Diff for /imach/src/imach.c between versions 1.48 and 1.96

version 1.48, 2002/06/10 13:12:49 version 1.96, 2003/07/15 15:38:55
Line 1 Line 1
 /* $Id$  /* $Id$
    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
   probability 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 "gnuplot"    (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  
 #ifdef windows  */
 #define DIRSEPARATOR '\\'  /*
 #else     Interpolated Markov Chain
 #define DIRSEPARATOR '/'  
 #endif    Short summary of the programme:
     
 char version[80]="Imach version 0.8h, May 2002, INED-EUROREVES ";    This program computes Healthy Life Expectancies from
 int erreur; /* Error number */    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 int nvar;    first survey ("cross") where individuals from different ages are
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    interviewed on their health status or degree of disability (in the
 int npar=NPARMAX;    case of a health survey which is our main interest) -2- at least a
 int nlstate=2; /* Number of live states */    second wave of interviews ("longitudinal") which measure each change
 int ndeath=1; /* Number of dead states */    (if any) in individual health status.  Health expectancies are
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    computed from the time spent in each health state according to a
 int popbased=0;    model. More health states you consider, more time is necessary to reach the
     Maximum Likelihood of the parameters involved in the model.  The
 int *wav; /* Number of waves for this individuual 0 is possible */    simplest model is the multinomial logistic model where pij is the
 int maxwav; /* Maxim number of waves */    probability to be observed in state j at the second wave
 int jmin, jmax; /* min, max spacing between 2 waves */    conditional to be observed in state i at the first wave. Therefore
 int mle, weightopt;    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    'age' is age and 'sex' is a covariate. If you want to have a more
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    complex model than "constant and age", you should modify the program
 double jmean; /* Mean space between 2 waves */    where the markup *Covariates have to be included here again* invites
 double **oldm, **newm, **savm; /* Working pointers to matrices */    you to do it.  More covariates you add, slower the
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    convergence.
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;    The advantage of this computer programme, compared to a simple
 FILE *fichtm; /* Html File */    multinomial logistic model, is clear when the delay between waves is not
 FILE *ficreseij;    identical for each individual. Also, if a individual missed an
 char filerese[FILENAMELENGTH];    intermediate interview, the information is lost, but taken into
 FILE  *ficresvij;    account using an interpolation or extrapolation.  
 char fileresv[FILENAMELENGTH];  
 FILE  *ficresvpl;    hPijx is the probability to be observed in state i at age x+h
 char fileresvpl[FILENAMELENGTH];    conditional to the observed state i at age x. The delay 'h' can be
 char title[MAXLINE];    split into an exact number (nh*stepm) of unobserved intermediate
 char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    states. This elementary transition (by month, quarter,
 char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    semester or year) is modelled as a multinomial logistic.  The hPx
     matrix is simply the matrix product of nh*stepm elementary matrices
 char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];    and the contribution of each individual to the likelihood is simply
     hPijx.
 char filerest[FILENAMELENGTH];  
 char fileregp[FILENAMELENGTH];    Also this programme outputs the covariance matrix of the parameters but also
 char popfile[FILENAMELENGTH];    of the life expectancies. It also computes the stable prevalence. 
     
 char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
              Institut national d'études démographiques, Paris.
 #define NR_END 1    This software have been partly granted by Euro-REVES, a concerted action
 #define FREE_ARG char*    from the European Union.
 #define FTOL 1.0e-10    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
 #define NRANSI    can be accessed at http://euroreves.ined.fr/imach .
 #define ITMAX 200  
     Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 #define TOL 2.0e-4    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
     
 #define CGOLD 0.3819660    **********************************************************************/
 #define ZEPS 1.0e-10  /*
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    main
     read parameterfile
 #define GOLD 1.618034    read datafile
 #define GLIMIT 100.0    concatwav
 #define TINY 1.0e-20    freqsummary
     if (mle >= 1)
 static double maxarg1,maxarg2;      mlikeli
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    print results files
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    if mle==1 
         computes hessian
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    read end of parameter file: agemin, agemax, bage, fage, estepm
 #define rint(a) floor(a+0.5)        begin-prev-date,...
     open gnuplot file
 static double sqrarg;    open html file
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    stable prevalence
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}     for age prevalim()
     h Pij x
 int imx;    variance of p varprob
 int stepm;    forecasting if prevfcast==1 prevforecast call prevalence()
 /* Stepm, step in month: minimum step interpolation*/    health expectancies
     Variance-covariance of DFLE
 int estepm;    prevalence()
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/     movingaverage()
     varevsij() 
 int m,nb;    if popbased==1 varevsij(,popbased)
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    total life expectancies
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Variance of stable prevalence
 double **pmmij, ***probs, ***mobaverage;   end
 double dateintmean=0;  */
   
 double *weight;  
 int **s; /* Status */  
 double *agedc, **covar, idx;   
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  #include <math.h>
   #include <stdio.h>
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  #include <stdlib.h>
 double ftolhess; /* Tolerance for computing hessian */  #include <unistd.h>
   
 /**************** split *************************/  #include <sys/time.h>
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  #include <time.h>
 {  #include "timeval.h"
    char *s;                             /* pointer */  
    int  l1, l2;                         /* length counters */  /* #include <libintl.h> */
   /* #define _(String) gettext (String) */
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  #define MAXLINE 256
    s = strrchr( path,  DIRSEPARATOR );          /* find last / */  #define GNUPLOTPROGRAM "gnuplot"
    if ( s == NULL ) {                   /* no directory, so use current */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 #if     defined(__bsd__)                /* get current working directory */  #define FILENAMELENGTH 132
       extern char       *getwd( );  /*#define DEBUG*/
   /*#define windows*/
       if ( getwd( dirc ) == NULL ) {  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 #else  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
       extern char       *getcwd( );  
   #define MAXPARM 30 /* Maximum number of parameters for the optimization */
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 #endif  
          return( GLOCK_ERROR_GETCWD );  #define NINTERVMAX 8
       }  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
       strcpy( name, path );             /* we've got it */  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
    } else {                             /* strip direcotry from path */  #define NCOVMAX 8 /* Maximum number of covariates */
       s++;                              /* after this, the filename */  #define MAXN 20000
       l2 = strlen( s );                 /* length of filename */  #define YEARM 12. /* Number of months per year */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  #define AGESUP 130
       strcpy( name, s );                /* save file name */  #define AGEBASE 40
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  #ifdef unix
       dirc[l1-l2] = 0;                  /* add zero */  #define DIRSEPARATOR '/'
    }  #define ODIRSEPARATOR '\\'
    l1 = strlen( dirc );                 /* length of directory */  #else
 #ifdef windows  #define DIRSEPARATOR '\\'
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  #define ODIRSEPARATOR '/'
 #else  #endif
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  
 #endif  /* $Id$ */
    s = strrchr( name, '.' );            /* find last / */  /* $State$ */
    s++;  
    strcpy(ext,s);                       /* save extension */  char version[]="Imach version 0.96c, July 2003, INED-EUROREVES ";
    l1= strlen( name);  char fullversion[]="$Revision$ $Date$"; 
    l2= strlen( s)+1;  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
    strncpy( finame, name, l1-l2);  int nvar;
    finame[l1-l2]= 0;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
    return( 0 );                         /* we're done */  int npar=NPARMAX;
 }  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;
   
 void replace(char *s, char*t)  int *wav; /* Number of waves for this individuual 0 is possible */
 {  int maxwav; /* Maxim number of waves */
   int i;  int jmin, jmax; /* min, max spacing between 2 waves */
   int lg=20;  int gipmx, gsw; /* Global variables on the number of contributions 
   i=0;                     to the likelihood and the sum of weights (done by funcone)*/
   lg=strlen(t);  int mle, weightopt;
   for(i=0; i<= lg; i++) {  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
     (s[i] = t[i]);  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
     if (t[i]== '\\') s[i]='/';  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 */
   double **oldm, **newm, **savm; /* Working pointers to matrices */
 int nbocc(char *s, char occ)  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 {  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   int i,j=0;  FILE *ficlog, *ficrespow;
   int lg=20;  int globpr; /* Global variable for printing or not */
   i=0;  double fretone; /* Only one call to likelihood */
   lg=strlen(s);  long ipmx; /* Number of contributions */
   for(i=0; i<= lg; i++) {  double sw; /* Sum of weights */
   if  (s[i] == occ ) j++;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   }  FILE *ficresilk;
   return j;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 }  FILE *ficresprobmorprev;
   FILE *fichtm, *fichtmcov; /* Html File */
 void cutv(char *u,char *v, char*t, char occ)  FILE *ficreseij;
 {  char filerese[FILENAMELENGTH];
   int i,lg,j,p=0;  FILE  *ficresvij;
   i=0;  char fileresv[FILENAMELENGTH];
   for(j=0; j<=strlen(t)-1; j++) {  FILE  *ficresvpl;
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  char fileresvpl[FILENAMELENGTH];
   }  char title[MAXLINE];
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   lg=strlen(t);  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   for(j=0; j<p; j++) {  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
     (u[j] = t[j]);  char command[FILENAMELENGTH];
   }  int  outcmd=0;
      u[p]='\0';  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);  char filelog[FILENAMELENGTH]; /* Log file */
   }  char filerest[FILENAMELENGTH];
 }  char fileregp[FILENAMELENGTH];
   char popfile[FILENAMELENGTH];
 /********************** nrerror ********************/  
   char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 void nrerror(char error_text[])  
 {  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   fprintf(stderr,"ERREUR ...\n");  struct timezone tzp;
   fprintf(stderr,"%s\n",error_text);  extern int gettimeofday();
   exit(1);  struct tm tmg, tm, tmf, *gmtime(), *localtime();
 }  long time_value;
 /*********************** vector *******************/  extern long time();
 double *vector(int nl, int nh)  char strcurr[80], strfor[80];
 {  
   double *v;  #define NR_END 1
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  #define FREE_ARG char*
   if (!v) nrerror("allocation failure in vector");  #define FTOL 1.0e-10
   return v-nl+NR_END;  
 }  #define NRANSI 
   #define ITMAX 200 
 /************************ free vector ******************/  
 void free_vector(double*v, int nl, int nh)  #define TOL 2.0e-4 
 {  
   free((FREE_ARG)(v+nl-NR_END));  #define CGOLD 0.3819660 
 }  #define ZEPS 1.0e-10 
   #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 /************************ivector *******************************/  
 int *ivector(long nl,long nh)  #define GOLD 1.618034 
 {  #define GLIMIT 100.0 
   int *v;  #define TINY 1.0e-20 
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");  static double maxarg1,maxarg2;
   return v-nl+NR_END;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 }  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     
 /******************free ivector **************************/  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
 void free_ivector(int *v, long nl, long nh)  #define rint(a) floor(a+0.5)
 {  
   free((FREE_ARG)(v+nl-NR_END));  static double sqrarg;
 }  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 /******************* imatrix *******************************/  
 int **imatrix(long nrl, long nrh, long ncl, long nch)  int imx; 
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  int stepm;
 {  /* Stepm, step in month: minimum step interpolation*/
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;  int estepm;
    /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  int m,nb;
   if (!m) nrerror("allocation failure 1 in matrix()");  long *num;
   m += NR_END;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
   m -= nrl;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
    double **pmmij, ***probs;
    double dateintmean=0;
   /* allocate rows and set pointers to them */  
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  double *weight;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int **s; /* Status */
   m[nrl] += NR_END;  double *agedc, **covar, idx;
   m[nrl] -= ncl;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
    
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
    double ftolhess; /* Tolerance for computing hessian */
   /* return pointer to array of pointers to rows */  
   return m;  /**************** split *************************/
 }  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   {
 /****************** free_imatrix *************************/    char  *ss;                            /* pointer */
 void free_imatrix(m,nrl,nrh,ncl,nch)    int   l1, l2;                         /* length counters */
       int **m;  
       long nch,ncl,nrh,nrl;    l1 = strlen(path );                   /* length of path */
      /* free an int matrix allocated by imatrix() */    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
 {    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    if ( ss == NULL ) {                   /* no directory, so use current */
   free((FREE_ARG) (m+nrl-NR_END));      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 }        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       /* get current working directory */
 /******************* matrix *******************************/      /*    extern  char* getcwd ( char *buf , int len);*/
 double **matrix(long nrl, long nrh, long ncl, long nch)      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 {        return( GLOCK_ERROR_GETCWD );
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;      }
   double **m;      strcpy( name, path );               /* we've got it */
     } else {                              /* strip direcotry from path */
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));      ss++;                               /* after this, the filename */
   if (!m) nrerror("allocation failure 1 in matrix()");      l2 = strlen( ss );                  /* length of filename */
   m += NR_END;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   m -= nrl;      strcpy( name, ss );         /* save file name */
       strncpy( dirc, path, l1 - l2 );     /* now the directory */
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));      dirc[l1-l2] = 0;                    /* add zero */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    }
   m[nrl] += NR_END;    l1 = strlen( dirc );                  /* length of directory */
   m[nrl] -= ncl;    /*#ifdef windows
     if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #else
   return m;    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
 }  #endif
     */
 /*************************free matrix ************************/    ss = strrchr( name, '.' );            /* find last / */
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    ss++;
 {    strcpy(ext,ss);                       /* save extension */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    l1= strlen( name);
   free((FREE_ARG)(m+nrl-NR_END));    l2= strlen(ss)+1;
 }    strncpy( finame, name, l1-l2);
     finame[l1-l2]= 0;
 /******************* ma3x *******************************/    return( 0 );                          /* we're done */
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  }
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;  /******************************************/
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  void replace_back_to_slash(char *s, char*t)
   if (!m) nrerror("allocation failure 1 in matrix()");  {
   m += NR_END;    int i;
   m -= nrl;    int lg=0;
     i=0;
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    lg=strlen(t);
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    for(i=0; i<= lg; i++) {
   m[nrl] += NR_END;      (s[i] = t[i]);
   m[nrl] -= ncl;      if (t[i]== '\\') s[i]='/';
     }
   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)));  int nbocc(char *s, char occ)
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  {
   m[nrl][ncl] += NR_END;    int i,j=0;
   m[nrl][ncl] -= nll;    int lg=20;
   for (j=ncl+1; j<=nch; j++)    i=0;
     m[nrl][j]=m[nrl][j-1]+nlay;    lg=strlen(s);
      for(i=0; i<= lg; i++) {
   for (i=nrl+1; i<=nrh; i++) {    if  (s[i] == occ ) j++;
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    }
     for (j=ncl+1; j<=nch; j++)    return j;
       m[i][j]=m[i][j-1]+nlay;  }
   }  
   return m;  void cutv(char *u,char *v, char*t, char occ)
 }  {
     /* cuts string t into u and v where u is ended by char occ excluding it
 /*************************free ma3x ************************/       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)       gives u="abcedf" and v="ghi2j" */
 {    int i,lg,j,p=0;
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    i=0;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    for(j=0; j<=strlen(t)-1; j++) {
   free((FREE_ARG)(m+nrl-NR_END));      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 }    }
   
 /***************** f1dim *************************/    lg=strlen(t);
 extern int ncom;    for(j=0; j<p; j++) {
 extern double *pcom,*xicom;      (u[j] = t[j]);
 extern double (*nrfunc)(double []);    }
         u[p]='\0';
 double f1dim(double x)  
 {     for(j=0; j<= lg; j++) {
   int j;      if (j>=(p+1))(v[j-p-1] = t[j]);
   double f;    }
   double *xt;  }
    
   xt=vector(1,ncom);  /********************** nrerror ********************/
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  
   f=(*nrfunc)(xt);  void nrerror(char error_text[])
   free_vector(xt,1,ncom);  {
   return f;    fprintf(stderr,"ERREUR ...\n");
 }    fprintf(stderr,"%s\n",error_text);
     exit(EXIT_FAILURE);
 /*****************brent *************************/  }
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  /*********************** vector *******************/
 {  double *vector(int nl, int nh)
   int iter;  {
   double a,b,d,etemp;    double *v;
   double fu,fv,fw,fx;    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   double ftemp;    if (!v) nrerror("allocation failure in vector");
   double p,q,r,tol1,tol2,u,v,w,x,xm;    return v-nl+NR_END;
   double e=0.0;  }
    
   a=(ax < cx ? ax : cx);  /************************ free vector ******************/
   b=(ax > cx ? ax : cx);  void free_vector(double*v, int nl, int nh)
   x=w=v=bx;  {
   fw=fv=fx=(*f)(x);    free((FREE_ARG)(v+nl-NR_END));
   for (iter=1;iter<=ITMAX;iter++) {  }
     xm=0.5*(a+b);  
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  /************************ivector *******************************/
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  int *ivector(long nl,long nh)
     printf(".");fflush(stdout);  {
 #ifdef DEBUG    int *v;
     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);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    if (!v) nrerror("allocation failure in ivector");
 #endif    return v-nl+NR_END;
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  }
       *xmin=x;  
       return fx;  /******************free ivector **************************/
     }  void free_ivector(int *v, long nl, long nh)
     ftemp=fu;  {
     if (fabs(e) > tol1) {    free((FREE_ARG)(v+nl-NR_END));
       r=(x-w)*(fx-fv);  }
       q=(x-v)*(fx-fw);  
       p=(x-v)*q-(x-w)*r;  /************************lvector *******************************/
       q=2.0*(q-r);  long *lvector(long nl,long nh)
       if (q > 0.0) p = -p;  {
       q=fabs(q);    long *v;
       etemp=e;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       e=d;    if (!v) nrerror("allocation failure in ivector");
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    return v-nl+NR_END;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  }
       else {  
         d=p/q;  /******************free lvector **************************/
         u=x+d;  void free_lvector(long *v, long nl, long nh)
         if (u-a < tol2 || b-u < tol2)  {
           d=SIGN(tol1,xm-x);    free((FREE_ARG)(v+nl-NR_END));
       }  }
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  /******************* imatrix *******************************/
     }  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
     fu=(*f)(u);  { 
     if (fu <= fx) {    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       if (u >= x) a=x; else b=x;    int **m; 
       SHFT(v,w,x,u)    
         SHFT(fv,fw,fx,fu)    /* allocate pointers to rows */ 
         } else {    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
           if (u < x) a=u; else b=u;    if (!m) nrerror("allocation failure 1 in matrix()"); 
           if (fu <= fw || w == x) {    m += NR_END; 
             v=w;    m -= nrl; 
             w=u;    
             fv=fw;    
             fw=fu;    /* allocate rows and set pointers to them */ 
           } else if (fu <= fv || v == x || v == w) {    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
             v=u;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
             fv=fu;    m[nrl] += NR_END; 
           }    m[nrl] -= ncl; 
         }    
   }    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
   nrerror("Too many iterations in brent");    
   *xmin=x;    /* return pointer to array of pointers to rows */ 
   return fx;    return m; 
 }  } 
   
