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version 1.38, 2002/04/03 12:19:36 version 1.97, 2004/02/20 13:25:42
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 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.97  2004/02/20 13:25:42  lievre
      Version 0.96d. Population forecasting command line is (temporarily)
   This program computes Healthy Life Expectancies from    suppressed.
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a  
   first survey ("cross") where individuals from different ages are    Revision 1.96  2003/07/15 15:38:55  brouard
   interviewed on their health status or degree of disability (in the    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   case of a health survey which is our main interest) -2- at least a    rewritten within the same printf. Workaround: many printfs.
   second wave of interviews ("longitudinal") which measure each change  
   (if any) in individual health status.  Health expectancies are    Revision 1.95  2003/07/08 07:54:34  brouard
   computed from the time spent in each health state according to a    * imach.c (Repository):
   model. More health states you consider, more time is necessary to reach the    (Repository): Using imachwizard code to output a more meaningful covariance
   Maximum Likelihood of the parameters involved in the model.  The    matrix (cov(a12,c31) instead of numbers.
   simplest model is the multinomial logistic model where pij is the  
   probabibility to be observed in state j at the second wave    Revision 1.94  2003/06/27 13:00:02  brouard
   conditional to be observed in state i at the first wave. Therefore    Just cleaning
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where  
   'age' is age and 'sex' is a covariate. If you want to have a more    Revision 1.93  2003/06/25 16:33:55  brouard
   complex model than "constant and age", you should modify the program    (Module): On windows (cygwin) function asctime_r doesn't
   where the markup *Covariates have to be included here again* invites    exist so I changed back to asctime which exists.
   you to do it.  More covariates you add, slower the    (Module): Version 0.96b
   convergence.  
     Revision 1.92  2003/06/25 16:30:45  brouard
   The advantage of this computer programme, compared to a simple    (Module): On windows (cygwin) function asctime_r doesn't
   multinomial logistic model, is clear when the delay between waves is not    exist so I changed back to asctime which exists.
   identical for each individual. Also, if a individual missed an  
   intermediate interview, the information is lost, but taken into    Revision 1.91  2003/06/25 15:30:29  brouard
   account using an interpolation or extrapolation.      * imach.c (Repository): Duplicated warning errors corrected.
     (Repository): Elapsed time after each iteration is now output. It
   hPijx is the probability to be observed in state i at age x+h    helps to forecast when convergence will be reached. Elapsed time
   conditional to the observed state i at age x. The delay 'h' can be    is stamped in powell.  We created a new html file for the graphs
   split into an exact number (nh*stepm) of unobserved intermediate    concerning matrix of covariance. It has extension -cov.htm.
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Revision 1.90  2003/06/24 12:34:15  brouard
   matrix is simply the matrix product of nh*stepm elementary matrices    (Module): Some bugs corrected for windows. Also, when
   and the contribution of each individual to the likelihood is simply    mle=-1 a template is output in file "or"mypar.txt with the design
   hPijx.    of the covariance matrix to be input.
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.89  2003/06/24 12:30:52  brouard
   of the life expectancies. It also computes the prevalence limits.    (Module): Some bugs corrected for windows. Also, when
      mle=-1 a template is output in file "or"mypar.txt with the design
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    of the covariance matrix to be input.
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.88  2003/06/23 17:54:56  brouard
   from the European Union.    * 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.
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.87  2003/06/18 12:26:01  brouard
   can be accessed at http://euroreves.ined.fr/imach .    Version 0.96
   **********************************************************************/  
      Revision 1.86  2003/06/17 20:04:08  brouard
 #include <math.h>    (Module): Change position of html and gnuplot routines and added
 #include <stdio.h>    routine fileappend.
 #include <stdlib.h>  
 #include <unistd.h>    Revision 1.85  2003/06/17 13:12:43  brouard
     * imach.c (Repository): Check when date of death was earlier that
 #define MAXLINE 256    current date of interview. It may happen when the death was just
 #define GNUPLOTPROGRAM "wgnuplot"    prior to the death. In this case, dh was negative and likelihood
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    was wrong (infinity). We still send an "Error" but patch by
 #define FILENAMELENGTH 80    assuming that the date of death was just one stepm after the
 /*#define DEBUG*/    interview.
 #define windows    (Repository): Because some people have very long ID (first column)
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    we changed int to long in num[] and we added a new lvector for
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    memory allocation. But we also truncated to 8 characters (left
     truncation)
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    (Repository): No more line truncation errors.
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     Revision 1.84  2003/06/13 21:44:43  brouard
 #define NINTERVMAX 8    * imach.c (Repository): Replace "freqsummary" at a correct
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    place. It differs from routine "prevalence" which may be called
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    many times. Probs is memory consuming and must be used with
 #define NCOVMAX 8 /* Maximum number of covariates */    parcimony.
 #define MAXN 20000    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Revision 1.83  2003/06/10 13:39:11  lievre
 #define AGEBASE 40    *** empty log message ***
   
     Revision 1.82  2003/06/05 15:57:20  brouard
 int erreur; /* Error number */    Add log in  imach.c and  fullversion number is now printed.
 int nvar;  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  */
 int npar=NPARMAX;  /*
 int nlstate=2; /* Number of live states */     Interpolated Markov Chain
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Short summary of the programme:
 int popbased=0;    
     This program computes Healthy Life Expectancies from
 int *wav; /* Number of waves for this individuual 0 is possible */    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 int maxwav; /* Maxim number of waves */    first survey ("cross") where individuals from different ages are
 int jmin, jmax; /* min, max spacing between 2 waves */    interviewed on their health status or degree of disability (in the
 int mle, weightopt;    case of a health survey which is our main interest) -2- at least a
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    second wave of interviews ("longitudinal") which measure each change
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    (if any) in individual health status.  Health expectancies are
 double jmean; /* Mean space between 2 waves */    computed from the time spent in each health state according to a
 double **oldm, **newm, **savm; /* Working pointers to matrices */    model. More health states you consider, more time is necessary to reach the
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    Maximum Likelihood of the parameters involved in the model.  The
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    simplest model is the multinomial logistic model where pij is the
 FILE *ficgp,*ficresprob,*ficpop;    probability to be observed in state j at the second wave
 FILE *ficreseij;    conditional to be observed in state i at the first wave. Therefore
   char filerese[FILENAMELENGTH];    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
  FILE  *ficresvij;    'age' is age and 'sex' is a covariate. If you want to have a more
   char fileresv[FILENAMELENGTH];    complex model than "constant and age", you should modify the program
  FILE  *ficresvpl;    where the markup *Covariates have to be included here again* invites
   char fileresvpl[FILENAMELENGTH];    you to do it.  More covariates you add, slower the
     convergence.
 #define NR_END 1  
 #define FREE_ARG char*    The advantage of this computer programme, compared to a simple
 #define FTOL 1.0e-10    multinomial logistic model, is clear when the delay between waves is not
     identical for each individual. Also, if a individual missed an
 #define NRANSI    intermediate interview, the information is lost, but taken into
 #define ITMAX 200    account using an interpolation or extrapolation.  
   
 #define TOL 2.0e-4    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
 #define CGOLD 0.3819660    split into an exact number (nh*stepm) of unobserved intermediate
 #define ZEPS 1.0e-10    states. This elementary transition (by month, quarter,
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    semester or year) is modelled as a multinomial logistic.  The hPx
     matrix is simply the matrix product of nh*stepm elementary matrices
 #define GOLD 1.618034    and the contribution of each individual to the likelihood is simply
 #define GLIMIT 100.0    hPijx.
 #define TINY 1.0e-20  
     Also this programme outputs the covariance matrix of the parameters but also
 static double maxarg1,maxarg2;    of the life expectancies. It also computes the stable prevalence. 
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
               Institut national d'études démographiques, Paris.
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    This software have been partly granted by Euro-REVES, a concerted action
 #define rint(a) floor(a+0.5)    from the European Union.
     It is copyrighted identically to a GNU software product, ie programme and
 static double sqrarg;    software can be distributed freely for non commercial use. Latest version
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    can be accessed at http://euroreves.ined.fr/imach .
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 int imx;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 int stepm;    
 /* Stepm, step in month: minimum step interpolation*/    **********************************************************************/
   /*
 int estepm;    main
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    read parameterfile
     read datafile
 int m,nb;    concatwav
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    freqsummary
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    if (mle >= 1)
 double **pmmij, ***probs, ***mobaverage;      mlikeli
 double dateintmean=0;    print results files
     if mle==1 
 double *weight;       computes hessian
 int **s; /* Status */    read end of parameter file: agemin, agemax, bage, fage, estepm
 double *agedc, **covar, idx;        begin-prev-date,...
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    open gnuplot file
     open html file
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    stable prevalence
 double ftolhess; /* Tolerance for computing hessian */     for age prevalim()
     h Pij x
 /**************** split *************************/    variance of p varprob
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    forecasting if prevfcast==1 prevforecast call prevalence()
 {    health expectancies
    char *s;                             /* pointer */    Variance-covariance of DFLE
    int  l1, l2;                         /* length counters */    prevalence()
      movingaverage()
    l1 = strlen( path );                 /* length of path */    varevsij() 
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    if popbased==1 varevsij(,popbased)
 #ifdef windows    total life expectancies
    s = strrchr( path, '\\' );           /* find last / */    Variance of stable prevalence
 #else   end
    s = strrchr( path, '/' );            /* find last / */  */
 #endif  
    if ( s == NULL ) {                   /* no directory, so use current */  
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );   
   #include <math.h>
       if ( getwd( dirc ) == NULL ) {  #include <stdio.h>
 #else  #include <stdlib.h>
       extern char       *getcwd( );  #include <unistd.h>
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  #include <sys/time.h>
 #endif  #include <time.h>
          return( GLOCK_ERROR_GETCWD );  #include "timeval.h"
       }  
       strcpy( name, path );             /* we've got it */  /* #include <libintl.h> */
    } else {                             /* strip direcotry from path */  /* #define _(String) gettext (String) */
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */  #define MAXLINE 256
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  #define GNUPLOTPROGRAM "gnuplot"
       strcpy( name, s );                /* save file name */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  #define FILENAMELENGTH 132
       dirc[l1-l2] = 0;                  /* add zero */  /*#define DEBUG*/
    }  /*#define windows*/
    l1 = strlen( dirc );                 /* length of directory */  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #ifdef windows  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #else  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 #endif  
    s = strrchr( name, '.' );            /* find last / */  #define NINTERVMAX 8
    s++;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
    strcpy(ext,s);                       /* save extension */  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
    l1= strlen( name);  #define NCOVMAX 8 /* Maximum number of covariates */
    l2= strlen( s)+1;  #define MAXN 20000
    strncpy( finame, name, l1-l2);  #define YEARM 12. /* Number of months per year */
    finame[l1-l2]= 0;  #define AGESUP 130
    return( 0 );                         /* we're done */  #define AGEBASE 40
 }  #ifdef unix
   #define DIRSEPARATOR '/'
   #define ODIRSEPARATOR '\\'
 /******************************************/  #else
   #define DIRSEPARATOR '\\'
 void replace(char *s, char*t)  #define ODIRSEPARATOR '/'
 {  #endif
   int i;  
   int lg=20;  /* $Id$ */
   i=0;  /* $State$ */
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {  char version[]="Imach version 0.96d, February 2004, INED-EUROREVES ";
     (s[i] = t[i]);  char fullversion[]="$Revision$ $Date$"; 
     if (t[i]== '\\') s[i]='/';  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   }  int nvar;
 }  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   int npar=NPARMAX;
 int nbocc(char *s, char occ)  int nlstate=2; /* Number of live states */
 {  int ndeath=1; /* Number of dead states */
   int i,j=0;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int lg=20;  int popbased=0;
   i=0;  
   lg=strlen(s);  int *wav; /* Number of waves for this individuual 0 is possible */
   for(i=0; i<= lg; i++) {  int maxwav; /* Maxim number of waves */
   if  (s[i] == occ ) j++;  int jmin, jmax; /* min, max spacing between 2 waves */
   }  int gipmx, gsw; /* Global variables on the number of contributions 
   return j;                     to the likelihood and the sum of weights (done by funcone)*/
 }  int mle, weightopt;
   int **mw; /* mw[mi][i] is number of the mi wave for this individual */
 void cutv(char *u,char *v, char*t, char occ)  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 {  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   int i,lg,j,p=0;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   i=0;  double jmean; /* Mean space between 2 waves */
   for(j=0; j<=strlen(t)-1; j++) {  double **oldm, **newm, **savm; /* Working pointers to matrices */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   }  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   FILE *ficlog, *ficrespow;
   lg=strlen(t);  int globpr; /* Global variable for printing or not */
   for(j=0; j<p; j++) {  double fretone; /* Only one call to likelihood */
     (u[j] = t[j]);  long ipmx; /* Number of contributions */
   }  double sw; /* Sum of weights */
      u[p]='\0';  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   FILE *ficresilk;
    for(j=0; j<= lg; j++) {  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
     if (j>=(p+1))(v[j-p-1] = t[j]);  FILE *ficresprobmorprev;
   }  FILE *fichtm, *fichtmcov; /* Html File */
 }  FILE *ficreseij;
   char filerese[FILENAMELENGTH];
 /********************** nrerror ********************/  FILE  *ficresvij;
   char fileresv[FILENAMELENGTH];
 void nrerror(char error_text[])  FILE  *ficresvpl;
 {  char fileresvpl[FILENAMELENGTH];
   fprintf(stderr,"ERREUR ...\n");  char title[MAXLINE];
   fprintf(stderr,"%s\n",error_text);  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   exit(1);  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 }  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
 /*********************** vector *******************/  char command[FILENAMELENGTH];
 double *vector(int nl, int nh)  int  outcmd=0;
 {  
   double *v;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");  char filelog[FILENAMELENGTH]; /* Log file */
   return v-nl+NR_END;  char filerest[FILENAMELENGTH];
 }  char fileregp[FILENAMELENGTH];
   char popfile[FILENAMELENGTH];
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 {  
   free((FREE_ARG)(v+nl-NR_END));  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
 }  struct timezone tzp;
   extern int gettimeofday();
 /************************ivector *******************************/  struct tm tmg, tm, tmf, *gmtime(), *localtime();
 int *ivector(long nl,long nh)  long time_value;
 {  extern long time();
   int *v;  char strcurr[80], strfor[80];
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");  #define NR_END 1
   return v-nl+NR_END;  #define FREE_ARG char*
 }  #define FTOL 1.0e-10
   
 /******************free ivector **************************/  #define NRANSI 
 void free_ivector(int *v, long nl, long nh)  #define ITMAX 200 
 {  
   free((FREE_ARG)(v+nl-NR_END));  #define TOL 2.0e-4 
 }  
   #define CGOLD 0.3819660 
 /******************* imatrix *******************************/  #define ZEPS 1.0e-10 
 int **imatrix(long nrl, long nrh, long ncl, long nch)  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {  #define GOLD 1.618034 
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  #define GLIMIT 100.0 
   int **m;  #define TINY 1.0e-20 
    
   /* allocate pointers to rows */  static double maxarg1,maxarg2;
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   if (!m) nrerror("allocation failure 1 in matrix()");  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   m += NR_END;    
   m -= nrl;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
    #define rint(a) floor(a+0.5)
    
   /* allocate rows and set pointers to them */  static double sqrarg;
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  int imx; 
    int stepm;
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  /* Stepm, step in month: minimum step interpolation*/
    
   /* return pointer to array of pointers to rows */  int estepm;
   return m;  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
 }  
   int m,nb;
 /****************** free_imatrix *************************/  long *num;
 void free_imatrix(m,nrl,nrh,ncl,nch)  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
       int **m;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
       long nch,ncl,nrh,nrl;  double **pmmij, ***probs;
      /* free an int matrix allocated by imatrix() */  double dateintmean=0;
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  double *weight;
   free((FREE_ARG) (m+nrl-NR_END));  int **s; /* Status */
 }  double *agedc, **covar, idx;
   int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 {  double ftolhess; /* Tolerance for computing hessian */
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;  /**************** split *************************/
   static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  {
   if (!m) nrerror("allocation failure 1 in matrix()");    char  *ss;                            /* pointer */
   m += NR_END;    int   l1, l2;                         /* length counters */
   m -= nrl;  
     l1 = strlen(path );                   /* length of path */
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   m[nrl] += NR_END;    if ( ss == NULL ) {                   /* no directory, so use current */
   m[nrl] -= ncl;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
         printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;      /* get current working directory */
   return m;      /*    extern  char* getcwd ( char *buf , int len);*/
 }      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
         return( GLOCK_ERROR_GETCWD );
 /*************************free matrix ************************/      }
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)      strcpy( name, path );               /* we've got it */
 {    } else {                              /* strip direcotry from path */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));      ss++;                               /* after this, the filename */
   free((FREE_ARG)(m+nrl-NR_END));      l2 = strlen( ss );                  /* length of filename */
 }      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       strcpy( name, ss );         /* save file name */
 /******************* ma3x *******************************/      strncpy( dirc, path, l1 - l2 );     /* now the directory */
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)      dirc[l1-l2] = 0;                    /* add zero */
 {    }
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    l1 = strlen( dirc );                  /* length of directory */
   double ***m;    /*#ifdef windows
     if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #else
   if (!m) nrerror("allocation failure 1 in matrix()");    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   m += NR_END;  #endif
   m -= nrl;    */
     ss = strrchr( name, '.' );            /* find last / */
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    ss++;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    strcpy(ext,ss);                       /* save extension */
   m[nrl] += NR_END;    l1= strlen( name);
   m[nrl] -= ncl;    l2= strlen(ss)+1;
     strncpy( finame, name, l1-l2);
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    finame[l1-l2]= 0;
     return( 0 );                          /* we're done */
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  }
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;  
   m[nrl][ncl] -= nll;  /******************************************/
   for (j=ncl+1; j<=nch; j++)  
     m[nrl][j]=m[nrl][j-1]+nlay;  void replace_back_to_slash(char *s, char*t)
    {
   for (i=nrl+1; i<=nrh; i++) {    int i;
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    int lg=0;
     for (j=ncl+1; j<=nch; j++)    i=0;
       m[i][j]=m[i][j-1]+nlay;    lg=strlen(t);
   }    for(i=0; i<= lg; i++) {
   return m;      (s[i] = t[i]);
 }      if (t[i]== '\\') s[i]='/';
     }
 /*************************free ma3x ************************/  }
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  
 {  int nbocc(char *s, char occ)
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  {
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    int i,j=0;
   free((FREE_ARG)(m+nrl-NR_END));    int lg=20;
 }    i=0;
     lg=strlen(s);
 /***************** f1dim *************************/    for(i=0; i<= lg; i++) {
 extern int ncom;    if  (s[i] == occ ) j++;
 extern double *pcom,*xicom;    }
 extern double (*nrfunc)(double []);    return j;
    }
 double f1dim(double x)  
 {  void cutv(char *u,char *v, char*t, char occ)
   int j;  {
   double f;    /* cuts string t into u and v where u is ended by char occ excluding it
   double *xt;       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
         gives u="abcedf" and v="ghi2j" */
   xt=vector(1,ncom);    int i,lg,j,p=0;
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    i=0;
   f=(*nrfunc)(xt);    for(j=0; j<=strlen(t)-1; j++) {
   free_vector(xt,1,ncom);      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   return f;    }
 }  
     lg=strlen(t);
 /*****************brent *************************/    for(j=0; j<p; j++) {
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)      (u[j] = t[j]);
 {    }
   int iter;       u[p]='\0';
   double a,b,d,etemp;  
   double fu,fv,fw,fx;     for(j=0; j<= lg; j++) {
   double ftemp;      if (j>=(p+1))(v[j-p-1] = t[j]);
   double p,q,r,tol1,tol2,u,v,w,x,xm;    }
   double e=0.0;  }
    
