Diff for /imach/src/imach.c between versions 1.50 and 1.97

version 1.50, 2002/06/26 23:25:02 version 1.97, 2004/02/20 13:25:42
Line 1 Line 1
 /* $Id$  /* $Id$
    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  
   probability 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 "gnuplot"    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 ***
 #ifdef windows  
 #define DIRSEPARATOR '\\'    Revision 1.82  2003/06/05 15:57:20  brouard
 #define ODIRSEPARATOR '/'    Add log in  imach.c and  fullversion number is now printed.
 #else  
 #define DIRSEPARATOR '/'  */
 #define ODIRSEPARATOR '\\'  /*
 #endif     Interpolated Markov Chain
   
 char version[80]="Imach version 0.8i, June 2002, INED-EUROREVES ";    Short summary of the programme:
 int erreur; /* Error number */    
 int nvar;    This program computes Healthy Life Expectancies from
 int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 int npar=NPARMAX;    first survey ("cross") where individuals from different ages are
 int nlstate=2; /* Number of live states */    interviewed on their health status or degree of disability (in the
 int ndeath=1; /* Number of dead states */    case of a health survey which is our main interest) -2- at least a
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    second wave of interviews ("longitudinal") which measure each change
 int popbased=0;    (if any) in individual health status.  Health expectancies are
     computed from the time spent in each health state according to a
 int *wav; /* Number of waves for this individuual 0 is possible */    model. More health states you consider, more time is necessary to reach the
 int maxwav; /* Maxim number of waves */    Maximum Likelihood of the parameters involved in the model.  The
 int jmin, jmax; /* min, max spacing between 2 waves */    simplest model is the multinomial logistic model where pij is the
 int mle, weightopt;    probability to be observed in state j at the second wave
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    conditional to be observed in state i at the first wave. Therefore
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 double jmean; /* Mean space between 2 waves */    'age' is age and 'sex' is a covariate. If you want to have a more
 double **oldm, **newm, **savm; /* Working pointers to matrices */    complex model than "constant and age", you should modify the program
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    where the markup *Covariates have to be included here again* invites
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    you to do it.  More covariates you add, slower the
 FILE *ficlog;    convergence.
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;  
 FILE *ficresprobmorprev;    The advantage of this computer programme, compared to a simple
 FILE *fichtm; /* Html File */    multinomial logistic model, is clear when the delay between waves is not
 FILE *ficreseij;    identical for each individual. Also, if a individual missed an
 char filerese[FILENAMELENGTH];    intermediate interview, the information is lost, but taken into
 FILE  *ficresvij;    account using an interpolation or extrapolation.  
 char fileresv[FILENAMELENGTH];  
 FILE  *ficresvpl;    hPijx is the probability to be observed in state i at age x+h
 char fileresvpl[FILENAMELENGTH];    conditional to the observed state i at age x. The delay 'h' can be
 char title[MAXLINE];    split into an exact number (nh*stepm) of unobserved intermediate
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    states. This elementary transition (by month, quarter,
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    semester or year) is modelled as a multinomial logistic.  The hPx
     matrix is simply the matrix product of nh*stepm elementary matrices
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    and the contribution of each individual to the likelihood is simply
 char filelog[FILENAMELENGTH]; /* Log file */    hPijx.
 char filerest[FILENAMELENGTH];  
 char fileregp[FILENAMELENGTH];    Also this programme outputs the covariance matrix of the parameters but also
 char popfile[FILENAMELENGTH];    of the life expectancies. It also computes the stable prevalence. 
     
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
              Institut national d'études démographiques, Paris.
 #define NR_END 1    This software have been partly granted by Euro-REVES, a concerted action
 #define FREE_ARG char*    from the European Union.
 #define FTOL 1.0e-10    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
 #define NRANSI    can be accessed at http://euroreves.ined.fr/imach .
 #define ITMAX 200  
     Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #define TOL 2.0e-4    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
     
 #define CGOLD 0.3819660    **********************************************************************/
 #define ZEPS 1.0e-10  /*
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    main
     read parameterfile
 #define GOLD 1.618034    read datafile
 #define GLIMIT 100.0    concatwav
 #define TINY 1.0e-20    freqsummary
     if (mle >= 1)
 static double maxarg1,maxarg2;      mlikeli
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    print results files
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    if mle==1 
         computes hessian
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    read end of parameter file: agemin, agemax, bage, fage, estepm
 #define rint(a) floor(a+0.5)        begin-prev-date,...
     open gnuplot file
 static double sqrarg;    open html file
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    stable prevalence
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}     for age prevalim()
     h Pij x
 int imx;    variance of p varprob
 int stepm;    forecasting if prevfcast==1 prevforecast call prevalence()
 /* Stepm, step in month: minimum step interpolation*/    health expectancies
     Variance-covariance of DFLE
 int estepm;    prevalence()
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/     movingaverage()
     varevsij() 
 int m,nb;    if popbased==1 varevsij(,popbased)
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    total life expectancies
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Variance of stable prevalence
 double **pmmij, ***probs, ***mobaverage;   end
 double dateintmean=0;  */
   
 double *weight;  
 int **s; /* Status */  
 double *agedc, **covar, idx;   
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  #include <math.h>
   #include <stdio.h>
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  #include <stdlib.h>
 double ftolhess; /* Tolerance for computing hessian */  #include <unistd.h>
   
 /**************** split *************************/  #include <sys/time.h>
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  #include <time.h>
 {  #include "timeval.h"
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */  /* #include <libintl.h> */
   /* #define _(String) gettext (String) */
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  #define MAXLINE 256
    s= strrchr( path, DIRSEPARATOR );            /* find last / */  #define GNUPLOTPROGRAM "gnuplot"
    if ( s == NULL ) {                   /* no directory, so use current */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
      /*if(strrchr(path, ODIRSEPARATOR )==NULL)  #define FILENAMELENGTH 132
        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/  /*#define DEBUG*/
 #if     defined(__bsd__)                /* get current working directory */  /*#define windows*/
       extern char       *getwd( );  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
       if ( getwd( dirc ) == NULL ) {  
 #else  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
       extern char       *getcwd( );  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  #define NINTERVMAX 8
 #endif  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
          return( GLOCK_ERROR_GETCWD );  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
       }  #define NCOVMAX 8 /* Maximum number of covariates */
       strcpy( name, path );             /* we've got it */  #define MAXN 20000
    } else {                             /* strip direcotry from path */  #define YEARM 12. /* Number of months per year */
       s++;                              /* after this, the filename */  #define AGESUP 130
       l2 = strlen( s );                 /* length of filename */  #define AGEBASE 40
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  #ifdef unix
       strcpy( name, s );                /* save file name */  #define DIRSEPARATOR '/'
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  #define ODIRSEPARATOR '\\'
       dirc[l1-l2] = 0;                  /* add zero */  #else
    }  #define DIRSEPARATOR '\\'
    l1 = strlen( dirc );                 /* length of directory */  #define ODIRSEPARATOR '/'
 #ifdef windows  #endif
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
 #else  /* $Id$ */
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  /* $State$ */
 #endif  
    s = strrchr( name, '.' );            /* find last / */  char version[]="Imach version 0.96d, February 2004, INED-EUROREVES ";
    s++;  char fullversion[]="$Revision$ $Date$"; 
    strcpy(ext,s);                       /* save extension */  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
    l1= strlen( name);  int nvar;
    l2= strlen( s)+1;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
    strncpy( finame, name, l1-l2);  int npar=NPARMAX;
    finame[l1-l2]= 0;  int nlstate=2; /* Number of live states */
    return( 0 );                         /* we're done */  int ndeath=1; /* Number of dead states */
 }  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int popbased=0;
   
 /******************************************/  int *wav; /* Number of waves for this individuual 0 is possible */
   int maxwav; /* Maxim number of waves */
 void replace(char *s, char*t)  int jmin, jmax; /* min, max spacing between 2 waves */
 {  int gipmx, gsw; /* Global variables on the number of contributions 
   int i;                     to the likelihood and the sum of weights (done by funcone)*/
   int lg=20;  int mle, weightopt;
   i=0;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   lg=strlen(t);  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   for(i=0; i<= lg; i++) {  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
     (s[i] = t[i]);             * wave mi and wave mi+1 is not an exact multiple of stepm. */
     if (t[i]== '\\') s[i]='/';  double jmean; /* Mean space between 2 waves */
   }  double **oldm, **newm, **savm; /* Working pointers to matrices */
 }  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 int nbocc(char *s, char occ)  FILE *ficlog, *ficrespow;
 {  int globpr; /* Global variable for printing or not */
   int i,j=0;  double fretone; /* Only one call to likelihood */
   int lg=20;  long ipmx; /* Number of contributions */
   i=0;  double sw; /* Sum of weights */
   lg=strlen(s);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   for(i=0; i<= lg; i++) {  FILE *ficresilk;
   if  (s[i] == occ ) j++;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   }  FILE *ficresprobmorprev;
   return j;  FILE *fichtm, *fichtmcov; /* Html File */
 }  FILE *ficreseij;
   char filerese[FILENAMELENGTH];
 void cutv(char *u,char *v, char*t, char occ)  FILE  *ficresvij;
 {  char fileresv[FILENAMELENGTH];
   /* cuts string t into u and v where u is ended by char occ excluding it  FILE  *ficresvpl;
      and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)  char fileresvpl[FILENAMELENGTH];
      gives u="abcedf" and v="ghi2j" */  char title[MAXLINE];
   int i,lg,j,p=0;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   i=0;  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   for(j=0; j<=strlen(t)-1; j++) {  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  char command[FILENAMELENGTH];
   }  int  outcmd=0;
   
   lg=strlen(t);  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   for(j=0; j<p; j++) {  
     (u[j] = t[j]);  char filelog[FILENAMELENGTH]; /* Log file */
   }  char filerest[FILENAMELENGTH];
      u[p]='\0';  char fileregp[FILENAMELENGTH];
   char popfile[FILENAMELENGTH];
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   }  
 }  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   struct timezone tzp;
 /********************** nrerror ********************/  extern int gettimeofday();
   struct tm tmg, tm, tmf, *gmtime(), *localtime();
 void nrerror(char error_text[])  long time_value;
 {  extern long time();
   fprintf(stderr,"ERREUR ...\n");  char strcurr[80], strfor[80];
   fprintf(stderr,"%s\n",error_text);  
   exit(1);  #define NR_END 1
 }  #define FREE_ARG char*
 /*********************** vector *******************/  #define FTOL 1.0e-10
 double *vector(int nl, int nh)  
 {  #define NRANSI 
   double *v;  #define ITMAX 200 
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");  #define TOL 2.0e-4 
   return v-nl+NR_END;  
 }  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
 /************************ free vector ******************/  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 void free_vector(double*v, int nl, int nh)  
 {  #define GOLD 1.618034 
   free((FREE_ARG)(v+nl-NR_END));  #define GLIMIT 100.0 
 }  #define TINY 1.0e-20 
   
 /************************ivector *******************************/  static double maxarg1,maxarg2;
 int *ivector(long nl,long nh)  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 {  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   int *v;    
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   if (!v) nrerror("allocation failure in ivector");  #define rint(a) floor(a+0.5)
   return v-nl+NR_END;  
 }  static double sqrarg;
   #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
 /******************free ivector **************************/  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 void free_ivector(int *v, long nl, long nh)  
 {  int imx; 
   free((FREE_ARG)(v+nl-NR_END));  int stepm;
 }  /* Stepm, step in month: minimum step interpolation*/
   
 /******************* imatrix *******************************/  int estepm;
 int **imatrix(long nrl, long nrh, long ncl, long nch)  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {  int m,nb;
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  long *num;
   int **m;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
    double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   /* allocate pointers to rows */  double **pmmij, ***probs;
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  double dateintmean=0;
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  double *weight;
   m -= nrl;  int **s; /* Status */
    double *agedc, **covar, idx;
    int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   /* allocate rows and set pointers to them */  
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  double ftolhess; /* Tolerance for computing hessian */
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  /**************** split *************************/
    static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  {
      char  *ss;                            /* pointer */
   /* return pointer to array of pointers to rows */    int   l1, l2;                         /* length counters */
   return m;  
 }    l1 = strlen(path );                   /* length of path */
     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 /****************** free_imatrix *************************/    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
 void free_imatrix(m,nrl,nrh,ncl,nch)    if ( ss == NULL ) {                   /* no directory, so use current */
       int **m;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       long nch,ncl,nrh,nrl;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
      /* free an int matrix allocated by imatrix() */      /* get current working directory */
 {      /*    extern  char* getcwd ( char *buf , int len);*/
   free((FREE_ARG) (m[nrl]+ncl-NR_END));      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   free((FREE_ARG) (m+nrl-NR_END));        return( GLOCK_ERROR_GETCWD );
 }      }
       strcpy( name, path );               /* we've got it */
 /******************* matrix *******************************/    } else {                              /* strip direcotry from path */
 double **matrix(long nrl, long nrh, long ncl, long nch)      ss++;                               /* after this, the filename */
 {      l2 = strlen( ss );                  /* length of filename */
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   double **m;      strcpy( name, ss );         /* save file name */
       strncpy( dirc, path, l1 - l2 );     /* now the directory */
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));      dirc[l1-l2] = 0;                    /* add zero */
   if (!m) nrerror("allocation failure 1 in matrix()");    }
   m += NR_END;    l1 = strlen( dirc );                  /* length of directory */
   m -= nrl;    /*#ifdef windows
     if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #else
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   m[nrl] += NR_END;  #endif
   m[nrl] -= ncl;    */
     ss = strrchr( name, '.' );            /* find last / */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    ss++;
   return m;    strcpy(ext,ss);                       /* save extension */
 }    l1= strlen( name);
     l2= strlen(ss)+1;
 /*************************free matrix ************************/    strncpy( finame, name, l1-l2);
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    finame[l1-l2]= 0;
 {    return( 0 );                          /* we're done */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  }
   free((FREE_ARG)(m+nrl-NR_END));  
 }  
   /******************************************/
 /******************* ma3x *******************************/  
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  void replace_back_to_slash(char *s, char*t)
 {  {
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    int i;
   double ***m;    int lg=0;
     i=0;
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    lg=strlen(t);
   if (!m) nrerror("allocation failure 1 in matrix()");    for(i=0; i<= lg; i++) {
   m += NR_END;      (s[i] = t[i]);
   m -= nrl;      if (t[i]== '\\') s[i]='/';
     }
   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;  int nbocc(char *s, char occ)
   m[nrl] -= ncl;  {
     int i,j=0;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    int lg=20;
     i=0;
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));    lg=strlen(s);
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");    for(i=0; i<= lg; i++) {
   m[nrl][ncl] += NR_END;    if  (s[i] == occ ) j++;
   m[nrl][ncl] -= nll;    }
   for (j=ncl+1; j<=nch; j++)    return j;
     m[nrl][j]=m[nrl][j-1]+nlay;  }
    
   for (i=nrl+1; i<=nrh; i++) {  void cutv(char *u,char *v, char*t, char occ)
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  {
     for (j=ncl+1; j<=nch; j++)    /* cuts string t into u and v where u is ended by char occ excluding it
       m[i][j]=m[i][j-1]+nlay;       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   }       gives u="abcedf" and v="ghi2j" */
   return m;    int i,lg,j,p=0;
 }    i=0;
     for(j=0; j<=strlen(t)-1; j++) {
 /*************************free ma3x ************************/      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    }
 {  
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    lg=strlen(t);
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    for(j=0; j<p; j++) {
   free((FREE_ARG)(m+nrl-NR_END));      (u[j] = t[j]);
 }    }
        u[p]='\0';
 /***************** f1dim *************************/  
 extern int ncom;     for(j=0; j<= lg; j++) {
 extern double *pcom,*xicom;      if (j>=(p+1))(v[j-p-1] = t[j]);
 extern double (*nrfunc)(double []);    }
    }
 double f1dim(double x)  
 {  /********************** nrerror ********************/
   int j;  
   double f;  void nrerror(char error_text[])
   double *xt;  {
      fprintf(stderr,"ERREUR ...\n");
   xt=vector(1,ncom);    fprintf(stderr,"%s\n",error_text);
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    exit(EXIT_FAILURE);
   f=(*nrfunc)(xt);  }
   free_vector(xt,1,ncom);  /*********************** vector *******************/
   return f;  double *vector(int nl, int nh)
 }  {
     double *v;
 /*****************brent *************************/    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    if (!v) nrerror("allocation failure in vector");
 {    return v-nl+NR_END;
   int iter;  }
   double a,b,d,etemp;  
   double fu,fv,fw,fx;  /************************ free vector ******************/
   double ftemp;  void free_vector(double*v, int nl, int nh)
   double p,q,r,tol1,tol2,u,v,w,x,xm;  {
   double e=0.0;    free((FREE_ARG)(v+nl-NR_END));
    }
   a=(ax < cx ? ax : cx);  
   b=(ax > cx ? ax : cx);  /************************ivector *******************************/
   x=w=v=bx;  int *ivector(long nl,long nh)
   fw=fv=fx=(*f)(x);  {
   for (iter=1;iter<=ITMAX;iter++) {    int *v;
     xm=0.5*(a+b);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);    if (!v) nrerror("allocation failure in ivector");
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    return v-nl+NR_END;
     printf(".");fflush(stdout);  }
     fprintf(ficlog,".");fflush(ficlog);  
 #ifdef DEBUG  /******************free ivector **************************/
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  void free_ivector(int *v, long nl, long nh)
     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)))) { */    free((FREE_ARG)(v+nl-NR_END));
 #endif  }
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  
       *xmin=x;  /************************lvector *******************************/
       return fx;  long *lvector(long nl,long nh)
     }  {
     ftemp=fu;    long *v;
     if (fabs(e) > tol1) {    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       r=(x-w)*(fx-fv);    if (!v) nrerror("allocation failure in ivector");
       q=(x-v)*(fx-fw);    return v-nl+NR_END;
       p=(x-v)*q-(x-w)*r;  }
       q=2.0*(q-r);  
       if (q > 0.0) p = -p;  /******************free lvector **************************/
       q=fabs(q);  void free_lvector(long *v, long nl, long nh)
       etemp=e;  {
       e=d;    free((FREE_ARG)(v+nl-NR_END));
       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));  
       else {  /******************* imatrix *******************************/
         d=p/q;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
         u=x+d;       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
         if (u-a < tol2 || b-u < tol2)  { 
           d=SIGN(tol1,xm-x);    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       }    int **m; 
     } else {    
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    /* allocate pointers to rows */ 
     }    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    if (!m) nrerror("allocation failure 1 in matrix()"); 
     fu=(*f)(u);    m += NR_END; 
     if (fu <= fx) {    m -= nrl; 
       if (u >= x) a=x; else b=x;    
       SHFT(v,w,x,u)    
         SHFT(fv,fw,fx,fu)    /* allocate rows and set pointers to them */ 
         } else {    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
           if (u < x) a=u; else b=u;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
           if (fu <= fw || w == x) {    m[nrl] += NR_END; 
             v=w;    m[nrl] -= ncl; 
             w=u;    
             fv=fw;    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
             fw=fu;    
           } else if (fu <= fv || v == x || v == w) {    /* return pointer to array of pointers to rows */ 
             v=u;    return m; 
             fv=fu;  } 
           }  
         }  /****************** free_imatrix *************************/
   }  void free_imatrix(m,nrl,nrh,ncl,nch)
   nrerror("Too many iterations in brent");        int **m;
   *xmin=x;        long nch,ncl,nrh,nrl; 
   return fx;       /* free an int matrix allocated by imatrix() */ 
 }  { 
     free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
 /****************** mnbrak ***********************/    free((FREE_ARG) (m+nrl-NR_END)); 
   } 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  
             double (*func)(double))  /******************* matrix *******************************/
 {  double **matrix(long nrl, long nrh, long ncl, long nch)
   double ulim,u,r,q, dum;  {
   double fu;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
      double **m;
   *fa=(*func)(*ax);  
   *fb=(*func)(*bx);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   if (*fb > *fa) {    if (!m) nrerror("allocation failure 1 in matrix()");
     SHFT(dum,*ax,*bx,dum)    m += NR_END;
       SHFT(dum,*fb,*fa,dum)    m -= nrl;
       }  
   *cx=(*bx)+GOLD*(*bx-*ax);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   *fc=(*func)(*cx);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   while (*fb > *fc) {    m[nrl] += NR_END;
     r=(*bx-*ax)*(*fb-*fc);    m[nrl] -= ncl;
     q=(*bx-*cx)*(*fb-*fa);  
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    return m;
     ulim=(*bx)+GLIMIT*(*cx-*bx);    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
     if ((*bx-u)*(u-*cx) > 0.0) {     */
       fu=(*func)(u);  }
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);  /*************************free matrix ************************/
       if (fu < *fc) {  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  {
           SHFT(*fb,*fc,fu,(*func)(u))    free((FREE_ARG)(m[nrl]+ncl-NR_END));
           }    free((FREE_ARG)(m+nrl-NR_END));
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  }
       u=ulim;  
       fu=(*func)(u);  /******************* ma3x *******************************/
     } else {  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       u=(*cx)+GOLD*(*cx-*bx);  {
       fu=(*func)(u);    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     }    double ***m;
     SHFT(*ax,*bx,*cx,u)  
       SHFT(*fa,*fb,*fc,fu)    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       }    if (!m) nrerror("allocation failure 1 in matrix()");
 }    m += NR_END;
     m -= nrl;
 /*************** linmin ************************/  
     m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 int ncom;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
 double *pcom,*xicom;    m[nrl] += NR_END;
 double (*nrfunc)(double []);    m[nrl] -= ncl;
    
