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version 1.41.2.1, 2003/06/12 10:43:20 version 1.97, 2004/02/20 13:25:42
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 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.97  2004/02/20 13:25:42  lievre
      Version 0.96d. Population forecasting command line is (temporarily)
   This program computes Healthy Life Expectancies from    suppressed.
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a  
   first survey ("cross") where individuals from different ages are    Revision 1.96  2003/07/15 15:38:55  brouard
   interviewed on their health status or degree of disability (in the    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
   case of a health survey which is our main interest) -2- at least a    rewritten within the same printf. Workaround: many printfs.
   second wave of interviews ("longitudinal") which measure each change  
   (if any) in individual health status.  Health expectancies are    Revision 1.95  2003/07/08 07:54:34  brouard
   computed from the time spent in each health state according to a    * imach.c (Repository):
   model. More health states you consider, more time is necessary to reach the    (Repository): Using imachwizard code to output a more meaningful covariance
   Maximum Likelihood of the parameters involved in the model.  The    matrix (cov(a12,c31) instead of numbers.
   simplest model is the multinomial logistic model where pij is the  
   probability to be observed in state j at the second wave    Revision 1.94  2003/06/27 13:00:02  brouard
   conditional to be observed in state i at the first wave. Therefore    Just cleaning
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where  
   'age' is age and 'sex' is a covariate. If you want to have a more    Revision 1.93  2003/06/25 16:33:55  brouard
   complex model than "constant and age", you should modify the program    (Module): On windows (cygwin) function asctime_r doesn't
   where the markup *Covariates have to be included here again* invites    exist so I changed back to asctime which exists.
   you to do it.  More covariates you add, slower the    (Module): Version 0.96b
   convergence.  
     Revision 1.92  2003/06/25 16:30:45  brouard
   The advantage of this computer programme, compared to a simple    (Module): On windows (cygwin) function asctime_r doesn't
   multinomial logistic model, is clear when the delay between waves is not    exist so I changed back to asctime which exists.
   identical for each individual. Also, if a individual missed an  
   intermediate interview, the information is lost, but taken into    Revision 1.91  2003/06/25 15:30:29  brouard
   account using an interpolation or extrapolation.      * imach.c (Repository): Duplicated warning errors corrected.
     (Repository): Elapsed time after each iteration is now output. It
   hPijx is the probability to be observed in state i at age x+h    helps to forecast when convergence will be reached. Elapsed time
   conditional to the observed state i at age x. The delay 'h' can be    is stamped in powell.  We created a new html file for the graphs
   split into an exact number (nh*stepm) of unobserved intermediate    concerning matrix of covariance. It has extension -cov.htm.
   states. This elementary transition (by month or quarter trimester,  
   semester or year) is model as a multinomial logistic.  The hPx    Revision 1.90  2003/06/24 12:34:15  brouard
   matrix is simply the matrix product of nh*stepm elementary matrices    (Module): Some bugs corrected for windows. Also, when
   and the contribution of each individual to the likelihood is simply    mle=-1 a template is output in file "or"mypar.txt with the design
   hPijx.    of the covariance matrix to be input.
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.89  2003/06/24 12:30:52  brouard
   of the life expectancies. It also computes the prevalence limits.    (Module): Some bugs corrected for windows. Also, when
      mle=-1 a template is output in file "or"mypar.txt with the design
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    of the covariance matrix to be input.
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.88  2003/06/23 17:54:56  brouard
   from the European Union.    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.87  2003/06/18 12:26:01  brouard
   can be accessed at http://euroreves.ined.fr/imach .    Version 0.96
   **********************************************************************/  
      Revision 1.86  2003/06/17 20:04:08  brouard
 #include <math.h>    (Module): Change position of html and gnuplot routines and added
 #include <stdio.h>    routine fileappend.
 #include <stdlib.h>  
 #include <unistd.h>    Revision 1.85  2003/06/17 13:12:43  brouard
     * imach.c (Repository): Check when date of death was earlier that
 #define MAXLINE 256    current date of interview. It may happen when the death was just
 #define GNUPLOTPROGRAM "wgnuplot"    prior to the death. In this case, dh was negative and likelihood
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/    was wrong (infinity). We still send an "Error" but patch by
 #define FILENAMELENGTH 80    assuming that the date of death was just one stepm after the
 /*#define DEBUG*/    interview.
     (Repository): Because some people have very long ID (first column)
 /*#define windows*/    we changed int to long in num[] and we added a new lvector for
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    memory allocation. But we also truncated to 8 characters (left
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    truncation)
     (Repository): No more line truncation errors.
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Revision 1.84  2003/06/13 21:44:43  brouard
     * imach.c (Repository): Replace "freqsummary" at a correct
 #define NINTERVMAX 8    place. It differs from routine "prevalence" which may be called
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    many times. Probs is memory consuming and must be used with
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    parcimony.
 #define NCOVMAX 8 /* Maximum number of covariates */    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Revision 1.83  2003/06/10 13:39:11  lievre
 #define AGESUP 130    *** empty log message ***
 #define AGEBASE 40  
     Revision 1.82  2003/06/05 15:57:20  brouard
     Add log in  imach.c and  fullversion number is now printed.
 int erreur; /* Error number */  
 int nvar;  */
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  /*
 int npar=NPARMAX;     Interpolated Markov Chain
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Short summary of the programme:
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    
 int popbased=0;    This program computes Healthy Life Expectancies from
     cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 int *wav; /* Number of waves for this individuual 0 is possible */    first survey ("cross") where individuals from different ages are
 int maxwav; /* Maxim number of waves */    interviewed on their health status or degree of disability (in the
 int jmin, jmax; /* min, max spacing between 2 waves */    case of a health survey which is our main interest) -2- at least a
 int mle, weightopt;    second wave of interviews ("longitudinal") which measure each change
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    (if any) in individual health status.  Health expectancies are
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    computed from the time spent in each health state according to a
 double jmean; /* Mean space between 2 waves */    model. More health states you consider, more time is necessary to reach the
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Maximum Likelihood of the parameters involved in the model.  The
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    simplest model is the multinomial logistic model where pij is the
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    probability to be observed in state j at the second wave
 FILE *ficgp,*ficresprob,*ficpop;    conditional to be observed in state i at the first wave. Therefore
 FILE *ficreseij;    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   char filerese[FILENAMELENGTH];    'age' is age and 'sex' is a covariate. If you want to have a more
  FILE  *ficresvij;    complex model than "constant and age", you should modify the program
   char fileresv[FILENAMELENGTH];    where the markup *Covariates have to be included here again* invites
  FILE  *ficresvpl;    you to do it.  More covariates you add, slower the
   char fileresvpl[FILENAMELENGTH];    convergence.
   
 #define NR_END 1    The advantage of this computer programme, compared to a simple
 #define FREE_ARG char*    multinomial logistic model, is clear when the delay between waves is not
 #define FTOL 1.0e-10    identical for each individual. Also, if a individual missed an
     intermediate interview, the information is lost, but taken into
 #define NRANSI    account using an interpolation or extrapolation.  
 #define ITMAX 200  
     hPijx is the probability to be observed in state i at age x+h
 #define TOL 2.0e-4    conditional to the observed state i at age x. The delay 'h' can be
     split into an exact number (nh*stepm) of unobserved intermediate
 #define CGOLD 0.3819660    states. This elementary transition (by month, quarter,
 #define ZEPS 1.0e-10    semester or year) is modelled as a multinomial logistic.  The hPx
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    matrix is simply the matrix product of nh*stepm elementary matrices
     and the contribution of each individual to the likelihood is simply
 #define GOLD 1.618034    hPijx.
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Also this programme outputs the covariance matrix of the parameters but also
     of the life expectancies. It also computes the stable prevalence. 
 static double maxarg1,maxarg2;    
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))             Institut national d'études démographiques, Paris.
      This software have been partly granted by Euro-REVES, a concerted action
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    from the European Union.
 #define rint(a) floor(a+0.5)    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
 static double sqrarg;    can be accessed at http://euroreves.ined.fr/imach .
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 int imx;    
 int stepm;    **********************************************************************/
 /* Stepm, step in month: minimum step interpolation*/  /*
     main
 int estepm;    read parameterfile
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    read datafile
     concatwav
 int m,nb;    freqsummary
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    if (mle >= 1)
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;      mlikeli
 double **pmmij, ***probs, ***mobaverage;    print results files
 double dateintmean=0;    if mle==1 
        computes hessian
 double *weight;    read end of parameter file: agemin, agemax, bage, fage, estepm
 int **s; /* Status */        begin-prev-date,...
 double *agedc, **covar, idx;    open gnuplot file
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    open html file
     stable prevalence
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */     for age prevalim()
 double ftolhess; /* Tolerance for computing hessian */    h Pij x
     variance of p varprob
 /**************** split *************************/    forecasting if prevfcast==1 prevforecast call prevalence()
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    health expectancies
 {    Variance-covariance of DFLE
    char *s;                             /* pointer */    prevalence()
    int  l1, l2;                         /* length counters */     movingaverage()
     varevsij() 
    l1 = strlen( path );                 /* length of path */    if popbased==1 varevsij(,popbased)
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    total life expectancies
 #ifdef windows    Variance of stable prevalence
    s = strrchr( path, '\\' );           /* find last / */   end
 #else  */
    s = strrchr( path, '/' );            /* find last / */  
 #endif  
    if ( s == NULL ) {                   /* no directory, so use current */  
 #if     defined(__bsd__)                /* get current working directory */   
       extern char       *getwd( );  #include <math.h>
   #include <stdio.h>
       if ( getwd( dirc ) == NULL ) {  #include <stdlib.h>
 #else  #include <unistd.h>
       extern char       *getcwd( );  
   #include <sys/time.h>
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  #include <time.h>
 #endif  #include "timeval.h"
          return( GLOCK_ERROR_GETCWD );  
       }  /* #include <libintl.h> */
       strcpy( name, path );             /* we've got it */  /* #define _(String) gettext (String) */
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */  #define MAXLINE 256
       l2 = strlen( s );                 /* length of filename */  #define GNUPLOTPROGRAM "gnuplot"
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
       strcpy( name, s );                /* save file name */  #define FILENAMELENGTH 132
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  /*#define DEBUG*/
       dirc[l1-l2] = 0;                  /* add zero */  /*#define windows*/
    }  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
    l1 = strlen( dirc );                 /* length of directory */  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 #ifdef windows  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 #else  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  
 #endif  #define NINTERVMAX 8
    s = strrchr( name, '.' );            /* find last / */  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
    s++;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
    strcpy(ext,s);                       /* save extension */  #define NCOVMAX 8 /* Maximum number of covariates */
    l1= strlen( name);  #define MAXN 20000
    l2= strlen( s)+1;  #define YEARM 12. /* Number of months per year */
    strncpy( finame, name, l1-l2);  #define AGESUP 130
    finame[l1-l2]= 0;  #define AGEBASE 40
    return( 0 );                         /* we're done */  #ifdef unix
 }  #define DIRSEPARATOR '/'
   #define ODIRSEPARATOR '\\'
   #else
 /******************************************/  #define DIRSEPARATOR '\\'
   #define ODIRSEPARATOR '/'
 void replace(char *s, char*t)  #endif
 {  
   int i;  /* $Id$ */
   int lg=20;  /* $State$ */
   i=0;  
   lg=strlen(t);  char version[]="Imach version 0.96d, February 2004, INED-EUROREVES ";
   for(i=0; i<= lg; i++) {  char fullversion[]="$Revision$ $Date$"; 
     (s[i] = t[i]);  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
     if (t[i]== '\\') s[i]='/';  int nvar;
   }  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 }  int npar=NPARMAX;
   int nlstate=2; /* Number of live states */
 int nbocc(char *s, char occ)  int ndeath=1; /* Number of dead states */
 {  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   int i,j=0;  int popbased=0;
   int lg=20;  
   i=0;  int *wav; /* Number of waves for this individuual 0 is possible */
   lg=strlen(s);  int maxwav; /* Maxim number of waves */
   for(i=0; i<= lg; i++) {  int jmin, jmax; /* min, max spacing between 2 waves */
   if  (s[i] == occ ) j++;  int gipmx, gsw; /* Global variables on the number of contributions 
   }                     to the likelihood and the sum of weights (done by funcone)*/
   return j;  int mle, weightopt;
 }  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
 void cutv(char *u,char *v, char*t, char occ)  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. */
   int i,lg,j,p=0;  double jmean; /* Mean space between 2 waves */
   i=0;  double **oldm, **newm, **savm; /* Working pointers to matrices */
   for(j=0; j<=strlen(t)-1; j++) {  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   }  FILE *ficlog, *ficrespow;
   int globpr; /* Global variable for printing or not */
   lg=strlen(t);  double fretone; /* Only one call to likelihood */
   for(j=0; j<p; j++) {  long ipmx; /* Number of contributions */
     (u[j] = t[j]);  double sw; /* Sum of weights */
   }  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
      u[p]='\0';  FILE *ficresilk;
   FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
    for(j=0; j<= lg; j++) {  FILE *ficresprobmorprev;
     if (j>=(p+1))(v[j-p-1] = t[j]);  FILE *fichtm, *fichtmcov; /* Html File */
   }  FILE *ficreseij;
 }  char filerese[FILENAMELENGTH];
   FILE  *ficresvij;
 /********************** nrerror ********************/  char fileresv[FILENAMELENGTH];
   FILE  *ficresvpl;
 void nrerror(char error_text[])  char fileresvpl[FILENAMELENGTH];
 {  char title[MAXLINE];
   fprintf(stderr,"ERREUR ...\n");  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   fprintf(stderr,"%s\n",error_text);  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   exit(1);  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
 }  char command[FILENAMELENGTH];
 /*********************** vector *******************/  int  outcmd=0;
 double *vector(int nl, int nh)  
 {  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  char filelog[FILENAMELENGTH]; /* Log file */
   if (!v) nrerror("allocation failure in vector");  char filerest[FILENAMELENGTH];
   return v-nl+NR_END;  char fileregp[FILENAMELENGTH];
 }  char popfile[FILENAMELENGTH];
   