 /****************** mnbrak ***********************/  /****************** free_imatrix *************************/
   void free_imatrix(m,nrl,nrh,ncl,nch)
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,        int **m;
             double (*func)(double))        long nch,ncl,nrh,nrl; 
 {       /* free an int matrix allocated by imatrix() */ 
   double ulim,u,r,q, dum;  { 
   double fu;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
      free((FREE_ARG) (m+nrl-NR_END)); 
   *fa=(*func)(*ax);  } 
   *fb=(*func)(*bx);  
   if (*fb > *fa) {  /******************* matrix *******************************/
     SHFT(dum,*ax,*bx,dum)  double **matrix(long nrl, long nrh, long ncl, long nch)
       SHFT(dum,*fb,*fa,dum)  {
       }    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   *cx=(*bx)+GOLD*(*bx-*ax);    double **m;
   *fc=(*func)(*cx);  
   while (*fb > *fc) {    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     r=(*bx-*ax)*(*fb-*fc);    if (!m) nrerror("allocation failure 1 in matrix()");
     q=(*bx-*cx)*(*fb-*fa);    m += NR_END;
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    m -= nrl;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  
     ulim=(*bx)+GLIMIT*(*cx-*bx);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if ((*bx-u)*(u-*cx) > 0.0) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       fu=(*func)(u);    m[nrl] += NR_END;
     } else if ((*cx-u)*(u-ulim) > 0.0) {    m[nrl] -= ncl;
       fu=(*func)(u);  
       if (fu < *fc) {    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    return m;
           SHFT(*fb,*fc,fu,(*func)(u))    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
           }     */
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  }
       u=ulim;  
       fu=(*func)(u);  /*************************free matrix ************************/
     } else {  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       u=(*cx)+GOLD*(*cx-*bx);  {
       fu=(*func)(u);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     }    free((FREE_ARG)(m+nrl-NR_END));
     SHFT(*ax,*bx,*cx,u)  }
       SHFT(*fa,*fb,*fc,fu)  
       }  /******************* ma3x *******************************/
 }  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   {
 /*************** linmin ************************/    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     double ***m;
 int ncom;  
 double *pcom,*xicom;    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 double (*nrfunc)(double []);    if (!m) nrerror("allocation failure 1 in matrix()");
      m += NR_END;
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    m -= nrl;
 {  
   double brent(double ax, double bx, double cx,    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
                double (*f)(double), double tol, double *xmin);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   double f1dim(double x);    m[nrl] += NR_END;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    m[nrl] -= ncl;
               double *fc, double (*func)(double));  
   int j;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   double xx,xmin,bx,ax;  
   double fx,fb,fa;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
      if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   ncom=n;    m[nrl][ncl] += NR_END;
   pcom=vector(1,n);    m[nrl][ncl] -= nll;
   xicom=vector(1,n);    for (j=ncl+1; j<=nch; j++) 
   nrfunc=func;      m[nrl][j]=m[nrl][j-1]+nlay;
   for (j=1;j<=n;j++) {    
     pcom[j]=p[j];    for (i=nrl+1; i<=nrh; i++) {
     xicom[j]=xi[j];      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
   }      for (j=ncl+1; j<=nch; j++) 
   ax=0.0;        m[i][j]=m[i][j-1]+nlay;
   xx=1.0;    }
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    return m; 
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
 #ifdef DEBUG             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    */
 #endif  }
   for (j=1;j<=n;j++) {  
     xi[j] *= xmin;  /*************************free ma3x ************************/
     p[j] += xi[j];  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   }  {
   free_vector(xicom,1,n);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   free_vector(pcom,1,n);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
 }    free((FREE_ARG)(m+nrl-NR_END));
   }
 /*************** powell ************************/  
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  /*************** function subdirf ***********/
             double (*func)(double []))  char *subdirf(char fileres[])
 {  {
   void linmin(double p[], double xi[], int n, double *fret,    /* Caution optionfilefiname is hidden */
               double (*func)(double []));    strcpy(tmpout,optionfilefiname);
   int i,ibig,j;    strcat(tmpout,"/"); /* Add to the right */
   double del,t,*pt,*ptt,*xit;    strcat(tmpout,fileres);
   double fp,fptt;    return tmpout;
   double *xits;  }
   pt=vector(1,n);  
   ptt=vector(1,n);  /*************** function subdirf2 ***********/
   xit=vector(1,n);  char *subdirf2(char fileres[], char *preop)
   xits=vector(1,n);  {
   *fret=(*func)(p);    
   for (j=1;j<=n;j++) pt[j]=p[j];    /* Caution optionfilefiname is hidden */
   for (*iter=1;;++(*iter)) {    strcpy(tmpout,optionfilefiname);
     fp=(*fret);    strcat(tmpout,"/");
     ibig=0;    strcat(tmpout,preop);
     del=0.0;    strcat(tmpout,fileres);
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    return tmpout;
     for (i=1;i<=n;i++)  }
       printf(" %d %.12f",i, p[i]);  
     printf("\n");  /*************** function subdirf3 ***********/
     for (i=1;i<=n;i++) {  char *subdirf3(char fileres[], char *preop, char *preop2)
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  {
       fptt=(*fret);    
 #ifdef DEBUG    /* Caution optionfilefiname is hidden */
       printf("fret=%lf \n",*fret);    strcpy(tmpout,optionfilefiname);
 #endif    strcat(tmpout,"/");
       printf("%d",i);fflush(stdout);    strcat(tmpout,preop);
       linmin(p,xit,n,fret,func);    strcat(tmpout,preop2);
       if (fabs(fptt-(*fret)) > del) {    strcat(tmpout,fileres);
         del=fabs(fptt-(*fret));    return tmpout;
         ibig=i;  }
       }  
 #ifdef DEBUG  /***************** f1dim *************************/
       printf("%d %.12e",i,(*fret));  extern int ncom; 
       for (j=1;j<=n;j++) {  extern double *pcom,*xicom;
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  extern double (*nrfunc)(double []); 
         printf(" x(%d)=%.12e",j,xit[j]);   
       }  double f1dim(double x) 
       for(j=1;j<=n;j++)  { 
         printf(" p=%.12e",p[j]);    int j; 
       printf("\n");    double f;
 #endif    double *xt; 
     }   
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    xt=vector(1,ncom); 
 #ifdef DEBUG    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
       int k[2],l;    f=(*nrfunc)(xt); 
       k[0]=1;    free_vector(xt,1,ncom); 
       k[1]=-1;    return f; 
       printf("Max: %.12e",(*func)(p));  } 
       for (j=1;j<=n;j++)  
         printf(" %.12e",p[j]);  /*****************brent *************************/
       printf("\n");  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
       for(l=0;l<=1;l++) {  { 
         for (j=1;j<=n;j++) {    int iter; 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    double a,b,d,etemp;
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    double fu,fv,fw,fx;
         }    double ftemp;
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       }    double e=0.0; 
 #endif   
     a=(ax < cx ? ax : cx); 
     b=(ax > cx ? ax : cx); 
       free_vector(xit,1,n);    x=w=v=bx; 
       free_vector(xits,1,n);    fw=fv=fx=(*f)(x); 
       free_vector(ptt,1,n);    for (iter=1;iter<=ITMAX;iter++) { 
       free_vector(pt,1,n);      xm=0.5*(a+b); 
       return;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     }      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");      printf(".");fflush(stdout);
     for (j=1;j<=n;j++) {      fprintf(ficlog,".");fflush(ficlog);
       ptt[j]=2.0*p[j]-pt[j];  #ifdef DEBUG
       xit[j]=p[j]-pt[j];      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);
       pt[j]=p[j];      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     }      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     fptt=(*func)(ptt);  #endif
     if (fptt < fp) {      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);        *xmin=x; 
       if (t < 0.0) {        return fx; 
         linmin(p,xit,n,fret,func);      } 
         for (j=1;j<=n;j++) {      ftemp=fu;
           xi[j][ibig]=xi[j][n];      if (fabs(e) > tol1) { 
           xi[j][n]=xit[j];        r=(x-w)*(fx-fv); 
         }        q=(x-v)*(fx-fw); 
 #ifdef DEBUG        p=(x-v)*q-(x-w)*r; 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);        q=2.0*(q-r); 
         for(j=1;j<=n;j++)        if (q > 0.0) p = -p; 
           printf(" %.12e",xit[j]);        q=fabs(q); 
         printf("\n");        etemp=e; 
 #endif        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)); 
   }        else { 
 }          d=p/q; 
           u=x+d; 
 /**** Prevalence limit ****************/          if (u-a < tol2 || b-u < tol2) 
             d=SIGN(tol1,xm-x); 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)        } 
 {      } else { 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
      matrix by transitions matrix until convergence is reached */      } 
       u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   int i, ii,j,k;      fu=(*f)(u); 
   double min, max, maxmin, maxmax,sumnew=0.;      if (fu <= fx) { 
   double **matprod2();        if (u >= x) a=x; else b=x; 
   double **out, cov[NCOVMAX], **pmij();        SHFT(v,w,x,u) 
   double **newm;          SHFT(fv,fw,fx,fu) 
   double agefin, delaymax=50 ; /* Max number of years to converge */          } else { 
             if (u < x) a=u; else b=u; 
   for (ii=1;ii<=nlstate+ndeath;ii++)            if (fu <= fw || w == x) { 
     for (j=1;j<=nlstate+ndeath;j++){              v=w; 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);              w=u; 
     }              fv=fw; 
               fw=fu; 
    cov[1]=1.;            } else if (fu <= fv || v == x || v == w) { 
                v=u; 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */              fv=fu; 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){            } 
     newm=savm;          } 
     /* Covariates have to be included here again */    } 
      cov[2]=agefin;    nrerror("Too many iterations in brent"); 
      *xmin=x; 
       for (k=1; k<=cptcovn;k++) {    return fx; 
         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]]);*/  
       }  /****************** mnbrak ***********************/
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  
       for (k=1; k<=cptcovprod;k++)  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];              double (*func)(double)) 
   { 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    double ulim,u,r,q, dum;
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    double fu; 
       /*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);    *fa=(*func)(*ax); 
     *fb=(*func)(*bx); 
     savm=oldm;    if (*fb > *fa) { 
     oldm=newm;      SHFT(dum,*ax,*bx,dum) 
     maxmax=0.;        SHFT(dum,*fb,*fa,dum) 
     for(j=1;j<=nlstate;j++){        } 
       min=1.;    *cx=(*bx)+GOLD*(*bx-*ax); 
       max=0.;    *fc=(*func)(*cx); 
       for(i=1; i<=nlstate; i++) {    while (*fb > *fc) { 
         sumnew=0;      r=(*bx-*ax)*(*fb-*fc); 
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];      q=(*bx-*cx)*(*fb-*fa); 
         prlim[i][j]= newm[i][j]/(1-sumnew);      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         max=FMAX(max,prlim[i][j]);        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
         min=FMIN(min,prlim[i][j]);      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       }      if ((*bx-u)*(u-*cx) > 0.0) { 
       maxmin=max-min;        fu=(*func)(u); 
       maxmax=FMAX(maxmax,maxmin);      } else if ((*cx-u)*(u-ulim) > 0.0) { 
     }        fu=(*func)(u); 
     if(maxmax < ftolpl){        if (fu < *fc) { 
       return prlim;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
     }            SHFT(*fb,*fc,fu,(*func)(u)) 
   }            } 
 }      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
         u=ulim; 
 /*************** transition probabilities ***************/        fu=(*func)(u); 
       } else { 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )        u=(*cx)+GOLD*(*cx-*bx); 
 {        fu=(*func)(u); 
   double s1, s2;      } 
   /*double t34;*/      SHFT(*ax,*bx,*cx,u) 
   int i,j,j1, nc, ii, jj;        SHFT(*fa,*fb,*fc,fu) 
         } 
     for(i=1; i<= nlstate; i++){  } 
     for(j=1; j<i;j++){  
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  /*************** linmin ************************/
         /*s2 += param[i][j][nc]*cov[nc];*/  
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  int ncom; 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  double *pcom,*xicom;
       }  double (*nrfunc)(double []); 
       ps[i][j]=s2;   
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
     }  { 
     for(j=i+1; j<=nlstate+ndeath;j++){    double brent(double ax, double bx, double cx, 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){                 double (*f)(double), double tol, double *xmin); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    double f1dim(double x); 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       }                double *fc, double (*func)(double)); 
       ps[i][j]=s2;    int j; 
     }    double xx,xmin,bx,ax; 
   }    double fx,fb,fa;
     /*ps[3][2]=1;*/   
     ncom=n; 
   for(i=1; i<= nlstate; i++){    pcom=vector(1,n); 
      s1=0;    xicom=vector(1,n); 
     for(j=1; j<i; j++)    nrfunc=func; 
       s1+=exp(ps[i][j]);    for (j=1;j<=n;j++) { 
     for(j=i+1; j<=nlstate+ndeath; j++)      pcom[j]=p[j]; 
       s1+=exp(ps[i][j]);      xicom[j]=xi[j]; 
     ps[i][i]=1./(s1+1.);    } 
     for(j=1; j<i; j++)    ax=0.0; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    xx=1.0; 
     for(j=i+1; j<=nlstate+ndeath; j++)    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  #ifdef DEBUG
   } /* end i */    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  #endif
     for(jj=1; jj<= nlstate+ndeath; jj++){    for (j=1;j<=n;j++) { 
       ps[ii][jj]=0;      xi[j] *= xmin; 
       ps[ii][ii]=1;      p[j] += xi[j]; 
     }    } 
   }    free_vector(xicom,1,n); 
     free_vector(pcom,1,n); 
   } 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){  char *asc_diff_time(long time_sec, char ascdiff[])
      printf("%lf ",ps[ii][jj]);  {
    }    long sec_left, days, hours, minutes;
     printf("\n ");    days = (time_sec) / (60*60*24);
     }    sec_left = (time_sec) % (60*60*24);
     printf("\n ");printf("%lf ",cov[2]);*/    hours = (sec_left) / (60*60) ;
 /*    sec_left = (sec_left) %(60*60);
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    minutes = (sec_left) /60;
   goto end;*/    sec_left = (sec_left) % (60);
     return ps;    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
 }    return ascdiff;
   }
 /**************** Product of 2 matrices ******************/  
   /*************** powell ************************/
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
 {              double (*func)(double [])) 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  { 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    void linmin(double p[], double xi[], int n, double *fret, 
   /* in, b, out are matrice of pointers which should have been initialized                double (*func)(double [])); 
      before: only the contents of out is modified. The function returns    int i,ibig,j; 
      a pointer to pointers identical to out */    double del,t,*pt,*ptt,*xit;
   long i, j, k;    double fp,fptt;
   for(i=nrl; i<= nrh; i++)    double *xits;
     for(k=ncolol; k<=ncoloh; k++)    int niterf, itmp;
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  
         out[i][k] +=in[i][j]*b[j][k];    pt=vector(1,n); 
     ptt=vector(1,n); 
   return out;    xit=vector(1,n); 
 }    xits=vector(1,n); 
     *fret=(*func)(p); 
     for (j=1;j<=n;j++) pt[j]=p[j]; 
 /************* Higher Matrix Product ***************/    for (*iter=1;;++(*iter)) { 
       fp=(*fret); 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      ibig=0; 
 {      del=0.0; 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      last_time=curr_time;
      duration (i.e. until      (void) gettimeofday(&curr_time,&tzp);
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.      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);
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step      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);
      (typically every 2 years instead of every month which is too big).      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
      Model is determined by parameters x and covariates have to be      for (i=1;i<=n;i++) {
      included manually here.        printf(" %d %.12f",i, p[i]);
         fprintf(ficlog," %d %.12lf",i, p[i]);
      */        fprintf(ficrespow," %.12lf", p[i]);
       }
   int i, j, d, h, k;      printf("\n");
   double **out, cov[NCOVMAX];      fprintf(ficlog,"\n");
   double **newm;      fprintf(ficrespow,"\n");fflush(ficrespow);
       if(*iter <=3){
   /* Hstepm could be zero and should return the unit matrix */        tm = *localtime(&curr_time.tv_sec);
   for (i=1;i<=nlstate+ndeath;i++)        strcpy(strcurr,asctime(&tmf));
     for (j=1;j<=nlstate+ndeath;j++){  /*       asctime_r(&tm,strcurr); */
       oldm[i][j]=(i==j ? 1.0 : 0.0);        forecast_time=curr_time;
       po[i][j][0]=(i==j ? 1.0 : 0.0);        itmp = strlen(strcurr);
     }        if(strcurr[itmp-1]=='\n')
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */          strcurr[itmp-1]='\0';
   for(h=1; h <=nhstepm; h++){        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     for(d=1; d <=hstepm; d++){        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       newm=savm;        for(niterf=10;niterf<=30;niterf+=10){
       /* Covariates have to be included here again */          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
       cov[1]=1.;          tmf = *localtime(&forecast_time.tv_sec);
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  /*      asctime_r(&tmf,strfor); */
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];          strcpy(strfor,asctime(&tmf));
       for (k=1; k<=cptcovage;k++)          itmp = strlen(strfor);
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          if(strfor[itmp-1]=='\n')
       for (k=1; k<=cptcovprod;k++)          strfor[itmp-1]='\0';
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];          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);
         }
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      }
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      for (i=1;i<=n;i++) { 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        fptt=(*fret); 
       savm=oldm;  #ifdef DEBUG
       oldm=newm;        printf("fret=%lf \n",*fret);
     }        fprintf(ficlog,"fret=%lf \n",*fret);
     for(i=1; i<=nlstate+ndeath; i++)  #endif
       for(j=1;j<=nlstate+ndeath;j++) {        printf("%d",i);fflush(stdout);
         po[i][j][h]=newm[i][j];        fprintf(ficlog,"%d",i);fflush(ficlog);
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);        linmin(p,xit,n,fret,func); 
          */        if (fabs(fptt-(*fret)) > del) { 
       }          del=fabs(fptt-(*fret)); 
   } /* end h */          ibig=i; 
   return po;        } 
 }  #ifdef DEBUG
         printf("%d %.12e",i,(*fret));
         fprintf(ficlog,"%d %.12e",i,(*fret));
 /*************** log-likelihood *************/        for (j=1;j<=n;j++) {
 double func( double *x)          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
 {          printf(" x(%d)=%.12e",j,xit[j]);
   int i, ii, j, k, mi, d, kk;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        }
   double **out;        for(j=1;j<=n;j++) {
   double sw; /* Sum of weights */          printf(" p=%.12e",p[j]);
   double lli; /* Individual log likelihood */          fprintf(ficlog," p=%.12e",p[j]);
   long ipmx;        }
   /*extern weight */        printf("\n");
   /* We are differentiating ll according to initial status */        fprintf(ficlog,"\n");
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/  #endif
   /*for(i=1;i<imx;i++)      } 
     printf(" %d\n",s[4][i]);      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   */  #ifdef DEBUG
   cov[1]=1.;        int k[2],l;
         k[0]=1;
   for(k=1; k<=nlstate; k++) ll[k]=0.;        k[1]=-1;
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        printf("Max: %.12e",(*func)(p));
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        fprintf(ficlog,"Max: %.12e",(*func)(p));
     for(mi=1; mi<= wav[i]-1; mi++){        for (j=1;j<=n;j++) {
       for (ii=1;ii<=nlstate+ndeath;ii++)          printf(" %.12e",p[j]);
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);          fprintf(ficlog," %.12e",p[j]);
       for(d=0; d<dh[mi][i]; d++){        }
         newm=savm;        printf("\n");
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;        fprintf(ficlog,"\n");
         for (kk=1; kk<=cptcovage;kk++) {        for(l=0;l<=1;l++) {
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];          for (j=1;j<=n;j++) {
         }            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
                    printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));          }
         savm=oldm;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         oldm=newm;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
                }
          #endif
       } /* end mult */  
        
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        free_vector(xit,1,n); 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        free_vector(xits,1,n); 
       ipmx +=1;        free_vector(ptt,1,n); 
       sw += weight[i];        free_vector(pt,1,n); 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        return; 
     } /* end of wave */      } 
   } /* end of individual */      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       for (j=1;j<=n;j++) { 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        ptt[j]=2.0*p[j]-pt[j]; 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */        xit[j]=p[j]-pt[j]; 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */        pt[j]=p[j]; 
   return -l;      } 
 }      fptt=(*func)(ptt); 
       if (fptt < fp) { 
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
 /*********** Maximum Likelihood Estimation ***************/        if (t < 0.0) { 
           linmin(p,xit,n,fret,func); 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))          for (j=1;j<=n;j++) { 
 {            xi[j][ibig]=xi[j][n]; 
   int i,j, iter;            xi[j][n]=xit[j]; 
   double **xi,*delti;          }
   double fret;  #ifdef DEBUG
   xi=matrix(1,npar,1,npar);          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   for (i=1;i<=npar;i++)          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     for (j=1;j<=npar;j++)          for(j=1;j<=n;j++){
       xi[i][j]=(i==j ? 1.0 : 0.0);            printf(" %.12e",xit[j]);
   printf("Powell\n");            fprintf(ficlog," %.12e",xit[j]);
   powell(p,xi,npar,ftol,&iter,&fret,func);          }
           printf("\n");
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));          fprintf(ficlog,"\n");
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));  #endif
         }
 }      } 
     } 
 /**** Computes Hessian and covariance matrix ***/  } 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  
 {  /**** Prevalence limit (stable prevalence)  ****************/
   double  **a,**y,*x,pd;  
   double **hess;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   int i, j,jk;  {
   int *indx;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
        matrix by transitions matrix until convergence is reached */
   double hessii(double p[], double delta, int theta, double delti[]);  
   double hessij(double p[], double delti[], int i, int j);    int i, ii,j,k;
   void lubksb(double **a, int npar, int *indx, double b[]) ;    double min, max, maxmin, maxmax,sumnew=0.;
   void ludcmp(double **a, int npar, int *indx, double *d) ;    double **matprod2();
     double **out, cov[NCOVMAX], **pmij();
   hess=matrix(1,npar,1,npar);    double **newm;
     double agefin, delaymax=50 ; /* Max number of years to converge */
   printf("\nCalculation of the hessian matrix. Wait...\n");  
   for (i=1;i<=npar;i++){    for (ii=1;ii<=nlstate+ndeath;ii++)
     printf("%d",i);fflush(stdout);      for (j=1;j<=nlstate+ndeath;j++){
     hess[i][i]=hessii(p,ftolhess,i,delti);        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     /*printf(" %f ",p[i]);*/      }
     /*printf(" %lf ",hess[i][i]);*/  
   }     cov[1]=1.;
     
   for (i=1;i<=npar;i++) {   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for (j=1;j<=npar;j++)  {    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       if (j>i) {      newm=savm;
         printf(".%d%d",i,j);fflush(stdout);      /* Covariates have to be included here again */
         hess[i][j]=hessij(p,delti,i,j);       cov[2]=agefin;
         hess[j][i]=hess[i][j];        
         /*printf(" %lf ",hess[i][j]);*/        for (k=1; k<=cptcovn;k++) {
       }          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]]);*/
   }        }
   printf("\n");        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++)
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
    