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 {  
   double brent(double ax, double bx, double cx,    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
                double (*f)(double), double tol, double *xmin);    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   double f1dim(double x);    m[nrl][ncl] += NR_END;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    m[nrl][ncl] -= nll;
               double *fc, double (*func)(double));    for (j=ncl+1; j<=nch; j++) 
   int j;      m[nrl][j]=m[nrl][j-1]+nlay;
   double xx,xmin,bx,ax;    
   double fx,fb,fa;    for (i=nrl+1; i<=nrh; i++) {
        m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   ncom=n;      for (j=ncl+1; j<=nch; j++) 
   pcom=vector(1,n);        m[i][j]=m[i][j-1]+nlay;
   xicom=vector(1,n);    }
   nrfunc=func;    return m; 
   for (j=1;j<=n;j++) {    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     pcom[j]=p[j];             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     xicom[j]=xi[j];    */
   }  }
   ax=0.0;  
   xx=1.0;  /*************************free ma3x ************************/
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  {
 #ifdef DEBUG    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    free((FREE_ARG)(m+nrl-NR_END));
 #endif  }
   for (j=1;j<=n;j++) {  
     xi[j] *= xmin;  /*************** function subdirf ***********/
     p[j] += xi[j];  char *subdirf(char fileres[])
   }  {
   free_vector(xicom,1,n);    /* Caution optionfilefiname is hidden */
   free_vector(pcom,1,n);    strcpy(tmpout,optionfilefiname);
 }    strcat(tmpout,"/"); /* Add to the right */
     strcat(tmpout,fileres);
 /*************** powell ************************/    return tmpout;
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  }
             double (*func)(double []))  
 {  /*************** function subdirf2 ***********/
   void linmin(double p[], double xi[], int n, double *fret,  char *subdirf2(char fileres[], char *preop)
               double (*func)(double []));  {
   int i,ibig,j;    
   double del,t,*pt,*ptt,*xit;    /* Caution optionfilefiname is hidden */
   double fp,fptt;    strcpy(tmpout,optionfilefiname);
   double *xits;    strcat(tmpout,"/");
   pt=vector(1,n);    strcat(tmpout,preop);
   ptt=vector(1,n);    strcat(tmpout,fileres);
   xit=vector(1,n);    return tmpout;
   xits=vector(1,n);  }
   *fret=(*func)(p);  
   for (j=1;j<=n;j++) pt[j]=p[j];  /*************** function subdirf3 ***********/
   for (*iter=1;;++(*iter)) {  char *subdirf3(char fileres[], char *preop, char *preop2)
     fp=(*fret);  {
     ibig=0;    
     del=0.0;    /* Caution optionfilefiname is hidden */
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    strcpy(tmpout,optionfilefiname);
     fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    strcat(tmpout,"/");
     for (i=1;i<=n;i++)    strcat(tmpout,preop);
       printf(" %d %.12f",i, p[i]);    strcat(tmpout,preop2);
     fprintf(ficlog," %d %.12f",i, p[i]);    strcat(tmpout,fileres);
     printf("\n");    return tmpout;
     fprintf(ficlog,"\n");  }
     for (i=1;i<=n;i++) {  
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  /***************** f1dim *************************/
       fptt=(*fret);  extern int ncom; 
 #ifdef DEBUG  extern double *pcom,*xicom;
       printf("fret=%lf \n",*fret);  extern double (*nrfunc)(double []); 
       fprintf(ficlog,"fret=%lf \n",*fret);   
 #endif  double f1dim(double x) 
       printf("%d",i);fflush(stdout);  { 
       fprintf(ficlog,"%d",i);fflush(ficlog);    int j; 
       linmin(p,xit,n,fret,func);    double f;
       if (fabs(fptt-(*fret)) > del) {    double *xt; 
         del=fabs(fptt-(*fret));   
         ibig=i;    xt=vector(1,ncom); 
       }    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
 #ifdef DEBUG    f=(*nrfunc)(xt); 
       printf("%d %.12e",i,(*fret));    free_vector(xt,1,ncom); 
       fprintf(ficlog,"%d %.12e",i,(*fret));    return f; 
       for (j=1;j<=n;j++) {  } 
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  
         printf(" x(%d)=%.12e",j,xit[j]);  /*****************brent *************************/
         fprintf(ficlog," x(%d)=%.12e",j,xit[j]);  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
       }  { 
       for(j=1;j<=n;j++) {    int iter; 
         printf(" p=%.12e",p[j]);    double a,b,d,etemp;
         fprintf(ficlog," p=%.12e",p[j]);    double fu,fv,fw,fx;
       }    double ftemp;
       printf("\n");    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       fprintf(ficlog,"\n");    double e=0.0; 
 #endif   
     }    a=(ax < cx ? ax : cx); 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    b=(ax > cx ? ax : cx); 
 #ifdef DEBUG    x=w=v=bx; 
       int k[2],l;    fw=fv=fx=(*f)(x); 
       k[0]=1;    for (iter=1;iter<=ITMAX;iter++) { 
       k[1]=-1;      xm=0.5*(a+b); 
       printf("Max: %.12e",(*func)(p));      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       fprintf(ficlog,"Max: %.12e",(*func)(p));      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
       for (j=1;j<=n;j++) {      printf(".");fflush(stdout);
         printf(" %.12e",p[j]);      fprintf(ficlog,".");fflush(ficlog);
         fprintf(ficlog," %.12e",p[j]);  #ifdef DEBUG
       }      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       printf("\n");      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);
       fprintf(ficlog,"\n");      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       for(l=0;l<=1;l++) {  #endif
         for (j=1;j<=n;j++) {      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];        *xmin=x; 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);        return fx; 
           fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);      } 
         }      ftemp=fu;
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));      if (fabs(e) > tol1) { 
         fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));        r=(x-w)*(fx-fv); 
       }        q=(x-v)*(fx-fw); 
 #endif        p=(x-v)*q-(x-w)*r; 
         q=2.0*(q-r); 
         if (q > 0.0) p = -p; 
       free_vector(xit,1,n);        q=fabs(q); 
       free_vector(xits,1,n);        etemp=e; 
       free_vector(ptt,1,n);        e=d; 
       free_vector(pt,1,n);        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
       return;          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     }        else { 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");          d=p/q; 
     for (j=1;j<=n;j++) {          u=x+d; 
       ptt[j]=2.0*p[j]-pt[j];          if (u-a < tol2 || b-u < tol2) 
       xit[j]=p[j]-pt[j];            d=SIGN(tol1,xm-x); 
       pt[j]=p[j];        } 
     }      } else { 
     fptt=(*func)(ptt);        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
     if (fptt < fp) {      } 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       if (t < 0.0) {      fu=(*f)(u); 
         linmin(p,xit,n,fret,func);      if (fu <= fx) { 
         for (j=1;j<=n;j++) {        if (u >= x) a=x; else b=x; 
           xi[j][ibig]=xi[j][n];        SHFT(v,w,x,u) 
           xi[j][n]=xit[j];          SHFT(fv,fw,fx,fu) 
         }          } else { 
 #ifdef DEBUG            if (u < x) a=u; else b=u; 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);            if (fu <= fw || w == x) { 
         fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);              v=w; 
         for(j=1;j<=n;j++){              w=u; 
           printf(" %.12e",xit[j]);              fv=fw; 
           fprintf(ficlog," %.12e",xit[j]);              fw=fu; 
         }            } else if (fu <= fv || v == x || v == w) { 
         printf("\n");              v=u; 
         fprintf(ficlog,"\n");              fv=fu; 
 #endif            } 
       }          } 
     }    } 
   }    nrerror("Too many iterations in brent"); 
 }    *xmin=x; 
     return fx; 
 /**** Prevalence limit ****************/  } 
   
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  /****************** mnbrak ***********************/
 {  
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
      matrix by transitions matrix until convergence is reached */              double (*func)(double)) 
   { 
   int i, ii,j,k;    double ulim,u,r,q, dum;
   double min, max, maxmin, maxmax,sumnew=0.;    double fu; 
   double **matprod2();   
   double **out, cov[NCOVMAX], **pmij();    *fa=(*func)(*ax); 
   double **newm;    *fb=(*func)(*bx); 
   double agefin, delaymax=50 ; /* Max number of years to converge */    if (*fb > *fa) { 
       SHFT(dum,*ax,*bx,dum) 
   for (ii=1;ii<=nlstate+ndeath;ii++)        SHFT(dum,*fb,*fa,dum) 
     for (j=1;j<=nlstate+ndeath;j++){        } 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    *cx=(*bx)+GOLD*(*bx-*ax); 
     }    *fc=(*func)(*cx); 
     while (*fb > *fc) { 
    cov[1]=1.;      r=(*bx-*ax)*(*fb-*fc); 
        q=(*bx-*cx)*(*fb-*fa); 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
     newm=savm;      ulim=(*bx)+GLIMIT*(*cx-*bx); 
     /* Covariates have to be included here again */      if ((*bx-u)*(u-*cx) > 0.0) { 
      cov[2]=agefin;        fu=(*func)(u); 
        } else if ((*cx-u)*(u-ulim) > 0.0) { 
       for (k=1; k<=cptcovn;k++) {        fu=(*func)(u); 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        if (fu < *fc) { 
         /*      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]]);*/          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
       }            SHFT(*fb,*fc,fu,(*func)(u)) 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];            } 
       for (k=1; k<=cptcovprod;k++)      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        u=ulim; 
         fu=(*func)(u); 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      } else { 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/        u=(*cx)+GOLD*(*cx-*bx); 
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/        fu=(*func)(u); 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);      } 
       SHFT(*ax,*bx,*cx,u) 
     savm=oldm;        SHFT(*fa,*fb,*fc,fu) 
     oldm=newm;        } 
     maxmax=0.;  } 
     for(j=1;j<=nlstate;j++){  
       min=1.;  /*************** linmin ************************/
       max=0.;  
       for(i=1; i<=nlstate; i++) {  int ncom; 
         sumnew=0;  double *pcom,*xicom;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  double (*nrfunc)(double []); 
         prlim[i][j]= newm[i][j]/(1-sumnew);   
         max=FMAX(max,prlim[i][j]);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
         min=FMIN(min,prlim[i][j]);  { 
       }    double brent(double ax, double bx, double cx, 
       maxmin=max-min;                 double (*f)(double), double tol, double *xmin); 
       maxmax=FMAX(maxmax,maxmin);    double f1dim(double x); 
     }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     if(maxmax < ftolpl){                double *fc, double (*func)(double)); 
       return prlim;    int j; 
     }    double xx,xmin,bx,ax; 
   }    double fx,fb,fa;
 }   
     ncom=n; 
 /*************** transition probabilities ***************/    pcom=vector(1,n); 
     xicom=vector(1,n); 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    nrfunc=func; 
 {    for (j=1;j<=n;j++) { 
   double s1, s2;      pcom[j]=p[j]; 
   /*double t34;*/      xicom[j]=xi[j]; 
   int i,j,j1, nc, ii, jj;    } 
     ax=0.0; 
     for(i=1; i<= nlstate; i++){    xx=1.0; 
     for(j=1; j<i;j++){    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
         /*s2 += param[i][j][nc]*cov[nc];*/  #ifdef DEBUG
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
       }  #endif
       ps[i][j]=s2;    for (j=1;j<=n;j++) { 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/      xi[j] *= xmin; 
     }      p[j] += xi[j]; 
     for(j=i+1; j<=nlstate+ndeath;j++){    } 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    free_vector(xicom,1,n); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    free_vector(pcom,1,n); 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/  } 
       }  
       ps[i][j]=s2;  char *asc_diff_time(long time_sec, char ascdiff[])
     }  {
   }    long sec_left, days, hours, minutes;
     /*ps[3][2]=1;*/    days = (time_sec) / (60*60*24);
     sec_left = (time_sec) % (60*60*24);
   for(i=1; i<= nlstate; i++){    hours = (sec_left) / (60*60) ;
      s1=0;    sec_left = (sec_left) %(60*60);
     for(j=1; j<i; j++)    minutes = (sec_left) /60;
       s1+=exp(ps[i][j]);    sec_left = (sec_left) % (60);
     for(j=i+1; j<=nlstate+ndeath; j++)    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
       s1+=exp(ps[i][j]);    return ascdiff;
     ps[i][i]=1./(s1+1.);  }
     for(j=1; j<i; j++)  
       ps[i][j]= exp(ps[i][j])*ps[i][i];  /*************** powell ************************/
     for(j=i+1; j<=nlstate+ndeath; j++)  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       ps[i][j]= exp(ps[i][j])*ps[i][i];              double (*func)(double [])) 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  { 
   } /* end i */    void linmin(double p[], double xi[], int n, double *fret, 
                 double (*func)(double [])); 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    int i,ibig,j; 
     for(jj=1; jj<= nlstate+ndeath; jj++){    double del,t,*pt,*ptt,*xit;
       ps[ii][jj]=0;    double fp,fptt;
       ps[ii][ii]=1;    double *xits;
     }    int niterf, itmp;
   }  
     pt=vector(1,n); 
     ptt=vector(1,n); 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    xit=vector(1,n); 
     for(jj=1; jj<= nlstate+ndeath; jj++){    xits=vector(1,n); 
      printf("%lf ",ps[ii][jj]);    *fret=(*func)(p); 
    }    for (j=1;j<=n;j++) pt[j]=p[j]; 
     printf("\n ");    for (*iter=1;;++(*iter)) { 
     }      fp=(*fret); 
     printf("\n ");printf("%lf ",cov[2]);*/      ibig=0; 
 /*      del=0.0; 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);      last_time=curr_time;
   goto end;*/      (void) gettimeofday(&curr_time,&tzp);
     return ps;      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);
 }      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
       fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
 /**************** Product of 2 matrices ******************/      for (i=1;i<=n;i++) {
         printf(" %d %.12f",i, p[i]);
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)        fprintf(ficlog," %d %.12lf",i, p[i]);
 {        fprintf(ficrespow," %.12lf", p[i]);
   /* 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(...) */      printf("\n");
   /* in, b, out are matrice of pointers which should have been initialized      fprintf(ficlog,"\n");
      before: only the contents of out is modified. The function returns      fprintf(ficrespow,"\n");fflush(ficrespow);
      a pointer to pointers identical to out */      if(*iter <=3){
   long i, j, k;        tm = *localtime(&curr_time.tv_sec);
   for(i=nrl; i<= nrh; i++)        strcpy(strcurr,asctime(&tmf));
     for(k=ncolol; k<=ncoloh; k++)  /*       asctime_r(&tm,strcurr); */
       for(j=ncl,out[i][k]=0.; j<=nch; j++)        forecast_time=curr_time;
         out[i][k] +=in[i][j]*b[j][k];        itmp = strlen(strcurr);
         if(strcurr[itmp-1]=='\n')
   return out;          strcurr[itmp-1]='\0';
 }        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         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){
 /************* Higher Matrix Product ***************/          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
           tmf = *localtime(&forecast_time.tv_sec);
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  /*      asctime_r(&tmf,strfor); */
 {          strcpy(strfor,asctime(&tmf));
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month          itmp = strlen(strfor);
      duration (i.e. until          if(strfor[itmp-1]=='\n')
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.          strfor[itmp-1]='\0';
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step          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);
      (typically every 2 years instead of every month which is too big).          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);
      Model is determined by parameters x and covariates have to be        }
      included manually here.      }
       for (i=1;i<=n;i++) { 
      */        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         fptt=(*fret); 
   int i, j, d, h, k;  #ifdef DEBUG
   double **out, cov[NCOVMAX];        printf("fret=%lf \n",*fret);
   double **newm;        fprintf(ficlog,"fret=%lf \n",*fret);
   #endif
   /* Hstepm could be zero and should return the unit matrix */        printf("%d",i);fflush(stdout);
   for (i=1;i<=nlstate+ndeath;i++)        fprintf(ficlog,"%d",i);fflush(ficlog);
     for (j=1;j<=nlstate+ndeath;j++){        linmin(p,xit,n,fret,func); 
       oldm[i][j]=(i==j ? 1.0 : 0.0);        if (fabs(fptt-(*fret)) > del) { 
       po[i][j][0]=(i==j ? 1.0 : 0.0);          del=fabs(fptt-(*fret)); 
     }          ibig=i; 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */        } 
   for(h=1; h <=nhstepm; h++){  #ifdef DEBUG
     for(d=1; d <=hstepm; d++){        printf("%d %.12e",i,(*fret));
       newm=savm;        fprintf(ficlog,"%d %.12e",i,(*fret));
       /* Covariates have to be included here again */        for (j=1;j<=n;j++) {
       cov[1]=1.;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;          printf(" x(%d)=%.12e",j,xit[j]);
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
       for (k=1; k<=cptcovage;k++)        }
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        for(j=1;j<=n;j++) {
       for (k=1; k<=cptcovprod;k++)          printf(" p=%.12e",p[j]);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          fprintf(ficlog," p=%.12e",p[j]);
         }
         printf("\n");
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        fprintf(ficlog,"\n");
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  #endif
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      } 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
       savm=oldm;  #ifdef DEBUG
       oldm=newm;        int k[2],l;
     }        k[0]=1;
     for(i=1; i<=nlstate+ndeath; i++)        k[1]=-1;
       for(j=1;j<=nlstate+ndeath;j++) {        printf("Max: %.12e",(*func)(p));
         po[i][j][h]=newm[i][j];        fprintf(ficlog,"Max: %.12e",(*func)(p));
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);        for (j=1;j<=n;j++) {
          */          printf(" %.12e",p[j]);
       }          fprintf(ficlog," %.12e",p[j]);
   } /* end h */        }
   return po;        printf("\n");
 }        fprintf(ficlog,"\n");
         for(l=0;l<=1;l++) {
           for (j=1;j<=n;j++) {
 /*************** log-likelihood *************/            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
 double func( 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]);
 {            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   int i, ii, j, k, mi, d, kk;          }
   double l, ll[NLSTATEMAX], cov[NCOVMAX];          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   double **out;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   double sw; /* Sum of weights */        }
   double lli; /* Individual log likelihood */  #endif
   long ipmx;  
   /*extern weight */  
   /* We are differentiating ll according to initial status */        free_vector(xit,1,n); 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        free_vector(xits,1,n); 
   /*for(i=1;i<imx;i++)        free_vector(ptt,1,n); 
     printf(" %d\n",s[4][i]);        free_vector(pt,1,n); 
   */        return; 
   cov[1]=1.;      } 
       if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   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++){        ptt[j]=2.0*p[j]-pt[j]; 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        xit[j]=p[j]-pt[j]; 
     for(mi=1; mi<= wav[i]-1; mi++){        pt[j]=p[j]; 
       for (ii=1;ii<=nlstate+ndeath;ii++)      } 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      fptt=(*func)(ptt); 
       for(d=0; d<dh[mi][i]; d++){      if (fptt < fp) { 
         newm=savm;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;        if (t < 0.0) { 
         for (kk=1; kk<=cptcovage;kk++) {          linmin(p,xit,n,fret,func); 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];          for (j=1;j<=n;j++) { 
         }            xi[j][ibig]=xi[j][n]; 
                    xi[j][n]=xit[j]; 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,          }
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  #ifdef DEBUG
         savm=oldm;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         oldm=newm;          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++){
                    printf(" %.12e",xit[j]);
       } /* end mult */            fprintf(ficlog," %.12e",xit[j]);
                }
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);          printf("\n");
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/          fprintf(ficlog,"\n");
       ipmx +=1;  #endif
       sw += weight[i];        }
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;      } 
     } /* end of wave */    } 
   } /* end of individual */  } 
   
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  /**** Prevalence limit (stable prevalence)  ****************/
   /* 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 */  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   return -l;  {
 }    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
        matrix by transitions matrix until convergence is reached */
   
 /*********** Maximum Likelihood Estimation ***************/    int i, ii,j,k;
     double min, max, maxmin, maxmax,sumnew=0.;
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    double **matprod2();
 {    double **out, cov[NCOVMAX], **pmij();
   int i,j, iter;    double **newm;
   double **xi,*delti;    double agefin, delaymax=50 ; /* Max number of years to converge */
   double fret;  
   xi=matrix(1,npar,1,npar);    for (ii=1;ii<=nlstate+ndeath;ii++)
   for (i=1;i<=npar;i++)      for (j=1;j<=nlstate+ndeath;j++){
     for (j=1;j<=npar;j++)        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       xi[i][j]=(i==j ? 1.0 : 0.0);      }
   printf("Powell\n");  fprintf(ficlog,"Powell\n");  
   powell(p,xi,npar,ftol,&iter,&fret,func);     cov[1]=1.;
    
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   fprintf(ficlog,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));      newm=savm;
       /* Covariates have to be included here again */
 }       cov[2]=agefin;
     
 /**** Computes Hessian and covariance matrix ***/        for (k=1; k<=cptcovn;k++) {
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
 {          /*      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]]);*/
   double  **a,**y,*x,pd;        }
   double **hess;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   int i, j,jk;        for (k=1; k<=cptcovprod;k++)
   int *indx;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
   double hessii(double p[], double delta, int theta, double delti[]);        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   double hessij(double p[], double delti[], int i, int j);        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   void lubksb(double **a, int npar, int *indx, double b[]) ;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   void ludcmp(double **a, int npar, int *indx, double *d) ;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   
   hess=matrix(1,npar,1,npar);      savm=oldm;
       oldm=newm;
   printf("\nCalculation of the hessian matrix. Wait...\n");      maxmax=0.;
   fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");      for(j=1;j<=nlstate;j++){
   for (i=1;i<=npar;i++){        min=1.;
     printf("%d",i);fflush(stdout);        max=0.;
     fprintf(ficlog,"%d",i);fflush(ficlog);        for(i=1; i<=nlstate; i++) {
     hess[i][i]=hessii(p,ftolhess,i,delti);          sumnew=0;
     /*printf(" %f ",p[i]);*/          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     /*printf(" %lf ",hess[i][i]);*/          prlim[i][j]= newm[i][j]/(1-sumnew);
   }          max=FMAX(max,prlim[i][j]);
            min=FMIN(min,prlim[i][j]);
   for (i=1;i<=npar;i++) {        }
     for (j=1;j<=npar;j++)  {        maxmin=max-min;
       if (j>i) {        maxmax=FMAX(maxmax,maxmin);
         printf(".%d%d",i,j);fflush(stdout);      }
         fprintf(ficlog,".%d%d",i,j);fflush(ficlog);      if(maxmax < ftolpl){
         hess[i][j]=hessij(p,delti,i,j);        return prlim;
         hess[j][i]=hess[i][j];          }
         /*printf(" %lf ",hess[i][j]);*/    }
       }  }
     }  
   }  /*************** transition probabilities ***************/ 
   printf("\n");  
   fprintf(ficlog,"\n");  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   {
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    double s1, s2;
   fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");    /*double t34;*/
      int i,j,j1, nc, ii, jj;
   a=matrix(1,npar,1,npar);  
   y=matrix(1,npar,1,npar);      for(i=1; i<= nlstate; i++){
   x=vector(1,npar);      for(j=1; j<i;j++){
   indx=ivector(1,npar);        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   for (i=1;i<=npar;i++)          /*s2 += param[i][j][nc]*cov[nc];*/
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   ludcmp(a,npar,indx,&pd);          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
         }
   for (j=1;j<=npar;j++) {        ps[i][j]=s2;
     for (i=1;i<=npar;i++) x[i]=0;        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
     x[j]=1;      }
     lubksb(a,npar,indx,x);      for(j=i+1; j<=nlstate+ndeath;j++){
     for (i=1;i<=npar;i++){        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       matcov[i][j]=x[i];          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);*/
   }        }
         ps[i][j]=s2;
   printf("\n#Hessian matrix#\n");      }
   fprintf(ficlog,"\n#Hessian matrix#\n");    }
   for (i=1;i<=npar;i++) {      /*ps[3][2]=1;*/
     for (j=1;j<=npar;j++) {  
       printf("%.3e ",hess[i][j]);    for(i=1; i<= nlstate; i++){
       fprintf(ficlog,"%.3e ",hess[i][j]);       s1=0;
     }      for(j=1; j<i; j++)
     printf("\n");        s1+=exp(ps[i][j]);
     fprintf(ficlog,"\n");      for(j=i+1; j<=nlstate+ndeath; j++)
   }        s1+=exp(ps[i][j]);
       ps[i][i]=1./(s1+1.);
   /* Recompute Inverse */      for(j=1; j<i; j++)
   for (i=1;i<=npar;i++)        ps[i][j]= exp(ps[i][j])*ps[i][i];
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];      for(j=i+1; j<=nlstate+ndeath; j++)
   ludcmp(a,npar,indx,&pd);        ps[i][j]= exp(ps[i][j])*ps[i][i];
       /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   /*  printf("\n#Hessian matrix recomputed#\n");    } /* end i */
   
   for (j=1;j<=npar;j++) {    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     for (i=1;i<=npar;i++) x[i]=0;      for(jj=1; jj<= nlstate+ndeath; jj++){
     x[j]=1;        ps[ii][jj]=0;
     lubksb(a,npar,indx,x);        ps[ii][ii]=1;
     for (i=1;i<=npar;i++){      }
       y[i][j]=x[i];    }
       printf("%.3e ",y[i][j]);  
       fprintf(ficlog,"%.3e ",y[i][j]);  
     }    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
     printf("\n");      for(jj=1; jj<= nlstate+ndeath; jj++){
     fprintf(ficlog,"\n");       printf("%lf ",ps[ii][jj]);
   }     }
   */      printf("\n ");
       }
   free_matrix(a,1,npar,1,npar);      printf("\n ");printf("%lf ",cov[2]);*/
   free_matrix(y,1,npar,1,npar);  /*
   free_vector(x,1,npar);    for(i=1; i<= npar; i++) printf("%f ",x[i]);
   free_ivector(indx,1,npar);    goto end;*/
   free_matrix(hess,1,npar,1,npar);      return ps;
   }
   