 /************************ free vector ******************/  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 void free_vector(double*v, int nl, int nh)  
 {  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   free((FREE_ARG)(v+nl-NR_END));  struct timezone tzp;
 }  extern int gettimeofday();
   struct tm tmg, tm, tmf, *gmtime(), *localtime();
 /************************ivector *******************************/  long time_value;
 int *ivector(long nl,long nh)  extern long time();
 {  char strcurr[80], strfor[80];
   int *v;  
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  #define NR_END 1
   if (!v) nrerror("allocation failure in ivector");  #define FREE_ARG char*
   return v-nl+NR_END;  #define FTOL 1.0e-10
 }  
   #define NRANSI 
 /******************free ivector **************************/  #define ITMAX 200 
 void free_ivector(int *v, long nl, long nh)  
 {  #define TOL 2.0e-4 
   free((FREE_ARG)(v+nl-NR_END));  
 }  #define CGOLD 0.3819660 
   #define ZEPS 1.0e-10 
 /******************* imatrix *******************************/  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
 int **imatrix(long nrl, long nrh, long ncl, long nch)  
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  #define GOLD 1.618034 
 {  #define GLIMIT 100.0 
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  #define TINY 1.0e-20 
   int **m;  
    static double maxarg1,maxarg2;
   /* allocate pointers to rows */  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   if (!m) nrerror("allocation failure 1 in matrix()");    
   m += NR_END;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   m -= nrl;  #define rint(a) floor(a+0.5)
    
    static double sqrarg;
   /* allocate rows and set pointers to them */  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  int imx; 
   m[nrl] -= ncl;  int stepm;
    /* Stepm, step in month: minimum step interpolation*/
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
    int estepm;
   /* return pointer to array of pointers to rows */  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   return m;  
 }  int m,nb;
   long *num;
 /****************** free_imatrix *************************/  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;
 void free_imatrix(m,nrl,nrh,ncl,nch)  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
       int **m;  double **pmmij, ***probs;
       long nch,ncl,nrh,nrl;  double dateintmean=0;
      /* free an int matrix allocated by imatrix() */  
 {  double *weight;
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  int **s; /* Status */
   free((FREE_ARG) (m+nrl-NR_END));  double *agedc, **covar, idx;
 }  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   
 /******************* matrix *******************************/  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 double **matrix(long nrl, long nrh, long ncl, long nch)  double ftolhess; /* Tolerance for computing hessian */
 {  
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  /**************** split *************************/
   double **m;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   {
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    char  *ss;                            /* pointer */
   if (!m) nrerror("allocation failure 1 in matrix()");    int   l1, l2;                         /* length counters */
   m += NR_END;  
   m -= nrl;    l1 = strlen(path );                   /* length of path */
     if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    if ( ss == NULL ) {                   /* no directory, so use current */
   m[nrl] += NR_END;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   m[nrl] -= ncl;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       /* get current working directory */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;      /*    extern  char* getcwd ( char *buf , int len);*/
   return m;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 }        return( GLOCK_ERROR_GETCWD );
       }
 /*************************free matrix ************************/      strcpy( name, path );               /* we've got it */
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)    } else {                              /* strip direcotry from path */
 {      ss++;                               /* after this, the filename */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));      l2 = strlen( ss );                  /* length of filename */
   free((FREE_ARG)(m+nrl-NR_END));      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 }      strcpy( name, ss );         /* save file name */
       strncpy( dirc, path, l1 - l2 );     /* now the directory */
 /******************* ma3x *******************************/      dirc[l1-l2] = 0;                    /* add zero */
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)    }
 {    l1 = strlen( dirc );                  /* length of directory */
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;    /*#ifdef windows
   double ***m;    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }
   #else
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }
   if (!m) nrerror("allocation failure 1 in matrix()");  #endif
   m += NR_END;    */
   m -= nrl;    ss = strrchr( name, '.' );            /* find last / */
     ss++;
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));    strcpy(ext,ss);                       /* save extension */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    l1= strlen( name);
   m[nrl] += NR_END;    l2= strlen(ss)+1;
   m[nrl] -= ncl;    strncpy( finame, name, l1-l2);
     finame[l1-l2]= 0;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;    return( 0 );                          /* we're done */
   }
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;  /******************************************/
   m[nrl][ncl] -= nll;  
   for (j=ncl+1; j<=nch; j++)  void replace_back_to_slash(char *s, char*t)
     m[nrl][j]=m[nrl][j-1]+nlay;  {
      int i;
   for (i=nrl+1; i<=nrh; i++) {    int lg=0;
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;    i=0;
     for (j=ncl+1; j<=nch; j++)    lg=strlen(t);
       m[i][j]=m[i][j-1]+nlay;    for(i=0; i<= lg; i++) {
   }      (s[i] = t[i]);
   return m;      if (t[i]== '\\') s[i]='/';
 }    }
   }
 /*************************free ma3x ************************/  
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  int nbocc(char *s, char occ)
 {  {
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));    int i,j=0;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));    int lg=20;
   free((FREE_ARG)(m+nrl-NR_END));    i=0;
 }    lg=strlen(s);
     for(i=0; i<= lg; i++) {
 /***************** f1dim *************************/    if  (s[i] == occ ) j++;
 extern int ncom;    }
 extern double *pcom,*xicom;    return j;
 extern double (*nrfunc)(double []);  }
    
 double f1dim(double x)  void cutv(char *u,char *v, char*t, char occ)
 {  {
   int j;    /* cuts string t into u and v where u is ended by char occ excluding it
   double f;       and v is after occ excluding it too : ex cutv(u,v,"abcdef2ghi2j",2)
   double *xt;       gives u="abcedf" and v="ghi2j" */
      int i,lg,j,p=0;
   xt=vector(1,ncom);    i=0;
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];    for(j=0; j<=strlen(t)-1; j++) {
   f=(*nrfunc)(xt);      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   free_vector(xt,1,ncom);    }
   return f;  
 }    lg=strlen(t);
     for(j=0; j<p; j++) {
 /*****************brent *************************/      (u[j] = t[j]);
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)    }
 {       u[p]='\0';
   int iter;  
   double a,b,d,etemp;     for(j=0; j<= lg; j++) {
   double fu,fv,fw,fx;      if (j>=(p+1))(v[j-p-1] = t[j]);
   double ftemp;    }
   double p,q,r,tol1,tol2,u,v,w,x,xm;  }
   double e=0.0;  
    /********************** nrerror ********************/
   a=(ax < cx ? ax : cx);  
   b=(ax > cx ? ax : cx);  void nrerror(char error_text[])
   x=w=v=bx;  {
   fw=fv=fx=(*f)(x);    fprintf(stderr,"ERREUR ...\n");
   for (iter=1;iter<=ITMAX;iter++) {    fprintf(stderr,"%s\n",error_text);
     xm=0.5*(a+b);    exit(EXIT_FAILURE);
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  }
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  /*********************** vector *******************/
     printf(".");fflush(stdout);  double *vector(int nl, int nh)
 #ifdef DEBUG  {
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);    double *v;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 #endif    if (!v) nrerror("allocation failure in vector");
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    return v-nl+NR_END;
       *xmin=x;  }
       return fx;  
     }  /************************ free vector ******************/
     ftemp=fu;  void free_vector(double*v, int nl, int nh)
     if (fabs(e) > tol1) {  {
       r=(x-w)*(fx-fv);    free((FREE_ARG)(v+nl-NR_END));
       q=(x-v)*(fx-fw);  }
       p=(x-v)*q-(x-w)*r;  
       q=2.0*(q-r);  /************************ivector *******************************/
       if (q > 0.0) p = -p;  int *ivector(long nl,long nh)
       q=fabs(q);  {
       etemp=e;    int *v;
       e=d;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    if (!v) nrerror("allocation failure in ivector");
         d=CGOLD*(e=(x >= xm ? a-x : b-x));    return v-nl+NR_END;
       else {  }
         d=p/q;  
         u=x+d;  /******************free ivector **************************/
         if (u-a < tol2 || b-u < tol2)  void free_ivector(int *v, long nl, long nh)
           d=SIGN(tol1,xm-x);  {
       }    free((FREE_ARG)(v+nl-NR_END));
     } else {  }
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }  /************************lvector *******************************/
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  long *lvector(long nl,long nh)
     fu=(*f)(u);  {
     if (fu <= fx) {    long *v;
       if (u >= x) a=x; else b=x;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       SHFT(v,w,x,u)    if (!v) nrerror("allocation failure in ivector");
         SHFT(fv,fw,fx,fu)    return v-nl+NR_END;
         } else {  }
           if (u < x) a=u; else b=u;  
           if (fu <= fw || w == x) {  /******************free lvector **************************/
             v=w;  void free_lvector(long *v, long nl, long nh)
             w=u;  {
             fv=fw;    free((FREE_ARG)(v+nl-NR_END));
             fw=fu;  }
           } else if (fu <= fv || v == x || v == w) {  
             v=u;  /******************* imatrix *******************************/
             fv=fu;  int **imatrix(long nrl, long nrh, long ncl, long nch) 
           }       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
         }  { 
   }    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   nrerror("Too many iterations in brent");    int **m; 
   *xmin=x;    
   return fx;    /* allocate pointers to rows */ 
 }    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     if (!m) nrerror("allocation failure 1 in matrix()"); 
 /****************** mnbrak ***********************/    m += NR_END; 
     m -= nrl; 
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    
             double (*func)(double))    
 {    /* allocate rows and set pointers to them */ 
   double ulim,u,r,q, dum;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   double fu;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
      m[nrl] += NR_END; 
   *fa=(*func)(*ax);    m[nrl] -= ncl; 
   *fb=(*func)(*bx);    
   if (*fb > *fa) {    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     SHFT(dum,*ax,*bx,dum)    
       SHFT(dum,*fb,*fa,dum)    /* return pointer to array of pointers to rows */ 
       }    return m; 
   *cx=(*bx)+GOLD*(*bx-*ax);  } 
   *fc=(*func)(*cx);  
   while (*fb > *fc) {  /****************** free_imatrix *************************/
     r=(*bx-*ax)*(*fb-*fc);  void free_imatrix(m,nrl,nrh,ncl,nch)
     q=(*bx-*cx)*(*fb-*fa);        int **m;
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/        long nch,ncl,nrh,nrl; 
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));       /* free an int matrix allocated by imatrix() */ 
     ulim=(*bx)+GLIMIT*(*cx-*bx);  { 
     if ((*bx-u)*(u-*cx) > 0.0) {    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       fu=(*func)(u);    free((FREE_ARG) (m+nrl-NR_END)); 
     } else if ((*cx-u)*(u-ulim) > 0.0) {  } 
       fu=(*func)(u);  
       if (fu < *fc) {  /******************* matrix *******************************/
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  double **matrix(long nrl, long nrh, long ncl, long nch)
           SHFT(*fb,*fc,fu,(*func)(u))  {
           }    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    double **m;
       u=ulim;  
       fu=(*func)(u);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     } else {    if (!m) nrerror("allocation failure 1 in matrix()");
       u=(*cx)+GOLD*(*cx-*bx);    m += NR_END;
       fu=(*func)(u);    m -= nrl;
     }  
     SHFT(*ax,*bx,*cx,u)    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       SHFT(*fa,*fb,*fc,fu)    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       }    m[nrl] += NR_END;
 }    m[nrl] -= ncl;
   
 /*************** linmin ************************/    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     return m;
 int ncom;    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
 double *pcom,*xicom;     */
 double (*nrfunc)(double []);  }
    