   a=(ax < cx ? ax : cx);  /********************** nrerror ********************/
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;  void nrerror(char error_text[])
   fw=fv=fx=(*f)(x);  {
   for (iter=1;iter<=ITMAX;iter++) {    fprintf(stderr,"ERREUR ...\n");
     xm=0.5*(a+b);    fprintf(stderr,"%s\n",error_text);
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    exit(EXIT_FAILURE);
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  }
     printf(".");fflush(stdout);  /*********************** vector *******************/
 #ifdef DEBUG  double *vector(int nl, int nh)
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  {
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    double *v;
 #endif    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    if (!v) nrerror("allocation failure in vector");
       *xmin=x;    return v-nl+NR_END;
       return fx;  }
     }  
     ftemp=fu;  /************************ free vector ******************/
     if (fabs(e) > tol1) {  void free_vector(double*v, int nl, int nh)
       r=(x-w)*(fx-fv);  {
       q=(x-v)*(fx-fw);    free((FREE_ARG)(v+nl-NR_END));
       p=(x-v)*q-(x-w)*r;  }
       q=2.0*(q-r);  
       if (q > 0.0) p = -p;  /************************ivector *******************************/
       q=fabs(q);  int *ivector(long nl,long nh)
       etemp=e;  {
       e=d;    int *v;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    if (!v) nrerror("allocation failure in ivector");
       else {    return v-nl+NR_END;
         d=p/q;  }
         u=x+d;  
         if (u-a < tol2 || b-u < tol2)  /******************free ivector **************************/
           d=SIGN(tol1,xm-x);  void free_ivector(int *v, long nl, long nh)
       }  {
     } else {    free((FREE_ARG)(v+nl-NR_END));
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  }
     }  
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  /************************lvector *******************************/
     fu=(*f)(u);  long *lvector(long nl,long nh)
     if (fu <= fx) {  {
       if (u >= x) a=x; else b=x;    long *v;
       SHFT(v,w,x,u)    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
         SHFT(fv,fw,fx,fu)    if (!v) nrerror("allocation failure in ivector");
         } else {    return v-nl+NR_END;
           if (u < x) a=u; else b=u;  }
           if (fu <= fw || w == x) {  
             v=w;  /******************free lvector **************************/
             w=u;  void free_lvector(long *v, long nl, long nh)
             fv=fw;  {
             fw=fu;    free((FREE_ARG)(v+nl-NR_END));
           } else if (fu <= fv || v == x || v == w) {  }
             v=u;  
             fv=fu;  /******************* imatrix *******************************/
           }  int **imatrix(long nrl, long nrh, long ncl, long nch) 
         }       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   }  { 
   nrerror("Too many iterations in brent");    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   *xmin=x;    int **m; 
   return fx;    
 }    /* allocate pointers to rows */ 
     m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 /****************** mnbrak ***********************/    if (!m) nrerror("allocation failure 1 in matrix()"); 
     m += NR_END; 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    m -= nrl; 
             double (*func)(double))    
 {    
   double ulim,u,r,q, dum;    /* allocate rows and set pointers to them */ 
   double fu;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
      if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   *fa=(*func)(*ax);    m[nrl] += NR_END; 
   *fb=(*func)(*bx);    m[nrl] -= ncl; 
   if (*fb > *fa) {    
     SHFT(dum,*ax,*bx,dum)    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       SHFT(dum,*fb,*fa,dum)    
       }    /* return pointer to array of pointers to rows */ 
   *cx=(*bx)+GOLD*(*bx-*ax);    return m; 
   *fc=(*func)(*cx);  } 
   while (*fb > *fc) {  
     r=(*bx-*ax)*(*fb-*fc);  /****************** free_imatrix *************************/
     q=(*bx-*cx)*(*fb-*fa);  void free_imatrix(m,nrl,nrh,ncl,nch)
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/        int **m;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));        long nch,ncl,nrh,nrl; 
     ulim=(*bx)+GLIMIT*(*cx-*bx);       /* free an int matrix allocated by imatrix() */ 
     if ((*bx-u)*(u-*cx) > 0.0) {  { 
       fu=(*func)(u);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     } else if ((*cx-u)*(u-ulim) > 0.0) {    free((FREE_ARG) (m+nrl-NR_END)); 
       fu=(*func)(u);  } 
       if (fu < *fc) {  
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  /******************* matrix *******************************/
           SHFT(*fb,*fc,fu,(*func)(u))  double **matrix(long nrl, long nrh, long ncl, long nch)
           }  {
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       u=ulim;    double **m;
       fu=(*func)(u);  
     } else {    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       u=(*cx)+GOLD*(*cx-*bx);    if (!m) nrerror("allocation failure 1 in matrix()");
       fu=(*func)(u);    m += NR_END;
     }    m -= nrl;
     SHFT(*ax,*bx,*cx,u)  
       SHFT(*fa,*fb,*fc,fu)    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;
 /*************** linmin ************************/  
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 int ncom;    return m;
 double *pcom,*xicom;    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
 double (*nrfunc)(double []);     */
    }
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  
 {  /*************************free matrix ************************/
   double brent(double ax, double bx, double cx,  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
                double (*f)(double), double tol, double *xmin);  {
   double f1dim(double x);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    free((FREE_ARG)(m+nrl-NR_END));
               double *fc, double (*func)(double));  }
   int j;  
   double xx,xmin,bx,ax;  /******************* ma3x *******************************/
   double fx,fb,fa;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
    {
   ncom=n;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   pcom=vector(1,n);    double ***m;
   xicom=vector(1,n);  
   nrfunc=func;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   for (j=1;j<=n;j++) {    if (!m) nrerror("allocation failure 1 in matrix()");
     pcom[j]=p[j];    m += NR_END;
     xicom[j]=xi[j];    m -= nrl;
   }  
   ax=0.0;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   xx=1.0;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    m[nrl] += NR_END;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    m[nrl] -= ncl;
 #ifdef DEBUG  
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 #endif  
   for (j=1;j<=n;j++) {    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     xi[j] *= xmin;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     p[j] += xi[j];    m[nrl][ncl] += NR_END;
   }    m[nrl][ncl] -= nll;
   free_vector(xicom,1,n);    for (j=ncl+1; j<=nch; j++) 
   free_vector(pcom,1,n);      m[nrl][j]=m[nrl][j-1]+nlay;
 }    
     for (i=nrl+1; i<=nrh; i++) {
 /*************** powell ************************/      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,      for (j=ncl+1; j<=nch; j++) 
             double (*func)(double []))        m[i][j]=m[i][j-1]+nlay;
 {    }
   void linmin(double p[], double xi[], int n, double *fret,    return m; 
               double (*func)(double []));    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   int i,ibig,j;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   double del,t,*pt,*ptt,*xit;    */
   double fp,fptt;  }
   double *xits;  
   pt=vector(1,n);  /*************************free ma3x ************************/
   ptt=vector(1,n);  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   xit=vector(1,n);  {
   xits=vector(1,n);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   *fret=(*func)(p);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   for (j=1;j<=n;j++) pt[j]=p[j];    free((FREE_ARG)(m+nrl-NR_END));
   for (*iter=1;;++(*iter)) {  }
     fp=(*fret);  
     ibig=0;  /*************** function subdirf ***********/
     del=0.0;  char *subdirf(char fileres[])
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  {
     for (i=1;i<=n;i++)    /* Caution optionfilefiname is hidden */
       printf(" %d %.12f",i, p[i]);    strcpy(tmpout,optionfilefiname);
     printf("\n");    strcat(tmpout,"/"); /* Add to the right */
     for (i=1;i<=n;i++) {    strcat(tmpout,fileres);
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    return tmpout;
       fptt=(*fret);  }
 #ifdef DEBUG  
       printf("fret=%lf \n",*fret);  /*************** function subdirf2 ***********/
 #endif  char *subdirf2(char fileres[], char *preop)
       printf("%d",i);fflush(stdout);  {
       linmin(p,xit,n,fret,func);    
       if (fabs(fptt-(*fret)) > del) {    /* Caution optionfilefiname is hidden */
         del=fabs(fptt-(*fret));    strcpy(tmpout,optionfilefiname);
         ibig=i;    strcat(tmpout,"/");
       }    strcat(tmpout,preop);
 #ifdef DEBUG    strcat(tmpout,fileres);
       printf("%d %.12e",i,(*fret));    return tmpout;
       for (j=1;j<=n;j++) {  }
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  
         printf(" x(%d)=%.12e",j,xit[j]);  /*************** function subdirf3 ***********/
       }  char *subdirf3(char fileres[], char *preop, char *preop2)
       for(j=1;j<=n;j++)  {
         printf(" p=%.12e",p[j]);    
       printf("\n");    /* Caution optionfilefiname is hidden */
 #endif    strcpy(tmpout,optionfilefiname);
     }    strcat(tmpout,"/");
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    strcat(tmpout,preop);
 #ifdef DEBUG    strcat(tmpout,preop2);
       int k[2],l;    strcat(tmpout,fileres);
       k[0]=1;    return tmpout;
       k[1]=-1;  }
       printf("Max: %.12e",(*func)(p));  
       for (j=1;j<=n;j++)  /***************** f1dim *************************/
         printf(" %.12e",p[j]);  extern int ncom; 
       printf("\n");  extern double *pcom,*xicom;
       for(l=0;l<=1;l++) {  extern double (*nrfunc)(double []); 
         for (j=1;j<=n;j++) {   
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  double f1dim(double x) 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  { 
         }    int j; 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    double f;
       }    double *xt; 
 #endif   
     xt=vector(1,ncom); 
     for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       free_vector(xit,1,n);    f=(*nrfunc)(xt); 
       free_vector(xits,1,n);    free_vector(xt,1,ncom); 
       free_vector(ptt,1,n);    return f; 
       free_vector(pt,1,n);  } 
       return;  
     }  /*****************brent *************************/
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     for (j=1;j<=n;j++) {  { 
       ptt[j]=2.0*p[j]-pt[j];    int iter; 
       xit[j]=p[j]-pt[j];    double a,b,d,etemp;
       pt[j]=p[j];    double fu,fv,fw,fx;
     }    double ftemp;
     fptt=(*func)(ptt);    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     if (fptt < fp) {    double e=0.0; 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);   
       if (t < 0.0) {    a=(ax < cx ? ax : cx); 
         linmin(p,xit,n,fret,func);    b=(ax > cx ? ax : cx); 
         for (j=1;j<=n;j++) {    x=w=v=bx; 
           xi[j][ibig]=xi[j][n];    fw=fv=fx=(*f)(x); 
           xi[j][n]=xit[j];    for (iter=1;iter<=ITMAX;iter++) { 
         }      xm=0.5*(a+b); 
 #ifdef DEBUG      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
         for(j=1;j<=n;j++)      printf(".");fflush(stdout);
           printf(" %.12e",xit[j]);      fprintf(ficlog,".");fflush(ficlog);
         printf("\n");  #ifdef DEBUG
 #endif      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);
       }      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)))) { */
   }  #endif
 }      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
         *xmin=x; 
 /**** Prevalence limit ****************/        return fx; 
       } 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)      ftemp=fu;
 {      if (fabs(e) > tol1) { 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit        r=(x-w)*(fx-fv); 
      matrix by transitions matrix until convergence is reached */        q=(x-v)*(fx-fw); 
         p=(x-v)*q-(x-w)*r; 
   int i, ii,j,k;        q=2.0*(q-r); 
   double min, max, maxmin, maxmax,sumnew=0.;        if (q > 0.0) p = -p; 
   double **matprod2();        q=fabs(q); 
   double **out, cov[NCOVMAX], **pmij();        etemp=e; 
   double **newm;        e=d; 
   double agefin, delaymax=50 ; /* Max number of years to converge */        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
           d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   for (ii=1;ii<=nlstate+ndeath;ii++)        else { 
     for (j=1;j<=nlstate+ndeath;j++){          d=p/q; 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);          u=x+d; 
     }          if (u-a < tol2 || b-u < tol2) 
             d=SIGN(tol1,xm-x); 
    cov[1]=1.;        } 
        } else { 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){      } 
     newm=savm;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     /* Covariates have to be included here again */      fu=(*f)(u); 
      cov[2]=agefin;      if (fu <= fx) { 
          if (u >= x) a=x; else b=x; 
       for (k=1; k<=cptcovn;k++) {        SHFT(v,w,x,u) 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];          SHFT(fv,fw,fx,fu) 
         /*      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]]);*/          } else { 
       }            if (u < x) a=u; else b=u; 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];            if (fu <= fw || w == x) { 
       for (k=1; k<=cptcovprod;k++)              v=w; 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];              w=u; 
               fv=fw; 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/              fw=fu; 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/            } else if (fu <= fv || v == x || v == w) { 
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/              v=u; 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);              fv=fu; 
             } 
     savm=oldm;          } 
     oldm=newm;    } 
     maxmax=0.;    nrerror("Too many iterations in brent"); 
     for(j=1;j<=nlstate;j++){    *xmin=x; 
       min=1.;    return fx; 
       max=0.;  } 
       for(i=1; i<=nlstate; i++) {  
         sumnew=0;  /****************** mnbrak ***********************/
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  
         prlim[i][j]= newm[i][j]/(1-sumnew);  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
         max=FMAX(max,prlim[i][j]);              double (*func)(double)) 
         min=FMIN(min,prlim[i][j]);  { 
       }    double ulim,u,r,q, dum;
       maxmin=max-min;    double fu; 
       maxmax=FMAX(maxmax,maxmin);   
     }    *fa=(*func)(*ax); 
     if(maxmax < ftolpl){    *fb=(*func)(*bx); 
       return prlim;    if (*fb > *fa) { 
     }      SHFT(dum,*ax,*bx,dum) 
   }        SHFT(dum,*fb,*fa,dum) 
 }        } 
     *cx=(*bx)+GOLD*(*bx-*ax); 
 /*************** transition probabilities ***************/    *fc=(*func)(*cx); 
     while (*fb > *fc) { 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )      r=(*bx-*ax)*(*fb-*fc); 
 {      q=(*bx-*cx)*(*fb-*fa); 
   double s1, s2;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   /*double t34;*/        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   int i,j,j1, nc, ii, jj;      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       if ((*bx-u)*(u-*cx) > 0.0) { 
     for(i=1; i<= nlstate; i++){        fu=(*func)(u); 
     for(j=1; j<i;j++){      } else if ((*cx-u)*(u-ulim) > 0.0) { 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        fu=(*func)(u); 
         /*s2 += param[i][j][nc]*cov[nc];*/        if (fu < *fc) { 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/            SHFT(*fb,*fc,fu,(*func)(u)) 
       }            } 
       ps[i][j]=s2;      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        u=ulim; 
     }        fu=(*func)(u); 
     for(j=i+1; j<=nlstate+ndeath;j++){      } else { 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        u=(*cx)+GOLD*(*cx-*bx); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        fu=(*func)(u); 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/      } 
       }      SHFT(*ax,*bx,*cx,u) 
       ps[i][j]=s2;        SHFT(*fa,*fb,*fc,fu) 
     }        } 
   }  } 
     /*ps[3][2]=1;*/  
   /*************** linmin ************************/
   for(i=1; i<= nlstate; i++){  
      s1=0;  int ncom; 
     for(j=1; j<i; j++)  double *pcom,*xicom;
       s1+=exp(ps[i][j]);  double (*nrfunc)(double []); 
     for(j=i+1; j<=nlstate+ndeath; j++)   
       s1+=exp(ps[i][j]);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     ps[i][i]=1./(s1+1.);  { 
     for(j=1; j<i; j++)    double brent(double ax, double bx, double cx, 
       ps[i][j]= exp(ps[i][j])*ps[i][i];                 double (*f)(double), double tol, double *xmin); 
     for(j=i+1; j<=nlstate+ndeath; j++)    double f1dim(double x); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */                double *fc, double (*func)(double)); 
   } /* end i */    int j; 
     double xx,xmin,bx,ax; 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    double fx,fb,fa;
     for(jj=1; jj<= nlstate+ndeath; jj++){   
       ps[ii][jj]=0;    ncom=n; 
       ps[ii][ii]=1;    pcom=vector(1,n); 
     }    xicom=vector(1,n); 
   }    nrfunc=func; 
     for (j=1;j<=n;j++) { 
       pcom[j]=p[j]; 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){      xicom[j]=xi[j]; 
     for(jj=1; jj<= nlstate+ndeath; jj++){    } 
      printf("%lf ",ps[ii][jj]);    ax=0.0; 
    }    xx=1.0; 
     printf("\n ");    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     }    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     printf("\n ");printf("%lf ",cov[2]);*/  #ifdef DEBUG
 /*    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   goto end;*/  #endif
     return ps;    for (j=1;j<=n;j++) { 
 }      xi[j] *= xmin; 
       p[j] += xi[j]; 
 /**************** Product of 2 matrices ******************/    } 
     free_vector(xicom,1,n); 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    free_vector(pcom,1,n); 
 {  } 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  char *asc_diff_time(long time_sec, char ascdiff[])
   /* in, b, out are matrice of pointers which should have been initialized  {
      before: only the contents of out is modified. The function returns    long sec_left, days, hours, minutes;
      a pointer to pointers identical to out */    days = (time_sec) / (60*60*24);
   long i, j, k;    sec_left = (time_sec) % (60*60*24);
   for(i=nrl; i<= nrh; i++)    hours = (sec_left) / (60*60) ;
     for(k=ncolol; k<=ncoloh; k++)    sec_left = (sec_left) %(60*60);
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    minutes = (sec_left) /60;
         out[i][k] +=in[i][j]*b[j][k];    sec_left = (sec_left) % (60);
     sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   return out;    return ascdiff;
 }  }
   