 }  /**************** Product of 2 matrices ******************/
   
 /*************** hessian matrix ****************/  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
 double hessii( double x[], double delta, int theta, double delti[])  {
 {    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   int i;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   int l=1, lmax=20;    /* in, b, out are matrice of pointers which should have been initialized 
   double k1,k2;       before: only the contents of out is modified. The function returns
   double p2[NPARMAX+1];       a pointer to pointers identical to out */
   double res;    long i, j, k;
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;    for(i=nrl; i<= nrh; i++)
   double fx;      for(k=ncolol; k<=ncoloh; k++)
   int k=0,kmax=10;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
   double l1;          out[i][k] +=in[i][j]*b[j][k];
   
   fx=func(x);    return out;
   for (i=1;i<=npar;i++) p2[i]=x[i];  }
   for(l=0 ; l <=lmax; l++){  
     l1=pow(10,l);  
     delts=delt;  /************* Higher Matrix Product ***************/
     for(k=1 ; k <kmax; k=k+1){  
       delt = delta*(l1*k);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
       p2[theta]=x[theta] +delt;  {
       k1=func(p2)-fx;    /* Computes the transition matrix starting at age 'age' over 
       p2[theta]=x[theta]-delt;       'nhstepm*hstepm*stepm' months (i.e. until
       k2=func(p2)-fx;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
       /*res= (k1-2.0*fx+k2)/delt/delt; */       nhstepm*hstepm matrices. 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
             (typically every 2 years instead of every month which is too big 
 #ifdef DEBUG       for the memory).
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);       Model is determined by parameters x and covariates have to be 
       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);       included manually here. 
 #endif  
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */       */
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  
         k=kmax;    int i, j, d, h, k;
       }    double **out, cov[NCOVMAX];
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    double **newm;
         k=kmax; l=lmax*10.;  
       }    /* Hstepm could be zero and should return the unit matrix */
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    for (i=1;i<=nlstate+ndeath;i++)
         delts=delt;      for (j=1;j<=nlstate+ndeath;j++){
       }        oldm[i][j]=(i==j ? 1.0 : 0.0);
     }        po[i][j][0]=(i==j ? 1.0 : 0.0);
   }      }
   delti[theta]=delts;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   return res;    for(h=1; h <=nhstepm; h++){
        for(d=1; d <=hstepm; d++){
 }        newm=savm;
         /* Covariates have to be included here again */
 double hessij( double x[], double delti[], int thetai,int thetaj)        cov[1]=1.;
 {        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   int i;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   int l=1, l1, lmax=20;        for (k=1; k<=cptcovage;k++)
   double k1,k2,k3,k4,res,fx;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   double p2[NPARMAX+1];        for (k=1; k<=cptcovprod;k++)
   int k;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   
   fx=func(x);  
   for (k=1; k<=2; k++) {        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
     for (i=1;i<=npar;i++) p2[i]=x[i];        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
     p2[thetai]=x[thetai]+delti[thetai]/k;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     k1=func(p2)-fx;        savm=oldm;
          oldm=newm;
     p2[thetai]=x[thetai]+delti[thetai]/k;      }
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      for(i=1; i<=nlstate+ndeath; i++)
     k2=func(p2)-fx;        for(j=1;j<=nlstate+ndeath;j++) {
            po[i][j][h]=newm[i][j];
     p2[thetai]=x[thetai]-delti[thetai]/k;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;           */
     k3=func(p2)-fx;        }
      } /* end h */
     p2[thetai]=x[thetai]-delti[thetai]/k;    return po;
     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  /*************** log-likelihood *************/
     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 func( double *x)
     fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);  {
 #endif    int i, ii, j, k, mi, d, kk;
   }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   return res;    double **out;
 }    double sw; /* Sum of weights */
     double lli; /* Individual log likelihood */
 /************** Inverse of matrix **************/    int s1, s2;
 void ludcmp(double **a, int n, int *indx, double *d)    double bbh, survp;
 {    long ipmx;
   int i,imax,j,k;    /*extern weight */
   double big,dum,sum,temp;    /* We are differentiating ll according to initial status */
   double *vv;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
      /*for(i=1;i<imx;i++) 
   vv=vector(1,n);      printf(" %d\n",s[4][i]);
   *d=1.0;    */
   for (i=1;i<=n;i++) {    cov[1]=1.;
     big=0.0;  
     for (j=1;j<=n;j++)    for(k=1; k<=nlstate; k++) ll[k]=0.;
       if ((temp=fabs(a[i][j])) > big) big=temp;  
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    if(mle==1){
     vv[i]=1.0/big;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   for (j=1;j<=n;j++) {        for(mi=1; mi<= wav[i]-1; mi++){
     for (i=1;i<j;i++) {          for (ii=1;ii<=nlstate+ndeath;ii++)
       sum=a[i][j];            for (j=1;j<=nlstate+ndeath;j++){
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       a[i][j]=sum;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     }            }
     big=0.0;          for(d=0; d<dh[mi][i]; d++){
     for (i=j;i<=n;i++) {            newm=savm;
       sum=a[i][j];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for (k=1;k<j;k++)            for (kk=1; kk<=cptcovage;kk++) {
         sum -= a[i][k]*a[k][j];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       a[i][j]=sum;            }
       if ( (dum=vv[i]*fabs(sum)) >= big) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         big=dum;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         imax=i;            savm=oldm;
       }            oldm=newm;
     }          } /* end mult */
     if (j != imax) {        
       for (k=1;k<=n;k++) {          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         dum=a[imax][k];          /* But now since version 0.9 we anticipate for bias and large stepm.
         a[imax][k]=a[j][k];           * If stepm is larger than one month (smallest stepm) and if the exact delay 
         a[j][k]=dum;           * (in months) between two waves is not a multiple of stepm, we rounded to 
       }           * the nearest (and in case of equal distance, to the lowest) interval but now
       *d = -(*d);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       vv[imax]=vv[j];           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
     }           * probability in order to take into account the bias as a fraction of the way
     indx[j]=imax;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     if (a[j][j] == 0.0) a[j][j]=TINY;           * -stepm/2 to stepm/2 .
     if (j != n) {           * For stepm=1 the results are the same as for previous versions of Imach.
       dum=1.0/(a[j][j]);           * For stepm > 1 the results are less biased than in previous versions. 
       for (i=j+1;i<=n;i++) a[i][j] *= dum;           */
     }          s1=s[mw[mi][i]][i];
   }          s2=s[mw[mi+1][i]][i];
   free_vector(vv,1,n);  /* Doesn't work */          bbh=(double)bh[mi][i]/(double)stepm; 
 ;          /* bias is positive if real duration
 }           * is higher than the multiple of stepm and negative otherwise.
            */
 void lubksb(double **a, int n, int *indx, double b[])          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
 {          if( s2 > nlstate){ 
   int i,ii=0,ip,j;            /* i.e. if s2 is a death state and if the date of death is known then the contribution
   double sum;               to the likelihood is the probability to die between last step unit time and current 
                 step unit time, which is also the differences between probability to die before dh 
   for (i=1;i<=n;i++) {               and probability to die before dh-stepm . 
     ip=indx[i];               In version up to 0.92 likelihood was computed
     sum=b[ip];          as if date of death was unknown. Death was treated as any other
     b[ip]=b[i];          health state: the date of the interview describes the actual state
     if (ii)          and not the date of a change in health state. The former idea was
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          to consider that at each interview the state was recorded
     else if (sum) ii=i;          (healthy, disable or death) and IMaCh was corrected; but when we
     b[i]=sum;          introduced the exact date of death then we should have modified
   }          the contribution of an exact death to the likelihood. This new
   for (i=n;i>=1;i--) {          contribution is smaller and very dependent of the step unit
     sum=b[i];          stepm. It is no more the probability to die between last interview
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          and month of death but the probability to survive from last
     b[i]=sum/a[i][i];          interview up to one month before death multiplied by the
   }          probability to die within a month. Thanks to Chris
 }          Jackson for correcting this bug.  Former versions increased
           mortality artificially. The bad side is that we add another loop
 /************ Frequencies ********************/          which slows down the processing. The difference can be up to 10%
 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)          lower mortality.
 {  /* Some frequencies */            */
              lli=log(out[s1][s2] - savm[s1][s2]);
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          }else{
   int first;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   double ***freq; /* Frequencies */            /*  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 */
   double *pp;          } 
   double pos, k2, dateintsum=0,k2cpt=0;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   FILE *ficresp;          /*if(lli ==000.0)*/
   char fileresp[FILENAMELENGTH];          /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
            ipmx +=1;
   pp=vector(1,nlstate);          sw += weight[i];
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   strcpy(fileresp,"p");        } /* end of wave */
   strcat(fileresp,fileres);      } /* end of individual */
   if((ficresp=fopen(fileresp,"w"))==NULL) {    }  else if(mle==2){
     printf("Problem with prevalence resultfile: %s\n", fileresp);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     exit(0);        for(mi=1; mi<= wav[i]-1; mi++){
   }          for (ii=1;ii<=nlstate+ndeath;ii++)
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);            for (j=1;j<=nlstate+ndeath;j++){
   j1=0;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                savm[ii][j]=(ii==j ? 1.0 : 0.0);
   j=cptcoveff;            }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          for(d=0; d<=dh[mi][i]; d++){
             newm=savm;
   first=1;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
   for(k1=1; k1<=j;k1++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for(i1=1; i1<=ncodemax[k1];i1++){            }
       j1++;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         scanf("%d", i);*/            savm=oldm;
       for (i=-1; i<=nlstate+ndeath; i++)              oldm=newm;
         for (jk=-1; jk<=nlstate+ndeath; jk++)            } /* end mult */
           for(m=agemin; m <= agemax+3; m++)        
             freq[i][jk][m]=0;          s1=s[mw[mi][i]][i];
                s2=s[mw[mi+1][i]][i];
       dateintsum=0;          bbh=(double)bh[mi][i]/(double)stepm; 
       k2cpt=0;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
       for (i=1; i<=imx; i++) {          ipmx +=1;
         bool=1;          sw += weight[i];
         if  (cptcovn>0) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           for (z1=1; z1<=cptcoveff; z1++)        } /* end of wave */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      } /* end of individual */
               bool=0;    }  else if(mle==3){  /* exponential inter-extrapolation */
         }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         if (bool==1) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           for(m=firstpass; m<=lastpass; m++){        for(mi=1; mi<= wav[i]-1; mi++){
             k2=anint[m][i]+(mint[m][i]/12.);          for (ii=1;ii<=nlstate+ndeath;ii++)
             if ((k2>=dateprev1) && (k2<=dateprev2)) {            for (j=1;j<=nlstate+ndeath;j++){
               if(agev[m][i]==0) agev[m][i]=agemax+1;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               if(agev[m][i]==1) agev[m][i]=agemax+2;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
               if (m<lastpass) {            }
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          for(d=0; d<dh[mi][i]; d++){
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];            newm=savm;
               }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                          for (kk=1; kk<=cptcovage;kk++) {
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                 dateintsum=dateintsum+k2;            }
                 k2cpt++;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
               }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             }            savm=oldm;
           }            oldm=newm;
         }          } /* end mult */
       }        
                  s1=s[mw[mi][i]][i];
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
       if  (cptcovn>0) {          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
         fprintf(ficresp, "\n#********** Variable ");          ipmx +=1;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          sw += weight[i];
         fprintf(ficresp, "**********\n#");          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       }        } /* end of wave */
       for(i=1; i<=nlstate;i++)      } /* end of individual */
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    }else if (mle==4){  /* ml=4 no inter-extrapolation */
       fprintf(ficresp, "\n");      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
              for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(i=(int)agemin; i <= (int)agemax+3; i++){        for(mi=1; mi<= wav[i]-1; mi++){
         if(i==(int)agemax+3){          for (ii=1;ii<=nlstate+ndeath;ii++)
           fprintf(ficlog,"Total");            for (j=1;j<=nlstate+ndeath;j++){
         }else{              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           if(first==1){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             first=0;            }
             printf("See log file for details...\n");          for(d=0; d<dh[mi][i]; d++){
           }            newm=savm;
           fprintf(ficlog,"Age %d", i);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         }            for (kk=1; kk<=cptcovage;kk++) {
         for(jk=1; jk <=nlstate ; jk++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            }
             pp[jk] += freq[jk][m][i];          
         }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         for(jk=1; jk <=nlstate ; jk++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           for(m=-1, pos=0; m <=0 ; m++)            savm=oldm;
             pos += freq[jk][m][i];            oldm=newm;
           if(pp[jk]>=1.e-10){          } /* end mult */
             if(first==1){        
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          s1=s[mw[mi][i]][i];
             }          s2=s[mw[mi+1][i]][i];
             fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);          if( s2 > nlstate){ 
           }else{            lli=log(out[s1][s2] - savm[s1][s2]);
             if(first==1)          }else{
               printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
             fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          }
           }          ipmx +=1;
         }          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]); */
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)        } /* end of wave */
             pp[jk] += freq[jk][m][i];      } /* end of individual */
         }    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for(jk=1,pos=0; jk <=nlstate ; jk++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           pos += pp[jk];        for(mi=1; mi<= wav[i]-1; mi++){
         for(jk=1; jk <=nlstate ; jk++){          for (ii=1;ii<=nlstate+ndeath;ii++)
           if(pos>=1.e-5){            for (j=1;j<=nlstate+ndeath;j++){
             if(first==1)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);            }
           }else{          for(d=0; d<dh[mi][i]; d++){
             if(first==1)            newm=savm;
               printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);            for (kk=1; kk<=cptcovage;kk++) {
           }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           if( i <= (int) agemax){            }
             if(pos>=1.e-5){          
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
               probs[i][jk][j1]= pp[jk]/pos;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/            savm=oldm;
             }            oldm=newm;
             else          } /* end mult */
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        
           }          s1=s[mw[mi][i]][i];
         }          s2=s[mw[mi+1][i]][i];
                  lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         for(jk=-1; jk <=nlstate+ndeath; jk++)          ipmx +=1;
           for(m=-1; m <=nlstate+ndeath; m++)          sw += weight[i];
             if(freq[jk][m][i] !=0 ) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             if(first==1)          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
               printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        } /* end of wave */
               fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);      } /* end of individual */
             }    } /* End of if */
         if(i <= (int) agemax)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
           fprintf(ficresp,"\n");    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         if(first==1)    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
           printf("Others in log...\n");    return -l;
         fprintf(ficlog,"\n");  }
       }  
     }  /*************** log-likelihood *************/
   }  double funcone( double *x)
   dateintmean=dateintsum/k2cpt;  {
      /* Same as likeli but slower because of a lot of printf and if */
   fclose(ficresp);    int i, ii, j, k, mi, d, kk;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   free_vector(pp,1,nlstate);    double **out;
      double lli; /* Individual log likelihood */
   /* End of Freq */    double llt;
 }    int s1, s2;
     double bbh, survp;
 /************ Prevalence ********************/    /*extern weight */
 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)    /* We are differentiating ll according to initial status */
 {  /* Some frequencies */    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
      /*for(i=1;i<imx;i++) 
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;      printf(" %d\n",s[4][i]);
   double ***freq; /* Frequencies */    */
   double *pp;    cov[1]=1.;
   double pos, k2;  
     for(k=1; k<=nlstate; k++) ll[k]=0.;
   pp=vector(1,nlstate);  
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      for(mi=1; mi<= wav[i]-1; mi++){
   j1=0;        for (ii=1;ii<=nlstate+ndeath;ii++)
            for (j=1;j<=nlstate+ndeath;j++){
   j=cptcoveff;            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            savm[ii][j]=(ii==j ? 1.0 : 0.0);
            }
   for(k1=1; k1<=j;k1++){        for(d=0; d<dh[mi][i]; d++){
     for(i1=1; i1<=ncodemax[k1];i1++){          newm=savm;
       j1++;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                for (kk=1; kk<=cptcovage;kk++) {
       for (i=-1; i<=nlstate+ndeath; i++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         for (jk=-1; jk<=nlstate+ndeath; jk++)            }
           for(m=agemin; m <= agemax+3; m++)          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             freq[i][jk][m]=0;                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                savm=oldm;
       for (i=1; i<=imx; i++) {          oldm=newm;
         bool=1;        } /* end mult */
         if  (cptcovn>0) {        
           for (z1=1; z1<=cptcoveff; z1++)        s1=s[mw[mi][i]][i];
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        s2=s[mw[mi+1][i]][i];
               bool=0;        bbh=(double)bh[mi][i]/(double)stepm; 
         }        /* bias is positive if real duration
         if (bool==1) {         * is higher than the multiple of stepm and negative otherwise.
           for(m=firstpass; m<=lastpass; m++){         */
             k2=anint[m][i]+(mint[m][i]/12.);        if( s2 > nlstate && (mle <5) ){  /* Jackson */
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          lli=log(out[s1][s2] - savm[s1][s2]);
               if(agev[m][i]==0) agev[m][i]=agemax+1;        } else if (mle==1){
               if(agev[m][i]==1) agev[m][i]=agemax+2;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
               if (m<lastpass) {        } else if(mle==2){
                 if (calagedate>0)          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];        } else if(mle==3){  /* exponential inter-extrapolation */
                 else          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 */
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        } else if (mle==4){  /* mle=4 no inter-extrapolation */
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];          lli=log(out[s1][s2]); /* Original formula */
               }        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
             }          lli=log(out[s1][s2]); /* Original formula */
           }        } /* End of if */
         }        ipmx +=1;
       }        sw += weight[i];
       for(i=(int)agemin; i <= (int)agemax+3; 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]); */
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        if(globpr){
             pp[jk] += freq[jk][m][i];          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
         }   %10.6f %10.6f %10.6f ", \
         for(jk=1; jk <=nlstate ; jk++){                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
           for(m=-1, pos=0; m <=0 ; m++)                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
             pos += freq[jk][m][i];          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
         }            llt +=ll[k]*gipmx/gsw;
                    fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
         for(jk=1; jk <=nlstate ; jk++){          }
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          fprintf(ficresilk," %10.6f\n", -llt);
             pp[jk] += freq[jk][m][i];        }
         }      } /* end of wave */
            } /* end of individual */
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
            /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         for(jk=1; jk <=nlstate ; jk++){        l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
           if( i <= (int) agemax){    if(globpr==0){ /* First time we count the contributions and weights */
             if(pos>=1.e-5){      gipmx=ipmx;
               probs[i][jk][j1]= pp[jk]/pos;      gsw=sw;
             }    }
           }    return -l;
         }/* end jk */  }
       }/* end i */  
     } /* end i1 */  
   } /* end k1 */  /*************** function likelione ***********/
   void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
    {
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    /* This routine should help understanding what is done with 
   free_vector(pp,1,nlstate);       the selection of individuals/waves and
         to check the exact contribution to the likelihood.
 }  /* End of Freq */       Plotting could be done.
      */
 /************* Waves Concatenation ***************/    int k;
   
