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version 1.37, 2002/03/29 15:31:59 version 1.96, 2003/07/15 15:38:55
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 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.96  2003/07/15 15:38:55  brouard
      * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   This program computes Healthy Life Expectancies from    rewritten within the same printf. Workaround: many printfs.
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a  
   first survey ("cross") where individuals from different ages are    Revision 1.95  2003/07/08 07:54:34  brouard
   interviewed on their health status or degree of disability (in the    * imach.c (Repository):
   case of a health survey which is our main interest) -2- at least a    (Repository): Using imachwizard code to output a more meaningful covariance
   second wave of interviews ("longitudinal") which measure each change    matrix (cov(a12,c31) instead of numbers.
   (if any) in individual health status.  Health expectancies are  
   computed from the time spent in each health state according to a    Revision 1.94  2003/06/27 13:00:02  brouard
   model. More health states you consider, more time is necessary to reach the    Just cleaning
   Maximum Likelihood of the parameters involved in the model.  The  
   simplest model is the multinomial logistic model where pij is the    Revision 1.93  2003/06/25 16:33:55  brouard
   probabibility to be observed in state j at the second wave    (Module): On windows (cygwin) function asctime_r doesn't
   conditional to be observed in state i at the first wave. Therefore    exist so I changed back to asctime which exists.
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    (Module): Version 0.96b
   'age' is age and 'sex' is a covariate. If you want to have a more  
   complex model than "constant and age", you should modify the program    Revision 1.92  2003/06/25 16:30:45  brouard
   where the markup *Covariates have to be included here again* invites    (Module): On windows (cygwin) function asctime_r doesn't
   you to do it.  More covariates you add, slower the    exist so I changed back to asctime which exists.
   convergence.  
     Revision 1.91  2003/06/25 15:30:29  brouard
   The advantage of this computer programme, compared to a simple    * imach.c (Repository): Duplicated warning errors corrected.
   multinomial logistic model, is clear when the delay between waves is not    (Repository): Elapsed time after each iteration is now output. It
   identical for each individual. Also, if a individual missed an    helps to forecast when convergence will be reached. Elapsed time
   intermediate interview, the information is lost, but taken into    is stamped in powell.  We created a new html file for the graphs
   account using an interpolation or extrapolation.      concerning matrix of covariance. It has extension -cov.htm.
   
   hPijx is the probability to be observed in state i at age x+h    Revision 1.90  2003/06/24 12:34:15  brouard
   conditional to the observed state i at age x. The delay 'h' can be    (Module): Some bugs corrected for windows. Also, when
   split into an exact number (nh*stepm) of unobserved intermediate    mle=-1 a template is output in file "or"mypar.txt with the design
   states. This elementary transition (by month or quarter trimester,    of the covariance matrix to be input.
   semester or year) is model as a multinomial logistic.  The hPx  
   matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.89  2003/06/24 12:30:52  brouard
   and the contribution of each individual to the likelihood is simply    (Module): Some bugs corrected for windows. Also, when
   hPijx.    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.88  2003/06/23 17:54:56  brouard
      * 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.
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.87  2003/06/18 12:26:01  brouard
   This software have been partly granted by Euro-REVES, a concerted action    Version 0.96
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.86  2003/06/17 20:04:08  brouard
   software can be distributed freely for non commercial use. Latest version    (Module): Change position of html and gnuplot routines and added
   can be accessed at http://euroreves.ined.fr/imach .    routine fileappend.
   **********************************************************************/  
      Revision 1.85  2003/06/17 13:12:43  brouard
 #include <math.h>    * imach.c (Repository): Check when date of death was earlier that
 #include <stdio.h>    current date of interview. It may happen when the death was just
 #include <stdlib.h>    prior to the death. In this case, dh was negative and likelihood
 #include <unistd.h>    was wrong (infinity). We still send an "Error" but patch by
     assuming that the date of death was just one stepm after the
 #define MAXLINE 256    interview.
 #define GNUPLOTPROGRAM "wgnuplot"    (Repository): Because some people have very long ID (first column)
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    we changed int to long in num[] and we added a new lvector for
 #define FILENAMELENGTH 80    memory allocation. But we also truncated to 8 characters (left
 /*#define DEBUG*/    truncation)
 #define windows    (Repository): No more line truncation errors.
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Revision 1.84  2003/06/13 21:44:43  brouard
     * imach.c (Repository): Replace "freqsummary" at a correct
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    place. It differs from routine "prevalence" which may be called
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    many times. Probs is memory consuming and must be used with
     parcimony.
 #define NINTERVMAX 8    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.83  2003/06/10 13:39:11  lievre
 #define NCOVMAX 8 /* Maximum number of covariates */    *** empty log message ***
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Revision 1.82  2003/06/05 15:57:20  brouard
 #define AGESUP 130    Add log in  imach.c and  fullversion number is now printed.
 #define AGEBASE 40  
   */
   /*
 int erreur; /* Error number */     Interpolated Markov Chain
 int nvar;  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Short summary of the programme:
 int npar=NPARMAX;    
 int nlstate=2; /* Number of live states */    This program computes Healthy Life Expectancies from
 int ndeath=1; /* Number of dead states */    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    first survey ("cross") where individuals from different ages are
 int popbased=0;    interviewed on their health status or degree of disability (in the
     case of a health survey which is our main interest) -2- at least a
 int *wav; /* Number of waves for this individuual 0 is possible */    second wave of interviews ("longitudinal") which measure each change
 int maxwav; /* Maxim number of waves */    (if any) in individual health status.  Health expectancies are
 int jmin, jmax; /* min, max spacing between 2 waves */    computed from the time spent in each health state according to a
 int mle, weightopt;    model. More health states you consider, more time is necessary to reach the
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Maximum Likelihood of the parameters involved in the model.  The
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    simplest model is the multinomial logistic model where pij is the
 double jmean; /* Mean space between 2 waves */    probability to be observed in state j at the second wave
 double **oldm, **newm, **savm; /* Working pointers to matrices */    conditional to be observed in state i at the first wave. Therefore
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    'age' is age and 'sex' is a covariate. If you want to have a more
 FILE *ficgp,*ficresprob,*ficpop;    complex model than "constant and age", you should modify the program
 FILE *ficreseij;    where the markup *Covariates have to be included here again* invites
   char filerese[FILENAMELENGTH];    you to do it.  More covariates you add, slower the
  FILE  *ficresvij;    convergence.
   char fileresv[FILENAMELENGTH];  
  FILE  *ficresvpl;    The advantage of this computer programme, compared to a simple
   char fileresvpl[FILENAMELENGTH];    multinomial logistic model, is clear when the delay between waves is not
     identical for each individual. Also, if a individual missed an
 #define NR_END 1    intermediate interview, the information is lost, but taken into
 #define FREE_ARG char*    account using an interpolation or extrapolation.  
 #define FTOL 1.0e-10  
     hPijx is the probability to be observed in state i at age x+h
 #define NRANSI    conditional to the observed state i at age x. The delay 'h' can be
 #define ITMAX 200    split into an exact number (nh*stepm) of unobserved intermediate
     states. This elementary transition (by month, quarter,
 #define TOL 2.0e-4    semester or year) is modelled as a multinomial logistic.  The hPx
     matrix is simply the matrix product of nh*stepm elementary matrices
 #define CGOLD 0.3819660    and the contribution of each individual to the likelihood is simply
 #define ZEPS 1.0e-10    hPijx.
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     Also this programme outputs the covariance matrix of the parameters but also
 #define GOLD 1.618034    of the life expectancies. It also computes the stable prevalence. 
 #define GLIMIT 100.0    
 #define TINY 1.0e-20    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
              Institut national d'études démographiques, Paris.
 static double maxarg1,maxarg2;    This software have been partly granted by Euro-REVES, a concerted action
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    from the European Union.
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    It is copyrighted identically to a GNU software product, ie programme and
      software can be distributed freely for non commercial use. Latest version
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    can be accessed at http://euroreves.ined.fr/imach .
 #define rint(a) floor(a+0.5)  
     Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 static double sqrarg;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    **********************************************************************/
   /*
 int imx;    main
 int stepm;    read parameterfile
 /* Stepm, step in month: minimum step interpolation*/    read datafile
     concatwav
 int estepm;    freqsummary
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    if (mle >= 1)
       mlikeli
 int m,nb;    print results files
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    if mle==1 
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;       computes hessian
 double **pmmij, ***probs, ***mobaverage;    read end of parameter file: agemin, agemax, bage, fage, estepm
 double dateintmean=0;        begin-prev-date,...
     open gnuplot file
 double *weight;    open html file
 int **s; /* Status */    stable prevalence
 double *agedc, **covar, idx;     for age prevalim()
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    h Pij x
     variance of p varprob
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    forecasting if prevfcast==1 prevforecast call prevalence()
 double ftolhess; /* Tolerance for computing hessian */    health expectancies
     Variance-covariance of DFLE
 /**************** split *************************/    prevalence()
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )     movingaverage()
 {    varevsij() 
    char *s;                             /* pointer */    if popbased==1 varevsij(,popbased)
    int  l1, l2;                         /* length counters */    total life expectancies
     Variance of stable prevalence
    l1 = strlen( path );                 /* length of path */   end
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  */
 #ifdef windows  
    s = strrchr( path, '\\' );           /* find last / */  
 #else  
    s = strrchr( path, '/' );            /* find last / */   
 #endif  #include <math.h>
    if ( s == NULL ) {                   /* no directory, so use current */  #include <stdio.h>
 #if     defined(__bsd__)                /* get current working directory */  #include <stdlib.h>
       extern char       *getwd( );  #include <unistd.h>
   
       if ( getwd( dirc ) == NULL ) {  #include <sys/time.h>
 #else  #include <time.h>
       extern char       *getcwd( );  #include "timeval.h"
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  /* #include <libintl.h> */
 #endif  /* #define _(String) gettext (String) */
          return( GLOCK_ERROR_GETCWD );  
       }  #define MAXLINE 256
       strcpy( name, path );             /* we've got it */  #define GNUPLOTPROGRAM "gnuplot"
    } else {                             /* strip direcotry from path */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
       s++;                              /* after this, the filename */  #define FILENAMELENGTH 132
       l2 = strlen( s );                 /* length of filename */  /*#define DEBUG*/
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  /*#define windows*/
       strcpy( name, s );                /* save file name */  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
       dirc[l1-l2] = 0;                  /* add zero */  
    }  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
    l1 = strlen( dirc );                 /* length of directory */  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 #ifdef windows  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  #define NINTERVMAX 8
 #else  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 #endif  #define NCOVMAX 8 /* Maximum number of covariates */
    s = strrchr( name, '.' );            /* find last / */  #define MAXN 20000
    s++;  #define YEARM 12. /* Number of months per year */
    strcpy(ext,s);                       /* save extension */  #define AGESUP 130
    l1= strlen( name);  #define AGEBASE 40
    l2= strlen( s)+1;  #ifdef unix
    strncpy( finame, name, l1-l2);  #define DIRSEPARATOR '/'
    finame[l1-l2]= 0;  #define ODIRSEPARATOR '\\'
    return( 0 );                         /* we're done */  #else
 }  #define DIRSEPARATOR '\\'
   #define ODIRSEPARATOR '/'
   #endif
 /******************************************/  
   /* $Id$ */
 void replace(char *s, char*t)  /* $State$ */
 {  
   int i;  char version[]="Imach version 0.96c, July 2003, INED-EUROREVES ";
   int lg=20;  char fullversion[]="$Revision$ $Date$"; 
   i=0;  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   lg=strlen(t);  int nvar;
   for(i=0; i<= lg; i++) {  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
     (s[i] = t[i]);  int npar=NPARMAX;
     if (t[i]== '\\') s[i]='/';  int nlstate=2; /* Number of live states */
   }  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 nbocc(char *s, char occ)  
 {  int *wav; /* Number of waves for this individuual 0 is possible */
   int i,j=0;  int maxwav; /* Maxim number of waves */
   int lg=20;  int jmin, jmax; /* min, max spacing between 2 waves */
   i=0;  int gipmx, gsw; /* Global variables on the number of contributions 
   lg=strlen(s);                     to the likelihood and the sum of weights (done by funcone)*/
   for(i=0; i<= lg; i++) {  int mle, weightopt;
   if  (s[i] == occ ) j++;  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   }  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   return j;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 }             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   double jmean; /* Mean space between 2 waves */
 void cutv(char *u,char *v, char*t, char occ)  double **oldm, **newm, **savm; /* Working pointers to matrices */
 {  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   int i,lg,j,p=0;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   i=0;  FILE *ficlog, *ficrespow;
   for(j=0; j<=strlen(t)-1; j++) {  int globpr; /* Global variable for printing or not */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  double fretone; /* Only one call to likelihood */
   }  long ipmx; /* Number of contributions */
   double sw; /* Sum of weights */
   lg=strlen(t);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   for(j=0; j<p; j++) {  FILE *ficresilk;
     (u[j] = t[j]);  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   }  FILE *ficresprobmorprev;
      u[p]='\0';  FILE *fichtm, *fichtmcov; /* Html File */
   FILE *ficreseij;
    for(j=0; j<= lg; j++) {  char filerese[FILENAMELENGTH];
     if (j>=(p+1))(v[j-p-1] = t[j]);  FILE  *ficresvij;
   }  char fileresv[FILENAMELENGTH];
 }  FILE  *ficresvpl;
   char fileresvpl[FILENAMELENGTH];
 /********************** nrerror ********************/  char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
 void nrerror(char error_text[])  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
 {  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   fprintf(stderr,"ERREUR ...\n");  char command[FILENAMELENGTH];
   fprintf(stderr,"%s\n",error_text);  int  outcmd=0;
   exit(1);  
 }  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 /*********************** vector *******************/  
 double *vector(int nl, int nh)  char filelog[FILENAMELENGTH]; /* Log file */
 {  char filerest[FILENAMELENGTH];
   double *v;  char fileregp[FILENAMELENGTH];
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  char popfile[FILENAMELENGTH];
   if (!v) nrerror("allocation failure in vector");  
   return v-nl+NR_END;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 }  
   struct timeval start_time, end_time, curr_time, last_time, forecast_time;
 /************************ free vector ******************/  struct timezone tzp;
 void free_vector(double*v, int nl, int nh)  extern int gettimeofday();
 {  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   free((FREE_ARG)(v+nl-NR_END));  long time_value;
 }  extern long time();
   char strcurr[80], strfor[80];
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)  #define NR_END 1
 {  #define FREE_ARG char*
   int *v;  #define FTOL 1.0e-10
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");  #define NRANSI 
   return v-nl+NR_END;  #define ITMAX 200 
 }  
   #define TOL 2.0e-4 
 /******************free ivector **************************/  
 void free_ivector(int *v, long nl, long nh)  #define CGOLD 0.3819660 
 {  #define ZEPS 1.0e-10 
   free((FREE_ARG)(v+nl-NR_END));  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 }  
   #define GOLD 1.618034 
 /******************* imatrix *******************************/  #define GLIMIT 100.0 
 int **imatrix(long nrl, long nrh, long ncl, long nch)  #define TINY 1.0e-20 
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {  static double maxarg1,maxarg2;
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   int **m;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
      
   /* allocate pointers to rows */  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  #define rint(a) floor(a+0.5)
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  static double sqrarg;
   m -= nrl;  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
    #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
    
   /* allocate rows and set pointers to them */  int imx; 
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  int stepm;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  /* Stepm, step in month: minimum step interpolation*/
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  int estepm;
    /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
    int m,nb;
   /* return pointer to array of pointers to rows */  long *num;
   return m;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 }  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
   double **pmmij, ***probs;
 /****************** free_imatrix *************************/  double dateintmean=0;
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;  double *weight;
       long nch,ncl,nrh,nrl;  int **s; /* Status */
      /* free an int matrix allocated by imatrix() */  double *agedc, **covar, idx;
 {  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 }  double ftolhess; /* Tolerance for computing hessian */
   
 /******************* matrix *******************************/  /**************** split *************************/
 double **matrix(long nrl, long nrh, long ncl, long nch)  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 {  {
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;    char  *ss;                            /* pointer */
   double **m;    int   l1, l2;                         /* length counters */
   
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    l1 = strlen(path );                   /* length of path */
   if (!m) nrerror("allocation failure 1 in matrix()");    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   m += NR_END;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   m -= nrl;    if ( ss == NULL ) {                   /* no directory, so use current */
       /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");      /* get current working directory */
   m[nrl] += NR_END;      /*    extern  char* getcwd ( char *buf , int len);*/
   m[nrl] -= ncl;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
         return( GLOCK_ERROR_GETCWD );
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;      }
   return m;      strcpy( name, path );               /* we've got it */
 }    } else {                              /* strip direcotry from path */
       ss++;                               /* after this, the filename */
 /*************************free matrix ************************/      l2 = strlen( ss );                  /* length of filename */
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 {      strcpy( name, ss );         /* save file name */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   free((FREE_ARG)(m+nrl-NR_END));      dirc[l1-l2] = 0;                    /* add zero */
 }    }
     l1 = strlen( dirc );                  /* length of directory */
 /******************* ma3x *******************************/    /*#ifdef windows
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
 {  #else
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   double ***m;  #endif
     */
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    ss = strrchr( name, '.' );            /* find last / */
   if (!m) nrerror("allocation failure 1 in matrix()");    ss++;
   m += NR_END;    strcpy(ext,ss);                       /* save extension */
   m -= nrl;    l1= strlen( name);
     l2= strlen(ss)+1;
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    strncpy( finame, name, l1-l2);
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    finame[l1-l2]= 0;
   m[nrl] += NR_END;    return( 0 );                          /* we're done */
   m[nrl] -= ncl;  }
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   /******************************************/
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  void replace_back_to_slash(char *s, char*t)
   m[nrl][ncl] += NR_END;  {
   m[nrl][ncl] -= nll;    int i;
   for (j=ncl+1; j<=nch; j++)    int lg=0;
     m[nrl][j]=m[nrl][j-1]+nlay;    i=0;
      lg=strlen(t);
   for (i=nrl+1; i<=nrh; i++) {    for(i=0; i<= lg; i++) {
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;      (s[i] = t[i]);
     for (j=ncl+1; j<=nch; j++)      if (t[i]== '\\') s[i]='/';
       m[i][j]=m[i][j-1]+nlay;    }
   }  }
   return m;  
 }  int nbocc(char *s, char occ)
   {
 /*************************free ma3x ************************/    int i,j=0;
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)    int lg=20;
 {    i=0;
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    lg=strlen(s);
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    for(i=0; i<= lg; i++) {
   free((FREE_ARG)(m+nrl-NR_END));    if  (s[i] == occ ) j++;
 }    }
     return j;
 /***************** f1dim *************************/  }
 extern int ncom;  
 extern double *pcom,*xicom;  void cutv(char *u,char *v, char*t, char occ)
 extern double (*nrfunc)(double []);  {
      /* cuts string t into u and v where u is ended by char occ excluding it
 double f1dim(double x)       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
 {       gives u="abcedf" and v="ghi2j" */
   int j;    int i,lg,j,p=0;
   double f;    i=0;
   double *xt;    for(j=0; j<=strlen(t)-1; j++) {
        if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   xt=vector(1,ncom);    }
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  
   f=(*nrfunc)(xt);    lg=strlen(t);
   free_vector(xt,1,ncom);    for(j=0; j<p; j++) {
   return f;      (u[j] = t[j]);
 }    }
        u[p]='\0';
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)     for(j=0; j<= lg; j++) {
 {      if (j>=(p+1))(v[j-p-1] = t[j]);
   int iter;    }
   double a,b,d,etemp;  }
   double fu,fv,fw,fx;  
   double ftemp;  /********************** nrerror ********************/
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;  void nrerror(char error_text[])
    {
   a=(ax < cx ? ax : cx);    fprintf(stderr,"ERREUR ...\n");
   b=(ax > cx ? ax : cx);    fprintf(stderr,"%s\n",error_text);
   x=w=v=bx;    exit(EXIT_FAILURE);
   fw=fv=fx=(*f)(x);  }
   for (iter=1;iter<=ITMAX;iter++) {  /*********************** vector *******************/
     xm=0.5*(a+b);  double *vector(int nl, int nh)
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  {
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/    double *v;
     printf(".");fflush(stdout);    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 #ifdef DEBUG    if (!v) nrerror("allocation failure in vector");
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    return v-nl+NR_END;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  }
 #endif  
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  /************************ free vector ******************/
       *xmin=x;  void free_vector(double*v, int nl, int nh)
       return fx;  {
     }    free((FREE_ARG)(v+nl-NR_END));
     ftemp=fu;  }
     if (fabs(e) > tol1) {  
       r=(x-w)*(fx-fv);  /************************ivector *******************************/
       q=(x-v)*(fx-fw);  int *ivector(long nl,long nh)
       p=(x-v)*q-(x-w)*r;  {
       q=2.0*(q-r);    int *v;
       if (q > 0.0) p = -p;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       q=fabs(q);    if (!v) nrerror("allocation failure in ivector");
       etemp=e;    return v-nl+NR_END;
       e=d;  }
       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));  /******************free ivector **************************/
       else {  void free_ivector(int *v, long nl, long nh)
         d=p/q;  {
         u=x+d;    free((FREE_ARG)(v+nl-NR_END));
         if (u-a < tol2 || b-u < tol2)  }
           d=SIGN(tol1,xm-x);  
       }  /************************lvector *******************************/
     } else {  long *lvector(long nl,long nh)
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  {
     }    long *v;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     fu=(*f)(u);    if (!v) nrerror("allocation failure in ivector");
     if (fu <= fx) {    return v-nl+NR_END;
       if (u >= x) a=x; else b=x;  }
       SHFT(v,w,x,u)  
         SHFT(fv,fw,fx,fu)  /******************free lvector **************************/
         } else {  void free_lvector(long *v, long nl, long nh)
           if (u < x) a=u; else b=u;  {
           if (fu <= fw || w == x) {    free((FREE_ARG)(v+nl-NR_END));
             v=w;  }
             w=u;  
             fv=fw;  /******************* imatrix *******************************/
             fw=fu;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
           } else if (fu <= fv || v == x || v == w) {       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
             v=u;  { 
             fv=fu;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
           }    int **m; 
         }    
   }    /* allocate pointers to rows */ 
   nrerror("Too many iterations in brent");    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   *xmin=x;    if (!m) nrerror("allocation failure 1 in matrix()"); 
   return fx;    m += NR_END; 
 }    m -= nrl; 
     