   a=matrix(1,npar,1,npar);        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   y=matrix(1,npar,1,npar);        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   x=vector(1,npar);        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   indx=ivector(1,npar);      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];      savm=oldm;
   ludcmp(a,npar,indx,&pd);      oldm=newm;
       maxmax=0.;
   for (j=1;j<=npar;j++) {      for(j=1;j<=nlstate;j++){
     for (i=1;i<=npar;i++) x[i]=0;        min=1.;
     x[j]=1;        max=0.;
     lubksb(a,npar,indx,x);        for(i=1; i<=nlstate; i++) {
     for (i=1;i<=npar;i++){          sumnew=0;
       matcov[i][j]=x[i];          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     }          prlim[i][j]= newm[i][j]/(1-sumnew);
   }          max=FMAX(max,prlim[i][j]);
           min=FMIN(min,prlim[i][j]);
   printf("\n#Hessian matrix#\n");        }
   for (i=1;i<=npar;i++) {        maxmin=max-min;
     for (j=1;j<=npar;j++) {        maxmax=FMAX(maxmax,maxmin);
       printf("%.3e ",hess[i][j]);      }
     }      if(maxmax < ftolpl){
     printf("\n");        return prlim;
   }      }
     }
   /* Recompute Inverse */  }
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  /*************** transition probabilities ***************/ 
   ludcmp(a,npar,indx,&pd);  
   double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   /*  printf("\n#Hessian matrix recomputed#\n");  {
     double s1, s2;
   for (j=1;j<=npar;j++) {    /*double t34;*/
     for (i=1;i<=npar;i++) x[i]=0;    int i,j,j1, nc, ii, jj;
     x[j]=1;  
     lubksb(a,npar,indx,x);      for(i=1; i<= nlstate; i++){
     for (i=1;i<=npar;i++){      for(j=1; j<i;j++){
       y[i][j]=x[i];        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       printf("%.3e ",y[i][j]);          /*s2 += param[i][j][nc]*cov[nc];*/
     }          s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     printf("\n");          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
   }        }
   */        ps[i][j]=s2;
         /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
   free_matrix(a,1,npar,1,npar);      }
   free_matrix(y,1,npar,1,npar);      for(j=i+1; j<=nlstate+ndeath;j++){
   free_vector(x,1,npar);        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   free_ivector(indx,1,npar);          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   free_matrix(hess,1,npar,1,npar);          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
         }
         ps[i][j]=s2;
 }      }
     }
 /*************** hessian matrix ****************/      /*ps[3][2]=1;*/
 double hessii( double x[], double delta, int theta, double delti[])  
 {    for(i=1; i<= nlstate; i++){
   int i;       s1=0;
   int l=1, lmax=20;      for(j=1; j<i; j++)
   double k1,k2;        s1+=exp(ps[i][j]);
   double p2[NPARMAX+1];      for(j=i+1; j<=nlstate+ndeath; j++)
   double res;        s1+=exp(ps[i][j]);
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      ps[i][i]=1./(s1+1.);
   double fx;      for(j=1; j<i; j++)
   int k=0,kmax=10;        ps[i][j]= exp(ps[i][j])*ps[i][i];
   double l1;      for(j=i+1; j<=nlstate+ndeath; j++)
         ps[i][j]= exp(ps[i][j])*ps[i][i];
   fx=func(x);      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   for (i=1;i<=npar;i++) p2[i]=x[i];    } /* end i */
   for(l=0 ; l <=lmax; l++){  
     l1=pow(10,l);    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     delts=delt;      for(jj=1; jj<= nlstate+ndeath; jj++){
     for(k=1 ; k <kmax; k=k+1){        ps[ii][jj]=0;
       delt = delta*(l1*k);        ps[ii][ii]=1;
       p2[theta]=x[theta] +delt;      }
       k1=func(p2)-fx;    }
       p2[theta]=x[theta]-delt;  
       k2=func(p2)-fx;  
       /*res= (k1-2.0*fx+k2)/delt/delt; */    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */      for(jj=1; jj<= nlstate+ndeath; jj++){
             printf("%lf ",ps[ii][jj]);
 #ifdef DEBUG     }
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);      printf("\n ");
 #endif      }
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */      printf("\n ");printf("%lf ",cov[2]);*/
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  /*
         k=kmax;    for(i=1; i<= npar; i++) printf("%f ",x[i]);
       }    goto end;*/
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */      return ps;
         k=kmax; l=lmax*10.;  }
       }  
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  /**************** Product of 2 matrices ******************/
         delts=delt;  
       }  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
     }  {
   }    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   delti[theta]=delts;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
   return res;    /* in, b, out are matrice of pointers which should have been initialized 
         before: only the contents of out is modified. The function returns
 }       a pointer to pointers identical to out */
     long i, j, k;
 double hessij( double x[], double delti[], int thetai,int thetaj)    for(i=nrl; i<= nrh; i++)
 {      for(k=ncolol; k<=ncoloh; k++)
   int i;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
   int l=1, l1, lmax=20;          out[i][k] +=in[i][j]*b[j][k];
   double k1,k2,k3,k4,res,fx;  
   double p2[NPARMAX+1];    return out;
   int k;  }
   
   fx=func(x);  
   for (k=1; k<=2; k++) {  /************* Higher Matrix Product ***************/
     for (i=1;i<=npar;i++) p2[i]=x[i];  
     p2[thetai]=x[thetai]+delti[thetai]/k;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  {
     k1=func(p2)-fx;    /* Computes the transition matrix starting at age 'age' over 
         'nhstepm*hstepm*stepm' months (i.e. until
     p2[thetai]=x[thetai]+delti[thetai]/k;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;       nhstepm*hstepm matrices. 
     k2=func(p2)-fx;       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
         (typically every 2 years instead of every month which is too big 
     p2[thetai]=x[thetai]-delti[thetai]/k;       for the memory).
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;       Model is determined by parameters x and covariates have to be 
     k3=func(p2)-fx;       included manually here. 
    
     p2[thetai]=x[thetai]-delti[thetai]/k;       */
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k4=func(p2)-fx;    int i, j, d, h, k;
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    double **out, cov[NCOVMAX];
 #ifdef DEBUG    double **newm;
     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);  
 #endif    /* Hstepm could be zero and should return the unit matrix */
   }    for (i=1;i<=nlstate+ndeath;i++)
   return res;      for (j=1;j<=nlstate+ndeath;j++){
 }        oldm[i][j]=(i==j ? 1.0 : 0.0);
         po[i][j][0]=(i==j ? 1.0 : 0.0);
 /************** Inverse of matrix **************/      }
 void ludcmp(double **a, int n, int *indx, double *d)    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
 {    for(h=1; h <=nhstepm; h++){
   int i,imax,j,k;      for(d=1; d <=hstepm; d++){
   double big,dum,sum,temp;        newm=savm;
   double *vv;        /* Covariates have to be included here again */
          cov[1]=1.;
   vv=vector(1,n);        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
   *d=1.0;        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   for (i=1;i<=n;i++) {        for (k=1; k<=cptcovage;k++)
     big=0.0;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     for (j=1;j<=n;j++)        for (k=1; k<=cptcovprod;k++)
       if ((temp=fabs(a[i][j])) > big) big=temp;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");  
     vv[i]=1.0/big;  
   }        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   for (j=1;j<=n;j++) {        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
     for (i=1;i<j;i++) {        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
       sum=a[i][j];                     pmij(pmmij,cov,ncovmodel,x,nlstate));
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        savm=oldm;
       a[i][j]=sum;        oldm=newm;
     }      }
     big=0.0;      for(i=1; i<=nlstate+ndeath; i++)
     for (i=j;i<=n;i++) {        for(j=1;j<=nlstate+ndeath;j++) {
       sum=a[i][j];          po[i][j][h]=newm[i][j];
       for (k=1;k<j;k++)          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
         sum -= a[i][k]*a[k][j];           */
       a[i][j]=sum;        }
       if ( (dum=vv[i]*fabs(sum)) >= big) {    } /* end h */
         big=dum;    return po;
         imax=i;  }
       }  
     }  
     if (j != imax) {  /*************** log-likelihood *************/
       for (k=1;k<=n;k++) {  double func( double *x)
         dum=a[imax][k];  {
         a[imax][k]=a[j][k];    int i, ii, j, k, mi, d, kk;
         a[j][k]=dum;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
       }    double **out;
       *d = -(*d);    double sw; /* Sum of weights */
       vv[imax]=vv[j];    double lli; /* Individual log likelihood */
     }    int s1, s2;
     indx[j]=imax;    double bbh, survp;
     if (a[j][j] == 0.0) a[j][j]=TINY;    long ipmx;
     if (j != n) {    /*extern weight */
       dum=1.0/(a[j][j]);    /* We are differentiating ll according to initial status */
       for (i=j+1;i<=n;i++) a[i][j] *= dum;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     }    /*for(i=1;i<imx;i++) 
   }      printf(" %d\n",s[4][i]);
   free_vector(vv,1,n);  /* Doesn't work */    */
 ;    cov[1]=1.;
 }  
     for(k=1; k<=nlstate; k++) ll[k]=0.;
 void lubksb(double **a, int n, int *indx, double b[])  
 {    if(mle==1){
   int i,ii=0,ip,j;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double sum;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          for(mi=1; mi<= wav[i]-1; mi++){
   for (i=1;i<=n;i++) {          for (ii=1;ii<=nlstate+ndeath;ii++)
     ip=indx[i];            for (j=1;j<=nlstate+ndeath;j++){
     sum=b[ip];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     b[ip]=b[i];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     if (ii)            }
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];          for(d=0; d<dh[mi][i]; d++){
     else if (sum) ii=i;            newm=savm;
     b[i]=sum;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   }            for (kk=1; kk<=cptcovage;kk++) {
   for (i=n;i>=1;i--) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     sum=b[i];            }
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     b[i]=sum/a[i][i];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   }            savm=oldm;
 }            oldm=newm;
           } /* end mult */
 /************ Frequencies ********************/        
 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)          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
 {  /* Some frequencies */          /* But now since version 0.9 we anticipate for bias and large stepm.
             * If stepm is larger than one month (smallest stepm) and if the exact delay 
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;           * (in months) between two waves is not a multiple of stepm, we rounded to 
   double ***freq; /* Frequencies */           * the nearest (and in case of equal distance, to the lowest) interval but now
   double *pp;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   double pos, k2, dateintsum=0,k2cpt=0;           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
   FILE *ficresp;           * probability in order to take into account the bias as a fraction of the way
   char fileresp[FILENAMELENGTH];           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
             * -stepm/2 to stepm/2 .
   pp=vector(1,nlstate);           * For stepm=1 the results are the same as for previous versions of Imach.
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);           * For stepm > 1 the results are less biased than in previous versions. 
   strcpy(fileresp,"p");           */
   strcat(fileresp,fileres);          s1=s[mw[mi][i]][i];
   if((ficresp=fopen(fileresp,"w"))==NULL) {          s2=s[mw[mi+1][i]][i];
     printf("Problem with prevalence resultfile: %s\n", fileresp);          bbh=(double)bh[mi][i]/(double)stepm; 
     exit(0);          /* bias is positive if real duration
   }           * is higher than the multiple of stepm and negative otherwise.
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);           */
   j1=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){ 
   j=cptcoveff;            /* i.e. if s2 is a death state and if the date of death is known then the contribution
   if (cptcovn<1) {j=1;ncodemax[1]=1;}               to the likelihood is the probability to die between last step unit time and current 
                 step unit time, which is also the differences between probability to die before dh 
   for(k1=1; k1<=j;k1++){               and probability to die before dh-stepm . 
     for(i1=1; i1<=ncodemax[k1];i1++){               In version up to 0.92 likelihood was computed
       j1++;          as if date of death was unknown. Death was treated as any other
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);          health state: the date of the interview describes the actual state
         scanf("%d", i);*/          and not the date of a change in health state. The former idea was
       for (i=-1; i<=nlstate+ndeath; i++)            to consider that at each interview the state was recorded
         for (jk=-1; jk<=nlstate+ndeath; jk++)            (healthy, disable or death) and IMaCh was corrected; but when we
           for(m=agemin; m <= agemax+3; m++)          introduced the exact date of death then we should have modified
             freq[i][jk][m]=0;          the contribution of an exact death to the likelihood. This new
                contribution is smaller and very dependent of the step unit
       dateintsum=0;          stepm. It is no more the probability to die between last interview
       k2cpt=0;          and month of death but the probability to survive from last
       for (i=1; i<=imx; i++) {          interview up to one month before death multiplied by the
         bool=1;          probability to die within a month. Thanks to Chris
         if  (cptcovn>0) {          Jackson for correcting this bug.  Former versions increased
           for (z1=1; z1<=cptcoveff; z1++)          mortality artificially. The bad side is that we add another loop
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          which slows down the processing. The difference can be up to 10%
               bool=0;          lower mortality.
         }            */
         if (bool==1) {            lli=log(out[s1][s2] - savm[s1][s2]);
           for(m=firstpass; m<=lastpass; m++){          }else{
             k2=anint[m][i]+(mint[m][i]/12.);            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
             if ((k2>=dateprev1) && (k2<=dateprev2)) {            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
               if(agev[m][i]==0) agev[m][i]=agemax+1;          } 
               if(agev[m][i]==1) agev[m][i]=agemax+2;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
               if (m<lastpass) {          /*if(lli ==000.0)*/
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          /*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); */
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          ipmx +=1;
               }          sw += weight[i];
                        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {        } /* end of wave */
                 dateintsum=dateintsum+k2;      } /* end of individual */
                 k2cpt++;    }  else if(mle==2){
               }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           }        for(mi=1; mi<= wav[i]-1; mi++){
         }          for (ii=1;ii<=nlstate+ndeath;ii++)
       }            for (j=1;j<=nlstate+ndeath;j++){
                      oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
       if  (cptcovn>0) {          for(d=0; d<=dh[mi][i]; d++){
         fprintf(ficresp, "\n#********** Variable ");            newm=savm;
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         fprintf(ficresp, "**********\n#");            for (kk=1; kk<=cptcovage;kk++) {
       }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for(i=1; i<=nlstate;i++)            }
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       fprintf(ficresp, "\n");                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                  savm=oldm;
       for(i=(int)agemin; i <= (int)agemax+3; i++){            oldm=newm;
         if(i==(int)agemax+3)          } /* end mult */
           printf("Total");        
         else          s1=s[mw[mi][i]][i];
           printf("Age %d", i);          s2=s[mw[mi+1][i]][i];
         for(jk=1; jk <=nlstate ; jk++){          bbh=(double)bh[mi][i]/(double)stepm; 
           for(m=-1, 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];
         for(jk=1; jk <=nlstate ; jk++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           for(m=-1, pos=0; m <=0 ; m++)        } /* end of wave */
             pos += freq[jk][m][i];      } /* end of individual */
           if(pp[jk]>=1.e-10)    }  else if(mle==3){  /* exponential inter-extrapolation */
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           else        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);        for(mi=1; mi<= wav[i]-1; mi++){
         }          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
         for(jk=1; jk <=nlstate ; jk++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             pp[jk] += freq[jk][m][i];            }
         }          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
         for(jk=1,pos=0; jk <=nlstate ; jk++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           pos += pp[jk];            for (kk=1; kk<=cptcovage;kk++) {
         for(jk=1; jk <=nlstate ; jk++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           if(pos>=1.e-5)            }
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           else                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);            savm=oldm;
           if( i <= (int) agemax){            oldm=newm;
             if(pos>=1.e-5){          } /* end mult */
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        
               probs[i][jk][j1]= pp[jk]/pos;          s1=s[mw[mi][i]][i];
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/          s2=s[mw[mi+1][i]][i];
             }          bbh=(double)bh[mi][i]/(double)stepm; 
             else          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          ipmx +=1;
           }          sw += weight[i];
         }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
                } /* end of wave */
         for(jk=-1; jk <=nlstate+ndeath; jk++)      } /* end of individual */
           for(m=-1; m <=nlstate+ndeath; m++)    }else if (mle==4){  /* ml=4 no inter-extrapolation */
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         if(i <= (int) agemax)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           fprintf(ficresp,"\n");        for(mi=1; mi<= wav[i]-1; mi++){
         printf("\n");          for (ii=1;ii<=nlstate+ndeath;ii++)
       }            for (j=1;j<=nlstate+ndeath;j++){
     }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   dateintmean=dateintsum/k2cpt;            }
            for(d=0; d<dh[mi][i]; d++){
   fclose(ficresp);            newm=savm;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   free_vector(pp,1,nlstate);            for (kk=1; kk<=cptcovage;kk++) {
                cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   /* End of Freq */            }
 }          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 /************ Prevalence ********************/                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 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)            savm=oldm;
 {  /* Some frequencies */            oldm=newm;
            } /* end mult */
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;        
   double ***freq; /* Frequencies */          s1=s[mw[mi][i]][i];
   double *pp;          s2=s[mw[mi+1][i]][i];
   double pos, k2;          if( s2 > nlstate){ 
             lli=log(out[s1][s2] - savm[s1][s2]);
   pp=vector(1,nlstate);          }else{
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
            }
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          ipmx +=1;
   j1=0;          sw += weight[i];
            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   j=cptcoveff;  /*      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<1) {j=1;ncodemax[1]=1;}        } /* end of wave */
        } /* end of individual */
   for(k1=1; k1<=j;k1++){    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
     for(i1=1; i1<=ncodemax[k1];i1++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       j1++;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
              for(mi=1; mi<= wav[i]-1; mi++){
       for (i=-1; i<=nlstate+ndeath; i++)            for (ii=1;ii<=nlstate+ndeath;ii++)
         for (jk=-1; jk<=nlstate+ndeath; jk++)              for (j=1;j<=nlstate+ndeath;j++){
           for(m=agemin; m <= agemax+3; m++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             freq[i][jk][m]=0;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                  }
       for (i=1; i<=imx; i++) {          for(d=0; d<dh[mi][i]; d++){
         bool=1;            newm=savm;
         if  (cptcovn>0) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for (z1=1; z1<=cptcoveff; z1++)            for (kk=1; kk<=cptcovage;kk++) {
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
               bool=0;            }
         }          
         if (bool==1) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           for(m=firstpass; m<=lastpass; m++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             k2=anint[m][i]+(mint[m][i]/12.);            savm=oldm;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {            oldm=newm;
               if(agev[m][i]==0) agev[m][i]=agemax+1;          } /* end mult */
               if(agev[m][i]==1) agev[m][i]=agemax+2;        
               if (m<lastpass) {          s1=s[mw[mi][i]][i];
                 if (calagedate>0)          s2=s[mw[mi+1][i]][i];
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
                 else          ipmx +=1;
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          sw += weight[i];
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
               }          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
             }        } /* end of wave */
           }      } /* end of individual */
         }    } /* End of if */
       }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       for(i=(int)agemin; i <= (int)agemax+3; i++){    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         for(jk=1; jk <=nlstate ; jk++){    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    return -l;
             pp[jk] += freq[jk][m][i];  }
         }  
         for(jk=1; jk <=nlstate ; jk++){  /*************** log-likelihood *************/
           for(m=-1, pos=0; m <=0 ; m++)  double funcone( double *x)
             pos += freq[jk][m][i];  {
         }    /* Same as likeli but slower because of a lot of printf and if */
            int i, ii, j, k, mi, d, kk;
         for(jk=1; jk <=nlstate ; jk++){    double l, ll[NLSTATEMAX], cov[NCOVMAX];
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)    double **out;
             pp[jk] += freq[jk][m][i];    double lli; /* Individual log likelihood */
         }    double llt;
            int s1, s2;
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];    double bbh, survp;
            /*extern weight */
         for(jk=1; jk <=nlstate ; jk++){        /* We are differentiating ll according to initial status */
           if( i <= (int) agemax){    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
             if(pos>=1.e-5){    /*for(i=1;i<imx;i++) 
               probs[i][jk][j1]= pp[jk]/pos;      printf(" %d\n",s[4][i]);
             }    */
           }    cov[1]=1.;
         }  
            for(k=1; k<=nlstate; k++) ll[k]=0.;
       }  
     }    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   }      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){
          for (ii=1;ii<=nlstate+ndeath;ii++)
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          for (j=1;j<=nlstate+ndeath;j++){
   free_vector(pp,1,nlstate);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 }  /* End of Freq */          }
         for(d=0; d<dh[mi][i]; d++){
 /************* Waves Concatenation ***************/          newm=savm;
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 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 (kk=1; kk<=cptcovage;kk++) {
 {            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.          }
      Death is a valid wave (if date is known).          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          savm=oldm;
      and mw[mi+1][i]. dh depends on stepm.          oldm=newm;
      */        } /* end mult */
         