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    if(*globpri !=0){ /* Just counts and sums, no printings */
 {      strcpy(fileresilk,"ilk"); 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.      strcat(fileresilk,fileres);
      Death is a valid wave (if date is known).      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i        printf("Problem with resultfile: %s\n", fileresilk);
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
      and mw[mi+1][i]. dh depends on stepm.      }
      */      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 ");
   int i, mi, m;      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      for(k=1; k<=nlstate; k++) 
      double sum=0., jmean=0.;*/        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   int first;      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   int j, k=0,jk, ju, jl;    }
   double sum=0.;  
   first=0;    *fretone=(*funcone)(p);
   jmin=1e+5;    if(*globpri !=0){
   jmax=-1;      fclose(ficresilk);
   jmean=0.;      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   for(i=1; i<=imx; i++){      fflush(fichtm); 
     mi=0;    } 
     m=firstpass;    return;
     while(s[m][i] <= nlstate){  }
       if(s[m][i]>=1)  
         mw[++mi][i]=m;  
       if(m >=lastpass)  /*********** Maximum Likelihood Estimation ***************/
         break;  
       else  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
         m++;  {
     }/* end while */    int i,j, iter;
     if (s[m][i] > nlstate){    double **xi;
       mi++;     /* Death is another wave */    double fret;
       /* if(mi==0)  never been interviewed correctly before death */    double fretone; /* Only one call to likelihood */
          /* Only death is a correct wave */    char filerespow[FILENAMELENGTH];
       mw[mi][i]=m;    xi=matrix(1,npar,1,npar);
     }    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++)
     wav[i]=mi;        xi[i][j]=(i==j ? 1.0 : 0.0);
     if(mi==0){    printf("Powell\n");  fprintf(ficlog,"Powell\n");
       if(first==0){    strcpy(filerespow,"pow"); 
         printf("Warning, no any valid information for:%d line=%d and may be others, see log file\n",num[i],i);    strcat(filerespow,fileres);
         first=1;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
       }      printf("Problem with resultfile: %s\n", filerespow);
       if(first==1){      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Warning, no any valid information for:%d line=%d\n",num[i],i);    }
       }    fprintf(ficrespow,"# Powell\n# iter -2*LL");
     } /* end mi==0 */    for (i=1;i<=nlstate;i++)
   }      for(j=1;j<=nlstate+ndeath;j++)
         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   for(i=1; i<=imx; i++){    fprintf(ficrespow,"\n");
     for(mi=1; mi<wav[i];mi++){  
       if (stepm <=0)    powell(p,xi,npar,ftol,&iter,&fret,func);
         dh[mi][i]=1;  
       else{    fclose(ficrespow);
         if (s[mw[mi+1][i]][i] > nlstate) {    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
           if (agedc[i] < 2*AGESUP) {    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
           if(j==0) j=1;  /* Survives at least one month after exam */  
           k=k+1;  }
           if (j >= jmax) jmax=j;  
           if (j <= jmin) jmin=j;  /**** Computes Hessian and covariance matrix ***/
           sum=sum+j;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
           /*if (j<0) printf("j=%d num=%d \n",j,i); */  {
           }    double  **a,**y,*x,pd;
         }    double **hess;
         else{    int i, j,jk;
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    int *indx;
           k=k+1;  
           if (j >= jmax) jmax=j;    double hessii(double p[], double delta, int theta, double delti[]);
           else if (j <= jmin)jmin=j;    double hessij(double p[], double delti[], int i, int j);
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    void lubksb(double **a, int npar, int *indx, double b[]) ;
           sum=sum+j;    void ludcmp(double **a, int npar, int *indx, double *d) ;
         }  
         jk= j/stepm;    hess=matrix(1,npar,1,npar);
         jl= j -jk*stepm;  
         ju= j -(jk+1)*stepm;    printf("\nCalculation of the hessian matrix. Wait...\n");
         if(jl <= -ju)    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
           dh[mi][i]=jk;    for (i=1;i<=npar;i++){
         else      printf("%d",i);fflush(stdout);
           dh[mi][i]=jk+1;      fprintf(ficlog,"%d",i);fflush(ficlog);
         if(dh[mi][i]==0)      hess[i][i]=hessii(p,ftolhess,i,delti);
           dh[mi][i]=1; /* At least one step */      /*printf(" %f ",p[i]);*/
       }      /*printf(" %lf ",hess[i][i]);*/
     }    }
   }    
   jmean=sum/k;    for (i=1;i<=npar;i++) {
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);      for (j=1;j<=npar;j++)  {
   fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);        if (j>i) { 
  }          printf(".%d%d",i,j);fflush(stdout);
           fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
 /*********** Tricode ****************************/          hess[i][j]=hessij(p,delti,i,j);
 void tricode(int *Tvar, int **nbcode, int imx)          hess[j][i]=hess[i][j];    
 {          /*printf(" %lf ",hess[i][j]);*/
   int Ndum[20],ij=1, k, j, i;        }
   int cptcode=0;      }
   cptcoveff=0;    }
      printf("\n");
   for (k=0; k<19; k++) Ndum[k]=0;    fprintf(ficlog,"\n");
   for (k=1; k<=7; k++) ncodemax[k]=0;  
     printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     for (i=1; i<=imx; i++) {    
       ij=(int)(covar[Tvar[j]][i]);    a=matrix(1,npar,1,npar);
       Ndum[ij]++;    y=matrix(1,npar,1,npar);
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    x=vector(1,npar);
       if (ij > cptcode) cptcode=ij;    indx=ivector(1,npar);
     }    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     for (i=0; i<=cptcode; i++) {    ludcmp(a,npar,indx,&pd);
       if(Ndum[i]!=0) ncodemax[j]++;  
     }    for (j=1;j<=npar;j++) {
     ij=1;      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
       lubksb(a,npar,indx,x);
     for (i=1; i<=ncodemax[j]; i++) {      for (i=1;i<=npar;i++){ 
       for (k=0; k<=19; k++) {        matcov[i][j]=x[i];
         if (Ndum[k] != 0) {      }
           nbcode[Tvar[j]][ij]=k;    }
            
           ij++;    printf("\n#Hessian matrix#\n");
         }    fprintf(ficlog,"\n#Hessian matrix#\n");
         if (ij > ncodemax[j]) break;    for (i=1;i<=npar;i++) { 
       }        for (j=1;j<=npar;j++) { 
     }        printf("%.3e ",hess[i][j]);
   }          fprintf(ficlog,"%.3e ",hess[i][j]);
       }
  for (k=0; k<19; k++) Ndum[k]=0;      printf("\n");
       fprintf(ficlog,"\n");
  for (i=1; i<=ncovmodel-2; i++) {    }
    ij=Tvar[i];  
    Ndum[ij]++;    /* Recompute Inverse */
  }    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
  ij=1;    ludcmp(a,npar,indx,&pd);
  for (i=1; i<=10; i++) {  
    if((Ndum[i]!=0) && (i<=ncovcol)){    /*  printf("\n#Hessian matrix recomputed#\n");
      Tvaraff[ij]=i;  
      ij++;    for (j=1;j<=npar;j++) {
    }      for (i=1;i<=npar;i++) x[i]=0;
  }      x[j]=1;
        lubksb(a,npar,indx,x);
  cptcoveff=ij-1;      for (i=1;i<=npar;i++){ 
 }        y[i][j]=x[i];
         printf("%.3e ",y[i][j]);
 /*********** Health Expectancies ****************/        fprintf(ficlog,"%.3e ",y[i][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,double delti[],double **matcov )      printf("\n");
       fprintf(ficlog,"\n");
 {    }
   /* Health expectancies */    */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;  
   double age, agelim, hf;    free_matrix(a,1,npar,1,npar);
   double ***p3mat,***varhe;    free_matrix(y,1,npar,1,npar);
   double **dnewm,**doldm;    free_vector(x,1,npar);
   double *xp;    free_ivector(indx,1,npar);
   double **gp, **gm;    free_matrix(hess,1,npar,1,npar);
   double ***gradg, ***trgradg;  
   int theta;  
   }
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);  
   xp=vector(1,npar);  /*************** hessian matrix ****************/
   dnewm=matrix(1,nlstate*2,1,npar);  double hessii( double x[], double delta, int theta, double delti[])
   doldm=matrix(1,nlstate*2,1,nlstate*2);  {
      int i;
   fprintf(ficreseij,"# Health expectancies\n");    int l=1, lmax=20;
   fprintf(ficreseij,"# Age");    double k1,k2;
   for(i=1; i<=nlstate;i++)    double p2[NPARMAX+1];
     for(j=1; j<=nlstate;j++)    double res;
       fprintf(ficreseij," %1d-%1d (SE)",i,j);    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   fprintf(ficreseij,"\n");    double fx;
     int k=0,kmax=10;
   if(estepm < stepm){    double l1;
     printf ("Problem %d lower than %d\n",estepm, stepm);  
   }    fx=func(x);
   else  hstepm=estepm;      for (i=1;i<=npar;i++) p2[i]=x[i];
   /* We compute the life expectancy from trapezoids spaced every estepm months    for(l=0 ; l <=lmax; l++){
    * This is mainly to measure the difference between two models: for example      l1=pow(10,l);
    * if stepm=24 months pijx are given only every 2 years and by summing them      delts=delt;
    * we are calculating an estimate of the Life Expectancy assuming a linear      for(k=1 ; k <kmax; k=k+1){
    * progression inbetween and thus overestimating or underestimating according        delt = delta*(l1*k);
    * to the curvature of the survival function. If, for the same date, we        p2[theta]=x[theta] +delt;
    * estimate the model with stepm=1 month, we can keep estepm to 24 months        k1=func(p2)-fx;
    * to compare the new estimate of Life expectancy with the same linear        p2[theta]=x[theta]-delt;
    * hypothesis. A more precise result, taking into account a more precise        k2=func(p2)-fx;
    * curvature will be obtained if estepm is as small as stepm. */        /*res= (k1-2.0*fx+k2)/delt/delt; */
         res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   /* 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.  #ifdef DEBUG
      nhstepm is the number of hstepm from age to agelim        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);
      nstepm is the number of stepm from age to agelin.        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);
      Look at hpijx to understand the reason of that which relies in memory size  #endif
      and note for a fixed period like estepm months */        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
      survival function given by stepm (the optimization length). Unfortunately it          k=kmax;
      means that if the survival funtion is printed only each two years of age and if        }
      you sum them up and add 1 year (area under the trapezoids) you won't get the same        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
      results. So we changed our mind and took the option of the best precision.          k=kmax; l=lmax*10.;
   */        }
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           delts=delt;
   agelim=AGESUP;        }
   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);    delti[theta]=delts;
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    return res; 
     /* if (stepm >= YEARM) hstepm=1;*/    
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */  }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);  double hessij( double x[], double delti[], int thetai,int thetaj)
     gp=matrix(0,nhstepm,1,nlstate*2);  {
     gm=matrix(0,nhstepm,1,nlstate*2);    int i;
     int l=1, l1, lmax=20;
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    double k1,k2,k3,k4,res,fx;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    double p2[NPARMAX+1];
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      int k;
    
     fx=func(x);
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    for (k=1; k<=2; k++) {
       for (i=1;i<=npar;i++) p2[i]=x[i];
     /* Computing Variances of health expectancies */      p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
      for(theta=1; theta <=npar; theta++){      k1=func(p2)-fx;
       for(i=1; i<=npar; i++){    
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      p2[thetai]=x[thetai]+delti[thetai]/k;
       }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        k2=func(p2)-fx;
      
       cptj=0;      p2[thetai]=x[thetai]-delti[thetai]/k;
       for(j=1; j<= nlstate; j++){      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         for(i=1; i<=nlstate; i++){      k3=func(p2)-fx;
           cptj=cptj+1;    
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){      p2[thetai]=x[thetai]-delti[thetai]/k;
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;      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
            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);
            fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       for(i=1; i<=npar; i++)  #endif
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      return res;
        }
       cptj=0;  
       for(j=1; j<= nlstate; j++){  /************** Inverse of matrix **************/
         for(i=1;i<=nlstate;i++){  void ludcmp(double **a, int n, int *indx, double *d) 
           cptj=cptj+1;  { 
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){    int i,imax,j,k; 
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    double big,dum,sum,temp; 
           }    double *vv; 
         }   
       }    vv=vector(1,n); 
       for(j=1; j<= nlstate*2; j++)    *d=1.0; 
         for(h=0; h<=nhstepm-1; h++){    for (i=1;i<=n;i++) { 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      big=0.0; 
         }      for (j=1;j<=n;j++) 
      }        if ((temp=fabs(a[i][j])) > big) big=temp; 
          if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
 /* End theta */      vv[i]=1.0/big; 
     } 
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);    for (j=1;j<=n;j++) { 
       for (i=1;i<j;i++) { 
      for(h=0; h<=nhstepm-1; h++)        sum=a[i][j]; 
       for(j=1; j<=nlstate*2;j++)        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         for(theta=1; theta <=npar; theta++)        a[i][j]=sum; 
           trgradg[h][j][theta]=gradg[h][theta][j];      } 
            big=0.0; 
       for (i=j;i<=n;i++) { 
      for(i=1;i<=nlstate*2;i++)        sum=a[i][j]; 
       for(j=1;j<=nlstate*2;j++)        for (k=1;k<j;k++) 
         varhe[i][j][(int)age] =0.;          sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
      printf("%d|",(int)age);fflush(stdout);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);          big=dum; 
      for(h=0;h<=nhstepm-1;h++){          imax=i; 
       for(k=0;k<=nhstepm-1;k++){        } 
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);      } 
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);      if (j != imax) { 
         for(i=1;i<=nlstate*2;i++)        for (k=1;k<=n;k++) { 
           for(j=1;j<=nlstate*2;j++)          dum=a[imax][k]; 
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;          a[imax][k]=a[j][k]; 
       }          a[j][k]=dum; 
     }        } 
     /* Computing expectancies */        *d = -(*d); 
     for(i=1; i<=nlstate;i++)        vv[imax]=vv[j]; 
       for(j=1; j<=nlstate;j++)      } 
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){      indx[j]=imax; 
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;      if (a[j][j] == 0.0) a[j][j]=TINY; 
                if (j != n) { 
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/        dum=1.0/(a[j][j]); 
         for (i=j+1;i<=n;i++) a[i][j] *= dum; 
         }      } 
     } 
     fprintf(ficreseij,"%3.0f",age );    free_vector(vv,1,n);  /* Doesn't work */
     cptj=0;  ;
     for(i=1; i<=nlstate;i++)  } 
       for(j=1; j<=nlstate;j++){  
         cptj++;  void lubksb(double **a, int n, int *indx, double b[]) 
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );  { 
       }    int i,ii=0,ip,j; 
     fprintf(ficreseij,"\n");    double sum; 
       
     free_matrix(gm,0,nhstepm,1,nlstate*2);    for (i=1;i<=n;i++) { 
     free_matrix(gp,0,nhstepm,1,nlstate*2);      ip=indx[i]; 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);      sum=b[ip]; 
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);      b[ip]=b[i]; 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      if (ii) 
   }        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   printf("\n");      else if (sum) ii=i; 
   fprintf(ficlog,"\n");      b[i]=sum; 
     } 
   free_vector(xp,1,npar);    for (i=n;i>=1;i--) { 
   free_matrix(dnewm,1,nlstate*2,1,npar);      sum=b[i]; 
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);      b[i]=sum/a[i][i]; 
 }    } 
   } 
 /************ Variance ******************/  
 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)  /************ Frequencies ********************/
 {  void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint)
   /* Variance of health expectancies */  {  /* Some frequencies */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    
   /* double **newm;*/    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   double **dnewm,**doldm;    int first;
   double **dnewmp,**doldmp;    double ***freq; /* Frequencies */
   int i, j, nhstepm, hstepm, h, nstepm ;    double *pp, **prop;
   int k, cptcode;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   double *xp;    FILE *ficresp;
   double **gp, **gm;  /* for var eij */    char fileresp[FILENAMELENGTH];
   double ***gradg, ***trgradg; /*for var eij */    
   double **gradgp, **trgradgp; /* for var p point j */    pp=vector(1,nlstate);
   double *gpp, *gmp; /* for var p point j */    prop=matrix(1,nlstate,iagemin,iagemax+3);
   double **varppt; /* for var p point j nlstate to nlstate+ndeath */    strcpy(fileresp,"p");
   double ***p3mat;    strcat(fileresp,fileres);
   double age,agelim, hf;    if((ficresp=fopen(fileresp,"w"))==NULL) {
   int theta;      printf("Problem with prevalence resultfile: %s\n", fileresp);
   char digit[4];      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   char digitp[16];      exit(0);
     }
   char fileresprobmorprev[FILENAMELENGTH];    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
     j1=0;
   if(popbased==1)    
     strcpy(digitp,"-populbased-");    j=cptcoveff;
   else    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     strcpy(digitp,"-stablbased-");  
     first=1;
   strcpy(fileresprobmorprev,"prmorprev");  
   sprintf(digit,"%-d",ij);    for(k1=1; k1<=j;k1++){
   /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/      for(i1=1; i1<=ncodemax[k1];i1++){
   strcat(fileresprobmorprev,digit); /* Tvar to be done */        j1++;
   strcat(fileresprobmorprev,digitp); /* Popbased or not */        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   strcat(fileresprobmorprev,fileres);          scanf("%d", i);*/
   if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {        for (i=-1; i<=nlstate+ndeath; i++)  
     printf("Problem with resultfile: %s\n", fileresprobmorprev);          for (jk=-1; jk<=nlstate+ndeath; jk++)  
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);            for(m=iagemin; m <= iagemax+3; m++)
   }              freq[i][jk][m]=0;
   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);      for (i=1; i<=nlstate; i++)  
   fprintf(ficresprobmorprev,"# probabilities of dying during a year and weighted mean w1*p1j+w2*p2j+... stand dev in()\n");        for(m=iagemin; m <= iagemax+3; m++)
   fprintf(ficresprobmorprev,"# Age cov=%-d",ij);          prop[i][m]=0;
   for(j=nlstate+1; j<=(nlstate+ndeath);j++){        
     fprintf(ficresprobmorprev," p.%-d SE",j);        dateintsum=0;
     for(i=1; i<=nlstate;i++)        k2cpt=0;
       fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);        for (i=1; i<=imx; i++) {
   }            bool=1;
   fprintf(ficresprobmorprev,"\n");          if  (cptcovn>0) {
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {            for (z1=1; z1<=cptcoveff; z1++) 
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);                bool=0;
     exit(0);          }
   }          if (bool==1){
   else{            for(m=firstpass; m<=lastpass; m++){
     fprintf(ficgp,"\n# Routine varevsij");              k2=anint[m][i]+(mint[m][i]/12.);
   }              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     printf("Problem with html file: %s\n", optionfilehtm);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     exit(0);                if (m<lastpass) {
   }                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   else{                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
     fprintf(fichtm,"\n<li><h4> Computing step probabilities of dying and weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");                }
   }                
   varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                   dateintsum=dateintsum+k2;
   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");                  k2cpt++;
   fprintf(ficresvij,"# Age");                }
   for(i=1; i<=nlstate;i++)                /*}*/
     for(j=1; j<=nlstate;j++)            }
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          }
   fprintf(ficresvij,"\n");        }
          
   xp=vector(1,npar);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   dnewm=matrix(1,nlstate,1,npar);  
   doldm=matrix(1,nlstate,1,nlstate);        if  (cptcovn>0) {
   dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);          fprintf(ficresp, "\n#********** Variable "); 
   doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresp, "**********\n#");
   gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);        }
   gpp=vector(nlstate+1,nlstate+ndeath);        for(i=1; i<=nlstate;i++) 
   gmp=vector(nlstate+1,nlstate+ndeath);          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/        fprintf(ficresp, "\n");
          
   if(estepm < stepm){        for(i=iagemin; i <= iagemax+3; i++){
     printf ("Problem %d lower than %d\n",estepm, stepm);          if(i==iagemax+3){
   }            fprintf(ficlog,"Total");
   else  hstepm=estepm;            }else{
   /* For example we decided to compute the life expectancy with the smallest unit */            if(first==1){
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.              first=0;
      nhstepm is the number of hstepm from age to agelim              printf("See log file for details...\n");
      nstepm is the number of stepm from age to agelin.            }
      Look at hpijx to understand the reason of that which relies in memory size            fprintf(ficlog,"Age %d", i);
      and note for a fixed period like k years */          }
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the          for(jk=1; jk <=nlstate ; jk++){
      survival function given by stepm (the optimization length). Unfortunately it            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
      means that if the survival funtion is printed only each two years of age and if              pp[jk] += freq[jk][m][i]; 
      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.          for(jk=1; jk <=nlstate ; jk++){
   */            for(m=-1, pos=0; m <=0 ; m++)
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */              pos += freq[jk][m][i];
   agelim = AGESUP;            if(pp[jk]>=1.e-10){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */              if(first==1){
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */              }
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);            }else{
     gp=matrix(0,nhstepm,1,nlstate);              if(first==1)
     gm=matrix(0,nhstepm,1,nlstate);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             }
     for(theta=1; theta <=npar; theta++){          }
       for(i=1; i<=npar; i++){ /* Computes gradient */  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          for(jk=1; jk <=nlstate ; jk++){
       }            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                pp[jk] += freq[jk][m][i];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          }       
           for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
       if (popbased==1) {            pos += pp[jk];
         for(i=1; i<=nlstate;i++)            posprop += prop[jk][i];
           prlim[i][i]=probs[(int)age][i][ij];          }
       }          for(jk=1; jk <=nlstate ; jk++){
              if(pos>=1.e-5){
       for(j=1; j<= nlstate; j++){              if(first==1)
         for(h=0; h<=nhstepm; h++){                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];            }else{
         }              if(first==1)
       }                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       /* This for computing forces of mortality (h=1)as a weighted average */              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
       for(j=nlstate+1,gpp[j]=0.;j<=nlstate+ndeath;j++){            }
         for(i=1; i<= nlstate; i++)            if( i <= iagemax){
           gpp[j] += prlim[i][i]*p3mat[i][j][1];              if(pos>=1.e-5){
       }                    fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
       /* end force of mortality */                /*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]);*/
       for(i=1; i<=npar; i++) /* Computes gradient */              }
         xp[i] = x[i] - (i==theta ?delti[theta]:0);              else
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                  fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            }
            }
       if (popbased==1) {          
         for(i=1; i<=nlstate;i++)          for(jk=-1; jk <=nlstate+ndeath; jk++)
           prlim[i][i]=probs[(int)age][i][ij];            for(m=-1; m <=nlstate+ndeath; m++)
       }              if(freq[jk][m][i] !=0 ) {
               if(first==1)
       for(j=1; j<= nlstate; j++){                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
         for(h=0; h<=nhstepm; h++){                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)              }
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          if(i <= iagemax)
         }            fprintf(ficresp,"\n");
       }          if(first==1)
       /* This for computing force of mortality (h=1)as a weighted average */            printf("Others in log...\n");
       for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){          fprintf(ficlog,"\n");
         for(i=1; i<= nlstate; i++)        }
           gmp[j] += prlim[i][i]*p3mat[i][j][1];      }
       }        }
       /* end force of mortality */    dateintmean=dateintsum/k2cpt; 
    
       for(j=1; j<= nlstate; j++) /* vareij */    fclose(ficresp);
         for(h=0; h<=nhstepm; h++){    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    free_vector(pp,1,nlstate);
         }    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
       for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */    /* End of Freq */
         gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];  }
       }  
   /************ Prevalence ********************/
     } /* End theta */  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)
   {  
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
        in each health status at the date of interview (if between dateprev1 and dateprev2).
     for(h=0; h<=nhstepm; h++) /* veij */       We still use firstpass and lastpass as another selection.
       for(j=1; j<=nlstate;j++)    */
         for(theta=1; theta <=npar; theta++)   
           trgradg[h][j][theta]=gradg[h][theta][j];    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     double ***freq; /* Frequencies */
     for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */    double *pp, **prop;
       for(theta=1; theta <=npar; theta++)    double pos,posprop; 
         trgradgp[j][theta]=gradgp[theta][j];    double  y2; /* in fractional years */
     int iagemin, iagemax;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */  
     for(i=1;i<=nlstate;i++)    iagemin= (int) agemin;
       for(j=1;j<=nlstate;j++)    iagemax= (int) agemax;
         vareij[i][j][(int)age] =0.;    /*pp=vector(1,nlstate);*/
     prop=matrix(1,nlstate,iagemin,iagemax+3); 
     for(h=0;h<=nhstepm;h++){    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
       for(k=0;k<=nhstepm;k++){    j1=0;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    j=cptcoveff;
         for(i=1;i<=nlstate;i++)    if (cptcovn<1) {j=1;ncodemax[1]=1;}
           for(j=1;j<=nlstate;j++)    
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;    for(k1=1; k1<=j;k1++){
       }      for(i1=1; i1<=ncodemax[k1];i1++){
     }        j1++;
         