 /****************** mnbrak ***********************/    
     /* allocate rows and set pointers to them */ 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
             double (*func)(double))    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
 {    m[nrl] += NR_END; 
   double ulim,u,r,q, dum;    m[nrl] -= ncl; 
   double fu;    
      for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   *fa=(*func)(*ax);    
   *fb=(*func)(*bx);    /* return pointer to array of pointers to rows */ 
   if (*fb > *fa) {    return m; 
     SHFT(dum,*ax,*bx,dum)  } 
       SHFT(dum,*fb,*fa,dum)  
       }  /****************** free_imatrix *************************/
   *cx=(*bx)+GOLD*(*bx-*ax);  void free_imatrix(m,nrl,nrh,ncl,nch)
   *fc=(*func)(*cx);        int **m;
   while (*fb > *fc) {        long nch,ncl,nrh,nrl; 
     r=(*bx-*ax)*(*fb-*fc);       /* free an int matrix allocated by imatrix() */ 
     q=(*bx-*cx)*(*fb-*fa);  { 
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    free((FREE_ARG) (m+nrl-NR_END)); 
     ulim=(*bx)+GLIMIT*(*cx-*bx);  } 
     if ((*bx-u)*(u-*cx) > 0.0) {  
       fu=(*func)(u);  /******************* matrix *******************************/
     } else if ((*cx-u)*(u-ulim) > 0.0) {  double **matrix(long nrl, long nrh, long ncl, long nch)
       fu=(*func)(u);  {
       if (fu < *fc) {    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    double **m;
           SHFT(*fb,*fc,fu,(*func)(u))  
           }    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    if (!m) nrerror("allocation failure 1 in matrix()");
       u=ulim;    m += NR_END;
       fu=(*func)(u);    m -= nrl;
     } else {  
       u=(*cx)+GOLD*(*cx-*bx);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       fu=(*func)(u);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     }    m[nrl] += NR_END;
     SHFT(*ax,*bx,*cx,u)    m[nrl] -= ncl;
       SHFT(*fa,*fb,*fc,fu)  
       }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 }    return m;
     /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
 /*************** linmin ************************/     */
   }
 int ncom;  
 double *pcom,*xicom;  /*************************free matrix ************************/
 double (*nrfunc)(double []);  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
    {
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 {    free((FREE_ARG)(m+nrl-NR_END));
   double brent(double ax, double bx, double cx,  }
                double (*f)(double), double tol, double *xmin);  
   double f1dim(double x);  /******************* ma3x *******************************/
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
               double *fc, double (*func)(double));  {
   int j;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   double xx,xmin,bx,ax;    double ***m;
   double fx,fb,fa;  
      m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   ncom=n;    if (!m) nrerror("allocation failure 1 in matrix()");
   pcom=vector(1,n);    m += NR_END;
   xicom=vector(1,n);    m -= nrl;
   nrfunc=func;  
   for (j=1;j<=n;j++) {    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     pcom[j]=p[j];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     xicom[j]=xi[j];    m[nrl] += NR_END;
   }    m[nrl] -= ncl;
   ax=0.0;  
   xx=1.0;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
 #ifdef DEBUG    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    m[nrl][ncl] += NR_END;
 #endif    m[nrl][ncl] -= nll;
   for (j=1;j<=n;j++) {    for (j=ncl+1; j<=nch; j++) 
     xi[j] *= xmin;      m[nrl][j]=m[nrl][j-1]+nlay;
     p[j] += xi[j];    
   }    for (i=nrl+1; i<=nrh; i++) {
   free_vector(xicom,1,n);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   free_vector(pcom,1,n);      for (j=ncl+1; j<=nch; j++) 
 }        m[i][j]=m[i][j-1]+nlay;
     }
 /*************** powell ************************/    return m; 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
             double (*func)(double []))             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
 {    */
   void linmin(double p[], double xi[], int n, double *fret,  }
               double (*func)(double []));  
   int i,ibig,j;  /*************************free ma3x ************************/
   double del,t,*pt,*ptt,*xit;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   double fp,fptt;  {
   double *xits;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   pt=vector(1,n);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   ptt=vector(1,n);    free((FREE_ARG)(m+nrl-NR_END));
   xit=vector(1,n);  }
   xits=vector(1,n);  
   *fret=(*func)(p);  /*************** function subdirf ***********/
   for (j=1;j<=n;j++) pt[j]=p[j];  char *subdirf(char fileres[])
   for (*iter=1;;++(*iter)) {  {
     fp=(*fret);    /* Caution optionfilefiname is hidden */
     ibig=0;    strcpy(tmpout,optionfilefiname);
     del=0.0;    strcat(tmpout,"/"); /* Add to the right */
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    strcat(tmpout,fileres);
     for (i=1;i<=n;i++)    return tmpout;
       printf(" %d %.12f",i, p[i]);  }
     printf("\n");  
     for (i=1;i<=n;i++) {  /*************** function subdirf2 ***********/
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  char *subdirf2(char fileres[], char *preop)
       fptt=(*fret);  {
 #ifdef DEBUG    
       printf("fret=%lf \n",*fret);    /* Caution optionfilefiname is hidden */
 #endif    strcpy(tmpout,optionfilefiname);
       printf("%d",i);fflush(stdout);    strcat(tmpout,"/");
       linmin(p,xit,n,fret,func);    strcat(tmpout,preop);
       if (fabs(fptt-(*fret)) > del) {    strcat(tmpout,fileres);
         del=fabs(fptt-(*fret));    return tmpout;
         ibig=i;  }
       }  
 #ifdef DEBUG  /*************** function subdirf3 ***********/
       printf("%d %.12e",i,(*fret));  char *subdirf3(char fileres[], char *preop, char *preop2)
       for (j=1;j<=n;j++) {  {
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    
         printf(" x(%d)=%.12e",j,xit[j]);    /* Caution optionfilefiname is hidden */
       }    strcpy(tmpout,optionfilefiname);
       for(j=1;j<=n;j++)    strcat(tmpout,"/");
         printf(" p=%.12e",p[j]);    strcat(tmpout,preop);
       printf("\n");    strcat(tmpout,preop2);
 #endif    strcat(tmpout,fileres);
     }    return tmpout;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  }
 #ifdef DEBUG  
       int k[2],l;  /***************** f1dim *************************/
       k[0]=1;  extern int ncom; 
       k[1]=-1;  extern double *pcom,*xicom;
       printf("Max: %.12e",(*func)(p));  extern double (*nrfunc)(double []); 
       for (j=1;j<=n;j++)   
         printf(" %.12e",p[j]);  double f1dim(double x) 
       printf("\n");  { 
       for(l=0;l<=1;l++) {    int j; 
         for (j=1;j<=n;j++) {    double f;
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    double *xt; 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);   
         }    xt=vector(1,ncom); 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       }    f=(*nrfunc)(xt); 
 #endif    free_vector(xt,1,ncom); 
     return f; 
   } 
       free_vector(xit,1,n);  
       free_vector(xits,1,n);  /*****************brent *************************/
       free_vector(ptt,1,n);  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
       free_vector(pt,1,n);  { 
       return;    int iter; 
     }    double a,b,d,etemp;
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    double fu,fv,fw,fx;
     for (j=1;j<=n;j++) {    double ftemp;
       ptt[j]=2.0*p[j]-pt[j];    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       xit[j]=p[j]-pt[j];    double e=0.0; 
       pt[j]=p[j];   
     }    a=(ax < cx ? ax : cx); 
     fptt=(*func)(ptt);    b=(ax > cx ? ax : cx); 
     if (fptt < fp) {    x=w=v=bx; 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    fw=fv=fx=(*f)(x); 
       if (t < 0.0) {    for (iter=1;iter<=ITMAX;iter++) { 
         linmin(p,xit,n,fret,func);      xm=0.5*(a+b); 
         for (j=1;j<=n;j++) {      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
           xi[j][ibig]=xi[j][n];      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
           xi[j][n]=xit[j];      printf(".");fflush(stdout);
         }      fprintf(ficlog,".");fflush(ficlog);
 #ifdef DEBUG  #ifdef DEBUG
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      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);
         for(j=1;j<=n;j++)      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
           printf(" %.12e",xit[j]);      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
         printf("\n");  #endif
 #endif      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       }        *xmin=x; 
     }        return fx; 
   }      } 
 }      ftemp=fu;
       if (fabs(e) > tol1) { 
 /**** Prevalence limit ****************/        r=(x-w)*(fx-fv); 
         q=(x-v)*(fx-fw); 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)        p=(x-v)*q-(x-w)*r; 
 {        q=2.0*(q-r); 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit        if (q > 0.0) p = -p; 
      matrix by transitions matrix until convergence is reached */        q=fabs(q); 
         etemp=e; 
   int i, ii,j,k;        e=d; 
   double min, max, maxmin, maxmax,sumnew=0.;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   double **matprod2();          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   double **out, cov[NCOVMAX], **pmij();        else { 
   double **newm;          d=p/q; 
   double agefin, delaymax=50 ; /* Max number of years to converge */          u=x+d; 
           if (u-a < tol2 || b-u < tol2) 
   for (ii=1;ii<=nlstate+ndeath;ii++)            d=SIGN(tol1,xm-x); 
     for (j=1;j<=nlstate+ndeath;j++){        } 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);      } else { 
     }        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       } 
    cov[1]=1.;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
        fu=(*f)(u); 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */      if (fu <= fx) { 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){        if (u >= x) a=x; else b=x; 
     newm=savm;        SHFT(v,w,x,u) 
     /* Covariates have to be included here again */          SHFT(fv,fw,fx,fu) 
      cov[2]=agefin;          } else { 
              if (u < x) a=u; else b=u; 
       for (k=1; k<=cptcovn;k++) {            if (fu <= fw || w == x) { 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];              v=w; 
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/              w=u; 
       }              fv=fw; 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];              fw=fu; 
       for (k=1; k<=cptcovprod;k++)            } else if (fu <= fv || v == x || v == w) { 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];              v=u; 
               fv=fu; 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/            } 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/          } 
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/    } 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    nrerror("Too many iterations in brent"); 
     *xmin=x; 
     savm=oldm;    return fx; 
     oldm=newm;  } 
     maxmax=0.;  
     for(j=1;j<=nlstate;j++){  /****************** mnbrak ***********************/
       min=1.;  
       max=0.;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       for(i=1; i<=nlstate; i++) {              double (*func)(double)) 
         sumnew=0;  { 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];    double ulim,u,r,q, dum;
         prlim[i][j]= newm[i][j]/(1-sumnew);    double fu; 
         max=FMAX(max,prlim[i][j]);   
         min=FMIN(min,prlim[i][j]);    *fa=(*func)(*ax); 
       }    *fb=(*func)(*bx); 
       maxmin=max-min;    if (*fb > *fa) { 
       maxmax=FMAX(maxmax,maxmin);      SHFT(dum,*ax,*bx,dum) 
     }        SHFT(dum,*fb,*fa,dum) 
     if(maxmax < ftolpl){        } 
       return prlim;    *cx=(*bx)+GOLD*(*bx-*ax); 
     }    *fc=(*func)(*cx); 
   }    while (*fb > *fc) { 
 }      r=(*bx-*ax)*(*fb-*fc); 
       q=(*bx-*cx)*(*fb-*fa); 
 /*************** transition probabilities ***************/      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )      ulim=(*bx)+GLIMIT*(*cx-*bx); 
 {      if ((*bx-u)*(u-*cx) > 0.0) { 
   double s1, s2;        fu=(*func)(u); 
   /*double t34;*/      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   int i,j,j1, nc, ii, jj;        fu=(*func)(u); 
         if (fu < *fc) { 
     for(i=1; i<= nlstate; i++){          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     for(j=1; j<i;j++){            SHFT(*fb,*fc,fu,(*func)(u)) 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){            } 
         /*s2 += param[i][j][nc]*cov[nc];*/      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];        u=ulim; 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/        fu=(*func)(u); 
       }      } else { 
       ps[i][j]=s2;        u=(*cx)+GOLD*(*cx-*bx); 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        fu=(*func)(u); 
     }      } 
     for(j=i+1; j<=nlstate+ndeath;j++){      SHFT(*ax,*bx,*cx,u) 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        SHFT(*fa,*fb,*fc,fu) 
         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;  /*************** linmin ************************/
     }  
   }  int ncom; 
     /*ps[3][2]=1;*/  double *pcom,*xicom;
   double (*nrfunc)(double []); 
   for(i=1; i<= nlstate; i++){   
      s1=0;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     for(j=1; j<i; j++)  { 
       s1+=exp(ps[i][j]);    double brent(double ax, double bx, double cx, 
     for(j=i+1; j<=nlstate+ndeath; j++)                 double (*f)(double), double tol, double *xmin); 
       s1+=exp(ps[i][j]);    double f1dim(double x); 
     ps[i][i]=1./(s1+1.);    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     for(j=1; j<i; j++)                double *fc, double (*func)(double)); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    int j; 
     for(j=i+1; j<=nlstate+ndeath; j++)    double xx,xmin,bx,ax; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    double fx,fb,fa;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */   
   } /* end i */    ncom=n; 
     pcom=vector(1,n); 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    xicom=vector(1,n); 
     for(jj=1; jj<= nlstate+ndeath; jj++){    nrfunc=func; 
       ps[ii][jj]=0;    for (j=1;j<=n;j++) { 
       ps[ii][ii]=1;      pcom[j]=p[j]; 
     }      xicom[j]=xi[j]; 
   }    } 
     ax=0.0; 
     xx=1.0; 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     for(jj=1; jj<= nlstate+ndeath; jj++){    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
      printf("%lf ",ps[ii][jj]);  #ifdef DEBUG
    }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     printf("\n ");    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     }  #endif
     printf("\n ");printf("%lf ",cov[2]);*/    for (j=1;j<=n;j++) { 
 /*      xi[j] *= xmin; 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);      p[j] += xi[j]; 
   goto end;*/    } 
     return ps;    free_vector(xicom,1,n); 
 }    free_vector(pcom,1,n); 
   } 
 /**************** Product of 2 matrices ******************/  
   char *asc_diff_time(long time_sec, char ascdiff[])
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  {
 {    long sec_left, days, hours, minutes;
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    days = (time_sec) / (60*60*24);
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    sec_left = (time_sec) % (60*60*24);
   /* in, b, out are matrice of pointers which should have been initialized    hours = (sec_left) / (60*60) ;
      before: only the contents of out is modified. The function returns    sec_left = (sec_left) %(60*60);
      a pointer to pointers identical to out */    minutes = (sec_left) /60;
   long i, j, k;    sec_left = (sec_left) % (60);
   for(i=nrl; i<= nrh; i++)    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
     for(k=ncolol; k<=ncoloh; k++)    return ascdiff;
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  }
         out[i][k] +=in[i][j]*b[j][k];  
   /*************** powell ************************/
   return out;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
 }              double (*func)(double [])) 
   { 
     void linmin(double p[], double xi[], int n, double *fret, 
 /************* Higher Matrix Product ***************/                double (*func)(double [])); 
     int i,ibig,j; 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    double del,t,*pt,*ptt,*xit;
 {    double fp,fptt;
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    double *xits;
      duration (i.e. until    int niterf, itmp;
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    pt=vector(1,n); 
      (typically every 2 years instead of every month which is too big).    ptt=vector(1,n); 
      Model is determined by parameters x and covariates have to be    xit=vector(1,n); 
      included manually here.    xits=vector(1,n); 
     *fret=(*func)(p); 
      */    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for (*iter=1;;++(*iter)) { 
   int i, j, d, h, k;      fp=(*fret); 
   double **out, cov[NCOVMAX];      ibig=0; 
   double **newm;      del=0.0; 
       last_time=curr_time;
   /* Hstepm could be zero and should return the unit matrix */      (void) gettimeofday(&curr_time,&tzp);
   for (i=1;i<=nlstate+ndeath;i++)      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);
     for (j=1;j<=nlstate+ndeath;j++){      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);
       oldm[i][j]=(i==j ? 1.0 : 0.0);      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
       po[i][j][0]=(i==j ? 1.0 : 0.0);      for (i=1;i<=n;i++) {
     }        printf(" %d %.12f",i, p[i]);
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */        fprintf(ficlog," %d %.12lf",i, p[i]);
   for(h=1; h <=nhstepm; h++){        fprintf(ficrespow," %.12lf", p[i]);
     for(d=1; d <=hstepm; d++){      }
       newm=savm;      printf("\n");
       /* Covariates have to be included here again */      fprintf(ficlog,"\n");
       cov[1]=1.;      fprintf(ficrespow,"\n");fflush(ficrespow);
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      if(*iter <=3){
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        tm = *localtime(&curr_time.tv_sec);
       for (k=1; k<=cptcovage;k++)        strcpy(strcurr,asctime(&tmf));
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  /*       asctime_r(&tm,strcurr); */
       for (k=1; k<=cptcovprod;k++)        forecast_time=curr_time;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        itmp = strlen(strcurr);
         if(strcurr[itmp-1]=='\n')
           strcurr[itmp-1]='\0';
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,        for(niterf=10;niterf<=30;niterf+=10){
                    pmij(pmmij,cov,ncovmodel,x,nlstate));          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
       savm=oldm;          tmf = *localtime(&forecast_time.tv_sec);
       oldm=newm;  /*      asctime_r(&tmf,strfor); */
     }          strcpy(strfor,asctime(&tmf));
     for(i=1; i<=nlstate+ndeath; i++)          itmp = strlen(strfor);
       for(j=1;j<=nlstate+ndeath;j++) {          if(strfor[itmp-1]=='\n')
         po[i][j][h]=newm[i][j];          strfor[itmp-1]='\0';
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
          */          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
       }        }
   } /* end h */      }
   return po;      for (i=1;i<=n;i++) { 
 }        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
         fptt=(*fret); 
   #ifdef DEBUG
 /*************** log-likelihood *************/        printf("fret=%lf \n",*fret);
 double func( double *x)        fprintf(ficlog,"fret=%lf \n",*fret);
 {  #endif
   int i, ii, j, k, mi, d, kk;        printf("%d",i);fflush(stdout);
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        fprintf(ficlog,"%d",i);fflush(ficlog);
   double **out;        linmin(p,xit,n,fret,func); 
   double sw; /* Sum of weights */        if (fabs(fptt-(*fret)) > del) { 
   double lli; /* Individual log likelihood */          del=fabs(fptt-(*fret)); 
   long ipmx;          ibig=i; 
   /*extern weight */        } 
   /* We are differentiating ll according to initial status */  #ifdef DEBUG
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/        printf("%d %.12e",i,(*fret));
   /*for(i=1;i<imx;i++)        fprintf(ficlog,"%d %.12e",i,(*fret));
     printf(" %d\n",s[4][i]);        for (j=1;j<=n;j++) {
   */          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   cov[1]=1.;          printf(" x(%d)=%.12e",j,xit[j]);
           fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   for(k=1; k<=nlstate; k++) ll[k]=0.;        }
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        for(j=1;j<=n;j++) {
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];          printf(" p=%.12e",p[j]);
     for(mi=1; mi<= wav[i]-1; mi++){          fprintf(ficlog," p=%.12e",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);        printf("\n");
       for(d=0; d<dh[mi][i]; d++){        fprintf(ficlog,"\n");
         newm=savm;  #endif
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      } 
         for (kk=1; kk<=cptcovage;kk++) {      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  #ifdef DEBUG
         }        int k[2],l;
                k[0]=1;
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        k[1]=-1;
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        printf("Max: %.12e",(*func)(p));
         savm=oldm;        fprintf(ficlog,"Max: %.12e",(*func)(p));
         oldm=newm;        for (j=1;j<=n;j++) {
                  printf(" %.12e",p[j]);
                  fprintf(ficlog," %.12e",p[j]);
       } /* end mult */        }
              printf("\n");
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        fprintf(ficlog,"\n");
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        for(l=0;l<=1;l++) {
       ipmx +=1;          for (j=1;j<=n;j++) {
       sw += weight[i];            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     } /* end of wave */            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   } /* end of individual */          }
           printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   /* 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 */  #endif
   return -l;  
 }  
         free_vector(xit,1,n); 
         free_vector(xits,1,n); 
 /*********** Maximum Likelihood Estimation ***************/        free_vector(ptt,1,n); 
         free_vector(pt,1,n); 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        return; 
 {      } 
   int i,j, iter;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   double **xi,*delti;      for (j=1;j<=n;j++) { 
   double fret;        ptt[j]=2.0*p[j]-pt[j]; 
   xi=matrix(1,npar,1,npar);        xit[j]=p[j]-pt[j]; 
   for (i=1;i<=npar;i++)        pt[j]=p[j]; 
     for (j=1;j<=npar;j++)      } 
       xi[i][j]=(i==j ? 1.0 : 0.0);      fptt=(*func)(ptt); 
   printf("Powell\n");      if (fptt < fp) { 
   powell(p,xi,npar,ftol,&iter,&fret,func);        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         if (t < 0.0) { 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));          linmin(p,xit,n,fret,func); 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));          for (j=1;j<=n;j++) { 
             xi[j][ibig]=xi[j][n]; 
 }            xi[j][n]=xit[j]; 
           }
 /**** Computes Hessian and covariance matrix ***/  #ifdef DEBUG
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 {          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   double  **a,**y,*x,pd;          for(j=1;j<=n;j++){
   double **hess;            printf(" %.12e",xit[j]);
   int i, j,jk;            fprintf(ficlog," %.12e",xit[j]);
   int *indx;          }
           printf("\n");
   double hessii(double p[], double delta, int theta, double delti[]);          fprintf(ficlog,"\n");
   double hessij(double p[], double delti[], int i, int j);  #endif
   void lubksb(double **a, int npar, int *indx, double b[]) ;        }
   void ludcmp(double **a, int npar, int *indx, double *d) ;      } 
     } 
   hess=matrix(1,npar,1,npar);  } 
   