   int i, mi, m;        s1=s[mw[mi][i]][i];
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        s2=s[mw[mi+1][i]][i];
      double sum=0., jmean=0.;*/        bbh=(double)bh[mi][i]/(double)stepm; 
         /* bias is positive if real duration
   int j, k=0,jk, ju, jl;         * is higher than the multiple of stepm and negative otherwise.
   double sum=0.;         */
   jmin=1e+5;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   jmax=-1;          lli=log(out[s1][s2] - savm[s1][s2]);
   jmean=0.;        } else if (mle==1){
   for(i=1; i<=imx; i++){          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     mi=0;        } else if(mle==2){
     m=firstpass;          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 */
     while(s[m][i] <= nlstate){        } else if(mle==3){  /* exponential inter-extrapolation */
       if(s[m][i]>=1)          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
         mw[++mi][i]=m;        } else if (mle==4){  /* mle=4 no inter-extrapolation */
       if(m >=lastpass)          lli=log(out[s1][s2]); /* Original formula */
         break;        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
       else          lli=log(out[s1][s2]); /* Original formula */
         m++;        } /* End of if */
     }/* end while */        ipmx +=1;
     if (s[m][i] > nlstate){        sw += weight[i];
       mi++;     /* Death is another wave */        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       /* if(mi==0)  never been interviewed correctly before death */  /*       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]); */
          /* Only death is a correct wave */        if(globpr){
       mw[mi][i]=m;          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
     }   %10.6f %10.6f %10.6f ", \
                   num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
     wav[i]=mi;                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
     if(mi==0)          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);            llt +=ll[k]*gipmx/gsw;
   }            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           }
   for(i=1; i<=imx; i++){          fprintf(ficresilk," %10.6f\n", -llt);
     for(mi=1; mi<wav[i];mi++){        }
       if (stepm <=0)      } /* end of wave */
         dh[mi][i]=1;    } /* end of individual */
       else{    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         if (s[mw[mi+1][i]][i] > nlstate) {    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
           if (agedc[i] < 2*AGESUP) {    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);    if(globpr==0){ /* First time we count the contributions and weights */
           if(j==0) j=1;  /* Survives at least one month after exam */      gipmx=ipmx;
           k=k+1;      gsw=sw;
           if (j >= jmax) jmax=j;    }
           if (j <= jmin) jmin=j;    return -l;
           sum=sum+j;  }
           /*if (j<0) printf("j=%d num=%d \n",j,i); */  
           }  
         }  /*************** function likelione ***********/
         else{  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));  {
           k=k+1;    /* This routine should help understanding what is done with 
           if (j >= jmax) jmax=j;       the selection of individuals/waves and
           else if (j <= jmin)jmin=j;       to check the exact contribution to the likelihood.
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */       Plotting could be done.
           sum=sum+j;     */
         }    int k;
         jk= j/stepm;  
         jl= j -jk*stepm;    if(*globpri !=0){ /* Just counts and sums, no printings */
         ju= j -(jk+1)*stepm;      strcpy(fileresilk,"ilk"); 
         if(jl <= -ju)      strcat(fileresilk,fileres);
           dh[mi][i]=jk;      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         else        printf("Problem with resultfile: %s\n", fileresilk);
           dh[mi][i]=jk+1;        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
         if(dh[mi][i]==0)      }
           dh[mi][i]=1; /* At least one step */      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
       }      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     }      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   }      for(k=1; k<=nlstate; k++) 
   jmean=sum/k;        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
  }    }
 /*********** Tricode ****************************/  
 void tricode(int *Tvar, int **nbcode, int imx)    *fretone=(*funcone)(p);
 {    if(*globpri !=0){
   int Ndum[20],ij=1, k, j, i;      fclose(ficresilk);
   int cptcode=0;      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   cptcoveff=0;      fflush(fichtm); 
      } 
   for (k=0; k<19; k++) Ndum[k]=0;    return;
   for (k=1; k<=7; k++) ncodemax[k]=0;  }
   
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  
     for (i=1; i<=imx; i++) {  /*********** Maximum Likelihood Estimation ***************/
       ij=(int)(covar[Tvar[j]][i]);  
       Ndum[ij]++;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/  {
       if (ij > cptcode) cptcode=ij;    int i,j, iter;
     }    double **xi;
     double fret;
     for (i=0; i<=cptcode; i++) {    double fretone; /* Only one call to likelihood */
       if(Ndum[i]!=0) ncodemax[j]++;    char filerespow[FILENAMELENGTH];
     }    xi=matrix(1,npar,1,npar);
     ij=1;    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++)
         xi[i][j]=(i==j ? 1.0 : 0.0);
     for (i=1; i<=ncodemax[j]; i++) {    printf("Powell\n");  fprintf(ficlog,"Powell\n");
       for (k=0; k<=19; k++) {    strcpy(filerespow,"pow"); 
         if (Ndum[k] != 0) {    strcat(filerespow,fileres);
           nbcode[Tvar[j]][ij]=k;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
                printf("Problem with resultfile: %s\n", filerespow);
           ij++;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
         }    }
         if (ij > ncodemax[j]) break;    fprintf(ficrespow,"# Powell\n# iter -2*LL");
       }      for (i=1;i<=nlstate;i++)
     }      for(j=1;j<=nlstate+ndeath;j++)
   }          if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     fprintf(ficrespow,"\n");
  for (k=0; k<19; k++) Ndum[k]=0;  
     powell(p,xi,npar,ftol,&iter,&fret,func);
  for (i=1; i<=ncovmodel-2; i++) {  
       ij=Tvar[i];    fclose(ficrespow);
       Ndum[ij]++;    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     }    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
  ij=1;  
  for (i=1; i<=10; i++) {  }
    if((Ndum[i]!=0) && (i<=ncovcol)){  
      Tvaraff[ij]=i;  /**** Computes Hessian and covariance matrix ***/
      ij++;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
    }  {
  }    double  **a,**y,*x,pd;
      double **hess;
     cptcoveff=ij-1;    int i, j,jk;
 }    int *indx;
   
 /*********** Health Expectancies ****************/    double hessii(double p[], double delta, int theta, double delti[]);
     double hessij(double p[], double delti[], int i, int j);
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )    void lubksb(double **a, int npar, int *indx, double b[]) ;
     void ludcmp(double **a, int npar, int *indx, double *d) ;
 {  
   /* Health expectancies */    hess=matrix(1,npar,1,npar);
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;  
   double age, agelim, hf;    printf("\nCalculation of the hessian matrix. Wait...\n");
   double ***p3mat,***varhe;    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   double **dnewm,**doldm;    for (i=1;i<=npar;i++){
   double *xp;      printf("%d",i);fflush(stdout);
   double **gp, **gm;      fprintf(ficlog,"%d",i);fflush(ficlog);
   double ***gradg, ***trgradg;      hess[i][i]=hessii(p,ftolhess,i,delti);
   int theta;      /*printf(" %f ",p[i]);*/
       /*printf(" %lf ",hess[i][i]);*/
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);    }
   xp=vector(1,npar);    
   dnewm=matrix(1,nlstate*2,1,npar);    for (i=1;i<=npar;i++) {
   doldm=matrix(1,nlstate*2,1,nlstate*2);      for (j=1;j<=npar;j++)  {
          if (j>i) { 
   fprintf(ficreseij,"# Health expectancies\n");          printf(".%d%d",i,j);fflush(stdout);
   fprintf(ficreseij,"# Age");          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   for(i=1; i<=nlstate;i++)          hess[i][j]=hessij(p,delti,i,j);
     for(j=1; j<=nlstate;j++)          hess[j][i]=hess[i][j];    
       fprintf(ficreseij," %1d-%1d (SE)",i,j);          /*printf(" %lf ",hess[i][j]);*/
   fprintf(ficreseij,"\n");        }
       }
   if(estepm < stepm){    }
     printf ("Problem %d lower than %d\n",estepm, stepm);    printf("\n");
   }    fprintf(ficlog,"\n");
   else  hstepm=estepm;    
   /* We compute the life expectancy from trapezoids spaced every estepm months    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
    * This is mainly to measure the difference between two models: for example    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
    * 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    a=matrix(1,npar,1,npar);
    * progression inbetween and thus overestimating or underestimating according    y=matrix(1,npar,1,npar);
    * to the curvature of the survival function. If, for the same date, we    x=vector(1,npar);
    * estimate the model with stepm=1 month, we can keep estepm to 24 months    indx=ivector(1,npar);
    * 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      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
    * curvature will be obtained if estepm is as small as stepm. */    ludcmp(a,npar,indx,&pd);
   
   /* For example we decided to compute the life expectancy with the smallest unit */    for (j=1;j<=npar;j++) {
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.      for (i=1;i<=npar;i++) x[i]=0;
      nhstepm is the number of hstepm from age to agelim      x[j]=1;
      nstepm is the number of stepm from age to agelin.      lubksb(a,npar,indx,x);
      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 */        matcov[i][j]=x[i];
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the      }
      survival function given by stepm (the optimization length). Unfortunately it    }
      means that if the survival funtion is printed only each two years of age and if  
      you sum them up and add 1 year (area under the trapezoids) you won't get the same    printf("\n#Hessian matrix#\n");
      results. So we changed our mind and took the option of the best precision.    fprintf(ficlog,"\n#Hessian matrix#\n");
   */    for (i=1;i<=npar;i++) { 
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */      for (j=1;j<=npar;j++) { 
         printf("%.3e ",hess[i][j]);
   agelim=AGESUP;        fprintf(ficlog,"%.3e ",hess[i][j]);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      }
     /* nhstepm age range expressed in number of stepm */      printf("\n");
     nstepm=(int) rint((agelim-age)*YEARM/stepm);      fprintf(ficlog,"\n");
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    }
     /* if (stepm >= YEARM) hstepm=1;*/  
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    /* Recompute Inverse */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for (i=1;i<=npar;i++)
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     gp=matrix(0,nhstepm,1,nlstate*2);    ludcmp(a,npar,indx,&pd);
     gm=matrix(0,nhstepm,1,nlstate*2);  
     /*  printf("\n#Hessian matrix recomputed#\n");
     /* Computed by stepm unit matrices, product of hstepm matrices, stored  
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    for (j=1;j<=npar;j++) {
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);        for (i=1;i<=npar;i++) x[i]=0;
        x[j]=1;
       lubksb(a,npar,indx,x);
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      for (i=1;i<=npar;i++){ 
         y[i][j]=x[i];
     /* Computing Variances of health expectancies */        printf("%.3e ",y[i][j]);
         fprintf(ficlog,"%.3e ",y[i][j]);
      for(theta=1; theta <=npar; theta++){      }
       for(i=1; i<=npar; i++){      printf("\n");
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      fprintf(ficlog,"\n");
       }    }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      */
    
       cptj=0;    free_matrix(a,1,npar,1,npar);
       for(j=1; j<= nlstate; j++){    free_matrix(y,1,npar,1,npar);
         for(i=1; i<=nlstate; i++){    free_vector(x,1,npar);
           cptj=cptj+1;    free_ivector(indx,1,npar);
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){    free_matrix(hess,1,npar,1,npar);
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;  
           }  
         }  }
       }  
        /*************** hessian matrix ****************/
        double hessii( double x[], double delta, int theta, double delti[])
       for(i=1; i<=npar; i++)  {
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    int i;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      int l=1, lmax=20;
          double k1,k2;
       cptj=0;    double p2[NPARMAX+1];
       for(j=1; j<= nlstate; j++){    double res;
         for(i=1;i<=nlstate;i++){    double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
           cptj=cptj+1;    double fx;
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){    int k=0,kmax=10;
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    double l1;
           }  
         }    fx=func(x);
       }    for (i=1;i<=npar;i++) p2[i]=x[i];
       for(j=1; j<= nlstate*2; j++)    for(l=0 ; l <=lmax; l++){
         for(h=0; h<=nhstepm-1; h++){      l1=pow(10,l);
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      delts=delt;
         }      for(k=1 ; k <kmax; k=k+1){
      }        delt = delta*(l1*k);
            p2[theta]=x[theta] +delt;
 /* End theta */        k1=func(p2)-fx;
         p2[theta]=x[theta]-delt;
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);        k2=func(p2)-fx;
         /*res= (k1-2.0*fx+k2)/delt/delt; */
      for(h=0; h<=nhstepm-1; h++)        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
       for(j=1; j<=nlstate*2;j++)        
         for(theta=1; theta <=npar; theta++)  #ifdef DEBUG
           trgradg[h][j][theta]=gradg[h][theta][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);
              fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   #endif
      for(i=1;i<=nlstate*2;i++)        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
       for(j=1;j<=nlstate*2;j++)        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         varhe[i][j][(int)age] =0.;          k=kmax;
         }
      printf("%d|",(int)age);fflush(stdout);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
      for(h=0;h<=nhstepm-1;h++){          k=kmax; l=lmax*10.;
       for(k=0;k<=nhstepm-1;k++){        }
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);          delts=delt;
         for(i=1;i<=nlstate*2;i++)        }
           for(j=1;j<=nlstate*2;j++)      }
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;    }
       }    delti[theta]=delts;
     }    return res; 
     /* Computing expectancies */    
     for(i=1; i<=nlstate;i++)  }
       for(j=1; j<=nlstate;j++)  
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){  double hessij( double x[], double delti[], int thetai,int thetaj)
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;  {
              int i;
 /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/    int l=1, l1, lmax=20;
     double k1,k2,k3,k4,res,fx;
         }    double p2[NPARMAX+1];
     int k;
     fprintf(ficreseij,"%3.0f",age );  
     cptj=0;    fx=func(x);
     for(i=1; i<=nlstate;i++)    for (k=1; k<=2; k++) {
       for(j=1; j<=nlstate;j++){      for (i=1;i<=npar;i++) p2[i]=x[i];
         cptj++;      p2[thetai]=x[thetai]+delti[thetai]/k;
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       }      k1=func(p2)-fx;
     fprintf(ficreseij,"\n");    
          p2[thetai]=x[thetai]+delti[thetai]/k;
     free_matrix(gm,0,nhstepm,1,nlstate*2);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     free_matrix(gp,0,nhstepm,1,nlstate*2);      k2=func(p2)-fx;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);    
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);      p2[thetai]=x[thetai]-delti[thetai]/k;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   }      k3=func(p2)-fx;
   printf("\n");    
       p2[thetai]=x[thetai]-delti[thetai]/k;
   free_vector(xp,1,npar);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   free_matrix(dnewm,1,nlstate*2,1,npar);      k4=func(p2)-fx;
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);  #ifdef DEBUG
 }      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
       fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
 /************ Variance ******************/  #endif
 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)    }
 {    return res;
   /* Variance of health expectancies */  }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/  
   double **newm;  /************** Inverse of matrix **************/
   double **dnewm,**doldm;  void ludcmp(double **a, int n, int *indx, double *d) 
   int i, j, nhstepm, hstepm, h, nstepm ;  { 
   int k, cptcode;    int i,imax,j,k; 
   double *xp;    double big,dum,sum,temp; 
   double **gp, **gm;    double *vv; 
   double ***gradg, ***trgradg;   
   double ***p3mat;    vv=vector(1,n); 
   double age,agelim, hf;    *d=1.0; 
   int theta;    for (i=1;i<=n;i++) { 
       big=0.0; 
   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");      for (j=1;j<=n;j++) 
   fprintf(ficresvij,"# Age");        if ((temp=fabs(a[i][j])) > big) big=temp; 
   for(i=1; i<=nlstate;i++)      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     for(j=1; j<=nlstate;j++)      vv[i]=1.0/big; 
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    } 
   fprintf(ficresvij,"\n");    for (j=1;j<=n;j++) { 
       for (i=1;i<j;i++) { 
   xp=vector(1,npar);        sum=a[i][j]; 
   dnewm=matrix(1,nlstate,1,npar);        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   doldm=matrix(1,nlstate,1,nlstate);        a[i][j]=sum; 
        } 
   if(estepm < stepm){      big=0.0; 
     printf ("Problem %d lower than %d\n",estepm, stepm);      for (i=j;i<=n;i++) { 
   }        sum=a[i][j]; 
   else  hstepm=estepm;          for (k=1;k<j;k++) 
   /* For example we decided to compute the life expectancy with the smallest unit */          sum -= a[i][k]*a[k][j]; 
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        a[i][j]=sum; 
      nhstepm is the number of hstepm from age to agelim        if ( (dum=vv[i]*fabs(sum)) >= big) { 
      nstepm is the number of stepm from age to agelin.          big=dum; 
      Look at hpijx to understand the reason of that which relies in memory size          imax=i; 
      and note for a fixed period like k years */        } 
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the      } 
      survival function given by stepm (the optimization length). Unfortunately it      if (j != imax) { 
      means that if the survival funtion is printed only each two years of age and if        for (k=1;k<=n;k++) { 
      you sum them up and add 1 year (area under the trapezoids) you won't get the same          dum=a[imax][k]; 
      results. So we changed our mind and took the option of the best precision.          a[imax][k]=a[j][k]; 
   */          a[j][k]=dum; 
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        } 
   agelim = AGESUP;        *d = -(*d); 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        vv[imax]=vv[j]; 
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      } 
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      indx[j]=imax; 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      if (a[j][j] == 0.0) a[j][j]=TINY; 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      if (j != n) { 
     gp=matrix(0,nhstepm,1,nlstate);        dum=1.0/(a[j][j]); 
     gm=matrix(0,nhstepm,1,nlstate);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       } 
     for(theta=1; theta <=npar; theta++){    } 
       for(i=1; i<=npar; i++){ /* Computes gradient */    free_vector(vv,1,n);  /* Doesn't work */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  ;
       }  } 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  void lubksb(double **a, int n, int *indx, double b[]) 
   { 
       if (popbased==1) {    int i,ii=0,ip,j; 
         for(i=1; i<=nlstate;i++)    double sum; 
           prlim[i][i]=probs[(int)age][i][ij];   
       }    for (i=1;i<=n;i++) { 
        ip=indx[i]; 
       for(j=1; j<= nlstate; j++){      sum=b[ip]; 
         for(h=0; h<=nhstepm; h++){      b[ip]=b[i]; 
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)      if (ii) 
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
         }      else if (sum) ii=i; 
       }      b[i]=sum; 
        } 
       for(i=1; i<=npar; i++) /* Computes gradient */    for (i=n;i>=1;i--) { 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      sum=b[i]; 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      b[i]=sum/a[i][i]; 
      } 
       if (popbased==1) {  } 
         for(i=1; i<=nlstate;i++)  
           prlim[i][i]=probs[(int)age][i][ij];  /************ 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)
   {  /* Some frequencies */
       for(j=1; j<= nlstate; j++){    
         for(h=0; h<=nhstepm; h++){    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    int first;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    double ***freq; /* Frequencies */
         }    double *pp, **prop;
       }    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     FILE *ficresp;
       for(j=1; j<= nlstate; j++)    char fileresp[FILENAMELENGTH];
         for(h=0; h<=nhstepm; h++){    
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    pp=vector(1,nlstate);
         }    prop=matrix(1,nlstate,iagemin,iagemax+3);
     } /* End theta */    strcpy(fileresp,"p");
     strcat(fileresp,fileres);
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    if((ficresp=fopen(fileresp,"w"))==NULL) {
       printf("Problem with prevalence resultfile: %s\n", fileresp);
     for(h=0; h<=nhstepm; h++)      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       for(j=1; j<=nlstate;j++)      exit(0);
         for(theta=1; theta <=npar; theta++)    }
           trgradg[h][j][theta]=gradg[h][theta][j];    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
     j1=0;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    
     for(i=1;i<=nlstate;i++)    j=cptcoveff;
       for(j=1;j<=nlstate;j++)    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         vareij[i][j][(int)age] =0.;  
     first=1;
     for(h=0;h<=nhstepm;h++){  
       for(k=0;k<=nhstepm;k++){    for(k1=1; k1<=j;k1++){
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      for(i1=1; i1<=ncodemax[k1];i1++){
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        j1++;
         for(i=1;i<=nlstate;i++)        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           for(j=1;j<=nlstate;j++)          scanf("%d", i);*/
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;        for (i=-1; i<=nlstate+ndeath; i++)  
       }          for (jk=-1; jk<=nlstate+ndeath; jk++)  
     }            for(m=iagemin; m <= iagemax+3; m++)
               freq[i][jk][m]=0;
     fprintf(ficresvij,"%.0f ",age );  
     for(i=1; i<=nlstate;i++)      for (i=1; i<=nlstate; i++)  
       for(j=1; j<=nlstate;j++){        for(m=iagemin; m <= iagemax+3; m++)
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);          prop[i][m]=0;
       }        
     fprintf(ficresvij,"\n");        dateintsum=0;
     free_matrix(gp,0,nhstepm,1,nlstate);        k2cpt=0;
     free_matrix(gm,0,nhstepm,1,nlstate);        for (i=1; i<=imx; i++) {
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);          bool=1;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          if  (cptcovn>0) {
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for (z1=1; z1<=cptcoveff; z1++) 
   } /* End age */              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                  bool=0;
   free_vector(xp,1,npar);          }
   free_matrix(doldm,1,nlstate,1,npar);          if (bool==1){
   free_matrix(dnewm,1,nlstate,1,nlstate);            for(m=firstpass; m<=lastpass; m++){
               k2=anint[m][i]+(mint[m][i]/12.);
 }              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                 if(agev[m][i]==0) agev[m][i]=iagemax+1;
 /************ Variance of prevlim ******************/                if(agev[m][i]==1) agev[m][i]=iagemax+2;
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
 {                if (m<lastpass) {
   /* Variance of prevalence limit */                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
   double **newm;                }
   double **dnewm,**doldm;                
   int i, j, nhstepm, hstepm;                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   int k, cptcode;                  dateintsum=dateintsum+k2;
   double *xp;                  k2cpt++;
   double *gp, *gm;                }
   double **gradg, **trgradg;                /*}*/
   double age,agelim;            }
   int theta;          }
            }
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");         
   fprintf(ficresvpl,"# Age");        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   for(i=1; i<=nlstate;i++)  
       fprintf(ficresvpl," %1d-%1d",i,i);        if  (cptcovn>0) {
   fprintf(ficresvpl,"\n");          fprintf(ficresp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   xp=vector(1,npar);          fprintf(ficresp, "**********\n#");
   dnewm=matrix(1,nlstate,1,npar);        }
   doldm=matrix(1,nlstate,1,nlstate);        for(i=1; i<=nlstate;i++) 
            fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   hstepm=1*YEARM; /* Every year of age */        fprintf(ficresp, "\n");
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        
   agelim = AGESUP;        for(i=iagemin; i <= iagemax+3; i++){
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          if(i==iagemax+3){
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            fprintf(ficlog,"Total");
     if (stepm >= YEARM) hstepm=1;          }else{
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            if(first==1){
     gradg=matrix(1,npar,1,nlstate);              first=0;
     gp=vector(1,nlstate);              printf("See log file for details...\n");
     gm=vector(1,nlstate);            }
             fprintf(ficlog,"Age %d", i);
     for(theta=1; theta <=npar; theta++){          }
       for(i=1; i<=npar; i++){ /* Computes gradient */          for(jk=1; jk <=nlstate ; jk++){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
       }              pp[jk] += freq[jk][m][i]; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          }
       for(i=1;i<=nlstate;i++)          for(jk=1; jk <=nlstate ; jk++){
         gp[i] = prlim[i][i];            for(m=-1, pos=0; m <=0 ; m++)
                  pos += freq[jk][m][i];
       for(i=1; i<=npar; i++) /* Computes gradient */            if(pp[jk]>=1.e-10){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);              if(first==1){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       for(i=1;i<=nlstate;i++)              }
         gm[i] = prlim[i][i];              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
             }else{
       for(i=1;i<=nlstate;i++)              if(first==1)
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     } /* End theta */              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             }
     trgradg =matrix(1,nlstate,1,npar);          }
   
