=ncodemax[j]; i++) {
           }        for (k=0; k<= maxncov; k++) {
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;          if (Ndum[k] != 0) {
         }            nbcode[Tvar[j]][ij]=k; 
       }            /* 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; */
     }            
                ij++;
 }          }
           if (ij > ncodemax[j]) break; 
         }  
 /************** Forecasting ******************/      } 
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){    }  
    
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;   for (k=0; k< maxncov; k++) Ndum[k]=0;
   int *popage;  
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;   for (i=1; i<=ncovmodel-2; i++) { 
   double *popeffectif,*popcount;     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
   double ***p3mat;     ij=Tvar[i];
   char fileresf[FILENAMELENGTH];     Ndum[ij]++;
    }
  agelim=AGESUP;  
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;   ij=1;
    for (i=1; i<= maxncov; i++) {
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);     if((Ndum[i]!=0) && (i<=ncovcol)){
         Tvaraff[ij]=i; /*For printing */
         ij++;
   strcpy(fileresf,"f");     }
   strcat(fileresf,fileres);   }
   if((ficresf=fopen(fileresf,"w"))==NULL) {   
     printf("Problem with forecast resultfile: %s\n", fileresf);   cptcoveff=ij-1; /*Number of simple covariates*/
   }  }
   printf("Computing forecasting: result on file '%s' \n", fileresf);  
   /*********** Health Expectancies ****************/
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
   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 )
   if (mobilav==1) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  {
     movingaverage(agedeb, fage, ageminpar, mobaverage);    /* Health expectancies */
   }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     double age, agelim, hf;
   stepsize=(int) (stepm+YEARM-1)/YEARM;    double ***p3mat,***varhe;
   if (stepm<=12) stepsize=1;    double **dnewm,**doldm;
      double *xp;
   agelim=AGESUP;    double **gp, **gm;
      double ***gradg, ***trgradg;
   hstepm=1;    int theta;
   hstepm=hstepm/stepm;  
   yp1=modf(dateintmean,&yp);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   anprojmean=yp;    xp=vector(1,npar);
   yp2=modf((yp1*12),&yp);    dnewm=matrix(1,nlstate*nlstate,1,npar);
   mprojmean=yp;    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   yp1=modf((yp2*30.5),&yp);    
   jprojmean=yp;    fprintf(ficreseij,"# Health expectancies\n");
   if(jprojmean==0) jprojmean=1;    fprintf(ficreseij,"# Age");
   if(mprojmean==0) jprojmean=1;    for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++)
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);        fprintf(ficreseij," %1d-%1d (SE)",i,j);
      fprintf(ficreseij,"\n");
   for(cptcov=1;cptcov<=i2;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    if(estepm < stepm){
       k=k+1;      printf ("Problem %d lower than %d\n",estepm, stepm);
       fprintf(ficresf,"\n#******");    }
       for(j=1;j<=cptcoveff;j++) {    else  hstepm=estepm;   
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    /* We compute the life expectancy from trapezoids spaced every estepm months
       }     * This is mainly to measure the difference between two models: for example
       fprintf(ficresf,"******\n");     * if stepm=24 months pijx are given only every 2 years and by summing them
       fprintf(ficresf,"# StartingAge FinalAge");     * we are calculating an estimate of the Life Expectancy assuming a linear 
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);     * progression in between 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
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {     * to compare the new estimate of Life expectancy with the same linear 
         fprintf(ficresf,"\n");     * hypothesis. A more precise result, taking into account a more precise
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);       * curvature will be obtained if estepm is as small as stepm. */
   
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    /* For example we decided to compute the life expectancy with the smallest unit */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           nhstepm = nhstepm/hstepm;       nhstepm is the number of hstepm from age to agelim 
                 nstepm is the number of stepm from age to agelin. 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       Look at hpijx to understand the reason of that which relies in memory size
           oldm=oldms;savm=savms;       and note for a fixed period like estepm months */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      /* 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
           for (h=0; h<=nhstepm; h++){       means that if the survival funtion is printed only each two years of age and if
             if (h==(int) (calagedate+YEARM*cpt)) {       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);       results. So we changed our mind and took the option of the best precision.
             }    */
             for(j=1; j<=nlstate+ndeath;j++) {    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
               kk1=0.;kk2=0;  
               for(i=1; i<=nlstate;i++) {                  agelim=AGESUP;
                 if (mobilav==1)    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      /* nhstepm age range expressed in number of stepm */
                 else {      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
                 }      /* if (stepm >= YEARM) hstepm=1;*/
                      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
               }      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
               if (h==(int)(calagedate+12*cpt)){      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
                 fprintf(ficresf," %.3f", kk1);      gp=matrix(0,nhstepm,1,nlstate*nlstate);
                              gm=matrix(0,nhstepm,1,nlstate*nlstate);
               }  
             }      /* Computed by stepm unit matrices, product of hstepm matrices, stored
           }         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
         }   
       }  
     }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   }  
              /* Computing  Variances of health expectancies */
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
        for(theta=1; theta <=npar; theta++){
   fclose(ficresf);        for(i=1; i<=npar; i++){ 
 }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
 /************** Forecasting ******************/        }
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
      
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        cptj=0;
   int *popage;        for(j=1; j<= nlstate; j++){
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          for(i=1; i<=nlstate; i++){
   double *popeffectif,*popcount;            cptj=cptj+1;
   double ***p3mat,***tabpop,***tabpopprev;            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
   char filerespop[FILENAMELENGTH];              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
             }
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          }
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        }
   agelim=AGESUP;       
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;       
          for(i=1; i<=npar; i++) 
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
          
   strcpy(filerespop,"pop");        cptj=0;
   strcat(filerespop,fileres);        for(j=1; j<= nlstate; j++){
   if((ficrespop=fopen(filerespop,"w"))==NULL) {          for(i=1;i<=nlstate;i++){
     printf("Problem with forecast resultfile: %s\n", filerespop);            cptj=cptj+1;
   }            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   printf("Computing forecasting: result on file '%s' \n", filerespop);  
               gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;            }
           }
   if (mobilav==1) {        }
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(j=1; j<= nlstate*nlstate; j++)
     movingaverage(agedeb, fage, ageminpar, mobaverage);          for(h=0; h<=nhstepm-1; h++){
   }            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   stepsize=(int) (stepm+YEARM-1)/YEARM;       } 
   if (stepm<=12) stepsize=1;     
    /* End theta */
   agelim=AGESUP;  
         trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   hstepm=1;  
   hstepm=hstepm/stepm;       for(h=0; h<=nhstepm-1; h++)
          for(j=1; j<=nlstate*nlstate;j++)
   if (popforecast==1) {          for(theta=1; theta <=npar; theta++)
     if((ficpop=fopen(popfile,"r"))==NULL) {            trgradg[h][j][theta]=gradg[h][theta][j];
       printf("Problem with population file : %s\n",popfile);exit(0);       
     }  
     popage=ivector(0,AGESUP);       for(i=1;i<=nlstate*nlstate;i++)
     popeffectif=vector(0,AGESUP);        for(j=1;j<=nlstate*nlstate;j++)
     popcount=vector(0,AGESUP);          varhe[i][j][(int)age] =0.;
      