   /*************** powell ************************/
 /************* Higher Matrix Product ***************/  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
               double (*func)(double [])) 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  { 
 {    void linmin(double p[], double xi[], int n, double *fret, 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month                double (*func)(double [])); 
      duration (i.e. until    int i,ibig,j; 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    double del,t,*pt,*ptt,*xit;
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    double fp,fptt;
      (typically every 2 years instead of every month which is too big).    double *xits;
      Model is determined by parameters x and covariates have to be    int niterf, itmp;
      included manually here.  
     pt=vector(1,n); 
      */    ptt=vector(1,n); 
     xit=vector(1,n); 
   int i, j, d, h, k;    xits=vector(1,n); 
   double **out, cov[NCOVMAX];    *fret=(*func)(p); 
   double **newm;    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for (*iter=1;;++(*iter)) { 
   /* Hstepm could be zero and should return the unit matrix */      fp=(*fret); 
   for (i=1;i<=nlstate+ndeath;i++)      ibig=0; 
     for (j=1;j<=nlstate+ndeath;j++){      del=0.0; 
       oldm[i][j]=(i==j ? 1.0 : 0.0);      last_time=curr_time;
       po[i][j][0]=(i==j ? 1.0 : 0.0);      (void) gettimeofday(&curr_time,&tzp);
     }      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
   for(h=1; h <=nhstepm; h++){      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
     for(d=1; d <=hstepm; d++){      for (i=1;i<=n;i++) {
       newm=savm;        printf(" %d %.12f",i, p[i]);
       /* Covariates have to be included here again */        fprintf(ficlog," %d %.12lf",i, p[i]);
       cov[1]=1.;        fprintf(ficrespow," %.12lf", p[i]);
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      }
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      printf("\n");
       for (k=1; k<=cptcovage;k++)      fprintf(ficlog,"\n");
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      fprintf(ficrespow,"\n");fflush(ficrespow);
       for (k=1; k<=cptcovprod;k++)      if(*iter <=3){
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        tm = *localtime(&curr_time.tv_sec);
         strcpy(strcurr,asctime(&tmf));
   /*       asctime_r(&tm,strcurr); */
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        forecast_time=curr_time;
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        itmp = strlen(strcurr);
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,        if(strcurr[itmp-1]=='\n')
                    pmij(pmmij,cov,ncovmodel,x,nlstate));          strcurr[itmp-1]='\0';
       savm=oldm;        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       oldm=newm;        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){
     for(i=1; i<=nlstate+ndeath; i++)          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
       for(j=1;j<=nlstate+ndeath;j++) {          tmf = *localtime(&forecast_time.tv_sec);
         po[i][j][h]=newm[i][j];  /*      asctime_r(&tmf,strfor); */
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);          strcpy(strfor,asctime(&tmf));
          */          itmp = strlen(strfor);
       }          if(strfor[itmp-1]=='\n')
   } /* end h */          strfor[itmp-1]='\0';
   return po;          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
 }          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
         }
       }
 /*************** log-likelihood *************/      for (i=1;i<=n;i++) { 
 double func( double *x)        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
 {        fptt=(*fret); 
   int i, ii, j, k, mi, d, kk;  #ifdef DEBUG
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        printf("fret=%lf \n",*fret);
   double **out;        fprintf(ficlog,"fret=%lf \n",*fret);
   double sw; /* Sum of weights */  #endif
   double lli; /* Individual log likelihood */        printf("%d",i);fflush(stdout);
   long ipmx;        fprintf(ficlog,"%d",i);fflush(ficlog);
   /*extern weight */        linmin(p,xit,n,fret,func); 
   /* We are differentiating ll according to initial status */        if (fabs(fptt-(*fret)) > del) { 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/          del=fabs(fptt-(*fret)); 
   /*for(i=1;i<imx;i++)          ibig=i; 
     printf(" %d\n",s[4][i]);        } 
   */  #ifdef DEBUG
   cov[1]=1.;        printf("%d %.12e",i,(*fret));
         fprintf(ficlog,"%d %.12e",i,(*fret));
   for(k=1; k<=nlstate; k++) ll[k]=0.;        for (j=1;j<=n;j++) {
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];          printf(" x(%d)=%.12e",j,xit[j]);
     for(mi=1; mi<= wav[i]-1; mi++){          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       for (ii=1;ii<=nlstate+ndeath;ii++)        }
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        for(j=1;j<=n;j++) {
       for(d=0; d<dh[mi][i]; d++){          printf(" p=%.12e",p[j]);
         newm=savm;          fprintf(ficlog," p=%.12e",p[j]);
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;        }
         for (kk=1; kk<=cptcovage;kk++) {        printf("\n");
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        fprintf(ficlog,"\n");
         }  #endif
              } 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  #ifdef DEBUG
         savm=oldm;        int k[2],l;
         oldm=newm;        k[0]=1;
                k[1]=-1;
                printf("Max: %.12e",(*func)(p));
       } /* end mult */        fprintf(ficlog,"Max: %.12e",(*func)(p));
              for (j=1;j<=n;j++) {
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);          printf(" %.12e",p[j]);
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/          fprintf(ficlog," %.12e",p[j]);
       ipmx +=1;        }
       sw += weight[i];        printf("\n");
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        fprintf(ficlog,"\n");
     } /* end of wave */        for(l=0;l<=1;l++) {
   } /* end of individual */          for (j=1;j<=n;j++) {
             ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */          }
   return -l;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 }          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         }
   #endif
 /*********** Maximum Likelihood Estimation ***************/  
   
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        free_vector(xit,1,n); 
 {        free_vector(xits,1,n); 
   int i,j, iter;        free_vector(ptt,1,n); 
   double **xi,*delti;        free_vector(pt,1,n); 
   double fret;        return; 
   xi=matrix(1,npar,1,npar);      } 
   for (i=1;i<=npar;i++)      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     for (j=1;j<=npar;j++)      for (j=1;j<=n;j++) { 
       xi[i][j]=(i==j ? 1.0 : 0.0);        ptt[j]=2.0*p[j]-pt[j]; 
   printf("Powell\n");        xit[j]=p[j]-pt[j]; 
   powell(p,xi,npar,ftol,&iter,&fret,func);        pt[j]=p[j]; 
       } 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));      fptt=(*func)(ptt); 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      if (fptt < fp) { 
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
 }        if (t < 0.0) { 
           linmin(p,xit,n,fret,func); 
 /**** Computes Hessian and covariance matrix ***/          for (j=1;j<=n;j++) { 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))            xi[j][ibig]=xi[j][n]; 
 {            xi[j][n]=xit[j]; 
   double  **a,**y,*x,pd;          }
   double **hess;  #ifdef DEBUG
   int i, j,jk;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   int *indx;          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++){
   double hessii(double p[], double delta, int theta, double delti[]);            printf(" %.12e",xit[j]);
   double hessij(double p[], double delti[], int i, int j);            fprintf(ficlog," %.12e",xit[j]);
   void lubksb(double **a, int npar, int *indx, double b[]) ;          }
   void ludcmp(double **a, int npar, int *indx, double *d) ;          printf("\n");
           fprintf(ficlog,"\n");
   hess=matrix(1,npar,1,npar);  #endif
         }
   printf("\nCalculation of the hessian matrix. Wait...\n");      } 
   for (i=1;i<=npar;i++){    } 
     printf("%d",i);fflush(stdout);  } 
     hess[i][i]=hessii(p,ftolhess,i,delti);  
     /*printf(" %f ",p[i]);*/  /**** Prevalence limit (stable prevalence)  ****************/
     /*printf(" %lf ",hess[i][i]);*/  
   }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
    {
   for (i=1;i<=npar;i++) {    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     for (j=1;j<=npar;j++)  {       matrix by transitions matrix until convergence is reached */
       if (j>i) {  
         printf(".%d%d",i,j);fflush(stdout);    int i, ii,j,k;
         hess[i][j]=hessij(p,delti,i,j);    double min, max, maxmin, maxmax,sumnew=0.;
         hess[j][i]=hess[i][j];        double **matprod2();
         /*printf(" %lf ",hess[i][j]);*/    double **out, cov[NCOVMAX], **pmij();
       }    double **newm;
     }    double agefin, delaymax=50 ; /* Max number of years to converge */
   }  
   printf("\n");    for (ii=1;ii<=nlstate+ndeath;ii++)
       for (j=1;j<=nlstate+ndeath;j++){
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
        }
   a=matrix(1,npar,1,npar);  
   y=matrix(1,npar,1,npar);     cov[1]=1.;
   x=vector(1,npar);   
   indx=ivector(1,npar);   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   for (i=1;i<=npar;i++)    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];      newm=savm;
   ludcmp(a,npar,indx,&pd);      /* Covariates have to be included here again */
        cov[2]=agefin;
   for (j=1;j<=npar;j++) {    
     for (i=1;i<=npar;i++) x[i]=0;        for (k=1; k<=cptcovn;k++) {
     x[j]=1;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     lubksb(a,npar,indx,x);          /*      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++){        }
       matcov[i][j]=x[i];        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]]];
   
   printf("\n#Hessian matrix#\n");        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   for (i=1;i<=npar;i++) {        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     for (j=1;j<=npar;j++) {        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       printf("%.3e ",hess[i][j]);      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
     }  
     printf("\n");      savm=oldm;
   }      oldm=newm;
       maxmax=0.;
   /* Recompute Inverse */      for(j=1;j<=nlstate;j++){
   for (i=1;i<=npar;i++)        min=1.;
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        max=0.;
   ludcmp(a,npar,indx,&pd);        for(i=1; i<=nlstate; i++) {
           sumnew=0;
   /*  printf("\n#Hessian matrix recomputed#\n");          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
           prlim[i][j]= newm[i][j]/(1-sumnew);
   for (j=1;j<=npar;j++) {          max=FMAX(max,prlim[i][j]);
     for (i=1;i<=npar;i++) x[i]=0;          min=FMIN(min,prlim[i][j]);
     x[j]=1;        }
     lubksb(a,npar,indx,x);        maxmin=max-min;
     for (i=1;i<=npar;i++){        maxmax=FMAX(maxmax,maxmin);
       y[i][j]=x[i];      }
       printf("%.3e ",y[i][j]);      if(maxmax < ftolpl){
     }        return prlim;
     printf("\n");      }
   }    }
   */  }
   
   free_matrix(a,1,npar,1,npar);  /*************** transition probabilities ***************/ 
   free_matrix(y,1,npar,1,npar);  
   free_vector(x,1,npar);  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   free_ivector(indx,1,npar);  {
   free_matrix(hess,1,npar,1,npar);    double s1, s2;
     /*double t34;*/
     int i,j,j1, nc, ii, jj;
 }  
       for(i=1; i<= nlstate; i++){
 /*************** hessian matrix ****************/      for(j=1; j<i;j++){
 double hessii( double x[], double delta, int theta, double delti[])        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
 {          /*s2 += param[i][j][nc]*cov[nc];*/
   int i;          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   int l=1, lmax=20;          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
   double k1,k2;        }
   double p2[NPARMAX+1];        ps[i][j]=s2;
   double res;        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      }
   double fx;      for(j=i+1; j<=nlstate+ndeath;j++){
   int k=0,kmax=10;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   double l1;          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);*/
   fx=func(x);        }
   for (i=1;i<=npar;i++) p2[i]=x[i];        ps[i][j]=s2;
   for(l=0 ; l <=lmax; l++){      }
     l1=pow(10,l);    }
     delts=delt;      /*ps[3][2]=1;*/
     for(k=1 ; k <kmax; k=k+1){  
       delt = delta*(l1*k);    for(i=1; i<= nlstate; i++){
       p2[theta]=x[theta] +delt;       s1=0;
       k1=func(p2)-fx;      for(j=1; j<i; j++)
       p2[theta]=x[theta]-delt;        s1+=exp(ps[i][j]);
       k2=func(p2)-fx;      for(j=i+1; j<=nlstate+ndeath; j++)
       /*res= (k1-2.0*fx+k2)/delt/delt; */        s1+=exp(ps[i][j]);
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */      ps[i][i]=1./(s1+1.);
            for(j=1; j<i; j++)
 #ifdef DEBUG        ps[i][j]= exp(ps[i][j])*ps[i][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);      for(j=i+1; j<=nlstate+ndeath; j++)
 #endif        ps[i][j]= exp(ps[i][j])*ps[i][i];
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){    } /* end i */
         k=kmax;  
       }    for(ii=nlstate+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.;        ps[ii][jj]=0;
       }        ps[ii][ii]=1;
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      }
         delts=delt;    }
       }  
     }  
   }    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   delti[theta]=delts;      for(jj=1; jj<= nlstate+ndeath; jj++){
   return res;       printf("%lf ",ps[ii][jj]);
       }
 }      printf("\n ");
       }
 double hessij( double x[], double delti[], int thetai,int thetaj)      printf("\n ");printf("%lf ",cov[2]);*/
 {  /*
   int i;    for(i=1; i<= npar; i++) printf("%f ",x[i]);
   int l=1, l1, lmax=20;    goto end;*/
   double k1,k2,k3,k4,res,fx;      return ps;
   double p2[NPARMAX+1];  }
   int k;  
   /**************** Product of 2 matrices ******************/
   fx=func(x);  
   for (k=1; k<=2; k++) {  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
     for (i=1;i<=npar;i++) p2[i]=x[i];  {
     p2[thetai]=x[thetai]+delti[thetai]/k;    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     k1=func(p2)-fx;    /* in, b, out are matrice of pointers which should have been initialized 
         before: only the contents of out is modified. The function returns
     p2[thetai]=x[thetai]+delti[thetai]/k;       a pointer to pointers identical to out */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    long i, j, k;
     k2=func(p2)-fx;    for(i=nrl; i<= nrh; 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];
     k3=func(p2)-fx;  
      return out;
     p2[thetai]=x[thetai]-delti[thetai]/k;  }
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k4=func(p2)-fx;  
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  /************* Higher Matrix Product ***************/
 #ifdef DEBUG  
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
 #endif  {
   }    /* Computes the transition matrix starting at age 'age' over 
   return res;       'nhstepm*hstepm*stepm' months (i.e. until
 }       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
        nhstepm*hstepm matrices. 
 /************** Inverse of matrix **************/       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
 void ludcmp(double **a, int n, int *indx, double *d)       (typically every 2 years instead of every month which is too big 
 {       for the memory).
   int i,imax,j,k;       Model is determined by parameters x and covariates have to be 
   double big,dum,sum,temp;       included manually here. 
   double *vv;  
         */
   vv=vector(1,n);  
   *d=1.0;    int i, j, d, h, k;
   for (i=1;i<=n;i++) {    double **out, cov[NCOVMAX];
     big=0.0;    double **newm;
     for (j=1;j<=n;j++)  
       if ((temp=fabs(a[i][j])) > big) big=temp;    /* Hstepm could be zero and should return the unit matrix */
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    for (i=1;i<=nlstate+ndeath;i++)
     vv[i]=1.0/big;      for (j=1;j<=nlstate+ndeath;j++){
   }        oldm[i][j]=(i==j ? 1.0 : 0.0);
   for (j=1;j<=n;j++) {        po[i][j][0]=(i==j ? 1.0 : 0.0);
     for (i=1;i<j;i++) {      }
       sum=a[i][j];    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];    for(h=1; h <=nhstepm; h++){
       a[i][j]=sum;      for(d=1; d <=hstepm; d++){
     }        newm=savm;
     big=0.0;        /* Covariates have to be included here again */
     for (i=j;i<=n;i++) {        cov[1]=1.;
       sum=a[i][j];        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
       for (k=1;k<j;k++)        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         sum -= a[i][k]*a[k][j];        for (k=1; k<=cptcovage;k++)
       a[i][j]=sum;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       if ( (dum=vv[i]*fabs(sum)) >= big) {        for (k=1; k<=cptcovprod;k++)
         big=dum;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         imax=i;  
       }  
     }        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
     if (j != imax) {        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
       for (k=1;k<=n;k++) {        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
         dum=a[imax][k];                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         a[imax][k]=a[j][k];        savm=oldm;
         a[j][k]=dum;        oldm=newm;
       }      }
       *d = -(*d);      for(i=1; i<=nlstate+ndeath; i++)
       vv[imax]=vv[j];        for(j=1;j<=nlstate+ndeath;j++) {
     }          po[i][j][h]=newm[i][j];
     indx[j]=imax;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
     if (a[j][j] == 0.0) a[j][j]=TINY;           */
     if (j != n) {        }
       dum=1.0/(a[j][j]);    } /* end h */
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    return po;
     }  }
   }  
   free_vector(vv,1,n);  /* Doesn't work */  
 ;  /*************** log-likelihood *************/
 }  double func( double *x)
   {
 void lubksb(double **a, int n, int *indx, double b[])    int i, ii, j, k, mi, d, kk;
 {    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   int i,ii=0,ip,j;    double **out;
   double sum;    double sw; /* Sum of weights */
      double lli; /* Individual log likelihood */
   for (i=1;i<=n;i++) {    int s1, s2;
     ip=indx[i];    double bbh, survp;
     sum=b[ip];    long ipmx;
     b[ip]=b[i];    /*extern weight */
     if (ii)    /* We are differentiating ll according to initial status */
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     else if (sum) ii=i;    /*for(i=1;i<imx;i++) 
     b[i]=sum;      printf(" %d\n",s[4][i]);
   }    */
   for (i=n;i>=1;i--) {    cov[1]=1.;
     sum=b[i];  
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];    for(k=1; k<=nlstate; k++) ll[k]=0.;
     b[i]=sum/a[i][i];  
   }    if(mle==1){
 }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 /************ Frequencies ********************/        for(mi=1; mi<= wav[i]-1; mi++){
 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 (ii=1;ii<=nlstate+ndeath;ii++)
 {  /* Some frequencies */            for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double ***freq; /* Frequencies */            }
   double *pp;          for(d=0; d<dh[mi][i]; d++){
   double pos, k2, dateintsum=0,k2cpt=0;            newm=savm;
   FILE *ficresp;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   char fileresp[FILENAMELENGTH];            for (kk=1; kk<=cptcovage;kk++) {
                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   pp=vector(1,nlstate);            }
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   strcpy(fileresp,"p");                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   strcat(fileresp,fileres);            savm=oldm;
   if((ficresp=fopen(fileresp,"w"))==NULL) {            oldm=newm;
     printf("Problem with prevalence resultfile: %s\n", fileresp);          } /* end mult */
     exit(0);        
   }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          /* But now since version 0.9 we anticipate for bias and large stepm.
   j1=0;           * If stepm is larger than one month (smallest stepm) and if the exact delay 
             * (in months) between two waves is not a multiple of stepm, we rounded to 
   j=cptcoveff;           * the nearest (and in case of equal distance, to the lowest) interval but now
   if (cptcovn<1) {j=1;ncodemax[1]=1;}           * we keep into memory the bias bh[mi][i] and also the previous matrix product
             * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   for(k1=1; k1<=j;k1++){           * probability in order to take into account the bias as a fraction of the way
     for(i1=1; i1<=ncodemax[k1];i1++){           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
       j1++;           * -stepm/2 to stepm/2 .
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);           * For stepm=1 the results are the same as for previous versions of Imach.
         scanf("%d", i);*/           * For stepm > 1 the results are less biased than in previous versions. 
       for (i=-1; i<=nlstate+ndeath; i++)             */
         for (jk=-1; jk<=nlstate+ndeath; jk++)            s1=s[mw[mi][i]][i];
           for(m=agemin; m <= agemax+3; m++)          s2=s[mw[mi+1][i]][i];
             freq[i][jk][m]=0;          bbh=(double)bh[mi][i]/(double)stepm; 
                /* bias is positive if real duration
       dateintsum=0;           * is higher than the multiple of stepm and negative otherwise.
       k2cpt=0;           */
       for (i=1; i<=imx; 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]));*/
         bool=1;          if( s2 > nlstate){ 
         if  (cptcovn>0) {            /* i.e. if s2 is a death state and if the date of death is known then the contribution
           for (z1=1; z1<=cptcoveff; z1++)               to the likelihood is the probability to die between last step unit time and current 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])               step unit time, which is also the differences between probability to die before dh 
               bool=0;               and probability to die before dh-stepm . 
         }               In version up to 0.92 likelihood was computed
         if (bool==1) {          as if date of death was unknown. Death was treated as any other
           for(m=firstpass; m<=lastpass; m++){          health state: the date of the interview describes the actual state
             k2=anint[m][i]+(mint[m][i]/12.);          and not the date of a change in health state. The former idea was
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          to consider that at each interview the state was recorded
               if(agev[m][i]==0) agev[m][i]=agemax+1;          (healthy, disable or death) and IMaCh was corrected; but when we
               if(agev[m][i]==1) agev[m][i]=agemax+2;          introduced the exact date of death then we should have modified
               if (m<lastpass) {          the contribution of an exact death to the likelihood. This new
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          contribution is smaller and very dependent of the step unit
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          stepm. It is no more the probability to die between last interview
               }          and month of death but the probability to survive from last
                        interview up to one month before death multiplied by the
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {          probability to die within a month. Thanks to Chris
                 dateintsum=dateintsum+k2;          Jackson for correcting this bug.  Former versions increased
                 k2cpt++;          mortality artificially. The bad side is that we add another loop
               }          which slows down the processing. The difference can be up to 10%
             }          lower mortality.
           }            */
         }            lli=log(out[s1][s2] - savm[s1][s2]);
       }          }else{
                    lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
           } 
       if  (cptcovn>0) {          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         fprintf(ficresp, "\n#********** Variable ");          /*if(lli ==000.0)*/
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
         fprintf(ficresp, "**********\n#");          ipmx +=1;
       }          sw += weight[i];
       for(i=1; i<=nlstate;i++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        } /* end of wave */
       fprintf(ficresp, "\n");      } /* end of individual */
          }  else if(mle==2){
       for(i=(int)agemin; i <= (int)agemax+3; i++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         if(i==(int)agemax+3)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           printf("Total");        for(mi=1; mi<= wav[i]-1; mi++){
         else          for (ii=1;ii<=nlstate+ndeath;ii++)
           printf("Age %d", i);            for (j=1;j<=nlstate+ndeath;j++){
         for(jk=1; jk <=nlstate ; jk++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             pp[jk] += freq[jk][m][i];            }
         }          for(d=0; d<=dh[mi][i]; d++){
         for(jk=1; jk <=nlstate ; jk++){            newm=savm;
           for(m=-1, pos=0; m <=0 ; m++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             pos += freq[jk][m][i];            for (kk=1; kk<=cptcovage;kk++) {
           if(pp[jk]>=1.e-10)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);            }
           else            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         }            savm=oldm;
             oldm=newm;
         for(jk=1; jk <=nlstate ; jk++){          } /* end mult */
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        
             pp[jk] += freq[jk][m][i];          s1=s[mw[mi][i]][i];
         }          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
         for(jk=1,pos=0; jk <=nlstate ; 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 */
           pos += pp[jk];          ipmx +=1;
         for(jk=1; jk <=nlstate ; jk++){          sw += weight[i];
           if(pos>=1.e-5)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        } /* end of wave */
           else      } /* end of individual */
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    }  else if(mle==3){  /* exponential inter-extrapolation */
           if( i <= (int) agemax){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             if(pos>=1.e-5){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        for(mi=1; mi<= wav[i]-1; mi++){
               probs[i][jk][j1]= pp[jk]/pos;          for (ii=1;ii<=nlstate+ndeath;ii++)
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/            for (j=1;j<=nlstate+ndeath;j++){
             }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             else              savm[ii][j]=(ii==j ? 1.0 : 0.0);
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);            }
           }          for(d=0; d<dh[mi][i]; d++){
         }            newm=savm;
                    cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         for(jk=-1; jk <=nlstate+ndeath; jk++)            for (kk=1; kk<=cptcovage;kk++) {
           for(m=-1; m <=nlstate+ndeath; m++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);            }
         if(i <= (int) agemax)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           fprintf(ficresp,"\n");                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         printf("\n");            savm=oldm;
       }            oldm=newm;
     }          } /* end mult */
   }        
   dateintmean=dateintsum/k2cpt;          s1=s[mw[mi][i]][i];
            s2=s[mw[mi+1][i]][i];
   fclose(ficresp);          bbh=(double)bh[mi][i]/(double)stepm; 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          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 */
   free_vector(pp,1,nlstate);          ipmx +=1;
            sw += weight[i];
   /* End of Freq */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 }        } /* end of wave */
       } /* end of individual */
 /************ Prevalence ********************/    }else if (mle==4){  /* ml=4 no inter-extrapolation */
 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 (i=1,ipmx=0, sw=0.; i<=imx; i++){
 {  /* Some frequencies */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          for(mi=1; mi<= wav[i]-1; mi++){
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          for (ii=1;ii<=nlstate+ndeath;ii++)
   double ***freq; /* Frequencies */            for (j=1;j<=nlstate+ndeath;j++){
   double *pp;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double pos, k2;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
   pp=vector(1,nlstate);          for(d=0; d<dh[mi][i]; d++){
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);            for (kk=1; kk<=cptcovage;kk++) {
   j1=0;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
              }
   j=cptcoveff;          
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                           1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
  for(k1=1; k1<=j;k1++){            savm=oldm;
     for(i1=1; i1<=ncodemax[k1];i1++){            oldm=newm;
       j1++;          } /* end mult */
          