   printf("\nCalculation of the hessian matrix. Wait...\n");  /**** Prevalence limit (stable prevalence)  ****************/
   for (i=1;i<=npar;i++){  
     printf("%d",i);fflush(stdout);  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     hess[i][i]=hessii(p,ftolhess,i,delti);  {
     /*printf(" %f ",p[i]);*/    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     /*printf(" %lf ",hess[i][i]);*/       matrix by transitions matrix until convergence is reached */
   }  
      int i, ii,j,k;
   for (i=1;i<=npar;i++) {    double min, max, maxmin, maxmax,sumnew=0.;
     for (j=1;j<=npar;j++)  {    double **matprod2();
       if (j>i) {    double **out, cov[NCOVMAX], **pmij();
         printf(".%d%d",i,j);fflush(stdout);    double **newm;
         hess[i][j]=hessij(p,delti,i,j);    double agefin, delaymax=50 ; /* Max number of years to converge */
         hess[j][i]=hess[i][j];      
         /*printf(" %lf ",hess[i][j]);*/    for (ii=1;ii<=nlstate+ndeath;ii++)
       }      for (j=1;j<=nlstate+ndeath;j++){
     }        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   }      }
   printf("\n");  
      cov[1]=1.;
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");   
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   a=matrix(1,npar,1,npar);    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   y=matrix(1,npar,1,npar);      newm=savm;
   x=vector(1,npar);      /* Covariates have to be included here again */
   indx=ivector(1,npar);       cov[2]=agefin;
   for (i=1;i<=npar;i++)    
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        for (k=1; k<=cptcovn;k++) {
   ludcmp(a,npar,indx,&pd);          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]]);*/
   for (j=1;j<=npar;j++) {        }
     for (i=1;i<=npar;i++) x[i]=0;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     x[j]=1;        for (k=1; k<=cptcovprod;k++)
     lubksb(a,npar,indx,x);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     for (i=1;i<=npar;i++){  
       matcov[i][j]=x[i];        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     }        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   }        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   printf("\n#Hessian matrix#\n");  
   for (i=1;i<=npar;i++) {      savm=oldm;
     for (j=1;j<=npar;j++) {      oldm=newm;
       printf("%.3e ",hess[i][j]);      maxmax=0.;
     }      for(j=1;j<=nlstate;j++){
     printf("\n");        min=1.;
   }        max=0.;
         for(i=1; i<=nlstate; i++) {
   /* Recompute Inverse */          sumnew=0;
   for (i=1;i<=npar;i++)          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];          prlim[i][j]= newm[i][j]/(1-sumnew);
   ludcmp(a,npar,indx,&pd);          max=FMAX(max,prlim[i][j]);
           min=FMIN(min,prlim[i][j]);
   /*  printf("\n#Hessian matrix recomputed#\n");        }
         maxmin=max-min;
   for (j=1;j<=npar;j++) {        maxmax=FMAX(maxmax,maxmin);
     for (i=1;i<=npar;i++) x[i]=0;      }
     x[j]=1;      if(maxmax < ftolpl){
     lubksb(a,npar,indx,x);        return prlim;
     for (i=1;i<=npar;i++){      }
       y[i][j]=x[i];    }
       printf("%.3e ",y[i][j]);  }
     }  
     printf("\n");  /*************** transition probabilities ***************/ 
   }  
   */  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   {
   free_matrix(a,1,npar,1,npar);    double s1, s2;
   free_matrix(y,1,npar,1,npar);    /*double t34;*/
   free_vector(x,1,npar);    int i,j,j1, nc, ii, jj;
   free_ivector(indx,1,npar);  
   free_matrix(hess,1,npar,1,npar);      for(i=1; i<= nlstate; i++){
       for(j=1; j<i;j++){
         for (nc=1, s2=0.;nc <=ncovmodel; nc++){
 }          /*s2 += param[i][j][nc]*cov[nc];*/
           s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
 /*************** hessian matrix ****************/          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
 double hessii( double x[], double delta, int theta, double delti[])        }
 {        ps[i][j]=s2;
   int i;        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
   int l=1, lmax=20;      }
   double k1,k2;      for(j=i+1; j<=nlstate+ndeath;j++){
   double p2[NPARMAX+1];        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   double res;          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
   double fx;        }
   int k=0,kmax=10;        ps[i][j]=s2;
   double l1;      }
     }
   fx=func(x);      /*ps[3][2]=1;*/
   for (i=1;i<=npar;i++) p2[i]=x[i];  
   for(l=0 ; l <=lmax; l++){    for(i=1; i<= nlstate; i++){
     l1=pow(10,l);       s1=0;
     delts=delt;      for(j=1; j<i; j++)
     for(k=1 ; k <kmax; k=k+1){        s1+=exp(ps[i][j]);
       delt = delta*(l1*k);      for(j=i+1; j<=nlstate+ndeath; j++)
       p2[theta]=x[theta] +delt;        s1+=exp(ps[i][j]);
       k1=func(p2)-fx;      ps[i][i]=1./(s1+1.);
       p2[theta]=x[theta]-delt;      for(j=1; j<i; j++)
       k2=func(p2)-fx;        ps[i][j]= exp(ps[i][j])*ps[i][i];
       /*res= (k1-2.0*fx+k2)/delt/delt; */      for(j=i+1; j<=nlstate+ndeath; j++)
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        ps[i][j]= exp(ps[i][j])*ps[i][i];
            /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
 #ifdef DEBUG    } /* end i */
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);  
 #endif    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */      for(jj=1; jj<= nlstate+ndeath; jj++){
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){        ps[ii][jj]=0;
         k=kmax;        ps[ii][ii]=1;
       }      }
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */    }
         k=kmax; l=lmax*10.;  
       }  
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
         delts=delt;      for(jj=1; jj<= nlstate+ndeath; jj++){
       }       printf("%lf ",ps[ii][jj]);
     }     }
   }      printf("\n ");
   delti[theta]=delts;      }
   return res;      printf("\n ");printf("%lf ",cov[2]);*/
    /*
 }    for(i=1; i<= npar; i++) printf("%f ",x[i]);
     goto end;*/
 double hessij( double x[], double delti[], int thetai,int thetaj)      return ps;
 {  }
   int i;  
   int l=1, l1, lmax=20;  /**************** Product of 2 matrices ******************/
   double k1,k2,k3,k4,res,fx;  
   double p2[NPARMAX+1];  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   int k;  {
     /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   fx=func(x);       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   for (k=1; k<=2; k++) {    /* in, b, out are matrice of pointers which should have been initialized 
     for (i=1;i<=npar;i++) p2[i]=x[i];       before: only the contents of out is modified. The function returns
     p2[thetai]=x[thetai]+delti[thetai]/k;       a pointer to pointers identical to out */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    long i, j, k;
     k1=func(p2)-fx;    for(i=nrl; i<= nrh; i++)
        for(k=ncolol; k<=ncoloh; k++)
     p2[thetai]=x[thetai]+delti[thetai]/k;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          out[i][k] +=in[i][j]*b[j][k];
     k2=func(p2)-fx;  
      return out;
     p2[thetai]=x[thetai]-delti[thetai]/k;  }
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k3=func(p2)-fx;  
    /************* Higher Matrix Product ***************/
     p2[thetai]=x[thetai]-delti[thetai]/k;  
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     k4=func(p2)-fx;  {
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    /* Computes the transition matrix starting at age 'age' over 
 #ifdef DEBUG       'nhstepm*hstepm*stepm' months (i.e. until
     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);       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
 #endif       nhstepm*hstepm matrices. 
   }       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   return res;       (typically every 2 years instead of every month which is too big 
 }       for the memory).
        Model is determined by parameters x and covariates have to be 
 /************** Inverse of matrix **************/       included manually here. 
 void ludcmp(double **a, int n, int *indx, double *d)  
 {       */
   int i,imax,j,k;  
   double big,dum,sum,temp;    int i, j, d, h, k;
   double *vv;    double **out, cov[NCOVMAX];
      double **newm;
   vv=vector(1,n);  
   *d=1.0;    /* Hstepm could be zero and should return the unit matrix */
   for (i=1;i<=n;i++) {    for (i=1;i<=nlstate+ndeath;i++)
     big=0.0;      for (j=1;j<=nlstate+ndeath;j++){
     for (j=1;j<=n;j++)        oldm[i][j]=(i==j ? 1.0 : 0.0);
       if ((temp=fabs(a[i][j])) > big) big=temp;        po[i][j][0]=(i==j ? 1.0 : 0.0);
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");      }
     vv[i]=1.0/big;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   }    for(h=1; h <=nhstepm; h++){
   for (j=1;j<=n;j++) {      for(d=1; d <=hstepm; d++){
     for (i=1;i<j;i++) {        newm=savm;
       sum=a[i][j];        /* Covariates have to be included here again */
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        cov[1]=1.;
       a[i][j]=sum;        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     }        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     big=0.0;        for (k=1; k<=cptcovage;k++)
     for (i=j;i<=n;i++) {          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       sum=a[i][j];        for (k=1; k<=cptcovprod;k++)
       for (k=1;k<j;k++)          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;  
       if ( (dum=vv[i]*fabs(sum)) >= big) {        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         big=dum;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         imax=i;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
       }                     pmij(pmmij,cov,ncovmodel,x,nlstate));
     }        savm=oldm;
     if (j != imax) {        oldm=newm;
       for (k=1;k<=n;k++) {      }
         dum=a[imax][k];      for(i=1; i<=nlstate+ndeath; i++)
         a[imax][k]=a[j][k];        for(j=1;j<=nlstate+ndeath;j++) {
         a[j][k]=dum;          po[i][j][h]=newm[i][j];
       }          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
       *d = -(*d);           */
       vv[imax]=vv[j];        }
     }    } /* end h */
     indx[j]=imax;    return po;
     if (a[j][j] == 0.0) a[j][j]=TINY;  }
     if (j != n) {  
       dum=1.0/(a[j][j]);  
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  /*************** log-likelihood *************/
     }  double func( double *x)
   }  {
   free_vector(vv,1,n);  /* Doesn't work */    int i, ii, j, k, mi, d, kk;
 ;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
 }    double **out;
     double sw; /* Sum of weights */
 void lubksb(double **a, int n, int *indx, double b[])    double lli; /* Individual log likelihood */
 {    int s1, s2;
   int i,ii=0,ip,j;    double bbh, survp;
   double sum;    long ipmx;
      /*extern weight */
   for (i=1;i<=n;i++) {    /* We are differentiating ll according to initial status */
     ip=indx[i];    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     sum=b[ip];    /*for(i=1;i<imx;i++) 
     b[ip]=b[i];      printf(" %d\n",s[4][i]);
     if (ii)    */
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    cov[1]=1.;
     else if (sum) ii=i;  
     b[i]=sum;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   }  
   for (i=n;i>=1;i--) {    if(mle==1){
     sum=b[i];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     b[i]=sum/a[i][i];        for(mi=1; mi<= wav[i]-1; mi++){
   }          for (ii=1;ii<=nlstate+ndeath;ii++)
 }            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 /************ Frequencies ********************/              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 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)            }
 {  /* Some frequencies */          for(d=0; d<dh[mi][i]; d++){
              newm=savm;
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double ***freq; /* Frequencies */            for (kk=1; kk<=cptcovage;kk++) {
   double *pp;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double pos, k2, dateintsum=0,k2cpt=0;            }
   FILE *ficresp;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   char fileresp[FILENAMELENGTH];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              savm=oldm;
   pp=vector(1,nlstate);            oldm=newm;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          } /* end mult */
   strcpy(fileresp,"p");        
   strcat(fileresp,fileres);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   if((ficresp=fopen(fileresp,"w"))==NULL) {          /* But now since version 0.9 we anticipate for bias and large stepm.
     printf("Problem with prevalence resultfile: %s\n", fileresp);           * If stepm is larger than one month (smallest stepm) and if the exact delay 
     exit(0);           * (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
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   j1=0;           * (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
   j=cptcoveff;           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
   if (cptcovn<1) {j=1;ncodemax[1]=1;}           * -stepm/2 to stepm/2 .
             * For stepm=1 the results are the same as for previous versions of Imach.
   for(k1=1; k1<=j;k1++){           * For stepm > 1 the results are less biased than in previous versions. 
     for(i1=1; i1<=ncodemax[k1];i1++){           */
       j1++;          s1=s[mw[mi][i]][i];
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);          s2=s[mw[mi+1][i]][i];
         scanf("%d", i);*/          bbh=(double)bh[mi][i]/(double)stepm; 
       for (i=-1; i<=nlstate+ndeath; i++)            /* bias is positive if real duration
         for (jk=-1; jk<=nlstate+ndeath; jk++)             * is higher than the multiple of stepm and negative otherwise.
           for(m=agemin; m <= agemax+3; m++)           */
             freq[i][jk][m]=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]));*/
                if( s2 > nlstate){ 
       dateintsum=0;            /* i.e. if s2 is a death state and if the date of death is known then the contribution
       k2cpt=0;               to the likelihood is the probability to die between last step unit time and current 
       for (i=1; i<=imx; i++) {               step unit time, which is also the differences between probability to die before dh 
         bool=1;               and probability to die before dh-stepm . 
         if  (cptcovn>0) {               In version up to 0.92 likelihood was computed
           for (z1=1; z1<=cptcoveff; z1++)          as if date of death was unknown. Death was treated as any other
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          health state: the date of the interview describes the actual state
               bool=0;          and not the date of a change in health state. The former idea was
         }          to consider that at each interview the state was recorded
         if (bool==1) {          (healthy, disable or death) and IMaCh was corrected; but when we
           for(m=firstpass; m<=lastpass; m++){          introduced the exact date of death then we should have modified
             k2=anint[m][i]+(mint[m][i]/12.);          the contribution of an exact death to the likelihood. This new
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          contribution is smaller and very dependent of the step unit
               if(agev[m][i]==0) agev[m][i]=agemax+1;          stepm. It is no more the probability to die between last interview
               if(agev[m][i]==1) agev[m][i]=agemax+2;          and month of death but the probability to survive from last
               if (m<lastpass) {          interview up to one month before death multiplied by the
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          probability to die within a month. Thanks to Chris
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          Jackson for correcting this bug.  Former versions increased
               }          mortality artificially. The bad side is that we add another loop
                        which slows down the processing. The difference can be up to 10%
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {          lower mortality.
                 dateintsum=dateintsum+k2;            */
                 k2cpt++;            lli=log(out[s1][s2] - savm[s1][s2]);
               }          }else{
             }            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           }            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
         }          } 
       }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
                  /*if(lli ==000.0)*/
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          /*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;
       if  (cptcovn>0) {          sw += weight[i];
         fprintf(ficresp, "\n#********** Variable ");          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        } /* end of wave */
         fprintf(ficresp, "**********\n#");      } /* end of individual */
       }    }  else if(mle==2){
       for(i=1; i<=nlstate;i++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       fprintf(ficresp, "\n");        for(mi=1; mi<= wav[i]-1; mi++){
                for (ii=1;ii<=nlstate+ndeath;ii++)
       for(i=(int)agemin; i <= (int)agemax+3; i++){            for (j=1;j<=nlstate+ndeath;j++){
         if(i==(int)agemax+3)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           printf("Total");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         else            }
           printf("Age %d", i);          for(d=0; d<=dh[mi][i]; d++){
         for(jk=1; jk <=nlstate ; jk++){            newm=savm;
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             pp[jk] += freq[jk][m][i];            for (kk=1; kk<=cptcovage;kk++) {
         }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         for(jk=1; jk <=nlstate ; jk++){            }
           for(m=-1, pos=0; m <=0 ; m++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             pos += freq[jk][m][i];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           if(pp[jk]>=1.e-10)            savm=oldm;
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);            oldm=newm;
           else          } /* end mult */
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        
         }          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
         for(jk=1; jk <=nlstate ; jk++){          bbh=(double)bh[mi][i]/(double)stepm; 
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          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 */
             pp[jk] += freq[jk][m][i];          ipmx +=1;
         }          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         for(jk=1,pos=0; jk <=nlstate ; jk++)        } /* end of wave */
           pos += pp[jk];      } /* end of individual */
         for(jk=1; jk <=nlstate ; jk++){    }  else if(mle==3){  /* exponential inter-extrapolation */
           if(pos>=1.e-5)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           else        for(mi=1; mi<= wav[i]-1; mi++){
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);          for (ii=1;ii<=nlstate+ndeath;ii++)
           if( i <= (int) agemax){            for (j=1;j<=nlstate+ndeath;j++){
             if(pos>=1.e-5){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
               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(d=0; d<dh[mi][i]; d++){
             }            newm=savm;
             else            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);            for (kk=1; kk<=cptcovage;kk++) {
           }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         }            }
                    out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         for(jk=-1; jk <=nlstate+ndeath; jk++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           for(m=-1; m <=nlstate+ndeath; m++)            savm=oldm;
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);            oldm=newm;
         if(i <= (int) agemax)          } /* end mult */
           fprintf(ficresp,"\n");        
         printf("\n");          s1=s[mw[mi][i]][i];
       }          s2=s[mw[mi+1][i]][i];
     }          bbh=(double)bh[mi][i]/(double)stepm; 
   }          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 */
   dateintmean=dateintsum/k2cpt;          ipmx +=1;
            sw += weight[i];
   fclose(ficresp);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        } /* end of wave */
   free_vector(pp,1,nlstate);      } /* end of individual */
      }else if (mle==4){  /* ml=4 no inter-extrapolation */
   /* End of Freq */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
 /************ Prevalence ********************/          for (ii=1;ii<=nlstate+ndeath;ii++)
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)            for (j=1;j<=nlstate+ndeath;j++){
 {  /* Some frequencies */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;            }
   double ***freq; /* Frequencies */          for(d=0; d<dh[mi][i]; d++){
   double *pp;            newm=savm;
   double pos, k2;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
   pp=vector(1,nlstate);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            }
            