     /* pptj */        for (i=1; i<=nlstate; i++)  
     matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);          for(m=iagemin; m <= iagemax+3; m++)
     matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);            prop[i][m]=0.0;
     for(j=nlstate+1;j<=nlstate+ndeath;j++)       
       for(i=nlstate+1;i<=nlstate+ndeath;i++)        for (i=1; i<=imx; i++) { /* Each individual */
         varppt[j][i]=doldmp[j][i];          bool=1;
     /* end ppptj */          if  (cptcovn>0) {
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);              for (z1=1; z1<=cptcoveff; z1++) 
     prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                  bool=0;
     if (popbased==1) {          } 
       for(i=1; i<=nlstate;i++)          if (bool==1) { 
         prlim[i][i]=probs[(int)age][i][ij];            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     }              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
                  if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
     /* This for computing force of mortality (h=1)as a weighted average */                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     for(j=nlstate+1,gmp[j]=0.;j<=nlstate+ndeath;j++){                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       for(i=1; i<= nlstate; i++)                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); 
         gmp[j] += prlim[i][i]*p3mat[i][j][1];                if (s[m][i]>0 && s[m][i]<=nlstate) { 
     }                      /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
     /* end force of mortality */                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                   prop[s[m][i]][iagemax+3] += weight[i]; 
     fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);                } 
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){              }
       fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));            } /* end selection of waves */
       for(i=1; i<=nlstate;i++){          }
         fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);        }
       }        for(i=iagemin; i <= iagemax+3; i++){  
     }          
     fprintf(ficresprobmorprev,"\n");          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
             posprop += prop[jk][i]; 
     fprintf(ficresvij,"%.0f ",age );          } 
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){          for(jk=1; jk <=nlstate ; jk++){     
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);            if( i <=  iagemax){ 
       }              if(posprop>=1.e-5){ 
     fprintf(ficresvij,"\n");                probs[i][jk][j1]= prop[jk][i]/posprop;
     free_matrix(gp,0,nhstepm,1,nlstate);              } 
     free_matrix(gm,0,nhstepm,1,nlstate);            } 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);          }/* end jk */ 
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);        }/* end i */ 
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      } /* end i1 */
   } /* End age */    } /* end k1 */
   free_vector(gpp,nlstate+1,nlstate+ndeath);    
   free_vector(gmp,nlstate+1,nlstate+ndeath);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);    /*free_vector(pp,1,nlstate);*/
   free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
   fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");  }  /* End of prevalence */
   /* 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)\";");  /************* Waves Concatenation ***************/
   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm);  
   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm);  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,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm);  {
   fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",fileresprobmorprev,fileresprobmorprev);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   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);       Death is a valid wave (if date is known).
   fprintf(ficgp,"\nset out \"varmuptjgr%s%s.png\";replot;",digitp,digit);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
        dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   free_vector(xp,1,npar);       and mw[mi+1][i]. dh depends on stepm.
   free_matrix(doldm,1,nlstate,1,nlstate);       */
   free_matrix(dnewm,1,nlstate,1,npar);  
   free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);    int i, mi, m;
   free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);       double sum=0., jmean=0.;*/
   fclose(ficresprobmorprev);    int first;
   fclose(ficgp);    int j, k=0,jk, ju, jl;
   fclose(fichtm);    double sum=0.;
     first=0;
 }    jmin=1e+5;
     jmax=-1;
 /************ Variance of prevlim ******************/    jmean=0.;
 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<=imx; i++){
 {      mi=0;
   /* Variance of prevalence limit */      m=firstpass;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      while(s[m][i] <= nlstate){
   double **newm;        if(s[m][i]>=1)
   double **dnewm,**doldm;          mw[++mi][i]=m;
   int i, j, nhstepm, hstepm;        if(m >=lastpass)
   int k, cptcode;          break;
   double *xp;        else
   double *gp, *gm;          m++;
   double **gradg, **trgradg;      }/* end while */
   double age,agelim;      if (s[m][i] > nlstate){
   int theta;        mi++;     /* Death is another wave */
            /* if(mi==0)  never been interviewed correctly before death */
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");           /* Only death is a correct wave */
   fprintf(ficresvpl,"# Age");        mw[mi][i]=m;
   for(i=1; i<=nlstate;i++)      }
       fprintf(ficresvpl," %1d-%1d",i,i);  
   fprintf(ficresvpl,"\n");      wav[i]=mi;
       if(mi==0){
   xp=vector(1,npar);        nbwarn++;
   dnewm=matrix(1,nlstate,1,npar);        if(first==0){
   doldm=matrix(1,nlstate,1,nlstate);          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
            first=1;
   hstepm=1*YEARM; /* Every year of age */        }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        if(first==1){
   agelim = AGESUP;          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      } /* end mi==0 */
     if (stepm >= YEARM) hstepm=1;    } /* End individuals */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
     gradg=matrix(1,npar,1,nlstate);    for(i=1; i<=imx; i++){
     gp=vector(1,nlstate);      for(mi=1; mi<wav[i];mi++){
     gm=vector(1,nlstate);        if (stepm <=0)
           dh[mi][i]=1;
     for(theta=1; theta <=npar; theta++){        else{
       for(i=1; i<=npar; i++){ /* Computes gradient */          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            if (agedc[i] < 2*AGESUP) {
       }              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              if(j==0) j=1;  /* Survives at least one month after exam */
       for(i=1;i<=nlstate;i++)              else if(j<0){
         gp[i] = prlim[i][i];                nberr++;
                    printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       for(i=1; i<=npar; i++) /* Computes gradient */                j=1; /* Temporary Dangerous patch */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);                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);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);                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);
         gm[i] = prlim[i][i];              }
               k=k+1;
       for(i=1;i<=nlstate;i++)              if (j >= jmax) jmax=j;
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];              if (j <= jmin) jmin=j;
     } /* End theta */              sum=sum+j;
               /*if (j<0) printf("j=%d num=%d \n",j,i);*/
     trgradg =matrix(1,nlstate,1,npar);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             }
     for(j=1; j<=nlstate;j++)          }
       for(theta=1; theta <=npar; theta++)          else{
         trgradg[j][theta]=gradg[theta][j];            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
             /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     for(i=1;i<=nlstate;i++)            k=k+1;
       varpl[i][(int)age] =0.;            if (j >= jmax) jmax=j;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);            else if (j <= jmin)jmin=j;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
     for(i=1;i<=nlstate;i++)            /*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]);*/
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */            if(j<0){
               nberr++;
     fprintf(ficresvpl,"%.0f ",age );              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     for(i=1; i<=nlstate;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]);
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));            }
     fprintf(ficresvpl,"\n");            sum=sum+j;
     free_vector(gp,1,nlstate);          }
     free_vector(gm,1,nlstate);          jk= j/stepm;
     free_matrix(gradg,1,npar,1,nlstate);          jl= j -jk*stepm;
     free_matrix(trgradg,1,nlstate,1,npar);          ju= j -(jk+1)*stepm;
   } /* End age */          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
             if(jl==0){
   free_vector(xp,1,npar);              dh[mi][i]=jk;
   free_matrix(doldm,1,nlstate,1,npar);              bh[mi][i]=0;
   free_matrix(dnewm,1,nlstate,1,nlstate);            }else{ /* We want a negative bias in order to only have interpolation ie
                     * at the price of an extra matrix product in likelihood */
 }              dh[mi][i]=jk+1;
               bh[mi][i]=ju;
 /************ Variance of one-step probabilities  ******************/            }
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)          }else{
 {            if(jl <= -ju){
   int i, j=0,  i1, k1, l1, t, tj;              dh[mi][i]=jk;
   int k2, l2, j1,  z1;              bh[mi][i]=jl;       /* bias is positive if real duration
   int k=0,l, cptcode;                                   * is higher than the multiple of stepm and negative otherwise.
   int first=1, first1;                                   */
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;            }
   double **dnewm,**doldm;            else{
   double *xp;              dh[mi][i]=jk+1;
   double *gp, *gm;              bh[mi][i]=ju;
   double **gradg, **trgradg;            }
   double **mu;            if(dh[mi][i]==0){
   double age,agelim, cov[NCOVMAX];              dh[mi][i]=1; /* At least one step */
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */              bh[mi][i]=ju; /* At least one step */
   int theta;              /*  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);*/
   char fileresprob[FILENAMELENGTH];            }
   char fileresprobcov[FILENAMELENGTH];          } /* end if mle */
   char fileresprobcor[FILENAMELENGTH];        }
       } /* end wave */
   double ***varpij;    }
     jmean=sum/k;
   strcpy(fileresprob,"prob");    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   strcat(fileresprob,fileres);    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {   }
     printf("Problem with resultfile: %s\n", fileresprob);  
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);  /*********** Tricode ****************************/
   }  void tricode(int *Tvar, int **nbcode, int imx)
   strcpy(fileresprobcov,"probcov");  {
   strcat(fileresprobcov,fileres);    
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {    int Ndum[20],ij=1, k, j, i, maxncov=19;
     printf("Problem with resultfile: %s\n", fileresprobcov);    int cptcode=0;
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);    cptcoveff=0; 
   }   
   strcpy(fileresprobcor,"probcor");    for (k=0; k<maxncov; k++) Ndum[k]=0;
   strcat(fileresprobcor,fileres);    for (k=1; k<=7; k++) ncodemax[k]=0;
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {  
     printf("Problem with resultfile: %s\n", fileresprobcor);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
     fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
   }                                 modality*/ 
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
   fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);        Ndum[ij]++; /*store the modality */
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);                                         Tvar[j]. If V=sex and male is 0 and 
   fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);                                         female is 1, then  cptcode=1.*/
        }
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");  
   fprintf(ficresprob,"# Age");      for (i=0; i<=cptcode; i++) {
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");        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 */
   fprintf(ficresprobcov,"# Age");      }
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");  
   fprintf(ficresprobcov,"# Age");      ij=1; 
       for (i=1; i<=ncodemax[j]; i++) {
         for (k=0; k<= maxncov; k++) {
   for(i=1; i<=nlstate;i++)          if (Ndum[k] != 0) {
     for(j=1; j<=(nlstate+ndeath);j++){            nbcode[Tvar[j]][ij]=k; 
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);            /* 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; */
       fprintf(ficresprobcov," p%1d-%1d ",i,j);            
       fprintf(ficresprobcor," p%1d-%1d ",i,j);            ij++;
     }            }
   fprintf(ficresprob,"\n");          if (ij > ncodemax[j]) break; 
   fprintf(ficresprobcov,"\n");        }  
   fprintf(ficresprobcor,"\n");      } 
   xp=vector(1,npar);    }  
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);  
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));   for (k=0; k< maxncov; k++) Ndum[k]=0;
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);  
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);   for (i=1; i<=ncovmodel-2; i++) { 
   first=1;     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {     ij=Tvar[i];
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);     Ndum[ij]++;
     fprintf(ficlog,"Problem with gnuplot file: %s\n", optionfilegnuplot);   }
     exit(0);  
   }   ij=1;
   else{   for (i=1; i<= maxncov; i++) {
     fprintf(ficgp,"\n# Routine varprob");     if((Ndum[i]!=0) && (i<=ncovcol)){
   }       Tvaraff[ij]=i; /*For printing */
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {       ij++;
     printf("Problem with html file: %s\n", optionfilehtm);     }
     fprintf(ficlog,"Problem with html file: %s\n", optionfilehtm);   }
     exit(0);   
   }   cptcoveff=ij-1; /*Number of simple covariates*/
   else{  }
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");  
     fprintf(fichtm,"\n");  /*********** Health Expectancies ****************/
   
     fprintf(fichtm,"\n<li><h4> Computing matrix of variance-covariance of step probabilities</h4></li>\n");  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 )
     fprintf(fichtm,"\nWe have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");  
     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");  {
     /* Health expectancies */
   }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     double age, agelim, hf;
      double ***p3mat,***varhe;
   cov[1]=1;    double **dnewm,**doldm;
   tj=cptcoveff;    double *xp;
   if (cptcovn<1) {tj=1;ncodemax[1]=1;}    double **gp, **gm;
   j1=0;    double ***gradg, ***trgradg;
   for(t=1; t<=tj;t++){    int theta;
     for(i1=1; i1<=ncodemax[t];i1++){  
       j1++;    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
          xp=vector(1,npar);
       if  (cptcovn>0) {    dnewm=matrix(1,nlstate*nlstate,1,npar);
         fprintf(ficresprob, "\n#********** Variable ");    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    
         fprintf(ficresprob, "**********\n#");    fprintf(ficreseij,"# Health expectancies\n");
         fprintf(ficresprobcov, "\n#********** Variable ");    fprintf(ficreseij,"# Age");
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    for(i=1; i<=nlstate;i++)
         fprintf(ficresprobcov, "**********\n#");      for(j=1; j<=nlstate;j++)
                fprintf(ficreseij," %1d-%1d (SE)",i,j);
         fprintf(ficgp, "\n#********** Variable ");    fprintf(ficreseij,"\n");
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
         fprintf(ficgp, "**********\n#");    if(estepm < stepm){
              printf ("Problem %d lower than %d\n",estepm, stepm);
            }
         fprintf(fichtm, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable ");    else  hstepm=estepm;   
         for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    /* We compute the life expectancy from trapezoids spaced every estepm months
         fprintf(fichtm, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");     * 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
         fprintf(ficresprobcor, "\n#********** Variable ");         * we are calculating an estimate of the Life Expectancy assuming a linear 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);     * progression in between and thus overestimating or underestimating according
         fprintf(ficgp, "**********\n#");         * to the curvature of the survival function. If, for the same date, we 
       }     * estimate the model with stepm=1 month, we can keep estepm to 24 months
           * to compare the new estimate of Life expectancy with the same linear 
       for (age=bage; age<=fage; age ++){     * hypothesis. A more precise result, taking into account a more precise
         cov[2]=age;     * curvature will be obtained if estepm is as small as stepm. */
         for (k=1; k<=cptcovn;k++) {  
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];    /* 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. 
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];       nhstepm is the number of hstepm from age to agelim 
         for (k=1; k<=cptcovprod;k++)       nstepm is the number of stepm from age to agelin. 
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];       Look at hpijx to understand the reason of that which relies in memory size
               and note for a fixed period like estepm months */
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);       survival function given by stepm (the optimization length). Unfortunately it
         gp=vector(1,(nlstate)*(nlstate+ndeath));       means that if the survival funtion is printed only each two years of age and if
         gm=vector(1,(nlstate)*(nlstate+ndeath));       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.
         for(theta=1; theta <=npar; theta++){    */
           for(i=1; i<=npar; i++)    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
             xp[i] = x[i] + (i==theta ?delti[theta]:0);  
              agelim=AGESUP;
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                /* nhstepm age range expressed in number of stepm */
           k=0;      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
           for(i=1; i<= (nlstate); i++){      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
             for(j=1; j<=(nlstate+ndeath);j++){      /* if (stepm >= YEARM) hstepm=1;*/
               k=k+1;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
               gp[k]=pmmij[i][j];      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);
           for(i=1; i<=npar; i++)  
             xp[i] = x[i] - (i==theta ?delti[theta]:0);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
             in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
           pmij(pmmij,cov,ncovmodel,xp,nlstate);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
           k=0;   
           for(i=1; i<=(nlstate); i++){  
             for(j=1; j<=(nlstate+ndeath);j++){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
               k=k+1;  
               gm[k]=pmmij[i][j];      /* Computing  Variances of health expectancies */
             }  
           }       for(theta=1; theta <=npar; theta++){
              for(i=1; i<=npar; i++){ 
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)          xp[i] = x[i] + (i==theta ?delti[theta]:0);
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];          }
         }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)        cptj=0;
           for(theta=1; theta <=npar; theta++)        for(j=1; j<= nlstate; j++){
             trgradg[j][theta]=gradg[theta][j];          for(i=1; i<=nlstate; i++){
                    cptj=cptj+1;
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
                    }
         pmij(pmmij,cov,ncovmodel,x,nlstate);          }
                }
         k=0;       
         for(i=1; i<=(nlstate); i++){       
           for(j=1; j<=(nlstate+ndeath);j++){        for(i=1; i<=npar; i++) 
             k=k+1;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
             mu[k][(int) age]=pmmij[i][j];        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           }        
         }        cptj=0;
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)        for(j=1; j<= nlstate; j++){
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)          for(i=1;i<=nlstate;i++){
             varpij[i][j][(int)age] = doldm[i][j];            cptj=cptj+1;
             for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
         /*printf("\n%d ",(int)age);  
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));            }
        fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));          }
      }*/        }
         for(j=1; j<= nlstate*nlstate; j++)
         fprintf(ficresprob,"\n%d ",(int)age);          for(h=0; h<=nhstepm-1; h++){
         fprintf(ficresprobcov,"\n%d ",(int)age);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
         fprintf(ficresprobcor,"\n%d ",(int)age);          }
        } 
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)     
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));  /* End theta */
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){  
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);  
         }       for(h=0; h<=nhstepm-1; h++)
         i=0;        for(j=1; j<=nlstate*nlstate;j++)
         for (k=1; k<=(nlstate);k++){          for(theta=1; theta <=npar; theta++)
           for (l=1; l<=(nlstate+ndeath);l++){            trgradg[h][j][theta]=gradg[h][theta][j];
             i=i++;       
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);  
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);       for(i=1;i<=nlstate*nlstate;i++)
             for (j=1; j<=i;j++){        for(j=1;j<=nlstate*nlstate;j++)
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);          varhe[i][j][(int)age] =0.;
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));  
             }       printf("%d|",(int)age);fflush(stdout);
           }       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
         }/* end of loop for state */       for(h=0;h<=nhstepm-1;h++){
       } /* end of loop for age */        for(k=0;k<=nhstepm-1;k++){
           matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
       /* Confidence intervalle of pij  */          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
       /*          for(i=1;i<=nlstate*nlstate;i++)
       fprintf(ficgp,"\nset noparametric;unset label");            for(j=1;j<=nlstate*nlstate;j++)
       fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");        }
       fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);      }
       fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);      /* Computing expectancies */
       fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);      for(i=1; i<=nlstate;i++)
       fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);        for(j=1; j<=nlstate;j++)
       */          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
       /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/            
       first1=1;  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
       for (k1=1; k1<=(nlstate);k1++){  
         for (l1=1; l1<=(nlstate+ndeath);l1++){          }
           if(l1==k1) continue;  
           i=(k1-1)*(nlstate+ndeath)+l1;      fprintf(ficreseij,"%3.0f",age );
           for (k2=1; k2<=(nlstate);k2++){      cptj=0;
             for (l2=1; l2<=(nlstate+ndeath);l2++){      for(i=1; i<=nlstate;i++)
               if(l2==k2) continue;        for(j=1; j<=nlstate;j++){
               j=(k2-1)*(nlstate+ndeath)+l2;          cptj++;
               if(j<=i) continue;          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
               for (age=bage; age<=fage; age ++){        }
                 if ((int)age %5==0){      fprintf(ficreseij,"\n");
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;     
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
                   mu1=mu[i][(int) age]/stepm*YEARM ;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
                   mu2=mu[j][(int) age]/stepm*YEARM;      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
                   /* Computing eigen value of matrix of covariance */      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));    }
                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));    printf("\n");
                   if(first1==1){    fprintf(ficlog,"\n");
                     first1=0;  
                     printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\nOthers in log...\n",v1,v2,cv12,lc1,lc2);    free_vector(xp,1,npar);
                   }    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
                   fprintf(ficlog,"Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
                   /* Eigen vectors */    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));  }
                   v21=sqrt(1.-v11*v11);  
                   v12=-v21;  /************ Variance ******************/
                   v22=v11;  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
                   /*printf(fignu*/  {
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */    /* Variance of health expectancies */
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
                   if(first==1){    /* double **newm;*/
                     first=0;    double **dnewm,**doldm;
                     fprintf(ficgp,"\nset parametric;set nolabel");    double **dnewmp,**doldmp;
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);    int i, j, nhstepm, hstepm, h, nstepm ;
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");    int k, cptcode;
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%d%1d%1d-%1d%1d.png\">varpijgr%s%d%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1,optionfilefiname, j1,k2,l2,k1,l1);    double *xp;
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%d%1d%1d-%1d%1d.png\"> ",optionfilefiname, j1,k2,l2,k1,l1);    double **gp, **gm;  /* for var eij */
                     fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\"",optionfilefiname, j1,k2,l2,k1,l1);    double ***gradg, ***trgradg; /*for var eij */
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);    double **gradgp, **trgradgp; /* for var p point j */
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);    double *gpp, *gmp; /* for var p point j */
                     /*              fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    double ***p3mat;
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);    double age,agelim, hf;
                     */    double ***mobaverage;
                     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",\    int theta;
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    char digit[4];
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));    char digitp[25];
                   }else{  
                     first=0;    char fileresprobmorprev[FILENAMELENGTH];
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);  
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);    if(popbased==1){
                     /*      if(mobilav!=0)
                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\        strcpy(digitp,"-populbased-mobilav-");
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \      else strcpy(digitp,"-populbased-nomobil-");
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);    }
                     */    else 
                     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",\      strcpy(digitp,"-stablbased-");
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \  
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2));    if (mobilav!=0) {
                   }/* if first */      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                 } /* age mod 5 */      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
               } /* end loop age */        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
               fprintf(ficgp,"\nset out \"varpijgr%s%d%1d%1d-%1d%1d.png\";replot;",optionfilefiname, j1,k2,l2,k1,l1);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
               first=1;      }
             } /*l12 */    }
           } /* k12 */  
         } /*l1 */    strcpy(fileresprobmorprev,"prmorprev"); 
       }/* k1 */    sprintf(digit,"%-d",ij);
     } /* loop covariates */    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    strcat(fileresprobmorprev,fileres);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   }    }
   free_vector(xp,1,npar);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   fclose(ficresprob);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   fclose(ficresprobcov);    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);
   fclose(ficresprobcor);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   fclose(ficgp);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   fclose(fichtm);      fprintf(ficresprobmorprev," p.%-d SE",j);
 }      for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
 /******************* Printing html file ***********/    fprintf(ficresprobmorprev,"\n");
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \    fprintf(ficgp,"\n# Routine varevsij");
                   int lastpass, int stepm, int weightopt, char model[],\    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");
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
                   int popforecast, int estepm ,\  /*   } */
                   double jprev1, double mprev1,double anprev1, \    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                   double jprev2, double mprev2,double anprev2){  
   int jj1, k1, i1, cpt;    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");
   /*char optionfilehtm[FILENAMELENGTH];*/    fprintf(ficresvij,"# Age");
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {    for(i=1; i<=nlstate;i++)
     printf("Problem with %s \n",optionfilehtm), exit(0);      for(j=1; j<=nlstate;j++)
     fprintf(ficlog,"Problem with %s \n",optionfilehtm), exit(0);        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   }    fprintf(ficresvij,"\n");
   
    fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n    xp=vector(1,npar);
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n    dnewm=matrix(1,nlstate,1,npar);
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n    doldm=matrix(1,nlstate,1,nlstate);
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
  - Life expectancies by age and initial health status (estepm=%2d months):    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    <a href=\"e%s\">e%s</a> <br>\n</li>", \  
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
 fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");    gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
  m=cptcoveff;    
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
  jj1=0;    }
  for(k1=1; k1<=m;k1++){    else  hstepm=estepm;   
    for(i1=1; i1<=ncodemax[k1];i1++){    /* For example we decided to compute the life expectancy with the smallest unit */
      jj1++;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
      if (cptcovn > 0) {       nhstepm is the number of hstepm from age to agelim 
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");       nstepm is the number of stepm from age to agelin. 
        for (cpt=1; cpt<=cptcoveff;cpt++)       Look at hpijx to understand the reason of that which relies in memory size
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);       and note for a fixed period like k years */
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    /* 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
      /* Pij */       means that if the survival funtion is printed every two years of age and if
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);           results. So we changed our mind and took the option of the best precision.
      /* Quasi-incidences */    */
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);    agelim = AGESUP;
        /* Stable prevalence in each health state */    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
        for(cpt=1; cpt<nlstate;cpt++){      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        }      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
      for(cpt=1; cpt<=nlstate;cpt++) {      gp=matrix(0,nhstepm,1,nlstate);
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>      gm=matrix(0,nhstepm,1,nlstate);
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);  
      }  
      fprintf(fichtm,"\n<br>- Total life expectancy by age and      for(theta=1; theta <=npar; theta++){
 health expectancies in states (1) and (2): e%s%d.png<br>        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
    } /* end i1 */        }
  }/* End k1 */        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
  fprintf(fichtm,"</ul>");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
         if (popbased==1) {
  fprintf(fichtm,"\n<br><li><h4> Result files (second order: variances)</h4>\n          if(mobilav ==0){
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n            for(i=1; i<=nlstate;i++)
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n              prlim[i][i]=probs[(int)age][i][ij];
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n          }else{ /* mobilav */ 
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n            for(i=1; i<=nlstate;i++)
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n              prlim[i][i]=mobaverage[(int)age][i][ij];
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n          }
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);        }
     
  if(popforecast==1) fprintf(fichtm,"\n        for(j=1; j<= nlstate; j++){
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n          for(h=0; h<=nhstepm; h++){
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
         <br>",fileres,fileres,fileres,fileres);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
  else          }
    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model);        }
 fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");        /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
  m=cptcoveff;           as a weighted average of prlim.
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
  jj1=0;          for(i=1,gpp[j]=0.; i<= nlstate; i++)
  for(k1=1; k1<=m;k1++){            gpp[j] += prlim[i][i]*p3mat[i][j][1];
    for(i1=1; i1<=ncodemax[k1];i1++){        }    
      jj1++;        /* end probability of death */
      if (cptcovn > 0) {  
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
        for (cpt=1; cpt<=cptcoveff;cpt++)          xp[i] = x[i] - (i==theta ?delti[theta]:0);
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
      }   
      for(cpt=1; cpt<=nlstate;cpt++) {        if (popbased==1) {
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident          if(mobilav ==0){
 interval) in state (%d): v%s%d%d.png <br>            for(i=1; i<=nlstate;i++)
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);                prlim[i][i]=probs[(int)age][i][ij];
      }          }else{ /* mobilav */ 
    } /* end i1 */            for(i=1; i<=nlstate;i++)
  }/* End k1 */              prlim[i][i]=mobaverage[(int)age][i][ij];
  fprintf(fichtm,"</ul>");          }
 fclose(fichtm);        }
 }  
         for(j=1; j<= nlstate; j++){
 /******************* Gnuplot file **************/          for(h=0; h<=nhstepm; h++){
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;          }
   int ng;        }
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {        /* This for computing probability of death (h=1 means
     printf("Problem with file %s",optionfilegnuplot);           computed over hstepm matrices product = hstepm*stepm months) 
     fprintf(ficlog,"Problem with file %s",optionfilegnuplot);           as a weighted average of prlim.
   }        */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
 #ifdef windows          for(i=1,gmp[j]=0.; i<= nlstate; i++)
     fprintf(ficgp,"cd \"%s\" \n",pathc);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
 #endif        }    
 m=pow(2,cptcoveff);        /* end probability of death */
    