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  /*************************free matrix ************************/
 {  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   double brent(double ax, double bx, double cx,  {
                double (*f)(double), double tol, double *xmin);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double f1dim(double x);    free((FREE_ARG)(m+nrl-NR_END));
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  }
               double *fc, double (*func)(double));  
   int j;  /******************* ma3x *******************************/
   double xx,xmin,bx,ax;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   double fx,fb,fa;  {
      long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   ncom=n;    double ***m;
   pcom=vector(1,n);  
   xicom=vector(1,n);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   nrfunc=func;    if (!m) nrerror("allocation failure 1 in matrix()");
   for (j=1;j<=n;j++) {    m += NR_END;
     pcom[j]=p[j];    m -= nrl;
     xicom[j]=xi[j];  
   }    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   ax=0.0;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   xx=1.0;    m[nrl] += NR_END;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    m[nrl] -= ncl;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  
 #ifdef DEBUG    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  
 #endif    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
   for (j=1;j<=n;j++) {    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     xi[j] *= xmin;    m[nrl][ncl] += NR_END;
     p[j] += xi[j];    m[nrl][ncl] -= nll;
   }    for (j=ncl+1; j<=nch; j++) 
   free_vector(xicom,1,n);      m[nrl][j]=m[nrl][j-1]+nlay;
   free_vector(pcom,1,n);    
 }    for (i=nrl+1; i<=nrh; i++) {
       m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
 /*************** powell ************************/      for (j=ncl+1; j<=nch; j++) 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,        m[i][j]=m[i][j-1]+nlay;
             double (*func)(double []))    }
 {    return m; 
   void linmin(double p[], double xi[], int n, double *fret,    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
               double (*func)(double []));             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   int i,ibig,j;    */
   double del,t,*pt,*ptt,*xit;  }
   double fp,fptt;  
   double *xits;  /*************************free ma3x ************************/
   pt=vector(1,n);  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   ptt=vector(1,n);  {
   xit=vector(1,n);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   xits=vector(1,n);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   *fret=(*func)(p);    free((FREE_ARG)(m+nrl-NR_END));
   for (j=1;j<=n;j++) pt[j]=p[j];  }
   for (*iter=1;;++(*iter)) {  
     fp=(*fret);  /*************** function subdirf ***********/
     ibig=0;  char *subdirf(char fileres[])
     del=0.0;  {
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    /* Caution optionfilefiname is hidden */
     for (i=1;i<=n;i++)    strcpy(tmpout,optionfilefiname);
       printf(" %d %.12f",i, p[i]);    strcat(tmpout,"/"); /* Add to the right */
     printf("\n");    strcat(tmpout,fileres);
     for (i=1;i<=n;i++) {    return tmpout;
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  }
       fptt=(*fret);  
 #ifdef DEBUG  /*************** function subdirf2 ***********/
       printf("fret=%lf \n",*fret);  char *subdirf2(char fileres[], char *preop)
 #endif  {
       printf("%d",i);fflush(stdout);    
       linmin(p,xit,n,fret,func);    /* Caution optionfilefiname is hidden */
       if (fabs(fptt-(*fret)) > del) {    strcpy(tmpout,optionfilefiname);
         del=fabs(fptt-(*fret));    strcat(tmpout,"/");
         ibig=i;    strcat(tmpout,preop);
       }    strcat(tmpout,fileres);
 #ifdef DEBUG    return tmpout;
       printf("%d %.12e",i,(*fret));  }
       for (j=1;j<=n;j++) {  
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  /*************** function subdirf3 ***********/
         printf(" x(%d)=%.12e",j,xit[j]);  char *subdirf3(char fileres[], char *preop, char *preop2)
       }  {
       for(j=1;j<=n;j++)    
         printf(" p=%.12e",p[j]);    /* Caution optionfilefiname is hidden */
       printf("\n");    strcpy(tmpout,optionfilefiname);
 #endif    strcat(tmpout,"/");
     }    strcat(tmpout,preop);
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    strcat(tmpout,preop2);
 #ifdef DEBUG    strcat(tmpout,fileres);
       int k[2],l;    return tmpout;
       k[0]=1;  }
       k[1]=-1;  
       printf("Max: %.12e",(*func)(p));  /***************** f1dim *************************/
       for (j=1;j<=n;j++)  extern int ncom; 
         printf(" %.12e",p[j]);  extern double *pcom,*xicom;
       printf("\n");  extern double (*nrfunc)(double []); 
       for(l=0;l<=1;l++) {   
         for (j=1;j<=n;j++) {  double f1dim(double x) 
           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]);    int j; 
         }    double f;
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    double *xt; 
       }   
 #endif    xt=vector(1,ncom); 
     for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     f=(*nrfunc)(xt); 
       free_vector(xit,1,n);    free_vector(xt,1,ncom); 
       free_vector(xits,1,n);    return f; 
       free_vector(ptt,1,n);  } 
       free_vector(pt,1,n);  
       return;  /*****************brent *************************/
     }  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  { 
     for (j=1;j<=n;j++) {    int iter; 
       ptt[j]=2.0*p[j]-pt[j];    double a,b,d,etemp;
       xit[j]=p[j]-pt[j];    double fu,fv,fw,fx;
       pt[j]=p[j];    double ftemp;
     }    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     fptt=(*func)(ptt);    double e=0.0; 
     if (fptt < fp) {   
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    a=(ax < cx ? ax : cx); 
       if (t < 0.0) {    b=(ax > cx ? ax : cx); 
         linmin(p,xit,n,fret,func);    x=w=v=bx; 
         for (j=1;j<=n;j++) {    fw=fv=fx=(*f)(x); 
           xi[j][ibig]=xi[j][n];    for (iter=1;iter<=ITMAX;iter++) { 
           xi[j][n]=xit[j];      xm=0.5*(a+b); 
         }      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
 #ifdef DEBUG      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      printf(".");fflush(stdout);
         for(j=1;j<=n;j++)      fprintf(ficlog,".");fflush(ficlog);
           printf(" %.12e",xit[j]);  #ifdef DEBUG
         printf("\n");      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
 #endif      fprintf(ficlog,"br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
       }      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
     }  #endif
   }      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
 }        *xmin=x; 
         return fx; 
 /**** Prevalence limit ****************/      } 
       ftemp=fu;
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)      if (fabs(e) > tol1) { 
 {        r=(x-w)*(fx-fv); 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit        q=(x-v)*(fx-fw); 
      matrix by transitions matrix until convergence is reached */        p=(x-v)*q-(x-w)*r; 
         q=2.0*(q-r); 
   int i, ii,j,k;        if (q > 0.0) p = -p; 
   double min, max, maxmin, maxmax,sumnew=0.;        q=fabs(q); 
   double **matprod2();        etemp=e; 
   double **out, cov[NCOVMAX], **pmij();        e=d; 
   double **newm;        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   double agefin, delaymax=50 ; /* Max number of years to converge */          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         else { 
   for (ii=1;ii<=nlstate+ndeath;ii++)          d=p/q; 
     for (j=1;j<=nlstate+ndeath;j++){          u=x+d; 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);          if (u-a < tol2 || b-u < tol2) 
     }            d=SIGN(tol1,xm-x); 
         } 
    cov[1]=1.;      } else { 
          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */      } 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
     newm=savm;      fu=(*f)(u); 
     /* Covariates have to be included here again */      if (fu <= fx) { 
      cov[2]=agefin;        if (u >= x) a=x; else b=x; 
          SHFT(v,w,x,u) 
       for (k=1; k<=cptcovn;k++) {          SHFT(fv,fw,fx,fu) 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];          } else { 
         /*      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]]);*/            if (u < x) a=u; else b=u; 
       }            if (fu <= fw || w == x) { 
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];              v=w; 
       for (k=1; k<=cptcovprod;k++)              w=u; 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];              fv=fw; 
               fw=fu; 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/            } else if (fu <= fv || v == x || v == w) { 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/              v=u; 
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/              fv=fu; 
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);            } 
           } 
     savm=oldm;    } 
     oldm=newm;    nrerror("Too many iterations in brent"); 
     maxmax=0.;    *xmin=x; 
     for(j=1;j<=nlstate;j++){    return fx; 
       min=1.;  } 
       max=0.;  
       for(i=1; i<=nlstate; i++) {  /****************** mnbrak ***********************/
         sumnew=0;  
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
         prlim[i][j]= newm[i][j]/(1-sumnew);              double (*func)(double)) 
         max=FMAX(max,prlim[i][j]);  { 
         min=FMIN(min,prlim[i][j]);    double ulim,u,r,q, dum;
       }    double fu; 
       maxmin=max-min;   
       maxmax=FMAX(maxmax,maxmin);    *fa=(*func)(*ax); 
     }    *fb=(*func)(*bx); 
     if(maxmax < ftolpl){    if (*fb > *fa) { 
       return prlim;      SHFT(dum,*ax,*bx,dum) 
     }        SHFT(dum,*fb,*fa,dum) 
   }        } 
 }    *cx=(*bx)+GOLD*(*bx-*ax); 
     *fc=(*func)(*cx); 
 /*************** transition probabilities ***************/    while (*fb > *fc) { 
       r=(*bx-*ax)*(*fb-*fc); 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )      q=(*bx-*cx)*(*fb-*fa); 
 {      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   double s1, s2;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   /*double t34;*/      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   int i,j,j1, nc, ii, jj;      if ((*bx-u)*(u-*cx) > 0.0) { 
         fu=(*func)(u); 
     for(i=1; i<= nlstate; i++){      } else if ((*cx-u)*(u-ulim) > 0.0) { 
     for(j=1; j<i;j++){        fu=(*func)(u); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        if (fu < *fc) { 
         /*s2 += param[i][j][nc]*cov[nc];*/          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];            SHFT(*fb,*fc,fu,(*func)(u)) 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/            } 
       }      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       ps[i][j]=s2;        u=ulim; 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        fu=(*func)(u); 
     }      } else { 
     for(j=i+1; j<=nlstate+ndeath;j++){        u=(*cx)+GOLD*(*cx-*bx); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){        fu=(*func)(u); 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      } 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/      SHFT(*ax,*bx,*cx,u) 
       }        SHFT(*fa,*fb,*fc,fu) 
       ps[i][j]=s2;        } 
     }  } 
   }  
     /*ps[3][2]=1;*/  /*************** linmin ************************/
   
   for(i=1; i<= nlstate; i++){  int ncom; 
      s1=0;  double *pcom,*xicom;
     for(j=1; j<i; j++)  double (*nrfunc)(double []); 
       s1+=exp(ps[i][j]);   
     for(j=i+1; j<=nlstate+ndeath; j++)  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       s1+=exp(ps[i][j]);  { 
     ps[i][i]=1./(s1+1.);    double brent(double ax, double bx, double cx, 
     for(j=1; j<i; j++)                 double (*f)(double), double tol, double *xmin); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    double f1dim(double x); 
     for(j=i+1; j<=nlstate+ndeath; j++)    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
       ps[i][j]= exp(ps[i][j])*ps[i][i];                double *fc, double (*func)(double)); 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    int j; 
   } /* end i */    double xx,xmin,bx,ax; 
     double fx,fb,fa;
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){   
     for(jj=1; jj<= nlstate+ndeath; jj++){    ncom=n; 
       ps[ii][jj]=0;    pcom=vector(1,n); 
       ps[ii][ii]=1;    xicom=vector(1,n); 
     }    nrfunc=func; 
   }    for (j=1;j<=n;j++) { 
       pcom[j]=p[j]; 
       xicom[j]=xi[j]; 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    } 
     for(jj=1; jj<= nlstate+ndeath; jj++){    ax=0.0; 
      printf("%lf ",ps[ii][jj]);    xx=1.0; 
    }    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     printf("\n ");    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
     }  #ifdef DEBUG
     printf("\n ");printf("%lf ",cov[2]);*/    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 /*    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  #endif
   goto end;*/    for (j=1;j<=n;j++) { 
     return ps;      xi[j] *= xmin; 
 }      p[j] += xi[j]; 
     } 
 /**************** Product of 2 matrices ******************/    free_vector(xicom,1,n); 
     free_vector(pcom,1,n); 
 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  char *asc_diff_time(long time_sec, char ascdiff[])
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  {
   /* in, b, out are matrice of pointers which should have been initialized    long sec_left, days, hours, minutes;
      before: only the contents of out is modified. The function returns    days = (time_sec) / (60*60*24);
      a pointer to pointers identical to out */    sec_left = (time_sec) % (60*60*24);
   long i, j, k;    hours = (sec_left) / (60*60) ;
   for(i=nrl; i<= nrh; i++)    sec_left = (sec_left) %(60*60);
     for(k=ncolol; k<=ncoloh; k++)    minutes = (sec_left) /60;
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    sec_left = (sec_left) % (60);
         out[i][k] +=in[i][j]*b[j][k];    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
     return ascdiff;
   return out;  }
 }  
   /*************** powell ************************/
   void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
 /************* Higher Matrix Product ***************/              double (*func)(double [])) 
   { 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    void linmin(double p[], double xi[], int n, double *fret, 
 {                double (*func)(double [])); 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    int i,ibig,j; 
      duration (i.e. until    double del,t,*pt,*ptt,*xit;
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    double fp,fptt;
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    double *xits;
      (typically every 2 years instead of every month which is too big).    int niterf, itmp;
      Model is determined by parameters x and covariates have to be  
      included manually here.    pt=vector(1,n); 
     ptt=vector(1,n); 
      */    xit=vector(1,n); 
     xits=vector(1,n); 
   int i, j, d, h, k;    *fret=(*func)(p); 
   double **out, cov[NCOVMAX];    for (j=1;j<=n;j++) pt[j]=p[j]; 
   double **newm;    for (*iter=1;;++(*iter)) { 
       fp=(*fret); 
   /* Hstepm could be zero and should return the unit matrix */      ibig=0; 
   for (i=1;i<=nlstate+ndeath;i++)      del=0.0; 
     for (j=1;j<=nlstate+ndeath;j++){      last_time=curr_time;
       oldm[i][j]=(i==j ? 1.0 : 0.0);      (void) gettimeofday(&curr_time,&tzp);
       po[i][j][0]=(i==j ? 1.0 : 0.0);      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
     }      fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
   for(h=1; h <=nhstepm; h++){      for (i=1;i<=n;i++) {
     for(d=1; d <=hstepm; d++){        printf(" %d %.12f",i, p[i]);
       newm=savm;        fprintf(ficlog," %d %.12lf",i, p[i]);
       /* Covariates have to be included here again */        fprintf(ficrespow," %.12lf", p[i]);
       cov[1]=1.;      }
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      printf("\n");
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      fprintf(ficlog,"\n");
       for (k=1; k<=cptcovage;k++)      fprintf(ficrespow,"\n");fflush(ficrespow);
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      if(*iter <=3){
       for (k=1; k<=cptcovprod;k++)        tm = *localtime(&curr_time.tv_sec);
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        strcpy(strcurr,asctime(&tmf));
   /*       asctime_r(&tm,strcurr); */
         forecast_time=curr_time;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/        itmp = strlen(strcurr);
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        if(strcurr[itmp-1]=='\n')
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,          strcurr[itmp-1]='\0';
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       savm=oldm;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       oldm=newm;        for(niterf=10;niterf<=30;niterf+=10){
     }          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
     for(i=1; i<=nlstate+ndeath; i++)          tmf = *localtime(&forecast_time.tv_sec);
       for(j=1;j<=nlstate+ndeath;j++) {  /*      asctime_r(&tmf,strfor); */
         po[i][j][h]=newm[i][j];          strcpy(strfor,asctime(&tmf));
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);          itmp = strlen(strfor);
          */          if(strfor[itmp-1]=='\n')
       }          strfor[itmp-1]='\0';
   } /* end h */          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
   return po;          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s or\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
 }        }
       }
       for (i=1;i<=n;i++) { 
 /*************** log-likelihood *************/        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
 double func( double *x)        fptt=(*fret); 
 {  #ifdef DEBUG
   int i, ii, j, k, mi, d, kk;        printf("fret=%lf \n",*fret);
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        fprintf(ficlog,"fret=%lf \n",*fret);
   double **out;  #endif
   double sw; /* Sum of weights */        printf("%d",i);fflush(stdout);
   double lli; /* Individual log likelihood */        fprintf(ficlog,"%d",i);fflush(ficlog);
   long ipmx;        linmin(p,xit,n,fret,func); 
   /*extern weight */        if (fabs(fptt-(*fret)) > del) { 
   /* We are differentiating ll according to initial status */          del=fabs(fptt-(*fret)); 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/          ibig=i; 
   /*for(i=1;i<imx;i++)        } 
     printf(" %d\n",s[4][i]);  #ifdef DEBUG
   */        printf("%d %.12e",i,(*fret));
   cov[1]=1.;        fprintf(ficlog,"%d %.12e",i,(*fret));
         for (j=1;j<=n;j++) {
   for(k=1; k<=nlstate; k++) ll[k]=0.;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){          printf(" x(%d)=%.12e",j,xit[j]);
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     for(mi=1; mi<= wav[i]-1; mi++){        }
       for (ii=1;ii<=nlstate+ndeath;ii++)        for(j=1;j<=n;j++) {
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);          printf(" p=%.12e",p[j]);
       for(d=0; d<dh[mi][i]; d++){          fprintf(ficlog," p=%.12e",p[j]);
         newm=savm;        }
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;        printf("\n");
         for (kk=1; kk<=cptcovage;kk++) {        fprintf(ficlog,"\n");
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  #endif
         }      } 
              if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  #ifdef DEBUG
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        int k[2],l;
         savm=oldm;        k[0]=1;
         oldm=newm;        k[1]=-1;
                printf("Max: %.12e",(*func)(p));
                fprintf(ficlog,"Max: %.12e",(*func)(p));
       } /* end mult */        for (j=1;j<=n;j++) {
                printf(" %.12e",p[j]);
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);          fprintf(ficlog," %.12e",p[j]);
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        }
       ipmx +=1;        printf("\n");
       sw += weight[i];        fprintf(ficlog,"\n");
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        for(l=0;l<=1;l++) {
     } /* end of wave */          for (j=1;j<=n;j++) {
   } /* end of individual */            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]);
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */          }
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   return -l;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 }        }
   #endif
   