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   j1=0;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              savm=oldm;
   j=cptcoveff;            oldm=newm;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          } /* end mult */
          
  for(k1=1; k1<=j;k1++){          s1=s[mw[mi][i]][i];
     for(i1=1; i1<=ncodemax[k1];i1++){          s2=s[mw[mi+1][i]][i];
       j1++;          if( s2 > nlstate){ 
              lli=log(out[s1][s2] - savm[s1][s2]);
       for (i=-1; i<=nlstate+ndeath; i++)            }else{
         for (jk=-1; jk<=nlstate+ndeath; jk++)              lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           for(m=agemin; m <= agemax+3; m++)          }
             freq[i][jk][m]=0;          ipmx +=1;
                sw += weight[i];
       for (i=1; i<=imx; i++) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         bool=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]); */
         if  (cptcovn>0) {        } /* end of wave */
           for (z1=1; z1<=cptcoveff; z1++)      } /* end of individual */
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
               bool=0;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         if (bool==1) {        for(mi=1; mi<= wav[i]-1; mi++){
           for(m=firstpass; m<=lastpass; m++){          for (ii=1;ii<=nlstate+ndeath;ii++)
             k2=anint[m][i]+(mint[m][i]/12.);            for (j=1;j<=nlstate+ndeath;j++){
             if ((k2>=dateprev1) && (k2<=dateprev2)) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               if(agev[m][i]==0) agev[m][i]=agemax+1;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
               if(agev[m][i]==1) agev[m][i]=agemax+2;            }
               if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          for(d=0; d<dh[mi][i]; d++){
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];  */            newm=savm;
             }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           }            for (kk=1; kk<=cptcovage;kk++) {
         }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       }            }
         for(i=(int)agemin; i <= (int)agemax+3; i++){          
           for(jk=1; jk <=nlstate ; jk++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
               pp[jk] += freq[jk][m][i];            savm=oldm;
           }            oldm=newm;
           for(jk=1; jk <=nlstate ; jk++){          } /* end mult */
             for(m=-1, pos=0; m <=0 ; m++)        
             pos += freq[jk][m][i];          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 ; jk++){          ipmx +=1;
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          sw += weight[i];
              pp[jk] += freq[jk][m][i];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          }          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
                  } /* end of wave */
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      } /* end of individual */
     } /* End of if */
          for(jk=1; jk <=nlstate ; jk++){              for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
            if( i <= (int) agemax){    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
              if(pos>=1.e-5){    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
                probs[i][jk][j1]= pp[jk]/pos;    return -l;
              }  }
            }  
          }  /*************** log-likelihood *************/
            double funcone( double *x)
         }  {
     }    /* Same as likeli but slower because of a lot of printf and if */
   }    int i, ii, j, k, mi, d, kk;
      double l, ll[NLSTATEMAX], cov[NCOVMAX];
      double **out;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    double lli; /* Individual log likelihood */
   free_vector(pp,1,nlstate);    double llt;
      int s1, s2;
 }  /* End of Freq */    double bbh, survp;
     /*extern weight */
 /************* Waves Concatenation ***************/    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    /*for(i=1;i<imx;i++) 
 {      printf(" %d\n",s[4][i]);
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    */
      Death is a valid wave (if date is known).    cov[1]=1.;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    for(k=1; k<=nlstate; k++) ll[k]=0.;
      and mw[mi+1][i]. dh depends on stepm.  
      */    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int i, mi, m;      for(mi=1; mi<= wav[i]-1; mi++){
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        for (ii=1;ii<=nlstate+ndeath;ii++)
      double sum=0., jmean=0.;*/          for (j=1;j<=nlstate+ndeath;j++){
             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int j, k=0,jk, ju, jl;            savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double sum=0.;          }
   jmin=1e+5;        for(d=0; d<dh[mi][i]; d++){
   jmax=-1;          newm=savm;
   jmean=0.;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   for(i=1; i<=imx; i++){          for (kk=1; kk<=cptcovage;kk++) {
     mi=0;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     m=firstpass;          }
     while(s[m][i] <= nlstate){          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       if(s[m][i]>=1)                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         mw[++mi][i]=m;          savm=oldm;
       if(m >=lastpass)          oldm=newm;
         break;        } /* end mult */
       else        
         m++;        s1=s[mw[mi][i]][i];
     }/* end while */        s2=s[mw[mi+1][i]][i];
     if (s[m][i] > nlstate){        bbh=(double)bh[mi][i]/(double)stepm; 
       mi++;     /* Death is another wave */        /* bias is positive if real duration
       /* if(mi==0)  never been interviewed correctly before death */         * is higher than the multiple of stepm and negative otherwise.
          /* Only death is a correct wave */         */
       mw[mi][i]=m;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
     }          lli=log(out[s1][s2] - savm[s1][s2]);
         } else if (mle==1){
     wav[i]=mi;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     if(mi==0)        } else if(mle==2){
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   }        } else if(mle==3){  /* exponential inter-extrapolation */
           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 */
   for(i=1; i<=imx; i++){        } else if (mle==4){  /* mle=4 no inter-extrapolation */
     for(mi=1; mi<wav[i];mi++){          lli=log(out[s1][s2]); /* Original formula */
       if (stepm <=0)        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
         dh[mi][i]=1;          lli=log(out[s1][s2]); /* Original formula */
       else{        } /* End of if */
         if (s[mw[mi+1][i]][i] > nlstate) {        ipmx +=1;
           if (agedc[i] < 2*AGESUP) {        sw += weight[i];
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           if(j==0) j=1;  /* Survives at least one month after exam */  /*       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]); */
           k=k+1;        if(globpr){
           if (j >= jmax) jmax=j;          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
           if (j <= jmin) jmin=j;   %10.6f %10.6f %10.6f ", \
           sum=sum+j;                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
           /*if (j<0) printf("j=%d num=%d \n",j,i); */                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
           }          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
         }            llt +=ll[k]*gipmx/gsw;
         else{            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          }
           k=k+1;          fprintf(ficresilk," %10.6f\n", -llt);
           if (j >= jmax) jmax=j;        }
           else if (j <= jmin)jmin=j;      } /* end of wave */
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    } /* end of individual */
           sum=sum+j;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         jk= j/stepm;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         jl= j -jk*stepm;    if(globpr==0){ /* First time we count the contributions and weights */
         ju= j -(jk+1)*stepm;      gipmx=ipmx;
         if(jl <= -ju)      gsw=sw;
           dh[mi][i]=jk;    }
         else    return -l;
           dh[mi][i]=jk+1;  }
         if(dh[mi][i]==0)  
           dh[mi][i]=1; /* At least one step */  
       }  /*************** function likelione ***********/
     }  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   }  {
   jmean=sum/k;    /* This routine should help understanding what is done with 
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);       the selection of individuals/waves and
  }       to check the exact contribution to the likelihood.
 /*********** Tricode ****************************/       Plotting could be done.
 void tricode(int *Tvar, int **nbcode, int imx)     */
 {    int k;
   int Ndum[20],ij=1, k, j, i;  
   int cptcode=0;    if(*globpri !=0){ /* Just counts and sums, no printings */
   cptcoveff=0;      strcpy(fileresilk,"ilk"); 
        strcat(fileresilk,fileres);
   for (k=0; k<19; k++) Ndum[k]=0;      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   for (k=1; k<=7; k++) ncodemax[k]=0;        printf("Problem with resultfile: %s\n", fileresilk);
         fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {      }
     for (i=1; i<=imx; i++) {      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");
       ij=(int)(covar[Tvar[j]][i]);      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       Ndum[ij]++;      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/      for(k=1; k<=nlstate; k++) 
       if (ij > cptcode) cptcode=ij;        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
     }      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     }
     for (i=0; i<=cptcode; i++) {  
       if(Ndum[i]!=0) ncodemax[j]++;    *fretone=(*funcone)(p);
     }    if(*globpri !=0){
     ij=1;      fclose(ficresilk);
       fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       fflush(fichtm); 
     for (i=1; i<=ncodemax[j]; i++) {    } 
       for (k=0; k<=19; k++) {    return;
         if (Ndum[k] != 0) {  }
           nbcode[Tvar[j]][ij]=k;  
           /*     printf("nbcodeaaaaaaaaaaa=%d Tvar[j]=%d ij=%d j=%d",nbcode[Tvar[j]][ij],Tvar[j],ij,j);*/  
           ij++;  /*********** Maximum Likelihood Estimation ***************/
         }  
         if (ij > ncodemax[j]) break;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       }    {
     }    int i,j, iter;
   }      double **xi;
     double fret;
  for (k=0; k<19; k++) Ndum[k]=0;    double fretone; /* Only one call to likelihood */
     char filerespow[FILENAMELENGTH];
  for (i=1; i<=ncovmodel-2; i++) {    xi=matrix(1,npar,1,npar);
       ij=Tvar[i];    for (i=1;i<=npar;i++)
       Ndum[ij]++;      for (j=1;j<=npar;j++)
     }        xi[i][j]=(i==j ? 1.0 : 0.0);
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
  ij=1;    strcpy(filerespow,"pow"); 
  for (i=1; i<=10; i++) {    strcat(filerespow,fileres);
    if((Ndum[i]!=0) && (i<=ncovcol)){    if((ficrespow=fopen(filerespow,"w"))==NULL) {
      Tvaraff[ij]=i;      printf("Problem with resultfile: %s\n", filerespow);
      ij++;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
    }    }
  }    fprintf(ficrespow,"# Powell\n# iter -2*LL");
      for (i=1;i<=nlstate;i++)
     cptcoveff=ij-1;      for(j=1;j<=nlstate+ndeath;j++)
 }        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     fprintf(ficrespow,"\n");
 /*********** Health Expectancies ****************/  
     powell(p,xi,npar,ftol,&iter,&fret,func);
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm)  
 {    fclose(ficrespow);
   /* Health expectancies */    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   int i, j, nhstepm, hstepm, h, nstepm;    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   double age, agelim, hf;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   double ***p3mat;  
    }
   fprintf(ficreseij,"# Health expectancies\n");  
   fprintf(ficreseij,"# Age");  /**** Computes Hessian and covariance matrix ***/
   for(i=1; i<=nlstate;i++)  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     for(j=1; j<=nlstate;j++)  {
       fprintf(ficreseij," %1d-%1d",i,j);    double  **a,**y,*x,pd;
   fprintf(ficreseij,"\n");    double **hess;
     int i, j,jk;
   if(estepm < stepm){    int *indx;
     printf ("Problem %d lower than %d\n",estepm, stepm);  
   }    double hessii(double p[], double delta, int theta, double delti[]);
   else  hstepm=estepm;      double hessij(double p[], double delti[], int i, int j);
   /* We compute the life expectancy from trapezoids spaced every estepm months    void lubksb(double **a, int npar, int *indx, double b[]) ;
    * This is mainly to measure the difference between two models: for example    void ludcmp(double **a, int npar, int *indx, double *d) ;
    * if stepm=24 months pijx are given only every 2 years and by summing them  
    * we are calculating an estimate of the Life Expectancy assuming a linear    hess=matrix(1,npar,1,npar);
    * progression inbetween and thus overestimating or underestimating according  
    * to the curvature of the survival function. If, for the same date, we    printf("\nCalculation of the hessian matrix. Wait...\n");
    * estimate the model with stepm=1 month, we can keep estepm to 24 months    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
    * to compare the new estimate of Life expectancy with the same linear    for (i=1;i<=npar;i++){
    * hypothesis. A more precise result, taking into account a more precise      printf("%d",i);fflush(stdout);
    * curvature will be obtained if estepm is as small as stepm. */      fprintf(ficlog,"%d",i);fflush(ficlog);
       hess[i][i]=hessii(p,ftolhess,i,delti);
   /* For example we decided to compute the life expectancy with the smallest unit */      /*printf(" %f ",p[i]);*/
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.      /*printf(" %lf ",hess[i][i]);*/
      nhstepm is the number of hstepm from age to agelim    }
      nstepm is the number of stepm from age to agelin.    
      Look at hpijx to understand the reason of that which relies in memory size    for (i=1;i<=npar;i++) {
      and note for a fixed period like estepm months */      for (j=1;j<=npar;j++)  {
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the        if (j>i) { 
      survival function given by stepm (the optimization length). Unfortunately it          printf(".%d%d",i,j);fflush(stdout);
      means that if the survival funtion is printed only each two years of age and if          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
      you sum them up and add 1 year (area under the trapezoids) you won't get the same          hess[i][j]=hessij(p,delti,i,j);
      results. So we changed our mind and took the option of the best precision.          hess[j][i]=hess[i][j];    
   */          /*printf(" %lf ",hess[i][j]);*/
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        }
       }
   agelim=AGESUP;    }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    printf("\n");
     /* nhstepm age range expressed in number of stepm */    fprintf(ficlog,"\n");
     nstepm=(int) rint((agelim-age)*YEARM/stepm);  
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     /* if (stepm >= YEARM) hstepm=1;*/    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    a=matrix(1,npar,1,npar);
     /* Computed by stepm unit matrices, product of hstepm matrices, stored    y=matrix(1,npar,1,npar);
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    x=vector(1,npar);
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      indx=ivector(1,npar);
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    for (i=1;i<=npar;i++)
     for(i=1; i<=nlstate;i++)      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
       for(j=1; j<=nlstate;j++)    ludcmp(a,npar,indx,&pd);
         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;    for (j=1;j<=npar;j++) {
           /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/      for (i=1;i<=npar;i++) x[i]=0;
         }      x[j]=1;
     fprintf(ficreseij,"%3.0f",age );      lubksb(a,npar,indx,x);
     for(i=1; i<=nlstate;i++)      for (i=1;i<=npar;i++){ 
       for(j=1; j<=nlstate;j++){        matcov[i][j]=x[i];
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);      }
       }    }
     fprintf(ficreseij,"\n");  
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    printf("\n#Hessian matrix#\n");
   }    fprintf(ficlog,"\n#Hessian matrix#\n");
 }    for (i=1;i<=npar;i++) { 
       for (j=1;j<=npar;j++) { 
 /************ Variance ******************/        printf("%.3e ",hess[i][j]);
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm)        fprintf(ficlog,"%.3e ",hess[i][j]);
 {      }
   /* Variance of health expectancies */      printf("\n");
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      fprintf(ficlog,"\n");
   double **newm;    }
   double **dnewm,**doldm;  
   int i, j, nhstepm, hstepm, h, nstepm ;    /* Recompute Inverse */
   int k, cptcode;    for (i=1;i<=npar;i++)
   double *xp;      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   double **gp, **gm;    ludcmp(a,npar,indx,&pd);
   double ***gradg, ***trgradg;  
   double ***p3mat;    /*  printf("\n#Hessian matrix recomputed#\n");
   double age,agelim, hf;  
   int theta;    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
    fprintf(ficresvij,"# Covariances of life expectancies\n");      x[j]=1;
   fprintf(ficresvij,"# Age");      lubksb(a,npar,indx,x);
   for(i=1; i<=nlstate;i++)      for (i=1;i<=npar;i++){ 
     for(j=1; j<=nlstate;j++)        y[i][j]=x[i];
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        printf("%.3e ",y[i][j]);
   fprintf(ficresvij,"\n");        fprintf(ficlog,"%.3e ",y[i][j]);
       }
   xp=vector(1,npar);      printf("\n");
   dnewm=matrix(1,nlstate,1,npar);      fprintf(ficlog,"\n");
   doldm=matrix(1,nlstate,1,nlstate);    }
      */
   if(estepm < stepm){  
     printf ("Problem %d lower than %d\n",estepm, stepm);    free_matrix(a,1,npar,1,npar);
   }    free_matrix(y,1,npar,1,npar);
   else  hstepm=estepm;      free_vector(x,1,npar);
   /* For example we decided to compute the life expectancy with the smallest unit */    free_ivector(indx,1,npar);
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    free_matrix(hess,1,npar,1,npar);
      nhstepm is the number of hstepm from age to agelim  
      nstepm is the number of stepm from age to agelin.  
      Look at hpijx to understand the reason of that which relies in memory size  }
      and note for a fixed period like k years */  
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the  /*************** hessian matrix ****************/
      survival function given by stepm (the optimization length). Unfortunately it  double hessii( double x[], double delta, int theta, double delti[])
      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    int i;
      results. So we changed our mind and took the option of the best precision.    int l=1, lmax=20;
   */    double k1,k2;
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    double p2[NPARMAX+1];
   agelim = AGESUP;    double res;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    double fx;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    int k=0,kmax=10;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double l1;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);  
     gp=matrix(0,nhstepm,1,nlstate);    fx=func(x);
     gm=matrix(0,nhstepm,1,nlstate);    for (i=1;i<=npar;i++) p2[i]=x[i];
     for(l=0 ; l <=lmax; l++){
     for(theta=1; theta <=npar; theta++){      l1=pow(10,l);
       for(i=1; i<=npar; i++){ /* Computes gradient */      delts=delt;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      for(k=1 ; k <kmax; k=k+1){
       }        delt = delta*(l1*k);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          p2[theta]=x[theta] +delt;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        k1=func(p2)-fx;
         p2[theta]=x[theta]-delt;
       if (popbased==1) {        k2=func(p2)-fx;
         for(i=1; i<=nlstate;i++)        /*res= (k1-2.0*fx+k2)/delt/delt; */
           prlim[i][i]=probs[(int)age][i][ij];        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
       }        
    #ifdef DEBUG
       for(j=1; j<= nlstate; j++){        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         for(h=0; h<=nhstepm; h++){        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)  #endif
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         }        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
       }          k=kmax;
            }
       for(i=1; i<=npar; i++) /* Computes gradient */        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          k=kmax; l=lmax*10.;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
            delts=delt;
       if (popbased==1) {        }
         for(i=1; i<=nlstate;i++)      }
           prlim[i][i]=probs[(int)age][i][ij];    }
       }    delti[theta]=delts;
     return res; 
       for(j=1; j<= nlstate; j++){    
         for(h=0; h<=nhstepm; h++){  }
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)  
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];  double hessij( double x[], double delti[], int thetai,int thetaj)
         }  {
       }    int i;
     int l=1, l1, lmax=20;
       for(j=1; j<= nlstate; j++)    double k1,k2,k3,k4,res,fx;
         for(h=0; h<=nhstepm; h++){    double p2[NPARMAX+1];
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    int k;
         }  
     } /* End theta */    fx=func(x);
     for (k=1; k<=2; k++) {
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);      for (i=1;i<=npar;i++) p2[i]=x[i];
       p2[thetai]=x[thetai]+delti[thetai]/k;
     for(h=0; h<=nhstepm; h++)      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       for(j=1; j<=nlstate;j++)      k1=func(p2)-fx;
         for(theta=1; theta <=npar; theta++)    
           trgradg[h][j][theta]=gradg[h][theta][j];      p2[thetai]=x[thetai]+delti[thetai]/k;
       p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      k2=func(p2)-fx;
     for(i=1;i<=nlstate;i++)    
       for(j=1;j<=nlstate;j++)      p2[thetai]=x[thetai]-delti[thetai]/k;
         vareij[i][j][(int)age] =0.;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k3=func(p2)-fx;
     for(h=0;h<=nhstepm;h++){    
       for(k=0;k<=nhstepm;k++){      p2[thetai]=x[thetai]-delti[thetai]/k;
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);      k4=func(p2)-fx;
         for(i=1;i<=nlstate;i++)      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
           for(j=1;j<=nlstate;j++)  #ifdef DEBUG
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;      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);
     }  #endif
     }
     fprintf(ficresvij,"%.0f ",age );    return res;
     for(i=1; i<=nlstate;i++)  }
       for(j=1; j<=nlstate;j++){  
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);  /************** Inverse of matrix **************/
       }  void ludcmp(double **a, int n, int *indx, double *d) 
     fprintf(ficresvij,"\n");  { 
     free_matrix(gp,0,nhstepm,1,nlstate);    int i,imax,j,k; 
     free_matrix(gm,0,nhstepm,1,nlstate);    double big,dum,sum,temp; 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    double *vv; 
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);   
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    vv=vector(1,n); 
   } /* End age */    *d=1.0; 
      for (i=1;i<=n;i++) { 
   free_vector(xp,1,npar);      big=0.0; 
   free_matrix(doldm,1,nlstate,1,npar);      for (j=1;j<=n;j++) 
   free_matrix(dnewm,1,nlstate,1,nlstate);        if ((temp=fabs(a[i][j])) > big) big=temp; 
       if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
 }      vv[i]=1.0/big; 
     } 
 /************ Variance of prevlim ******************/    for (j=1;j<=n;j++) { 
 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<j;i++) { 
 {        sum=a[i][j]; 
   /* Variance of prevalence limit */        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        a[i][j]=sum; 
   double **newm;      } 
   double **dnewm,**doldm;      big=0.0; 
   int i, j, nhstepm, hstepm;      for (i=j;i<=n;i++) { 
   int k, cptcode;        sum=a[i][j]; 
   double *xp;        for (k=1;k<j;k++) 
   double *gp, *gm;          sum -= a[i][k]*a[k][j]; 
   double **gradg, **trgradg;        a[i][j]=sum; 
   double age,agelim;        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   int theta;          big=dum; 
              imax=i; 
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");        } 
   fprintf(ficresvpl,"# Age");      } 
   for(i=1; i<=nlstate;i++)      if (j != imax) { 
       fprintf(ficresvpl," %1d-%1d",i,i);        for (k=1;k<=n;k++) { 
   fprintf(ficresvpl,"\n");          dum=a[imax][k]; 
           a[imax][k]=a[j][k]; 
   xp=vector(1,npar);          a[j][k]=dum; 
   dnewm=matrix(1,nlstate,1,npar);        } 
   doldm=matrix(1,nlstate,1,nlstate);        *d = -(*d); 
          vv[imax]=vv[j]; 
   hstepm=1*YEARM; /* Every year of age */      } 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      indx[j]=imax; 
   agelim = AGESUP;      if (a[j][j] == 0.0) a[j][j]=TINY; 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      if (j != n) { 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        dum=1.0/(a[j][j]); 
     if (stepm >= YEARM) hstepm=1;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      } 
     gradg=matrix(1,npar,1,nlstate);    } 
     gp=vector(1,nlstate);    free_vector(vv,1,n);  /* Doesn't work */
     gm=vector(1,nlstate);  ;
   } 
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++){ /* Computes gradient */  void lubksb(double **a, int n, int *indx, double b[]) 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  { 
       }    int i,ii=0,ip,j; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double sum; 
       for(i=1;i<=nlstate;i++)   
         gp[i] = prlim[i][i];    for (i=1;i<=n;i++) { 
          ip=indx[i]; 
       for(i=1; i<=npar; i++) /* Computes gradient */      sum=b[ip]; 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      b[ip]=b[i]; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      if (ii) 
       for(i=1;i<=nlstate;i++)        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
         gm[i] = prlim[i][i];      else if (sum) ii=i; 
       b[i]=sum; 
       for(i=1;i<=nlstate;i++)    } 
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    for (i=n;i>=1;i--) { 
     } /* End theta */      sum=b[i]; 
       for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     trgradg =matrix(1,nlstate,1,npar);      b[i]=sum/a[i][i]; 
     } 
     for(j=1; j<=nlstate;j++)  } 
       for(theta=1; theta <=npar; theta++)  
         trgradg[j][theta]=gradg[theta][j];  /************ Frequencies ********************/
   void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint)
     for(i=1;i<=nlstate;i++)  {  /* Some frequencies */
       varpl[i][(int)age] =0.;    
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    int first;
     for(i=1;i<=nlstate;i++)    double ***freq; /* Frequencies */
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    double *pp, **prop;
     double pos,posprop, k2, dateintsum=0,k2cpt=0;
     fprintf(ficresvpl,"%.0f ",age );    FILE *ficresp;
     for(i=1; i<=nlstate;i++)    char fileresp[FILENAMELENGTH];
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    
     fprintf(ficresvpl,"\n");    pp=vector(1,nlstate);
     free_vector(gp,1,nlstate);    prop=matrix(1,nlstate,iagemin,iagemax+3);
     free_vector(gm,1,nlstate);    strcpy(fileresp,"p");
     free_matrix(gradg,1,npar,1,nlstate);    strcat(fileresp,fileres);
     free_matrix(trgradg,1,nlstate,1,npar);    if((ficresp=fopen(fileresp,"w"))==NULL) {
   } /* End age */      printf("Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   free_vector(xp,1,npar);      exit(0);
   free_matrix(doldm,1,nlstate,1,npar);    }
   free_matrix(dnewm,1,nlstate,1,nlstate);    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
     j1=0;
 }    
     j=cptcoveff;
 /************ Variance of one-step probabilities  ******************/    if (cptcovn<1) {j=1;ncodemax[1]=1;}
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)  
 {    first=1;
   int i, j;  
   int k=0, cptcode;    for(k1=1; k1<=j;k1++){
   double **dnewm,**doldm;      for(i1=1; i1<=ncodemax[k1];i1++){
   double *xp;        j1++;
   double *gp, *gm;        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   double **gradg, **trgradg;          scanf("%d", i);*/
   double age,agelim, cov[NCOVMAX];        for (i=-1; i<=nlstate+ndeath; i++)  
   int theta;          for (jk=-1; jk<=nlstate+ndeath; jk++)  
   char fileresprob[FILENAMELENGTH];            for(m=iagemin; m <= iagemax+3; m++)
               freq[i][jk][m]=0;
   strcpy(fileresprob,"prob");  
   strcat(fileresprob,fileres);      for (i=1; i<=nlstate; i++)  
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {        for(m=iagemin; m <= iagemax+3; m++)
     printf("Problem with resultfile: %s\n", fileresprob);          prop[i][m]=0;
   }        
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);        dateintsum=0;
          k2cpt=0;
         for (i=1; i<=imx; i++) {
   xp=vector(1,npar);          bool=1;
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          if  (cptcovn>0) {
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));            for (z1=1; z1<=cptcoveff; z1++) 
                if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   cov[1]=1;                bool=0;
   for (age=bage; age<=fage; age ++){          }
     cov[2]=age;          if (bool==1){
     gradg=matrix(1,npar,1,9);            for(m=firstpass; m<=lastpass; m++){
     trgradg=matrix(1,9,1,npar);              k2=anint[m][i]+(mint[m][i]/12.);
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                    if(agev[m][i]==1) agev[m][i]=iagemax+2;
     for(theta=1; theta <=npar; theta++){                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
       for(i=1; i<=npar; i++)                if (m<lastpass) {
         xp[i] = x[i] + (i==theta ?delti[theta]:0);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                        freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
       pmij(pmmij,cov,ncovmodel,xp,nlstate);                }
                    