       for (i=-1; i<=nlstate+ndeath; i++)            s1=s[mw[mi][i]][i];
         for (jk=-1; jk<=nlstate+ndeath; jk++)            s2=s[mw[mi+1][i]][i];
           for(m=agemin; m <= agemax+3; m++)          if( s2 > nlstate){ 
             freq[i][jk][m]=0;            lli=log(out[s1][s2] - savm[s1][s2]);
                }else{
       for (i=1; i<=imx; i++) {            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         bool=1;          }
         if  (cptcovn>0) {          ipmx +=1;
           for (z1=1; z1<=cptcoveff; z1++)          sw += weight[i];
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
               bool=0;  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
         }        } /* end of wave */
         if (bool==1) {      } /* end of individual */
           for(m=firstpass; m<=lastpass; m++){    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
             k2=anint[m][i]+(mint[m][i]/12.);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
               if(agev[m][i]==0) agev[m][i]=agemax+1;        for(mi=1; mi<= wav[i]-1; mi++){
               if(agev[m][i]==1) agev[m][i]=agemax+2;          for (ii=1;ii<=nlstate+ndeath;ii++)
               if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];            for (j=1;j<=nlstate+ndeath;j++){
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           }            }
         }          for(d=0; d<dh[mi][i]; d++){
       }            newm=savm;
         for(i=(int)agemin; i <= (int)agemax+3; i++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for(jk=1; jk <=nlstate ; jk++){            for (kk=1; kk<=cptcovage;kk++) {
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
               pp[jk] += freq[jk][m][i];            }
           }          
           for(jk=1; jk <=nlstate ; jk++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             for(m=-1, pos=0; m <=0 ; m++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             pos += freq[jk][m][i];            savm=oldm;
         }            oldm=newm;
                  } /* end mult */
          for(jk=1; jk <=nlstate ; jk++){        
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          s1=s[mw[mi][i]][i];
              pp[jk] += freq[jk][m][i];          s2=s[mw[mi+1][i]][i];
          }          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
                    ipmx +=1;
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          for(jk=1; jk <=nlstate ; jk++){                    /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
            if( i <= (int) agemax){        } /* end of wave */
              if(pos>=1.e-5){      } /* end of individual */
                probs[i][jk][j1]= pp[jk]/pos;    } /* End of if */
              }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
            }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
          }    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
              return -l;
         }  }
     }  
   }  /*************** log-likelihood *************/
    double funcone( double *x)
    {
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    /* Same as likeli but slower because of a lot of printf and if */
   free_vector(pp,1,nlstate);    int i, ii, j, k, mi, d, kk;
      double l, ll[NLSTATEMAX], cov[NCOVMAX];
 }  /* End of Freq */    double **out;
     double lli; /* Individual log likelihood */
 /************* Waves Concatenation ***************/    double llt;
     int s1, s2;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    double bbh, survp;
 {    /*extern weight */
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    /* We are differentiating ll according to initial status */
      Death is a valid wave (if date is known).    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i    /*for(i=1;i<imx;i++) 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]      printf(" %d\n",s[4][i]);
      and mw[mi+1][i]. dh depends on stepm.    */
      */    cov[1]=1.;
   
   int i, mi, m;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  
      double sum=0., jmean=0.;*/    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int j, k=0,jk, ju, jl;      for(mi=1; mi<= wav[i]-1; mi++){
   double sum=0.;        for (ii=1;ii<=nlstate+ndeath;ii++)
   jmin=1e+5;          for (j=1;j<=nlstate+ndeath;j++){
   jmax=-1;            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   jmean=0.;            savm[ii][j]=(ii==j ? 1.0 : 0.0);
   for(i=1; i<=imx; i++){          }
     mi=0;        for(d=0; d<dh[mi][i]; d++){
     m=firstpass;          newm=savm;
     while(s[m][i] <= nlstate){          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       if(s[m][i]>=1)          for (kk=1; kk<=cptcovage;kk++) {
         mw[++mi][i]=m;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       if(m >=lastpass)          }
         break;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       else                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         m++;          savm=oldm;
     }/* end while */          oldm=newm;
     if (s[m][i] > nlstate){        } /* end mult */
       mi++;     /* Death is another wave */        
       /* if(mi==0)  never been interviewed correctly before death */        s1=s[mw[mi][i]][i];
          /* Only death is a correct wave */        s2=s[mw[mi+1][i]][i];
       mw[mi][i]=m;        bbh=(double)bh[mi][i]/(double)stepm; 
     }        /* bias is positive if real duration
          * is higher than the multiple of stepm and negative otherwise.
     wav[i]=mi;         */
     if(mi==0)        if( s2 > nlstate && (mle <5) ){  /* Jackson */
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          lli=log(out[s1][s2] - savm[s1][s2]);
   }        } else if (mle==1){
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   for(i=1; i<=imx; i++){        } else if(mle==2){
     for(mi=1; mi<wav[i];mi++){          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
       if (stepm <=0)        } else if(mle==3){  /* exponential inter-extrapolation */
         dh[mi][i]=1;          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
       else{        } else if (mle==4){  /* mle=4 no inter-extrapolation */
         if (s[mw[mi+1][i]][i] > nlstate) {          lli=log(out[s1][s2]); /* Original formula */
           if (agedc[i] < 2*AGESUP) {        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          lli=log(out[s1][s2]); /* Original formula */
           if(j==0) j=1;  /* Survives at least one month after exam */        } /* End of if */
           k=k+1;        ipmx +=1;
           if (j >= jmax) jmax=j;        sw += weight[i];
           if (j <= jmin) jmin=j;        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           sum=sum+j;  /*       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 (j<0) printf("j=%d num=%d \n",j,i); */        if(globpr){
           }          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
         }   %10.6f %10.6f %10.6f ", \
         else{                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
           k=k+1;          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
           if (j >= jmax) jmax=j;            llt +=ll[k]*gipmx/gsw;
           else if (j <= jmin)jmin=j;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          }
           sum=sum+j;          fprintf(ficresilk," %10.6f\n", -llt);
         }        }
         jk= j/stepm;      } /* end of wave */
         jl= j -jk*stepm;    } /* end of individual */
         ju= j -(jk+1)*stepm;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         if(jl <= -ju)    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
           dh[mi][i]=jk;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         else    if(globpr==0){ /* First time we count the contributions and weights */
           dh[mi][i]=jk+1;      gipmx=ipmx;
         if(dh[mi][i]==0)      gsw=sw;
           dh[mi][i]=1; /* At least one step */    }
       }    return -l;
     }  }
   }  
   jmean=sum/k;  
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);  /*************** function likelione ***********/
  }  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
 /*********** Tricode ****************************/  {
 void tricode(int *Tvar, int **nbcode, int imx)    /* This routine should help understanding what is done with 
 {       the selection of individuals/waves and
   int Ndum[20],ij=1, k, j, i;       to check the exact contribution to the likelihood.
   int cptcode=0;       Plotting could be done.
   cptcoveff=0;     */
      int k;
   for (k=0; k<19; k++) Ndum[k]=0;  
   for (k=1; k<=7; k++) ncodemax[k]=0;    if(*globpri !=0){ /* Just counts and sums, no printings */
       strcpy(fileresilk,"ilk"); 
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {      strcat(fileresilk,fileres);
     for (i=1; i<=imx; i++) {      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
       ij=(int)(covar[Tvar[j]][i]);        printf("Problem with resultfile: %s\n", fileresilk);
       Ndum[ij]++;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/      }
       if (ij > cptcode) cptcode=ij;      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
     }      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     for (i=0; i<=cptcode; i++) {      for(k=1; k<=nlstate; k++) 
       if(Ndum[i]!=0) ncodemax[j]++;        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
     }      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     ij=1;    }
   
     *fretone=(*funcone)(p);
     for (i=1; i<=ncodemax[j]; i++) {    if(*globpri !=0){
       for (k=0; k<=19; k++) {      fclose(ficresilk);
         if (Ndum[k] != 0) {      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
           nbcode[Tvar[j]][ij]=k;      fflush(fichtm); 
           /*     printf("nbcodeaaaaaaaaaaa=%d Tvar[j]=%d ij=%d j=%d",nbcode[Tvar[j]][ij],Tvar[j],ij,j);*/    } 
           ij++;    return;
         }  }
         if (ij > ncodemax[j]) break;  
       }    
     }  /*********** Maximum Likelihood Estimation ***************/
   }    
   void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
  for (k=0; k<19; k++) Ndum[k]=0;  {
     int i,j, iter;
  for (i=1; i<=ncovmodel-2; i++) {    double **xi;
       ij=Tvar[i];    double fret;
       Ndum[ij]++;    double fretone; /* Only one call to likelihood */
     }    char filerespow[FILENAMELENGTH];
     xi=matrix(1,npar,1,npar);
  ij=1;    for (i=1;i<=npar;i++)
  for (i=1; i<=10; i++) {      for (j=1;j<=npar;j++)
    if((Ndum[i]!=0) && (i<=ncovcol)){        xi[i][j]=(i==j ? 1.0 : 0.0);
      Tvaraff[ij]=i;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
      ij++;    strcpy(filerespow,"pow"); 
    }    strcat(filerespow,fileres);
  }    if((ficrespow=fopen(filerespow,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", filerespow);
     cptcoveff=ij-1;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
 }    }
     fprintf(ficrespow,"# Powell\n# iter -2*LL");
 /*********** Health Expectancies ****************/    for (i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate+ndeath;j++)
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm)        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
 {    fprintf(ficrespow,"\n");
   /* Health expectancies */  
   int i, j, nhstepm, hstepm, h, nstepm;    powell(p,xi,npar,ftol,&iter,&fret,func);
   double age, agelim, hf;  
   double ***p3mat;    fclose(ficrespow);
      printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   fprintf(ficreseij,"# Health expectancies\n");    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   fprintf(ficreseij,"# Age");    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=nlstate;j++)  }
       fprintf(ficreseij," %1d-%1d",i,j);  
   fprintf(ficreseij,"\n");  /**** Computes Hessian and covariance matrix ***/
   void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   if(estepm < stepm){  {
     printf ("Problem %d lower than %d\n",estepm, stepm);    double  **a,**y,*x,pd;
   }    double **hess;
   else  hstepm=estepm;      int i, j,jk;
   /* We compute the life expectancy from trapezoids spaced every estepm months    int *indx;
    * This is mainly to measure the difference between two models: for example  
    * if stepm=24 months pijx are given only every 2 years and by summing them    double hessii(double p[], double delta, int theta, double delti[]);
    * we are calculating an estimate of the Life Expectancy assuming a linear    double hessij(double p[], double delti[], int i, int j);
    * progression inbetween and thus overestimating or underestimating according    void lubksb(double **a, int npar, int *indx, double b[]) ;
    * to the curvature of the survival function. If, for the same date, we    void ludcmp(double **a, int npar, int *indx, double *d) ;
    * estimate the model with stepm=1 month, we can keep estepm to 24 months  
    * to compare the new estimate of Life expectancy with the same linear    hess=matrix(1,npar,1,npar);
    * hypothesis. A more precise result, taking into account a more precise  
    * curvature will be obtained if estepm is as small as stepm. */    printf("\nCalculation of the hessian matrix. Wait...\n");
     fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   /* 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.      printf("%d",i);fflush(stdout);
      nhstepm is the number of hstepm from age to agelim      fprintf(ficlog,"%d",i);fflush(ficlog);
      nstepm is the number of stepm from age to agelin.      hess[i][i]=hessii(p,ftolhess,i,delti);
      Look at hpijx to understand the reason of that which relies in memory size      /*printf(" %f ",p[i]);*/
      and note for a fixed period like estepm months */      /*printf(" %lf ",hess[i][i]);*/
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    }
      survival function given by stepm (the optimization length). Unfortunately it    
      means that if the survival funtion is printed only each two years of age and if    for (i=1;i<=npar;i++) {
      you sum them up and add 1 year (area under the trapezoids) you won't get the same      for (j=1;j<=npar;j++)  {
      results. So we changed our mind and took the option of the best precision.        if (j>i) { 
   */          printf(".%d%d",i,j);fflush(stdout);
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
           hess[i][j]=hessij(p,delti,i,j);
   agelim=AGESUP;          hess[j][i]=hess[i][j];    
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          /*printf(" %lf ",hess[i][j]);*/
     /* nhstepm age range expressed in number of stepm */        }
     nstepm=(int) rint((agelim-age)*YEARM/stepm);      }
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    }
     /* if (stepm >= YEARM) hstepm=1;*/    printf("\n");
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    fprintf(ficlog,"\n");
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    a=matrix(1,npar,1,npar);
     for(i=1; i<=nlstate;i++)    y=matrix(1,npar,1,npar);
       for(j=1; j<=nlstate;j++)    x=vector(1,npar);
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    indx=ivector(1,npar);
           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]);*/      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
         }    ludcmp(a,npar,indx,&pd);
     fprintf(ficreseij,"%3.0f",age );  
     for(i=1; i<=nlstate;i++)    for (j=1;j<=npar;j++) {
       for(j=1; j<=nlstate;j++){      for (i=1;i<=npar;i++) x[i]=0;
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);      x[j]=1;
       }      lubksb(a,npar,indx,x);
     fprintf(ficreseij,"\n");      for (i=1;i<=npar;i++){ 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        matcov[i][j]=x[i];
   }      }
 }    }
   