 /*********** Maximum Likelihood Estimation ***************/  
         free_vector(xit,1,n); 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        free_vector(xits,1,n); 
 {        free_vector(ptt,1,n); 
   int i,j, iter;        free_vector(pt,1,n); 
   double **xi,*delti;        return; 
   double fret;      } 
   xi=matrix(1,npar,1,npar);      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   for (i=1;i<=npar;i++)      for (j=1;j<=n;j++) { 
     for (j=1;j<=npar;j++)        ptt[j]=2.0*p[j]-pt[j]; 
       xi[i][j]=(i==j ? 1.0 : 0.0);        xit[j]=p[j]-pt[j]; 
   printf("Powell\n");        pt[j]=p[j]; 
   powell(p,xi,npar,ftol,&iter,&fret,func);      } 
       fptt=(*func)(ptt); 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));      if (fptt < fp) { 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         if (t < 0.0) { 
 }          linmin(p,xit,n,fret,func); 
           for (j=1;j<=n;j++) { 
 /**** Computes Hessian and covariance matrix ***/            xi[j][ibig]=xi[j][n]; 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))            xi[j][n]=xit[j]; 
 {          }
   double  **a,**y,*x,pd;  #ifdef DEBUG
   double **hess;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   int i, j,jk;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   int *indx;          for(j=1;j<=n;j++){
             printf(" %.12e",xit[j]);
   double hessii(double p[], double delta, int theta, double delti[]);            fprintf(ficlog," %.12e",xit[j]);
   double hessij(double p[], double delti[], int i, int j);          }
   void lubksb(double **a, int npar, int *indx, double b[]) ;          printf("\n");
   void ludcmp(double **a, int npar, int *indx, double *d) ;          fprintf(ficlog,"\n");
   #endif
   hess=matrix(1,npar,1,npar);        }
       } 
   printf("\nCalculation of the hessian matrix. Wait...\n");    } 
   for (i=1;i<=npar;i++){  } 
     printf("%d",i);fflush(stdout);  
     hess[i][i]=hessii(p,ftolhess,i,delti);  /**** Prevalence limit (stable prevalence)  ****************/
     /*printf(" %f ",p[i]);*/  
     /*printf(" %lf ",hess[i][i]);*/  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   }  {
      /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   for (i=1;i<=npar;i++) {       matrix by transitions matrix until convergence is reached */
     for (j=1;j<=npar;j++)  {  
       if (j>i) {    int i, ii,j,k;
         printf(".%d%d",i,j);fflush(stdout);    double min, max, maxmin, maxmax,sumnew=0.;
         hess[i][j]=hessij(p,delti,i,j);    double **matprod2();
         hess[j][i]=hess[i][j];        double **out, cov[NCOVMAX], **pmij();
         /*printf(" %lf ",hess[i][j]);*/    double **newm;
       }    double agefin, delaymax=50 ; /* Max number of years to converge */
     }  
   }    for (ii=1;ii<=nlstate+ndeath;ii++)
   printf("\n");      for (j=1;j<=nlstate+ndeath;j++){
         oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");      }
    
   a=matrix(1,npar,1,npar);     cov[1]=1.;
   y=matrix(1,npar,1,npar);   
   x=vector(1,npar);   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   indx=ivector(1,npar);    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   for (i=1;i<=npar;i++)      newm=savm;
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];      /* Covariates have to be included here again */
   ludcmp(a,npar,indx,&pd);       cov[2]=agefin;
     
   for (j=1;j<=npar;j++) {        for (k=1; k<=cptcovn;k++) {
     for (i=1;i<=npar;i++) x[i]=0;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     x[j]=1;          /*      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]]);*/
     lubksb(a,npar,indx,x);        }
     for (i=1;i<=npar;i++){        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       matcov[i][j]=x[i];        for (k=1; k<=cptcovprod;k++)
     }          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   }  
         /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
   printf("\n#Hessian matrix#\n");        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   for (i=1;i<=npar;i++) {        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     for (j=1;j<=npar;j++) {      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
       printf("%.3e ",hess[i][j]);  
     }      savm=oldm;
     printf("\n");      oldm=newm;
   }      maxmax=0.;
       for(j=1;j<=nlstate;j++){
   /* Recompute Inverse */        min=1.;
   for (i=1;i<=npar;i++)        max=0.;
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        for(i=1; i<=nlstate; i++) {
   ludcmp(a,npar,indx,&pd);          sumnew=0;
           for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   /*  printf("\n#Hessian matrix recomputed#\n");          prlim[i][j]= newm[i][j]/(1-sumnew);
           max=FMAX(max,prlim[i][j]);
   for (j=1;j<=npar;j++) {          min=FMIN(min,prlim[i][j]);
     for (i=1;i<=npar;i++) x[i]=0;        }
     x[j]=1;        maxmin=max-min;
     lubksb(a,npar,indx,x);        maxmax=FMAX(maxmax,maxmin);
     for (i=1;i<=npar;i++){      }
       y[i][j]=x[i];      if(maxmax < ftolpl){
       printf("%.3e ",y[i][j]);        return prlim;
     }      }
     printf("\n");    }
   }  }
   */  
   /*************** transition probabilities ***************/ 
   free_matrix(a,1,npar,1,npar);  
   free_matrix(y,1,npar,1,npar);  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   free_vector(x,1,npar);  {
   free_ivector(indx,1,npar);    double s1, s2;
   free_matrix(hess,1,npar,1,npar);    /*double t34;*/
     int i,j,j1, nc, ii, jj;
   
 }      for(i=1; i<= nlstate; i++){
       for(j=1; j<i;j++){
 /*************** hessian matrix ****************/        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
 double hessii( double x[], double delta, int theta, double delti[])          /*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 i;          /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/
   int l=1, lmax=20;        }
   double k1,k2;        ps[i][j]=s2;
   double p2[NPARMAX+1];        /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/
   double res;      }
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      for(j=i+1; j<=nlstate+ndeath;j++){
   double fx;        for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   int k=0,kmax=10;          s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   double l1;          /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/
         }
   fx=func(x);        ps[i][j]=s2;
   for (i=1;i<=npar;i++) p2[i]=x[i];      }
   for(l=0 ; l <=lmax; l++){    }
     l1=pow(10,l);      /*ps[3][2]=1;*/
     delts=delt;  
     for(k=1 ; k <kmax; k=k+1){    for(i=1; i<= nlstate; i++){
       delt = delta*(l1*k);       s1=0;
       p2[theta]=x[theta] +delt;      for(j=1; j<i; j++)
       k1=func(p2)-fx;        s1+=exp(ps[i][j]);
       p2[theta]=x[theta]-delt;      for(j=i+1; j<=nlstate+ndeath; j++)
       k2=func(p2)-fx;        s1+=exp(ps[i][j]);
       /*res= (k1-2.0*fx+k2)/delt/delt; */      ps[i][i]=1./(s1+1.);
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */      for(j=1; j<i; j++)
              ps[i][j]= exp(ps[i][j])*ps[i][i];
 #ifdef DEBUG      for(j=i+1; j<=nlstate+ndeath; 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);        ps[i][j]= exp(ps[i][j])*ps[i][i];
 #endif      /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    } /* end i */
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  
         k=kmax;    for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       }      for(jj=1; jj<= nlstate+ndeath; jj++){
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */        ps[ii][jj]=0;
         k=kmax; l=lmax*10.;        ps[ii][ii]=1;
       }      }
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){    }
         delts=delt;  
       }  
     }    /*   for(ii=1; ii<= nlstate+ndeath; ii++){
   }      for(jj=1; jj<= nlstate+ndeath; jj++){
   delti[theta]=delts;       printf("%lf ",ps[ii][jj]);
   return res;     }
        printf("\n ");
 }      }
       printf("\n ");printf("%lf ",cov[2]);*/
 double hessij( double x[], double delti[], int thetai,int thetaj)  /*
 {    for(i=1; i<= npar; i++) printf("%f ",x[i]);
   int i;    goto end;*/
   int l=1, l1, lmax=20;      return ps;
   double k1,k2,k3,k4,res,fx;  }
   double p2[NPARMAX+1];  
   int k;  /**************** Product of 2 matrices ******************/
   
   fx=func(x);  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
   for (k=1; k<=2; k++) {  {
     for (i=1;i<=npar;i++) p2[i]=x[i];    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
     p2[thetai]=x[thetai]+delti[thetai]/k;       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;    /* in, b, out are matrice of pointers which should have been initialized 
     k1=func(p2)-fx;       before: only the contents of out is modified. The function returns
         a pointer to pointers identical to out */
     p2[thetai]=x[thetai]+delti[thetai]/k;    long i, j, k;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    for(i=nrl; i<= nrh; i++)
     k2=func(p2)-fx;      for(k=ncolol; k<=ncoloh; k++)
          for(j=ncl,out[i][k]=0.; j<=nch; j++)
     p2[thetai]=x[thetai]-delti[thetai]/k;          out[i][k] +=in[i][j]*b[j][k];
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k3=func(p2)-fx;    return out;
    }
     p2[thetai]=x[thetai]-delti[thetai]/k;  
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k4=func(p2)-fx;  /************* Higher Matrix Product ***************/
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */  
 #ifdef DEBUG  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     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    /* Computes the transition matrix starting at age 'age' over 
   }       'nhstepm*hstepm*stepm' months (i.e. until
   return res;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
 }       nhstepm*hstepm matrices. 
        Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
 /************** Inverse of matrix **************/       (typically every 2 years instead of every month which is too big 
 void ludcmp(double **a, int n, int *indx, double *d)       for the memory).
 {       Model is determined by parameters x and covariates have to be 
   int i,imax,j,k;       included manually here. 
   double big,dum,sum,temp;  
   double *vv;       */
    
   vv=vector(1,n);    int i, j, d, h, k;
   *d=1.0;    double **out, cov[NCOVMAX];
   for (i=1;i<=n;i++) {    double **newm;
     big=0.0;  
     for (j=1;j<=n;j++)    /* Hstepm could be zero and should return the unit matrix */
       if ((temp=fabs(a[i][j])) > big) big=temp;    for (i=1;i<=nlstate+ndeath;i++)
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");      for (j=1;j<=nlstate+ndeath;j++){
     vv[i]=1.0/big;        oldm[i][j]=(i==j ? 1.0 : 0.0);
   }        po[i][j][0]=(i==j ? 1.0 : 0.0);
   for (j=1;j<=n;j++) {      }
     for (i=1;i<j;i++) {    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       sum=a[i][j];    for(h=1; h <=nhstepm; h++){
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];      for(d=1; d <=hstepm; d++){
       a[i][j]=sum;        newm=savm;
     }        /* Covariates have to be included here again */
     big=0.0;        cov[1]=1.;
     for (i=j;i<=n;i++) {        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
       sum=a[i][j];        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       for (k=1;k<j;k++)        for (k=1; k<=cptcovage;k++)
         sum -= a[i][k]*a[k][j];          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       a[i][j]=sum;        for (k=1; k<=cptcovprod;k++)
       if ( (dum=vv[i]*fabs(sum)) >= big) {          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         big=dum;  
         imax=i;  
       }        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
     }        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
     if (j != imax) {        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
       for (k=1;k<=n;k++) {                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         dum=a[imax][k];        savm=oldm;
         a[imax][k]=a[j][k];        oldm=newm;
         a[j][k]=dum;      }
       }      for(i=1; i<=nlstate+ndeath; i++)
       *d = -(*d);        for(j=1;j<=nlstate+ndeath;j++) {
       vv[imax]=vv[j];          po[i][j][h]=newm[i][j];
     }          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
     indx[j]=imax;           */
     if (a[j][j] == 0.0) a[j][j]=TINY;        }
     if (j != n) {    } /* end h */
       dum=1.0/(a[j][j]);    return po;
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  }
     }  
   }  
   free_vector(vv,1,n);  /* Doesn't work */  /*************** log-likelihood *************/
 ;  double func( double *x)
 }  {
     int i, ii, j, k, mi, d, kk;
 void lubksb(double **a, int n, int *indx, double b[])    double l, ll[NLSTATEMAX], cov[NCOVMAX];
 {    double **out;
   int i,ii=0,ip,j;    double sw; /* Sum of weights */
   double sum;    double lli; /* Individual log likelihood */
      int s1, s2;
   for (i=1;i<=n;i++) {    double bbh, survp;
     ip=indx[i];    long ipmx;
     sum=b[ip];    /*extern weight */
     b[ip]=b[i];    /* We are differentiating ll according to initial status */
     if (ii)    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    /*for(i=1;i<imx;i++) 
     else if (sum) ii=i;      printf(" %d\n",s[4][i]);
     b[i]=sum;    */
   }    cov[1]=1.;
   for (i=n;i>=1;i--) {  
     sum=b[i];    for(k=1; k<=nlstate; k++) ll[k]=0.;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  
     b[i]=sum/a[i][i];    if(mle==1){
   }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
 /************ Frequencies ********************/          for (ii=1;ii<=nlstate+ndeath;ii++)
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)            for (j=1;j<=nlstate+ndeath;j++){
 {  /* Some frequencies */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                savm[ii][j]=(ii==j ? 1.0 : 0.0);
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;            }
   double ***freq; /* Frequencies */          for(d=0; d<dh[mi][i]; d++){
   double *pp;            newm=savm;
   double pos, k2, dateintsum=0,k2cpt=0;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   FILE *ficresp;            for (kk=1; kk<=cptcovage;kk++) {
   char fileresp[FILENAMELENGTH];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
              }
   pp=vector(1,nlstate);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   strcpy(fileresp,"p");            savm=oldm;
   strcat(fileresp,fileres);            oldm=newm;
   if((ficresp=fopen(fileresp,"w"))==NULL) {          } /* end mult */
     printf("Problem with prevalence resultfile: %s\n", fileresp);        
     exit(0);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
   }          /* But now since version 0.9 we anticipate for bias and large stepm.
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   j1=0;           * (in months) between two waves is not a multiple of stepm, we rounded to 
             * the nearest (and in case of equal distance, to the lowest) interval but now
   j=cptcoveff;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
   if (cptcovn<1) {j=1;ncodemax[1]=1;}           * (i.e to dh[mi][i]-1) saved in 'savm'. The we inter(extra)polate the
             * probability in order to take into account the bias as a fraction of the way
   for(k1=1; k1<=j;k1++){           * from savm to out if bh is neagtive or even beyond if bh is positive. bh varies
     for(i1=1; i1<=ncodemax[k1];i1++){           * -stepm/2 to stepm/2 .
       j1++;           * For stepm=1 the results are the same as for previous versions of Imach.
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);           * For stepm > 1 the results are less biased than in previous versions. 
         scanf("%d", i);*/           */
       for (i=-1; i<=nlstate+ndeath; i++)            s1=s[mw[mi][i]][i];
         for (jk=-1; jk<=nlstate+ndeath; jk++)            s2=s[mw[mi+1][i]][i];
           for(m=agemin; m <= agemax+3; m++)          bbh=(double)bh[mi][i]/(double)stepm; 
             freq[i][jk][m]=0;          /* bias is positive if real duration
                 * is higher than the multiple of stepm and negative otherwise.
       dateintsum=0;           */
       k2cpt=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]));*/
       for (i=1; i<=imx; i++) {          if( s2 > nlstate){ 
         bool=1;            /* i.e. if s2 is a death state and if the date of death is known then the contribution
         if  (cptcovn>0) {               to the likelihood is the probability to die between last step unit time and current 
           for (z1=1; z1<=cptcoveff; z1++)               step unit time, which is also the differences between probability to die before dh 
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])               and probability to die before dh-stepm . 
               bool=0;               In version up to 0.92 likelihood was computed
         }          as if date of death was unknown. Death was treated as any other
         if (bool==1) {          health state: the date of the interview describes the actual state
           for(m=firstpass; m<=lastpass; m++){          and not the date of a change in health state. The former idea was
             k2=anint[m][i]+(mint[m][i]/12.);          to consider that at each interview the state was recorded
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          (healthy, disable or death) and IMaCh was corrected; but when we
               if(agev[m][i]==0) agev[m][i]=agemax+1;          introduced the exact date of death then we should have modified
               if(agev[m][i]==1) agev[m][i]=agemax+2;          the contribution of an exact death to the likelihood. This new
               if (m<lastpass) {          contribution is smaller and very dependent of the step unit
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          stepm. It is no more the probability to die between last interview
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          and month of death but the probability to survive from last
               }          interview up to one month before death multiplied by the
                        probability to die within a month. Thanks to Chris
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {          Jackson for correcting this bug.  Former versions increased
                 dateintsum=dateintsum+k2;          mortality artificially. The bad side is that we add another loop
                 k2cpt++;          which slows down the processing. The difference can be up to 10%
               }          lower mortality.
             }            */
           }            lli=log(out[s1][s2] - savm[s1][s2]);
         }          }else{
       }            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
                    /*  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 */
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          } 
           /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
       if  (cptcovn>0) {          /*if(lli ==000.0)*/
         fprintf(ficresp, "\n#********** Variable ");          /*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); */
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          ipmx +=1;
         fprintf(ficresp, "**********\n#");          sw += weight[i];
       }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for(i=1; i<=nlstate;i++)        } /* end of wave */
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      } /* end of individual */
       fprintf(ficresp, "\n");    }  else if(mle==2){
            for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for(i=(int)agemin; i <= (int)agemax+3; i++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         if(i==(int)agemax+3)        for(mi=1; mi<= wav[i]-1; mi++){
           printf("Total");          for (ii=1;ii<=nlstate+ndeath;ii++)
         else            for (j=1;j<=nlstate+ndeath;j++){
           printf("Age %d", i);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         for(jk=1; jk <=nlstate ; jk++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)            }
             pp[jk] += freq[jk][m][i];          for(d=0; d<=dh[mi][i]; d++){
         }            newm=savm;
         for(jk=1; jk <=nlstate ; jk++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for(m=-1, pos=0; m <=0 ; m++)            for (kk=1; kk<=cptcovage;kk++) {
             pos += freq[jk][m][i];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           if(pp[jk]>=1.e-10)            }
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           else                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);            savm=oldm;
         }            oldm=newm;
           } /* end mult */
         for(jk=1; jk <=nlstate ; jk++){        
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          s1=s[mw[mi][i]][i];
             pp[jk] += freq[jk][m][i];          s2=s[mw[mi+1][i]][i];
         }          bbh=(double)bh[mi][i]/(double)stepm; 
           lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
         for(jk=1,pos=0; jk <=nlstate ; jk++)          ipmx +=1;
           pos += pp[jk];          sw += weight[i];
         for(jk=1; jk <=nlstate ; jk++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           if(pos>=1.e-5)        } /* end of wave */
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);      } /* end of individual */
           else    }  else if(mle==3){  /* exponential inter-extrapolation */
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);      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];
             if(pos>=1.e-5){        for(mi=1; mi<= wav[i]-1; mi++){
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          for (ii=1;ii<=nlstate+ndeath;ii++)
               probs[i][jk][j1]= pp[jk]/pos;            for (j=1;j<=nlstate+ndeath;j++){
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             else            }
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);          for(d=0; d<dh[mi][i]; d++){
           }            newm=savm;
         }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                    for (kk=1; kk<=cptcovage;kk++) {
         for(jk=-1; jk <=nlstate+ndeath; jk++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           for(m=-1; m <=nlstate+ndeath; m++)            }
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         if(i <= (int) agemax)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           fprintf(ficresp,"\n");            savm=oldm;
         printf("\n");            oldm=newm;
       }          } /* end mult */
     }        
   }          s1=s[mw[mi][i]][i];
   dateintmean=dateintsum/k2cpt;          s2=s[mw[mi+1][i]][i];
            bbh=(double)bh[mi][i]/(double)stepm; 
   fclose(ficresp);          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          ipmx +=1;
   free_vector(pp,1,nlstate);          sw += weight[i];
            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /* End of Freq */        } /* end of wave */
 }      } /* end of individual */
     }else if (mle==4){  /* ml=4 no inter-extrapolation */
 /************ Prevalence ********************/      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 void prevalence(int agemin, float agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 {  /* Some frequencies */        for(mi=1; mi<= wav[i]-1; mi++){
            for (ii=1;ii<=nlstate+ndeath;ii++)
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;            for (j=1;j<=nlstate+ndeath;j++){
   double ***freq; /* Frequencies */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double *pp;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double pos, k2;            }
           for(d=0; d<dh[mi][i]; d++){
   pp=vector(1,nlstate);            newm=savm;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
              for (kk=1; kk<=cptcovage;kk++) {
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   j1=0;            }
            