       k=0;                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
       for(i=1; i<= (nlstate+ndeath); i++){                  dateintsum=dateintsum+k2;
         for(j=1; j<=(nlstate+ndeath);j++){                  k2cpt++;
            k=k+1;                }
           gp[k]=pmmij[i][j];                /*}*/
         }            }
       }          }
         }
       for(i=1; i<=npar; i++)         
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
      
         if  (cptcovn>0) {
       pmij(pmmij,cov,ncovmodel,xp,nlstate);          fprintf(ficresp, "\n#********** Variable "); 
       k=0;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       for(i=1; i<=(nlstate+ndeath); i++){          fprintf(ficresp, "**********\n#");
         for(j=1; j<=(nlstate+ndeath);j++){        }
           k=k+1;        for(i=1; i<=nlstate;i++) 
           gm[k]=pmmij[i][j];          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         }        fprintf(ficresp, "\n");
       }        
              for(i=iagemin; i <= iagemax+3; i++){
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)          if(i==iagemax+3){
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];              fprintf(ficlog,"Total");
     }          }else{
             if(first==1){
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)              first=0;
       for(theta=1; theta <=npar; theta++)              printf("See log file for details...\n");
       trgradg[j][theta]=gradg[theta][j];            }
              fprintf(ficlog,"Age %d", i);
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);          }
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
      pmij(pmmij,cov,ncovmodel,x,nlstate);              pp[jk] += freq[jk][m][i]; 
           }
      k=0;          for(jk=1; jk <=nlstate ; jk++){
      for(i=1; i<=(nlstate+ndeath); i++){            for(m=-1, pos=0; m <=0 ; m++)
        for(j=1; j<=(nlstate+ndeath);j++){              pos += freq[jk][m][i];
          k=k+1;            if(pp[jk]>=1.e-10){
          gm[k]=pmmij[i][j];              if(first==1){
         }              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
      }              }
                    fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
      /*printf("\n%d ",(int)age);            }else{
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){              if(first==1)
                        printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));            }
      }*/          }
   
   fprintf(ficresprob,"\n%d ",(int)age);          for(jk=1; jk <=nlstate ; jk++){
             for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){              pp[jk] += freq[jk][m][i];
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);          }       
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   }            pos += pp[jk];
             posprop += prop[jk][i];
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));          }
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));          for(jk=1; jk <=nlstate ; jk++){
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            if(pos>=1.e-5){
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);              if(first==1)
 }                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
  free_vector(xp,1,npar);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
 fclose(ficresprob);            }else{
               if(first==1)
 }                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 /******************* Printing html file ***********/            }
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \            if( i <= iagemax){
  int lastpass, int stepm, int weightopt, char model[],\              if(pos>=1.e-5){
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\                /*probs[i][jk][j1]= pp[jk]/pos;*/
  char version[], int popforecast, int estepm ){                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   int jj1, k1, i1, cpt;              }
   FILE *fichtm;              else
   /*char optionfilehtm[FILENAMELENGTH];*/                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
             }
   strcpy(optionfilehtm,optionfile);          }
   strcat(optionfilehtm,".htm");          
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          for(jk=-1; jk <=nlstate+ndeath; jk++)
     printf("Problem with %s \n",optionfilehtm), exit(0);            for(m=-1; m <=nlstate+ndeath; m++)
   }              if(freq[jk][m][i] !=0 ) {
               if(first==1)
  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
 \n              }
 Total number of observations=%d <br>\n          if(i <= iagemax)
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n            fprintf(ficresp,"\n");
 <hr  size=\"2\" color=\"#EC5E5E\">          if(first==1)
  <ul><li>Outputs files<br>\n            printf("Others in log...\n");
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n          fprintf(ficlog,"\n");
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n        }
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n      }
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n    }
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n    dateintmean=dateintsum/k2cpt; 
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,estepm);   
     fclose(ficresp);
  fprintf(fichtm,"\n    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n    free_vector(pp,1,nlstate);
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n    /* End of Freq */
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);  }
   
  if(popforecast==1) fprintf(fichtm,"\n  /************ Prevalence ********************/
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n  {  
         <br>",fileres,fileres,fileres,fileres);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
  else       in each health status at the date of interview (if between dateprev1 and dateprev2).
    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);       We still use firstpass and lastpass as another selection.
 fprintf(fichtm," <li>Graphs</li><p>");    */
    
  m=cptcoveff;    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    double ***freq; /* Frequencies */
     double *pp, **prop;
  jj1=0;    double pos,posprop; 
  for(k1=1; k1<=m;k1++){    double  y2; /* in fractional years */
    for(i1=1; i1<=ncodemax[k1];i1++){    int iagemin, iagemax;
        jj1++;  
        if (cptcovn > 0) {    iagemin= (int) agemin;
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    iagemax= (int) agemax;
          for (cpt=1; cpt<=cptcoveff;cpt++)    /*pp=vector(1,nlstate);*/
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
        }    j1=0;
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);        j=cptcoveff;
        for(cpt=1; cpt<nlstate;cpt++){    if (cptcovn<1) {j=1;ncodemax[1]=1;}
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    for(k1=1; k1<=j;k1++){
        }      for(i1=1; i1<=ncodemax[k1];i1++){
     for(cpt=1; cpt<=nlstate;cpt++) {        j1++;
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident        
 interval) in state (%d): v%s%d%d.gif <br>        for (i=1; i<=nlstate; i++)  
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            for(m=iagemin; m <= iagemax+3; m++)
      }            prop[i][m]=0.0;
      for(cpt=1; cpt<=nlstate;cpt++) {       
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>        for (i=1; i<=imx; i++) { /* Each individual */
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          bool=1;
      }          if  (cptcovn>0) {
      fprintf(fichtm,"\n<br>- Total life expectancy by age and            for (z1=1; z1<=cptcoveff; z1++) 
 health expectancies in states (1) and (2): e%s%d.gif<br>              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);                bool=0;
 fprintf(fichtm,"\n</body>");          } 
    }          if (bool==1) { 
    }            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
 fclose(fichtm);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
 }              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                 if(agev[m][i]==0) agev[m][i]=iagemax+1;
 /******************* Gnuplot file **************/                if(agev[m][i]==1) agev[m][i]=iagemax+2;
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
                 if (s[m][i]>0 && s[m][i]<=nlstate) { 
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;                  /*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]]);*/
                   prop[s[m][i]][(int)agev[m][i]] += weight[i];
   strcpy(optionfilegnuplot,optionfilefiname);                  prop[s[m][i]][iagemax+3] += weight[i]; 
   strcat(optionfilegnuplot,".gp.txt");                } 
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {              }
     printf("Problem with file %s",optionfilegnuplot);            } /* end selection of waves */
   }          }
         }
 #ifdef windows        for(i=iagemin; i <= iagemax+3; i++){  
     fprintf(ficgp,"cd \"%s\" \n",pathc);          
 #endif          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
 m=pow(2,cptcoveff);            posprop += prop[jk][i]; 
            } 
  /* 1eme*/  
   for (cpt=1; cpt<= nlstate ; cpt ++) {          for(jk=1; jk <=nlstate ; jk++){     
    for (k1=1; k1<= m ; k1 ++) {            if( i <=  iagemax){ 
               if(posprop>=1.e-5){ 
 #ifdef windows                probs[i][jk][j1]= prop[jk][i]/posprop;
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);              } 
 #endif            } 
 #ifdef unix          }/* end jk */ 
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);        }/* end i */ 
 #endif      } /* end i1 */
     } /* end k1 */
 for (i=1; i<= nlstate ; i ++) {    
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   else fprintf(ficgp," \%%*lf (\%%*lf)");    /*free_vector(pp,1,nlstate);*/
 }    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);  }  /* End of prevalence */
     for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  /************* Waves Concatenation ***************/
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);  {
      for (i=1; i<= nlstate ; i ++) {    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");       Death is a valid wave (if date is known).
   else fprintf(ficgp," \%%*lf (\%%*lf)");       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
 }         dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));       and mw[mi+1][i]. dh depends on stepm.
 #ifdef unix       */
 fprintf(ficgp,"\nset ter gif small size 400,300");  
 #endif    int i, mi, m;
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
    }       double sum=0., jmean=0.;*/
   }    int first;
   /*2 eme*/    int j, k=0,jk, ju, jl;
     double sum=0.;
   for (k1=1; k1<= m ; k1 ++) {    first=0;
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);    jmin=1e+5;
        jmax=-1;
     for (i=1; i<= nlstate+1 ; i ++) {    jmean=0.;
       k=2*i;    for(i=1; i<=imx; i++){
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);      mi=0;
       for (j=1; j<= nlstate+1 ; j ++) {      m=firstpass;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      while(s[m][i] <= nlstate){
   else fprintf(ficgp," \%%*lf (\%%*lf)");        if(s[m][i]>=1)
 }            mw[++mi][i]=m;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        if(m >=lastpass)
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          break;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);        else
       for (j=1; j<= nlstate+1 ; j ++) {          m++;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      }/* end while */
         else fprintf(ficgp," \%%*lf (\%%*lf)");      if (s[m][i] > nlstate){
 }          mi++;     /* Death is another wave */
       fprintf(ficgp,"\" t\"\" w l 0,");        /* if(mi==0)  never been interviewed correctly before death */
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);           /* Only death is a correct wave */
       for (j=1; j<= nlstate+1 ; j ++) {        mw[mi][i]=m;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      }
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }        wav[i]=mi;
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");      if(mi==0){
       else fprintf(ficgp,"\" t\"\" w l 0,");        nbwarn++;
     }        if(first==0){
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
   }          first=1;
          }
   /*3eme*/        if(first==1){
           fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
   for (k1=1; k1<= m ; k1 ++) {        }
     for (cpt=1; cpt<= nlstate ; cpt ++) {      } /* end mi==0 */
       k=2+nlstate*(cpt-1);    } /* End individuals */
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);  
       for (i=1; i< nlstate ; i ++) {    for(i=1; i<=imx; i++){
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);      for(mi=1; mi<wav[i];mi++){
       }        if (stepm <=0)
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          dh[mi][i]=1;
     }        else{
     }          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
              if (agedc[i] < 2*AGESUP) {
   /* CV preval stat */              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     for (k1=1; k1<= m ; k1 ++) {              if(j==0) j=1;  /* Survives at least one month after exam */
     for (cpt=1; cpt<nlstate ; cpt ++) {              else if(j<0){
       k=3;                nberr++;
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                 j=1; /* Temporary Dangerous patch */
       for (i=1; i< nlstate ; i ++)                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
         fprintf(ficgp,"+$%d",k+i+1);                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
                    }
       l=3+(nlstate+ndeath)*cpt;              k=k+1;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);              if (j >= jmax) jmax=j;
       for (i=1; i< nlstate ; i ++) {              if (j <= jmin) jmin=j;
         l=3+(nlstate+ndeath)*cpt;              sum=sum+j;
         fprintf(ficgp,"+$%d",l+i+1);              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
       }              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);              }
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          }
     }          else{
   }              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);*/
   /* proba elementaires */            k=k+1;
    for(i=1,jk=1; i <=nlstate; i++){            if (j >= jmax) jmax=j;
     for(k=1; k <=(nlstate+ndeath); k++){            else if (j <= jmin)jmin=j;
       if (k != i) {            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
         for(j=1; j <=ncovmodel; j++){            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
                    if(j<0){
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);              nberr++;
           jk++;              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
           fprintf(ficgp,"\n");              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
         }            }
       }            sum=sum+j;
     }          }
     }          jk= j/stepm;
           jl= j -jk*stepm;
     for(jk=1; jk <=m; jk++) {          ju= j -(jk+1)*stepm;
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
    i=1;            if(jl==0){
    for(k2=1; k2<=nlstate; k2++) {              dh[mi][i]=jk;
      k3=i;              bh[mi][i]=0;
      for(k=1; k<=(nlstate+ndeath); k++) {            }else{ /* We want a negative bias in order to only have interpolation ie
        if (k != k2){                    * at the price of an extra matrix product in likelihood */
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);              dh[mi][i]=jk+1;
 ij=1;              bh[mi][i]=ju;
         for(j=3; j <=ncovmodel; j++) {            }
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          }else{
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            if(jl <= -ju){
             ij++;              dh[mi][i]=jk;
           }              bh[mi][i]=jl;       /* bias is positive if real duration
           else                                   * is higher than the multiple of stepm and negative otherwise.
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);                                   */
         }            }
           fprintf(ficgp,")/(1");            else{
                      dh[mi][i]=jk+1;
         for(k1=1; k1 <=nlstate; k1++){                bh[mi][i]=ju;
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);            }
 ij=1;            if(dh[mi][i]==0){
           for(j=3; j <=ncovmodel; j++){              dh[mi][i]=1; /* At least one step */
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              bh[mi][i]=ju; /* At least one step */
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
             ij++;            }
           }          } /* end if mle */
           else        }
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      } /* end wave */
           }    }
           fprintf(ficgp,")");    jmean=sum/k;
         }    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");   }
         i=i+ncovmodel;  
        }  /*********** Tricode ****************************/
      }  void tricode(int *Tvar, int **nbcode, int imx)
    }  {
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    
    }    int Ndum[20],ij=1, k, j, i, maxncov=19;
        int cptcode=0;
   fclose(ficgp);    cptcoveff=0; 
 }  /* end gnuplot */   
     for (k=0; k<maxncov; k++) Ndum[k]=0;
     for (k=1; k<=7; k++) ncodemax[k]=0;
 /*************** Moving average **************/  
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
       for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
   int i, cpt, cptcod;                                 modality*/ 
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
       for (i=1; i<=nlstate;i++)        Ndum[ij]++; /*store the modality */
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
           mobaverage[(int)agedeb][i][cptcod]=0.;        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
                                             Tvar[j]. If V=sex and male is 0 and 
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){                                         female is 1, then  cptcode=1.*/
       for (i=1; i<=nlstate;i++){      }
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
           for (cpt=0;cpt<=4;cpt++){      for (i=0; i<=cptcode; i++) {
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];        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 */
           }      }
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;  
         }      ij=1; 
       }      for (i=1; i<=ncodemax[j]; i++) {
     }        for (k=0; k<= maxncov; k++) {
              if (Ndum[k] != 0) {
 }            nbcode[Tvar[j]][ij]=k; 
             /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
             