  /* 1eme*/        for(j=1; j<= nlstate; j++) /* vareij */
   for (cpt=1; cpt<= nlstate ; cpt ++) {          for(h=0; h<=nhstepm; h++){
    for (k1=1; k1<= m ; k1 ++) {            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
 #ifdef windows  
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
 #endif        }
 #ifdef unix  
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);      } /* End theta */
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);  
 #endif      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
 for (i=1; i<= nlstate ; i ++) {      for(h=0; h<=nhstepm; h++) /* veij */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        for(j=1; j<=nlstate;j++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for(theta=1; theta <=npar; theta++)
 }            trgradg[h][j][theta]=gradg[h][theta][j];
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);  
     for (i=1; i<= nlstate ; i ++) {      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        for(theta=1; theta <=npar; theta++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");          trgradgp[j][theta]=gradgp[theta][j];
 }    
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  
      for (i=1; i<= nlstate ; i ++) {      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      for(i=1;i<=nlstate;i++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for(j=1;j<=nlstate;j++)
 }            vareij[i][j][(int)age] =0.;
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));  
 #ifdef unix      for(h=0;h<=nhstepm;h++){
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");        for(k=0;k<=nhstepm;k++){
 #endif          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
    }          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   }          for(i=1;i<=nlstate;i++)
   /*2 eme*/            for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   for (k1=1; k1<= m ; k1 ++) {        }
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);      }
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);    
          /* pptj */
     for (i=1; i<= nlstate+1 ; i ++) {      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       k=2*i;      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);      for(j=nlstate+1;j<=nlstate+ndeath;j++)
       for (j=1; j<= nlstate+1 ; j ++) {        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          varppt[j][i]=doldmp[j][i];
   else fprintf(ficgp," \%%*lf (\%%*lf)");      /* end ppptj */
 }        /*  x centered again */
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);   
       for (j=1; j<= nlstate+1 ; j ++) {      if (popbased==1) {
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        if(mobilav ==0){
         else fprintf(ficgp," \%%*lf (\%%*lf)");          for(i=1; i<=nlstate;i++)
 }              prlim[i][i]=probs[(int)age][i][ij];
       fprintf(ficgp,"\" t\"\" w l 0,");        }else{ /* mobilav */ 
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);          for(i=1; i<=nlstate;i++)
       for (j=1; j<= nlstate+1 ; j ++) {            prlim[i][i]=mobaverage[(int)age][i][ij];
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        }
   else fprintf(ficgp," \%%*lf (\%%*lf)");      }
 }                 
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");      /* This for computing probability of death (h=1 means
       else fprintf(ficgp,"\" t\"\" w l 0,");         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
     }         as a weighted average of prlim.
   }      */
        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   /*3eme*/        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   for (k1=1; k1<= m ; k1 ++) {      }    
     for (cpt=1; cpt<= nlstate ; cpt ++) {      /* end probability of death */
       k=2+nlstate*(2*cpt-2);  
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");        for(i=1; i<=nlstate;i++){
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);        }
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");      } 
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);      fprintf(ficresprobmorprev,"\n");
   
 */      fprintf(ficresvij,"%.0f ",age );
       for (i=1; i< nlstate ; 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+2*i,cpt,i+1);        for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
       }        }
     }      fprintf(ficresvij,"\n");
   }      free_matrix(gp,0,nhstepm,1,nlstate);
        free_matrix(gm,0,nhstepm,1,nlstate);
   /* CV preval stat */      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
     for (k1=1; k1<= m ; k1 ++) {      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     for (cpt=1; cpt<nlstate ; cpt ++) {      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       k=3;    } /* End age */
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    free_vector(gpp,nlstate+1,nlstate+ndeath);
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);    free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
       for (i=1; i< nlstate ; i ++)    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
         fprintf(ficgp,"+$%d",k+i+1);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
          fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
       l=3+(nlstate+ndeath)*cpt;  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
       for (i=1; i< nlstate ; i ++) {  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
         l=3+(nlstate+ndeath)*cpt;    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
         fprintf(ficgp,"+$%d",l+i+1);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
       }    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     }    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   }      /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
    */
   /* proba elementaires */  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
    for(i=1,jk=1; i <=nlstate; i++){    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     for(k=1; k <=(nlstate+ndeath); k++){  
       if (k != i) {    free_vector(xp,1,npar);
         for(j=1; j <=ncovmodel; j++){    free_matrix(doldm,1,nlstate,1,nlstate);
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    free_matrix(dnewm,1,nlstate,1,npar);
           jk++;    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           fprintf(ficgp,"\n");    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
         }    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       }    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     }    fclose(ficresprobmorprev);
    }    fflush(ficgp);
     fflush(fichtm); 
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/  }  /* end varevsij */
      for(jk=1; jk <=m; jk++) {  
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);  /************ Variance of prevlim ******************/
        if (ng==2)  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");  {
        else    /* Variance of prevalence limit */
          fprintf(ficgp,"\nset title \"Probability\"\n");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);    double **newm;
        i=1;    double **dnewm,**doldm;
        for(k2=1; k2<=nlstate; k2++) {    int i, j, nhstepm, hstepm;
          k3=i;    int k, cptcode;
          for(k=1; k<=(nlstate+ndeath); k++) {    double *xp;
            if (k != k2){    double *gp, *gm;
              if(ng==2)    double **gradg, **trgradg;
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);    double age,agelim;
              else    int theta;
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);     
              ij=1;    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
              for(j=3; j <=ncovmodel; j++) {    fprintf(ficresvpl,"# Age");
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    for(i=1; i<=nlstate;i++)
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        fprintf(ficresvpl," %1d-%1d",i,i);
                  ij++;    fprintf(ficresvpl,"\n");
                }  
                else    xp=vector(1,npar);
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    dnewm=matrix(1,nlstate,1,npar);
              }    doldm=matrix(1,nlstate,1,nlstate);
              fprintf(ficgp,")/(1");    
                  hstepm=1*YEARM; /* Every year of age */
              for(k1=1; k1 <=nlstate; k1++){      hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    agelim = AGESUP;
                ij=1;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                for(j=3; j <=ncovmodel; j++){      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      if (stepm >= YEARM) hstepm=1;
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
                    ij++;      gradg=matrix(1,npar,1,nlstate);
                  }      gp=vector(1,nlstate);
                  else      gm=vector(1,nlstate);
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  
                }      for(theta=1; theta <=npar; theta++){
                fprintf(ficgp,")");        for(i=1; i<=npar; i++){ /* Computes gradient */
              }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);        }
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
              i=i+ncovmodel;        for(i=1;i<=nlstate;i++)
            }          gp[i] = prlim[i][i];
          } /* end k */      
        } /* end k2 */        for(i=1; i<=npar; i++) /* Computes gradient */
      } /* end jk */          xp[i] = x[i] - (i==theta ?delti[theta]:0);
    } /* end ng */        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    fclose(ficgp);        for(i=1;i<=nlstate;i++)
 }  /* end gnuplot */          gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
 /*************** Moving average **************/          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){      } /* End theta */
   
   int i, cpt, cptcod;      trgradg =matrix(1,nlstate,1,npar);
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)  
       for (i=1; i<=nlstate;i++)      for(j=1; j<=nlstate;j++)
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)        for(theta=1; theta <=npar; theta++)
           mobaverage[(int)agedeb][i][cptcod]=0.;          trgradg[j][theta]=gradg[theta][j];
      
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){      for(i=1;i<=nlstate;i++)
       for (i=1; i<=nlstate;i++){        varpl[i][(int)age] =0.;
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
           for (cpt=0;cpt<=4;cpt++){      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];      for(i=1;i<=nlstate;i++)
           }        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;  
         }      fprintf(ficresvpl,"%.0f ",age );
       }      for(i=1; i<=nlstate;i++)
     }        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
          fprintf(ficresvpl,"\n");
 }      free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
 /************** Forecasting ******************/      free_matrix(trgradg,1,nlstate,1,npar);
 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){    } /* End age */
    
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    free_vector(xp,1,npar);
   int *popage;    free_matrix(doldm,1,nlstate,1,npar);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    free_matrix(dnewm,1,nlstate,1,nlstate);
   double *popeffectif,*popcount;  
   double ***p3mat;  }
   char fileresf[FILENAMELENGTH];  
   /************ Variance of one-step probabilities  ******************/
  agelim=AGESUP;  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;  {
     int i, j=0,  i1, k1, l1, t, tj;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    int k2, l2, j1,  z1;
      int k=0,l, cptcode;
      int first=1, first1;
   strcpy(fileresf,"f");    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   strcat(fileresf,fileres);    double **dnewm,**doldm;
   if((ficresf=fopen(fileresf,"w"))==NULL) {    double *xp;
     printf("Problem with forecast resultfile: %s\n", fileresf);    double *gp, *gm;
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);    double **gradg, **trgradg;
   }    double **mu;
   printf("Computing forecasting: result on file '%s' \n", fileresf);    double age,agelim, cov[NCOVMAX];
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
   if (mobilav==1) {    char fileresprobcor[FILENAMELENGTH];
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
     movingaverage(agedeb, fage, ageminpar, mobaverage);    double ***varpij;
   }  
     strcpy(fileresprob,"prob"); 
   stepsize=(int) (stepm+YEARM-1)/YEARM;    strcat(fileresprob,fileres);
   if (stepm<=12) stepsize=1;    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprob);
   agelim=AGESUP;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
      }
   hstepm=1;    strcpy(fileresprobcov,"probcov"); 
   hstepm=hstepm/stepm;    strcat(fileresprobcov,fileres);
   yp1=modf(dateintmean,&yp);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
   anprojmean=yp;      printf("Problem with resultfile: %s\n", fileresprobcov);
   yp2=modf((yp1*12),&yp);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   mprojmean=yp;    }
   yp1=modf((yp2*30.5),&yp);    strcpy(fileresprobcor,"probcor"); 
   jprojmean=yp;    strcat(fileresprobcor,fileres);
   if(jprojmean==0) jprojmean=1;    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   if(mprojmean==0) jprojmean=1;      printf("Problem with resultfile: %s\n", fileresprobcor);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    }
      printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   for(cptcov=1;cptcov<=i2;cptcov++){    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
       k=k+1;    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
       fprintf(ficresf,"\n#******");    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
       for(j=1;j<=cptcoveff;j++) {    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    
       }    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
       fprintf(ficresf,"******\n");    fprintf(ficresprob,"# Age");
       fprintf(ficresf,"# StartingAge FinalAge");    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    fprintf(ficresprobcov,"# Age");
          fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
          fprintf(ficresprobcov,"# Age");
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {  
         fprintf(ficresf,"\n");  
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        fprintf(ficresprobcov," p%1d-%1d ",i,j);
           nhstepm = nhstepm/hstepm;        fprintf(ficresprobcor," p%1d-%1d ",i,j);
                }  
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   /* fprintf(ficresprob,"\n");
           oldm=oldms;savm=savms;    fprintf(ficresprobcov,"\n");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      fprintf(ficresprobcor,"\n");
           */
           for (h=0; h<=nhstepm; h++){   xp=vector(1,npar);
             if (h==(int) (calagedate+YEARM*cpt)) {    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
             }    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
             for(j=1; j<=nlstate+ndeath;j++) {    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
               kk1=0.;kk2=0;    first=1;
               for(i=1; i<=nlstate;i++) {                  fprintf(ficgp,"\n# Routine varprob");
                 if (mobilav==1)    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    fprintf(fichtm,"\n");
                 else {  
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    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);
               }    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
               if (h==(int)(calagedate+12*cpt)){  and drawn. It helps understanding how is the covariance between two incidences.\
                 fprintf(ficresf," %.3f", kk1);   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
                            fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
               }  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
             }  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
           }  standard deviations wide on each axis. <br>\
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
         }   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
       }  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
     }  
   }    cov[1]=1;
            tj=cptcoveff;
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
   fclose(ficresf);    for(t=1; t<=tj;t++){
 }      for(i1=1; i1<=ncodemax[t];i1++){ 
 /************** Forecasting ******************/        j1++;
 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){        if  (cptcovn>0) {
            fprintf(ficresprob, "\n#********** Variable "); 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   int *popage;          fprintf(ficresprob, "**********\n#\n");
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          fprintf(ficresprobcov, "\n#********** Variable "); 
   double *popeffectif,*popcount;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   double ***p3mat,***tabpop,***tabpopprev;          fprintf(ficresprobcov, "**********\n#\n");
   char filerespop[FILENAMELENGTH];          
           fprintf(ficgp, "\n#********** Variable "); 
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          fprintf(ficgp, "**********\n#\n");
   agelim=AGESUP;          
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;          
            fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          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\">");
            
   strcpy(filerespop,"pop");          fprintf(ficresprobcor, "\n#********** Variable ");    
   strcat(filerespop,fileres);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   if((ficrespop=fopen(filerespop,"w"))==NULL) {          fprintf(ficresprobcor, "**********\n#");    
     printf("Problem with forecast resultfile: %s\n", filerespop);        }
     fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);        
   }        for (age=bage; age<=fage; age ++){ 
   printf("Computing forecasting: result on file '%s' \n", filerespop);          cov[2]=age;
   fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);          for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
   if (cptcoveff==0) ncodemax[cptcoveff]=1;          }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   if (mobilav==1) {          for (k=1; k<=cptcovprod;k++)
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     movingaverage(agedeb, fage, ageminpar, mobaverage);          
   }          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   stepsize=(int) (stepm+YEARM-1)/YEARM;          gp=vector(1,(nlstate)*(nlstate+ndeath));
   if (stepm<=12) stepsize=1;          gm=vector(1,(nlstate)*(nlstate+ndeath));
        
   agelim=AGESUP;          for(theta=1; theta <=npar; theta++){
              for(i=1; i<=npar; i++)
   hstepm=1;              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
   hstepm=hstepm/stepm;            
              pmij(pmmij,cov,ncovmodel,xp,nlstate);
   if (popforecast==1) {            
     if((ficpop=fopen(popfile,"r"))==NULL) {            k=0;
       printf("Problem with population file : %s\n",popfile);exit(0);            for(i=1; i<= (nlstate); i++){
       fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);              for(j=1; j<=(nlstate+ndeath);j++){
     }                k=k+1;
     popage=ivector(0,AGESUP);                gp[k]=pmmij[i][j];
     popeffectif=vector(0,AGESUP);              }
     popcount=vector(0,AGESUP);            }
                
     i=1;              for(i=1; i<=npar; i++)
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
          