   j=cptcoveff;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   if (cptcovn<1) {j=1;ncodemax[1]=1;}                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              savm=oldm;
  for(k1=1; k1<=j;k1++){            oldm=newm;
     for(i1=1; i1<=ncodemax[k1];i1++){          } /* end mult */
       j1++;        
            s1=s[mw[mi][i]][i];
       for (i=-1; i<=nlstate+ndeath; i++)            s2=s[mw[mi+1][i]][i];
         for (jk=-1; jk<=nlstate+ndeath; jk++)            if( s2 > nlstate){ 
           for(m=agemin; m <= agemax+3; m++)            lli=log(out[s1][s2] - savm[s1][s2]);
             freq[i][jk][m]=0;          }else{
                  lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       for (i=1; i<=imx; i++) {          }
         bool=1;          ipmx +=1;
         if  (cptcovn>0) {          sw += weight[i];
           for (z1=1; z1<=cptcoveff; z1++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  /*      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]); */
               bool=0;        } /* end of wave */
         }      } /* end of individual */
         if (bool==1) {    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
           for(m=firstpass; m<=lastpass; m++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             k2=anint[m][i]+(mint[m][i]/12.);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        for(mi=1; mi<= wav[i]-1; mi++){
               if(agev[m][i]==0) agev[m][i]=agemax+1;          for (ii=1;ii<=nlstate+ndeath;ii++)
               if(agev[m][i]==1) agev[m][i]=agemax+2;            for (j=1;j<=nlstate+ndeath;j++){
               if (m<lastpass)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                 if (calagedate>0) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
               else            }
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          for(d=0; d<dh[mi][i]; d++){
                freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];            newm=savm;
             }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           }            for (kk=1; kk<=cptcovage;kk++) {
         }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       }            }
         for(i=(int)agemin; i <= (int)agemax+3; i++){          
           for(jk=1; jk <=nlstate ; jk++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
               pp[jk] += freq[jk][m][i];            savm=oldm;
           }            oldm=newm;
           for(jk=1; jk <=nlstate ; jk++){          } /* end mult */
             for(m=-1, pos=0; m <=0 ; m++)        
             pos += freq[jk][m][i];          s1=s[mw[mi][i]][i];
         }          s2=s[mw[mi+1][i]][i];
                  lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
          for(jk=1; jk <=nlstate ; jk++){          ipmx +=1;
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          sw += weight[i];
              pp[jk] += freq[jk][m][i];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
          }          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
                  } /* end of wave */
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];      } /* end of individual */
     } /* End of if */
          for(jk=1; jk <=nlstate ; jk++){              for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
            if( i <= (int) agemax){    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
              if(pos>=1.e-5){    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
                probs[i][jk][j1]= pp[jk]/pos;    return -l;
              }  }
            }  
          }  /*************** log-likelihood *************/
            double funcone( double *x)
         }  {
     }    /* Same as likeli but slower because of a lot of printf and if */
   }    int i, ii, j, k, mi, d, kk;
     double l, ll[NLSTATEMAX], cov[NCOVMAX];
      double **out;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);    double lli; /* Individual log likelihood */
   free_vector(pp,1,nlstate);    double llt;
      int s1, s2;
 }  /* End of Freq */    double bbh, survp;
     /*extern weight */
 /************* Waves Concatenation ***************/    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)    /*for(i=1;i<imx;i++) 
 {      printf(" %d\n",s[4][i]);
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.    */
      Death is a valid wave (if date is known).    cov[1]=1.;
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i  
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]    for(k=1; k<=nlstate; k++) ll[k]=0.;
      and mw[mi+1][i]. dh depends on stepm.  
      */    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int i, mi, m;      for(mi=1; mi<= wav[i]-1; mi++){
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;        for (ii=1;ii<=nlstate+ndeath;ii++)
      double sum=0., jmean=0.;*/          for (j=1;j<=nlstate+ndeath;j++){
             oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int j, k=0,jk, ju, jl;            savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double sum=0.;          }
   jmin=1e+5;        for(d=0; d<dh[mi][i]; d++){
   jmax=-1;          newm=savm;
   jmean=0.;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   for(i=1; i<=imx; i++){          for (kk=1; kk<=cptcovage;kk++) {
     mi=0;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     m=firstpass;          }
     while(s[m][i] <= nlstate){          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       if(s[m][i]>=1)                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         mw[++mi][i]=m;          savm=oldm;
       if(m >=lastpass)          oldm=newm;
         break;        } /* end mult */
       else        
         m++;        s1=s[mw[mi][i]][i];
     }/* end while */        s2=s[mw[mi+1][i]][i];
     if (s[m][i] > nlstate){        bbh=(double)bh[mi][i]/(double)stepm; 
       mi++;     /* Death is another wave */        /* bias is positive if real duration
       /* if(mi==0)  never been interviewed correctly before death */         * is higher than the multiple of stepm and negative otherwise.
          /* Only death is a correct wave */         */
       mw[mi][i]=m;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
     }          lli=log(out[s1][s2] - savm[s1][s2]);
         } else if (mle==1){
     wav[i]=mi;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     if(mi==0)        } else if(mle==2){
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   }        } else if(mle==3){  /* exponential inter-extrapolation */
           lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   for(i=1; i<=imx; i++){        } else if (mle==4){  /* mle=4 no inter-extrapolation */
     for(mi=1; mi<wav[i];mi++){          lli=log(out[s1][s2]); /* Original formula */
       if (stepm <=0)        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
         dh[mi][i]=1;          lli=log(out[s1][s2]); /* Original formula */
       else{        } /* End of if */
         if (s[mw[mi+1][i]][i] > nlstate) {        ipmx +=1;
           if (agedc[i] < 2*AGESUP) {        sw += weight[i];
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           if(j==0) j=1;  /* Survives at least one month after exam */  /*       printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
           k=k+1;        if(globpr){
           if (j >= jmax) jmax=j;          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
           if (j <= jmin) jmin=j;   %10.6f %10.6f %10.6f ", \
           sum=sum+j;                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
           /*if (j<0) printf("j=%d num=%d \n",j,i); */                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
           }          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
         }            llt +=ll[k]*gipmx/gsw;
         else{            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          }
           k=k+1;          fprintf(ficresilk," %10.6f\n", -llt);
           if (j >= jmax) jmax=j;        }
           else if (j <= jmin)jmin=j;      } /* end of wave */
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */    } /* end of individual */
           sum=sum+j;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         jk= j/stepm;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         jl= j -jk*stepm;    if(globpr==0){ /* First time we count the contributions and weights */
         ju= j -(jk+1)*stepm;      gipmx=ipmx;
         if(jl <= -ju)      gsw=sw;
           dh[mi][i]=jk;    }
         else    return -l;
           dh[mi][i]=jk+1;  }
         if(dh[mi][i]==0)  
           dh[mi][i]=1; /* At least one step */  
       }  /*************** function likelione ***********/
     }  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   }  {
   jmean=sum/k;    /* This routine should help understanding what is done with 
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);       the selection of individuals/waves and
  }       to check the exact contribution to the likelihood.
 /*********** Tricode ****************************/       Plotting could be done.
 void tricode(int *Tvar, int **nbcode, int imx)     */
 {    int k;
   int Ndum[20],ij=1, k, j, i;  
   int cptcode=0;    if(*globpri !=0){ /* Just counts and sums, no printings */
   cptcoveff=0;      strcpy(fileresilk,"ilk"); 
        strcat(fileresilk,fileres);
   for (k=0; k<19; k++) Ndum[k]=0;      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   for (k=1; k<=7; k++) ncodemax[k]=0;        printf("Problem with resultfile: %s\n", fileresilk);
         fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {      }
     for (i=1; i<=imx; i++) {      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
       ij=(int)(covar[Tvar[j]][i]);      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       Ndum[ij]++;      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/      for(k=1; k<=nlstate; k++) 
       if (ij > cptcode) cptcode=ij;        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
     }      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     }
     for (i=0; i<=cptcode; i++) {  
       if(Ndum[i]!=0) ncodemax[j]++;    *fretone=(*funcone)(p);
     }    if(*globpri !=0){
     ij=1;      fclose(ficresilk);
       fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
       fflush(fichtm); 
     for (i=1; i<=ncodemax[j]; i++) {    } 
       for (k=0; k<=19; k++) {    return;
         if (Ndum[k] != 0) {  }
           nbcode[Tvar[j]][ij]=k;  
            