 /************** Forecasting ******************/            ij++;
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){          }
            if (ij > ncodemax[j]) break; 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        }  
   int *popage;      } 
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;    }  
   double *popeffectif,*popcount;  
   double ***p3mat;   for (k=0; k< maxncov; k++) Ndum[k]=0;
   char fileresf[FILENAMELENGTH];  
    for (i=1; i<=ncovmodel-2; i++) { 
  agelim=AGESUP;     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;     ij=Tvar[i];
      Ndum[ij]++;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);   }
    
     ij=1;
   strcpy(fileresf,"f");   for (i=1; i<= maxncov; i++) {
   strcat(fileresf,fileres);     if((Ndum[i]!=0) && (i<=ncovcol)){
   if((ficresf=fopen(fileresf,"w"))==NULL) {       Tvaraff[ij]=i; /*For printing */
     printf("Problem with forecast resultfile: %s\n", fileresf);       ij++;
   }     }
   printf("Computing forecasting: result on file '%s' \n", fileresf);   }
    
   if (cptcoveff==0) ncodemax[cptcoveff]=1;   cptcoveff=ij-1; /*Number of simple covariates*/
   }
   if (mobilav==1) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  /*********** Health Expectancies ****************/
     movingaverage(agedeb, fage, ageminpar, mobaverage);  
   }  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 )
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;  {
   if (stepm<=12) stepsize=1;    /* Health expectancies */
      int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
   agelim=AGESUP;    double age, agelim, hf;
      double ***p3mat,***varhe;
   hstepm=1;    double **dnewm,**doldm;
   hstepm=hstepm/stepm;    double *xp;
   yp1=modf(dateintmean,&yp);    double **gp, **gm;
   anprojmean=yp;    double ***gradg, ***trgradg;
   yp2=modf((yp1*12),&yp);    int theta;
   mprojmean=yp;  
   yp1=modf((yp2*30.5),&yp);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   jprojmean=yp;    xp=vector(1,npar);
   if(jprojmean==0) jprojmean=1;    dnewm=matrix(1,nlstate*nlstate,1,npar);
   if(mprojmean==0) jprojmean=1;    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
      
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);    fprintf(ficreseij,"# Health expectancies\n");
      fprintf(ficreseij,"# Age");
   for(cptcov=1;cptcov<=i2;cptcov++){    for(i=1; i<=nlstate;i++)
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      for(j=1; j<=nlstate;j++)
       k=k+1;        fprintf(ficreseij," %1d-%1d (SE)",i,j);
       fprintf(ficresf,"\n#******");    fprintf(ficreseij,"\n");
       for(j=1;j<=cptcoveff;j++) {  
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    if(estepm < stepm){
       }      printf ("Problem %d lower than %d\n",estepm, stepm);
       fprintf(ficresf,"******\n");    }
       fprintf(ficresf,"# StartingAge FinalAge");    else  hstepm=estepm;   
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);    /* We compute the life expectancy from trapezoids spaced every estepm months
           * This is mainly to measure the difference between two models: for example
           * if stepm=24 months pijx are given only every 2 years and by summing them
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {     * we are calculating an estimate of the Life Expectancy assuming a linear 
         fprintf(ficresf,"\n");     * progression in between and thus overestimating or underestimating according
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);       * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){     * to compare the new estimate of Life expectancy with the same linear 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);     * hypothesis. A more precise result, taking into account a more precise
           nhstepm = nhstepm/hstepm;     * curvature will be obtained if estepm is as small as stepm. */
            
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /* For example we decided to compute the life expectancy with the smallest unit */
           oldm=oldms;savm=savms;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);         nhstepm is the number of hstepm from age to agelim 
               nstepm is the number of stepm from age to agelin. 
           for (h=0; h<=nhstepm; h++){       Look at hpijx to understand the reason of that which relies in memory size
             if (h==(int) (calagedate+YEARM*cpt)) {       and note for a fixed period like estepm months */
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
             }       survival function given by stepm (the optimization length). Unfortunately it
             for(j=1; j<=nlstate+ndeath;j++) {       means that if the survival funtion is printed only each two years of age and if
               kk1=0.;kk2=0;       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
               for(i=1; i<=nlstate;i++) {                     results. So we changed our mind and took the option of the best precision.
                 if (mobilav==1)    */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
                 else {  
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    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); 
               if (h==(int)(calagedate+12*cpt)){      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
                 fprintf(ficresf," %.3f", kk1);      /* if (stepm >= YEARM) hstepm=1;*/
                              nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
               }      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             }      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
           }      gp=matrix(0,nhstepm,1,nlstate*nlstate);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      gm=matrix(0,nhstepm,1,nlstate*nlstate);
         }  
       }      /* Computed by stepm unit matrices, product of hstepm matrices, stored
     }         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
           
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);  
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   fclose(ficresf);  
 }      /* Computing  Variances of health expectancies */
 /************** Forecasting ******************/  
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){       for(theta=1; theta <=npar; theta++){
          for(i=1; i<=npar; i++){ 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   int *popage;        }
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   double *popeffectif,*popcount;    
   double ***p3mat,***tabpop,***tabpopprev;        cptj=0;
   char filerespop[FILENAMELENGTH];        for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            cptj=cptj+1;
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
   agelim=AGESUP;              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;            }
            }
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);        }
         
         
   strcpy(filerespop,"pop");        for(i=1; i<=npar; i++) 
   strcat(filerespop,fileres);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   if((ficrespop=fopen(filerespop,"w"))==NULL) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     printf("Problem with forecast resultfile: %s\n", filerespop);        
   }        cptj=0;
   printf("Computing forecasting: result on file '%s' \n", filerespop);        for(j=1; j<= nlstate; j++){
           for(i=1;i<=nlstate;i++){
   if (cptcoveff==0) ncodemax[cptcoveff]=1;            cptj=cptj+1;
             for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   if (mobilav==1) {  
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     movingaverage(agedeb, fage, ageminpar, mobaverage);            }
   }          }
         }
   stepsize=(int) (stepm+YEARM-1)/YEARM;        for(j=1; j<= nlstate*nlstate; j++)
   if (stepm<=12) stepsize=1;          for(h=0; h<=nhstepm-1; h++){
              gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   agelim=AGESUP;          }
         } 
   hstepm=1;     
   hstepm=hstepm/stepm;  /* End theta */
    
   if (popforecast==1) {       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     if((ficpop=fopen(popfile,"r"))==NULL) {  
       printf("Problem with population file : %s\n",popfile);exit(0);       for(h=0; h<=nhstepm-1; h++)
     }        for(j=1; j<=nlstate*nlstate;j++)
     popage=ivector(0,AGESUP);          for(theta=1; theta <=npar; theta++)
     popeffectif=vector(0,AGESUP);            trgradg[h][j][theta]=gradg[h][theta][j];
     popcount=vector(0,AGESUP);       
      
     i=1;         for(i=1;i<=nlstate*nlstate;i++)
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;        for(j=1;j<=nlstate*nlstate;j++)
              varhe[i][j][(int)age] =0.;
     imx=i;  
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];       printf("%d|",(int)age);fflush(stdout);
   }       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        for(h=0;h<=nhstepm-1;h++){
   for(cptcov=1;cptcov<=i2;cptcov++){        for(k=0;k<=nhstepm-1;k++){
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
       k=k+1;          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
       fprintf(ficrespop,"\n#******");          for(i=1;i<=nlstate*nlstate;i++)
       for(j=1;j<=cptcoveff;j++) {            for(j=1;j<=nlstate*nlstate;j++)
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
       }        }
       fprintf(ficrespop,"******\n");      }
       fprintf(ficrespop,"# Age");      /* Computing expectancies */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);      for(i=1; i<=nlstate;i++)
       if (popforecast==1)  fprintf(ficrespop," [Population]");        for(j=1; j<=nlstate;j++)
                for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       for (cpt=0; cpt<=0;cpt++) {            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);              
          /* 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 (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          }
           nhstepm = nhstepm/hstepm;  
                fprintf(ficreseij,"%3.0f",age );
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      cptj=0;
           oldm=oldms;savm=savms;      for(i=1; i<=nlstate;i++)
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          for(j=1; j<=nlstate;j++){
                  cptj++;
           for (h=0; h<=nhstepm; h++){          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
             if (h==(int) (calagedate+YEARM*cpt)) {        }
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      fprintf(ficreseij,"\n");
             }     
             for(j=1; j<=nlstate+ndeath;j++) {      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
               kk1=0.;kk2=0;      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
               for(i=1; i<=nlstate;i++) {                    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
                 if (mobilav==1)      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                 else {    }
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    printf("\n");
                 }    fprintf(ficlog,"\n");
               }  
               if (h==(int)(calagedate+12*cpt)){    free_vector(xp,1,npar);
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
                   /*fprintf(ficrespop," %.3f", kk1);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
               }  }
             }  
             for(i=1; i<=nlstate;i++){  /************ Variance ******************/
               kk1=0.;  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)
                 for(j=1; j<=nlstate;j++){  {
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    /* Variance of health expectancies */
                 }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];    /* double **newm;*/
             }    double **dnewm,**doldm;
     double **dnewmp,**doldmp;
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)    int i, j, nhstepm, hstepm, h, nstepm ;
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    int k, cptcode;
           }    double *xp;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double **gp, **gm;  /* for var eij */
         }    double ***gradg, ***trgradg; /*for var eij */
       }    double **gradgp, **trgradgp; /* for var p point j */
      double *gpp, *gmp; /* for var p point j */
   /******/    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     double ***p3mat;
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    double age,agelim, hf;
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      double ***mobaverage;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    int theta;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    char digit[4];
           nhstepm = nhstepm/hstepm;    char digitp[25];
            
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    char fileresprobmorprev[FILENAMELENGTH];
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      if(popbased==1){
           for (h=0; h<=nhstepm; h++){      if(mobilav!=0)
             if (h==(int) (calagedate+YEARM*cpt)) {        strcpy(digitp,"-populbased-mobilav-");
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);      else strcpy(digitp,"-populbased-nomobil-");
             }    }
             for(j=1; j<=nlstate+ndeath;j++) {    else 
               kk1=0.;kk2=0;      strcpy(digitp,"-stablbased-");
               for(i=1; i<=nlstate;i++) {                
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];        if (mobilav!=0) {
               }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);      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);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      }
         }    }
       }  
    }    strcpy(fileresprobmorprev,"prmorprev"); 
   }    sprintf(digit,"%-d",ij);
      /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   if (popforecast==1) {    strcat(fileresprobmorprev,fileres);
     free_ivector(popage,0,AGESUP);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
     free_vector(popeffectif,0,AGESUP);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
     free_vector(popcount,0,AGESUP);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   }    }
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   fclose(ficrespop);    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
 }    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
 /***********************************************/      fprintf(ficresprobmorprev," p.%-d SE",j);
 /**************** Main Program *****************/      for(i=1; i<=nlstate;i++)
 /***********************************************/        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
 int main(int argc, char *argv[])    fprintf(ficresprobmorprev,"\n");
 {    fprintf(ficgp,"\n# Routine varevsij");
     fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   double agedeb, agefin,hf;  /*   } */
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
   double fret;    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
   double **xi,tmp,delta;    fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
   double dum; /* Dummy variable */      for(j=1; j<=nlstate;j++)
   double ***p3mat;        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
   int *indx;    fprintf(ficresvij,"\n");
   char line[MAXLINE], linepar[MAXLINE];  
   char title[MAXLINE];    xp=vector(1,npar);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    dnewm=matrix(1,nlstate,1,npar);
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    doldm=matrix(1,nlstate,1,nlstate);
      dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
   char filerest[FILENAMELENGTH];    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   char fileregp[FILENAMELENGTH];    gpp=vector(nlstate+1,nlstate+ndeath);
   char popfile[FILENAMELENGTH];    gmp=vector(nlstate+1,nlstate+ndeath);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   int firstobs=1, lastobs=10;    
   int sdeb, sfin; /* Status at beginning and end */    if(estepm < stepm){
   int c,  h , cpt,l;      printf ("Problem %d lower than %d\n",estepm, stepm);
   int ju,jl, mi;    }
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    else  hstepm=estepm;   
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    /* For example we decided to compute the life expectancy with the smallest unit */
   int mobilav=0,popforecast=0;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   int hstepm, nhstepm;       nhstepm is the number of hstepm from age to agelim 
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;       nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
   double bage, fage, age, agelim, agebase;       and note for a fixed period like k years */
   double ftolpl=FTOL;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   double **prlim;       survival function given by stepm (the optimization length). Unfortunately it
   double *severity;       means that if the survival funtion is printed every two years of age and if
   double ***param; /* Matrix of parameters */       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   double  *p;       results. So we changed our mind and took the option of the best precision.
   double **matcov; /* Matrix of covariance */    */
   double ***delti3; /* Scale */    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   double *delti; /* Scale */    agelim = AGESUP;
   double ***eij, ***vareij;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   double **varpl; /* Variances of prevalence limits by age */      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   double *epj, vepp;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   double kk1, kk2;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
        gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   char version[80]="Imach version 0.8b, March 2002, INED-EUROREVES ";  
   char *alph[]={"a","a","b","c","d","e"}, str[4];  
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   char z[1]="c", occ;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
 #include <sys/time.h>        }
 #include <time.h>        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
   /* long total_usecs;        if (popbased==1) {
   struct timeval start_time, end_time;          if(mobilav ==0){
              for(i=1; i<=nlstate;i++)
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */              prlim[i][i]=probs[(int)age][i][ij];
   getcwd(pathcd, size);          }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
   printf("\n%s",version);              prlim[i][i]=mobaverage[(int)age][i][ij];
   if(argc <=1){          }
     printf("\nEnter the parameter file name: ");        }
     scanf("%s",pathtot);    
   }        for(j=1; j<= nlstate; j++){
   else{          for(h=0; h<=nhstepm; h++){
     strcpy(pathtot,argv[1]);            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   }              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/          }
   /*cygwin_split_path(pathtot,path,optionfile);        }
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/        /* This for computing probability of death (h=1 means
   /* cutv(path,optionfile,pathtot,'\\');*/           computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);        */
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   chdir(path);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
   replace(pathc,path);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
 /*-------- arguments in the command line --------*/        /* end probability of death */
   
   strcpy(fileres,"r");        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   strcat(fileres, optionfilefiname);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   strcat(fileres,".txt");    /* Other files have txt extension */        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   /*---------arguments file --------*/   
         if (popbased==1) {
   if((ficpar=fopen(optionfile,"r"))==NULL)    {          if(mobilav ==0){
     printf("Problem with optionfile %s\n",optionfile);            for(i=1; i<=nlstate;i++)
     goto end;              prlim[i][i]=probs[(int)age][i][ij];
   }          }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
   strcpy(filereso,"o");              prlim[i][i]=mobaverage[(int)age][i][ij];
   strcat(filereso,fileres);          }
   if((ficparo=fopen(filereso,"w"))==NULL) {        }
     printf("Problem with Output resultfile: %s\n", filereso);goto end;  
   }        for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
   /* Reads comments: lines beginning with '#' */            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   while((c=getc(ficpar))=='#' && c!= EOF){              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);        }
     puts(line);        /* This for computing probability of death (h=1 means
     fputs(line,ficparo);           computed over hstepm matrices product = hstepm*stepm months) 
   }           as a weighted average of prlim.
   ungetc(c,ficpar);        */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   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);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);        }    
 while((c=getc(ficpar))=='#' && c!= EOF){        /* end probability of death */
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);        for(j=1; j<= nlstate; j++) /* vareij */
     puts(line);          for(h=0; h<=nhstepm; h++){
     fputs(line,ficparo);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   }          }
   ungetc(c,ficpar);  
          for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
              gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   covar=matrix(0,NCOVMAX,1,n);        }
   cptcovn=0;  
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;      } /* End theta */
   