     i=1;         printf("%d|",(int)age);fflush(stdout);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
           for(h=0;h<=nhstepm-1;h++){
     imx=i;        for(k=0;k<=nhstepm-1;k++){
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
   }          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
           for(i=1;i<=nlstate*nlstate;i++)
   for(cptcov=1;cptcov<=i2;cptcov++){            for(j=1;j<=nlstate*nlstate;j++)
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
       k=k+1;        }
       fprintf(ficrespop,"\n#******");      }
       for(j=1;j<=cptcoveff;j++) {      /* Computing expectancies */
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for(i=1; i<=nlstate;i++)
       }        for(j=1; j<=nlstate;j++)
       fprintf(ficrespop,"******\n");          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       fprintf(ficrespop,"# Age");            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);            
       if (popforecast==1)  fprintf(ficrespop," [Population]");  /* 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 (cpt=0; cpt<=0;cpt++) {          }
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);    
              fprintf(ficreseij,"%3.0f",age );
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){      cptj=0;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      for(i=1; i<=nlstate;i++)
           nhstepm = nhstepm/hstepm;        for(j=1; j<=nlstate;j++){
                    cptj++;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
           oldm=oldms;savm=savms;        }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        fprintf(ficreseij,"\n");
             
           for (h=0; h<=nhstepm; h++){      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
             if (h==(int) (calagedate+YEARM*cpt)) {      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
             }      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
             for(j=1; j<=nlstate+ndeath;j++) {      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
               kk1=0.;kk2=0;    }
               for(i=1; i<=nlstate;i++) {                  printf("\n");
                 if (mobilav==1)    fprintf(ficlog,"\n");
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];  
                 else {    free_vector(xp,1,npar);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
                 }    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
               }    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
               if (h==(int)(calagedate+12*cpt)){  }
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;  
                   /*fprintf(ficrespop," %.3f", kk1);  /************ Variance ******************/
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
               }  {
             }    /* Variance of health expectancies */
             for(i=1; i<=nlstate;i++){    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
               kk1=0.;    /* double **newm;*/
                 for(j=1; j<=nlstate;j++){    double **dnewm,**doldm;
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    double **dnewmp,**doldmp;
                 }    int i, j, nhstepm, hstepm, h, nstepm ;
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    int k, cptcode;
             }    double *xp;
     double **gp, **gm;  /* for var eij */
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)    double ***gradg, ***trgradg; /*for var eij */
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    double **gradgp, **trgradgp; /* for var p point j */
           }    double *gpp, *gmp; /* for var p point j */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
         }    double ***p3mat;
       }    double age,agelim, hf;
      double ***mobaverage;
   /******/    int theta;
     char digit[4];
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    char digitp[25];
         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--){    char fileresprobmorprev[FILENAMELENGTH];
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
           nhstepm = nhstepm/hstepm;    if(popbased==1){
                if(mobilav!=0)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        strcpy(digitp,"-populbased-mobilav-");
           oldm=oldms;savm=savms;      else strcpy(digitp,"-populbased-nomobil-");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      }
           for (h=0; h<=nhstepm; h++){    else 
             if (h==(int) (calagedate+YEARM*cpt)) {      strcpy(digitp,"-stablbased-");
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  
             }    if (mobilav!=0) {
             for(j=1; j<=nlstate+ndeath;j++) {      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
               kk1=0.;kk2=0;      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
               for(i=1; i<=nlstate;i++) {                      fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];            printf(" Error in movingaverage mobilav=%d\n",mobilav);
               }      }
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);    }
             }  
           }    strcpy(fileresprobmorprev,"prmorprev"); 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    sprintf(digit,"%-d",ij);
         }    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
       }    strcat(fileresprobmorprev,digit); /* Tvar to be done */
    }    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   }    strcat(fileresprobmorprev,fileres);
      if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   if (popforecast==1) {    }
     free_ivector(popage,0,AGESUP);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     free_vector(popeffectif,0,AGESUP);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     free_vector(popcount,0,AGESUP);    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);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      fprintf(ficresprobmorprev," p.%-d SE",j);
   fclose(ficrespop);      for(i=1; i<=nlstate;i++)
 }        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
 /***********************************************/    fprintf(ficresprobmorprev,"\n");
 /**************** Main Program *****************/    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(fichtm,"\n<br>%s  <br>\n",digitp);
 int main(int argc, char *argv[])  /*   } */
 {    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    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 agedeb, agefin,hf;    fprintf(ficresvij,"# Age");
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
   double fret;        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   double **xi,tmp,delta;    fprintf(ficresvij,"\n");
   
   double dum; /* Dummy variable */    xp=vector(1,npar);
   double ***p3mat;    dnewm=matrix(1,nlstate,1,npar);
   int *indx;    doldm=matrix(1,nlstate,1,nlstate);
   char line[MAXLINE], linepar[MAXLINE];    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   char title[MAXLINE];    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];  
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
      gpp=vector(nlstate+1,nlstate+ndeath);
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   char filerest[FILENAMELENGTH];    
   char fileregp[FILENAMELENGTH];    if(estepm < stepm){
   char popfile[FILENAMELENGTH];      printf ("Problem %d lower than %d\n",estepm, stepm);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    }
   int firstobs=1, lastobs=10;    else  hstepm=estepm;   
   int sdeb, sfin; /* Status at beginning and end */    /* For example we decided to compute the life expectancy with the smallest unit */
   int c,  h , cpt,l;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   int ju,jl, mi;       nhstepm is the number of hstepm from age to agelim 
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;       nstepm is the number of stepm from age to agelin. 
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;       Look at hpijx to understand the reason of that which relies in memory size
   int mobilav=0,popforecast=0;       and note for a fixed period like k years */
   int hstepm, nhstepm;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;       survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed every two years of age and if
   double bage, fage, age, agelim, agebase;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   double ftolpl=FTOL;       results. So we changed our mind and took the option of the best precision.
   double **prlim;    */
   double *severity;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   double ***param; /* Matrix of parameters */    agelim = AGESUP;
   double  *p;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   double **matcov; /* Matrix of covariance */      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   double ***delti3; /* Scale */      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   double *delti; /* Scale */      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   double ***eij, ***vareij;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   double **varpl; /* Variances of prevalence limits by age */      gp=matrix(0,nhstepm,1,nlstate);
   double *epj, vepp;      gm=matrix(0,nhstepm,1,nlstate);
   double kk1, kk2;  
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;  
        for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   char version[80]="Imach version 0.8a, March 2002, INED-EUROREVES ";          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   char *alph[]={"a","a","b","c","d","e"}, str[4];        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   char z[1]="c", occ;  
 #include <sys/time.h>        if (popbased==1) {
 #include <time.h>          if(mobilav ==0){
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];            for(i=1; i<=nlstate;i++)
                prlim[i][i]=probs[(int)age][i][ij];
   /* long total_usecs;          }else{ /* mobilav */ 
   struct timeval start_time, end_time;            for(i=1; i<=nlstate;i++)
                prlim[i][i]=mobaverage[(int)age][i][ij];
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */          }
   getcwd(pathcd, size);        }
     