 /************ Variance ******************/    printf("\n#Hessian matrix#\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)    fprintf(ficlog,"\n#Hessian matrix#\n");
 {    for (i=1;i<=npar;i++) { 
   /* Variance of health expectancies */      for (j=1;j<=npar;j++) { 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        printf("%.3e ",hess[i][j]);
   double **newm;        fprintf(ficlog,"%.3e ",hess[i][j]);
   double **dnewm,**doldm;      }
   int i, j, nhstepm, hstepm, h, nstepm ;      printf("\n");
   int k, cptcode;      fprintf(ficlog,"\n");
   double *xp;    }
   double **gp, **gm;  
   double ***gradg, ***trgradg;    /* Recompute Inverse */
   double ***p3mat;    for (i=1;i<=npar;i++)
   double age,agelim, hf;      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   int theta;    ludcmp(a,npar,indx,&pd);
   
    fprintf(ficresvij,"# Covariances of life expectancies\n");    /*  printf("\n#Hessian matrix recomputed#\n");
   fprintf(ficresvij,"# Age");  
   for(i=1; i<=nlstate;i++)    for (j=1;j<=npar;j++) {
     for(j=1; j<=nlstate;j++)      for (i=1;i<=npar;i++) x[i]=0;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      x[j]=1;
   fprintf(ficresvij,"\n");      lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
   xp=vector(1,npar);        y[i][j]=x[i];
   dnewm=matrix(1,nlstate,1,npar);        printf("%.3e ",y[i][j]);
   doldm=matrix(1,nlstate,1,nlstate);        fprintf(ficlog,"%.3e ",y[i][j]);
        }
   if(estepm < stepm){      printf("\n");
     printf ("Problem %d lower than %d\n",estepm, stepm);      fprintf(ficlog,"\n");
   }    }
   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.    free_matrix(a,1,npar,1,npar);
      nhstepm is the number of hstepm from age to agelim    free_matrix(y,1,npar,1,npar);
      nstepm is the number of stepm from age to agelin.    free_vector(x,1,npar);
      Look at hpijx to understand the reason of that which relies in memory size    free_ivector(indx,1,npar);
      and note for a fixed period like k years */    free_matrix(hess,1,npar,1,npar);
   /* 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  
      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.  /*************** hessian matrix ****************/
   */  double hessii( double x[], double delta, int theta, double delti[])
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */  {
   agelim = AGESUP;    int i;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    int l=1, lmax=20;
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    double k1,k2;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    double p2[NPARMAX+1];
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double res;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     gp=matrix(0,nhstepm,1,nlstate);    double fx;
     gm=matrix(0,nhstepm,1,nlstate);    int k=0,kmax=10;
     double l1;
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient */    fx=func(x);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    for (i=1;i<=npar;i++) p2[i]=x[i];
       }    for(l=0 ; l <=lmax; l++){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        l1=pow(10,l);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      delts=delt;
       for(k=1 ; k <kmax; k=k+1){
       if (popbased==1) {        delt = delta*(l1*k);
         for(i=1; i<=nlstate;i++)        p2[theta]=x[theta] +delt;
           prlim[i][i]=probs[(int)age][i][ij];        k1=func(p2)-fx;
       }        p2[theta]=x[theta]-delt;
          k2=func(p2)-fx;
       for(j=1; j<= nlstate; j++){        /*res= (k1-2.0*fx+k2)/delt/delt; */
         for(h=0; h<=nhstepm; h++){        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)        
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];  #ifdef DEBUG
         }        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
       }        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
       for(i=1; i<=npar; i++) /* Computes gradient */        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            k=kmax;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        }
          else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       if (popbased==1) {          k=kmax; l=lmax*10.;
         for(i=1; i<=nlstate;i++)        }
           prlim[i][i]=probs[(int)age][i][ij];        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
       }          delts=delt;
         }
       for(j=1; j<= nlstate; j++){      }
         for(h=0; h<=nhstepm; h++){    }
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    delti[theta]=delts;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    return res; 
         }    
       }  }
   
       for(j=1; j<= nlstate; j++)  double hessij( double x[], double delti[], int thetai,int thetaj)
         for(h=0; h<=nhstepm; h++){  {
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    int i;
         }    int l=1, l1, lmax=20;
     } /* End theta */    double k1,k2,k3,k4,res,fx;
     double p2[NPARMAX+1];
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    int k;
   
     for(h=0; h<=nhstepm; h++)    fx=func(x);
       for(j=1; j<=nlstate;j++)    for (k=1; k<=2; k++) {
         for(theta=1; theta <=npar; theta++)      for (i=1;i<=npar;i++) p2[i]=x[i];
           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. */      k1=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;
       k2=func(p2)-fx;
     for(h=0;h<=nhstepm;h++){    
       for(k=0;k<=nhstepm;k++){      p2[thetai]=x[thetai]-delti[thetai]/k;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      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] += doldm[i][j]*hf*hf;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       }      k4=func(p2)-fx;
     }      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   #ifdef DEBUG
     fprintf(ficresvij,"%.0f ",age );      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(i=1; i<=nlstate;i++)      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(j=1; j<=nlstate;j++){  #endif
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);    }
       }    return res;
     fprintf(ficresvij,"\n");  }
     free_matrix(gp,0,nhstepm,1,nlstate);  
     free_matrix(gm,0,nhstepm,1,nlstate);  /************** Inverse of matrix **************/
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);  void ludcmp(double **a, int n, int *indx, double *d) 
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);  { 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int i,imax,j,k; 
   } /* End age */    double big,dum,sum,temp; 
      double *vv; 
   free_vector(xp,1,npar);   
   free_matrix(doldm,1,nlstate,1,npar);    vv=vector(1,n); 
   free_matrix(dnewm,1,nlstate,1,nlstate);    *d=1.0; 
     for (i=1;i<=n;i++) { 
 }      big=0.0; 
       for (j=1;j<=n;j++) 
 /************ Variance of prevlim ******************/        if ((temp=fabs(a[i][j])) > big) big=temp; 
 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)      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
 {      vv[i]=1.0/big; 
   /* Variance of prevalence limit */    } 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    for (j=1;j<=n;j++) { 
   double **newm;      for (i=1;i<j;i++) { 
   double **dnewm,**doldm;        sum=a[i][j]; 
   int i, j, nhstepm, hstepm;        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   int k, cptcode;        a[i][j]=sum; 
   double *xp;      } 
   double *gp, *gm;      big=0.0; 
   double **gradg, **trgradg;      for (i=j;i<=n;i++) { 
   double age,agelim;        sum=a[i][j]; 
   int theta;        for (k=1;k<j;k++) 
              sum -= a[i][k]*a[k][j]; 
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");        a[i][j]=sum; 
   fprintf(ficresvpl,"# Age");        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   for(i=1; i<=nlstate;i++)          big=dum; 
       fprintf(ficresvpl," %1d-%1d",i,i);          imax=i; 
   fprintf(ficresvpl,"\n");        } 
       } 
   xp=vector(1,npar);      if (j != imax) { 
   dnewm=matrix(1,nlstate,1,npar);        for (k=1;k<=n;k++) { 
   doldm=matrix(1,nlstate,1,nlstate);          dum=a[imax][k]; 
            a[imax][k]=a[j][k]; 
   hstepm=1*YEARM; /* Every year of age */          a[j][k]=dum; 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        } 
   agelim = AGESUP;        *d = -(*d); 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        vv[imax]=vv[j]; 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      } 
     if (stepm >= YEARM) hstepm=1;      indx[j]=imax; 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      if (a[j][j] == 0.0) a[j][j]=TINY; 
     gradg=matrix(1,npar,1,nlstate);      if (j != n) { 
     gp=vector(1,nlstate);        dum=1.0/(a[j][j]); 
     gm=vector(1,nlstate);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       } 
     for(theta=1; theta <=npar; theta++){    } 
       for(i=1; i<=npar; i++){ /* Computes gradient */    free_vector(vv,1,n);  /* Doesn't work */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  ;
       }  } 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)  void lubksb(double **a, int n, int *indx, double b[]) 
         gp[i] = prlim[i][i];  { 
        int i,ii=0,ip,j; 
       for(i=1; i<=npar; i++) /* Computes gradient */    double sum; 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);   
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    for (i=1;i<=n;i++) { 
       for(i=1;i<=nlstate;i++)      ip=indx[i]; 
         gm[i] = prlim[i][i];      sum=b[ip]; 
       b[ip]=b[i]; 
       for(i=1;i<=nlstate;i++)      if (ii) 
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
     } /* End theta */      else if (sum) ii=i; 
       b[i]=sum; 
     trgradg =matrix(1,nlstate,1,npar);    } 
     for (i=n;i>=1;i--) { 
     for(j=1; j<=nlstate;j++)      sum=b[i]; 
       for(theta=1; theta <=npar; theta++)      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
         trgradg[j][theta]=gradg[theta][j];      b[i]=sum/a[i][i]; 
     } 
     for(i=1;i<=nlstate;i++)  } 
       varpl[i][(int)age] =0.;  
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);  /************ Frequencies ********************/
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);  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(i=1;i<=nlstate;i++)  {  /* Some frequencies */
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    
     int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     fprintf(ficresvpl,"%.0f ",age );    int first;
     for(i=1; i<=nlstate;i++)    double ***freq; /* Frequencies */
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    double *pp, **prop;
     fprintf(ficresvpl,"\n");    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     free_vector(gp,1,nlstate);    FILE *ficresp;
     free_vector(gm,1,nlstate);    char fileresp[FILENAMELENGTH];
     free_matrix(gradg,1,npar,1,nlstate);    
     free_matrix(trgradg,1,nlstate,1,npar);    pp=vector(1,nlstate);
   } /* End age */    prop=matrix(1,nlstate,iagemin,iagemax+3);
     strcpy(fileresp,"p");
   free_vector(xp,1,npar);    strcat(fileresp,fileres);
   free_matrix(doldm,1,nlstate,1,npar);    if((ficresp=fopen(fileresp,"w"))==NULL) {
   free_matrix(dnewm,1,nlstate,1,nlstate);      printf("Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
 }      exit(0);
     }
 /************ Variance of one-step probabilities  ******************/    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)    j1=0;
 {    
   int i, j;    j=cptcoveff;
   int k=0, cptcode;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   double **dnewm,**doldm;  
   double *xp;    first=1;
   double *gp, *gm;  
   double **gradg, **trgradg;    for(k1=1; k1<=j;k1++){
   double age,agelim, cov[NCOVMAX];      for(i1=1; i1<=ncodemax[k1];i1++){
   int theta;        j1++;
   char fileresprob[FILENAMELENGTH];        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           scanf("%d", i);*/
   strcpy(fileresprob,"prob");        for (i=-1; i<=nlstate+ndeath; i++)  
   strcat(fileresprob,fileres);          for (jk=-1; jk<=nlstate+ndeath; jk++)  
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {            for(m=iagemin; m <= iagemax+3; m++)
     printf("Problem with resultfile: %s\n", fileresprob);              freq[i][jk][m]=0;
   }  
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);      for (i=1; i<=nlstate; i++)  
          for(m=iagemin; m <= iagemax+3; m++)
           prop[i][m]=0;
   xp=vector(1,npar);        
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        dateintsum=0;
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));        k2cpt=0;
          for (i=1; i<=imx; i++) {
   cov[1]=1;          bool=1;
   for (age=bage; age<=fage; age ++){          if  (cptcovn>0) {
     cov[2]=age;            for (z1=1; z1<=cptcoveff; z1++) 
     gradg=matrix(1,npar,1,9);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     trgradg=matrix(1,9,1,npar);                bool=0;
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          }
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          if (bool==1){
                for(m=firstpass; m<=lastpass; m++){
     for(theta=1; theta <=npar; theta++){              k2=anint[m][i]+(mint[m][i]/12.);
       for(i=1; i<=npar; i++)              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
         xp[i] = x[i] + (i==theta ?delti[theta]:0);                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                      if(agev[m][i]==1) agev[m][i]=iagemax+2;
       pmij(pmmij,cov,ncovmodel,xp,nlstate);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
                    if (m<lastpass) {
       k=0;                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
       for(i=1; i<= (nlstate+ndeath); i++){                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
         for(j=1; j<=(nlstate+ndeath);j++){                }
            k=k+1;                
           gp[k]=pmmij[i][j];                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
         }                  dateintsum=dateintsum+k2;
       }                  k2cpt++;
                 }
       for(i=1; i<=npar; i++)                /*}*/
         xp[i] = x[i] - (i==theta ?delti[theta]:0);            }
              }
         }
       pmij(pmmij,cov,ncovmodel,xp,nlstate);         
       k=0;        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       for(i=1; i<=(nlstate+ndeath); i++){  
         for(j=1; j<=(nlstate+ndeath);j++){        if  (cptcovn>0) {
           k=k+1;          fprintf(ficresp, "\n#********** Variable "); 
           gm[k]=pmmij[i][j];          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         }          fprintf(ficresp, "**********\n#");
       }        }
              for(i=1; i<=nlstate;i++) 
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];          fprintf(ficresp, "\n");
     }        
         for(i=iagemin; i <= iagemax+3; i++){
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)          if(i==iagemax+3){
       for(theta=1; theta <=npar; theta++)            fprintf(ficlog,"Total");
       trgradg[j][theta]=gradg[theta][j];          }else{
              if(first==1){
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);              first=0;
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);              printf("See log file for details...\n");
             }
      pmij(pmmij,cov,ncovmodel,x,nlstate);            fprintf(ficlog,"Age %d", i);
           }
      k=0;          for(jk=1; jk <=nlstate ; jk++){
      for(i=1; i<=(nlstate+ndeath); i++){            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
        for(j=1; j<=(nlstate+ndeath);j++){              pp[jk] += freq[jk][m][i]; 
          k=k+1;          }
          gm[k]=pmmij[i][j];          for(jk=1; jk <=nlstate ; jk++){
         }            for(m=-1, pos=0; m <=0 ; m++)
      }              pos += freq[jk][m][i];
                  if(pp[jk]>=1.e-10){
      /*printf("\n%d ",(int)age);              if(first==1){
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                      }
               fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));            }else{
      }*/              if(first==1)
                 printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   fprintf(ficresprob,"\n%d ",(int)age);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             }
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);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++){
   }            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
               pp[jk] += freq[jk][m][i];
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));          }       
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            pos += pp[jk];
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            posprop += prop[jk][i];
 }          }
  free_vector(xp,1,npar);          for(jk=1; jk <=nlstate ; jk++){
 fclose(ficresprob);            if(pos>=1.e-5){
               if(first==1)
 }                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
               fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
 /******************* Printing html file ***********/            }else{
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \              if(first==1)
  int lastpass, int stepm, int weightopt, char model[],\                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\            }
  char version[], int popforecast, int estepm ){            if( i <= iagemax){
   int jj1, k1, i1, cpt;              if(pos>=1.e-5){
   FILE *fichtm;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   /*char optionfilehtm[FILENAMELENGTH];*/                /*probs[i][jk][j1]= pp[jk]/pos;*/
                 /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   strcpy(optionfilehtm,optionfile);              }
   strcat(optionfilehtm,".htm");              else
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     printf("Problem with %s \n",optionfilehtm), exit(0);            }
   }          }
           