     for(j=1; j<=nlstate;j++)          for(jk=1; jk <=nlstate ; jk++){
       for(theta=1; theta <=npar; theta++)            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
         trgradg[j][theta]=gradg[theta][j];              pp[jk] += freq[jk][m][i];
           }       
     for(i=1;i<=nlstate;i++)          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
       varpl[i][(int)age] =0.;            pos += pp[jk];
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);            posprop += prop[jk][i];
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          }
     for(i=1;i<=nlstate;i++)          for(jk=1; jk <=nlstate ; jk++){
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */            if(pos>=1.e-5){
               if(first==1)
     fprintf(ficresvpl,"%.0f ",age );                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     for(i=1; i<=nlstate;i++)              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));            }else{
     fprintf(ficresvpl,"\n");              if(first==1)
     free_vector(gp,1,nlstate);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     free_vector(gm,1,nlstate);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     free_matrix(gradg,1,npar,1,nlstate);            }
     free_matrix(trgradg,1,nlstate,1,npar);            if( i <= iagemax){
   } /* End age */              if(pos>=1.e-5){
                 fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   free_vector(xp,1,npar);                /*probs[i][jk][j1]= pp[jk]/pos;*/
   free_matrix(doldm,1,nlstate,1,npar);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   free_matrix(dnewm,1,nlstate,1,nlstate);              }
               else
 }                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
             }
 /************ Variance of one-step probabilities  ******************/          }
 void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)          
 {          for(jk=-1; jk <=nlstate+ndeath; jk++)
   int i, j,  i1, k1, l1;            for(m=-1; m <=nlstate+ndeath; m++)
   int k2, l2, j1,  z1;              if(freq[jk][m][i] !=0 ) {
   int k=0,l, cptcode;              if(first==1)
   int first=1;                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   double **dnewm,**doldm;              }
   double *xp;          if(i <= iagemax)
   double *gp, *gm;            fprintf(ficresp,"\n");
   double **gradg, **trgradg;          if(first==1)
   double **mu;            printf("Others in log...\n");
   double age,agelim, cov[NCOVMAX];          fprintf(ficlog,"\n");
   double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */        }
   int theta;      }
   char fileresprob[FILENAMELENGTH];    }
   char fileresprobcov[FILENAMELENGTH];    dateintmean=dateintsum/k2cpt; 
   char fileresprobcor[FILENAMELENGTH];   
     fclose(ficresp);
   double ***varpij;    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
     free_vector(pp,1,nlstate);
   strcpy(fileresprob,"prob");    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   strcat(fileresprob,fileres);    /* End of Freq */
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {  }
     printf("Problem with resultfile: %s\n", fileresprob);  
   }  /************ Prevalence ********************/
   strcpy(fileresprobcov,"probcov");  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)
   strcat(fileresprobcov,fileres);  {  
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
     printf("Problem with resultfile: %s\n", fileresprobcov);       in each health status at the date of interview (if between dateprev1 and dateprev2).
   }       We still use firstpass and lastpass as another selection.
   strcpy(fileresprobcor,"probcor");    */
   strcat(fileresprobcor,fileres);   
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     printf("Problem with resultfile: %s\n", fileresprobcor);    double ***freq; /* Frequencies */
   }    double *pp, **prop;
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);    double pos,posprop; 
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);    double  y2; /* in fractional years */
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);    int iagemin, iagemax;
    
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");    iagemin= (int) agemin;
   fprintf(ficresprob,"# Age");    iagemax= (int) agemax;
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");    /*pp=vector(1,nlstate);*/
   fprintf(ficresprobcov,"# Age");    prop=matrix(1,nlstate,iagemin,iagemax+3); 
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   fprintf(ficresprobcov,"# Age");    j1=0;
     
     j=cptcoveff;
   for(i=1; i<=nlstate;i++)    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     for(j=1; j<=(nlstate+ndeath);j++){    
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);    for(k1=1; k1<=j;k1++){
       fprintf(ficresprobcov," p%1d-%1d ",i,j);      for(i1=1; i1<=ncodemax[k1];i1++){
       fprintf(ficresprobcor," p%1d-%1d ",i,j);        j1++;
     }          
   fprintf(ficresprob,"\n");        for (i=1; i<=nlstate; i++)  
   fprintf(ficresprobcov,"\n");          for(m=iagemin; m <= iagemax+3; m++)
   fprintf(ficresprobcor,"\n");            prop[i][m]=0.0;
   xp=vector(1,npar);       
   dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);        for (i=1; i<=imx; i++) { /* Each individual */
   doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));          bool=1;
   mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);          if  (cptcovn>0) {
   varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);            for (z1=1; z1<=cptcoveff; z1++) 
   first=1;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {                bool=0;
     printf("Problem with gnuplot file: %s\n", optionfilegnuplot);          } 
     exit(0);          if (bool==1) { 
   }            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
   else{              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
     fprintf(ficgp,"\n# Routine varprob");              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
   }                if(agev[m][i]==0) agev[m][i]=iagemax+1;
   if((fichtm=fopen(optionfilehtm,"a"))==NULL) {                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     printf("Problem with html file: %s\n", optionfilehtm);                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); 
     exit(0);                if (s[m][i]>0 && s[m][i]<=nlstate) { 
   }                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
   else{                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
     fprintf(fichtm,"\n<H2> Computing matrix of variance-covariance of step probabilities</h2>\n");                  prop[s[m][i]][iagemax+3] += weight[i]; 
     fprintf(fichtm,"\n<br> We have drawn ellipsoids of confidence around the p<inf>ij</inf>, p<inf>kl</inf> to understand the covariance between two incidences. They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");                } 
     fprintf(fichtm,"\n<br> We have drawn x'cov<sup>-1</sup>x = 4 where x is the column vector (pij,pkl). It means that if pij and pkl where uncorrelated the (2X2) matrix would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 standard deviations wide on each axis. <br> When both incidences are correlated we diagonalised the inverse of the covariance matrix and made the appropriate rotation.<br> \n");              }
             } /* end selection of waves */
   }          }
   cov[1]=1;        }
   j=cptcoveff;        for(i=iagemin; i <= iagemax+3; i++){  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          
   j1=0;          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
   for(k1=1; k1<=1;k1++){            posprop += prop[jk][i]; 
     for(i1=1; i1<=ncodemax[k1];i1++){          } 
     j1++;  
           for(jk=1; jk <=nlstate ; jk++){     
     if  (cptcovn>0) {            if( i <=  iagemax){ 
       fprintf(ficresprob, "\n#********** Variable ");              if(posprop>=1.e-5){ 
       fprintf(ficresprobcov, "\n#********** Variable ");                probs[i][jk][j1]= prop[jk][i]/posprop;
       fprintf(ficgp, "\n#********** Variable ");              } 
       fprintf(fichtm, "\n<h4>********** Variable</h4>\n ");            } 
       fprintf(ficresprobcor, "\n#********** Variable ");          }/* end jk */ 
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);        }/* end i */ 
       fprintf(ficresprob, "**********\n#");      } /* end i1 */
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    } /* end k1 */
       fprintf(ficresprobcov, "**********\n#");    
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
       fprintf(ficgp, "**********\n#");    /*free_vector(pp,1,nlstate);*/
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, "# V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
       fprintf(ficgp, "**********\n#");  }  /* End of prevalence */
       for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
       fprintf(fichtm, "**********\n#");  /************* Waves Concatenation ***************/
     }  
      void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
       for (age=bage; age<=fage; age ++){  {
         cov[2]=age;    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
         for (k=1; k<=cptcovn;k++) {       Death is a valid wave (if date is known).
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];       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]
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];       and mw[mi+1][i]. dh depends on stepm.
         for (k=1; k<=cptcovprod;k++)       */
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  
            int i, mi, m;
         gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
         trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);       double sum=0., jmean=0.;*/
         gp=vector(1,(nlstate)*(nlstate+ndeath));    int first;
         gm=vector(1,(nlstate)*(nlstate+ndeath));    int j, k=0,jk, ju, jl;
        double sum=0.;
         for(theta=1; theta <=npar; theta++){    first=0;
           for(i=1; i<=npar; i++)    jmin=1e+5;
             xp[i] = x[i] + (i==theta ?delti[theta]:0);    jmax=-1;
              jmean=0.;
           pmij(pmmij,cov,ncovmodel,xp,nlstate);    for(i=1; i<=imx; i++){
                mi=0;
           k=0;      m=firstpass;
           for(i=1; i<= (nlstate); i++){      while(s[m][i] <= nlstate){
             for(j=1; j<=(nlstate+ndeath);j++){        if(s[m][i]>=1)
               k=k+1;          mw[++mi][i]=m;
               gp[k]=pmmij[i][j];        if(m >=lastpass)
             }          break;
           }        else
                    m++;
           for(i=1; i<=npar; i++)      }/* end while */
             xp[i] = x[i] - (i==theta ?delti[theta]:0);      if (s[m][i] > nlstate){
            mi++;     /* Death is another wave */
           pmij(pmmij,cov,ncovmodel,xp,nlstate);        /* if(mi==0)  never been interviewed correctly before death */
           k=0;           /* Only death is a correct wave */
           for(i=1; i<=(nlstate); i++){        mw[mi][i]=m;
             for(j=1; j<=(nlstate+ndeath);j++){      }
               k=k+1;  
               gm[k]=pmmij[i][j];      wav[i]=mi;
             }      if(mi==0){
           }        nbwarn++;
              if(first==0){
           for(i=1; i<= (nlstate)*(nlstate+ndeath); i++)          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];            first=1;
         }        }
         if(first==1){
         for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
           for(theta=1; theta <=npar; theta++)        }
             trgradg[j][theta]=gradg[theta][j];      } /* end mi==0 */
            } /* End individuals */
         matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov);  
         matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);    for(i=1; i<=imx; i++){
              for(mi=1; mi<wav[i];mi++){
         pmij(pmmij,cov,ncovmodel,x,nlstate);        if (stepm <=0)
                  dh[mi][i]=1;
         k=0;        else{
         for(i=1; i<=(nlstate); i++){          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
           for(j=1; j<=(nlstate+ndeath);j++){            if (agedc[i] < 2*AGESUP) {
             k=k+1;              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
             mu[k][(int) age]=pmmij[i][j];              if(j==0) j=1;  /* Survives at least one month after exam */
           }              else if(j<0){
         }                nberr++;
         for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
           for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)                j=1; /* Temporary Dangerous patch */
             varpij[i][j][(int)age] = doldm[i][j];                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(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]);
         /*printf("\n%d ",(int)age);                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
      for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){              }
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));              k=k+1;
      }*/              if (j >= jmax) jmax=j;
               if (j <= jmin) jmin=j;
         fprintf(ficresprob,"\n%d ",(int)age);              sum=sum+j;
         fprintf(ficresprobcov,"\n%d ",(int)age);              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
         fprintf(ficresprobcor,"\n%d ",(int)age);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             }
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)          }
           fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));          else{
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
           fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
           fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);            k=k+1;
         }            if (j >= jmax) jmax=j;
         i=0;            else if (j <= jmin)jmin=j;
         for (k=1; k<=(nlstate);k++){            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
           for (l=1; l<=(nlstate+ndeath);l++){            /*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]);*/
             i=i++;            if(j<0){
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);              nberr++;
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             for (j=1; j<=i;j++){              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
               fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);            }
               fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));            sum=sum+j;
             }          }
           }          jk= j/stepm;
         }/* end of loop for state */          jl= j -jk*stepm;
       } /* end of loop for age */          ju= j -(jk+1)*stepm;
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
       for (k1=1; k1<=(nlstate);k1++){            if(jl==0){
         for (l1=1; l1<=(nlstate+ndeath);l1++){              dh[mi][i]=jk;
           if(l1==k1) continue;              bh[mi][i]=0;
           i=(k1-1)*(nlstate+ndeath)+l1;            }else{ /* We want a negative bias in order to only have interpolation ie
           for (k2=1; k2<=(nlstate);k2++){                    * at the price of an extra matrix product in likelihood */
             for (l2=1; l2<=(nlstate+ndeath);l2++){              dh[mi][i]=jk+1;
               if(l2==k2) continue;              bh[mi][i]=ju;
               j=(k2-1)*(nlstate+ndeath)+l2;            }
               if(j<=i) continue;          }else{
               for (age=bage; age<=fage; age ++){            if(jl <= -ju){
                 if ((int)age %5==0){              dh[mi][i]=jk;
                   v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;              bh[mi][i]=jl;       /* bias is positive if real duration
                   v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;                                   * is higher than the multiple of stepm and negative otherwise.
                   cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;                                   */
                   mu1=mu[i][(int) age]/stepm*YEARM ;            }
                   mu2=mu[j][(int) age]/stepm*YEARM;            else{
                   /* Computing eigen value of matrix of covariance */              dh[mi][i]=jk+1;
                   lc1=(v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));              bh[mi][i]=ju;
                   lc2=(v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12));            }
                   printf("Var %.4e %.4e cov %.4e Eigen %.3e %.3e\n",v1,v2,cv12,lc1,lc2);            if(dh[mi][i]==0){
                   /* Eigen vectors */              dh[mi][i]=1; /* At least one step */
                   v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));              bh[mi][i]=ju; /* At least one step */
                   v21=sqrt(1.-v11*v11);              /*  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);*/
                   v12=-v21;            }
                   v22=v11;          } /* end if mle */
                   /*printf(fignu*/        }
                   /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */      } /* end wave */
                   /* mu2+ v21*lc1*cost + v21*lc2*sin(t) */    }
                   if(first==1){    jmean=sum/k;
                     first=0;    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
                     fprintf(ficgp,"\nset parametric;set nolabel");    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
                     fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k2,l2,k1,l1);   }
                     fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");  
                     fprintf(fichtm,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup> :<a href=\"varpijgr%s%1d%1d-%1d%1d.png\">varpijgr%s%1d%1d-%1d%1d.png</A>, ",k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1,optionfilefiname,k2,l2,k1,l1);  /*********** Tricode ****************************/
                     fprintf(fichtm,"\n<br><img src=\"varpijgr%s%1d%1d-%1d%1d.png\">, ",optionfilefiname,k2,l2,k1,l1);  void tricode(int *Tvar, int **nbcode, int imx)
                     fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\"",optionfilefiname,k2,l2,k1,l1);  {
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);    
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);    int Ndum[20],ij=1, k, j, i, maxncov=19;
                     fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\    int cptcode=0;
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \    cptcoveff=0; 
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);   
                   }else{    for (k=0; k<maxncov; k++) Ndum[k]=0;
                     first=0;    for (k=1; k<=7; k++) ncodemax[k]=0;
                     fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k2,l2,k1,l1);  
                     fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu2,mu1);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
                     fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(-%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) t \"%d\"",\      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                             mu2,std,v21,sqrt(lc1),v21,sqrt(lc2), \                                 modality*/ 
                             mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),(int) age);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
                   }/* if first */        Ndum[ij]++; /*store the modality */
                 } /* age mod 5 */        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
               } /* end loop age */        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
               fprintf(ficgp,"\nset out \"varpijgr%s%1d%1d-%1d%1d.png\";replot;",optionfilefiname,k2,l2,k1,l1);                                         Tvar[j]. If V=sex and male is 0 and 
               first=1;                                         female is 1, then  cptcode=1.*/
             } /*l12 */      }
           } /* k12 */  
         } /*l1 */      for (i=0; i<=cptcode; i++) {
       }/* k1 */        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 */
     } /* loop covariates */      }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);  
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));      ij=1; 
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));      for (i=1; i<=ncodemax[j]; i++) {
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);        for (k=0; k<= maxncov; k++) {
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          if (Ndum[k] != 0) {
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            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; */
   free_vector(xp,1,npar);            
   fclose(ficresprob);            ij++;
   fclose(ficresprobcov);          }
   fclose(ficresprobcor);          if (ij > ncodemax[j]) break; 
   fclose(ficgp);        }  
   fclose(fichtm);      } 
 }    }  
   
    for (k=0; k< maxncov; k++) Ndum[k]=0;
 /******************* Printing html file ***********/  
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \   for (i=1; i<=ncovmodel-2; i++) { 
                   int lastpass, int stepm, int weightopt, char model[],\     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
                   int imx,int jmin, int jmax, double jmeanint,char rfileres[],\     ij=Tvar[i];
                   int popforecast, int estepm ,\     Ndum[ij]++;
                   double jprev1, double mprev1,double anprev1, \   }
                   double jprev2, double mprev2,double anprev2){  
   int jj1, k1, i1, cpt;   ij=1;
   /*char optionfilehtm[FILENAMELENGTH];*/   for (i=1; i<= maxncov; i++) {
   if((fichtm=fopen(optionfilehtm,"a"))==NULL)    {     if((Ndum[i]!=0) && (i<=ncovcol)){
     printf("Problem with %s \n",optionfilehtm), exit(0);       Tvaraff[ij]=i; /*For printing */
   }       ij++;
      }
    fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n   }
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n   
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n   cptcoveff=ij-1; /*Number of simple covariates*/
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n  }
  - Life expectancies by age and initial health status (estepm=%2d months):  
    <a href=\"e%s\">e%s</a> <br>\n</li>", \  /*********** Health Expectancies ****************/
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);  
   void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )
  fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n  
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n  {
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n    /* Health expectancies */
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n    double age, agelim, hf;
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n    double ***p3mat,***varhe;
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n    double **dnewm,**doldm;
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);    double *xp;
     double **gp, **gm;
  if(popforecast==1) fprintf(fichtm,"\n    double ***gradg, ***trgradg;
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n    int theta;
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n  
         <br>",fileres,fileres,fileres,fileres);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
  else    xp=vector(1,npar);
    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);    dnewm=matrix(1,nlstate*nlstate,1,npar);
 fprintf(fichtm," <li>Graphs</li><p>");    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     
  m=cptcoveff;    fprintf(ficreseij,"# Health expectancies\n");
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    fprintf(ficreseij,"# Age");
     for(i=1; i<=nlstate;i++)
  jj1=0;      for(j=1; j<=nlstate;j++)
  for(k1=1; k1<=m;k1++){        fprintf(ficreseij," %1d-%1d (SE)",i,j);
    for(i1=1; i1<=ncodemax[k1];i1++){    fprintf(ficreseij,"\n");
      jj1++;  
      if (cptcovn > 0) {    if(estepm < stepm){
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");      printf ("Problem %d lower than %d\n",estepm, stepm);
        for (cpt=1; cpt<=cptcoveff;cpt++)    }
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);    else  hstepm=estepm;   
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    /* We compute the life expectancy from trapezoids spaced every estepm months
      }     * This is mainly to measure the difference between two models: for example
      /* Pij */     * if stepm=24 months pijx are given only every 2 years and by summing them
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>     * we are calculating an estimate of the Life Expectancy assuming a linear 
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);         * progression in between and thus overestimating or underestimating according
      /* Quasi-incidences */     * to the curvature of the survival function. If, for the same date, we 
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: pe%s%d2.png<br>     * estimate the model with stepm=1 month, we can keep estepm to 24 months
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);     * to compare the new estimate of Life expectancy with the same linear 
        /* Stable prevalence in each health state */     * hypothesis. A more precise result, taking into account a more precise
        for(cpt=1; cpt<nlstate;cpt++){     * curvature will be obtained if estepm is as small as stepm. */
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>  
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);    /* For example we decided to compute the life expectancy with the smallest unit */
        }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     for(cpt=1; cpt<=nlstate;cpt++) {       nhstepm is the number of hstepm from age to agelim 
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident       nstepm is the number of stepm from age to agelin. 
 interval) in state (%d): v%s%d%d.png <br>       Look at hpijx to understand the reason of that which relies in memory size
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);         and note for a fixed period like estepm months */
      }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
      for(cpt=1; cpt<=nlstate;cpt++) {       survival function given by stepm (the optimization length). Unfortunately it
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>       means that if the survival funtion is printed only each two years of age and if
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
      }       results. So we changed our mind and took the option of the best precision.
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    */
 health expectancies in states (1) and (2): e%s%d.png<br>    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);  
    }    agelim=AGESUP;
  }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 fclose(fichtm);      /* nhstepm age range expressed in number of stepm */
 }      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
 /******************* Gnuplot file **************/      /* if (stepm >= YEARM) hstepm=1;*/
 void printinggnuplot(char fileres[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   int ng;      gp=matrix(0,nhstepm,1,nlstate*nlstate);
   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) {      gm=matrix(0,nhstepm,1,nlstate*nlstate);
     printf("Problem with file %s",optionfilegnuplot);  
   }      /* Computed by stepm unit matrices, product of hstepm matrices, stored
          in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
 #ifdef windows      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
     fprintf(ficgp,"cd \"%s\" \n",pathc);   
 #endif  
 m=pow(2,cptcoveff);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
    