   printf("\n%s",version);        for(j=1; j<= nlstate; j++){
   if(argc <=1){          for(h=0; h<=nhstepm; h++){
     printf("\nEnter the parameter file name: ");            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
     scanf("%s",pathtot);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   }          }
   else{        }
     strcpy(pathtot,argv[1]);        /* This for computing probability of death (h=1 means
   }           computed over hstepm matrices product = hstepm*stepm months) 
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/           as a weighted average of prlim.
   /*cygwin_split_path(pathtot,path,optionfile);        */
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   /* cutv(path,optionfile,pathtot,'\\');*/          for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);        }    
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);        /* end probability of death */
   chdir(path);  
   replace(pathc,path);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
 /*-------- arguments in the command line --------*/        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   strcpy(fileres,"r");   
   strcat(fileres, optionfilefiname);        if (popbased==1) {
   strcat(fileres,".txt");    /* Other files have txt extension */          if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
   /*---------arguments file --------*/              prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
   if((ficpar=fopen(optionfile,"r"))==NULL)    {            for(i=1; i<=nlstate;i++)
     printf("Problem with optionfile %s\n",optionfile);              prlim[i][i]=mobaverage[(int)age][i][ij];
     goto end;          }
   }        }
   
   strcpy(filereso,"o");        for(j=1; j<= nlstate; j++){
   strcat(filereso,fileres);          for(h=0; h<=nhstepm; h++){
   if((ficparo=fopen(filereso,"w"))==NULL) {            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
     printf("Problem with Output resultfile: %s\n", filereso);goto end;              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   }          }
         }
   /* Reads comments: lines beginning with '#' */        /* This for computing probability of death (h=1 means
   while((c=getc(ficpar))=='#' && c!= EOF){           computed over hstepm matrices product = hstepm*stepm months) 
     ungetc(c,ficpar);           as a weighted average of prlim.
     fgets(line, MAXLINE, ficpar);        */
     puts(line);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     fputs(line,ficparo);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   }           gmp[j] += prlim[i][i]*p3mat[i][j][1];
   ungetc(c,ficpar);        }    
         /* end probability of death */
   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);  
   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);        for(j=1; j<= nlstate; j++) /* vareij */
   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);          for(h=0; h<=nhstepm; h++){
 while((c=getc(ficpar))=='#' && c!= EOF){            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);  
     puts(line);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
     fputs(line,ficparo);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   }        }
   ungetc(c,ficpar);  
        } /* End theta */
      
   covar=matrix(0,NCOVMAX,1,n);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   cptcovn=0;  
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;      for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
   ncovmodel=2+cptcovn;          for(theta=1; theta <=npar; theta++)
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */            trgradg[h][j][theta]=gradg[h][theta][j];
    
   /* Read guess parameters */      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   /* Reads comments: lines beginning with '#' */        for(theta=1; theta <=npar; theta++)
   while((c=getc(ficpar))=='#' && c!= EOF){          trgradgp[j][theta]=gradgp[theta][j];
     ungetc(c,ficpar);    
     fgets(line, MAXLINE, ficpar);  
     puts(line);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     fputs(line,ficparo);      for(i=1;i<=nlstate;i++)
   }        for(j=1;j<=nlstate;j++)
   ungetc(c,ficpar);          vareij[i][j][(int)age] =0.;
    
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      for(h=0;h<=nhstepm;h++){
     for(i=1; i <=nlstate; i++)        for(k=0;k<=nhstepm;k++){
     for(j=1; j <=nlstate+ndeath-1; j++){          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
       fscanf(ficpar,"%1d%1d",&i1,&j1);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
       fprintf(ficparo,"%1d%1d",i1,j1);          for(i=1;i<=nlstate;i++)
       printf("%1d%1d",i,j);            for(j=1;j<=nlstate;j++)
       for(k=1; k<=ncovmodel;k++){              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         fscanf(ficpar," %lf",&param[i][j][k]);        }
         printf(" %lf",param[i][j][k]);      }
         fprintf(ficparo," %lf",param[i][j][k]);    
       }      /* pptj */
       fscanf(ficpar,"\n");      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       printf("\n");      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       fprintf(ficparo,"\n");      for(j=nlstate+1;j<=nlstate+ndeath;j++)
     }        for(i=nlstate+1;i<=nlstate+ndeath;i++)
            varppt[j][i]=doldmp[j][i];
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;      /* end ppptj */
       /*  x centered again */
   p=param[1][1];      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
        prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   /* Reads comments: lines beginning with '#' */   
   while((c=getc(ficpar))=='#' && c!= EOF){      if (popbased==1) {
     ungetc(c,ficpar);        if(mobilav ==0){
     fgets(line, MAXLINE, ficpar);          for(i=1; i<=nlstate;i++)
     puts(line);            prlim[i][i]=probs[(int)age][i][ij];
     fputs(line,ficparo);        }else{ /* mobilav */ 
   }          for(i=1; i<=nlstate;i++)
   ungetc(c,ficpar);            prlim[i][i]=mobaverage[(int)age][i][ij];
         }
   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++){      /* This for computing probability of death (h=1 means
     for(j=1; j <=nlstate+ndeath-1; j++){         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
       fscanf(ficpar,"%1d%1d",&i1,&j1);         as a weighted average of prlim.
       printf("%1d%1d",i,j);      */
       fprintf(ficparo,"%1d%1d",i1,j1);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
       for(k=1; k<=ncovmodel;k++){        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
         fscanf(ficpar,"%le",&delti3[i][j][k]);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
         printf(" %le",delti3[i][j][k]);      }    
         fprintf(ficparo," %le",delti3[i][j][k]);      /* end probability of death */
       }  
       fscanf(ficpar,"\n");      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       printf("\n");      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficparo,"\n");        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     }        for(i=1; i<=nlstate;i++){
   }          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   delti=delti3[1][1];        }
        } 
   /* Reads comments: lines beginning with '#' */      fprintf(ficresprobmorprev,"\n");
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      fprintf(ficresvij,"%.0f ",age );
     fgets(line, MAXLINE, ficpar);      for(i=1; i<=nlstate;i++)
     puts(line);        for(j=1; j<=nlstate;j++){
     fputs(line,ficparo);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
   }        }
   ungetc(c,ficpar);      fprintf(ficresvij,"\n");
        free_matrix(gp,0,nhstepm,1,nlstate);
   matcov=matrix(1,npar,1,npar);      free_matrix(gm,0,nhstepm,1,nlstate);
   for(i=1; i <=npar; i++){      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
     fscanf(ficpar,"%s",&str);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     printf("%s",str);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fprintf(ficparo,"%s",str);    } /* End age */
     for(j=1; j <=i; j++){    free_vector(gpp,nlstate+1,nlstate+ndeath);
       fscanf(ficpar," %le",&matcov[i][j]);    free_vector(gmp,nlstate+1,nlstate+ndeath);
       printf(" %.5le",matcov[i][j]);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
       fprintf(ficparo," %.5le",matcov[i][j]);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     }    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     fscanf(ficpar,"\n");    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     printf("\n");    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
     fprintf(ficparo,"\n");  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   }  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   for(i=1; i <=npar; i++)  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     for(j=i+1;j<=npar;j++)    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
       matcov[i][j]=matcov[j][i];    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
        fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
   printf("\n");    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);
     /*  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);
     /*-------- Rewriting paramater file ----------*/  */
      strcpy(rfileres,"r");    /* "Rparameterfile */  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
      strcat(rfileres,".");    /* */  
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    free_vector(xp,1,npar);
     if((ficres =fopen(rfileres,"w"))==NULL) {    free_matrix(doldm,1,nlstate,1,nlstate);
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    free_matrix(dnewm,1,nlstate,1,npar);
     }    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     fprintf(ficres,"#%s\n",version);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
        free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     /*-------- data file ----------*/    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     if((fic=fopen(datafile,"r"))==NULL)    {    fclose(ficresprobmorprev);
       printf("Problem with datafile: %s\n", datafile);goto end;    fflush(ficgp);
     }    fflush(fichtm); 
   }  /* end varevsij */
     n= lastobs;  
     severity = vector(1,maxwav);  /************ Variance of prevlim ******************/
     outcome=imatrix(1,maxwav+1,1,n);  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)
     num=ivector(1,n);  {
     moisnais=vector(1,n);    /* Variance of prevalence limit */
     annais=vector(1,n);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     moisdc=vector(1,n);    double **newm;
     andc=vector(1,n);    double **dnewm,**doldm;
     agedc=vector(1,n);    int i, j, nhstepm, hstepm;
     cod=ivector(1,n);    int k, cptcode;
     weight=vector(1,n);    double *xp;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    double *gp, *gm;
     mint=matrix(1,maxwav,1,n);    double **gradg, **trgradg;
     anint=matrix(1,maxwav,1,n);    double age,agelim;
     s=imatrix(1,maxwav+1,1,n);    int theta;
     adl=imatrix(1,maxwav+1,1,n);         
     tab=ivector(1,NCOVMAX);    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
     ncodemax=ivector(1,8);    fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
     i=1;        fprintf(ficresvpl," %1d-%1d",i,i);
     while (fgets(line, MAXLINE, fic) != NULL)    {    fprintf(ficresvpl,"\n");
       if ((i >= firstobs) && (i <=lastobs)) {  
            xp=vector(1,npar);
         for (j=maxwav;j>=1;j--){    dnewm=matrix(1,nlstate,1,npar);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    doldm=matrix(1,nlstate,1,nlstate);
           strcpy(line,stra);    
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    hstepm=1*YEARM; /* Every year of age */
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
         }    agelim = AGESUP;
            for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);      if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);      gradg=matrix(1,npar,1,nlstate);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);      gp=vector(1,nlstate);
       gm=vector(1,nlstate);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);  
         for (j=ncovcol;j>=1;j--){      for(theta=1; theta <=npar; theta++){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);        for(i=1; i<=npar; i++){ /* Computes gradient */
         }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         num[i]=atol(stra);        }
                prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){        for(i=1;i<=nlstate;i++)
           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;}*/          gp[i] = prlim[i][i];
       