  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n          for(jk=-1; jk <=nlstate+ndeath; jk++)
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n            for(m=-1; m <=nlstate+ndeath; m++)
 \n              if(freq[jk][m][i] !=0 ) {
 Total number of observations=%d <br>\n              if(first==1)
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
 <hr  size=\"2\" color=\"#EC5E5E\">                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
  <ul><li>Outputs files<br>\n              }
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n          if(i <= iagemax)
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n            fprintf(ficresp,"\n");
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n          if(first==1)
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n            printf("Others in log...\n");
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n          fprintf(ficlog,"\n");
  - 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,estepm,fileres,fileres);        }
       }
  fprintf(fichtm,"\n    }
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n    dateintmean=dateintsum/k2cpt; 
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n   
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n    fclose(ficresp);
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
     free_vector(pp,1,nlstate);
  if(popforecast==1) fprintf(fichtm,"\n    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n    /* End of Freq */
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n  }
         <br>",fileres,fileres,fileres,fileres);  
  else  /************ Prevalence ********************/
    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);  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
 fprintf(fichtm," <li>Graphs</li><p>");  {  
     /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
  m=cptcoveff;       in each health status at the date of interview (if between dateprev1 and dateprev2).
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}       We still use firstpass and lastpass as another selection.
     */
  jj1=0;   
  for(k1=1; k1<=m;k1++){    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
    for(i1=1; i1<=ncodemax[k1];i1++){    double ***freq; /* Frequencies */
        jj1++;    double *pp, **prop;
        if (cptcovn > 0) {    double pos,posprop; 
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    double  y2; /* in fractional years */
          for (cpt=1; cpt<=cptcoveff;cpt++)    int iagemin, iagemax;
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);  
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    iagemin= (int) agemin;
        }    iagemax= (int) agemax;
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    /*pp=vector(1,nlstate);*/
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        prop=matrix(1,nlstate,iagemin,iagemax+3); 
        for(cpt=1; cpt<nlstate;cpt++){    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    j1=0;
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    
        }    j=cptcoveff;
     for(cpt=1; cpt<=nlstate;cpt++) {    if (cptcovn<1) {j=1;ncodemax[1]=1;}
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    
 interval) in state (%d): v%s%d%d.gif <br>    for(k1=1; k1<=j;k1++){
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        for(i1=1; i1<=ncodemax[k1];i1++){
      }        j1++;
      for(cpt=1; cpt<=nlstate;cpt++) {        
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>        for (i=1; i<=nlstate; i++)  
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          for(m=iagemin; m <= iagemax+3; m++)
      }            prop[i][m]=0.0;
      fprintf(fichtm,"\n<br>- Total life expectancy by age and       
 health expectancies in states (1) and (2): e%s%d.gif<br>        for (i=1; i<=imx; i++) { /* Each individual */
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          bool=1;
 fprintf(fichtm,"\n</body>");          if  (cptcovn>0) {
    }            for (z1=1; z1<=cptcoveff; z1++) 
    }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
 fclose(fichtm);                bool=0;
 }          } 
           if (bool==1) { 
 /******************* Gnuplot file **************/            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
               if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                 if(agev[m][i]==1) agev[m][i]=iagemax+2;
   strcpy(optionfilegnuplot,optionfilefiname);                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
   strcat(optionfilegnuplot,".gp.txt");                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
     printf("Problem with file %s",optionfilegnuplot);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
   }                  prop[s[m][i]][iagemax+3] += weight[i]; 
                 } 
 #ifdef windows              }
     fprintf(ficgp,"cd \"%s\" \n",pathc);            } /* end selection of waves */
 #endif          }
 m=pow(2,cptcoveff);        }
          for(i=iagemin; i <= iagemax+3; i++){  
  /* 1eme*/          
   for (cpt=1; cpt<= nlstate ; cpt ++) {          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
    for (k1=1; k1<= m ; k1 ++) {            posprop += prop[jk][i]; 
           } 
 #ifdef windows  
     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);          for(jk=1; jk <=nlstate ; jk++){     
 #endif            if( i <=  iagemax){ 
 #ifdef unix              if(posprop>=1.e-5){ 
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);                probs[i][jk][j1]= prop[jk][i]/posprop;
 #endif              } 
             } 
 for (i=1; i<= nlstate ; i ++) {          }/* end jk */ 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        }/* end i */ 
   else fprintf(ficgp," \%%*lf (\%%*lf)");      } /* end i1 */
 }    } /* end k1 */
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    
     for (i=1; i<= nlstate ; i ++) {    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    /*free_vector(pp,1,nlstate);*/
   else fprintf(ficgp," \%%*lf (\%%*lf)");    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
 }  }  /* End of prevalence */
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  
      for (i=1; i<= nlstate ; i ++) {  /************* Waves Concatenation ***************/
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
 }    {
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
 #ifdef unix       Death is a valid wave (if date is known).
 fprintf(ficgp,"\nset ter gif small size 400,300");       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
 #endif       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);       and mw[mi+1][i]. dh depends on stepm.
    }       */
   }  
   /*2 eme*/    int i, mi, m;
     /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   for (k1=1; k1<= m ; k1 ++) {       double sum=0., jmean=0.;*/
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);    int first;
        int j, k=0,jk, ju, jl;
     for (i=1; i<= nlstate+1 ; i ++) {    double sum=0.;
       k=2*i;    first=0;
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    jmin=1e+5;
       for (j=1; j<= nlstate+1 ; j ++) {    jmax=-1;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    jmean=0.;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    for(i=1; i<=imx; i++){
 }        mi=0;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");      m=firstpass;
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);      while(s[m][i] <= nlstate){
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);        if(s[m][i]>=1)
       for (j=1; j<= nlstate+1 ; j ++) {          mw[++mi][i]=m;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        if(m >=lastpass)
         else fprintf(ficgp," \%%*lf (\%%*lf)");          break;
 }          else
       fprintf(ficgp,"\" t\"\" w l 0,");          m++;
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      }/* end while */
       for (j=1; j<= nlstate+1 ; j ++) {      if (s[m][i] > nlstate){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        mi++;     /* Death is another wave */
   else fprintf(ficgp," \%%*lf (\%%*lf)");        /* if(mi==0)  never been interviewed correctly before death */
 }             /* Only death is a correct wave */
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");        mw[mi][i]=m;
       else fprintf(ficgp,"\" t\"\" w l 0,");      }
     }  
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);      wav[i]=mi;
   }      if(mi==0){
          nbwarn++;
   /*3eme*/        if(first==0){
           printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
   for (k1=1; k1<= m ; k1 ++) {          first=1;
     for (cpt=1; cpt<= nlstate ; cpt ++) {        }
       k=2+nlstate*(cpt-1);        if(first==1){
       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);          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
       for (i=1; i< nlstate ; i ++) {        }
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);      } /* end mi==0 */
       }    } /* End individuals */
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  
     }    for(i=1; i<=imx; i++){
     }      for(mi=1; mi<wav[i];mi++){
          if (stepm <=0)
   /* CV preval stat */          dh[mi][i]=1;
     for (k1=1; k1<= m ; k1 ++) {        else{
     for (cpt=1; cpt<nlstate ; cpt ++) {          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
       k=3;            if (agedc[i] < 2*AGESUP) {
       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/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
               if(j==0) j=1;  /* Survives at least one month after exam */
       for (i=1; i< nlstate ; i ++)              else if(j<0){
         fprintf(ficgp,"+$%d",k+i+1);                nberr++;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);                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]);
                      j=1; /* Temporary Dangerous patch */
       l=3+(nlstate+ndeath)*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);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       for (i=1; i< nlstate ; i ++) {                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
         l=3+(nlstate+ndeath)*cpt;              }
         fprintf(ficgp,"+$%d",l+i+1);              k=k+1;
       }              if (j >= jmax) jmax=j;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                if (j <= jmin) jmin=j;
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              sum=sum+j;
     }              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   }                /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
              }
   /* proba elementaires */          }
    for(i=1,jk=1; i <=nlstate; i++){          else{
     for(k=1; k <=(nlstate+ndeath); k++){            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
       if (k != i) {            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
         for(j=1; j <=ncovmodel; j++){            k=k+1;
                    if (j >= jmax) jmax=j;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);            else if (j <= jmin)jmin=j;
           jk++;            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
           fprintf(ficgp,"\n");            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
         }            if(j<0){
       }              nberr++;
     }              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     }              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             }
     for(jk=1; jk <=m; jk++) {            sum=sum+j;
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);          }
    i=1;          jk= j/stepm;
    for(k2=1; k2<=nlstate; k2++) {          jl= j -jk*stepm;
      k3=i;          ju= j -(jk+1)*stepm;
      for(k=1; k<=(nlstate+ndeath); k++) {          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
        if (k != k2){            if(jl==0){
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);              dh[mi][i]=jk;
 ij=1;              bh[mi][i]=0;
         for(j=3; j <=ncovmodel; j++) {            }else{ /* We want a negative bias in order to only have interpolation ie
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {                    * at the price of an extra matrix product in likelihood */
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);              dh[mi][i]=jk+1;
             ij++;              bh[mi][i]=ju;
           }            }
           else          }else{
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            if(jl <= -ju){
         }              dh[mi][i]=jk;
           fprintf(ficgp,")/(1");              bh[mi][i]=jl;       /* bias is positive if real duration
                                           * is higher than the multiple of stepm and negative otherwise.
         for(k1=1; k1 <=nlstate; k1++){                                     */
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);            }
 ij=1;            else{
           for(j=3; j <=ncovmodel; j++){              dh[mi][i]=jk+1;
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              bh[mi][i]=ju;
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            }
             ij++;            if(dh[mi][i]==0){
           }              dh[mi][i]=1; /* At least one step */
           else              bh[mi][i]=ju; /* At least one step */
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
           }            }
           fprintf(ficgp,")");          } /* end if mle */
         }        }
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);      } /* end wave */
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    }
         i=i+ncovmodel;    jmean=sum/k;
        }    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
      }    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
    }   }
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);  
    }  /*********** Tricode ****************************/
      void tricode(int *Tvar, int **nbcode, int imx)
   fclose(ficgp);  {
 }  /* end gnuplot */    
     int Ndum[20],ij=1, k, j, i, maxncov=19;
     int cptcode=0;
 /*************** Moving average **************/    cptcoveff=0; 
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){   
     for (k=0; k<maxncov; k++) Ndum[k]=0;
   int i, cpt, cptcod;    for (k=1; k<=7; k++) ncodemax[k]=0;
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)  
       for (i=1; i<=nlstate;i++)    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
           mobaverage[(int)agedeb][i][cptcod]=0.;                                 modality*/ 
            ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){        Ndum[ij]++; /*store the modality */
       for (i=1; i<=nlstate;i++){        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
           for (cpt=0;cpt<=4;cpt++){                                         Tvar[j]. If V=sex and male is 0 and 
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];                                         female is 1, then  cptcode=1.*/
           }      }
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;  
         }      for (i=0; i<=cptcode; i++) {
       }        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 */
     }      }
      
 }      ij=1; 
       for (i=1; i<=ncodemax[j]; i++) {
         for (k=0; k<= maxncov; k++) {
 /************** Forecasting ******************/          if (Ndum[k] != 0) {
 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){            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; */
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;            
   int *popage;            ij++;
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          }
   double *popeffectif,*popcount;          if (ij > ncodemax[j]) break; 
   double ***p3mat;        }  
   char fileresf[FILENAMELENGTH];      } 
     }  
  agelim=AGESUP;  
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;   for (k=0; k< maxncov; k++) Ndum[k]=0;
   
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);   for (i=1; i<=ncovmodel-2; i++) { 
       /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
       ij=Tvar[i];
   strcpy(fileresf,"f");     Ndum[ij]++;
   strcat(fileresf,fileres);   }
   if((ficresf=fopen(fileresf,"w"))==NULL) {  
     printf("Problem with forecast resultfile: %s\n", fileresf);   ij=1;
   }   for (i=1; i<= maxncov; i++) {
   printf("Computing forecasting: result on file '%s' \n", fileresf);     if((Ndum[i]!=0) && (i<=ncovcol)){
        Tvaraff[ij]=i; /*For printing */
   if (cptcoveff==0) ncodemax[cptcoveff]=1;       ij++;
      }
   if (mobilav==1) {   }
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);   
     movingaverage(agedeb, fage, ageminpar, mobaverage);   cptcoveff=ij-1; /*Number of simple covariates*/
   }  }
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;  /*********** Health Expectancies ****************/
   if (stepm<=12) stepsize=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 )
   agelim=AGESUP;  
    {
   hstepm=1;    /* Health expectancies */
   hstepm=hstepm/stepm;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
   yp1=modf(dateintmean,&yp);    double age, agelim, hf;
   anprojmean=yp;    double ***p3mat,***varhe;
   yp2=modf((yp1*12),&yp);    double **dnewm,**doldm;
   mprojmean=yp;    double *xp;
   yp1=modf((yp2*30.5),&yp);    double **gp, **gm;
   jprojmean=yp;    double ***gradg, ***trgradg;
   if(jprojmean==0) jprojmean=1;    int theta;
   if(mprojmean==0) jprojmean=1;  
      varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    xp=vector(1,npar);
      dnewm=matrix(1,nlstate*nlstate,1,npar);
   for(cptcov=1;cptcov<=i2;cptcov++){    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    
       k=k+1;    fprintf(ficreseij,"# Health expectancies\n");
       fprintf(ficresf,"\n#******");    fprintf(ficreseij,"# Age");
       for(j=1;j<=cptcoveff;j++) {    for(i=1; i<=nlstate;i++)
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for(j=1; j<=nlstate;j++)
       }        fprintf(ficreseij," %1d-%1d (SE)",i,j);
       fprintf(ficresf,"******\n");    fprintf(ficreseij,"\n");
       fprintf(ficresf,"# StartingAge FinalAge");  
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    if(estepm < stepm){
            printf ("Problem %d lower than %d\n",estepm, stepm);
          }
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    else  hstepm=estepm;   
         fprintf(ficresf,"\n");    /* We compute the life expectancy from trapezoids spaced every estepm months
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);       * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){     * we are calculating an estimate of the Life Expectancy assuming a linear 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);     * progression in between and thus overestimating or underestimating according
           nhstepm = nhstepm/hstepm;     * 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
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     * to compare the new estimate of Life expectancy with the same linear 
           oldm=oldms;savm=savms;     * hypothesis. A more precise result, taking into account a more precise
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);       * curvature will be obtained if estepm is as small as stepm. */
          
           for (h=0; h<=nhstepm; h++){    /* For example we decided to compute the life expectancy with the smallest unit */
             if (h==(int) (calagedate+YEARM*cpt)) {    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);       nhstepm is the number of hstepm from age to agelim 
             }       nstepm is the number of stepm from age to agelin. 
             for(j=1; j<=nlstate+ndeath;j++) {       Look at hpijx to understand the reason of that which relies in memory size
               kk1=0.;kk2=0;       and note for a fixed period like estepm months */
               for(i=1; i<=nlstate;i++) {                  /* We decided (b) to get a life expectancy respecting the most precise curvature of the
                 if (mobilav==1)       survival function given by stepm (the optimization length). Unfortunately it
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];       means that if the survival funtion is printed only each two years of age and if
                 else {       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];       results. So we changed our mind and took the option of the best precision.
                 }    */
                    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
               }  
               if (h==(int)(calagedate+12*cpt)){    agelim=AGESUP;
                 fprintf(ficresf," %.3f", kk1);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                              /* nhstepm age range expressed in number of stepm */
               }      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
             }      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
           }      /* if (stepm >= YEARM) hstepm=1;*/
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         }      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       }      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     }      gp=matrix(0,nhstepm,1,nlstate*nlstate);
   }      gm=matrix(0,nhstepm,1,nlstate*nlstate);
          
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
          in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   fclose(ficresf);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
 }   
 /************** 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){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
    
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      /* Computing  Variances of health expectancies */
   int *popage;  
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;       for(theta=1; theta <=npar; theta++){
   double *popeffectif,*popcount;        for(i=1; i<=npar; i++){ 
   double ***p3mat,***tabpop,***tabpopprev;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   char filerespop[FILENAMELENGTH];        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        cptj=0;
   agelim=AGESUP;        for(j=1; j<= nlstate; j++){
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;          for(i=1; i<=nlstate; i++){
              cptj=cptj+1;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
                gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
              }
   strcpy(filerespop,"pop");          }
   strcat(filerespop,fileres);        }
   if((ficrespop=fopen(filerespop,"w"))==NULL) {       
     printf("Problem with forecast resultfile: %s\n", filerespop);       
   }        for(i=1; i<=npar; i++) 
   printf("Computing forecasting: result on file '%s' \n", filerespop);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        
         cptj=0;
   if (mobilav==1) {        for(j=1; j<= nlstate; j++){
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for(i=1;i<=nlstate;i++){
     movingaverage(agedeb, fage, ageminpar, mobaverage);            cptj=cptj+1;
   }            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   if (stepm<=12) stepsize=1;            }
            }
   agelim=AGESUP;        }
          for(j=1; j<= nlstate*nlstate; j++)
   hstepm=1;          for(h=0; h<=nhstepm-1; h++){
   hstepm=hstepm/stepm;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
            }
   if (popforecast==1) {       } 
     if((ficpop=fopen(popfile,"r"))==NULL) {     
       printf("Problem with population file : %s\n",popfile);exit(0);  /* End theta */
     }  
     popage=ivector(0,AGESUP);       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     popeffectif=vector(0,AGESUP);  
     popcount=vector(0,AGESUP);       for(h=0; h<=nhstepm-1; h++)
            for(j=1; j<=nlstate*nlstate;j++)
     i=1;            for(theta=1; theta <=npar; theta++)
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;            trgradg[h][j][theta]=gradg[h][theta][j];
           
     imx=i;  
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];       for(i=1;i<=nlstate*nlstate;i++)
   }        for(j=1;j<=nlstate*nlstate;j++)
           varhe[i][j][(int)age] =0.;
   for(cptcov=1;cptcov<=i2;cptcov++){  
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){       printf("%d|",(int)age);fflush(stdout);
       k=k+1;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       fprintf(ficrespop,"\n#******");       for(h=0;h<=nhstepm-1;h++){
       for(j=1;j<=cptcoveff;j++) {        for(k=0;k<=nhstepm-1;k++){
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
       }          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
       fprintf(ficrespop,"******\n");          for(i=1;i<=nlstate*nlstate;i++)
       fprintf(ficrespop,"# Age");            for(j=1;j<=nlstate*nlstate;j++)
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
       if (popforecast==1)  fprintf(ficrespop," [Population]");        }
            }
       for (cpt=0; cpt<=0;cpt++) {      /* Computing expectancies */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);        for(i=1; i<=nlstate;i++)
                for(j=1; j<=nlstate;j++)
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
           nhstepm = nhstepm/hstepm;            
            /* 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]);*/
           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(ficreseij,"%3.0f",age );
           for (h=0; h<=nhstepm; h++){      cptj=0;
             if (h==(int) (calagedate+YEARM*cpt)) {      for(i=1; i<=nlstate;i++)
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        for(j=1; j<=nlstate;j++){
             }          cptj++;
             for(j=1; j<=nlstate+ndeath;j++) {          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
               kk1=0.;kk2=0;        }
               for(i=1; i<=nlstate;i++) {                    fprintf(ficreseij,"\n");
                 if (mobilav==1)     
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
                 else {      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
                 }      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
               }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
               if (h==(int)(calagedate+12*cpt)){    }
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    printf("\n");
                   /*fprintf(ficrespop," %.3f", kk1);    fprintf(ficlog,"\n");
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/  
               }    free_vector(xp,1,npar);
             }    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
             for(i=1; i<=nlstate;i++){    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
               kk1=0.;    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
                 for(j=1; j<=nlstate;j++){  }
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];  
                 }  /************ Variance ******************/
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-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 */
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    /* double **newm;*/
           }    double **dnewm,**doldm;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double **dnewmp,**doldmp;
         }    int i, j, nhstepm, hstepm, h, nstepm ;
       }    int k, cptcode;
      double *xp;
   /******/    double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    double **gradgp, **trgradgp; /* for var p point j */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      double *gpp, *gmp; /* for var p point j */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    double ***p3mat;
           nhstepm = nhstepm/hstepm;    double age,agelim, hf;
              double ***mobaverage;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int theta;
           oldm=oldms;savm=savms;    char digit[4];
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      char digitp[25];
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {    char fileresprobmorprev[FILENAMELENGTH];
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);  
             }    if(popbased==1){
             for(j=1; j<=nlstate+ndeath;j++) {      if(mobilav!=0)
               kk1=0.;kk2=0;        strcpy(digitp,"-populbased-mobilav-");
               for(i=1; i<=nlstate;i++) {                    else strcpy(digitp,"-populbased-nomobil-");
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        }
               }    else 
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);      strcpy(digitp,"-stablbased-");
             }  
           }    if (mobilav!=0) {
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      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);
   }      }
      }
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
     strcpy(fileresprobmorprev,"prmorprev"); 
   if (popforecast==1) {    sprintf(digit,"%-d",ij);
     free_ivector(popage,0,AGESUP);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     free_vector(popeffectif,0,AGESUP);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     free_vector(popcount,0,AGESUP);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   }    strcat(fileresprobmorprev,fileres);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
   fclose(ficrespop);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
 }    }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
 /***********************************************/    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
 /**************** Main Program *****************/    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
 /***********************************************/    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
 int main(int argc, char *argv[])      fprintf(ficresprobmorprev," p.%-d SE",j);
 {      for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    }  
   double agedeb, agefin,hf;    fprintf(ficresprobmorprev,"\n");
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    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");
   double fret;    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   double **xi,tmp,delta;  /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   double dum; /* Dummy variable */  
   double ***p3mat;    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");
   int *indx;    fprintf(ficresvij,"# Age");
   char line[MAXLINE], linepar[MAXLINE];    for(i=1; i<=nlstate;i++)
   char title[MAXLINE];      for(j=1; j<=nlstate;j++)
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    fprintf(ficresvij,"\n");
    
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
   char filerest[FILENAMELENGTH];    doldm=matrix(1,nlstate,1,nlstate);
   char fileregp[FILENAMELENGTH];    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   char popfile[FILENAMELENGTH];    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];  
   int firstobs=1, lastobs=10;    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   int sdeb, sfin; /* Status at beginning and end */    gpp=vector(nlstate+1,nlstate+ndeath);
   int c,  h , cpt,l;    gmp=vector(nlstate+1,nlstate+ndeath);
   int ju,jl, mi;    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    if(estepm < stepm){
   int mobilav=0,popforecast=0;      printf ("Problem %d lower than %d\n",estepm, stepm);
   int hstepm, nhstepm;    }
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;    else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
   double bage, fage, age, agelim, agebase;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   double ftolpl=FTOL;       nhstepm is the number of hstepm from age to agelim 
   double **prlim;       nstepm is the number of stepm from age to agelin. 
   double *severity;       Look at hpijx to understand the reason of that which relies in memory size
   double ***param; /* Matrix of parameters */       and note for a fixed period like k years */
   double  *p;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   double **matcov; /* Matrix of covariance */       survival function given by stepm (the optimization length). Unfortunately it
   double ***delti3; /* Scale */       means that if the survival funtion is printed every two years of age and if
   double *delti; /* Scale */       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   double ***eij, ***vareij;       results. So we changed our mind and took the option of the best precision.
   double **varpl; /* Variances of prevalence limits by age */    */
   double *epj, vepp;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   double kk1, kk2;    agelim = AGESUP;
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
        nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   char version[80]="Imach version 0.8b, March 2002, INED-EUROREVES ";      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   char *alph[]={"a","a","b","c","d","e"}, str[4];      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   char z[1]="c", occ;  
 #include <sys/time.h>  
 #include <time.h>      for(theta=1; theta <=npar; theta++){
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
            xp[i] = x[i] + (i==theta ?delti[theta]:0);
   /* long total_usecs;        }
   struct timeval start_time, end_time;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */  
   getcwd(pathcd, size);        if (popbased==1) {
           if(mobilav ==0){
   printf("\n%s",version);            for(i=1; i<=nlstate;i++)
   if(argc <=1){              prlim[i][i]=probs[(int)age][i][ij];
     printf("\nEnter the parameter file name: ");          }else{ /* mobilav */ 
     scanf("%s",pathtot);            for(i=1; i<=nlstate;i++)
   }              prlim[i][i]=mobaverage[(int)age][i][ij];
   else{          }
     strcpy(pathtot,argv[1]);        }
   }    
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/        for(j=1; j<= nlstate; j++){
   /*cygwin_split_path(pathtot,path,optionfile);          for(h=0; h<=nhstepm; h++){
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   /* cutv(path,optionfile,pathtot,'\\');*/              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);        }
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);        /* This for computing probability of death (h=1 means
   chdir(path);           computed over hstepm matrices product = hstepm*stepm months) 
   replace(pathc,path);           as a weighted average of prlim.
         */
 /*-------- arguments in the command line --------*/        for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
   strcpy(fileres,"r");            gpp[j] += prlim[i][i]*p3mat[i][j][1];
   strcat(fileres, optionfilefiname);        }    
   strcat(fileres,".txt");    /* Other files have txt extension */        /* end probability of death */
   