  /* 1eme*/      /* Computing  Variances of health expectancies */
   for (cpt=1; cpt<= nlstate ; cpt ++) {  
    for (k1=1; k1<= m ; k1 ++) {       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
 #ifdef windows          xp[i] = x[i] + (i==theta ?delti[theta]:0);
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        }
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 #endif    
 #ifdef unix        cptj=0;
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);        for(j=1; j<= nlstate; j++){
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);          for(i=1; i<=nlstate; i++){
 #endif            cptj=cptj+1;
             for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
 for (i=1; i<= nlstate ; i ++) {              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            }
   else fprintf(ficgp," \%%*lf (\%%*lf)");          }
 }        }
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);       
     for (i=1; i<= nlstate ; i ++) {       
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        for(i=1; i<=npar; i++) 
   else fprintf(ficgp," \%%*lf (\%%*lf)");          xp[i] = x[i] - (i==theta ?delti[theta]:0);
 }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);        
      for (i=1; i<= nlstate ; i ++) {        cptj=0;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        for(j=1; j<= nlstate; j++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for(i=1;i<=nlstate;i++){
 }              cptj=cptj+1;
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
 #ifdef unix  
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
 #endif            }
    }          }
   }        }
   /*2 eme*/        for(j=1; j<= nlstate*nlstate; j++)
           for(h=0; h<=nhstepm-1; h++){
   for (k1=1; k1<= m ; k1 ++) {            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);          }
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);       } 
         
     for (i=1; i<= nlstate+1 ; i ++) {  /* End theta */
       k=2*i;  
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
       for (j=1; j<= nlstate+1 ; j ++) {  
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");       for(h=0; h<=nhstepm-1; h++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");        for(j=1; j<=nlstate*nlstate;j++)
 }            for(theta=1; theta <=npar; theta++)
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");            trgradg[h][j][theta]=gradg[h][theta][j];
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);       
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {       for(i=1;i<=nlstate*nlstate;i++)
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        for(j=1;j<=nlstate*nlstate;j++)
         else fprintf(ficgp," \%%*lf (\%%*lf)");          varhe[i][j][(int)age] =0.;
 }    
       fprintf(ficgp,"\" t\"\" w l 0,");       printf("%d|",(int)age);fflush(stdout);
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
       for (j=1; j<= nlstate+1 ; j ++) {       for(h=0;h<=nhstepm-1;h++){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        for(k=0;k<=nhstepm-1;k++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
 }            matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");          for(i=1;i<=nlstate*nlstate;i++)
       else fprintf(ficgp,"\" t\"\" w l 0,");            for(j=1;j<=nlstate*nlstate;j++)
     }              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
   }        }
        }
   /*3eme*/      /* Computing expectancies */
       for(i=1; i<=nlstate;i++)
   for (k1=1; k1<= m ; k1 ++) {        for(j=1; j<=nlstate;j++)
     for (cpt=1; cpt<= nlstate ; cpt ++) {          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
       k=2+nlstate*(2*cpt-2);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);            
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);  /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);  
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");          }
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);  
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);      fprintf(ficreseij,"%3.0f",age );
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");      cptj=0;
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
 */          cptj++;
       for (i=1; i< nlstate ; i ++) {          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);        }
       fprintf(ficreseij,"\n");
       }     
     }      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   }      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
        free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   /* CV preval stat */      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     for (k1=1; k1<= m ; k1 ++) {      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     for (cpt=1; cpt<nlstate ; cpt ++) {    }
       k=3;    printf("\n");
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);    fprintf(ficlog,"\n");
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);  
     free_vector(xp,1,npar);
       for (i=1; i< nlstate ; i ++)    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
         fprintf(ficgp,"+$%d",k+i+1);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
        }
       l=3+(nlstate+ndeath)*cpt;  
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);  /************ Variance ******************/
       for (i=1; i< nlstate ; i ++) {  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
         l=3+(nlstate+ndeath)*cpt;  {
         fprintf(ficgp,"+$%d",l+i+1);    /* Variance of health expectancies */
       }    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      /* double **newm;*/
     }    double **dnewm,**doldm;
   }      double **dnewmp,**doldmp;
      int i, j, nhstepm, hstepm, h, nstepm ;
   /* proba elementaires */    int k, cptcode;
    for(i=1,jk=1; i <=nlstate; i++){    double *xp;
     for(k=1; k <=(nlstate+ndeath); k++){    double **gp, **gm;  /* for var eij */
       if (k != i) {    double ***gradg, ***trgradg; /*for var eij */
         for(j=1; j <=ncovmodel; j++){    double **gradgp, **trgradgp; /* for var p point j */
            double *gpp, *gmp; /* for var p point j */
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
           jk++;    double ***p3mat;
           fprintf(ficgp,"\n");    double age,agelim, hf;
         }    double ***mobaverage;
       }    int theta;
     }    char digit[4];
    }    char digitp[25];
   
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/    char fileresprobmorprev[FILENAMELENGTH];
      for(jk=1; jk <=m; jk++) {  
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);    if(popbased==1){
        if (ng==2)      if(mobilav!=0)
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");        strcpy(digitp,"-populbased-mobilav-");
        else      else strcpy(digitp,"-populbased-nomobil-");
          fprintf(ficgp,"\nset title \"Probability\"\n");    }
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);    else 
        i=1;      strcpy(digitp,"-stablbased-");
        for(k2=1; k2<=nlstate; k2++) {  
          k3=i;    if (mobilav!=0) {
          for(k=1; k<=(nlstate+ndeath); k++) {      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
            if (k != k2){      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
              if(ng==2)        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
              else      }
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    }
              ij=1;  
              for(j=3; j <=ncovmodel; j++) {    strcpy(fileresprobmorprev,"prmorprev"); 
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    sprintf(digit,"%-d",ij);
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
                  ij++;    strcat(fileresprobmorprev,digit); /* Tvar to be done */
                }    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
                else    strcat(fileresprobmorprev,fileres);
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
              }      printf("Problem with resultfile: %s\n", fileresprobmorprev);
              fprintf(ficgp,")/(1");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
                  }
              for(k1=1; k1 <=nlstate; k1++){      printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
                ij=1;    fprintf(ficresprobmorprev,"# probabilities of dying before estepm=%d months for people of exact age and weighted probabilities w1*p1j+w2*p2j+... stand dev in()\n",estepm);
                for(j=3; j <=ncovmodel; j++){    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      fprintf(ficresprobmorprev," p.%-d SE",j);
                    ij++;      for(i=1; i<=nlstate;i++)
                  }        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
                  else    }  
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    fprintf(ficresprobmorprev,"\n");
                }    fprintf(ficgp,"\n# Routine varevsij");
                fprintf(ficgp,")");    fprintf(fichtm,"\n<li><h4> Computing probabilities of dying over estepm months as a weighted average (i.e global mortality independent of initial healh state)</h4></li>\n");
              }    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);  /*   } */
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
              i=i+ncovmodel;  
            }    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
          }    fprintf(ficresvij,"# Age");
        }    for(i=1; i<=nlstate;i++)
      }      for(j=1; j<=nlstate;j++)
    }        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
    fclose(ficgp);    fprintf(ficresvij,"\n");
 }  /* end gnuplot */  
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
 /*************** Moving average **************/    doldm=matrix(1,nlstate,1,nlstate);
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   int i, cpt, cptcod;  
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
       for (i=1; i<=nlstate;i++)    gpp=vector(nlstate+1,nlstate+ndeath);
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)    gmp=vector(nlstate+1,nlstate+ndeath);
           mobaverage[(int)agedeb][i][cptcod]=0.;    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
        
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){    if(estepm < stepm){
       for (i=1; i<=nlstate;i++){      printf ("Problem %d lower than %d\n",estepm, stepm);
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    }
           for (cpt=0;cpt<=4;cpt++){    else  hstepm=estepm;   
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];    /* For example we decided to compute the life expectancy with the smallest unit */
           }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;       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
 }       survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed every two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
 /************** Forecasting ******************/       results. So we changed our mind and took the option of the best precision.
 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){    */
      hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;    agelim = AGESUP;
   int *popage;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   double *popeffectif,*popcount;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   double ***p3mat;      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   char fileresf[FILENAMELENGTH];      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
  agelim=AGESUP;      gm=matrix(0,nhstepm,1,nlstate);
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;  
   
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      for(theta=1; theta <=npar; theta++){
          for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
            xp[i] = x[i] + (i==theta ?delti[theta]:0);
   strcpy(fileresf,"f");        }
   strcat(fileresf,fileres);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   if((ficresf=fopen(fileresf,"w"))==NULL) {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     printf("Problem with forecast resultfile: %s\n", fileresf);  
   }        if (popbased==1) {
   printf("Computing forecasting: result on file '%s' \n", fileresf);          if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
   if (cptcoveff==0) ncodemax[cptcoveff]=1;              prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
   if (mobilav==1) {            for(i=1; i<=nlstate;i++)
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              prlim[i][i]=mobaverage[(int)age][i][ij];
     movingaverage(agedeb, fage, ageminpar, mobaverage);          }
   }        }
     
   stepsize=(int) (stepm+YEARM-1)/YEARM;        for(j=1; j<= nlstate; j++){
   if (stepm<=12) stepsize=1;          for(h=0; h<=nhstepm; h++){
              for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   agelim=AGESUP;              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
            }
   hstepm=1;        }
   hstepm=hstepm/stepm;        /* This for computing probability of death (h=1 means
   yp1=modf(dateintmean,&yp);           computed over hstepm matrices product = hstepm*stepm months) 
   anprojmean=yp;           as a weighted average of prlim.
   yp2=modf((yp1*12),&yp);        */
   mprojmean=yp;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
   yp1=modf((yp2*30.5),&yp);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
   jprojmean=yp;            gpp[j] += prlim[i][i]*p3mat[i][j][1];
   if(jprojmean==0) jprojmean=1;        }    
   if(mprojmean==0) jprojmean=1;        /* end probability of death */
    
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
            xp[i] = x[i] - (i==theta ?delti[theta]:0);
   for(cptcov=1;cptcov<=i2;cptcov++){        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       k=k+1;   
       fprintf(ficresf,"\n#******");        if (popbased==1) {
       for(j=1;j<=cptcoveff;j++) {          if(mobilav ==0){
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            for(i=1; i<=nlstate;i++)
       }              prlim[i][i]=probs[(int)age][i][ij];
       fprintf(ficresf,"******\n");          }else{ /* mobilav */ 
       fprintf(ficresf,"# StartingAge FinalAge");            for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);              prlim[i][i]=mobaverage[(int)age][i][ij];
                }
              }
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {  
         fprintf(ficresf,"\n");        for(j=1; j<= nlstate; j++){
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);            for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);          }
           nhstepm = nhstepm/hstepm;        }
                  /* This for computing probability of death (h=1 means
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);           computed over hstepm matrices product = hstepm*stepm months) 
           oldm=oldms;savm=savms;           as a weighted average of prlim.
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          */
                for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for (h=0; h<=nhstepm; h++){          for(i=1,gmp[j]=0.; i<= nlstate; i++)
             if (h==(int) (calagedate+YEARM*cpt)) {           gmp[j] += prlim[i][i]*p3mat[i][j][1];
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);        }    
             }        /* end probability of death */
             for(j=1; j<=nlstate+ndeath;j++) {  
               kk1=0.;kk2=0;        for(j=1; j<= nlstate; j++) /* vareij */
               for(i=1; i<=nlstate;i++) {                        for(h=0; h<=nhstepm; h++){
                 if (mobilav==1)            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
                   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];        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
                 }          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
                        }
               }  
               if (h==(int)(calagedate+12*cpt)){      } /* End theta */
                 fprintf(ficresf," %.3f", kk1);  
                              trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
               }  
             }      for(h=0; h<=nhstepm; h++) /* veij */
           }        for(j=1; j<=nlstate;j++)
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(theta=1; theta <=npar; theta++)
         }            trgradg[h][j][theta]=gradg[h][theta][j];
       }  
     }      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   }        for(theta=1; theta <=npar; theta++)
                  trgradgp[j][theta]=gradgp[theta][j];
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    
   
   fclose(ficresf);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
 }      for(i=1;i<=nlstate;i++)
 /************** Forecasting ******************/        for(j=1;j<=nlstate;j++)
 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){          vareij[i][j][(int)age] =0.;
    
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;      for(h=0;h<=nhstepm;h++){
   int *popage;        for(k=0;k<=nhstepm;k++){
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
   double *popeffectif,*popcount;          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   double ***p3mat,***tabpop,***tabpopprev;          for(i=1;i<=nlstate;i++)
   char filerespop[FILENAMELENGTH];            for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        }
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      }
   agelim=AGESUP;    
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;      /* pptj */
        matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
        for(j=nlstate+1;j<=nlstate+ndeath;j++)
          for(i=nlstate+1;i<=nlstate+ndeath;i++)
   strcpy(filerespop,"pop");          varppt[j][i]=doldmp[j][i];
   strcat(filerespop,fileres);      /* end ppptj */
   if((ficrespop=fopen(filerespop,"w"))==NULL) {      /*  x centered again */
     printf("Problem with forecast resultfile: %s\n", filerespop);      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
   }      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   printf("Computing forecasting: result on file '%s' \n", filerespop);   
       if (popbased==1) {
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
   if (mobilav==1) {            prlim[i][i]=probs[(int)age][i][ij];
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        }else{ /* mobilav */ 
     movingaverage(agedeb, fage, ageminpar, mobaverage);          for(i=1; i<=nlstate;i++)
   }            prlim[i][i]=mobaverage[(int)age][i][ij];
         }
   stepsize=(int) (stepm+YEARM-1)/YEARM;      }
   if (stepm<=12) stepsize=1;               
        /* This for computing probability of death (h=1 means
   agelim=AGESUP;         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
           as a weighted average of prlim.
   hstepm=1;      */
   hstepm=hstepm/stepm;      for(j=nlstate+1;j<=nlstate+ndeath;j++){
          for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   if (popforecast==1) {          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
     if((ficpop=fopen(popfile,"r"))==NULL) {      }    
       printf("Problem with population file : %s\n",popfile);exit(0);      /* end probability of death */
     }  
     popage=ivector(0,AGESUP);      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
     popeffectif=vector(0,AGESUP);      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     popcount=vector(0,AGESUP);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
            for(i=1; i<=nlstate;i++){
     i=1;            fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;        }
          } 
     imx=i;      fprintf(ficresprobmorprev,"\n");
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];  
   }      fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
   for(cptcov=1;cptcov<=i2;cptcov++){        for(j=1; j<=nlstate;j++){
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
       k=k+1;        }
       fprintf(ficrespop,"\n#******");      fprintf(ficresvij,"\n");
       for(j=1;j<=cptcoveff;j++) {      free_matrix(gp,0,nhstepm,1,nlstate);
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      free_matrix(gm,0,nhstepm,1,nlstate);
       }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       fprintf(ficrespop,"******\n");      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       fprintf(ficrespop,"# Age");      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    } /* End age */
       if (popforecast==1)  fprintf(ficrespop," [Population]");    free_vector(gpp,nlstate+1,nlstate+ndeath);
          free_vector(gmp,nlstate+1,nlstate+ndeath);
       for (cpt=0; cpt<=0;cpt++) {    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      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 (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
           nhstepm = nhstepm/hstepm;  /*   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); */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
           oldm=oldms;savm=savms;    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
            fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
           for (h=0; h<=nhstepm; h++){    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
             if (h==(int) (calagedate+YEARM*cpt)) {    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    /*  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);
             }  */
             for(j=1; j<=nlstate+ndeath;j++) {  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
               kk1=0.;kk2=0;    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
               for(i=1; i<=nlstate;i++) {                
                 if (mobilav==1)    free_vector(xp,1,npar);
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    free_matrix(doldm,1,nlstate,1,nlstate);
                 else {    free_matrix(dnewm,1,nlstate,1,npar);
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
                 }    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
               }    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
               if (h==(int)(calagedate+12*cpt)){    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    fclose(ficresprobmorprev);
                   /*fprintf(ficrespop," %.3f", kk1);    fflush(ficgp);
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/    fflush(fichtm); 
               }  }  /* end varevsij */
             }  
             for(i=1; i<=nlstate;i++){  /************ Variance of prevlim ******************/
               kk1=0.;  void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)
                 for(j=1; j<=nlstate;j++){  {
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    /* Variance of prevalence limit */
                 }    /*  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;
     int i, j, nhstepm, hstepm;
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)    int k, cptcode;
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);    double *xp;
           }    double *gp, *gm;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    double **gradg, **trgradg;
         }    double age,agelim;
       }    int theta;
       
   /******/    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
     fprintf(ficresvpl,"# Age");
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    for(i=1; i<=nlstate;i++)
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          fprintf(ficresvpl," %1d-%1d",i,i);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    fprintf(ficresvpl,"\n");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
           nhstepm = nhstepm/hstepm;    xp=vector(1,npar);
              dnewm=matrix(1,nlstate,1,npar);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    doldm=matrix(1,nlstate,1,nlstate);
           oldm=oldms;savm=savms;    
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      hstepm=1*YEARM; /* Every year of age */
           for (h=0; h<=nhstepm; h++){    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
             if (h==(int) (calagedate+YEARM*cpt)) {    agelim = AGESUP;
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
             }      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             for(j=1; j<=nlstate+ndeath;j++) {      if (stepm >= YEARM) hstepm=1;
               kk1=0.;kk2=0;      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
               for(i=1; i<=nlstate;i++) {                    gradg=matrix(1,npar,1,nlstate);
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];          gp=vector(1,nlstate);
               }      gm=vector(1,nlstate);
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);  
             }      for(theta=1; theta <=npar; theta++){
           }        for(i=1; i<=npar; i++){ /* Computes gradient */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }        }
       }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    }        for(i=1;i<=nlstate;i++)
   }          gp[i] = prlim[i][i];
        
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
   if (popforecast==1) {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     free_ivector(popage,0,AGESUP);        for(i=1;i<=nlstate;i++)
     free_vector(popeffectif,0,AGESUP);          gm[i] = prlim[i][i];
     free_vector(popcount,0,AGESUP);  
   }        for(i=1;i<=nlstate;i++)
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      } /* End theta */
   fclose(ficrespop);  
 }      trgradg =matrix(1,nlstate,1,npar);
   