   ncovmodel=2+cptcovn;      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  
        for(h=0; h<=nhstepm; h++) /* veij */
   /* Read guess parameters */        for(j=1; j<=nlstate;j++)
   /* Reads comments: lines beginning with '#' */          for(theta=1; theta <=npar; theta++)
   while((c=getc(ficpar))=='#' && c!= EOF){            trgradg[h][j][theta]=gradg[h][theta][j];
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     puts(line);        for(theta=1; theta <=npar; theta++)
     fputs(line,ficparo);          trgradgp[j][theta]=gradgp[theta][j];
   }    
   ungetc(c,ficpar);  
        hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      for(i=1;i<=nlstate;i++)
     for(i=1; i <=nlstate; i++)        for(j=1;j<=nlstate;j++)
     for(j=1; j <=nlstate+ndeath-1; j++){          vareij[i][j][(int)age] =0.;
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       fprintf(ficparo,"%1d%1d",i1,j1);      for(h=0;h<=nhstepm;h++){
       printf("%1d%1d",i,j);        for(k=0;k<=nhstepm;k++){
       for(k=1; k<=ncovmodel;k++){          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
         fscanf(ficpar," %lf",&param[i][j][k]);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
         printf(" %lf",param[i][j][k]);          for(i=1;i<=nlstate;i++)
         fprintf(ficparo," %lf",param[i][j][k]);            for(j=1;j<=nlstate;j++)
       }              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
       fscanf(ficpar,"\n");        }
       printf("\n");      }
       fprintf(ficparo,"\n");    
     }      /* pptj */
        matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
   p=param[1][1];        for(i=nlstate+1;i<=nlstate+ndeath;i++)
            varppt[j][i]=doldmp[j][i];
   /* Reads comments: lines beginning with '#' */      /* end ppptj */
   while((c=getc(ficpar))=='#' && c!= EOF){      /*  x centered again */
     ungetc(c,ficpar);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
     fgets(line, MAXLINE, ficpar);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
     puts(line);   
     fputs(line,ficparo);      if (popbased==1) {
   }        if(mobilav ==0){
   ungetc(c,ficpar);          for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        }else{ /* mobilav */ 
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */          for(i=1; i<=nlstate;i++)
   for(i=1; i <=nlstate; i++){            prlim[i][i]=mobaverage[(int)age][i][ij];
     for(j=1; j <=nlstate+ndeath-1; j++){        }
       fscanf(ficpar,"%1d%1d",&i1,&j1);      }
       printf("%1d%1d",i,j);               
       fprintf(ficparo,"%1d%1d",i1,j1);      /* This for computing probability of death (h=1 means
       for(k=1; k<=ncovmodel;k++){         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
         fscanf(ficpar,"%le",&delti3[i][j][k]);         as a weighted average of prlim.
         printf(" %le",delti3[i][j][k]);      */
         fprintf(ficparo," %le",delti3[i][j][k]);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
       }        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
       fscanf(ficpar,"\n");          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       printf("\n");      }    
       fprintf(ficparo,"\n");      /* end probability of death */
     }  
   }      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   delti=delti3[1][1];      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
          fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
   /* Reads comments: lines beginning with '#' */        for(i=1; i<=nlstate;i++){
   while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);      } 
     puts(line);      fprintf(ficresprobmorprev,"\n");
     fputs(line,ficparo);  
   }      fprintf(ficresvij,"%.0f ",age );
   ungetc(c,ficpar);      for(i=1; i<=nlstate;i++)
          for(j=1; j<=nlstate;j++){
   matcov=matrix(1,npar,1,npar);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
   for(i=1; i <=npar; i++){        }
     fscanf(ficpar,"%s",&str);      fprintf(ficresvij,"\n");
     printf("%s",str);      free_matrix(gp,0,nhstepm,1,nlstate);
     fprintf(ficparo,"%s",str);      free_matrix(gm,0,nhstepm,1,nlstate);
     for(j=1; j <=i; j++){      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       fscanf(ficpar," %le",&matcov[i][j]);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       printf(" %.5le",matcov[i][j]);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficparo," %.5le",matcov[i][j]);    } /* End age */
     }    free_vector(gpp,nlstate+1,nlstate+ndeath);
     fscanf(ficpar,"\n");    free_vector(gmp,nlstate+1,nlstate+ndeath);
     printf("\n");    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     fprintf(ficparo,"\n");    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   }    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
   for(i=1; i <=npar; i++)    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     for(j=i+1;j<=npar;j++)    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
       matcov[i][j]=matcov[j][i];  /*   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); */
   printf("\n");  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
     /*-------- Rewriting paramater file ----------*/    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
      strcpy(rfileres,"r");    /* "Rparameterfile */    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    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);
      strcat(rfileres,".");    /* */    /*  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);
      strcat(rfileres,optionfilext);    /* Other files have txt extension */  */
     if((ficres =fopen(rfileres,"w"))==NULL) {  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     }  
     fprintf(ficres,"#%s\n",version);    free_vector(xp,1,npar);
        free_matrix(doldm,1,nlstate,1,nlstate);
     /*-------- data file ----------*/    free_matrix(dnewm,1,nlstate,1,npar);
     if((fic=fopen(datafile,"r"))==NULL)    {    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       printf("Problem with datafile: %s\n", datafile);goto end;    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);
     n= lastobs;    fclose(ficresprobmorprev);
     severity = vector(1,maxwav);    fflush(ficgp);
     outcome=imatrix(1,maxwav+1,1,n);    fflush(fichtm); 
     num=ivector(1,n);  }  /* end varevsij */
     moisnais=vector(1,n);  
     annais=vector(1,n);  /************ Variance of prevlim ******************/
     moisdc=vector(1,n);  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
     andc=vector(1,n);  {
     agedc=vector(1,n);    /* Variance of prevalence limit */
     cod=ivector(1,n);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     weight=vector(1,n);    double **newm;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    double **dnewm,**doldm;
     mint=matrix(1,maxwav,1,n);    int i, j, nhstepm, hstepm;
     anint=matrix(1,maxwav,1,n);    int k, cptcode;
     s=imatrix(1,maxwav+1,1,n);    double *xp;
     adl=imatrix(1,maxwav+1,1,n);        double *gp, *gm;
     tab=ivector(1,NCOVMAX);    double **gradg, **trgradg;
     ncodemax=ivector(1,8);    double age,agelim;
     int theta;
     i=1;     
     while (fgets(line, MAXLINE, fic) != NULL)    {    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
       if ((i >= firstobs) && (i <=lastobs)) {    fprintf(ficresvpl,"# Age");
            for(i=1; i<=nlstate;i++)
         for (j=maxwav;j>=1;j--){        fprintf(ficresvpl," %1d-%1d",i,i);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    fprintf(ficresvpl,"\n");
           strcpy(line,stra);  
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    xp=vector(1,npar);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    dnewm=matrix(1,nlstate,1,npar);
         }    doldm=matrix(1,nlstate,1,nlstate);
            
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    hstepm=1*YEARM; /* Every year of age */
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
         for (j=ncovcol;j>=1;j--){      gradg=matrix(1,npar,1,nlstate);
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      gp=vector(1,nlstate);
         }      gm=vector(1,nlstate);
         num[i]=atol(stra);  
              for(theta=1; theta <=npar; theta++){
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){        for(i=1; i<=npar; i++){ /* Computes gradient */
           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;}*/          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         i=i+1;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       }        for(i=1;i<=nlstate;i++)
     }          gp[i] = prlim[i][i];
     /* printf("ii=%d", ij);      
        scanf("%d",i);*/        for(i=1; i<=npar; i++) /* Computes gradient */
   imx=i-1; /* Number of individuals */          xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   /* for (i=1; i<=imx; i++){        for(i=1;i<=nlstate;i++)
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;          gm[i] = prlim[i][i];
     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<=nlstate;i++)
     }*/          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
        } /* End theta */
   /* for (i=1; i<=imx; i++){  
      if (s[4][i]==9)  s[4][i]=-1;      trgradg =matrix(1,nlstate,1,npar);
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}  
   */      for(j=1; j<=nlstate;j++)
          for(theta=1; theta <=npar; theta++)
   /* Calculation of the number of parameter from char model*/          trgradg[j][theta]=gradg[theta][j];
   Tvar=ivector(1,15);  
   Tprod=ivector(1,15);      for(i=1;i<=nlstate;i++)
   Tvaraff=ivector(1,15);        varpl[i][(int)age] =0.;
   Tvard=imatrix(1,15,1,2);      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   Tage=ivector(1,15);            matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
          for(i=1;i<=nlstate;i++)
   if (strlen(model) >1){        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
     j=0, j1=0, k1=1, k2=1;  
     j=nbocc(model,'+');      fprintf(ficresvpl,"%.0f ",age );
     j1=nbocc(model,'*');      for(i=1; i<=nlstate;i++)
     cptcovn=j+1;        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
     cptcovprod=j1;      fprintf(ficresvpl,"\n");
          free_vector(gp,1,nlstate);
     strcpy(modelsav,model);      free_vector(gm,1,nlstate);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      free_matrix(gradg,1,npar,1,nlstate);
       printf("Error. Non available option model=%s ",model);      free_matrix(trgradg,1,nlstate,1,npar);
       goto end;    } /* End age */
     }  
        free_vector(xp,1,npar);
     for(i=(j+1); i>=1;i--){    free_matrix(doldm,1,nlstate,1,npar);
       cutv(stra,strb,modelsav,'+');    free_matrix(dnewm,1,nlstate,1,nlstate);
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);  
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/  }
       /*scanf("%d",i);*/  
       if (strchr(strb,'*')) {  /************ Variance of one-step probabilities  ******************/
         cutv(strd,strc,strb,'*');  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
         if (strcmp(strc,"age")==0) {  {
           cptcovprod--;    int i, j=0,  i1, k1, l1, t, tj;
           cutv(strb,stre,strd,'V');    int k2, l2, j1,  z1;
           Tvar[i]=atoi(stre);    int k=0,l, cptcode;
           cptcovage++;    int first=1, first1;
             Tage[cptcovage]=i;    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
             /*printf("stre=%s ", stre);*/    double **dnewm,**doldm;
         }    double *xp;
         else if (strcmp(strd,"age")==0) {    double *gp, *gm;
           cptcovprod--;    double **gradg, **trgradg;
           cutv(strb,stre,strc,'V');    double **mu;
           Tvar[i]=atoi(stre);    double age,agelim, cov[NCOVMAX];
           cptcovage++;    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
           Tage[cptcovage]=i;    int theta;
         }    char fileresprob[FILENAMELENGTH];
         else {    char fileresprobcov[FILENAMELENGTH];
           cutv(strb,stre,strc,'V');    char fileresprobcor[FILENAMELENGTH];
           Tvar[i]=ncovcol+k1;  
           cutv(strb,strc,strd,'V');    double ***varpij;
           Tprod[k1]=i;  
           Tvard[k1][1]=atoi(strc);    strcpy(fileresprob,"prob"); 
           Tvard[k1][2]=atoi(stre);    strcat(fileresprob,fileres);
           Tvar[cptcovn+k2]=Tvard[k1][1];    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
           Tvar[cptcovn+k2+1]=Tvard[k1][2];      printf("Problem with resultfile: %s\n", fileresprob);
           for (k=1; k<=lastobs;k++)      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    }
           k1++;    strcpy(fileresprobcov,"probcov"); 
           k2=k2+2;    strcat(fileresprobcov,fileres);
         }    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       }      printf("Problem with resultfile: %s\n", fileresprobcov);
       else {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    }
        /*  scanf("%d",i);*/    strcpy(fileresprobcor,"probcor"); 
       cutv(strd,strc,strb,'V');    strcat(fileresprobcor,fileres);
       Tvar[i]=atoi(strc);    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       }      printf("Problem with resultfile: %s\n", fileresprobcor);
       strcpy(modelsav,stra);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    }
         scanf("%d",i);*/    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     }    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
 }    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
      fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   printf("cptcovprod=%d ", cptcovprod);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   scanf("%d ",i);*/    
     fclose(fic);    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     /*  if(mle==1){*/    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     if (weightopt != 1) { /* Maximisation without weights*/    fprintf(ficresprobcov,"# Age");
       for(i=1;i<=n;i++) weight[i]=1.0;    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     }    fprintf(ficresprobcov,"# Age");
     /*-calculation of age at interview from date of interview and age at death -*/  
     agev=matrix(1,maxwav,1,imx);  
     for(i=1; i<=nlstate;i++)
     for (i=1; i<=imx; i++) {      for(j=1; j<=(nlstate+ndeath);j++){
       for(m=2; (m<= maxwav); m++) {        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){        fprintf(ficresprobcov," p%1d-%1d ",i,j);
          anint[m][i]=9999;        fprintf(ficresprobcor," p%1d-%1d ",i,j);
          s[m][i]=-1;      }  
        }   /* fprintf(ficresprob,"\n");
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;    fprintf(ficresprobcov,"\n");
       }    fprintf(ficresprobcor,"\n");
     }   */
    xp=vector(1,npar);
     for (i=1; i<=imx; i++)  {    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
       for(m=1; (m<= maxwav); m++){    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
         if(s[m][i] >0){    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
           if (s[m][i] >= nlstate+1) {    first=1;
             if(agedc[i]>0)    fprintf(ficgp,"\n# Routine varprob");
               if(moisdc[i]!=99 && andc[i]!=9999)    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
                 agev[m][i]=agedc[i];    fprintf(fichtm,"\n");
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/  
            else {    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
               if (andc[i]!=9999){    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    file %s<br>\n",optionfilehtmcov);
               agev[m][i]=-1;    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
               }  and drawn. It helps understanding how is the covariance between two incidences.\
             }   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. \
           else if(s[m][i] !=9){ /* Should no more exist */  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
             if(mint[m][i]==99 || anint[m][i]==9999)  standard deviations wide on each axis. <br>\
               agev[m][i]=1;   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
             else if(agev[m][i] <agemin){   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
               agemin=agev[m][i];  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/  
             }    cov[1]=1;
             else if(agev[m][i] >agemax){    tj=cptcoveff;
               agemax=agev[m][i];    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    j1=0;
             }    for(t=1; t<=tj;t++){
             /*agev[m][i]=anint[m][i]-annais[i];*/      for(i1=1; i1<=ncodemax[t];i1++){ 
             /*   agev[m][i] = age[i]+2*m;*/        j1++;
           }        if  (cptcovn>0) {
           else { /* =9 */          fprintf(ficresprob, "\n#********** Variable "); 
             agev[m][i]=1;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
             s[m][i]=-1;          fprintf(ficresprob, "**********\n#\n");
           }          fprintf(ficresprobcov, "\n#********** Variable "); 
         }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         else /*= 0 Unknown */          fprintf(ficresprobcov, "**********\n#\n");
           agev[m][i]=1;          
       }          fprintf(ficgp, "\n#********** Variable "); 
              for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     }          fprintf(ficgp, "**********\n#\n");
     for (i=1; i<=imx; i++)  {          
       for(m=1; (m<= maxwav); m++){          
         if (s[m][i] > (nlstate+ndeath)) {          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           printf("Error: Wrong value in nlstate or ndeath\n");            for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           goto end;          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
         }          
       }          fprintf(ficresprobcor, "\n#********** Variable ");    
     }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);        }
         
     free_vector(severity,1,maxwav);        for (age=bage; age<=fage; age ++){ 
     free_imatrix(outcome,1,maxwav+1,1,n);          cov[2]=age;
     free_vector(moisnais,1,n);          for (k=1; k<=cptcovn;k++) {
     free_vector(annais,1,n);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     /* free_matrix(mint,1,maxwav,1,n);          }
        free_matrix(anint,1,maxwav,1,n);*/          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     free_vector(moisdc,1,n);          for (k=1; k<=cptcovprod;k++)
     free_vector(andc,1,n);            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           
              gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
     wav=ivector(1,imx);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);          gp=vector(1,(nlstate)*(nlstate+ndeath));
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          gm=vector(1,(nlstate)*(nlstate+ndeath));
          
     /* Concatenates waves */          for(theta=1; theta <=npar; theta++){
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);            for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
       Tcode=ivector(1,100);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);            
       ncodemax[1]=1;            k=0;
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);            for(i=1; i<= (nlstate); i++){
                    for(j=1; j<=(nlstate+ndeath);j++){
    codtab=imatrix(1,100,1,10);                k=k+1;
    h=0;                gp[k]=pmmij[i][j];
    m=pow(2,cptcoveff);              }
              }
    for(k=1;k<=cptcoveff; k++){            
      for(i=1; i <=(m/pow(2,k));i++){            for(i=1; i<=npar; i++)
        for(j=1; j <= ncodemax[k]; j++){              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){      
            h++;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;            k=0;
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/            for(i=1; i<=(nlstate); i++){
          }              for(j=1; j<=(nlstate+ndeath);j++){
        }                k=k+1;
      }                gm[k]=pmmij[i][j];
    }              }
    /* 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(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
       for(k=1; k <=cptcovn; k++){              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);          }
       }  
       printf("\n");          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
       }            for(theta=1; theta <=npar; theta++)
       scanf("%d",i);*/              trgradg[j][theta]=gradg[theta][j];
              