   /*---------arguments file --------*/        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     printf("Problem with optionfile %s\n",optionfile);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     goto end;   
   }        if (popbased==1) {
           if(mobilav ==0){
   strcpy(filereso,"o");            for(i=1; i<=nlstate;i++)
   strcat(filereso,fileres);              prlim[i][i]=probs[(int)age][i][ij];
   if((ficparo=fopen(filereso,"w"))==NULL) {          }else{ /* mobilav */ 
     printf("Problem with Output resultfile: %s\n", filereso);goto end;            for(i=1; i<=nlstate;i++)
   }              prlim[i][i]=mobaverage[(int)age][i][ij];
           }
   /* Reads comments: lines beginning with '#' */        }
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);        for(j=1; j<= nlstate; j++){
     fgets(line, MAXLINE, ficpar);          for(h=0; h<=nhstepm; h++){
     puts(line);            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
     fputs(line,ficparo);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   }          }
   ungetc(c,ficpar);        }
         /* This for computing probability of death (h=1 means
   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);           computed over hstepm matrices product = hstepm*stepm months) 
   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);           as a weighted average of prlim.
   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);        */
 while((c=getc(ficpar))=='#' && c!= EOF){        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     ungetc(c,ficpar);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
     fgets(line, MAXLINE, ficpar);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
     puts(line);        }    
     fputs(line,ficparo);        /* end probability of death */
   }  
   ungetc(c,ficpar);        for(j=1; j<= nlstate; j++) /* vareij */
            for(h=0; h<=nhstepm; h++){
                gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   covar=matrix(0,NCOVMAX,1,n);          }
   cptcovn=0;  
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   ncovmodel=2+cptcovn;        }
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  
        } /* End theta */
   /* Read guess parameters */  
   /* Reads comments: lines beginning with '#' */      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      for(h=0; h<=nhstepm; h++) /* veij */
     fgets(line, MAXLINE, ficpar);        for(j=1; j<=nlstate;j++)
     puts(line);          for(theta=1; theta <=npar; theta++)
     fputs(line,ficparo);            trgradg[h][j][theta]=gradg[h][theta][j];
   }  
   ungetc(c,ficpar);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
          for(theta=1; theta <=npar; theta++)
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          trgradgp[j][theta]=gradgp[theta][j];
     for(i=1; i <=nlstate; i++)    
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       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] =0.;
         fscanf(ficpar," %lf",&param[i][j][k]);  
         printf(" %lf",param[i][j][k]);      for(h=0;h<=nhstepm;h++){
         fprintf(ficparo," %lf",param[i][j][k]);        for(k=0;k<=nhstepm;k++){
       }          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
       fscanf(ficpar,"\n");          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
       printf("\n");          for(i=1;i<=nlstate;i++)
       fprintf(ficparo,"\n");            for(j=1;j<=nlstate;j++)
     }              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
          }
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;      }
     
   p=param[1][1];      /* pptj */
        matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   /* Reads comments: lines beginning with '#' */      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   while((c=getc(ficpar))=='#' && c!= EOF){      for(j=nlstate+1;j<=nlstate+ndeath;j++)
     ungetc(c,ficpar);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
     fgets(line, MAXLINE, ficpar);          varppt[j][i]=doldmp[j][i];
     puts(line);      /* end ppptj */
     fputs(line,ficparo);      /*  x centered again */
   }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   ungetc(c,ficpar);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      if (popbased==1) {
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */        if(mobilav ==0){
   for(i=1; i <=nlstate; i++){          for(i=1; i<=nlstate;i++)
     for(j=1; j <=nlstate+ndeath-1; j++){            prlim[i][i]=probs[(int)age][i][ij];
       fscanf(ficpar,"%1d%1d",&i1,&j1);        }else{ /* mobilav */ 
       printf("%1d%1d",i,j);          for(i=1; i<=nlstate;i++)
       fprintf(ficparo,"%1d%1d",i1,j1);            prlim[i][i]=mobaverage[(int)age][i][ij];
       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]);      /* This for computing probability of death (h=1 means
       }         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
       fscanf(ficpar,"\n");         as a weighted average of prlim.
       printf("\n");      */
       fprintf(ficparo,"\n");      for(j=nlstate+1;j<=nlstate+ndeath;j++){
     }        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   }          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   delti=delti3[1][1];      }    
        /* end probability of death */
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
     ungetc(c,ficpar);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     fgets(line, MAXLINE, ficpar);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     puts(line);        for(i=1; i<=nlstate;i++){
     fputs(line,ficparo);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   }        }
   ungetc(c,ficpar);      } 
        fprintf(ficresprobmorprev,"\n");
   matcov=matrix(1,npar,1,npar);  
   for(i=1; i <=npar; i++){      fprintf(ficresvij,"%.0f ",age );
     fscanf(ficpar,"%s",&str);      for(i=1; i<=nlstate;i++)
     printf("%s",str);        for(j=1; j<=nlstate;j++){
     fprintf(ficparo,"%s",str);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
     for(j=1; j <=i; j++){        }
       fscanf(ficpar," %le",&matcov[i][j]);      fprintf(ficresvij,"\n");
       printf(" %.5le",matcov[i][j]);      free_matrix(gp,0,nhstepm,1,nlstate);
       fprintf(ficparo," %.5le",matcov[i][j]);      free_matrix(gm,0,nhstepm,1,nlstate);
     }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
     fscanf(ficpar,"\n");      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     printf("\n");      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     fprintf(ficparo,"\n");    } /* End age */
   }    free_vector(gpp,nlstate+1,nlstate+ndeath);
   for(i=1; i <=npar; i++)    free_vector(gmp,nlstate+1,nlstate+ndeath);
     for(j=i+1;j<=npar;j++)    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
       matcov[i][j]=matcov[j][i];    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");
   printf("\n");    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
     /*-------- Rewriting paramater file ----------*/  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
      strcpy(rfileres,"r");    /* "Rparameterfile */  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
      strcat(rfileres,".");    /* */    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
      strcat(rfileres,optionfilext);    /* Other files have txt extension */    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     if((ficres =fopen(rfileres,"w"))==NULL) {    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    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);
     fprintf(ficres,"#%s\n",version);  */
      /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     /*-------- data file ----------*/    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     if((fic=fopen(datafile,"r"))==NULL)    {  
       printf("Problem with datafile: %s\n", datafile);goto end;    free_vector(xp,1,npar);
     }    free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
     n= lastobs;    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     severity = vector(1,maxwav);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     outcome=imatrix(1,maxwav+1,1,n);    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     num=ivector(1,n);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     moisnais=vector(1,n);    fclose(ficresprobmorprev);
     annais=vector(1,n);    fflush(ficgp);
     moisdc=vector(1,n);    fflush(fichtm); 
     andc=vector(1,n);  }  /* end varevsij */
     agedc=vector(1,n);  
     cod=ivector(1,n);  /************ Variance of prevlim ******************/
     weight=vector(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)
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */  {
     mint=matrix(1,maxwav,1,n);    /* Variance of prevalence limit */
     anint=matrix(1,maxwav,1,n);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     s=imatrix(1,maxwav+1,1,n);    double **newm;
     adl=imatrix(1,maxwav+1,1,n);        double **dnewm,**doldm;
     tab=ivector(1,NCOVMAX);    int i, j, nhstepm, hstepm;
     ncodemax=ivector(1,8);    int k, cptcode;
     double *xp;
     i=1;    double *gp, *gm;
     while (fgets(line, MAXLINE, fic) != NULL)    {    double **gradg, **trgradg;
       if ((i >= firstobs) && (i <=lastobs)) {    double age,agelim;
            int theta;
         for (j=maxwav;j>=1;j--){     
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
           strcpy(line,stra);    fprintf(ficresvpl,"# Age");
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    for(i=1; i<=nlstate;i++)
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        fprintf(ficresvpl," %1d-%1d",i,i);
         }    fprintf(ficresvpl,"\n");
          
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    xp=vector(1,npar);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    agelim = AGESUP;
         for (j=ncovcol;j>=1;j--){    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
         }      if (stepm >= YEARM) hstepm=1;
         num[i]=atol(stra);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
              gradg=matrix(1,npar,1,nlstate);
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){      gp=vector(1,nlstate);
           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;}*/      gm=vector(1,nlstate);
   
         i=i+1;      for(theta=1; theta <=npar; theta++){
       }        for(i=1; i<=npar; i++){ /* Computes gradient */
     }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     /* printf("ii=%d", ij);        }
        scanf("%d",i);*/        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   imx=i-1; /* Number of individuals */        for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
   /* for (i=1; i<=imx; i++){      
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;        for(i=1; i<=npar; i++) /* Computes gradient */
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     }*/        for(i=1;i<=nlstate;i++)
            gm[i] = prlim[i][i];
   /* for (i=1; i<=imx; i++){  
      if (s[4][i]==9)  s[4][i]=-1;        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]));}          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   */      } /* End theta */
    
   /* Calculation of the number of parameter from char model*/      trgradg =matrix(1,nlstate,1,npar);
   Tvar=ivector(1,15);  
   Tprod=ivector(1,15);      for(j=1; j<=nlstate;j++)
   Tvaraff=ivector(1,15);        for(theta=1; theta <=npar; theta++)
   Tvard=imatrix(1,15,1,2);          trgradg[j][theta]=gradg[theta][j];
   Tage=ivector(1,15);        
          for(i=1;i<=nlstate;i++)
   if (strlen(model) >1){        varpl[i][(int)age] =0.;
     j=0, j1=0, k1=1, k2=1;      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
     j=nbocc(model,'+');      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
     j1=nbocc(model,'*');      for(i=1;i<=nlstate;i++)
     cptcovn=j+1;        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
     cptcovprod=j1;  
          fprintf(ficresvpl,"%.0f ",age );
     strcpy(modelsav,model);      for(i=1; i<=nlstate;i++)
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       printf("Error. Non available option model=%s ",model);      fprintf(ficresvpl,"\n");
       goto end;      free_vector(gp,1,nlstate);
     }      free_vector(gm,1,nlstate);
          free_matrix(gradg,1,npar,1,nlstate);
     for(i=(j+1); i>=1;i--){      free_matrix(trgradg,1,nlstate,1,npar);
       cutv(stra,strb,modelsav,'+');    } /* End age */
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);  
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    free_vector(xp,1,npar);
       /*scanf("%d",i);*/    free_matrix(doldm,1,nlstate,1,npar);
       if (strchr(strb,'*')) {    free_matrix(dnewm,1,nlstate,1,nlstate);
         cutv(strd,strc,strb,'*');  
         if (strcmp(strc,"age")==0) {  }
           cptcovprod--;  
           cutv(strb,stre,strd,'V');  /************ Variance of one-step probabilities  ******************/
           Tvar[i]=atoi(stre);  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
           cptcovage++;  {
             Tage[cptcovage]=i;    int i, j=0,  i1, k1, l1, t, tj;
             /*printf("stre=%s ", stre);*/    int k2, l2, j1,  z1;
         }    int k=0,l, cptcode;
         else if (strcmp(strd,"age")==0) {    int first=1, first1;
           cptcovprod--;    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
           cutv(strb,stre,strc,'V');    double **dnewm,**doldm;
           Tvar[i]=atoi(stre);    double *xp;
           cptcovage++;    double *gp, *gm;
           Tage[cptcovage]=i;    double **gradg, **trgradg;
         }    double **mu;
         else {    double age,agelim, cov[NCOVMAX];
           cutv(strb,stre,strc,'V');    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
           Tvar[i]=ncovcol+k1;    int theta;
           cutv(strb,strc,strd,'V');    char fileresprob[FILENAMELENGTH];
           Tprod[k1]=i;    char fileresprobcov[FILENAMELENGTH];
           Tvard[k1][1]=atoi(strc);    char fileresprobcor[FILENAMELENGTH];
           Tvard[k1][2]=atoi(stre);  
           Tvar[cptcovn+k2]=Tvard[k1][1];    double ***varpij;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];  
           for (k=1; k<=lastobs;k++)    strcpy(fileresprob,"prob"); 
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    strcat(fileresprob,fileres);
           k1++;    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
           k2=k2+2;      printf("Problem with resultfile: %s\n", fileresprob);
         }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
       }    }
       else {    strcpy(fileresprobcov,"probcov"); 
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    strcat(fileresprobcov,fileres);
        /*  scanf("%d",i);*/    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       cutv(strd,strc,strb,'V');      printf("Problem with resultfile: %s\n", fileresprobcov);
       Tvar[i]=atoi(strc);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
       }    }
       strcpy(modelsav,stra);      strcpy(fileresprobcor,"probcor"); 
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    strcat(fileresprobcor,fileres);
         scanf("%d",i);*/    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
     }      printf("Problem with resultfile: %s\n", fileresprobcor);
 }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
      }
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   printf("cptcovprod=%d ", cptcovprod);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   scanf("%d ",i);*/    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fclose(fic);    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     /*  if(mle==1){*/    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     if (weightopt != 1) { /* Maximisation without weights*/    
       for(i=1;i<=n;i++) weight[i]=1.0;    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     }    fprintf(ficresprob,"# Age");
     /*-calculation of age at interview from date of interview and age at death -*/    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     agev=matrix(1,maxwav,1,imx);    fprintf(ficresprobcov,"# Age");
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     for (i=1; i<=imx; i++) {    fprintf(ficresprobcov,"# Age");
       for(m=2; (m<= maxwav); m++) {  
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){  
          anint[m][i]=9999;    for(i=1; i<=nlstate;i++)
          s[m][i]=-1;      for(j=1; j<=(nlstate+ndeath);j++){
        }        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;        fprintf(ficresprobcov," p%1d-%1d ",i,j);
       }        fprintf(ficresprobcor," p%1d-%1d ",i,j);
     }      }  
    /* fprintf(ficresprob,"\n");
     for (i=1; i<=imx; i++)  {    fprintf(ficresprobcov,"\n");
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    fprintf(ficresprobcor,"\n");
       for(m=1; (m<= maxwav); m++){   */
         if(s[m][i] >0){   xp=vector(1,npar);
           if (s[m][i] >= nlstate+1) {    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
             if(agedc[i]>0)    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
               if(moisdc[i]!=99 && andc[i]!=9999)    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
                 agev[m][i]=agedc[i];    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/    first=1;
            else {    fprintf(ficgp,"\n# Routine varprob");
               if (andc[i]!=9999){    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    fprintf(fichtm,"\n");
               agev[m][i]=-1;  
               }    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
             }    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
           }    file %s<br>\n",optionfilehtmcov);
           else if(s[m][i] !=9){ /* Should no more exist */    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);  and drawn. It helps understanding how is the covariance between two incidences.\
             if(mint[m][i]==99 || anint[m][i]==9999)   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
               agev[m][i]=1;    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. \
             else if(agev[m][i] <agemin){  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
               agemin=agev[m][i];  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/  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(agev[m][i] >agemax){   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
               agemax=agev[m][i];  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/  
             }    cov[1]=1;
             /*agev[m][i]=anint[m][i]-annais[i];*/    tj=cptcoveff;
             /*   agev[m][i] = age[i]+2*m;*/    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
           }    j1=0;
           else { /* =9 */    for(t=1; t<=tj;t++){
             agev[m][i]=1;      for(i1=1; i1<=ncodemax[t];i1++){ 
             s[m][i]=-1;        j1++;
           }        if  (cptcovn>0) {
         }          fprintf(ficresprob, "\n#********** Variable "); 
         else /*= 0 Unknown */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           agev[m][i]=1;          fprintf(ficresprob, "**********\n#\n");
       }          fprintf(ficresprobcov, "\n#********** Variable "); 
              for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     }          fprintf(ficresprobcov, "**********\n#\n");
     for (i=1; i<=imx; i++)  {          
       for(m=1; (m<= maxwav); m++){          fprintf(ficgp, "\n#********** Variable "); 
         if (s[m][i] > (nlstate+ndeath)) {          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           printf("Error: Wrong value in nlstate or ndeath\n");            fprintf(ficgp, "**********\n#\n");
           goto end;          
         }          
       }          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
     }          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);          
           fprintf(ficresprobcor, "\n#********** Variable ");    
     free_vector(severity,1,maxwav);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     free_imatrix(outcome,1,maxwav+1,1,n);          fprintf(ficresprobcor, "**********\n#");    
     free_vector(moisnais,1,n);        }
     free_vector(annais,1,n);        
     /* free_matrix(mint,1,maxwav,1,n);        for (age=bage; age<=fage; age ++){ 
        free_matrix(anint,1,maxwav,1,n);*/          cov[2]=age;
     free_vector(moisdc,1,n);          for (k=1; k<=cptcovn;k++) {
     free_vector(andc,1,n);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           }
              for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     wav=ivector(1,imx);          for (k=1; k<=cptcovprod;k++)
     dh=imatrix(1,lastpass-firstpass+1,1,imx);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          
              gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
     /* Concatenates waves */          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);          gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
       
       Tcode=ivector(1,100);          for(theta=1; theta <=npar; theta++){
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);            for(i=1; i<=npar; i++)
       ncodemax[1]=1;              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);            
                  pmij(pmmij,cov,ncovmodel,xp,nlstate);
    codtab=imatrix(1,100,1,10);            
    h=0;            k=0;
    m=pow(2,cptcoveff);            for(i=1; i<= (nlstate); i++){
                for(j=1; j<=(nlstate+ndeath);j++){
    for(k=1;k<=cptcoveff; k++){                k=k+1;
      for(i=1; i <=(m/pow(2,k));i++){                gp[k]=pmmij[i][j];
        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;            for(i=1; i<=npar; i++)
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
          }      
        }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
      }            k=0;
    }            for(i=1; i<=(nlstate); i++){
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);              for(j=1; j<=(nlstate+ndeath);j++){
       codtab[1][2]=1;codtab[2][2]=2; */                k=k+1;
    /* for(i=1; i <=m ;i++){                gm[k]=pmmij[i][j];
       for(k=1; k <=cptcovn; k++){              }
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);            }
       }       
       printf("\n");            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
       }              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
       scanf("%d",i);*/          }
      