         i=i+1;        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);
     /* printf("ii=%d", ij);        for(i=1;i<=nlstate;i++)
        scanf("%d",i);*/          gm[i] = prlim[i][i];
   imx=i-1; /* Number of individuals */  
         for(i=1;i<=nlstate;i++)
   /* for (i=1; i<=imx; i++){          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;      } /* End theta */
     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;      trgradg =matrix(1,nlstate,1,npar);
     }*/  
        for(j=1; j<=nlstate;j++)
   /* for (i=1; i<=imx; i++){        for(theta=1; theta <=npar; theta++)
      if (s[4][i]==9)  s[4][i]=-1;          trgradg[j][theta]=gradg[theta][j];
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}  
   */      for(i=1;i<=nlstate;i++)
          varpl[i][(int)age] =0.;
   /* Calculation of the number of parameter from char model*/      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   Tvar=ivector(1,15);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   Tprod=ivector(1,15);      for(i=1;i<=nlstate;i++)
   Tvaraff=ivector(1,15);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   Tvard=imatrix(1,15,1,2);  
   Tage=ivector(1,15);            fprintf(ficresvpl,"%.0f ",age );
          for(i=1; i<=nlstate;i++)
   if (strlen(model) >1){        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
     j=0, j1=0, k1=1, k2=1;      fprintf(ficresvpl,"\n");
     j=nbocc(model,'+');      free_vector(gp,1,nlstate);
     j1=nbocc(model,'*');      free_vector(gm,1,nlstate);
     cptcovn=j+1;      free_matrix(gradg,1,npar,1,nlstate);
     cptcovprod=j1;      free_matrix(trgradg,1,nlstate,1,npar);
        } /* End age */
     strcpy(modelsav,model);  
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    free_vector(xp,1,npar);
       printf("Error. Non available option model=%s ",model);    free_matrix(doldm,1,nlstate,1,npar);
       goto end;    free_matrix(dnewm,1,nlstate,1,nlstate);
     }  
      }
     for(i=(j+1); i>=1;i--){  
       cutv(stra,strb,modelsav,'+');  /************ Variance of one-step probabilities  ******************/
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/  {
       /*scanf("%d",i);*/    int i, j=0,  i1, k1, l1, t, tj;
       if (strchr(strb,'*')) {    int k2, l2, j1,  z1;
         cutv(strd,strc,strb,'*');    int k=0,l, cptcode;
         if (strcmp(strc,"age")==0) {    int first=1, first1;
           cptcovprod--;    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
           cutv(strb,stre,strd,'V');    double **dnewm,**doldm;
           Tvar[i]=atoi(stre);    double *xp;
           cptcovage++;    double *gp, *gm;
             Tage[cptcovage]=i;    double **gradg, **trgradg;
             /*printf("stre=%s ", stre);*/    double **mu;
         }    double age,agelim, cov[NCOVMAX];
         else if (strcmp(strd,"age")==0) {    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
           cptcovprod--;    int theta;
           cutv(strb,stre,strc,'V');    char fileresprob[FILENAMELENGTH];
           Tvar[i]=atoi(stre);    char fileresprobcov[FILENAMELENGTH];
           cptcovage++;    char fileresprobcor[FILENAMELENGTH];
           Tage[cptcovage]=i;  
         }    double ***varpij;
         else {  
           cutv(strb,stre,strc,'V');    strcpy(fileresprob,"prob"); 
           Tvar[i]=ncovcol+k1;    strcat(fileresprob,fileres);
           cutv(strb,strc,strd,'V');    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
           Tprod[k1]=i;      printf("Problem with resultfile: %s\n", fileresprob);
           Tvard[k1][1]=atoi(strc);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
           Tvard[k1][2]=atoi(stre);    }
           Tvar[cptcovn+k2]=Tvard[k1][1];    strcpy(fileresprobcov,"probcov"); 
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    strcat(fileresprobcov,fileres);
           for (k=1; k<=lastobs;k++)    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];      printf("Problem with resultfile: %s\n", fileresprobcov);
           k1++;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
           k2=k2+2;    }
         }    strcpy(fileresprobcor,"probcor"); 
       }    strcat(fileresprobcor,fileres);
       else {    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/      printf("Problem with resultfile: %s\n", fileresprobcor);
        /*  scanf("%d",i);*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
       cutv(strd,strc,strb,'V');    }
       Tvar[i]=atoi(strc);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
       }    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
       strcpy(modelsav,stra);      printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
         scanf("%d",i);*/    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     }    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
 }    
      fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    fprintf(ficresprob,"# Age");
   printf("cptcovprod=%d ", cptcovprod);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
   scanf("%d ",i);*/    fprintf(ficresprobcov,"# Age");
     fclose(fic);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcov,"# Age");
     /*  if(mle==1){*/  
     if (weightopt != 1) { /* Maximisation without weights*/  
       for(i=1;i<=n;i++) weight[i]=1.0;    for(i=1; i<=nlstate;i++)
     }      for(j=1; j<=(nlstate+ndeath);j++){
     /*-calculation of age at interview from date of interview and age at death -*/        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
     agev=matrix(1,maxwav,1,imx);        fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
     for (i=1; i<=imx; i++) {      }  
       for(m=2; (m<= maxwav); m++) {   /* fprintf(ficresprob,"\n");
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    fprintf(ficresprobcov,"\n");
          anint[m][i]=9999;    fprintf(ficresprobcor,"\n");
          s[m][i]=-1;   */
        }   xp=vector(1,npar);
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;    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);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     for (i=1; i<=imx; i++)  {    first=1;
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    fprintf(ficgp,"\n# Routine varprob");
       for(m=1; (m<= maxwav); m++){    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
         if(s[m][i] >0){    fprintf(fichtm,"\n");
           if (s[m][i] >= nlstate+1) {  
             if(agedc[i]>0)    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
               if(moisdc[i]!=99 && andc[i]!=9999)    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
                 agev[m][i]=agedc[i];    file %s<br>\n",optionfilehtmcov);
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
            else {  and drawn. It helps understanding how is the covariance between two incidences.\
               if (andc[i]!=9999){   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
               agev[m][i]=-1;  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
               }  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>\
           }   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
           else if(s[m][i] !=9){ /* Should no more exist */   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
             if(mint[m][i]==99 || anint[m][i]==9999)  
               agev[m][i]=1;    cov[1]=1;
             else if(agev[m][i] <agemin){    tj=cptcoveff;
               agemin=agev[m][i];    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/    j1=0;
             }    for(t=1; t<=tj;t++){
             else if(agev[m][i] >agemax){      for(i1=1; i1<=ncodemax[t];i1++){ 
               agemax=agev[m][i];        j1++;
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/        if  (cptcovn>0) {
             }          fprintf(ficresprob, "\n#********** Variable "); 
             /*agev[m][i]=anint[m][i]-annais[i];*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
             /*   agev[m][i] = age[i]+2*m;*/          fprintf(ficresprob, "**********\n#\n");
           }          fprintf(ficresprobcov, "\n#********** Variable "); 
           else { /* =9 */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
             agev[m][i]=1;          fprintf(ficresprobcov, "**********\n#\n");
             s[m][i]=-1;          
           }          fprintf(ficgp, "\n#********** Variable "); 
         }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         else /*= 0 Unknown */          fprintf(ficgp, "**********\n#\n");
           agev[m][i]=1;          
       }          
              fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
     }          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     for (i=1; i<=imx; i++)  {          fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
       for(m=1; (m<= maxwav); m++){          
         if (s[m][i] > (nlstate+ndeath)) {          fprintf(ficresprobcor, "\n#********** Variable ");    
           printf("Error: Wrong value in nlstate or ndeath\n");            for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           goto end;          fprintf(ficresprobcor, "**********\n#");    
         }        }
       }        
     }        for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);          for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     free_vector(severity,1,maxwav);          }
     free_imatrix(outcome,1,maxwav+1,1,n);          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     free_vector(moisnais,1,n);          for (k=1; k<=cptcovprod;k++)
     free_vector(annais,1,n);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     /* free_matrix(mint,1,maxwav,1,n);          
        free_matrix(anint,1,maxwav,1,n);*/          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
     free_vector(moisdc,1,n);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(andc,1,n);          gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
          