     imx=i;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];            k=0;
   }            for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
   for(cptcov=1;cptcov<=i2;cptcov++){                k=k+1;
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){                gm[k]=pmmij[i][j];
       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]]);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
       }              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
       fprintf(ficrespop,"******\n");          }
       fprintf(ficrespop,"# Age");  
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
       if (popforecast==1)  fprintf(ficrespop," [Population]");            for(theta=1; theta <=npar; theta++)
                    trgradg[j][theta]=gradg[theta][j];
       for (cpt=0; cpt<=0;cpt++) {          
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
                  matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           nhstepm = nhstepm/hstepm;          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
                    free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;          pmij(pmmij,cov,ncovmodel,x,nlstate);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            
                  k=0;
           for (h=0; h<=nhstepm; h++){          for(i=1; i<=(nlstate); i++){
             if (h==(int) (calagedate+YEARM*cpt)) {            for(j=1; j<=(nlstate+ndeath);j++){
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);              k=k+1;
             }              mu[k][(int) age]=pmmij[i][j];
             for(j=1; j<=nlstate+ndeath;j++) {            }
               kk1=0.;kk2=0;          }
               for(i=1; i<=nlstate;i++) {                        for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
                 if (mobilav==1)            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];              varpij[i][j][(int)age] = doldm[i][j];
                 else {  
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          /*printf("\n%d ",(int)age);
                 }            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
               }            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
               if (h==(int)(calagedate+12*cpt)){            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;            }*/
                   /*fprintf(ficrespop," %.3f", kk1);  
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/          fprintf(ficresprob,"\n%d ",(int)age);
               }          fprintf(ficresprobcov,"\n%d ",(int)age);
             }          fprintf(ficresprobcor,"\n%d ",(int)age);
             for(i=1; i<=nlstate;i++){  
               kk1=0.;          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
                 for(j=1; j<=nlstate;j++){            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
                 }            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
             }          }
           i=0;
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)          for (k=1; k<=(nlstate);k++){
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);            for (l=1; l<=(nlstate+ndeath);l++){ 
           }              i=i++;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
         }              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
       }              for (j=1; j<=i;j++){
                  fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
   /******/                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {            }
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);            }/* end of loop for state */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){        } /* end of loop for age */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
           nhstepm = nhstepm/hstepm;        /* Confidence intervalle of pij  */
                  /*
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          fprintf(ficgp,"\nset noparametric;unset label");
           oldm=oldms;savm=savms;          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
           for (h=0; h<=nhstepm; h++){          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);
             if (h==(int) (calagedate+YEARM*cpt)) {          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
             }          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
             for(j=1; j<=nlstate+ndeath;j++) {        */
               kk1=0.;kk2=0;  
               for(i=1; i<=nlstate;i++) {                      /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];            first1=1;
               }        for (k2=1; k2<=(nlstate);k2++){
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             }            if(l2==k2) continue;
           }            j=(k2-1)*(nlstate+ndeath)+l2;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for (k1=1; k1<=(nlstate);k1++){
         }              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
       }                if(l1==k1) continue;
    }                i=(k1-1)*(nlstate+ndeath)+l1;
   }                if(i<=j) continue;
                  for (age=bage; age<=fage; age ++){ 
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                  if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   if (popforecast==1) {                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
     free_ivector(popage,0,AGESUP);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
     free_vector(popeffectif,0,AGESUP);                    mu1=mu[i][(int) age]/stepm*YEARM ;
     free_vector(popcount,0,AGESUP);                    mu2=mu[j][(int) age]/stepm*YEARM;
   }                    c12=cv12/sqrt(v1*v2);
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                    /* Computing eigen value of matrix of covariance */
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
   fclose(ficrespop);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
 }                    /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
 /***********************************************/                    /*v21=sqrt(1.-v11*v11); *//* error */
 /**************** Main Program *****************/                    v21=(lc1-v1)/cv12*v11;
 /***********************************************/                    v12=-v21;
                     v22=v11;
 int main(int argc, char *argv[])                    tnalp=v21/v11;
 {                    if(first1==1){
                       first1=0;
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;                      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);
   double agedeb, agefin,hf;                    }
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;                    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);
                     /*printf(fignu*/
   double fret;                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
   double **xi,tmp,delta;                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
   double dum; /* Dummy variable */                      first=0;
   double ***p3mat;                      fprintf(ficgp,"\nset parametric;unset label");
   int *indx;                      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);
   char line[MAXLINE], linepar[MAXLINE];                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   char path[80],pathc[80],pathcd[80],pathtot[80],model[80];                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
   int firstobs=1, lastobs=10;   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   int sdeb, sfin; /* Status at beginning and end */  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
   int c,  h , cpt,l;                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
   int ju,jl, mi;                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
   int mobilav=0,popforecast=0;                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   int hstepm, nhstepm;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
   double bage, fage, age, agelim, agebase;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   double ftolpl=FTOL;                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   double **prlim;                    }else{
   double *severity;                      first=0;
   double ***param; /* Matrix of parameters */                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
   double  *p;                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   double **matcov; /* Matrix of covariance */                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   double ***delti3; /* Scale */                      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",\
   double *delti; /* Scale */                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   double ***eij, ***vareij;                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   double **varpl; /* Variances of prevalence limits by age */                    }/* if first */
   double *epj, vepp;                  } /* age mod 5 */
   double kk1, kk2;                } /* end loop age */
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                  first=1;
               } /*l12 */
   char *alph[]={"a","a","b","c","d","e"}, str[4];            } /* k12 */
           } /*l1 */
         }/* k1 */
   char z[1]="c", occ;      } /* loop covariates */
 #include <sys/time.h>    }
 #include <time.h>    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
      free_vector(xp,1,npar);
   /* long total_usecs;    fclose(ficresprob);
   struct timeval start_time, end_time;    fclose(ficresprobcov);
      fclose(ficresprobcor);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    fflush(ficgp);
   getcwd(pathcd, size);    fflush(fichtmcov);
   }
   printf("\n%s",version);  
   if(argc <=1){  
     printf("\nEnter the parameter file name: ");  /******************* Printing html file ***********/
     scanf("%s",pathtot);  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
   }                    int lastpass, int stepm, int weightopt, char model[],\
   else{                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
     strcpy(pathtot,argv[1]);                    int popforecast, int estepm ,\
   }                    double jprev1, double mprev1,double anprev1, \
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/                    double jprev2, double mprev2,double anprev2){
   /*cygwin_split_path(pathtot,path,optionfile);    int jj1, k1, i1, cpt;
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/  
   /* cutv(path,optionfile,pathtot,'\\');*/     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 ",
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);     fprintf(fichtm,"\
   chdir(path);   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
   replace(pathc,path);             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
 /*-------- arguments in the command line --------*/   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
   /* Log file */     fprintf(fichtm,"\
   strcat(filelog, optionfilefiname);   - Life expectancies by age and initial health status (estepm=%2d months): \
   strcat(filelog,".log");    /* */     <a href=\"%s\">%s</a> <br>\n</li>",
   if((ficlog=fopen(filelog,"w"))==NULL)    {             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
     printf("Problem with logfile %s\n",filelog);  
     goto end;  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   }  
   fprintf(ficlog,"Log filename:%s\n",filelog);   m=cptcoveff;
   fprintf(ficlog,"\n%s",version);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   fprintf(ficlog,"\nEnter the parameter file name: ");  
   fprintf(ficlog,"pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);   jj1=0;
   fflush(ficlog);   for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
   /* */       jj1++;
   strcpy(fileres,"r");       if (cptcovn > 0) {
   strcat(fileres, optionfilefiname);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   strcat(fileres,".txt");    /* Other files have txt extension */         for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   /*---------arguments file --------*/         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
   if((ficpar=fopen(optionfile,"r"))==NULL)    {       /* Pij */
     printf("Problem with optionfile %s\n",optionfile);       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> \
     fprintf(ficlog,"Problem with optionfile %s\n",optionfile);  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
     goto end;       /* Quasi-incidences */
   }       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
   strcpy(filereso,"o");  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
   strcat(filereso,fileres);         /* Stable prevalence in each health state */
   if((ficparo=fopen(filereso,"w"))==NULL) {         for(cpt=1; cpt<nlstate;cpt++){
     printf("Problem with Output resultfile: %s\n", filereso);           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
     fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
     goto end;         }
   }       for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
   /* Reads comments: lines beginning with '#' */  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
   while((c=getc(ficpar))=='#' && c!= EOF){       }
     ungetc(c,ficpar);     } /* end i1 */
     fgets(line, MAXLINE, ficpar);   }/* End k1 */
     puts(line);   fprintf(fichtm,"</ul>");
     fputs(line,ficparo);  
   }  
   ungetc(c,ficpar);   fprintf(fichtm,"\
   \n<br><li><h4> Result files (second order: variances)</h4>\n\
   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);   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   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(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
 while((c=getc(ficpar))=='#' && c!= EOF){           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
     ungetc(c,ficpar);   fprintf(fichtm,"\
     fgets(line, MAXLINE, ficpar);   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
     puts(line);           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
     fputs(line,ficparo);  
   }   fprintf(fichtm,"\
   ungetc(c,ficpar);   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
             subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
       fprintf(fichtm,"\
   covar=matrix(0,NCOVMAX,1,n);   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
   cptcovn=0;           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;   fprintf(fichtm,"\
    - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
   ncovmodel=2+cptcovn;           subdirf2(fileres,"t"),subdirf2(fileres,"t"));
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */   fprintf(fichtm,"\
     - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
   /* Read guess parameters */           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){  /*  if(popforecast==1) fprintf(fichtm,"\n */
     ungetc(c,ficpar);  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
     fgets(line, MAXLINE, ficpar);  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
     puts(line);  /*      <br>",fileres,fileres,fileres,fileres); */
     fputs(line,ficparo);  /*  else  */
   }  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
   ungetc(c,ficpar);   fflush(fichtm);
     fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
     for(i=1; i <=nlstate; i++)   m=cptcoveff;
     for(j=1; j <=nlstate+ndeath-1; j++){   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       fprintf(ficparo,"%1d%1d",i1,j1);   jj1=0;
       if(mle==1)   for(k1=1; k1<=m;k1++){
         printf("%1d%1d",i,j);     for(i1=1; i1<=ncodemax[k1];i1++){
       fprintf(ficlog,"%1d%1d",i,j);       jj1++;
       for(k=1; k<=ncovmodel;k++){       if (cptcovn > 0) {
         fscanf(ficpar," %lf",&param[i][j][k]);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
         if(mle==1){         for (cpt=1; cpt<=cptcoveff;cpt++) 
           printf(" %lf",param[i][j][k]);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
           fprintf(ficlog," %lf",param[i][j][k]);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
         }       }
         else       for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(ficlog," %lf",param[i][j][k]);         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
         fprintf(ficparo," %lf",param[i][j][k]);  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
       }  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
       fscanf(ficpar,"\n");       }
       if(mle==1)       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
         printf("\n");  health expectancies in states (1) and (2): %s%d.png<br>\
       fprintf(ficlog,"\n");  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
       fprintf(ficparo,"\n");     } /* end i1 */
     }   }/* End k1 */
     fprintf(fichtm,"</ul>");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;   fflush(fichtm);
   }
   p=param[1][1];  
    /******************* Gnuplot file **************/
   /* Reads comments: lines beginning with '#' */  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    char dirfileres[132],optfileres[132];
     fgets(line, MAXLINE, ficpar);    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     puts(line);    int ng;
     fputs(line,ficparo);  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   }  /*     printf("Problem with file %s",optionfilegnuplot); */
   ungetc(c,ficpar);  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    /*#ifdef windows */
   for(i=1; i <=nlstate; i++){    fprintf(ficgp,"cd \"%s\" \n",pathc);
     for(j=1; j <=nlstate+ndeath-1; j++){      /*#endif */
       fscanf(ficpar,"%1d%1d",&i1,&j1);    m=pow(2,cptcoveff);
       printf("%1d%1d",i,j);  
       fprintf(ficparo,"%1d%1d",i1,j1);    strcpy(dirfileres,optionfilefiname);
       for(k=1; k<=ncovmodel;k++){    strcpy(optfileres,"vpl");
         fscanf(ficpar,"%le",&delti3[i][j][k]);   /* 1eme*/
         printf(" %le",delti3[i][j][k]);    for (cpt=1; cpt<= nlstate ; cpt ++) {
         fprintf(ficparo," %le",delti3[i][j][k]);     for (k1=1; k1<= m ; k1 ++) {
       }       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
       fscanf(ficpar,"\n");       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
       printf("\n");       fprintf(ficgp,"set xlabel \"Age\" \n\
       fprintf(ficparo,"\n");  set ylabel \"Probability\" \n\
     }  set ter png small\n\
   }  set size 0.65,0.65\n\
   delti=delti3[1][1];  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
    
   /* Reads comments: lines beginning with '#' */       for (i=1; i<= nlstate ; i ++) {
   while((c=getc(ficpar))=='#' && c!= EOF){         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     ungetc(c,ficpar);         else fprintf(ficgp," \%%*lf (\%%*lf)");
     fgets(line, MAXLINE, ficpar);       }
     puts(line);       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);
     fputs(line,ficparo);       for (i=1; i<= nlstate ; i ++) {
   }         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   ungetc(c,ficpar);         else fprintf(ficgp," \%%*lf (\%%*lf)");
         } 
   matcov=matrix(1,npar,1,npar);       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
   for(i=1; i <=npar; i++){       for (i=1; i<= nlstate ; i ++) {
     fscanf(ficpar,"%s",&str);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     if(mle==1)         else fprintf(ficgp," \%%*lf (\%%*lf)");
       printf("%s",str);       }  
     fprintf(ficlog,"%s",str);       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
     fprintf(ficparo,"%s",str);     }
     for(j=1; j <=i; j++){    }
       fscanf(ficpar," %le",&matcov[i][j]);    /*2 eme*/
       if(mle==1){    
         printf(" %.5le",matcov[i][j]);    for (k1=1; k1<= m ; k1 ++) { 
         fprintf(ficlog," %.5le",matcov[i][j]);      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       }      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       else      
         fprintf(ficlog," %.5le",matcov[i][j]);      for (i=1; i<= nlstate+1 ; i ++) {
       fprintf(ficparo," %.5le",matcov[i][j]);        k=2*i;
     }        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
     fscanf(ficpar,"\n");        for (j=1; j<= nlstate+1 ; j ++) {
     if(mle==1)          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       printf("\n");          else fprintf(ficgp," \%%*lf (\%%*lf)");
     fprintf(ficlog,"\n");        }   
     fprintf(ficparo,"\n");        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
   }        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
   for(i=1; i <=npar; i++)        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
     for(j=i+1;j<=npar;j++)        for (j=1; j<= nlstate+1 ; j ++) {
       matcov[i][j]=matcov[j][i];          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
              else fprintf(ficgp," \%%*lf (\%%*lf)");
   if(mle==1)        }   
     printf("\n");        fprintf(ficgp,"\" t\"\" w l 0,");
   fprintf(ficlog,"\n");        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     /*-------- Rewriting paramater file ----------*/          else fprintf(ficgp," \%%*lf (\%%*lf)");
      strcpy(rfileres,"r");    /* "Rparameterfile */        }   
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
      strcat(rfileres,".");    /* */        else fprintf(ficgp,"\" t\"\" w l 0,");
      strcat(rfileres,optionfilext);    /* Other files have txt extension */      }
     if((ficres =fopen(rfileres,"w"))==NULL) {    }
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;    /*3eme*/
     }    
     fprintf(ficres,"#%s\n",version);    for (k1=1; k1<= m ; k1 ++) { 
          for (cpt=1; cpt<= nlstate ; cpt ++) {
     /*-------- data file ----------*/        k=2+nlstate*(2*cpt-2);
     if((fic=fopen(datafile,"r"))==NULL)    {        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
       printf("Problem with datafile: %s\n", datafile);goto end;        fprintf(ficgp,"set ter png small\n\
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;  set size 0.65,0.65\n\
     }  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     n= lastobs;          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     severity = vector(1,maxwav);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     outcome=imatrix(1,maxwav+1,1,n);          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     num=ivector(1,n);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     moisnais=vector(1,n);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     annais=vector(1,n);          
     moisdc=vector(1,n);        */
     andc=vector(1,n);        for (i=1; i< nlstate ; i ++) {
     agedc=vector(1,n);          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);
     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);    /* CV preval stable (period) */
     adl=imatrix(1,maxwav+1,1,n);        for (k1=1; k1<= m ; k1 ++) { 
     tab=ivector(1,NCOVMAX);      for (cpt=1; cpt<=nlstate ; cpt ++) {
     ncodemax=ivector(1,8);        k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
     i=1;        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
     while (fgets(line, MAXLINE, fic) != NULL)    {  set ter png small\nset size 0.65,0.65\n\
       if ((i >= firstobs) && (i <=lastobs)) {  unset log y\n\
          plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         for (j=maxwav;j>=1;j--){        
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        for (i=1; i< nlstate ; i ++)
           strcpy(line,stra);          fprintf(ficgp,"+$%d",k+i+1);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        
         }        l=3+(nlstate+ndeath)*cpt;
                fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        for (i=1; i< nlstate ; i ++) {
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);          l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        }
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
         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);    /* proba elementaires */
         }    for(i=1,jk=1; i <=nlstate; i++){
         num[i]=atol(stra);      for(k=1; k <=(nlstate+ndeath); k++){
                if (k != i) {
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){          for(j=1; j <=ncovmodel; j++){
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
         i=i+1;            fprintf(ficgp,"\n");
       }          }
     }        }
     /* printf("ii=%d", ij);      }
        scanf("%d",i);*/     }
   imx=i-1; /* Number of individuals */  
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
   /* for (i=1; i<=imx; i++){       for(jk=1; jk <=m; jk++) {
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;         if (ng==2)
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
     }*/         else
    /*  for (i=1; i<=imx; i++){           fprintf(ficgp,"\nset title \"Probability\"\n");
      if (s[4][i]==9)  s[4][i]=-1;         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
      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]));}*/         i=1;
           for(k2=1; k2<=nlstate; k2++) {
             k3=i;
   /* Calculation of the number of parameter from char model*/           for(k=1; k<=(nlstate+ndeath); k++) {
   Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */             if (k != k2){
   Tprod=ivector(1,15);               if(ng==2)
   Tvaraff=ivector(1,15);                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
   Tvard=imatrix(1,15,1,2);               else
   Tage=ivector(1,15);                       fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                   ij=1;
   if (strlen(model) >1){               for(j=3; j <=ncovmodel; j++) {
     j=0, j1=0, k1=1, k2=1;                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
     j=nbocc(model,'+');                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
     j1=nbocc(model,'*');                   ij++;
     cptcovn=j+1;                 }
     cptcovprod=j1;                 else
                       fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
     strcpy(modelsav,model);               }
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){               fprintf(ficgp,")/(1");
       printf("Error. Non available option model=%s ",model);               
       fprintf(ficlog,"Error. Non available option model=%s ",model);               for(k1=1; k1 <=nlstate; k1++){   
       goto end;                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
     }                 ij=1;
                     for(j=3; j <=ncovmodel; j++){
     for(i=(j+1); i>=1;i--){                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
       cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyze it */                     ij++;
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/                   }
       /*scanf("%d",i);*/                   else
       if (strchr(strb,'*')) {  /* Model includes a product */                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
         cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/                 }
         if (strcmp(strc,"age")==0) { /* Vn*age */                 fprintf(ficgp,")");
           cptcovprod--;               }
           cutv(strb,stre,strd,'V');               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
           Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
           cptcovage++;               i=i+ncovmodel;
             Tage[cptcovage]=i;             }
             /*printf("stre=%s ", stre);*/           } /* end k */
         }         } /* end k2 */
         else if (strcmp(strd,"age")==0) { /* or age*Vn */       } /* end jk */
           cptcovprod--;     } /* end ng */
           cutv(strb,stre,strc,'V');     fflush(ficgp); 
           Tvar[i]=atoi(stre);  }  /* end gnuplot */
           cptcovage++;  
           Tage[cptcovage]=i;  
         }  /*************** Moving average **************/
         else {  /* Age is not in the model */  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
           cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/  
           Tvar[i]=ncovcol+k1;    int i, cpt, cptcod;
           cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */    int modcovmax =1;
           Tprod[k1]=i;    int mobilavrange, mob;
           Tvard[k1][1]=atoi(strc); /* m*/    double age;
           Tvard[k1][2]=atoi(stre); /* n */  
           Tvar[cptcovn+k2]=Tvard[k1][1];    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
           Tvar[cptcovn+k2+1]=Tvard[k1][2];                             a covariate has 2 modalities */
           for (k=1; k<=lastobs;k++)    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];  
           k1++;    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
           k2=k2+2;      if(mobilav==1) mobilavrange=5; /* default */
         }      else mobilavrange=mobilav;
       }      for (age=bage; age<=fage; age++)
       else { /* no more sum */        for (i=1; i<=nlstate;i++)
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/          for (cptcod=1;cptcod<=modcovmax;cptcod++)
        /*  scanf("%d",i);*/            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       cutv(strd,strc,strb,'V');      /* We keep the original values on the extreme ages bage, fage and for 
       Tvar[i]=atoi(strc);         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. 
       strcpy(modelsav,stra);        */ 
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);      for (mob=3;mob <=mobilavrange;mob=mob+2){
         scanf("%d",i);*/        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
     } /* end of loop + */          for (i=1; i<=nlstate;i++){
   } /* end model */            for (cptcod=1;cptcod<=modcovmax;cptcod++){
                mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);                for (cpt=1;cpt<=(mob-1)/2;cpt++){
   printf("cptcovprod=%d ", cptcovprod);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
   fprintf(ficlog,"cptcovprod=%d ", cptcovprod);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
   scanf("%d ",i);*/                }
     fclose(fic);              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
     /*  if(mle==1){*/          }
     if (weightopt != 1) { /* Maximisation without weights*/        }/* end age */
       for(i=1;i<=n;i++) weight[i]=1.0;      }/* end mob */
     }    }else return -1;
     /*-calculation of age at interview from date of interview and age at death -*/    return 0;
     agev=matrix(1,maxwav,1,imx);  }/* End movingaverage */
   
     for (i=1; i<=imx; i++) {  
       for(m=2; (m<= maxwav); m++) {  /************** Forecasting ******************/
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){  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){
          anint[m][i]=9999;    /* proj1, year, month, day of starting projection 
          s[m][i]=-1;       agemin, agemax range of age
        }       dateprev1 dateprev2 range of dates during which prevalence is computed
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;       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;
     for (i=1; i<=imx; i++)  {    double agec; /* generic age */
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
       for(m=1; (m<= maxwav); m++){    double *popeffectif,*popcount;
         if(s[m][i] >0){    double ***p3mat;
           if (s[m][i] >= nlstate+1) {    double ***mobaverage;
             if(agedc[i]>0)    char fileresf[FILENAMELENGTH];
               if(moisdc[i]!=99 && andc[i]!=9999)  
                 agev[m][i]=agedc[i];    agelim=AGESUP;
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
            else {   
               if (andc[i]!=9999){    strcpy(fileresf,"f"); 
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    strcat(fileresf,fileres);
               fprintf(ficlog,"Warning negative age at death: %d line:%d\n",num[i],i);    if((ficresf=fopen(fileresf,"w"))==NULL) {
               agev[m][i]=-1;      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);
           else if(s[m][i] !=9){ /* Should no more exist */    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);  
             if(mint[m][i]==99 || anint[m][i]==9999)    if (cptcoveff==0) ncodemax[cptcoveff]=1;
               agev[m][i]=1;  
             else if(agev[m][i] <agemin){    if (mobilav!=0) {
               agemin=agev[m][i];      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
             }        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
             else if(agev[m][i] >agemax){        printf(" Error in movingaverage mobilav=%d\n",mobilav);
               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];*/    stepsize=(int) (stepm+YEARM-1)/YEARM;
             /*   agev[m][i] = age[i]+2*m;*/    if (stepm<=12) stepsize=1;
           }    if(estepm < stepm){
           else { /* =9 */      printf ("Problem %d lower than %d\n",estepm, stepm);
             agev[m][i]=1;    }
             s[m][i]=-1;    else  hstepm=estepm;   
           }  
         }    hstepm=hstepm/stepm; 
         else /*= 0 Unknown */    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
           agev[m][i]=1;                                 fractional in yp1 */
       }    anprojmean=yp;
        yp2=modf((yp1*12),&yp);
     }    mprojmean=yp;
     for (i=1; i<=imx; i++)  {    yp1=modf((yp2*30.5),&yp);
       for(m=1; (m<= maxwav); m++){    jprojmean=yp;
         if (s[m][i] > (nlstate+ndeath)) {    if(jprojmean==0) jprojmean=1;
           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);      if(mprojmean==0) jprojmean=1;
           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;    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); 
     
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    fprintf(ficresf,"#****** Routine prevforecast **\n");
  fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);  
   /*            if (h==(int)(YEARM*yearp)){ */
     free_vector(severity,1,maxwav);    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
     free_imatrix(outcome,1,maxwav+1,1,n);      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
     free_vector(moisnais,1,n);        k=k+1;
     free_vector(annais,1,n);        fprintf(ficresf,"\n#******");
     /* free_matrix(mint,1,maxwav,1,n);        for(j=1;j<=cptcoveff;j++) {
        free_matrix(anint,1,maxwav,1,n);*/          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]]);
     free_vector(moisdc,1,n);        }
     free_vector(andc,1,n);        fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
            for(j=1; j<=nlstate+ndeath;j++){ 
     wav=ivector(1,imx);          for(i=1; i<=nlstate;i++)              
     dh=imatrix(1,lastpass-firstpass+1,1,imx);            fprintf(ficresf," p%d%d",i,j);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          fprintf(ficresf," p.%d",j);
            }
     /* Concatenates waves */        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);          fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
       Tcode=ivector(1,100);          for (agec=fage; agec>=(ageminpar-1); agec--){ 
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
       ncodemax[1]=1;            nhstepm = nhstepm/hstepm; 
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                  oldm=oldms;savm=savms;
    codtab=imatrix(1,100,1,10);            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
    h=0;          
    m=pow(2,cptcoveff);            for (h=0; h<=nhstepm; h++){
                if (h*hstepm/YEARM*stepm ==yearp) {
    for(k=1;k<=cptcoveff; k++){                fprintf(ficresf,"\n");
      for(i=1; i <=(m/pow(2,k));i++){                for(j=1;j<=cptcoveff;j++) 
        for(j=1; j <= ncodemax[k]; j++){                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
            h++;              } 
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;              for(j=1; j<=nlstate+ndeath;j++) {
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/                ppij=0.;
          }                for(i=1; i<=nlstate;i++) {
        }                  if (mobilav==1) 
      }                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
    }                  else {
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
       codtab[1][2]=1;codtab[2][2]=2; */                  }
    /* for(i=1; i <=m ;i++){                  if (h*hstepm/YEARM*stepm== yearp) {
       for(k=1; k <=cptcovn; k++){                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);                  }
       }                } /* end i */
       printf("\n");                if (h*hstepm/YEARM*stepm==yearp) {
       }                  fprintf(ficresf," %.3f", ppij);
       scanf("%d",i);*/                }
                  }/* end j */
    /* Calculates basic frequencies. Computes observed prevalence at single age            } /* end h */
        and prints on file fileres'p'. */            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
            } /* end yearp */
          } /* end cptcod */
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    } /* end  cptcov */
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */         
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    fclose(ficresf);
        }
     /* 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] */  /************** Forecasting *****not tested NB*************/
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */  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){
     
     if(mle==1){    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    int *popage;
     }    double calagedatem, agelim, kk1, kk2;
        double *popeffectif,*popcount;
     /*--------- results files --------------*/    double ***p3mat,***tabpop,***tabpopprev;
     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);    double ***mobaverage;
      char filerespop[FILENAMELENGTH];
   