    /* Calculates basic frequencies. Computes observed prevalence at single age          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
        and prints on file fileres'p'. */            for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
              
              matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
        
     /* For Powell, parameters are in a vector p[] starting at p[1]          pmij(pmmij,cov,ncovmodel,x,nlstate);
        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) */          k=0;
           for(i=1; i<=(nlstate); i++){
     if(mle==1){            for(j=1; j<=(nlstate+ndeath);j++){
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);              k=k+1;
     }              mu[k][(int) age]=pmmij[i][j];
                }
     /*--------- 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);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
              for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
    jk=1;  
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");          /*printf("\n%d ",(int)age);
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
    for(i=1,jk=1; i <=nlstate; i++){            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
      for(k=1; k <=(nlstate+ndeath); k++){            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
        if (k != i)            }*/
          {  
            printf("%d%d ",i,k);          fprintf(ficresprob,"\n%d ",(int)age);
            fprintf(ficres,"%1d%1d ",i,k);          fprintf(ficresprobcov,"\n%d ",(int)age);
            for(j=1; j <=ncovmodel; j++){          fprintf(ficresprobcor,"\n%d ",(int)age);
              printf("%f ",p[jk]);  
              fprintf(ficres,"%f ",p[jk]);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
              jk++;            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
            }          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
            printf("\n");            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
            fprintf(ficres,"\n");            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
          }          }
      }          i=0;
    }          for (k=1; k<=(nlstate);k++){
  if(mle==1){            for (l=1; l<=(nlstate+ndeath);l++){ 
     /* Computing hessian and covariance matrix */              i=i++;
     ftolhess=ftol; /* Usually correct */              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
     hesscov(matcov, p, npar, delti, ftolhess, func);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
  }              for (j=1; j<=i;j++){
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
     printf("# Scales (for hessian or gradient estimation)\n");                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
      for(i=1,jk=1; i <=nlstate; i++){              }
       for(j=1; j <=nlstate+ndeath; j++){            }
         if (j!=i) {          }/* end of loop for state */
           fprintf(ficres,"%1d%1d",i,j);        } /* end of loop for age */
           printf("%1d%1d",i,j);  
           for(k=1; k<=ncovmodel;k++){        /* Confidence intervalle of pij  */
             printf(" %.5e",delti[jk]);        /*
             fprintf(ficres," %.5e",delti[jk]);          fprintf(ficgp,"\nset noparametric;unset label");
             jk++;          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           }          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           printf("\n");          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(ficres,"\n");          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
         }          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
       }          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
      }        */
      
     k=1;        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
     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");        first1=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");        for (k2=1; k2<=(nlstate);k2++){
     for(i=1;i<=npar;i++){          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
       /*  if (k>nlstate) k=1;            if(l2==k2) continue;
       i1=(i-1)/(ncovmodel*nlstate)+1;            j=(k2-1)*(nlstate+ndeath)+l2;
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);            for (k1=1; k1<=(nlstate);k1++){
       printf("%s%d%d",alph[k],i1,tab[i]);*/              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
       fprintf(ficres,"%3d",i);                if(l1==k1) continue;
       printf("%3d",i);                i=(k1-1)*(nlstate+ndeath)+l1;
       for(j=1; j<=i;j++){                if(i<=j) continue;
         fprintf(ficres," %.5e",matcov[i][j]);                for (age=bage; age<=fage; age ++){ 
         printf(" %.5e",matcov[i][j]);                  if ((int)age %5==0){
       }                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
       fprintf(ficres,"\n");                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
       printf("\n");                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
       k++;                    mu1=mu[i][(int) age]/stepm*YEARM ;
     }                    mu2=mu[j][(int) age]/stepm*YEARM;
                        c12=cv12/sqrt(v1*v2);
     while((c=getc(ficpar))=='#' && c!= EOF){                    /* Computing eigen value of matrix of covariance */
       ungetc(c,ficpar);                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       fgets(line, MAXLINE, ficpar);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
       puts(line);                    /* Eigen vectors */
       fputs(line,ficparo);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
     }                    /*v21=sqrt(1.-v11*v11); *//* error */
     ungetc(c,ficpar);                    v21=(lc1-v1)/cv12*v11;
     estepm=0;                    v12=-v21;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);                    v22=v11;
     if (estepm==0 || estepm < stepm) estepm=stepm;                    tnalp=v21/v11;
     if (fage <= 2) {                    if(first1==1){
       bage = ageminpar;                      first1=0;
       fage = agemaxpar;                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
     }                    }
                        fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");                    /*printf(fignu*/
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                      if(first==1){
     while((c=getc(ficpar))=='#' && c!= EOF){                      first=0;
     ungetc(c,ficpar);                      fprintf(ficgp,"\nset parametric;unset label");
     fgets(line, MAXLINE, ficpar);                      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);
     puts(line);                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     fputs(line,ficparo);                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
   }   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   ungetc(c,ficpar);  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                                subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                            fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   while((c=getc(ficpar))=='#' && c!= EOF){                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
     ungetc(c,ficpar);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     fgets(line, MAXLINE, 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",\
     puts(line);                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
     fputs(line,ficparo);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   }                    }else{
   ungetc(c,ficpar);                      first=0;
                        fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
    dateprev1=anprev1+mprev1/12.+jprev1/365.;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
    dateprev2=anprev2+mprev2/12.+jprev2/365.;                      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",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   fscanf(ficpar,"pop_based=%d\n",&popbased);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   fprintf(ficparo,"pop_based=%d\n",popbased);                      }/* if first */
   fprintf(ficres,"pop_based=%d\n",popbased);                    } /* age mod 5 */
                  } /* end loop age */
   while((c=getc(ficpar))=='#' && c!= EOF){                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     ungetc(c,ficpar);                first=1;
     fgets(line, MAXLINE, ficpar);              } /*l12 */
     puts(line);            } /* k12 */
     fputs(line,ficparo);          } /*l1 */
   }        }/* k1 */
   ungetc(c,ficpar);      } /* loop covariates */
     }
   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);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
 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);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
 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);    free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
 while((c=getc(ficpar))=='#' && c!= EOF){    fclose(ficresprobcor);
     ungetc(c,ficpar);    fflush(ficgp);
     fgets(line, MAXLINE, ficpar);    fflush(fichtmcov);
     puts(line);  }
     fputs(line,ficparo);  
   }  
   ungetc(c,ficpar);  /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);                    int lastpass, int stepm, int weightopt, char model[],\
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);                    int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                    double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
 /*------------ gnuplot -------------*/  
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);     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 ",
 /*------------ free_vector  -------------*/             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
  chdir(path);     fprintf(fichtm,"\
     - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
  free_ivector(wav,1,imx);             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);     fprintf(fichtm,"\
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);     - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
  free_ivector(num,1,n);             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
  free_vector(agedc,1,n);     fprintf(fichtm,"\
  /*free_matrix(covar,1,NCOVMAX,1,n);*/   - Life expectancies by age and initial health status (estepm=%2d months): \
  fclose(ficparo);     <a href=\"%s\">%s</a> <br>\n</li>",
  fclose(ficres);             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   
 /*--------- index.htm --------*/  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);   m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
    
   /*--------------- Prevalence limit --------------*/   jj1=0;
     for(k1=1; k1<=m;k1++){
   strcpy(filerespl,"pl");     for(i1=1; i1<=ncodemax[k1];i1++){
   strcat(filerespl,fileres);       jj1++;
   if((ficrespl=fopen(filerespl,"w"))==NULL) {       if (cptcovn > 0) {
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   }         for (cpt=1; cpt<=cptcoveff;cpt++) 
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   fprintf(ficrespl,"#Prevalence limit\n");         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   fprintf(ficrespl,"#Age ");       }
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);       /* Pij */
   fprintf(ficrespl,"\n");       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
    <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
   prlim=matrix(1,nlstate,1,nlstate);       /* Quasi-incidences */
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */         /* Stable prevalence in each health state */
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */         for(cpt=1; cpt<nlstate;cpt++){
   k=0;           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
   agebase=ageminpar;  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
   agelim=agemaxpar;         }
   ftolpl=1.e-10;       for(cpt=1; cpt<=nlstate;cpt++) {
   i1=cptcoveff;          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
   if (cptcovn < 1){i1=1;}  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
   for(cptcov=1;cptcov<=i1;cptcov++){     } /* end i1 */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){   }/* End k1 */
         k=k+1;   fprintf(fichtm,"</ul>");
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/  
         fprintf(ficrespl,"\n#******");  
         for(j=1;j<=cptcoveff;j++)   fprintf(fichtm,"\
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  \n<br><li><h4> Result files (second order: variances)</h4>\n\
         fprintf(ficrespl,"******\n");   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
          
         for (age=agebase; age<=agelim; age++){   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
           fprintf(ficrespl,"%.0f",age );   fprintf(fichtm,"\
           for(i=1; i<=nlstate;i++)   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
           fprintf(ficrespl," %.5f", prlim[i][i]);           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
           fprintf(ficrespl,"\n");  
         }   fprintf(fichtm,"\
       }   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
     }           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
   fclose(ficrespl);   fprintf(fichtm,"\
    - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
   /*------------- h Pij x at various ages ------------*/           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
     fprintf(fichtm,"\
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
   if((ficrespij=fopen(filerespij,"w"))==NULL) {           subdirf2(fileres,"t"),subdirf2(fileres,"t"));
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;   fprintf(fichtm,"\
   }   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
   printf("Computing pij: result on file '%s' \n", filerespij);           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
    
   stepsize=(int) (stepm+YEARM-1)/YEARM;  /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*if (stepm<=24) stepsize=2;*/  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
   agelim=AGESUP;  /*      <br>",fileres,fileres,fileres,fileres); */
   hstepm=stepsize*YEARM; /* Every year of age */  /*  else  */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */  /*    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); */
     fflush(fichtm);
   k=0;   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){   m=cptcoveff;
       k=k+1;   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
         fprintf(ficrespij,"\n#****** ");  
         for(j=1;j<=cptcoveff;j++)   jj1=0;
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   for(k1=1; k1<=m;k1++){
         fprintf(ficrespij,"******\n");     for(i1=1; i1<=ncodemax[k1];i1++){
               jj1++;
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */       if (cptcovn > 0) {
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */         for (cpt=1; cpt<=cptcoveff;cpt++) 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
           oldm=oldms;savm=savms;         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);         }
           fprintf(ficrespij,"# Age");       for(cpt=1; cpt<=nlstate;cpt++) {
           for(i=1; i<=nlstate;i++)         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
             for(j=1; j<=nlstate+ndeath;j++)  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
               fprintf(ficrespij," %1d-%1d",i,j);  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
           fprintf(ficrespij,"\n");       }
           for (h=0; h<=nhstepm; h++){       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  health expectancies in states (1) and (2): %s%d.png<br>\
             for(i=1; i<=nlstate;i++)  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
               for(j=1; j<=nlstate+ndeath;j++)     } /* end i1 */
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);   }/* End k1 */
             fprintf(ficrespij,"\n");   fprintf(fichtm,"</ul>");
           }   fflush(fichtm);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  }
           fprintf(ficrespij,"\n");  
         }  /******************* Gnuplot file **************/
     }  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   }  
     char dirfileres[132],optfileres[132];
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   fclose(ficrespij);  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*---------- Forecasting ------------------*/  /*   } */
   if((stepm == 1) && (strcmp(model,".")==0)){  
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    /*#ifdef windows */
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    fprintf(ficgp,"cd \"%s\" \n",pathc);
     free_matrix(mint,1,maxwav,1,n);      /*#endif */
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    m=pow(2,cptcoveff);
     free_vector(weight,1,n);}  
   else{    strcpy(dirfileres,optionfilefiname);
     erreur=108;    strcpy(optfileres,"vpl");
     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);   /* 1eme*/
   }    for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
   /*---------- Health expectancies and variances ------------*/       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   strcpy(filerest,"t");  set ylabel \"Probability\" \n\
   strcat(filerest,fileres);  set ter png small\n\
   if((ficrest=fopen(filerest,"w"))==NULL) {  set size 0.65,0.65\n\
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   }  
   printf("Computing Total LEs with variances: file '%s' \n", filerest);       for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
   strcpy(filerese,"e");       }
   strcat(filerese,fileres);       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);
   if((ficreseij=fopen(filerese,"w"))==NULL) {       for (i=1; i<= nlstate ; i ++) {
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   }         else fprintf(ficgp," \%%*lf (\%%*lf)");
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);       } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
  strcpy(fileresv,"v");       for (i=1; i<= nlstate ; i ++) {
   strcat(fileresv,fileres);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   if((ficresvij=fopen(fileresv,"w"))==NULL) {         else fprintf(ficgp," \%%*lf (\%%*lf)");
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);       }  
   }       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);     }
     }
   k=0;    /*2 eme*/
   for(cptcov=1;cptcov<=i1;cptcov++){    
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    for (k1=1; k1<= m ; k1 ++) { 
       k=k+1;      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficrest,"\n#****** ");      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       for(j=1;j<=cptcoveff;j++)      
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for (i=1; i<= nlstate+1 ; i ++) {
       fprintf(ficrest,"******\n");        k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       fprintf(ficreseij,"\n#****** ");        for (j=1; j<= nlstate+1 ; j ++) {
       for(j=1;j<=cptcoveff;j++)          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          else fprintf(ficgp," \%%*lf (\%%*lf)");
       fprintf(ficreseij,"******\n");        }   
         if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
       fprintf(ficresvij,"\n#****** ");        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
       for(j=1;j<=cptcoveff;j++)        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for (j=1; j<= nlstate+1 ; j ++) {
       fprintf(ficresvij,"******\n");          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        }   
       oldm=oldms;savm=savms;        fprintf(ficgp,"\" t\"\" w l 0,");
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm);          fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        for (j=1; j<= nlstate+1 ; j ++) {
       oldm=oldms;savm=savms;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);          else fprintf(ficgp," \%%*lf (\%%*lf)");
            }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
          else fprintf(ficgp,"\" t\"\" w l 0,");
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      }
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    }
       fprintf(ficrest,"\n");    
     /*3eme*/
       epj=vector(1,nlstate+1);    
       for(age=bage; age <=fage ;age++){    for (k1=1; k1<= m ; k1 ++) { 
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      for (cpt=1; cpt<= nlstate ; cpt ++) {
         if (popbased==1) {        k=2+nlstate*(2*cpt-2);
           for(i=1; i<=nlstate;i++)        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
             prlim[i][i]=probs[(int)age][i][k];        fprintf(ficgp,"set ter png small\n\
         }  set size 0.65,0.65\n\
          plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         fprintf(ficrest," %4.0f",age);        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           for(i=1, epj[j]=0.;i <=nlstate;i++) {          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
             epj[j] += prlim[i][i]*eij[i][j][(int)age];          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           }          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           epj[nlstate+1] +=epj[j];          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
         }          
         for(i=1, vepp=0.;i <=nlstate;i++)        */
           for(j=1;j <=nlstate;j++)        for (i=1; i< nlstate ; i ++) {
             vepp += vareij[i][j][(int)age];          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);
         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");    
       }    /* CV preval stable (period) */
     }    for (k1=1; k1<= m ; k1 ++) { 
   }      for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
   fclose(ficreseij);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
   fclose(ficresvij);        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   fclose(ficrest);  set ter png small\nset size 0.65,0.65\n\
   fclose(ficpar);  unset log y\n\
   free_vector(epj,1,nlstate+1);  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
          
   /*------- Variance limit prevalence------*/          for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
   strcpy(fileresvpl,"vpl");        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
   strcat(fileresvpl,fileres);        
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {        l=3+(nlstate+ndeath)*cpt;
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
     exit(0);        for (i=1; i< nlstate ; i ++) {
   }          l=3+(nlstate+ndeath)*cpt;
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);          fprintf(ficgp,"+$%d",l+i+1);
         }
   k=0;        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
   for(cptcov=1;cptcov<=i1;cptcov++){      } 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    }  
       k=k+1;    
       fprintf(ficresvpl,"\n#****** ");    /* proba elementaires */
       for(j=1;j<=cptcoveff;j++)    for(i=1,jk=1; i <=nlstate; i++){
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for(k=1; k <=(nlstate+ndeath); k++){
       fprintf(ficresvpl,"******\n");        if (k != i) {
                for(j=1; j <=ncovmodel; j++){
       varpl=matrix(1,nlstate,(int) bage, (int) fage);            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
       oldm=oldms;savm=savms;            jk++; 
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);            fprintf(ficgp,"\n");
     }          }
  }        }
       }
   fclose(ficresvpl);     }
   
   /*---------- End : free ----------------*/     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);       for(jk=1; jk <=m; jk++) {
           fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);         if (ng==2)
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
           else
             fprintf(ficgp,"\nset title \"Probability\"\n");
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);         i=1;
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);         for(k2=1; k2<=nlstate; k2++) {
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);           k3=i;
             for(k=1; k<=(nlstate+ndeath); k++) {
   free_matrix(matcov,1,npar,1,npar);             if (k != k2){
   free_vector(delti,1,npar);               if(ng==2)
   free_matrix(agev,1,maxwav,1,imx);                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);               else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
   if(erreur >0)               ij=1;
     printf("End of Imach with error or warning %d\n",erreur);               for(j=3; j <=ncovmodel; j++) {
   else   printf("End of Imach\n");                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                     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);*/                 }
   /*printf("Total time was %d uSec.\n", total_usecs);*/                 else
   /*------ End -----------*/                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
  end:               
 #ifdef windows               for(k1=1; k1 <=nlstate; k1++){   
   /* chdir(pathcd);*/                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
 #endif                 ij=1;
  /*system("wgnuplot graph.plt");*/                 for(j=3; j <=ncovmodel; j++){
  /*system("../gp37mgw/wgnuplot graph.plt");*/                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
  /*system("cd ../gp37mgw");*/                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/                     ij++;
  strcpy(plotcmd,GNUPLOTPROGRAM);                   }
  strcat(plotcmd," ");                   else
  strcat(plotcmd,optionfilegnuplot);                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
  system(plotcmd);                 }
                  fprintf(ficgp,")");
 #ifdef windows               }
   while (z[0] != 'q') {               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
     /* chdir(path); */               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");               i=i+ncovmodel;
     scanf("%s",z);             }
     if (z[0] == 'c') system("./imach");           } /* end k */
     else if (z[0] == 'e') system(optionfilehtm);         } /* end k2 */
     else if (z[0] == 'g') system(plotcmd);       } /* end jk */
     else if (z[0] == 'q') exit(0);     } /* end ng */
   }     fflush(ficgp); 
 #endif  }  /* end gnuplot */
 }  
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** 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);
     for(i=1;i<=AGESUP;i++)
       for(j=1;j<=NCOVMAX;j++)
         for(k=1;k<=NCOVMAX;k++)
           probs[i][j][k]=0.;
   
     /*---------- 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.1.38  
changed lines
  Added in v.1.97

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