           ij++;  /*********** Maximum Likelihood Estimation ***************/
         }  
         if (ij > ncodemax[j]) break;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       }    {
     }    int i,j, iter;
   }      double **xi;
     double fret;
  for (k=0; k<19; k++) Ndum[k]=0;    double fretone; /* Only one call to likelihood */
     char filerespow[FILENAMELENGTH];
  for (i=1; i<=ncovmodel-2; i++) {    xi=matrix(1,npar,1,npar);
       ij=Tvar[i];    for (i=1;i<=npar;i++)
       Ndum[ij]++;      for (j=1;j<=npar;j++)
     }        xi[i][j]=(i==j ? 1.0 : 0.0);
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
  ij=1;    strcpy(filerespow,"pow"); 
  for (i=1; i<=10; i++) {    strcat(filerespow,fileres);
    if((Ndum[i]!=0) && (i<=ncovcol)){    if((ficrespow=fopen(filerespow,"w"))==NULL) {
      Tvaraff[ij]=i;      printf("Problem with resultfile: %s\n", filerespow);
      ij++;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
    }    }
  }    fprintf(ficrespow,"# Powell\n# iter -2*LL");
      for (i=1;i<=nlstate;i++)
     cptcoveff=ij-1;      for(j=1;j<=nlstate+ndeath;j++)
 }        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     fprintf(ficrespow,"\n");
 /*********** Health Expectancies ****************/  
     powell(p,xi,npar,ftol,&iter,&fret,func);
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )  
     fclose(ficrespow);
 {    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   /* Health expectancies */    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   double age, agelim, hf;  
   double ***p3mat,***varhe;  }
   double **dnewm,**doldm;  
   double *xp;  /**** Computes Hessian and covariance matrix ***/
   double **gp, **gm;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   double ***gradg, ***trgradg;  {
   int theta;    double  **a,**y,*x,pd;
     double **hess;
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);    int i, j,jk;
   xp=vector(1,npar);    int *indx;
   dnewm=matrix(1,nlstate*2,1,npar);  
   doldm=matrix(1,nlstate*2,1,nlstate*2);    double hessii(double p[], double delta, int theta, double delti[]);
      double hessij(double p[], double delti[], int i, int j);
   fprintf(ficreseij,"# Health expectancies\n");    void lubksb(double **a, int npar, int *indx, double b[]) ;
   fprintf(ficreseij,"# Age");    void ludcmp(double **a, int npar, int *indx, double *d) ;
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=nlstate;j++)    hess=matrix(1,npar,1,npar);
       fprintf(ficreseij," %1d-%1d (SE)",i,j);  
   fprintf(ficreseij,"\n");    printf("\nCalculation of the hessian matrix. Wait...\n");
     fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   if(estepm < stepm){    for (i=1;i<=npar;i++){
     printf ("Problem %d lower than %d\n",estepm, stepm);      printf("%d",i);fflush(stdout);
   }      fprintf(ficlog,"%d",i);fflush(ficlog);
   else  hstepm=estepm;        hess[i][i]=hessii(p,ftolhess,i,delti);
   /* We compute the life expectancy from trapezoids spaced every estepm months      /*printf(" %f ",p[i]);*/
    * This is mainly to measure the difference between two models: for example      /*printf(" %lf ",hess[i][i]);*/
    * 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    
    * progression inbetween and thus overestimating or underestimating according    for (i=1;i<=npar;i++) {
    * to the curvature of the survival function. If, for the same date, we      for (j=1;j<=npar;j++)  {
    * estimate the model with stepm=1 month, we can keep estepm to 24 months        if (j>i) { 
    * to compare the new estimate of Life expectancy with the same linear          printf(".%d%d",i,j);fflush(stdout);
    * hypothesis. A more precise result, taking into account a more precise          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
    * curvature will be obtained if estepm is as small as stepm. */          hess[i][j]=hessij(p,delti,i,j);
           hess[j][i]=hess[i][j];    
   /* For example we decided to compute the life expectancy with the smallest unit */          /*printf(" %lf ",hess[i][j]);*/
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        }
      nhstepm is the number of hstepm from age to agelim      }
      nstepm is the number of stepm from age to agelin.    }
      Look at hpijx to understand the reason of that which relies in memory size    printf("\n");
      and note for a fixed period like estepm months */    fprintf(ficlog,"\n");
   /* 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    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
      means that if the survival funtion is printed only each two years of age and if    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
      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.    a=matrix(1,npar,1,npar);
   */    y=matrix(1,npar,1,npar);
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    x=vector(1,npar);
     indx=ivector(1,npar);
   agelim=AGESUP;    for (i=1;i<=npar;i++)
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     /* nhstepm age range expressed in number of stepm */    ludcmp(a,npar,indx,&pd);
     nstepm=(int) rint((agelim-age)*YEARM/stepm);  
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */    for (j=1;j<=npar;j++) {
     /* if (stepm >= YEARM) hstepm=1;*/      for (i=1;i<=npar;i++) x[i]=0;
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */      x[j]=1;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      lubksb(a,npar,indx,x);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);      for (i=1;i<=npar;i++){ 
     gp=matrix(0,nhstepm,1,nlstate*2);        matcov[i][j]=x[i];
     gm=matrix(0,nhstepm,1,nlstate*2);      }
     }
     /* Computed by stepm unit matrices, product of hstepm matrices, stored  
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */    printf("\n#Hessian matrix#\n");
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);      fprintf(ficlog,"\n#Hessian matrix#\n");
      for (i=1;i<=npar;i++) { 
       for (j=1;j<=npar;j++) { 
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */        printf("%.3e ",hess[i][j]);
         fprintf(ficlog,"%.3e ",hess[i][j]);
     /* Computing Variances of health expectancies */      }
       printf("\n");
      for(theta=1; theta <=npar; theta++){      fprintf(ficlog,"\n");
       for(i=1; i<=npar; i++){    }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);  
       }    /* Recompute Inverse */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      for (i=1;i<=npar;i++)
        for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
       cptj=0;    ludcmp(a,npar,indx,&pd);
       for(j=1; j<= nlstate; j++){  
         for(i=1; i<=nlstate; i++){    /*  printf("\n#Hessian matrix recomputed#\n");
           cptj=cptj+1;  
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){    for (j=1;j<=npar;j++) {
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;      for (i=1;i<=npar;i++) x[i]=0;
           }      x[j]=1;
         }      lubksb(a,npar,indx,x);
       }      for (i=1;i<=npar;i++){ 
              y[i][j]=x[i];
              printf("%.3e ",y[i][j]);
       for(i=1; i<=npar; i++)        fprintf(ficlog,"%.3e ",y[i][j]);
         xp[i] = x[i] - (i==theta ?delti[theta]:0);      }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        printf("\n");
            fprintf(ficlog,"\n");
       cptj=0;    }
       for(j=1; j<= nlstate; j++){    */
         for(i=1;i<=nlstate;i++){  
           cptj=cptj+1;    free_matrix(a,1,npar,1,npar);
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){    free_matrix(y,1,npar,1,npar);
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    free_vector(x,1,npar);
           }    free_ivector(indx,1,npar);
         }    free_matrix(hess,1,npar,1,npar);
       }  
        
      }
   
       for(j=1; j<= nlstate*2; j++)  /*************** hessian matrix ****************/
         for(h=0; h<=nhstepm-1; h++){  double hessii( double x[], double delta, int theta, double delti[])
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  {
         }    int i;
     int l=1, lmax=20;
      }    double k1,k2;
        double p2[NPARMAX+1];
 /* End theta */    double res;
     double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);    double fx;
     int k=0,kmax=10;
      for(h=0; h<=nhstepm-1; h++)    double l1;
       for(j=1; j<=nlstate*2;j++)  
         for(theta=1; theta <=npar; theta++)    fx=func(x);
         trgradg[h][j][theta]=gradg[h][theta][j];    for (i=1;i<=npar;i++) p2[i]=x[i];
     for(l=0 ; l <=lmax; l++){
       l1=pow(10,l);
      for(i=1;i<=nlstate*2;i++)      delts=delt;
       for(j=1;j<=nlstate*2;j++)      for(k=1 ; k <kmax; k=k+1){
         varhe[i][j][(int)age] =0.;        delt = delta*(l1*k);
         p2[theta]=x[theta] +delt;
     for(h=0;h<=nhstepm-1;h++){        k1=func(p2)-fx;
       for(k=0;k<=nhstepm-1;k++){        p2[theta]=x[theta]-delt;
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);        k2=func(p2)-fx;
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);        /*res= (k1-2.0*fx+k2)/delt/delt; */
         for(i=1;i<=nlstate*2;i++)        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
           for(j=1;j<=nlstate*2;j++)        
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;  #ifdef DEBUG
       }        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
     }        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   #endif
              /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
     /* Computing expectancies */        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     for(i=1; i<=nlstate;i++)          k=kmax;
       for(j=1; j<=nlstate;j++)        }
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;          k=kmax; l=lmax*10.;
                  }
 /* 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]);*/        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           delts=delt;
         }        }
       }
     fprintf(ficreseij,"%3.0f",age );    }
     cptj=0;    delti[theta]=delts;
     for(i=1; i<=nlstate;i++)    return res; 
       for(j=1; j<=nlstate;j++){    
         cptj++;  }
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );  
       }  double hessij( double x[], double delti[], int thetai,int thetaj)
     fprintf(ficreseij,"\n");  {
        int i;
     free_matrix(gm,0,nhstepm,1,nlstate*2);    int l=1, l1, lmax=20;
     free_matrix(gp,0,nhstepm,1,nlstate*2);    double k1,k2,k3,k4,res,fx;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);    double p2[NPARMAX+1];
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);    int k;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
   }    fx=func(x);
   free_vector(xp,1,npar);    for (k=1; k<=2; k++) {
   free_matrix(dnewm,1,nlstate*2,1,npar);      for (i=1;i<=npar;i++) p2[i]=x[i];
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);      p2[thetai]=x[thetai]+delti[thetai]/k;
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
 }      k1=func(p2)-fx;
     
 /************ Variance ******************/      p2[thetai]=x[thetai]+delti[thetai]/k;
 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)      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
 {      k2=func(p2)-fx;
   /* Variance of health expectancies */    
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      p2[thetai]=x[thetai]-delti[thetai]/k;
   double **newm;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   double **dnewm,**doldm;      k3=func(p2)-fx;
   int i, j, nhstepm, hstepm, h, nstepm ;    
   int k, cptcode;      p2[thetai]=x[thetai]-delti[thetai]/k;
   double *xp;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   double **gp, **gm;      k4=func(p2)-fx;
   double ***gradg, ***trgradg;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   double ***p3mat;  #ifdef DEBUG
   double age,agelim, hf;      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   int theta;      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   #endif
    fprintf(ficresvij,"# Covariances of life expectancies\n");    }
   fprintf(ficresvij,"# Age");    return res;
   for(i=1; i<=nlstate;i++)  }
     for(j=1; j<=nlstate;j++)  
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);  /************** Inverse of matrix **************/
   fprintf(ficresvij,"\n");  void ludcmp(double **a, int n, int *indx, double *d) 
   { 
   xp=vector(1,npar);    int i,imax,j,k; 
   dnewm=matrix(1,nlstate,1,npar);    double big,dum,sum,temp; 
   doldm=matrix(1,nlstate,1,nlstate);    double *vv; 
     
   if(estepm < stepm){    vv=vector(1,n); 
     printf ("Problem %d lower than %d\n",estepm, stepm);    *d=1.0; 
   }    for (i=1;i<=n;i++) { 
   else  hstepm=estepm;        big=0.0; 
   /* For example we decided to compute the life expectancy with the smallest unit */      for (j=1;j<=n;j++) 
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.        if ((temp=fabs(a[i][j])) > big) big=temp; 
      nhstepm is the number of hstepm from age to agelim      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
      nstepm is the number of stepm from age to agelin.      vv[i]=1.0/big; 
      Look at hpijx to understand the reason of that which relies in memory size    } 
      and note for a fixed period like k years */    for (j=1;j<=n;j++) { 
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the      for (i=1;i<j;i++) { 
      survival function given by stepm (the optimization length). Unfortunately it        sum=a[i][j]; 
      means that if the survival funtion is printed only each two years of age and if        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
      you sum them up and add 1 year (area under the trapezoids) you won't get the same        a[i][j]=sum; 
      results. So we changed our mind and took the option of the best precision.      } 
   */      big=0.0; 
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */      for (i=j;i<=n;i++) { 
   agelim = AGESUP;        sum=a[i][j]; 
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        for (k=1;k<j;k++) 
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          sum -= a[i][k]*a[k][j]; 
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */        a[i][j]=sum; 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          big=dum; 
     gp=matrix(0,nhstepm,1,nlstate);          imax=i; 
     gm=matrix(0,nhstepm,1,nlstate);        } 
       } 
     for(theta=1; theta <=npar; theta++){      if (j != imax) { 
       for(i=1; i<=npar; i++){ /* Computes gradient */        for (k=1;k<=n;k++) { 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          dum=a[imax][k]; 
       }          a[imax][k]=a[j][k]; 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            a[j][k]=dum; 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        } 
         *d = -(*d); 
       if (popbased==1) {        vv[imax]=vv[j]; 
         for(i=1; i<=nlstate;i++)      } 
           prlim[i][i]=probs[(int)age][i][ij];      indx[j]=imax; 
       }      if (a[j][j] == 0.0) a[j][j]=TINY; 
        if (j != n) { 
       for(j=1; j<= nlstate; j++){        dum=1.0/(a[j][j]); 
         for(h=0; h<=nhstepm; h++){        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)      } 
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    } 
         }    free_vector(vv,1,n);  /* Doesn't work */
       }  ;
      } 
       for(i=1; i<=npar; i++) /* Computes gradient */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  void lubksb(double **a, int n, int *indx, double b[]) 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    { 
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    int i,ii=0,ip,j; 
      double sum; 
       if (popbased==1) {   
         for(i=1; i<=nlstate;i++)    for (i=1;i<=n;i++) { 
           prlim[i][i]=probs[(int)age][i][ij];      ip=indx[i]; 
       }      sum=b[ip]; 
       b[ip]=b[i]; 
       for(j=1; j<= nlstate; j++){      if (ii) 
         for(h=0; h<=nhstepm; h++){        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      else if (sum) ii=i; 
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];      b[i]=sum; 
         }    } 
       }    for (i=n;i>=1;i--) { 
       sum=b[i]; 
       for(j=1; j<= nlstate; j++)      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
         for(h=0; h<=nhstepm; h++){      b[i]=sum/a[i][i]; 
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    } 
         }  } 
     } /* End theta */  
   /************ Frequencies ********************/
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);  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(h=0; h<=nhstepm; h++)    
       for(j=1; j<=nlstate;j++)    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
         for(theta=1; theta <=npar; theta++)    int first;
           trgradg[h][j][theta]=gradg[h][theta][j];    double ***freq; /* Frequencies */
     double *pp, **prop;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     for(i=1;i<=nlstate;i++)    FILE *ficresp;
       for(j=1;j<=nlstate;j++)    char fileresp[FILENAMELENGTH];
         vareij[i][j][(int)age] =0.;    
     pp=vector(1,nlstate);
     for(h=0;h<=nhstepm;h++){    prop=matrix(1,nlstate,iagemin,iagemax+3);
       for(k=0;k<=nhstepm;k++){    strcpy(fileresp,"p");
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    strcat(fileresp,fileres);
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    if((ficresp=fopen(fileresp,"w"))==NULL) {
         for(i=1;i<=nlstate;i++)      printf("Problem with prevalence resultfile: %s\n", fileresp);
           for(j=1;j<=nlstate;j++)      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;      exit(0);
       }    }
     }    freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);
     j1=0;
     fprintf(ficresvij,"%.0f ",age );    
     for(i=1; i<=nlstate;i++)    j=cptcoveff;
       for(j=1; j<=nlstate;j++){    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);  
       }    first=1;
     fprintf(ficresvij,"\n");  
     free_matrix(gp,0,nhstepm,1,nlstate);    for(k1=1; k1<=j;k1++){
     free_matrix(gm,0,nhstepm,1,nlstate);      for(i1=1; i1<=ncodemax[k1];i1++){
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        j1++;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          scanf("%d", i);*/
   } /* End age */        for (i=-1; i<=nlstate+ndeath; i++)  
            for (jk=-1; jk<=nlstate+ndeath; jk++)  
   free_vector(xp,1,npar);            for(m=iagemin; m <= iagemax+3; m++)
   free_matrix(doldm,1,nlstate,1,npar);              freq[i][jk][m]=0;
   free_matrix(dnewm,1,nlstate,1,nlstate);  
       for (i=1; i<=nlstate; i++)  
 }        for(m=iagemin; m <= iagemax+3; m++)
           prop[i][m]=0;
 /************ Variance of prevlim ******************/        
 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)        dateintsum=0;
 {        k2cpt=0;
   /* Variance of prevalence limit */        for (i=1; i<=imx; i++) {
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          bool=1;
   double **newm;          if  (cptcovn>0) {
   double **dnewm,**doldm;            for (z1=1; z1<=cptcoveff; z1++) 
   int i, j, nhstepm, hstepm;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   int k, cptcode;                bool=0;
   double *xp;          }
   double *gp, *gm;          if (bool==1){
   double **gradg, **trgradg;            for(m=firstpass; m<=lastpass; m++){
   double age,agelim;              k2=anint[m][i]+(mint[m][i]/12.);
   int theta;              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                    if(agev[m][i]==0) agev[m][i]=iagemax+1;
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   fprintf(ficresvpl,"# Age");                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
   for(i=1; i<=nlstate;i++)                if (m<lastpass) {
       fprintf(ficresvpl," %1d-%1d",i,i);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   fprintf(ficresvpl,"\n");                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
                 }
   xp=vector(1,npar);                
   dnewm=matrix(1,nlstate,1,npar);                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
   doldm=matrix(1,nlstate,1,nlstate);                  dateintsum=dateintsum+k2;
                    k2cpt++;
   hstepm=1*YEARM; /* Every year of age */                }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */                /*}*/
   agelim = AGESUP;            }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        }
     if (stepm >= YEARM) hstepm=1;         
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
     gradg=matrix(1,npar,1,nlstate);  
     gp=vector(1,nlstate);        if  (cptcovn>0) {
     gm=vector(1,nlstate);          fprintf(ficresp, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     for(theta=1; theta <=npar; theta++){          fprintf(ficresp, "**********\n#");
       for(i=1; i<=npar; i++){ /* Computes gradient */        }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        for(i=1; i<=nlstate;i++) 
       }          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        fprintf(ficresp, "\n");
       for(i=1;i<=nlstate;i++)        
         gp[i] = prlim[i][i];        for(i=iagemin; i <= iagemax+3; i++){
              if(i==iagemax+3){
       for(i=1; i<=npar; i++) /* Computes gradient */            fprintf(ficlog,"Total");
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          }else{
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            if(first==1){
       for(i=1;i<=nlstate;i++)              first=0;
         gm[i] = prlim[i][i];              printf("See log file for details...\n");
             }
       for(i=1;i<=nlstate;i++)            fprintf(ficlog,"Age %d", i);
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];          }
     } /* End theta */          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     trgradg =matrix(1,nlstate,1,npar);              pp[jk] += freq[jk][m][i]; 
           }
     for(j=1; j<=nlstate;j++)          for(jk=1; jk <=nlstate ; jk++){
       for(theta=1; theta <=npar; theta++)            for(m=-1, pos=0; m <=0 ; m++)
         trgradg[j][theta]=gradg[theta][j];              pos += freq[jk][m][i];
             if(pp[jk]>=1.e-10){
     for(i=1;i<=nlstate;i++)              if(first==1){
       varpl[i][(int)age] =0.;              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);              }
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     for(i=1;i<=nlstate;i++)            }else{
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */              if(first==1)
                 printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     fprintf(ficresvpl,"%.0f ",age );              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     for(i=1; i<=nlstate;i++)            }
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));          }
     fprintf(ficresvpl,"\n");  
     free_vector(gp,1,nlstate);          for(jk=1; jk <=nlstate ; jk++){
     free_vector(gm,1,nlstate);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     free_matrix(gradg,1,npar,1,nlstate);              pp[jk] += freq[jk][m][i];
     free_matrix(trgradg,1,nlstate,1,npar);          }       
   } /* End age */          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
             pos += pp[jk];
   free_vector(xp,1,npar);            posprop += prop[jk][i];
   free_matrix(doldm,1,nlstate,1,npar);          }
   free_matrix(dnewm,1,nlstate,1,nlstate);          for(jk=1; jk <=nlstate ; jk++){
             if(pos>=1.e-5){
 }              if(first==1)
                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
 /************ Variance of one-step probabilities  ******************/              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)            }else{
 {              if(first==1)
   int i, j, i1, k1, j1, z1;                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   int k=0, cptcode;              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   double **dnewm,**doldm;            }
   double *xp;            if( i <= iagemax){
   double *gp, *gm;              if(pos>=1.e-5){
   double **gradg, **trgradg;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
   double age,agelim, cov[NCOVMAX];                /*probs[i][jk][j1]= pp[jk]/pos;*/
   int theta;                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
   char fileresprob[FILENAMELENGTH];              }
               else
   strcpy(fileresprob,"prob");                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   strcat(fileresprob,fileres);            }
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {          }
     printf("Problem with resultfile: %s\n", fileresprob);          
   }          for(jk=-1; jk <=nlstate+ndeath; jk++)
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);            for(m=-1; m <=nlstate+ndeath; m++)
                if(freq[jk][m][i] !=0 ) {
 fprintf(ficresprob,"#One-step probabilities and standard deviation in parentheses\n");              if(first==1)
   fprintf(ficresprob,"# Age");                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   for(i=1; i<=nlstate;i++)                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
     for(j=1; j<=(nlstate+ndeath);j++)              }
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);          if(i <= iagemax)
             fprintf(ficresp,"\n");
           if(first==1)
   fprintf(ficresprob,"\n");            printf("Others in log...\n");
           fprintf(ficlog,"\n");
         }
   xp=vector(1,npar);      }
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    }
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    dateintmean=dateintsum/k2cpt; 
     