 /***********************************************/      for(j=1; j<=nlstate;j++)
 /**************** Main Program *****************/        for(theta=1; theta <=npar; theta++)
 /***********************************************/          trgradg[j][theta]=gradg[theta][j];
   
 int main(int argc, char *argv[])      for(i=1;i<=nlstate;i++)
 {        varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
   double agedeb, agefin,hf;      for(i=1;i<=nlstate;i++)
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
   double fret;      fprintf(ficresvpl,"%.0f ",age );
   double **xi,tmp,delta;      for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
   double dum; /* Dummy variable */      fprintf(ficresvpl,"\n");
   double ***p3mat;      free_vector(gp,1,nlstate);
   int *indx;      free_vector(gm,1,nlstate);
   char line[MAXLINE], linepar[MAXLINE];      free_matrix(gradg,1,npar,1,nlstate);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];      free_matrix(trgradg,1,nlstate,1,npar);
   int firstobs=1, lastobs=10;    } /* End age */
   int sdeb, sfin; /* Status at beginning and end */  
   int c,  h , cpt,l;    free_vector(xp,1,npar);
   int ju,jl, mi;    free_matrix(doldm,1,nlstate,1,npar);
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    free_matrix(dnewm,1,nlstate,1,nlstate);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;  
   int mobilav=0,popforecast=0;  }
   int hstepm, nhstepm;  
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;  /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
   double bage, fage, age, agelim, agebase;  {
   double ftolpl=FTOL;    int i, j=0,  i1, k1, l1, t, tj;
   double **prlim;    int k2, l2, j1,  z1;
   double *severity;    int k=0,l, cptcode;
   double ***param; /* Matrix of parameters */    int first=1, first1;
   double  *p;    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   double **matcov; /* Matrix of covariance */    double **dnewm,**doldm;
   double ***delti3; /* Scale */    double *xp;
   double *delti; /* Scale */    double *gp, *gm;
   double ***eij, ***vareij;    double **gradg, **trgradg;
   double **varpl; /* Variances of prevalence limits by age */    double **mu;
   double *epj, vepp;    double age,agelim, cov[NCOVMAX];
   double kk1, kk2;    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    int theta;
      char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
   char *alph[]={"a","a","b","c","d","e"}, str[4];    char fileresprobcor[FILENAMELENGTH];
   
     double ***varpij;
   char z[1]="c", occ;  
 #include <sys/time.h>    strcpy(fileresprob,"prob"); 
 #include <time.h>    strcat(fileresprob,fileres);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprob);
   /* long total_usecs;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
   struct timeval start_time, end_time;    }
      strcpy(fileresprobcov,"probcov"); 
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    strcat(fileresprobcov,fileres);
   getcwd(pathcd, size);    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
   printf("\n%s",version);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
   if(argc <=1){    }
     printf("\nEnter the parameter file name: ");    strcpy(fileresprobcor,"probcor"); 
     scanf("%s",pathtot);    strcat(fileresprobcor,fileres);
   }    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
   else{      printf("Problem with resultfile: %s\n", fileresprobcor);
     strcpy(pathtot,argv[1]);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
   }    }
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
   /*cygwin_split_path(pathtot,path,optionfile);    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
   /* cutv(path,optionfile,pathtot,'\\');*/    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    
   chdir(path);    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
   replace(pathc,path);    fprintf(ficresprob,"# Age");
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
 /*-------- arguments in the command line --------*/    fprintf(ficresprobcov,"# Age");
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
   strcpy(fileres,"r");    fprintf(ficresprobcov,"# Age");
   strcat(fileres, optionfilefiname);  
   strcat(fileres,".txt");    /* Other files have txt extension */  
     for(i=1; i<=nlstate;i++)
   /*---------arguments file --------*/      for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {        fprintf(ficresprobcov," p%1d-%1d ",i,j);
     printf("Problem with optionfile %s\n",optionfile);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
     goto end;      }  
   }   /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
   strcpy(filereso,"o");    fprintf(ficresprobcor,"\n");
   strcat(filereso,fileres);   */
   if((ficparo=fopen(filereso,"w"))==NULL) {   xp=vector(1,npar);
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
   }    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
   /* Reads comments: lines beginning with '#' */    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
   while((c=getc(ficpar))=='#' && c!= EOF){    first=1;
     ungetc(c,ficpar);    fprintf(ficgp,"\n# Routine varprob");
     fgets(line, MAXLINE, ficpar);    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     puts(line);    fprintf(fichtm,"\n");
     fputs(line,ficparo);  
   }    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
   ungetc(c,ficpar);    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
   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);    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   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);  and drawn. It helps understanding how is the covariance between two incidences.\
   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);   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
 while((c=getc(ficpar))=='#' && c!= EOF){    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. \
     ungetc(c,ficpar);  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
     fgets(line, MAXLINE, ficpar);  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
     puts(line);  standard deviations wide on each axis. <br>\
     fputs(line,ficparo);   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
   }   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   ungetc(c,ficpar);  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
    
        cov[1]=1;
   covar=matrix(0,NCOVMAX,1,n);    tj=cptcoveff;
   cptcovn=0;    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    j1=0;
     for(t=1; t<=tj;t++){
   ncovmodel=2+cptcovn;      for(i1=1; i1<=ncodemax[t];i1++){ 
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */        j1++;
          if  (cptcovn>0) {
   /* Read guess parameters */          fprintf(ficresprob, "\n#********** Variable "); 
   /* Reads comments: lines beginning with '#' */          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficresprob, "**********\n#\n");
     ungetc(c,ficpar);          fprintf(ficresprobcov, "\n#********** Variable "); 
     fgets(line, MAXLINE, ficpar);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     puts(line);          fprintf(ficresprobcov, "**********\n#\n");
     fputs(line,ficparo);          
   }          fprintf(ficgp, "\n#********** Variable "); 
   ungetc(c,ficpar);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficgp, "**********\n#\n");
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);          
     for(i=1; i <=nlstate; i++)          
     for(j=1; j <=nlstate+ndeath-1; j++){          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
       fscanf(ficpar,"%1d%1d",&i1,&j1);          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       fprintf(ficparo,"%1d%1d",i1,j1);          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
       printf("%1d%1d",i,j);          
       for(k=1; k<=ncovmodel;k++){          fprintf(ficresprobcor, "\n#********** Variable ");    
         fscanf(ficpar," %lf",&param[i][j][k]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         printf(" %lf",param[i][j][k]);          fprintf(ficresprobcor, "**********\n#");    
         fprintf(ficparo," %lf",param[i][j][k]);        }
       }        
       fscanf(ficpar,"\n");        for (age=bage; age<=fage; age ++){ 
       printf("\n");          cov[2]=age;
       fprintf(ficparo,"\n");          for (k=1; k<=cptcovn;k++) {
     }            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
            }
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (k=1; k<=cptcovprod;k++)
   p=param[1][1];            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
            
   /* Reads comments: lines beginning with '#' */          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
   while((c=getc(ficpar))=='#' && c!= EOF){          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     ungetc(c,ficpar);          gp=vector(1,(nlstate)*(nlstate+ndeath));
     fgets(line, MAXLINE, ficpar);          gm=vector(1,(nlstate)*(nlstate+ndeath));
     puts(line);      
     fputs(line,ficparo);          for(theta=1; theta <=npar; theta++){
   }            for(i=1; i<=npar; i++)
   ungetc(c,ficpar);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */            
   for(i=1; i <=nlstate; i++){            k=0;
     for(j=1; j <=nlstate+ndeath-1; j++){            for(i=1; i<= (nlstate); i++){
       fscanf(ficpar,"%1d%1d",&i1,&j1);              for(j=1; j<=(nlstate+ndeath);j++){
       printf("%1d%1d",i,j);                k=k+1;
       fprintf(ficparo,"%1d%1d",i1,j1);                gp[k]=pmmij[i][j];
       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]);            for(i=1; i<=npar; i++)
       }              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       fscanf(ficpar,"\n");      
       printf("\n");            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       fprintf(ficparo,"\n");            k=0;
     }            for(i=1; i<=(nlstate); i++){
   }              for(j=1; j<=(nlstate+ndeath);j++){
   delti=delti3[1][1];                k=k+1;
                  gm[k]=pmmij[i][j];
   /* Reads comments: lines beginning with '#' */              }
   while((c=getc(ficpar))=='#' && c!= EOF){            }
     ungetc(c,ficpar);       
     fgets(line, MAXLINE, ficpar);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     puts(line);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
     fputs(line,ficparo);          }
   }  
   ungetc(c,ficpar);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
              for(theta=1; theta <=npar; theta++)
   matcov=matrix(1,npar,1,npar);              trgradg[j][theta]=gradg[theta][j];
   for(i=1; i <=npar; i++){          
     fscanf(ficpar,"%s",&str);          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
     printf("%s",str);          matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
     fprintf(ficparo,"%s",str);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
     for(j=1; j <=i; j++){          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
       fscanf(ficpar," %le",&matcov[i][j]);          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       printf(" %.5le",matcov[i][j]);          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
       fprintf(ficparo," %.5le",matcov[i][j]);  
     }          pmij(pmmij,cov,ncovmodel,x,nlstate);
     fscanf(ficpar,"\n");          
     printf("\n");          k=0;
     fprintf(ficparo,"\n");          for(i=1; i<=(nlstate); i++){
   }            for(j=1; j<=(nlstate+ndeath);j++){
   for(i=1; i <=npar; i++)              k=k+1;
     for(j=i+1;j<=npar;j++)              mu[k][(int) age]=pmmij[i][j];
       matcov[i][j]=matcov[j][i];            }
              }
   printf("\n");          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
     /*-------- Rewriting paramater file ----------*/  
      strcpy(rfileres,"r");    /* "Rparameterfile */          /*printf("\n%d ",(int)age);
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
      strcat(rfileres,".");    /* */            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
      strcat(rfileres,optionfilext);    /* Other files have txt extension */            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     if((ficres =fopen(rfileres,"w"))==NULL) {            }*/
       printf("Problem writing new parameter file: %s\n", fileres);goto end;  
     }          fprintf(ficresprob,"\n%d ",(int)age);
     fprintf(ficres,"#%s\n",version);          fprintf(ficresprobcov,"\n%d ",(int)age);
              fprintf(ficresprobcor,"\n%d ",(int)age);
     /*-------- data file ----------*/  
     if((fic=fopen(datafile,"r"))==NULL)    {          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
       printf("Problem with datafile: %s\n", datafile);goto end;            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
     }          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
     n= lastobs;            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
     severity = vector(1,maxwav);          }
     outcome=imatrix(1,maxwav+1,1,n);          i=0;
     num=ivector(1,n);          for (k=1; k<=(nlstate);k++){
     moisnais=vector(1,n);            for (l=1; l<=(nlstate+ndeath);l++){ 
     annais=vector(1,n);              i=i++;
     moisdc=vector(1,n);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
     andc=vector(1,n);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
     agedc=vector(1,n);              for (j=1; j<=i;j++){
     cod=ivector(1,n);                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
     weight=vector(1,n);                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */              }
     mint=matrix(1,maxwav,1,n);            }
     anint=matrix(1,maxwav,1,n);          }/* end of loop for state */
     s=imatrix(1,maxwav+1,1,n);        } /* end of loop for age */
     adl=imatrix(1,maxwav+1,1,n);      
     tab=ivector(1,NCOVMAX);        /* Confidence intervalle of pij  */
     ncodemax=ivector(1,8);        /*
           fprintf(ficgp,"\nset noparametric;unset label");
     i=1;          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
     while (fgets(line, MAXLINE, fic) != NULL)    {          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
       if ((i >= firstobs) && (i <=lastobs)) {          fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
                  fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
         for (j=maxwav;j>=1;j--){          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
           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);        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         }        first1=1;
                for (k2=1; k2<=(nlstate);k2++){
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);            if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);            for (k1=1; k1<=(nlstate);k1++){
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);                i=(k1-1)*(nlstate+ndeath)+l1;
         for (j=ncovcol;j>=1;j--){                if(i<=j) continue;
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);                for (age=bage; age<=fage; age ++){ 
         }                  if ((int)age %5==0){
         num[i]=atol(stra);                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                            v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
           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;}*/                    mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
         i=i+1;                    c12=cv12/sqrt(v1*v2);
       }                    /* Computing eigen value of matrix of covariance */
     }                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     /* printf("ii=%d", ij);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
        scanf("%d",i);*/                    /* Eigen vectors */
   imx=i-1; /* Number of individuals */                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
   /* for (i=1; i<=imx; i++){                    v21=(lc1-v1)/cv12*v11;
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;                    v12=-v21;
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;                    v22=v11;
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;                    tnalp=v21/v11;
     }*/                    if(first1==1){
    /*  for (i=1; i<=imx; i++){                      first1=0;
      if (s[4][i]==9)  s[4][i]=-1;                      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);
      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]));}*/                    }
                      fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
                      /*printf(fignu*/
   /* Calculation of the number of parameter from char model*/                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
   Tvar=ivector(1,15);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
   Tprod=ivector(1,15);                    if(first==1){
   Tvaraff=ivector(1,15);                      first=0;
   Tvard=imatrix(1,15,1,2);                      fprintf(ficgp,"\nset parametric;unset label");
   Tage=ivector(1,15);                            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");
   if (strlen(model) >1){                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
     j=0, j1=0, k1=1, k2=1;   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
     j=nbocc(model,'+');  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
     j1=nbocc(model,'*');                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
     cptcovn=j+1;                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     cptcovprod=j1;                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                          fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
     strcpy(modelsav,model);                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
       printf("Error. Non available option model=%s ",model);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
       goto end;                      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),\
                                  mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     for(i=(j+1); i>=1;i--){                    }else{
       cutv(stra,strb,modelsav,'+');                      first=0;
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
       /*scanf("%d",i);*/                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
       if (strchr(strb,'*')) {                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
         cutv(strd,strc,strb,'*');                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
         if (strcmp(strc,"age")==0) {                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
           cptcovprod--;                    }/* if first */
           cutv(strb,stre,strd,'V');                  } /* age mod 5 */
           Tvar[i]=atoi(stre);                } /* end loop age */
           cptcovage++;                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
             Tage[cptcovage]=i;                first=1;
             /*printf("stre=%s ", stre);*/              } /*l12 */
         }            } /* k12 */
         else if (strcmp(strd,"age")==0) {          } /*l1 */
           cptcovprod--;        }/* k1 */
           cutv(strb,stre,strc,'V');      } /* loop covariates */
           Tvar[i]=atoi(stre);    }
           cptcovage++;    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
           Tage[cptcovage]=i;    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
         }    free_vector(xp,1,npar);
         else {    fclose(ficresprob);
           cutv(strb,stre,strc,'V');    fclose(ficresprobcov);
           Tvar[i]=ncovcol+k1;    fclose(ficresprobcor);
           cutv(strb,strc,strd,'V');    fflush(ficgp);
           Tprod[k1]=i;    fflush(fichtmcov);
           Tvard[k1][1]=atoi(strc);  }
           Tvard[k1][2]=atoi(stre);  
           Tvar[cptcovn+k2]=Tvard[k1][1];  
           Tvar[cptcovn+k2+1]=Tvard[k1][2];  /******************* Printing html file ***********/
           for (k=1; k<=lastobs;k++)  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];                    int lastpass, int stepm, int weightopt, char model[],\
           k1++;                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
           k2=k2+2;                    int popforecast, int estepm ,\
         }                    double jprev1, double mprev1,double anprev1, \
       }                    double jprev2, double mprev2,double anprev2){
       else {    int jj1, k1, i1, cpt;
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/  
        /*  scanf("%d",i);*/     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
       cutv(strd,strc,strb,'V');   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
       Tvar[i]=atoi(strc);             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
       }     fprintf(fichtm,"\
       strcpy(modelsav,stra);     - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
         scanf("%d",i);*/     fprintf(fichtm,"\
     }   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
 }             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
       fprintf(fichtm,"\
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);   - Life expectancies by age and initial health status (estepm=%2d months): \
   printf("cptcovprod=%d ", cptcovprod);     <a href=\"%s\">%s</a> <br>\n</li>",
   scanf("%d ",i);*/             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
     fclose(fic);  
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
     /*  if(mle==1){*/  
     if (weightopt != 1) { /* Maximisation without weights*/   m=cptcoveff;
       for(i=1;i<=n;i++) weight[i]=1.0;   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     }  
     /*-calculation of age at interview from date of interview and age at death -*/   jj1=0;
     agev=matrix(1,maxwav,1,imx);   for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
     for (i=1; i<=imx; i++) {       jj1++;
       for(m=2; (m<= maxwav); m++) {       if (cptcovn > 0) {
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          anint[m][i]=9999;         for (cpt=1; cpt<=cptcoveff;cpt++) 
          s[m][i]=-1;           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
        }         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;       }
       }       /* Pij */
     }       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
     for (i=1; i<=imx; i++)  {       /* Quasi-incidences */
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
       for(m=1; (m<= maxwav); m++){   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
         if(s[m][i] >0){  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
           if (s[m][i] >= nlstate+1) {         /* Stable prevalence in each health state */
             if(agedc[i]>0)         for(cpt=1; cpt<nlstate;cpt++){
               if(moisdc[i]!=99 && andc[i]!=9999)           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
                 agev[m][i]=agedc[i];  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/         }
            else {       for(cpt=1; cpt<=nlstate;cpt++) {
               if (andc[i]!=9999){          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
               printf("Warning negative age at death: %d line:%d\n",num[i],i);  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
               agev[m][i]=-1;       }
               }     } /* end i1 */
             }   }/* End k1 */
           }   fprintf(fichtm,"</ul>");
           else if(s[m][i] !=9){ /* Should no more exist */  
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);  
             if(mint[m][i]==99 || anint[m][i]==9999)   fprintf(fichtm,"\
               agev[m][i]=1;  \n<br><li><h4> Result files (second order: variances)</h4>\n\
             else if(agev[m][i] <agemin){   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
               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);*/   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
             }           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
             else if(agev[m][i] >agemax){   fprintf(fichtm,"\
               agemax=agev[m][i];   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
             }  
             /*agev[m][i]=anint[m][i]-annais[i];*/   fprintf(fichtm,"\
             /*   agev[m][i] = age[i]+2*m;*/   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
           }           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
           else { /* =9 */   fprintf(fichtm,"\
             agev[m][i]=1;   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
             s[m][i]=-1;           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
           }   fprintf(fichtm,"\
         }   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
         else /*= 0 Unknown */           subdirf2(fileres,"t"),subdirf2(fileres,"t"));
           agev[m][i]=1;   fprintf(fichtm,"\
       }   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
               subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
     }  
     for (i=1; i<=imx; i++)  {  /*  if(popforecast==1) fprintf(fichtm,"\n */
       for(m=1; (m<= maxwav); m++){  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
         if (s[m][i] > (nlstate+ndeath)) {  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
           printf("Error: Wrong value in nlstate or ndeath\n");    /*      <br>",fileres,fileres,fileres,fileres); */
           goto end;  /*  else  */
         }  /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
       }   fflush(fichtm);
     }   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);   m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     free_vector(severity,1,maxwav);  
     free_imatrix(outcome,1,maxwav+1,1,n);   jj1=0;
     free_vector(moisnais,1,n);   for(k1=1; k1<=m;k1++){
     free_vector(annais,1,n);     for(i1=1; i1<=ncodemax[k1];i1++){
     /* free_matrix(mint,1,maxwav,1,n);       jj1++;
        free_matrix(anint,1,maxwav,1,n);*/       if (cptcovn > 0) {
     free_vector(moisdc,1,n);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     free_vector(andc,1,n);         for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
             fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
     wav=ivector(1,imx);       }
     dh=imatrix(1,lastpass-firstpass+1,1,imx);       for(cpt=1; cpt<=nlstate;cpt++) {
     mw=imatrix(1,lastpass-firstpass+1,1,imx);         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
      prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
     /* Concatenates waves */  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);       }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2): %s%d.png<br>\
       Tcode=ivector(1,100);  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);     } /* end i1 */
       ncodemax[1]=1;   }/* End k1 */
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);   fprintf(fichtm,"</ul>");
         fflush(fichtm);
    codtab=imatrix(1,100,1,10);  }
    h=0;  
    m=pow(2,cptcoveff);  /******************* Gnuplot file **************/
    void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
    for(k=1;k<=cptcoveff; k++){  
      for(i=1; i <=(m/pow(2,k));i++){    char dirfileres[132],optfileres[132];
        for(j=1; j <= ncodemax[k]; j++){    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    int ng;
            h++;  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;  /*     printf("Problem with file %s",optionfilegnuplot); */
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
          }  /*   } */
        }  
      }    /*#ifdef windows */
    }    fprintf(ficgp,"cd \"%s\" \n",pathc);
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);      /*#endif */
       codtab[1][2]=1;codtab[2][2]=2; */    m=pow(2,cptcoveff);
    /* for(i=1; i <=m ;i++){  
       for(k=1; k <=cptcovn; k++){    strcpy(dirfileres,optionfilefiname);
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);    strcpy(optfileres,"vpl");
       }   /* 1eme*/
       printf("\n");    for (cpt=1; cpt<= nlstate ; cpt ++) {
       }     for (k1=1; k1<= m ; k1 ++) {
       scanf("%d",i);*/       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
           fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
    /* Calculates basic frequencies. Computes observed prevalence at single age       fprintf(ficgp,"set xlabel \"Age\" \n\
        and prints on file fileres'p'. */  set ylabel \"Probability\" \n\
   set ter png small\n\
      set size 0.65,0.65\n\
      plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       for (i=1; i<= nlstate ; i ++) {
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */         else fprintf(ficgp," \%%*lf (\%%*lf)");
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */       }
             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 Powell, parameters are in a vector p[] starting at p[1]       for (i=1; i<= nlstate ; i ++) {
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */         else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
     if(mle==1){       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);       for (i=1; i<= nlstate ; i ++) {
     }         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
             else fprintf(ficgp," \%%*lf (\%%*lf)");
     /*--------- results files --------------*/       }  
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
       }
     }
    jk=1;    /*2 eme*/
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    for (k1=1; k1<= m ; k1 ++) { 
    for(i=1,jk=1; i <=nlstate; i++){      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
      for(k=1; k <=(nlstate+ndeath); k++){      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
        if (k != i)      
          {      for (i=1; i<= nlstate+1 ; i ++) {
            printf("%d%d ",i,k);        k=2*i;
            fprintf(ficres,"%1d%1d ",i,k);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
            for(j=1; j <=ncovmodel; j++){        for (j=1; j<= nlstate+1 ; j ++) {
              printf("%f ",p[jk]);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
              fprintf(ficres,"%f ",p[jk]);          else fprintf(ficgp," \%%*lf (\%%*lf)");
              jk++;        }   
            }        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
            printf("\n");        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
            fprintf(ficres,"\n");        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
          }        for (j=1; j<= nlstate+1 ; j ++) {
      }          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
    }          else fprintf(ficgp," \%%*lf (\%%*lf)");
  if(mle==1){        }   
     /* Computing hessian and covariance matrix */        fprintf(ficgp,"\" t\"\" w l 0,");
     ftolhess=ftol; /* Usually correct */        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
     hesscov(matcov, p, npar, delti, ftolhess, func);        for (j=1; j<= nlstate+1 ; j ++) {
  }          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");          else fprintf(ficgp," \%%*lf (\%%*lf)");
     printf("# Scales (for hessian or gradient estimation)\n");        }   
      for(i=1,jk=1; i <=nlstate; i++){        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
       for(j=1; j <=nlstate+ndeath; j++){        else fprintf(ficgp,"\" t\"\" w l 0,");
         if (j!=i) {      }
           fprintf(ficres,"%1d%1d",i,j);    }
           printf("%1d%1d",i,j);    
           for(k=1; k<=ncovmodel;k++){    /*3eme*/
             printf(" %.5e",delti[jk]);    
             fprintf(ficres," %.5e",delti[jk]);    for (k1=1; k1<= m ; k1 ++) { 
             jk++;      for (cpt=1; cpt<= nlstate ; cpt ++) {
           }        k=2+nlstate*(2*cpt-2);
           printf("\n");        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
           fprintf(ficres,"\n");        fprintf(ficgp,"set ter png small\n\
         }  set size 0.65,0.65\n\
       }  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
      }        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
              for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     k=1;          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
     for(i=1;i<=npar;i++){          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
       /*  if (k>nlstate) k=1;          
       i1=(i-1)/(ncovmodel*nlstate)+1;        */
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);        for (i=1; i< nlstate ; i ++) {
       printf("%s%d%d",alph[k],i1,tab[i]);*/          fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
       fprintf(ficres,"%3d",i);          
       printf("%3d",i);        } 
       for(j=1; j<=i;j++){      }
         fprintf(ficres," %.5e",matcov[i][j]);    }
         printf(" %.5e",matcov[i][j]);    
       }    /* CV preval stable (period) */
       fprintf(ficres,"\n");    for (k1=1; k1<= m ; k1 ++) { 
       printf("\n");      for (cpt=1; cpt<=nlstate ; cpt ++) {
       k++;        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\
     while((c=getc(ficpar))=='#' && c!= EOF){  set ter png small\nset size 0.65,0.65\n\
       ungetc(c,ficpar);  unset log y\n\
       fgets(line, MAXLINE, ficpar);  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
       puts(line);        
       fputs(line,ficparo);        for (i=1; i< nlstate ; i ++)
     }          fprintf(ficgp,"+$%d",k+i+1);
     ungetc(c,ficpar);        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
     estepm=0;        
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);        l=3+(nlstate+ndeath)*cpt;
     if (estepm==0 || estepm < stepm) estepm=stepm;        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
     if (fage <= 2) {        for (i=1; i< nlstate ; i ++) {
       bage = ageminpar;          l=3+(nlstate+ndeath)*cpt;
       fage = agemaxpar;          fprintf(ficgp,"+$%d",l+i+1);
     }        }
            fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      } 
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    }  
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);    
      /* proba elementaires */
     while((c=getc(ficpar))=='#' && c!= EOF){    for(i=1,jk=1; i <=nlstate; i++){
     ungetc(c,ficpar);      for(k=1; k <=(nlstate+ndeath); k++){
     fgets(line, MAXLINE, ficpar);        if (k != i) {
     puts(line);          for(j=1; j <=ncovmodel; j++){
     fputs(line,ficparo);            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
   }            jk++; 
   ungetc(c,ficpar);            fprintf(ficgp,"\n");
            }
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);        }
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);      }
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);     }
        