    /* Calculates basic frequencies. Computes observed prevalence at single age          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
        and prints on file fileres'p'. */          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
           free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
              free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
              free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          pmij(pmmij,cov,ncovmodel,x,nlstate);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */          k=0;
                for(i=1; i<=(nlstate); i++){
     /* For Powell, parameters are in a vector p[] starting at p[1]            for(j=1; j<=(nlstate+ndeath);j++){
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */              k=k+1;
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */              mu[k][(int) age]=pmmij[i][j];
             }
     if(mle==1){          }
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
     }            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
                  varpij[i][j][(int)age] = doldm[i][j];
     /*--------- results files --------------*/  
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);          /*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]));
    jk=1;            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");            }*/
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");  
    for(i=1,jk=1; i <=nlstate; i++){          fprintf(ficresprob,"\n%d ",(int)age);
      for(k=1; k <=(nlstate+ndeath); k++){          fprintf(ficresprobcov,"\n%d ",(int)age);
        if (k != i)          fprintf(ficresprobcor,"\n%d ",(int)age);
          {  
            printf("%d%d ",i,k);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
            fprintf(ficres,"%1d%1d ",i,k);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
            for(j=1; j <=ncovmodel; j++){          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
              printf("%f ",p[jk]);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
              fprintf(ficres,"%f ",p[jk]);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
              jk++;          }
            }          i=0;
            printf("\n");          for (k=1; k<=(nlstate);k++){
            fprintf(ficres,"\n");            for (l=1; l<=(nlstate+ndeath);l++){ 
          }              i=i++;
      }              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
    }              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
  if(mle==1){              for (j=1; j<=i;j++){
     /* Computing hessian and covariance matrix */                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
     ftolhess=ftol; /* Usually correct */                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
     hesscov(matcov, p, npar, delti, ftolhess, func);              }
  }            }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");          }/* end of loop for state */
     printf("# Scales (for hessian or gradient estimation)\n");        } /* end of loop for age */
      for(i=1,jk=1; i <=nlstate; i++){  
       for(j=1; j <=nlstate+ndeath; j++){        /* Confidence intervalle of pij  */
         if (j!=i) {        /*
           fprintf(ficres,"%1d%1d",i,j);          fprintf(ficgp,"\nset noparametric;unset label");
           printf("%1d%1d",i,j);          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
           for(k=1; k<=ncovmodel;k++){          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
             printf(" %.5e",delti[jk]);          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
             fprintf(ficres," %.5e",delti[jk]);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
             jk++;          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           }          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
           printf("\n");        */
           fprintf(ficres,"\n");  
         }        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
       }        first1=1;
      }        for (k2=1; k2<=(nlstate);k2++){
              for (l2=1; l2<=(nlstate+ndeath);l2++){ 
     k=1;            if(l2==k2) continue;
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");            j=(k2-1)*(nlstate+ndeath)+l2;
     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");            for (k1=1; k1<=(nlstate);k1++){
     for(i=1;i<=npar;i++){              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
       /*  if (k>nlstate) k=1;                if(l1==k1) continue;
       i1=(i-1)/(ncovmodel*nlstate)+1;                i=(k1-1)*(nlstate+ndeath)+l1;
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);                if(i<=j) continue;
       printf("%s%d%d",alph[k],i1,tab[i]);*/                for (age=bage; age<=fage; age ++){ 
       fprintf(ficres,"%3d",i);                  if ((int)age %5==0){
       printf("%3d",i);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
       for(j=1; j<=i;j++){                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
         fprintf(ficres," %.5e",matcov[i][j]);                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
         printf(" %.5e",matcov[i][j]);                    mu1=mu[i][(int) age]/stepm*YEARM ;
       }                    mu2=mu[j][(int) age]/stepm*YEARM;
       fprintf(ficres,"\n");                    c12=cv12/sqrt(v1*v2);
       printf("\n");                    /* Computing eigen value of matrix of covariance */
       k++;                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     }                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                        /* Eigen vectors */
     while((c=getc(ficpar))=='#' && c!= EOF){                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
       ungetc(c,ficpar);                    /*v21=sqrt(1.-v11*v11); *//* error */
       fgets(line, MAXLINE, ficpar);                    v21=(lc1-v1)/cv12*v11;
       puts(line);                    v12=-v21;
       fputs(line,ficparo);                    v22=v11;
     }                    tnalp=v21/v11;
     ungetc(c,ficpar);                    if(first1==1){
     estepm=0;                      first1=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);                      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);
     if (estepm==0 || estepm < stepm) estepm=stepm;                    }
     if (fage <= 2) {                    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);
       bage = ageminpar;                    /*printf(fignu*/
       fage = agemaxpar;                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
     }                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                        if(first==1){
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");                      first=0;
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                      fprintf(ficgp,"\nset parametric;unset label");
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                      fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     while((c=getc(ficpar))=='#' && c!= EOF){                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
     ungetc(c,ficpar);   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
     fgets(line, MAXLINE, ficpar);  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
     puts(line);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
     fputs(line,ficparo);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   }                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   ungetc(c,ficpar);                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                        fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                                    mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   while((c=getc(ficpar))=='#' && c!= EOF){                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     ungetc(c,ficpar);                    }else{
     fgets(line, MAXLINE, ficpar);                      first=0;
     puts(line);                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
     fputs(line,ficparo);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
   }                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   ungetc(c,ficpar);                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                                mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
    dateprev1=anprev1+mprev1/12.+jprev1/365.;                    }/* if first */
    dateprev2=anprev2+mprev2/12.+jprev2/365.;                  } /* age mod 5 */
                 } /* end loop age */
   fscanf(ficpar,"pop_based=%d\n",&popbased);                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   fprintf(ficparo,"pop_based=%d\n",popbased);                  first=1;
   fprintf(ficres,"pop_based=%d\n",popbased);                } /*l12 */
              } /* k12 */
   while((c=getc(ficpar))=='#' && c!= EOF){          } /*l1 */
     ungetc(c,ficpar);        }/* k1 */
     fgets(line, MAXLINE, ficpar);      } /* loop covariates */
     puts(line);    }
     fputs(line,ficparo);    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
   }    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
   ungetc(c,ficpar);    free_vector(xp,1,npar);
     fclose(ficresprob);
   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);    fclose(ficresprobcov);
 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);    fclose(ficresprobcor);
 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);    fflush(ficgp);
     fflush(fichtmcov);
   }
 while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  /******************* Printing html file ***********/
     puts(line);  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
     fputs(line,ficparo);                    int lastpass, int stepm, int weightopt, char model[],\
   }                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
   ungetc(c,ficpar);                    int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);                    double jprev2, double mprev2,double anprev2){
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    int jj1, k1, i1, cpt;
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);  
      fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
 /*------------ gnuplot -------------*/     fprintf(fichtm,"\
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
               stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
 /*------------ free_vector  -------------*/     fprintf(fichtm,"\
  chdir(path);   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
               subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
  free_ivector(wav,1,imx);     fprintf(fichtm,"\
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);   - Life expectancies by age and initial health status (estepm=%2d months): \
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);       <a href=\"%s\">%s</a> <br>\n</li>",
  free_ivector(num,1,n);             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
  free_vector(agedc,1,n);  
  /*free_matrix(covar,1,NCOVMAX,1,n);*/  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
  fclose(ficparo);  
  fclose(ficres);   m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
 /*--------- index.htm --------*/  
    jj1=0;
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);   for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
         jj1++;
   /*--------------- Prevalence limit --------------*/       if (cptcovn > 0) {
           fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   strcpy(filerespl,"pl");         for (cpt=1; cpt<=cptcoveff;cpt++) 
   strcat(filerespl,fileres);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;       }
   }       /* Pij */
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);       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(ficrespl,"#Prevalence limit\n");  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
   fprintf(ficrespl,"#Age ");       /* Quasi-incidences */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
   fprintf(ficrespl,"\n");   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
    <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
   prlim=matrix(1,nlstate,1,nlstate);         /* Stable prevalence in each health state */
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */         for(cpt=1; cpt<nlstate;cpt++){
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */         }
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */       for(cpt=1; cpt<=nlstate;cpt++) {
   k=0;          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
   agebase=ageminpar;  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
   agelim=agemaxpar;       }
   ftolpl=1.e-10;     } /* end i1 */
   i1=cptcoveff;   }/* End k1 */
   if (cptcovn < 1){i1=1;}   fprintf(fichtm,"</ul>");
   
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){   fprintf(fichtm,"\
         k=k+1;  \n<br><li><h4> Result files (second order: variances)</h4>\n\
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
         fprintf(ficrespl,"\n#******");  
         for(j=1;j<=cptcoveff;j++)   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
         fprintf(ficrespl,"******\n");   fprintf(fichtm,"\
           - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
         for (age=agebase; age<=agelim; age++){           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  
           fprintf(ficrespl,"%.0f",age );   fprintf(fichtm,"\
           for(i=1; i<=nlstate;i++)   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
           fprintf(ficrespl," %.5f", prlim[i][i]);           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
           fprintf(ficrespl,"\n");   fprintf(fichtm,"\
         }   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
       }           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
     }   fprintf(fichtm,"\
   fclose(ficrespl);   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"t"),subdirf2(fileres,"t"));
   /*------------- h Pij x at various ages ------------*/   fprintf(fichtm,"\
     - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   if((ficrespij=fopen(filerespij,"w"))==NULL) {  
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;  /*  if(popforecast==1) fprintf(fichtm,"\n */
   }  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
   printf("Computing pij: result on file '%s' \n", filerespij);  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
    /*      <br>",fileres,fileres,fileres,fileres); */
   stepsize=(int) (stepm+YEARM-1)/YEARM;  /*  else  */
   /*if (stepm<=24) stepsize=2;*/  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
   agelim=AGESUP;   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   hstepm=stepsize*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */   m=cptcoveff;
     if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   k=0;  
   for(cptcov=1;cptcov<=i1;cptcov++){   jj1=0;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){   for(k1=1; k1<=m;k1++){
       k=k+1;     for(i1=1; i1<=ncodemax[k1];i1++){
         fprintf(ficrespij,"\n#****** ");       jj1++;
         for(j=1;j<=cptcoveff;j++)       if (cptcovn > 0) {
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
         fprintf(ficrespij,"******\n");         for (cpt=1; cpt<=cptcoveff;cpt++) 
                   fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */       }
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */       for(cpt=1; cpt<=nlstate;cpt++) {
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
           oldm=oldms;savm=savms;  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
           fprintf(ficrespij,"# Age");       }
           for(i=1; i<=nlstate;i++)       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
             for(j=1; j<=nlstate+ndeath;j++)  health expectancies in states (1) and (2): %s%d.png<br>\
               fprintf(ficrespij," %1d-%1d",i,j);  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
           fprintf(ficrespij,"\n");     } /* end i1 */
           for (h=0; h<=nhstepm; h++){   }/* End k1 */
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );   fprintf(fichtm,"</ul>");
             for(i=1; i<=nlstate;i++)   fflush(fichtm);
               for(j=1; j<=nlstate+ndeath;j++)  }
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);  
             fprintf(ficrespij,"\n");  /******************* Gnuplot file **************/
           }  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           fprintf(ficrespij,"\n");    char dirfileres[132],optfileres[132];
         }    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     }    int ng;
   }  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   fclose(ficrespij);  
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
   /*---------- Forecasting ------------------*/      /*#endif */
   if((stepm == 1) && (strcmp(model,".")==0)){    m=pow(2,cptcoveff);
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);  
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);    strcpy(dirfileres,optionfilefiname);
     free_matrix(mint,1,maxwav,1,n);    strcpy(optfileres,"vpl");
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);   /* 1eme*/
     free_vector(weight,1,n);}    for (cpt=1; cpt<= nlstate ; cpt ++) {
   else{     for (k1=1; k1<= m ; k1 ++) {
     erreur=108;       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
     printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model);       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
   }       fprintf(ficgp,"set xlabel \"Age\" \n\
    set ylabel \"Probability\" \n\
   set ter png small\n\
   /*---------- Health expectancies and variances ------------*/  set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   strcpy(filerest,"t");  
   strcat(filerest,fileres);       for (i=1; i<= nlstate ; i ++) {
   if((ficrest=fopen(filerest,"w"))==NULL) {         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;         else fprintf(ficgp," \%%*lf (\%%*lf)");
   }       }
   printf("Computing Total LEs with variances: file '%s' \n", filerest);       fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   strcpy(filerese,"e");         else fprintf(ficgp," \%%*lf (\%%*lf)");
   strcat(filerese,fileres);       } 
   if((ficreseij=fopen(filerese,"w"))==NULL) {       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);       for (i=1; i<= nlstate ; i ++) {
   }         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);         else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
  strcpy(fileresv,"v");       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
   strcat(fileresv,fileres);     }
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    }
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    /*2 eme*/
   }    
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
   k=0;      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
   for(cptcov=1;cptcov<=i1;cptcov++){      
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      for (i=1; i<= nlstate+1 ; i ++) {
       k=k+1;        k=2*i;
       fprintf(ficrest,"\n#****** ");        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       for(j=1;j<=cptcoveff;j++)        for (j=1; j<= nlstate+1 ; j ++) {
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       fprintf(ficrest,"******\n");          else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
       fprintf(ficreseij,"\n#****** ");        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
       for(j=1;j<=cptcoveff;j++)        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
       fprintf(ficreseij,"******\n");        for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       fprintf(ficresvij,"\n#****** ");          else fprintf(ficgp," \%%*lf (\%%*lf)");
       for(j=1;j<=cptcoveff;j++)        }   
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        fprintf(ficgp,"\" t\"\" w l 0,");
       fprintf(ficresvij,"******\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 ++) {
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
       oldm=oldms;savm=savms;          else fprintf(ficgp," \%%*lf (\%%*lf)");
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm);          }   
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
       oldm=oldms;savm=savms;        else fprintf(ficgp,"\" t\"\" w l 0,");
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);      }
        }
     
      /*3eme*/
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficrest,"\n");      for (cpt=1; cpt<= nlstate ; cpt ++) {
         k=2+nlstate*(2*cpt-2);
       epj=vector(1,nlstate+1);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
       for(age=bage; age <=fage ;age++){        fprintf(ficgp,"set ter png small\n\
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  set size 0.65,0.65\n\
         if (popbased==1) {  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);
           for(i=1; i<=nlstate;i++)        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
             prlim[i][i]=probs[(int)age][i][k];          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
         }          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
                  fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
         fprintf(ficrest," %4.0f",age);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           for(i=1, epj[j]=0.;i <=nlstate;i++) {          
             epj[j] += prlim[i][i]*eij[i][j][(int)age];        */
           }        for (i=1; i< nlstate ; i ++) {
           epj[nlstate+1] +=epj[j];          fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
         }          
         for(i=1, vepp=0.;i <=nlstate;i++)        } 
           for(j=1;j <=nlstate;j++)      }
             vepp += vareij[i][j][(int)age];    }
         fprintf(ficrest," %7.2f (%7.2f)", epj[nlstate+1],sqrt(vepp));    
         for(j=1;j <=nlstate;j++){    /* CV preval stable (period) */
           fprintf(ficrest," %7.2f (%7.2f)", epj[j],sqrt(vareij[j][j][(int)age]));    for (k1=1; k1<= m ; k1 ++) { 
         }      for (cpt=1; cpt<=nlstate ; cpt ++) {
         fprintf(ficrest,"\n");        k=3;
       }        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
     }        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   }  set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   fclose(ficreseij);  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
   fclose(ficresvij);        
   fclose(ficrest);        for (i=1; i< nlstate ; i ++)
   fclose(ficpar);          fprintf(ficgp,"+$%d",k+i+1);
   free_vector(epj,1,nlstate+1);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
          
   /*------- Variance limit prevalence------*/          l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
   strcpy(fileresvpl,"vpl");        for (i=1; i< nlstate ; i ++) {
   strcat(fileresvpl,fileres);          l=3+(nlstate+ndeath)*cpt;
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {          fprintf(ficgp,"+$%d",l+i+1);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);        }
     exit(0);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
   }      } 
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    }  
     
   k=0;    /* proba elementaires */
   for(cptcov=1;cptcov<=i1;cptcov++){    for(i=1,jk=1; i <=nlstate; i++){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      for(k=1; k <=(nlstate+ndeath); k++){
       k=k+1;        if (k != i) {
       fprintf(ficresvpl,"\n#****** ");          for(j=1; j <=ncovmodel; j++){
       for(j=1;j<=cptcoveff;j++)            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            jk++; 
       fprintf(ficresvpl,"******\n");            fprintf(ficgp,"\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);     }
     }  
  }     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
   fclose(ficresvpl);         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
   /*---------- End : free ----------------*/           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);         else
             fprintf(ficgp,"\nset title \"Probability\"\n");
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);         i=1;
           for(k2=1; k2<=nlstate; k2++) {
             k3=i;
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);           for(k=1; k<=(nlstate+ndeath); k++) {
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);             if (k != k2){
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);               if(ng==2)
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);                 fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                 else
   free_matrix(matcov,1,npar,1,npar);                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
   free_vector(delti,1,npar);               ij=1;
   free_matrix(agev,1,maxwav,1,imx);               for(j=3; j <=ncovmodel; j++) {
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   if(erreur >0)                   ij++;
     printf("End of Imach with error or warning %d\n",erreur);                 }
   else   printf("End of Imach\n");                 else
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                 }
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/               fprintf(ficgp,")/(1");
   /*printf("Total time was %d uSec.\n", total_usecs);*/               
   /*------ End -----------*/               for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
  end:                 for(j=3; j <=ncovmodel; j++){
 #ifdef windows                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   /* chdir(pathcd);*/                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
 #endif                     ij++;
  /*system("wgnuplot graph.plt");*/                   }
  /*system("../gp37mgw/wgnuplot graph.plt");*/                   else
  /*system("cd ../gp37mgw");*/                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/                 }
  strcpy(plotcmd,GNUPLOTPROGRAM);                 fprintf(ficgp,")");
  strcat(plotcmd," ");               }
  strcat(plotcmd,optionfilegnuplot);               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
  system(plotcmd);               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
 #ifdef windows             }
   while (z[0] != 'q') {           } /* end k */
     /* chdir(path); */         } /* end k2 */
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");       } /* end jk */
     scanf("%s",z);     } /* end ng */
     if (z[0] == 'c') system("./imach");     fflush(ficgp); 
     else if (z[0] == 'e') system(optionfilehtm);  }  /* end gnuplot */
     else if (z[0] == 'g') system(plotcmd);  
     else if (z[0] == 'q') exit(0);  
   }  /*************** Moving average **************/
 #endif  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
 }  
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE]; 
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   
     char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char strstart[80], *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: ");
     fprintf(ficlog,"pathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
    
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     /* Read guess parameters */
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++){
       j=0;
       for(jj=1; jj <=nlstate+ndeath; jj++){
         if(jj==i) continue;
         j++;
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1 != i) && (j1 != j)){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);
         }
         fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)
           printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);
           if(mle==1){
             printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);
           }
           else
             fprintf(ficlog," %lf",param[i][j][k]);
           fprintf(ficparo," %lf",param[i][j][k]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     }  
     fflush(ficlog);
   
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1-i)*(j1-j)!=0){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);
         }
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         fprintf(ficlog,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);
           fprintf(ficlog," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
         fprintf(ficlog,"\n");
       }
     }
     fflush(ficlog);
   
     delti=delti3[1][1];
   
   
     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);
       if(mle==1)
         printf("%s",str);
       fprintf(ficlog,"%s",str);
       fprintf(ficparo,"%s",str);
       for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
           printf(" %.5le",matcov[i][j]);
         }
         fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       numlinepar++;
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
     for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];
      
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
   
     fflush(ficlog);
   
     /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         lstra=strlen(stra);
         if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
           stratrunc = &(stra[lstra-9]);
           num[i]=atol(stratrunc);
         }
         else
           num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);
     printf("\n");
     globpr=1; /* to print the contributions */
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);
     printf("\n");
     if(mle>=1){ /* Could be 1 or 2 */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
       
     /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           printf("%d%d ",i,k);
           fprintf(ficlog,"%d%d ",i,k);
           fprintf(ficres,"%1d%1d ",i,k);
           for(j=1; j <=ncovmodel; j++){
             printf("%f ",p[jk]);
             fprintf(ficlog,"%f ",p[jk]);
             fprintf(ficres,"%f ",p[jk]);
             jk++; 
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
     if(mle!=0){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);
             jk++;
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle>=1)
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
   
   
   /* Just to have a covariance matrix which will be more understandable
      even is we still don't want to manage dictionary of variables
   */
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               if(mle>=1)
                 printf("#%1d%1d%d",i,j,k);
               fprintf(ficlog,"#%1d%1d%d",i,j,k);
               fprintf(ficres,"#%1d%1d%d",i,j,k);
             }else{
               if(mle>=1)
                 printf("%1d%1d%d",i,j,k);
               fprintf(ficlog,"%1d%1d%d",i,j,k);
               fprintf(ficres,"%1d%1d%d",i,j,k);
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         if(mle>=1)
                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         if(mle>=1)
                           printf(" %.5e",matcov[jj][ll]); 
                         fprintf(ficlog," %.5e",matcov[jj][ll]); 
                         fprintf(ficres," %.5e",matcov[jj][ll]); 
                       }
                     }else{
                       if(itimes==1){
                         if(mle>=1)
                           printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         if(mle>=1)
                           printf(" %.5e",matcov[jj][ll]); 
                         fprintf(ficlog," %.5e",matcov[jj][ll]); 
                         fprintf(ficres," %.5e",matcov[jj][ll]); 
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             if(mle>=1)
               printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
     fflush(ficlog);
     fflush(ficres);
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
   
     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   
     replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     /*  chdir(path); */
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_lvector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     for(i=1;i<=AGESUP;i++)
       for(j=1;j<=NCOVMAX;j++)
         for(k=1;k<=NCOVMAX;k++)
           probs[i][j][k]=0.;
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
   /*      }  */
   /*      else{ */
   /*        erreur=108; */
   /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*      } */
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocaltime at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
     fclose(fichtm);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
     chdir(path);
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     if((outcmd=system(plotcmd)) != 0){
       printf(" Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   
Removed from v.1.37  
changed lines
  Added in v.1.96

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