     wav=ivector(1,imx);          for(theta=1; theta <=npar; theta++){
     dh=imatrix(1,lastpass-firstpass+1,1,imx);            for(i=1; i<=npar; i++)
     mw=imatrix(1,lastpass-firstpass+1,1,imx);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
                
     /* Concatenates waves */            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);            
             k=0;
             for(i=1; i<= (nlstate); i++){
       Tcode=ivector(1,100);              for(j=1; j<=(nlstate+ndeath);j++){
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);                k=k+1;
       ncodemax[1]=1;                gp[k]=pmmij[i][j];
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);              }
                  }
    codtab=imatrix(1,100,1,10);            
    h=0;            for(i=1; i<=npar; i++)
    m=pow(2,cptcoveff);              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
        
    for(k=1;k<=cptcoveff; k++){            pmij(pmmij,cov,ncovmodel,xp,nlstate);
      for(i=1; i <=(m/pow(2,k));i++){            k=0;
        for(j=1; j <= ncodemax[k]; j++){            for(i=1; i<=(nlstate); i++){
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){              for(j=1; j<=(nlstate+ndeath);j++){
            h++;                k=k+1;
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;                gm[k]=pmmij[i][j];
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/              }
          }            }
        }       
      }            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
    }              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
    /* 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(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
       for(k=1; k <=cptcovn; k++){            for(theta=1; theta <=npar; theta++)
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);              trgradg[j][theta]=gradg[theta][j];
       }          
       printf("\n");          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
       }          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
       scanf("%d",i);*/          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
              free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
    /* Calculates basic frequencies. Computes observed prevalence at single age          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
        and prints on file fileres'p'. */          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
              pmij(pmmij,cov,ncovmodel,x,nlstate);
              