   while((c=getc(ficpar))=='#' && c!= EOF){     for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
     ungetc(c,ficpar);       for(jk=1; jk <=m; jk++) {
     fgets(line, MAXLINE, ficpar);         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
     puts(line);         if (ng==2)
     fputs(line,ficparo);           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
   }         else
   ungetc(c,ficpar);           fprintf(ficgp,"\nset title \"Probability\"\n");
           fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
    dateprev1=anprev1+mprev1/12.+jprev1/365.;         for(k2=1; k2<=nlstate; k2++) {
    dateprev2=anprev2+mprev2/12.+jprev2/365.;           k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
   fscanf(ficpar,"pop_based=%d\n",&popbased);             if (k != k2){
   fprintf(ficparo,"pop_based=%d\n",popbased);                 if(ng==2)
   fprintf(ficres,"pop_based=%d\n",popbased);                   fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                 else
   while((c=getc(ficpar))=='#' && c!= EOF){                 fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
     ungetc(c,ficpar);               ij=1;
     fgets(line, MAXLINE, ficpar);               for(j=3; j <=ncovmodel; j++) {
     puts(line);                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
     fputs(line,ficparo);                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   }                   ij++;
   ungetc(c,ficpar);                 }
                  else
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);                   fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);               }
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);               fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
 while((c=getc(ficpar))=='#' && c!= EOF){                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
     ungetc(c,ficpar);                 ij=1;
     fgets(line, MAXLINE, ficpar);                 for(j=3; j <=ncovmodel; j++){
     puts(line);                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
     fputs(line,ficparo);                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   }                     ij++;
   ungetc(c,ficpar);                   }
                    else
   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(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   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);                 fprintf(ficgp,")");
                }
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
 /*------------ gnuplot -------------*/               i=i+ncovmodel;
   strcpy(optionfilegnuplot,optionfilefiname);             }
   strcat(optionfilegnuplot,".gp");           } /* end k */
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {         } /* end k2 */
     printf("Problem with file %s",optionfilegnuplot);       } /* end jk */
   }     } /* end ng */
   fclose(ficgp);     fflush(ficgp); 
  printinggnuplot(fileres, ageminpar,agemaxpar,fage, pathc,p);  }  /* end gnuplot */
 /*--------- index.htm --------*/  
   
   strcpy(optionfilehtm,optionfile);  /*************** Moving average **************/
   strcat(optionfilehtm,".htm");  int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {  
     printf("Problem with %s \n",optionfilehtm), exit(0);    int i, cpt, cptcod;
   }    int modcovmax =1;
     int mobilavrange, mob;
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n    double age;
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n  
 \n    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
 Total number of observations=%d <br>\n                             a covariate has 2 modalities */
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n    if (cptcovn<1) modcovmax=1; /* At least 1 pass */
 <hr  size=\"2\" color=\"#EC5E5E\">  
  <ul><li>Parameter files<br>\n    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n      if(mobilav==1) mobilavrange=5; /* default */
  - Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);      else mobilavrange=mobilav;
   fclose(fichtm);      for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);          for (cptcod=1;cptcod<=modcovmax;cptcod++)
              mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
 /*------------ free_vector  -------------*/      /* We keep the original values on the extreme ages bage, fage and for 
  chdir(path);         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. 
  free_ivector(wav,1,imx);      */ 
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      for (mob=3;mob <=mobilavrange;mob=mob+2){
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);          for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
  free_ivector(num,1,n);          for (i=1; i<=nlstate;i++){
  free_vector(agedc,1,n);            for (cptcod=1;cptcod<=modcovmax;cptcod++){
  /*free_matrix(covar,1,NCOVMAX,1,n);*/              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
  fclose(ficparo);                for (cpt=1;cpt<=(mob-1)/2;cpt++){
  fclose(ficres);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
   /*--------------- Prevalence limit --------------*/              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
              }
   strcpy(filerespl,"pl");          }
   strcat(filerespl,fileres);        }/* end age */
   if((ficrespl=fopen(filerespl,"w"))==NULL) {      }/* end mob */
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    }else return -1;
   }    return 0;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);  }/* End movingaverage */
   fprintf(ficrespl,"#Prevalence limit\n");  
   fprintf(ficrespl,"#Age ");  
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);  /************** Forecasting ******************/
   fprintf(ficrespl,"\n");  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 
   prlim=matrix(1,nlstate,1,nlstate);       agemin, agemax range of age
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       dateprev1 dateprev2 range of dates during which prevalence is computed
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */       anproj2 year of en of projection (same day and month as proj1).
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    */
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    int *popage;
   k=0;    double agec; /* generic age */
   agebase=ageminpar;    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
   agelim=agemaxpar;    double *popeffectif,*popcount;
   ftolpl=1.e-10;    double ***p3mat;
   i1=cptcoveff;    double ***mobaverage;
   if (cptcovn < 1){i1=1;}    char fileresf[FILENAMELENGTH];
   
   for(cptcov=1;cptcov<=i1;cptcov++){    agelim=AGESUP;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
         k=k+1;   
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    strcpy(fileresf,"f"); 
         fprintf(ficrespl,"\n#******");    strcat(fileresf,fileres);
         for(j=1;j<=cptcoveff;j++)    if((ficresf=fopen(fileresf,"w"))==NULL) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      printf("Problem with forecast resultfile: %s\n", fileresf);
         fprintf(ficrespl,"******\n");      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
            }
         for (age=agebase; age<=agelim; age++){    printf("Computing forecasting: result on file '%s' \n", fileresf);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
           fprintf(ficrespl,"%.0f",age );  
           for(i=1; i<=nlstate;i++)    if (cptcoveff==0) ncodemax[cptcoveff]=1;
           fprintf(ficrespl," %.5f", prlim[i][i]);  
           fprintf(ficrespl,"\n");    if (mobilav!=0) {
         }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       }      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
     }        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   fclose(ficrespl);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
   /*------------- h Pij x at various ages ------------*/    }
    
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    stepsize=(int) (stepm+YEARM-1)/YEARM;
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    if (stepm<=12) stepsize=1;
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    if(estepm < stepm){
   }      printf ("Problem %d lower than %d\n",estepm, stepm);
   printf("Computing pij: result on file '%s' \n", filerespij);    }
      else  hstepm=estepm;   
   stepsize=(int) (stepm+YEARM-1)/YEARM;  
   /*if (stepm<=24) stepsize=2;*/    hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
   agelim=AGESUP;                                 fractional in yp1 */
   hstepm=stepsize*YEARM; /* Every year of age */    anprojmean=yp;
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    yp2=modf((yp1*12),&yp);
      mprojmean=yp;
   k=0;    yp1=modf((yp2*30.5),&yp);
   for(cptcov=1;cptcov<=i1;cptcov++){    jprojmean=yp;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    if(jprojmean==0) jprojmean=1;
       k=k+1;    if(mprojmean==0) jprojmean=1;
         fprintf(ficrespij,"\n#****** ");  
         for(j=1;j<=cptcoveff;j++)    i1=cptcoveff;
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    if (cptcovn < 1){i1=1;}
         fprintf(ficrespij,"******\n");    
            fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    fprintf(ficresf,"#****** Routine prevforecast **\n");
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /*            if (h==(int)(YEARM*yearp)){ */
           oldm=oldms;savm=savms;    for(cptcov=1, k=0;cptcov<=i1;cptcov++){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
           fprintf(ficrespij,"# Age");        k=k+1;
           for(i=1; i<=nlstate;i++)        fprintf(ficresf,"\n#******");
             for(j=1; j<=nlstate+ndeath;j++)        for(j=1;j<=cptcoveff;j++) {
               fprintf(ficrespij," %1d-%1d",i,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(ficrespij,"\n");        }
            for (h=0; h<=nhstepm; h++){        fprintf(ficresf,"******\n");
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
             for(i=1; i<=nlstate;i++)        for(j=1; j<=nlstate+ndeath;j++){ 
               for(j=1; j<=nlstate+ndeath;j++)          for(i=1; i<=nlstate;i++)              
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);            fprintf(ficresf," p%d%d",i,j);
             fprintf(ficrespij,"\n");          fprintf(ficresf," p.%d",j);
              }        }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficrespij,"\n");          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); 
   varprob(optionfilefiname, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);            nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fclose(ficrespij);            oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
   /*---------- Forecasting ------------------*/            for (h=0; h<=nhstepm; h++){
   if((stepm == 1) && (strcmp(model,".")==0)){              if (h*hstepm/YEARM*stepm ==yearp) {
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);                fprintf(ficresf,"\n");
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);                for(j=1;j<=cptcoveff;j++) 
   }                  fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
   else{                fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
     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);              for(j=1; j<=nlstate+ndeath;j++) {
   }                ppij=0.;
                  for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
   /*---------- Health expectancies and variances ------------*/                    ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
   strcpy(filerest,"t");                    ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
   strcat(filerest,fileres);                  }
   if((ficrest=fopen(filerest,"w"))==NULL) {                  if (h*hstepm/YEARM*stepm== yearp) {
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;                    fprintf(ficresf," %.3f", p3mat[i][j][h]);
   }                  }
   printf("Computing Total LEs with variances: file '%s' \n", filerest);                } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
   strcpy(filerese,"e");                }
   strcat(filerese,fileres);              }/* end j */
   if((ficreseij=fopen(filerese,"w"))==NULL) {            } /* end h */
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }          } /* end agec */
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);        } /* end yearp */
       } /* end cptcod */
  strcpy(fileresv,"v");    } /* end  cptcov */
   strcat(fileresv,fileres);         
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  
   }    fclose(ficresf);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);  }
   calagedate=-1;  
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  /************** 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){
   k=0;    
   for(cptcov=1;cptcov<=i1;cptcov++){    int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    int *popage;
       k=k+1;    double calagedatem, agelim, kk1, kk2;
       fprintf(ficrest,"\n#****** ");    double *popeffectif,*popcount;
       for(j=1;j<=cptcoveff;j++)    double ***p3mat,***tabpop,***tabpopprev;
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    double ***mobaverage;
       fprintf(ficrest,"******\n");    char filerespop[FILENAMELENGTH];
   
       fprintf(ficreseij,"\n#****** ");    tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(j=1;j<=cptcoveff;j++)    tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    agelim=AGESUP;
       fprintf(ficreseij,"******\n");    calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
       fprintf(ficresvij,"\n#****** ");    prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       for(j=1;j<=cptcoveff;j++)    
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    
       fprintf(ficresvij,"******\n");    strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    if((ficrespop=fopen(filerespop,"w"))==NULL) {
       oldm=oldms;savm=savms;      printf("Problem with forecast resultfile: %s\n", filerespop);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);        fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
      }
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    printf("Computing forecasting: result on file '%s' \n", filerespop);
       oldm=oldms;savm=savms;    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);  
        if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
      if (mobilav!=0) {
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
       fprintf(ficrest,"\n");        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       epj=vector(1,nlstate+1);      }
       for(age=bage; age <=fage ;age++){    }
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);  
         if (popbased==1) {    stepsize=(int) (stepm+YEARM-1)/YEARM;
           for(i=1; i<=nlstate;i++)    if (stepm<=12) stepsize=1;
             prlim[i][i]=probs[(int)age][i][k];    
         }    agelim=AGESUP;
            
         fprintf(ficrest," %4.0f",age);    hstepm=1;
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    hstepm=hstepm/stepm; 
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    
             epj[j] += prlim[i][i]*eij[i][j][(int)age];    if (popforecast==1) {
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/      if((ficpop=fopen(popfile,"r"))==NULL) {
           }        printf("Problem with population file : %s\n",popfile);exit(0);
           epj[nlstate+1] +=epj[j];        fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
         }      } 
       popage=ivector(0,AGESUP);
         for(i=1, vepp=0.;i <=nlstate;i++)      popeffectif=vector(0,AGESUP);
           for(j=1;j <=nlstate;j++)      popcount=vector(0,AGESUP);
             vepp += vareij[i][j][(int)age];      
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));      i=1;   
         for(j=1;j <=nlstate;j++){      while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));     
         }      imx=i;
         fprintf(ficrest,"\n");      for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
       }    }
     }  
   }    for(cptcov=1,k=0;cptcov<=i2;cptcov++){
 free_matrix(mint,1,maxwav,1,n);     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);        k=k+1;
     free_vector(weight,1,n);        fprintf(ficrespop,"\n#******");
   fclose(ficreseij);        for(j=1;j<=cptcoveff;j++) {
   fclose(ficresvij);          fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
   fclose(ficrest);        }
   fclose(ficpar);        fprintf(ficrespop,"******\n");
   free_vector(epj,1,nlstate+1);        fprintf(ficrespop,"# Age");
          for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
   /*------- Variance limit prevalence------*/          if (popforecast==1)  fprintf(ficrespop," [Population]");
         
   strcpy(fileresvpl,"vpl");        for (cpt=0; cpt<=0;cpt++) { 
   strcat(fileresvpl,fileres);          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {          
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
     exit(0);            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
   }            nhstepm = nhstepm/hstepm; 
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);            
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   k=0;            oldm=oldms;savm=savms;
   for(cptcov=1;cptcov<=i1;cptcov++){            hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          
       k=k+1;            for (h=0; h<=nhstepm; h++){
       fprintf(ficresvpl,"\n#****** ");              if (h==(int) (calagedatem+YEARM*cpt)) {
       for(j=1;j<=cptcoveff;j++)                fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              } 
       fprintf(ficresvpl,"******\n");              for(j=1; j<=nlstate+ndeath;j++) {
                      kk1=0.;kk2=0;
       varpl=matrix(1,nlstate,(int) bage, (int) fage);                for(i=1; i<=nlstate;i++) {              
       oldm=oldms;savm=savms;                  if (mobilav==1) 
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);                    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];
                   }
   fclose(ficresvpl);                }
                 if (h==(int)(calagedatem+12*cpt)){
   /*---------- End : free ----------------*/                  tabpop[(int)(agedeb)][j][cptcod]=kk1;
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);                    /*fprintf(ficrespop," %.3f", kk1);
                        if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);                }
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);              }
                for(i=1; i<=nlstate;i++){
                  kk1=0.;
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);                  for(j=1; j<=nlstate;j++){
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);                    kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);                  }
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);                    tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
                }
   free_matrix(matcov,1,npar,1,npar);  
   free_vector(delti,1,npar);              if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
   free_matrix(agev,1,maxwav,1,imx);                fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);            }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fprintf(fichtm,"\n</body>");          }
   fclose(fichtm);        }
   fclose(ficgp);   
      /******/
   
   if(erreur >0)        for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
     printf("End of Imach with error or warning %d\n",erreur);          fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
   else   printf("End of Imach\n");          for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */            nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
              nhstepm = nhstepm/hstepm; 
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/            
   /*printf("Total time was %d uSec.\n", total_usecs);*/            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /*------ End -----------*/            oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
  end:              if (h==(int) (calagedatem+YEARM*cpt)) {
 #ifdef windows                fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
   /* chdir(pathcd);*/              } 
 #endif              for(j=1; j<=nlstate+ndeath;j++) {
  /*system("wgnuplot graph.plt");*/                kk1=0.;kk2=0;
  /*system("../gp37mgw/wgnuplot graph.plt");*/                for(i=1; i<=nlstate;i++) {              
  /*system("cd ../gp37mgw");*/                  kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/                }
  strcpy(plotcmd,GNUPLOTPROGRAM);                if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
  strcat(plotcmd," ");              }
  strcat(plotcmd,optionfilegnuplot);            }
  system(plotcmd);            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
 #ifdef windows        }
   while (z[0] != 'q') {     } 
     /* chdir(path); */    }
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");   
     scanf("%s",z);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     if (z[0] == 'c') system("./imach");  
     else if (z[0] == 'e') system(optionfilehtm);    if (popforecast==1) {
     else if (z[0] == 'g') system(plotcmd);      free_ivector(popage,0,AGESUP);
     else if (z[0] == 'q') exit(0);      free_vector(popeffectif,0,AGESUP);
   }      free_vector(popcount,0,AGESUP);
 #endif    }
 }    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.1.48  
changed lines
  Added in v.1.96


FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>