    jk=1;    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    agelim=AGESUP;
    fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
    for(i=1,jk=1; i <=nlstate; i++){    
      for(k=1; k <=(nlstate+ndeath); k++){    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
        if (k != i)    
          {    
            printf("%d%d ",i,k);    strcpy(filerespop,"pop"); 
            fprintf(ficlog,"%d%d ",i,k);    strcat(filerespop,fileres);
            fprintf(ficres,"%1d%1d ",i,k);    if((ficrespop=fopen(filerespop,"w"))==NULL) {
            for(j=1; j <=ncovmodel; j++){      printf("Problem with forecast resultfile: %s\n", filerespop);
              printf("%f ",p[jk]);      fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
              fprintf(ficlog,"%f ",p[jk]);    }
              fprintf(ficres,"%f ",p[jk]);    printf("Computing forecasting: result on file '%s' \n", filerespop);
              jk++;    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
            }  
            printf("\n");    if (cptcoveff==0) ncodemax[cptcoveff]=1;
            fprintf(ficlog,"\n");  
            fprintf(ficres,"\n");    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);
    if(mle==1){        printf(" Error in movingaverage mobilav=%d\n",mobilav);
      /* Computing hessian and covariance matrix */      }
      ftolhess=ftol; /* Usually correct */    }
      hesscov(matcov, p, npar, delti, ftolhess, func);  
    }    stepsize=(int) (stepm+YEARM-1)/YEARM;
    fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");    if (stepm<=12) stepsize=1;
    printf("# Scales (for hessian or gradient estimation)\n");    
    fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");    agelim=AGESUP;
    for(i=1,jk=1; i <=nlstate; i++){    
      for(j=1; j <=nlstate+ndeath; j++){    hstepm=1;
        if (j!=i) {    hstepm=hstepm/stepm; 
          fprintf(ficres,"%1d%1d",i,j);    
          printf("%1d%1d",i,j);    if (popforecast==1) {
          fprintf(ficlog,"%1d%1d",i,j);      if((ficpop=fopen(popfile,"r"))==NULL) {
          for(k=1; k<=ncovmodel;k++){        printf("Problem with population file : %s\n",popfile);exit(0);
            printf(" %.5e",delti[jk]);        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
            fprintf(ficlog," %.5e",delti[jk]);      } 
            fprintf(ficres," %.5e",delti[jk]);      popage=ivector(0,AGESUP);
            jk++;      popeffectif=vector(0,AGESUP);
          }      popcount=vector(0,AGESUP);
          printf("\n");      
          fprintf(ficlog,"\n");      i=1;   
          fprintf(ficres,"\n");      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];
        }
    k=1;  
    fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
    if(mle==1)     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
      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");        k=k+1;
    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");        fprintf(ficrespop,"\n#******");
    for(i=1;i<=npar;i++){        for(j=1;j<=cptcoveff;j++) {
      /*  if (k>nlstate) k=1;          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
          i1=(i-1)/(ncovmodel*nlstate)+1;        }
          fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);        fprintf(ficrespop,"******\n");
          printf("%s%d%d",alph[k],i1,tab[i]);*/        fprintf(ficrespop,"# Age");
      fprintf(ficres,"%3d",i);        for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
      if(mle==1)        if (popforecast==1)  fprintf(ficrespop," [Population]");
        printf("%3d",i);        
      fprintf(ficlog,"%3d",i);        for (cpt=0; cpt<=0;cpt++) { 
      for(j=1; j<=i;j++){          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
        fprintf(ficres," %.5e",matcov[i][j]);          
        if(mle==1)          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
          printf(" %.5e",matcov[i][j]);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
        fprintf(ficlog," %.5e",matcov[i][j]);            nhstepm = nhstepm/hstepm; 
      }            
      fprintf(ficres,"\n");            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
      if(mle==1)            oldm=oldms;savm=savms;
        printf("\n");            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
      fprintf(ficlog,"\n");          
      k++;            for (h=0; h<=nhstepm; h++){
    }              if (h==(int) (calagedatem+YEARM*cpt)) {
                    fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
    while((c=getc(ficpar))=='#' && c!= EOF){              } 
      ungetc(c,ficpar);              for(j=1; j<=nlstate+ndeath;j++) {
      fgets(line, MAXLINE, ficpar);                kk1=0.;kk2=0;
      puts(line);                for(i=1; i<=nlstate;i++) {              
      fputs(line,ficparo);                  if (mobilav==1) 
    }                    kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
    ungetc(c,ficpar);                  else {
    estepm=0;                    kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
    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) {                if (h==(int)(calagedatem+12*cpt)){
      bage = ageminpar;                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
      fage = agemaxpar;                    /*fprintf(ficrespop," %.3f", kk1);
    }                      if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                    }
    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);              for(i=1; i<=nlstate;i++){
    fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                kk1=0.;
                      for(j=1; j<=nlstate;j++){
    while((c=getc(ficpar))=='#' && c!= EOF){                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
      ungetc(c,ficpar);                  }
      fgets(line, MAXLINE, ficpar);                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
      puts(line);              }
      fputs(line,ficparo);  
    }              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
    ungetc(c,ficpar);                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
              }
    fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          }
    fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);        }
       
    while((c=getc(ficpar))=='#' && c!= EOF){    /******/
      ungetc(c,ficpar);  
      fgets(line, MAXLINE, ficpar);        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
      puts(line);          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
      fputs(line,ficparo);          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
    }            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
    ungetc(c,ficpar);            nhstepm = nhstepm/hstepm; 
              
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    dateprev1=anprev1+mprev1/12.+jprev1/365.;            oldm=oldms;savm=savms;
    dateprev2=anprev2+mprev2/12.+jprev2/365.;            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
   fscanf(ficpar,"pop_based=%d\n",&popbased);              if (h==(int) (calagedatem+YEARM*cpt)) {
   fprintf(ficparo,"pop_based=%d\n",popbased);                  fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
   fprintf(ficres,"pop_based=%d\n",popbased);                } 
                for(j=1; j<=nlstate+ndeath;j++) {
   while((c=getc(ficpar))=='#' && c!= EOF){                kk1=0.;kk2=0;
     ungetc(c,ficpar);                for(i=1; i<=nlstate;i++) {              
     fgets(line, MAXLINE, ficpar);                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
     puts(line);                }
     fputs(line,ficparo);                if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
   }              }
   ungetc(c,ficpar);            }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);          }
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);        }
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);     } 
     }
    
 while((c=getc(ficpar))=='#' && c!= EOF){    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    if (popforecast==1) {
     puts(line);      free_ivector(popage,0,AGESUP);
     fputs(line,ficparo);      free_vector(popeffectif,0,AGESUP);
   }      free_vector(popcount,0,AGESUP);
   ungetc(c,ficpar);    }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);    free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    fclose(ficrespop);
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);  } /* End of popforecast */
   
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  int fileappend(FILE *fichier, char *optionfich)
   {
 /*------------ gnuplot -------------*/    if((fichier=fopen(optionfich,"a"))==NULL) {
   strcpy(optionfilegnuplot,optionfilefiname);      printf("Problem with file: %s\n", optionfich);
   strcat(optionfilegnuplot,".gp");      fprintf(ficlog,"Problem with file: %s\n", optionfich);
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {      return (0);
     printf("Problem with file %s",optionfilegnuplot);    }
   }    fflush(fichier);
   fclose(ficgp);    return (1);
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);  }
 /*--------- index.htm --------*/  
   
   strcpy(optionfilehtm,optionfile);  /**************** function prwizard **********************/
   strcat(optionfilehtm,".htm");  void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {  {
     printf("Problem with %s \n",optionfilehtm), exit(0);  
   }    /* Wizard to print covariance matrix template */
   
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n    char ca[32], cb[32], cc[32];
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n    int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
 \n    int numlinepar;
 Total number of observations=%d <br>\n  
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
 <hr  size=\"2\" color=\"#EC5E5E\">    fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
  <ul><li><h4>Parameter files</h4>\n    for(i=1; i <=nlstate; i++){
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n      jj=0;
  - Log file of the run: <a href=\"%s\">%s</a><br>\n      for(j=1; j <=nlstate+ndeath; j++){
  - Gnuplot file name: <a href=\"%s\">%s</a></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,filelog,filelog,optionfilegnuplot,optionfilegnuplot);        if(j==i) continue;
   fclose(fichtm);        jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);        printf("%1d%1d",i,j);
          fprintf(ficparo,"%1d%1d",i,j);
 /*------------ free_vector  -------------*/        for(k=1; k<=ncovmodel;k++){
  chdir(path);          /*        printf(" %lf",param[i][j][k]); */
            /*        fprintf(ficparo," %lf",param[i][j][k]); */
  free_ivector(wav,1,imx);          printf(" 0.");
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);          fprintf(ficparo," 0.");
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);          }
  free_ivector(num,1,n);        printf("\n");
  free_vector(agedc,1,n);        fprintf(ficparo,"\n");
  /*free_matrix(covar,1,NCOVMAX,1,n);*/      }
  fclose(ficparo);    }
  fclose(ficres);    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*/ 
   /*--------------- Prevalence limit --------------*/    for(i=1; i <=nlstate; i++){
        jj=0;
   strcpy(filerespl,"pl");      for(j=1; j <=nlstate+ndeath; j++){
   strcat(filerespl,fileres);        if(j==i) continue;
   if((ficrespl=fopen(filerespl,"w"))==NULL) {        jj++;
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;        fprintf(ficparo,"%1d%1d",i,j);
     fprintf(ficlog,"Problem with Prev limit resultfile: %s\n", filerespl);goto end;        printf("%1d%1d",i,j);
   }        fflush(stdout);
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);        for(k=1; k<=ncovmodel;k++){
   fprintf(ficlog,"Computing prevalence limit: result on file '%s' \n", filerespl);          /*      printf(" %le",delti3[i][j][k]); */
   fprintf(ficrespl,"#Prevalence limit\n");          /*      fprintf(ficparo," %le",delti3[i][j][k]); */
   fprintf(ficrespl,"#Age ");          printf(" 0.");
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);          fprintf(ficparo," 0.");
   fprintf(ficrespl,"\n");        }
          numlinepar++;
   prlim=matrix(1,nlstate,1,nlstate);        printf("\n");
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        fprintf(ficparo,"\n");
   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 */    printf("# Covariance matrix\n");
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  /* # 121 Var(a12)\n\ */
   k=0;  /* # 122 Cov(b12,a12) Var(b12)\n\ */
   agebase=ageminpar;  /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   agelim=agemaxpar;  /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   ftolpl=1.e-10;  /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   i1=cptcoveff;  /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   if (cptcovn < 1){i1=1;}  /* # 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" */
   for(cptcov=1;cptcov<=i1;cptcov++){    fflush(stdout);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficparo,"# Covariance matrix\n");
         k=k+1;    /* # 121 Var(a12)\n\ */
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    /* # 122 Cov(b12,a12) Var(b12)\n\ */
         fprintf(ficrespl,"\n#******");    /* #   ...\n\ */
         printf("\n#******");    /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
         fprintf(ficlog,"\n#******");    
         for(j=1;j<=cptcoveff;j++) {    for(itimes=1;itimes<=2;itimes++){
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      jj=0;
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      for(i=1; i <=nlstate; i++){
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for(j=1; j <=nlstate+ndeath; j++){
         }          if(j==i) continue;
         fprintf(ficrespl,"******\n");          for(k=1; k<=ncovmodel;k++){
         printf("******\n");            jj++;
         fprintf(ficlog,"******\n");            ca[0]= k+'a'-1;ca[1]='\0';
                    if(itimes==1){
         for (age=agebase; age<=agelim; age++){              printf("#%1d%1d%d",i,j,k);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);              fprintf(ficparo,"#%1d%1d%d",i,j,k);
           fprintf(ficrespl,"%.0f",age );            }else{
           for(i=1; i<=nlstate;i++)              printf("%1d%1d%d",i,j,k);
           fprintf(ficrespl," %.5f", prlim[i][i]);              fprintf(ficparo,"%1d%1d%d",i,j,k);
           fprintf(ficrespl,"\n");              /*  printf(" %.5le",matcov[i][j]); */
         }            }
       }            ll=0;
     }            for(li=1;li <=nlstate; li++){
   fclose(ficrespl);              for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
   /*------------- h Pij x at various ages ------------*/                for(lk=1;lk<=ncovmodel;lk++){
                    ll++;
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);                  if(ll<=jj){
   if((ficrespij=fopen(filerespij,"w"))==NULL) {                    cb[0]= lk +'a'-1;cb[1]='\0';
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;                    if(ll<jj){
     fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;                      if(itimes==1){
   }                        printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
   printf("Computing pij: result on file '%s' \n", filerespij);                        fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
   fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);                      }else{
                          printf(" 0.");
   stepsize=(int) (stepm+YEARM-1)/YEARM;                        fprintf(ficparo," 0.");
   /*if (stepm<=24) stepsize=2;*/                      }
                     }else{
   agelim=AGESUP;                      if(itimes==1){
   hstepm=stepsize*YEARM; /* Every year of age */                        printf(" Var(%s%1d%1d)",ca,i,j);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */                        fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
   /* hstepm=1;   aff par mois*/                        printf(" 0.");
                         fprintf(ficparo," 0.");
   k=0;                      }
   for(cptcov=1;cptcov<=i1;cptcov++){                    }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                  }
       k=k+1;                } /* end lk */
         fprintf(ficrespij,"\n#****** ");              } /* end lj */
         for(j=1;j<=cptcoveff;j++)            } /* end li */
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            printf("\n");
         fprintf(ficrespij,"******\n");            fprintf(ficparo,"\n");
                    numlinepar++;
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */          } /* end k*/
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        } /*end j */
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      } /* end i */
     } /* end itimes */
           /*      nhstepm=nhstepm*YEARM; aff par mois*/  
   } /* end of prwizard */
           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,"# Age");  /**************** Main Program *****************/
           for(i=1; i<=nlstate;i++)  /***********************************************/
             for(j=1; j<=nlstate+ndeath;j++)  
               fprintf(ficrespij," %1d-%1d",i,j);  int main(int argc, char *argv[])
           fprintf(ficrespij,"\n");  {
            for (h=0; h<=nhstepm; h++){    int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
             fprintf(ficrespij,"%d %f %f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
             for(i=1; i<=nlstate;i++)    int jj, ll, li, lj, lk, imk;
               for(j=1; j<=nlstate+ndeath;j++)    int numlinepar=0; /* Current linenumber of parameter file */
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    int itimes;
             fprintf(ficrespij,"\n");  
              }    char ca[32], cb[32], cc[32];
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /*  FILE *fichtm; *//* Html File */
           fprintf(ficrespij,"\n");    /* FILE *ficgp;*/ /*Gnuplot File */
         }    double agedeb, agefin,hf;
     }    double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   }  
     double fret;
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);    double **xi,tmp,delta;
   
   fclose(ficrespij);    double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
   /*---------- Forecasting ------------------*/    int *indx;
   if((stepm == 1) && (strcmp(model,".")==0)){    char line[MAXLINE], linepar[MAXLINE];
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);    char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    char pathr[MAXLINE]; 
   }    int firstobs=1, lastobs=10;
   else{    int sdeb, sfin; /* Status at beginning and end */
     erreur=108;    int c,  h , cpt,l;
     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);    int ju,jl, mi;
     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);    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;
   /*---------- Health expectancies and variances ------------*/    int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
   strcpy(filerest,"t");    double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   strcat(filerest,fileres);  
   if((ficrest=fopen(filerest,"w"))==NULL) {    double bage, fage, age, agelim, agebase;
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    double ftolpl=FTOL;
     fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;    double **prlim;
   }    double *severity;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    double ***param; /* Matrix of parameters */
   fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest);    double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
   strcpy(filerese,"e");    double *delti; /* Scale */
   strcat(filerese,fileres);    double ***eij, ***vareij;
   if((ficreseij=fopen(filerese,"w"))==NULL) {    double **varpl; /* Variances of prevalence limits by age */
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    double *epj, vepp;
     fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    double kk1, kk2;
   }    double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);  
   fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);    char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   strcpy(fileresv,"v");  
   strcat(fileresv,fileres);    char z[1]="c", occ;
   if((ficresvij=fopen(fileresv,"w"))==NULL) {  
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);    char strstart[80], *strt, strtend[80];
   }    char *stratrunc;
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    int lstra;
   fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);  
   calagedate=-1;    long total_usecs;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);   
   /*   setlocale (LC_ALL, ""); */
   k=0;  /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   for(cptcov=1;cptcov<=i1;cptcov++){  /*   textdomain (PACKAGE); */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  /*   setlocale (LC_CTYPE, ""); */
       k=k+1;  /*   setlocale (LC_MESSAGES, ""); */
       fprintf(ficrest,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)    /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    (void) gettimeofday(&start_time,&tzp);
       fprintf(ficrest,"******\n");    curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
       fprintf(ficreseij,"\n#****** ");    tmg = *gmtime(&start_time.tv_sec);
       for(j=1;j<=cptcoveff;j++)    strcpy(strstart,asctime(&tm));
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficreseij,"******\n");  /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
       fprintf(ficresvij,"\n#****** ");  /*  tm = *localtime(&start_time.tv_sec); */
       for(j=1;j<=cptcoveff;j++)  /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
       fprintf(ficresvij,"******\n");  /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  /*   strt=asctime(&tmg); */
       oldm=oldms;savm=savms;  /*   printf("Time(after) =%s",strstart);  */
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);    /*  (void) time (&time_value);
    *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  *  tm = *localtime(&time_value);
       oldm=oldms;savm=savms;  *  strstart=asctime(&tm);
       varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0);  *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
       if(popbased==1){  */
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased);  
        }    nberr=0; /* Number of errors and warnings */
     nbwarn=0;
      getcwd(pathcd, size);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");  
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    printf("\n%s\n%s",version,fullversion);
       fprintf(ficrest,"\n");    if(argc <=1){
       printf("\nEnter the parameter file name: ");
       epj=vector(1,nlstate+1);      scanf("%s",pathtot);
       for(age=bage; age <=fage ;age++){    }
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    else{
         if (popbased==1) {      strcpy(pathtot,argv[1]);
           for(i=1; i<=nlstate;i++)    }
             prlim[i][i]=probs[(int)age][i][k];    /*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);*/
         fprintf(ficrest," %4.0f",age);    /* cutv(path,optionfile,pathtot,'\\');*/
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){  
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    split(pathtot,path,optionfile,optionfilext,optionfilefiname);
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/    chdir(path);
           }    strcpy(command,"mkdir ");
           epj[nlstate+1] +=epj[j];    strcat(command,optionfilefiname);
         }    if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
         for(i=1, vepp=0.;i <=nlstate;i++)      /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
           for(j=1;j <=nlstate;j++)      /* fclose(ficlog); */
             vepp += vareij[i][j][(int)age];  /*     exit(1); */
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));    }
         for(j=1;j <=nlstate;j++){  /*   if((imk=mkdir(optionfilefiname))<0){ */
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));  /*     perror("mkdir"); */
         }  /*   } */
         fprintf(ficrest,"\n");  
       }    /*-------- arguments in the command line --------*/
     }  
   }    /* Log file */
 free_matrix(mint,1,maxwav,1,n);    strcat(filelog, optionfilefiname);
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    strcat(filelog,".log");    /* */
     free_vector(weight,1,n);    if((ficlog=fopen(filelog,"w"))==NULL)    {
   fclose(ficreseij);      printf("Problem with logfile %s\n",filelog);
   fclose(ficresvij);      goto end;
   fclose(ficrest);    }
   fclose(ficpar);    fprintf(ficlog,"Log filename:%s\n",filelog);
   free_vector(epj,1,nlstate+1);    fprintf(ficlog,"\n%s\n%s",version,fullversion);
      fprintf(ficlog,"\nEnter the parameter file name: ");
   /*------- Variance limit prevalence------*/      fprintf(ficlog,"pathtot=%s\n\
    path=%s \n\
   strcpy(fileresvpl,"vpl");   optionfile=%s\n\
   strcat(fileresvpl,fileres);   optionfilext=%s\n\
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {   optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);  
     exit(0);    printf("Local time (at start):%s",strstart);
   }    fprintf(ficlog,"Local time (at start): %s",strstart);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   k=0;  /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    /* */
       k=k+1;    strcpy(fileres,"r");
       fprintf(ficresvpl,"\n#****** ");    strcat(fileres, optionfilefiname);
       for(j=1;j<=cptcoveff;j++)    strcat(fileres,".txt");    /* Other files have txt extension */
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficresvpl,"******\n");    /*---------arguments file --------*/
        
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    if((ficpar=fopen(optionfile,"r"))==NULL)    {
       oldm=oldms;savm=savms;      printf("Problem with optionfile %s\n",optionfile);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
     }      fflush(ficlog);
  }      goto end;
     }
   fclose(ficresvpl);  
   
   /*---------- End : free ----------------*/  
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    strcpy(filereso,"o");
      strcat(filereso,fileres);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);      printf("Problem with Output resultfile: %s\n", filereso);
        fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
        fflush(ficlog);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      goto end;
   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);    /* Reads comments: lines beginning with '#' */
      numlinepar=0;
   free_matrix(matcov,1,npar,1,npar);    while((c=getc(ficpar))=='#' && c!= EOF){
   free_vector(delti,1,npar);      ungetc(c,ficpar);
   free_matrix(agev,1,maxwav,1,imx);      fgets(line, MAXLINE, ficpar);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);      numlinepar++;
       puts(line);
   fprintf(fichtm,"\n</body>");      fputs(line,ficparo);
   fclose(fichtm);      fputs(line,ficlog);
   fclose(ficgp);    }
      ungetc(c,ficpar);
   
   if(erreur >0){    fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     printf("End of Imach with error or warning %d\n",erreur);    numlinepar++;
     fprintf(ficlog,"End of Imach with error or warning %d\n",erreur);    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);
   }else{    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);
    printf("End of Imach\n");    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);
    fprintf(ficlog,"End of Imach\n");    fflush(ficlog);
   }    while((c=getc(ficpar))=='#' && c!= EOF){
   printf("See log file on %s\n",filelog);      ungetc(c,ficpar);
   fclose(ficlog);      fgets(line, MAXLINE, ficpar);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      numlinepar++;
        puts(line);
   /* 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);*/      fputs(line,ficparo);
   /*printf("Total time was %d uSec.\n", total_usecs);*/      fputs(line,ficlog);
   /*------ End -----------*/    }
     ungetc(c,ficpar);
   
  end:     
 #ifdef windows    covar=matrix(0,NCOVMAX,1,n); 
   /* chdir(pathcd);*/    cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
 #endif    if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
  /*system("wgnuplot graph.plt");*/  
  /*system("../gp37mgw/wgnuplot graph.plt");*/    ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
  /*system("cd ../gp37mgw");*/    nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/   
  strcpy(plotcmd,GNUPLOTPROGRAM);    if(mle==-1){ /* Print a wizard for help writing covariance matrix */
  strcat(plotcmd," ");      prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
  strcat(plotcmd,optionfilegnuplot);      printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
  system(plotcmd);      fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fclose (ficparo);
 #ifdef windows      fclose (ficlog);
   while (z[0] != 'q') {      exit(0);
     /* chdir(path); */    }
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");    /* Read guess parameters */
     scanf("%s",z);    /* Reads comments: lines beginning with '#' */
     if (z[0] == 'c') system("./imach");    while((c=getc(ficpar))=='#' && c!= EOF){
     else if (z[0] == 'e') system(optionfilehtm);      ungetc(c,ficpar);
     else if (z[0] == 'g') system(plotcmd);      fgets(line, MAXLINE, ficpar);
     else if (z[0] == 'q') exit(0);      numlinepar++;
   }      puts(line);
 #endif      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);
     }
   }
   
   
   

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  Added in v.1.97


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