   cov[1]=1;    fclose(ficresp);
   j=cptcoveff;    free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    free_vector(pp,1,nlstate);
   j1=0;    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   for(k1=1; k1<=1;k1++){    /* End of Freq */
     for(i1=1; i1<=ncodemax[k1];i1++){  }
     j1++;  
   /************ Prevalence ********************/
     if  (cptcovn>0) {  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
       fprintf(ficresprob, "\n#********** Variable ");  {  
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
       fprintf(ficresprob, "**********\n#");       in each health status at the date of interview (if between dateprev1 and dateprev2).
     }       We still use firstpass and lastpass as another selection.
        */
       for (age=bage; age<=fage; age ++){   
         cov[2]=age;    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
         for (k=1; k<=cptcovn;k++) {    double ***freq; /* Frequencies */
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];    double *pp, **prop;
              double pos,posprop; 
         }    double  y2; /* in fractional years */
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    int iagemin, iagemax;
         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]]];    iagemin= (int) agemin;
            iagemax= (int) agemax;
         gradg=matrix(1,npar,1,9);    /*pp=vector(1,nlstate);*/
         trgradg=matrix(1,9,1,npar);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));    j1=0;
        
         for(theta=1; theta <=npar; theta++){    j=cptcoveff;
           for(i=1; i<=npar; i++)    if (cptcovn<1) {j=1;ncodemax[1]=1;}
             xp[i] = x[i] + (i==theta ?delti[theta]:0);    
              for(k1=1; k1<=j;k1++){
           pmij(pmmij,cov,ncovmodel,xp,nlstate);      for(i1=1; i1<=ncodemax[k1];i1++){
                  j1++;
           k=0;        
           for(i=1; i<= (nlstate+ndeath); i++){        for (i=1; i<=nlstate; i++)  
             for(j=1; j<=(nlstate+ndeath);j++){          for(m=iagemin; m <= iagemax+3; m++)
               k=k+1;            prop[i][m]=0.0;
               gp[k]=pmmij[i][j];       
             }        for (i=1; i<=imx; i++) { /* Each individual */
           }          bool=1;
                    if  (cptcovn>0) {
           for(i=1; i<=npar; i++)            for (z1=1; z1<=cptcoveff; z1++) 
             xp[i] = x[i] - (i==theta ?delti[theta]:0);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
                    bool=0;
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          } 
           k=0;          if (bool==1) { 
           for(i=1; i<=(nlstate+ndeath); i++){            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
             for(j=1; j<=(nlstate+ndeath);j++){              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
               k=k+1;              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
               gm[k]=pmmij[i][j];                if(agev[m][i]==0) agev[m][i]=iagemax+1;
             }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
           }                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
                      if (s[m][i]>0 && s[m][i]<=nlstate) { 
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)                  /*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]]);*/
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];                    prop[s[m][i]][(int)agev[m][i]] += weight[i];
         }                  prop[s[m][i]][iagemax+3] += weight[i]; 
                 } 
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)              }
           for(theta=1; theta <=npar; theta++)            } /* end selection of waves */
             trgradg[j][theta]=gradg[theta][j];          }
                }
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);        for(i=iagemin; i <= iagemax+3; i++){  
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);          
                  for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
         pmij(pmmij,cov,ncovmodel,x,nlstate);            posprop += prop[jk][i]; 
                  } 
         k=0;  
         for(i=1; i<=(nlstate+ndeath); i++){          for(jk=1; jk <=nlstate ; jk++){     
           for(j=1; j<=(nlstate+ndeath);j++){            if( i <=  iagemax){ 
             k=k+1;              if(posprop>=1.e-5){ 
             gm[k]=pmmij[i][j];                probs[i][jk][j1]= prop[jk][i]/posprop;
           }              } 
         }            } 
                }/* end jk */ 
      /*printf("\n%d ",(int)age);        }/* end i */ 
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){      } /* end i1 */
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    } /* end k1 */
      }*/    
     /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
         fprintf(ficresprob,"\n%d ",(int)age);    /*free_vector(pp,1,nlstate);*/
     free_matrix(prop,1,nlstate, iagemin,iagemax+3);
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)  }  /* End of prevalence */
           fprintf(ficresprob,"%.3e (%.3e) ",gm[i],sqrt(doldm[i][i]));  
    /************* 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)
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));  {
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);       Death is a valid wave (if date is known).
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   }       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
   free_vector(xp,1,npar);       and mw[mi+1][i]. dh depends on stepm.
   fclose(ficresprob);       */
    
 }    int i, mi, m;
     /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
 /******************* Printing html file ***********/       double sum=0., jmean=0.;*/
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \    int first;
  int lastpass, int stepm, int weightopt, char model[],\    int j, k=0,jk, ju, jl;
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \    double sum=0.;
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\    first=0;
  char version[], int popforecast, int estepm ){    jmin=1e+5;
   int jj1, k1, i1, cpt;    jmax=-1;
   FILE *fichtm;    jmean=0.;
   /*char optionfilehtm[FILENAMELENGTH];*/    for(i=1; i<=imx; i++){
       mi=0;
   strcpy(optionfilehtm,optionfile);      m=firstpass;
   strcat(optionfilehtm,".htm");      while(s[m][i] <= nlstate){
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {        if(s[m][i]>=1)
     printf("Problem with %s \n",optionfilehtm), exit(0);          mw[++mi][i]=m;
   }        if(m >=lastpass)
           break;
  fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n        else
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n          m++;
 \n      }/* end while */
 Total number of observations=%d <br>\n      if (s[m][i] > nlstate){
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n        mi++;     /* Death is another wave */
 <hr  size=\"2\" color=\"#EC5E5E\">        /* if(mi==0)  never been interviewed correctly before death */
  <ul><li>Outputs files<br>\n           /* Only death is a correct wave */
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n        mw[mi][i]=m;
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n      }
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n  
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n      wav[i]=mi;
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n      if(mi==0){
  - Life expectancies by age and initial health status (estepm=%2d months): <a href=\"e%s\">e%s</a> <br>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot,fileres,fileres,fileres,fileres,fileres,fileres,estepm,fileres,fileres);        nbwarn++;
         if(first==0){
  fprintf(fichtm,"\n          printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n          first=1;
   - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n        }
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n        if(first==1){
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);        }
       } /* end mi==0 */
  if(popforecast==1) fprintf(fichtm,"\n    } /* End individuals */
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n  
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n    for(i=1; i<=imx; i++){
         <br>",fileres,fileres,fileres,fileres);      for(mi=1; mi<wav[i];mi++){
  else        if (stepm <=0)
    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);          dh[mi][i]=1;
 fprintf(fichtm," <li>Graphs</li><p>");        else{
           if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
  m=cptcoveff;            if (agedc[i] < 2*AGESUP) {
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
               if(j==0) j=1;  /* Survives at least one month after exam */
  jj1=0;              else if(j<0){
  for(k1=1; k1<=m;k1++){                nberr++;
    for(i1=1; i1<=ncodemax[k1];i1++){                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]);
        jj1++;                j=1; /* Temporary Dangerous patch */
        if (cptcovn > 0) {                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview.\n  You MUST fix the contradiction between dates.\n",stepm);
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
          for (cpt=1; cpt<=cptcoveff;cpt++)                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);
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);              }
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");              k=k+1;
        }              if (j >= jmax) jmax=j;
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>              if (j <= jmin) jmin=j;
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);                  sum=sum+j;
        for(cpt=1; cpt<nlstate;cpt++){              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            }
        }          }
     for(cpt=1; cpt<=nlstate;cpt++) {          else{
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
 interval) in state (%d): v%s%d%d.gif <br>            /*      printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);              k=k+1;
      }            if (j >= jmax) jmax=j;
      for(cpt=1; cpt<=nlstate;cpt++) {            else if (j <= jmin)jmin=j;
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
      }            if(j<0){
      fprintf(fichtm,"\n<br>- Total life expectancy by age and              nberr++;
 health expectancies in states (1) and (2): e%s%d.gif<br>              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]);
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);              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(fichtm,"\n</body>");            }
    }            sum=sum+j;
    }          }
 fclose(fichtm);          jk= j/stepm;
 }          jl= j -jk*stepm;
           ju= j -(jk+1)*stepm;
 /******************* Gnuplot file **************/          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){            if(jl==0){
               dh[mi][i]=jk;
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;              bh[mi][i]=0;
             }else{ /* We want a negative bias in order to only have interpolation ie
   strcpy(optionfilegnuplot,optionfilefiname);                    * at the price of an extra matrix product in likelihood */
   strcat(optionfilegnuplot,".gp.txt");              dh[mi][i]=jk+1;
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {              bh[mi][i]=ju;
     printf("Problem with file %s",optionfilegnuplot);            }
   }          }else{
             if(jl <= -ju){
 #ifdef windows              dh[mi][i]=jk;
     fprintf(ficgp,"cd \"%s\" \n",pathc);              bh[mi][i]=jl;       /* bias is positive if real duration
 #endif                                   * is higher than the multiple of stepm and negative otherwise.
 m=pow(2,cptcoveff);                                   */
              }
  /* 1eme*/            else{
   for (cpt=1; cpt<= nlstate ; cpt ++) {              dh[mi][i]=jk+1;
    for (k1=1; k1<= m ; k1 ++) {              bh[mi][i]=ju;
             }
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);            if(dh[mi][i]==0){
               dh[mi][i]=1; /* At least one step */
 for (i=1; i<= nlstate ; i ++) {              bh[mi][i]=ju; /* At least one step */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              /*  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);*/
   else fprintf(ficgp," \%%*lf (\%%*lf)");            }
 }          } /* end if mle */
     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 ++) {      } /* end wave */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    }
   else fprintf(ficgp," \%%*lf (\%%*lf)");    jmean=sum/k;
 }    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
      for (i=1; i<= nlstate ; i ++) {   }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");  /*********** Tricode ****************************/
 }    void tricode(int *Tvar, int **nbcode, int imx)
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));  {
     