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          k=0;
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          for(i=1; i<=(nlstate); i++){
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            for(j=1; j<=(nlstate+ndeath);j++){
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              k=k+1;
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */              mu[k][(int) age]=pmmij[i][j];
                  }
     /* For Powell, parameters are in a vector p[] starting at p[1]          }
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
     if(mle==1){  
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);          /*printf("\n%d ",(int)age);
     }            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
                printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     /*--------- results files --------------*/            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);            }*/
    
           fprintf(ficresprob,"\n%d ",(int)age);
    jk=1;          fprintf(ficresprobcov,"\n%d ",(int)age);
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");          fprintf(ficresprobcor,"\n%d ",(int)age);
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");  
    for(i=1,jk=1; i <=nlstate; i++){          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
      for(k=1; k <=(nlstate+ndeath); k++){            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
        if (k != i)          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
          {            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
            printf("%d%d ",i,k);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
            fprintf(ficres,"%1d%1d ",i,k);          }
            for(j=1; j <=ncovmodel; j++){          i=0;
              printf("%f ",p[jk]);          for (k=1; k<=(nlstate);k++){
              fprintf(ficres,"%f ",p[jk]);            for (l=1; l<=(nlstate+ndeath);l++){ 
              jk++;              i=i++;
            }              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
            printf("\n");              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
            fprintf(ficres,"\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]));
    }              }
  if(mle==1){            }
     /* Computing hessian and covariance matrix */          }/* end of loop for state */
     ftolhess=ftol; /* Usually correct */        } /* end of loop for age */
     hesscov(matcov, p, npar, delti, ftolhess, func);  
  }        /* Confidence intervalle of pij  */
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");        /*
     printf("# Scales (for hessian or gradient estimation)\n");          fprintf(ficgp,"\nset noparametric;unset label");
      for(i=1,jk=1; i <=nlstate; i++){          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
       for(j=1; j <=nlstate+ndeath; j++){          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
         if (j!=i) {          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(ficres,"%1d%1d",i,j);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           printf("%1d%1d",i,j);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           for(k=1; k<=ncovmodel;k++){          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
             printf(" %.5e",delti[jk]);        */
             fprintf(ficres," %.5e",delti[jk]);  
             jk++;        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
           }        first1=1;
           printf("\n");        for (k2=1; k2<=(nlstate);k2++){
           fprintf(ficres,"\n");          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
         }            if(l2==k2) continue;
       }            j=(k2-1)*(nlstate+ndeath)+l2;
      }            for (k1=1; k1<=(nlstate);k1++){
                  for (l1=1; l1<=(nlstate+ndeath);l1++){ 
     k=1;                if(l1==k1) continue;
     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");                i=(k1-1)*(nlstate+ndeath)+l1;
     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");                if(i<=j) continue;
     for(i=1;i<=npar;i++){                for (age=bage; age<=fage; age ++){ 
       /*  if (k>nlstate) k=1;                  if ((int)age %5==0){
       i1=(i-1)/(ncovmodel*nlstate)+1;                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
       printf("%s%d%d",alph[k],i1,tab[i]);*/                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
       fprintf(ficres,"%3d",i);                    mu1=mu[i][(int) age]/stepm*YEARM ;
       printf("%3d",i);                    mu2=mu[j][(int) age]/stepm*YEARM;
       for(j=1; j<=i;j++){                    c12=cv12/sqrt(v1*v2);
         fprintf(ficres," %.5e",matcov[i][j]);                    /* Computing eigen value of matrix of covariance */
         printf(" %.5e",matcov[i][j]);                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       }                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       fprintf(ficres,"\n");                    /* Eigen vectors */
       printf("\n");                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
       k++;                    /*v21=sqrt(1.-v11*v11); *//* error */
     }                    v21=(lc1-v1)/cv12*v11;
                        v12=-v21;
     while((c=getc(ficpar))=='#' && c!= EOF){                    v22=v11;
       ungetc(c,ficpar);                    tnalp=v21/v11;
       fgets(line, MAXLINE, ficpar);                    if(first1==1){
       puts(line);                      first1=0;
       fputs(line,ficparo);                      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);
     }                    }
     ungetc(c,ficpar);                    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);
     estepm=0;                    /*printf(fignu*/
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
     if (estepm==0 || estepm < stepm) estepm=stepm;                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
     if (fage <= 2) {                    if(first==1){
       bage = ageminpar;                      first=0;
       fage = agemaxpar;                      fprintf(ficgp,"\nset parametric;unset label");
     }                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                                subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
     while((c=getc(ficpar))=='#' && c!= EOF){                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     ungetc(c,ficpar);                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     fgets(line, MAXLINE, ficpar);                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
     puts(line);                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     fputs(line,ficparo);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   }                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   ungetc(c,ficpar);                      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),\
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                    }else{
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                      first=0;
                            fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
   while((c=getc(ficpar))=='#' && c!= EOF){                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     ungetc(c,ficpar);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     fgets(line, MAXLINE, ficpar);                      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",\
     puts(line);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     fputs(line,ficparo);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   }                    }/* if first */
   ungetc(c,ficpar);                  } /* age mod 5 */
                  } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
    dateprev1=anprev1+mprev1/12.+jprev1/365.;                first=1;
    dateprev2=anprev2+mprev2/12.+jprev2/365.;              } /*l12 */
             } /* k12 */
   fscanf(ficpar,"pop_based=%d\n",&popbased);          } /*l1 */
   fprintf(ficparo,"pop_based=%d\n",popbased);          }/* k1 */
   fprintf(ficres,"pop_based=%d\n",popbased);        } /* loop covariates */
      }
   while((c=getc(ficpar))=='#' && c!= EOF){    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     ungetc(c,ficpar);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     fgets(line, MAXLINE, ficpar);    free_vector(xp,1,npar);
     puts(line);    fclose(ficresprob);
     fputs(line,ficparo);    fclose(ficresprobcov);
   }    fclose(ficresprobcor);
   ungetc(c,ficpar);    fflush(ficgp);
     fflush(fichtmcov);
   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);  }
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);  
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);  
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
 while((c=getc(ficpar))=='#' && c!= EOF){                    int lastpass, int stepm, int weightopt, char model[],\
     ungetc(c,ficpar);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
     fgets(line, MAXLINE, ficpar);                    int popforecast, int estepm ,\
     puts(line);                    double jprev1, double mprev1,double anprev1, \
     fputs(line,ficparo);                    double jprev2, double mprev2,double anprev2){
   }    int jj1, k1, i1, cpt;
   ungetc(c,ficpar);    /*char optionfilehtm[FILENAMELENGTH];*/
   /*   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    { */
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);  /*     printf("Problem with %s \n",optionfilehtm), exit(0); */
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);  /*     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0); */
   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,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);     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 \
 /*------------ gnuplot -------------*/   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n \
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n \
     - Life expectancies by age and initial health status (estepm=%2d months): \
 /*------------ free_vector  -------------*/     <a href=\"%s\">%s</a> <br>\n</li>", \
  chdir(path);             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"),\
               stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"),\
  free_ivector(wav,1,imx);             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"),\
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);    
  free_ivector(num,1,n);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
  free_vector(agedc,1,n);  
  /*free_matrix(covar,1,NCOVMAX,1,n);*/   m=cptcoveff;
  fclose(ficparo);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
  fclose(ficres);  
    jj1=0;
 /*--------- index.htm --------*/   for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);       jj1++;
        if (cptcovn > 0) {
           fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   /*--------------- Prevalence limit --------------*/         for (cpt=1; cpt<=cptcoveff;cpt++) 
             fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   strcpy(filerespl,"pl");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   strcat(filerespl,fileres);       }
   if((ficrespl=fopen(filerespl,"w"))==NULL) {       /* Pij */
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
   }  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);       /* Quasi-incidences */
   fprintf(ficrespl,"#Prevalence limit\n");       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
   fprintf(ficrespl,"#Age ");   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
   fprintf(ficrespl,"\n");         /* Stable prevalence in each health state */
           for(cpt=1; cpt<nlstate;cpt++){
   prlim=matrix(1,nlstate,1,nlstate);           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */         }
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       for(cpt=1; cpt<=nlstate;cpt++) {
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
   k=0;       }
   agebase=ageminpar;       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   agelim=agemaxpar;  health expectancies in states (1) and (2): %s%d.png<br>\
   ftolpl=1.e-10;  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
   i1=cptcoveff;     } /* end i1 */
   if (cptcovn < 1){i1=1;}   }/* End k1 */
    fprintf(fichtm,"</ul>");
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
         k=k+1;   fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n\
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n\
         fprintf(ficrespl,"\n#******");   - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
         for(j=1;j<=cptcoveff;j++)   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n\
         fprintf(ficrespl,"******\n");   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n\
           - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n\
         for (age=agebase; age<=agelim; age++){   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);           rfileres,rfileres,\
           fprintf(ficrespl,"%.0f",age );           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"),\
           for(i=1; i<=nlstate;i++)           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"),\
           fprintf(ficrespl," %.5f", prlim[i][i]);           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"),\
           fprintf(ficrespl,"\n");           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"),\
         }           subdirf2(fileres,"t"),subdirf2(fileres,"t"),\
       }           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
     }  
   fclose(ficrespl);  /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*------------- h Pij x at various ages ------------*/  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
    /*      <br>",fileres,fileres,fileres,fileres); */
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  /*  else  */
   if((ficrespij=fopen(filerespij,"w"))==NULL) {  /*    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); */
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;  fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   }  
   printf("Computing pij: result on file '%s' \n", filerespij);   m=cptcoveff;
     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   /*if (stepm<=24) stepsize=2;*/   jj1=0;
    for(k1=1; k1<=m;k1++){
   agelim=AGESUP;     for(i1=1; i1<=ncodemax[k1];i1++){
   hstepm=stepsize*YEARM; /* Every year of age */       jj1++;
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */       if (cptcovn > 0) {
           fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   k=0;         for (cpt=1; cpt<=cptcoveff;cpt++) 
   for(cptcov=1;cptcov<=i1;cptcov++){           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
       k=k+1;       }
         fprintf(ficrespij,"\n#****** ");       for(cpt=1; cpt<=nlstate;cpt++) {
         for(j=1;j<=cptcoveff;j++)         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
         fprintf(ficrespij,"******\n");  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
               }
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */     } /* end i1 */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */   }/* End k1 */
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */   fprintf(fichtm,"</ul>");
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   fflush(fichtm);
           oldm=oldms;savm=savms;  }
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
           fprintf(ficrespij,"# Age");  /******************* Gnuplot file **************/
           for(i=1; i<=nlstate;i++)  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
             for(j=1; j<=nlstate+ndeath;j++)  
               fprintf(ficrespij," %1d-%1d",i,j);    char dirfileres[132],optfileres[132];
           fprintf(ficrespij,"\n");    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
           for (h=0; h<=nhstepm; h++){    int ng;
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
             for(i=1; i<=nlstate;i++)  /*     printf("Problem with file %s",optionfilegnuplot); */
               for(j=1; j<=nlstate+ndeath;j++)  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);  /*   } */
             fprintf(ficrespij,"\n");  
           }    /*#ifdef windows */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficgp,"cd \"%s\" \n",pathc);
           fprintf(ficrespij,"\n");      /*#endif */
         }    m=pow(2,cptcoveff);
     }  
   }    strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/   /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
   fclose(ficrespij);     for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
   /*---------- Forecasting ------------------*/       fprintf(ficgp,"set xlabel \"Age\" \n\
   if((stepm == 1) && (strcmp(model,".")==0)){  set ylabel \"Probability\" \n\
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);  set ter png small\n\
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);  set size 0.65,0.65\n\
     free_matrix(mint,1,maxwav,1,n);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);  
     free_vector(weight,1,n);}       for (i=1; i<= nlstate ; i ++) {
   else{         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     erreur=108;         else fprintf(ficgp," \%%*lf (\%%*lf)");
     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(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)");
   /*---------- Health expectancies and variances ------------*/         else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
   strcpy(filerest,"t");       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
   strcat(filerest,fileres);       for (i=1; i<= nlstate ; i ++) {
   if((ficrest=fopen(filerest,"w"))==NULL) {         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;         else fprintf(ficgp," \%%*lf (\%%*lf)");
   }       }  
   printf("Computing Total LEs with variances: file '%s' \n", filerest);       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
   strcpy(filerese,"e");    /*2 eme*/
   strcat(filerese,fileres);    
   if((ficreseij=fopen(filerese,"w"))==NULL) {    for (k1=1; k1<= m ; k1 ++) { 
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
   }      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      
       for (i=1; i<= nlstate+1 ; i ++) {
  strcpy(fileresv,"v");        k=2*i;
   strcat(fileresv,fileres);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {        for (j=1; j<= nlstate+1 ; j ++) {
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   }          else fprintf(ficgp," \%%*lf (\%%*lf)");
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);        }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
   k=0;        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
   for(cptcov=1;cptcov<=i1;cptcov++){        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        for (j=1; j<= nlstate+1 ; j ++) {
       k=k+1;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       fprintf(ficrest,"\n#****** ");          else fprintf(ficgp," \%%*lf (\%%*lf)");
       for(j=1;j<=cptcoveff;j++)        }   
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficgp,"\" t\"\" w l 0,");
       fprintf(ficrest,"******\n");        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 ++) {
       fprintf(ficreseij,"\n#****** ");          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       for(j=1;j<=cptcoveff;j++)          else fprintf(ficgp," \%%*lf (\%%*lf)");
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        }   
       fprintf(ficreseij,"******\n");        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       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");    /*3eme*/
     
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    for (k1=1; k1<= m ; k1 ++) { 
       oldm=oldms;savm=savms;      for (cpt=1; cpt<= nlstate ; cpt ++) {
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm);          k=2+nlstate*(2*cpt-2);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
       oldm=oldms;savm=savms;        fprintf(ficgp,"set ter png small\n\
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);  set size 0.65,0.65\n\
      plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
            for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
       fprintf(ficrest,"\n");          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
       epj=vector(1,nlstate+1);          
       for(age=bage; age <=fage ;age++){        */
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        for (i=1; i< nlstate ; i ++) {
         if (popbased==1) {          fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
           for(i=1; i<=nlstate;i++)          
             prlim[i][i]=probs[(int)age][i][k];        } 
         }      }
            }
         fprintf(ficrest," %4.0f",age);    
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    /* CV preval stable (period) */
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    for (k1=1; k1<= m ; k1 ++) { 
             epj[j] += prlim[i][i]*eij[i][j][(int)age];      for (cpt=1; cpt<=nlstate ; cpt ++) {
           }        k=3;
           epj[nlstate+1] +=epj[j];        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         }        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
         for(i=1, vepp=0.;i <=nlstate;i++)  set ter png small\nset size 0.65,0.65\n\
           for(j=1;j <=nlstate;j++)  unset log y\n\
             vepp += vareij[i][j][(int)age];  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         fprintf(ficrest," %7.2f (%7.2f)", epj[nlstate+1],sqrt(vepp));        
         for(j=1;j <=nlstate;j++){        for (i=1; i< nlstate ; i ++)
           fprintf(ficrest," %7.2f (%7.2f)", epj[j],sqrt(vareij[j][j][(int)age]));          fprintf(ficgp,"+$%d",k+i+1);
         }        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         fprintf(ficrest,"\n");        
       }        l=3+(nlstate+ndeath)*cpt;
     }        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
   }        for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
   fclose(ficreseij);          fprintf(ficgp,"+$%d",l+i+1);
   fclose(ficresvij);        }
   fclose(ficrest);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
   fclose(ficpar);      } 
   free_vector(epj,1,nlstate+1);    }  
      
   /*------- Variance limit prevalence------*/      /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
   strcpy(fileresvpl,"vpl");      for(k=1; k <=(nlstate+ndeath); k++){
   strcat(fileresvpl,fileres);        if (k != i) {
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {          for(j=1; j <=ncovmodel; j++){
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
     exit(0);            jk++; 
   }            fprintf(ficgp,"\n");
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);          }
         }
   k=0;      }
   for(cptcov=1;cptcov<=i1;cptcov++){     }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
       fprintf(ficresvpl,"\n#****** ");       for(jk=1; jk <=m; jk++) {
       for(j=1;j<=cptcoveff;j++)         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);         if (ng==2)
       fprintf(ficresvpl,"******\n");           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
               else
       varpl=matrix(1,nlstate,(int) bage, (int) fage);           fprintf(ficgp,"\nset title \"Probability\"\n");
       oldm=oldms;savm=savms;         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);         i=1;
     }         for(k2=1; k2<=nlstate; k2++) {
  }           k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
   fclose(ficresvpl);             if (k != k2){
                if(ng==2)
   /*---------- End : free ----------------*/                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);               else
                   fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);               ij=1;
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);               for(j=3; j <=ncovmodel; j++) {
                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                     fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);                   ij++;
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);                 }
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);                 else
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                 }
   free_matrix(matcov,1,npar,1,npar);               fprintf(ficgp,")/(1");
   free_vector(delti,1,npar);               
   free_matrix(agev,1,maxwav,1,imx);               for(k1=1; k1 <=nlstate; k1++){   
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
   if(erreur >0)                 for(j=3; j <=ncovmodel; j++){
     printf("End of Imach with error or warning %d\n",erreur);                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   else   printf("End of Imach\n");                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */                     ij++;
                     }
   /* 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);*/                   else
   /*printf("Total time was %d uSec.\n", total_usecs);*/                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   /*------ End -----------*/                 }
                  fprintf(ficgp,")");
                }
  end:               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
 #ifdef windows               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
   /* chdir(pathcd);*/               i=i+ncovmodel;
 #endif             }
  /*system("wgnuplot graph.plt");*/           } /* end k */
  /*system("../gp37mgw/wgnuplot graph.plt");*/         } /* end k2 */
  /*system("cd ../gp37mgw");*/       } /* end jk */
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/     } /* end ng */
  strcpy(plotcmd,GNUPLOTPROGRAM);     fflush(ficgp); 
  strcat(plotcmd," ");  }  /* end gnuplot */
  strcat(plotcmd,optionfilegnuplot);  
  system(plotcmd);  
   /*************** Moving average **************/
 #ifdef windows  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   while (z[0] != 'q') {  
     /* chdir(path); */    int i, cpt, cptcod;
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");    int modcovmax =1;
     scanf("%s",z);    int mobilavrange, mob;
     if (z[0] == 'c') system("./imach");    double age;
     else if (z[0] == 'e') system(optionfilehtm);  
     else if (z[0] == 'g') system(plotcmd);    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
     else if (z[0] == 'q') exit(0);                             a covariate has 2 modalities */
   }    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
 #endif  
 }    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* 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, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
   
     char ca[32], cb[32], cc[32];
     /*  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;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: ");
     fprintf(ficlog,"pathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
    
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     /* Read guess parameters */
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++){
       j=0;
       for(jj=1; jj <=nlstate+ndeath; jj++){
         if(jj==i) continue;
         j++;
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1 != i) && (j1 != j)){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);
         }
         fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)
           printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);
           if(mle==1){
             printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);
           }
           else
             fprintf(ficlog," %lf",param[i][j][k]);
           fprintf(ficparo," %lf",param[i][j][k]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     }  
     fflush(ficlog);
   
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1-i)*(j1-j)!=0){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);
         }
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         fprintf(ficlog,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);
           fprintf(ficlog," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
         fprintf(ficlog,"\n");
       }
     }
     fflush(ficlog);
   
     delti=delti3[1][1];
   
   
     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);
       if(mle==1)
         printf("%s",str);
       fprintf(ficlog,"%s",str);
       fprintf(ficparo,"%s",str);
       for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
           printf(" %.5le",matcov[i][j]);
         }
         fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       numlinepar++;
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
     for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];
      
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
   
     fflush(ficlog);
   
     /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         lstra=strlen(stra);
         if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
           stratrunc = &(stra[lstra-9]);
           num[i]=atol(stratrunc);
         }
         else
           num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* 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);
     
   
     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");
   /* # 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" */
   
   
   /* Just to have a covariance matrix which will be more understandable
      even is we still don't want to manage dictionary of variables
   */
     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){
               if(mle>=1)
                 printf("#%1d%1d%d",i,j,k);
               fprintf(ficlog,"#%1d%1d%d",i,j,k);
               fprintf(ficres,"#%1d%1d%d",i,j,k);
             }else{
               if(mle>=1)
                 printf("%1d%1d%d",i,j,k);
               fprintf(ficlog,"%1d%1d%d",i,j,k);
               fprintf(ficres,"%1d%1d%d",i,j,k);
             }
             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){
                         if(mle>=1)
                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         if(mle>=1)
                           printf(" %.5e",matcov[jj][ll]); 
                         fprintf(ficlog," %.5e",matcov[jj][ll]); 
                         fprintf(ficres," %.5e",matcov[jj][ll]); 
                       }
                     }else{
                       if(itimes==1){
                         if(mle>=1)
                           printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         if(mle>=1)
                           printf(" %.5e",matcov[jj][ll]); 
                         fprintf(ficlog," %.5e",matcov[jj][ll]); 
                         fprintf(ficres," %.5e",matcov[jj][ll]); 
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             if(mle>=1)
               printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
     fflush(ficlog);
     fflush(ficres);
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   
     replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     /*  chdir(path); */
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_lvector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
   /*      }  */
   /*      else{ */
   /*        erreur=108; */
   /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*      } */
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocaltime at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
     fclose(fichtm);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
     chdir(path);
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     if((outcmd=system(plotcmd)) != 0){
       printf(" Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.36  
changed lines
  Added in v.1.95


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