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    int Ndum[20],ij=1, k, j, i, maxncov=19;
    }    int cptcode=0;
   }    cptcoveff=0; 
   /*2 eme*/   
     for (k=0; k<maxncov; k++) Ndum[k]=0;
   for (k1=1; k1<= m ; k1 ++) {    for (k=1; k<=7; k++) ncodemax[k]=0;
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);  
        for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
     for (i=1; i<= nlstate+1 ; i ++) {      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
       k=2*i;                                 modality*/ 
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
       for (j=1; j<= nlstate+1 ; j ++) {        Ndum[ij]++; /*store the modality */
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
   else fprintf(ficgp," \%%*lf (\%%*lf)");        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
 }                                           Tvar[j]. If V=sex and male is 0 and 
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");                                         female is 1, then  cptcode=1.*/
       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=0; i<=cptcode; i++) {
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        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 */
         else fprintf(ficgp," \%%*lf (\%%*lf)");      }
 }    
       fprintf(ficgp,"\" t\"\" w l 0,");      ij=1; 
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);      for (i=1; i<=ncodemax[j]; i++) {
       for (j=1; j<= nlstate+1 ; j ++) {        for (k=0; k<= maxncov; k++) {
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");          if (Ndum[k] != 0) {
   else fprintf(ficgp," \%%*lf (\%%*lf)");            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; */
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");            
       else fprintf(ficgp,"\" t\"\" w l 0,");            ij++;
     }          }
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);          if (ij > ncodemax[j]) break; 
   }        }  
        } 
   /*3eme*/    }  
   
   for (k1=1; k1<= m ; k1 ++) {   for (k=0; k< maxncov; k++) Ndum[k]=0;
     for (cpt=1; cpt<= nlstate ; cpt ++) {  
       k=2+nlstate*(2*cpt-2);   for (i=1; i<=ncovmodel-2; i++) { 
       fprintf(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);     /* Listing of all covariables in staement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);     ij=Tvar[i];
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");     Ndum[ij]++;
 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);  
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");   ij=1;
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);   for (i=1; i<= maxncov; i++) {
      if((Ndum[i]!=0) && (i<=ncovcol)){
 */       Tvaraff[ij]=i; /*For printing */
       for (i=1; i< nlstate ; i ++) {       ij++;
         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(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);   cptcoveff=ij-1; /*Number of simple covariates*/
     }  }
     }  
    /*********** Health Expectancies ****************/
   /* CV preval stat */  
     for (k1=1; k1<= m ; k1 ++) {  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 )
     for (cpt=1; cpt<nlstate ; cpt ++) {  
       k=3;  {
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);    /* Health expectancies */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
       for (i=1; i< nlstate ; i ++)    double age, agelim, hf;
         fprintf(ficgp,"+$%d",k+i+1);    double ***p3mat,***varhe;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    double **dnewm,**doldm;
          double *xp;
       l=3+(nlstate+ndeath)*cpt;    double **gp, **gm;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);    double ***gradg, ***trgradg;
       for (i=1; i< nlstate ; i ++) {    int theta;
         l=3+(nlstate+ndeath)*cpt;  
         fprintf(ficgp,"+$%d",l+i+1);    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
       }    xp=vector(1,npar);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      dnewm=matrix(1,nlstate*nlstate,1,npar);
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     }    
   }      fprintf(ficreseij,"# Health expectancies\n");
      fprintf(ficreseij,"# Age");
   /* proba elementaires */    for(i=1; i<=nlstate;i++)
    for(i=1,jk=1; i <=nlstate; i++){      for(j=1; j<=nlstate;j++)
     for(k=1; k <=(nlstate+ndeath); k++){        fprintf(ficreseij," %1d-%1d (SE)",i,j);
       if (k != i) {    fprintf(ficreseij,"\n");
         for(j=1; j <=ncovmodel; j++){  
            if(estepm < stepm){
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);      printf ("Problem %d lower than %d\n",estepm, stepm);
           jk++;    }
           fprintf(ficgp,"\n");    else  hstepm=estepm;   
         }    /* We compute the life expectancy from trapezoids spaced every estepm months
       }     * This is mainly to measure the difference between two models: for example
     }     * if stepm=24 months pijx are given only every 2 years and by summing them
     }     * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
     for(jk=1; jk <=m; jk++) {     * to the curvature of the survival function. If, for the same date, we 
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
    i=1;     * to compare the new estimate of Life expectancy with the same linear 
    for(k2=1; k2<=nlstate; k2++) {     * hypothesis. A more precise result, taking into account a more precise
      k3=i;     * curvature will be obtained if estepm is as small as stepm. */
      for(k=1; k<=(nlstate+ndeath); k++) {  
        if (k != k2){    /* For example we decided to compute the life expectancy with the smallest unit */
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
 ij=1;       nhstepm is the number of hstepm from age to agelim 
         for(j=3; j <=ncovmodel; j++) {       nstepm is the number of stepm from age to agelin. 
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {       Look at hpijx to understand the reason of that which relies in memory size
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);       and note for a fixed period like estepm months */
             ij++;    /* 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
           else       means that if the survival funtion is printed only each two years of age and if
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);       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(ficgp,")/(1");    */
            hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
         for(k1=1; k1 <=nlstate; k1++){    
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    agelim=AGESUP;
 ij=1;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
           for(j=3; j <=ncovmodel; j++){      /* nhstepm age range expressed in number of stepm */
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
             ij++;      /* if (stepm >= YEARM) hstepm=1;*/
           }      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
           else      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
           }      gp=matrix(0,nhstepm,1,nlstate*nlstate);
           fprintf(ficgp,")");      gm=matrix(0,nhstepm,1,nlstate*nlstate);
         }  
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
         i=i+ncovmodel;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
        }   
      }  
    }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);  
    }      /* Computing  Variances of health expectancies */
      
   fclose(ficgp);       for(theta=1; theta <=npar; theta++){
 }  /* end gnuplot */        for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
 /*************** Moving average **************/        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){    
         cptj=0;
   int i, cpt, cptcod;        for(j=1; j<= nlstate; j++){
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)          for(i=1; i<=nlstate; i++){
       for (i=1; i<=nlstate;i++)            cptj=cptj+1;
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
           mobaverage[(int)agedeb][i][cptcod]=0.;              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
                }
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){          }
       for (i=1; i<=nlstate;i++){        }
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){       
           for (cpt=0;cpt<=4;cpt++){       
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];        for(i=1; i<=npar; i++) 
           }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         }        
       }        cptj=0;
     }        for(j=1; j<= nlstate; j++){
              for(i=1;i<=nlstate;i++){
 }            cptj=cptj+1;
             for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   
 /************** Forecasting ******************/              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){            }
            }
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        }
   int *popage;        for(j=1; j<= nlstate*nlstate; j++)
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;          for(h=0; h<=nhstepm-1; h++){
   double *popeffectif,*popcount;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   double ***p3mat;          }
   char fileresf[FILENAMELENGTH];       } 
      
  agelim=AGESUP;  /* End theta */
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;  
        trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);  
         for(h=0; h<=nhstepm-1; h++)
          for(j=1; j<=nlstate*nlstate;j++)
   strcpy(fileresf,"f");          for(theta=1; theta <=npar; theta++)
   strcat(fileresf,fileres);            trgradg[h][j][theta]=gradg[h][theta][j];
   if((ficresf=fopen(fileresf,"w"))==NULL) {       
     printf("Problem with forecast resultfile: %s\n", fileresf);  
   }       for(i=1;i<=nlstate*nlstate;i++)
   printf("Computing forecasting: result on file '%s' \n", fileresf);        for(j=1;j<=nlstate*nlstate;j++)
           varhe[i][j][(int)age] =0.;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
        printf("%d|",(int)age);fflush(stdout);
   if (mobilav==1) {       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       for(h=0;h<=nhstepm-1;h++){
     movingaverage(agedeb, fage, ageminpar, mobaverage);        for(k=0;k<=nhstepm-1;k++){
   }          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]);
   stepsize=(int) (stepm+YEARM-1)/YEARM;          for(i=1;i<=nlstate*nlstate;i++)
   if (stepm<=12) stepsize=1;            for(j=1;j<=nlstate*nlstate;j++)
                varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
   agelim=AGESUP;        }
        }
   hstepm=1;      /* Computing expectancies */
   hstepm=hstepm/stepm;      for(i=1; i<=nlstate;i++)
   yp1=modf(dateintmean,&yp);        for(j=1; j<=nlstate;j++)
   anprojmean=yp;          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   yp2=modf((yp1*12),&yp);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   mprojmean=yp;            
   yp1=modf((yp2*30.5),&yp);  /* 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]);*/
   jprojmean=yp;  
   if(jprojmean==0) jprojmean=1;          }
   if(mprojmean==0) jprojmean=1;  
        fprintf(ficreseij,"%3.0f",age );
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);      cptj=0;
        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++){          cptj++;
       k=k+1;          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
       fprintf(ficresf,"\n#******");        }
       for(j=1;j<=cptcoveff;j++) {      fprintf(ficreseij,"\n");
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);     
       }      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
       fprintf(ficresf,"******\n");      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
       fprintf(ficresf,"# StartingAge FinalAge");      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
            free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
          }
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    printf("\n");
         fprintf(ficresf,"\n");    fprintf(ficlog,"\n");
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);    
     free_vector(xp,1,npar);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
           nhstepm = nhstepm/hstepm;    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
            }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;  /************ Variance ******************/
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav)
          {
           for (h=0; h<=nhstepm; h++){    /* Variance of health expectancies */
             if (h==(int) (calagedate+YEARM*cpt)) {    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);    /* double **newm;*/
             }    double **dnewm,**doldm;
             for(j=1; j<=nlstate+ndeath;j++) {    double **dnewmp,**doldmp;
               kk1=0.;kk2=0;    int i, j, nhstepm, hstepm, h, nstepm ;
               for(i=1; i<=nlstate;i++) {                  int k, cptcode;
                 if (mobilav==1)    double *xp;
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    double **gp, **gm;  /* for var eij */
                 else {    double ***gradg, ***trgradg; /*for var eij */
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    double **gradgp, **trgradgp; /* for var p point j */
                 }    double *gpp, *gmp; /* for var p point j */
                    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
               }    double ***p3mat;
               if (h==(int)(calagedate+12*cpt)){    double age,agelim, hf;
                 fprintf(ficresf," %.3f", kk1);    double ***mobaverage;
                            int theta;
               }    char digit[4];
             }    char digitp[25];
           }  
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    char fileresprobmorprev[FILENAMELENGTH];
         }  
       }    if(popbased==1){
     }      if(mobilav!=0)
   }        strcpy(digitp,"-populbased-mobilav-");
              else strcpy(digitp,"-populbased-nomobil-");
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    }
     else 
   fclose(ficresf);      strcpy(digitp,"-stablbased-");
 }  
 /************** Forecasting ******************/    if (mobilav!=0) {
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
        if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   int *popage;        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      }
   double *popeffectif,*popcount;    }
   double ***p3mat,***tabpop,***tabpopprev;  
   char filerespop[FILENAMELENGTH];    strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
   agelim=AGESUP;    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    strcat(fileresprobmorprev,fileres);
      if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
        fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
      }
   strcpy(filerespop,"pop");    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   strcat(filerespop,fileres);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    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);
     printf("Problem with forecast resultfile: %s\n", filerespop);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   }    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   printf("Computing forecasting: result on file '%s' \n", filerespop);      fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
   if (mobilav==1) {    fprintf(ficresprobmorprev,"\n");
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficgp,"\n# Routine varevsij");
     movingaverage(agedeb, fage, ageminpar, mobaverage);    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);
   /*   } */
   stepsize=(int) (stepm+YEARM-1)/YEARM;    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   if (stepm<=12) stepsize=1;  
      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");
   agelim=AGESUP;    fprintf(ficresvij,"# Age");
      for(i=1; i<=nlstate;i++)
   hstepm=1;      for(j=1; j<=nlstate;j++)
   hstepm=hstepm/stepm;        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
      fprintf(ficresvij,"\n");
   if (popforecast==1) {  
     if((ficpop=fopen(popfile,"r"))==NULL) {    xp=vector(1,npar);
       printf("Problem with population file : %s\n",popfile);exit(0);    dnewm=matrix(1,nlstate,1,npar);
     }    doldm=matrix(1,nlstate,1,nlstate);
     popage=ivector(0,AGESUP);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     popeffectif=vector(0,AGESUP);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     popcount=vector(0,AGESUP);  
        gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     i=1;      gpp=vector(nlstate+1,nlstate+ndeath);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    gmp=vector(nlstate+1,nlstate+ndeath);
        trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     imx=i;    
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    if(estepm < stepm){
   }      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
   for(cptcov=1;cptcov<=i2;cptcov++){    else  hstepm=estepm;   
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    /* For example we decided to compute the life expectancy with the smallest unit */
       k=k+1;    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       fprintf(ficrespop,"\n#******");       nhstepm is the number of hstepm from age to agelim 
       for(j=1;j<=cptcoveff;j++) {       nstepm is the number of stepm from age to agelin. 
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       Look at hpijx to understand the reason of that which relies in memory size
       }       and note for a fixed period like k years */
       fprintf(ficrespop,"******\n");    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       fprintf(ficrespop,"# Age");       survival function given by stepm (the optimization length). Unfortunately it
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);       means that if the survival funtion is printed every two years of age and if
       if (popforecast==1)  fprintf(ficrespop," [Population]");       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
             results. So we changed our mind and took the option of the best precision.
       for (cpt=0; cpt<=0;cpt++) {    */
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
            agelim = AGESUP;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm;      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
           oldm=oldms;savm=savms;      gp=matrix(0,nhstepm,1,nlstate);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        gm=matrix(0,nhstepm,1,nlstate);
          
           for (h=0; h<=nhstepm; h++){  
             if (h==(int) (calagedate+YEARM*cpt)) {      for(theta=1; theta <=npar; theta++){
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
             }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
             for(j=1; j<=nlstate+ndeath;j++) {        }
               kk1=0.;kk2=0;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
               for(i=1; i<=nlstate;i++) {                      prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
                 if (mobilav==1)  
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];        if (popbased==1) {
                 else {          if(mobilav ==0){
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];            for(i=1; i<=nlstate;i++)
                 }              prlim[i][i]=probs[(int)age][i][ij];
               }          }else{ /* mobilav */ 
               if (h==(int)(calagedate+12*cpt)){            for(i=1; i<=nlstate;i++)
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;              prlim[i][i]=mobaverage[(int)age][i][ij];
                   /*fprintf(ficrespop," %.3f", kk1);          }
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/        }
               }    
             }        for(j=1; j<= nlstate; j++){
             for(i=1; i<=nlstate;i++){          for(h=0; h<=nhstepm; h++){
               kk1=0.;            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
                 for(j=1; j<=nlstate;j++){              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];          }
                 }        }
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];        /* This for computing probability of death (h=1 means
             }           computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)        */
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);        for(j=nlstate+1;j<=nlstate+ndeath;j++){
           }          for(i=1,gpp[j]=0.; i<= nlstate; i++)
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }        }    
       }        /* end probability of death */
    
   /******/        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){   
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        if (popbased==1) {
           nhstepm = nhstepm/hstepm;          if(mobilav ==0){
                      for(i=1; i<=nlstate;i++)
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              prlim[i][i]=probs[(int)age][i][ij];
           oldm=oldms;savm=savms;          }else{ /* mobilav */ 
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);              for(i=1; i<=nlstate;i++)
           for (h=0; h<=nhstepm; h++){              prlim[i][i]=mobaverage[(int)age][i][ij];
             if (h==(int) (calagedate+YEARM*cpt)) {          }
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        }
             }  
             for(j=1; j<=nlstate+ndeath;j++) {        for(j=1; j<= nlstate; j++){
               kk1=0.;kk2=0;          for(h=0; h<=nhstepm; h++){
               for(i=1; i<=nlstate;i++) {                          for(i=1, gm[h][j]=0.;i<=nlstate;i++)
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                  gm[h][j] += prlim[i][i]*p3mat[i][j][h];
               }          }
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);        }
             }        /* This for computing probability of death (h=1 means
           }           computed over hstepm matrices product = hstepm*stepm months) 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);           as a weighted average of prlim.
         }        */
       }        for(j=nlstate+1;j<=nlstate+ndeath;j++){
    }          for(i=1,gmp[j]=0.; i<= nlstate; i++)
   }           gmp[j] += prlim[i][i]*p3mat[i][j][1];
          }    
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        /* end probability of death */
   
   if (popforecast==1) {        for(j=1; j<= nlstate; j++) /* vareij */
     free_ivector(popage,0,AGESUP);          for(h=0; h<=nhstepm; h++){
     free_vector(popeffectif,0,AGESUP);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     free_vector(popcount,0,AGESUP);          }
   }  
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
   fclose(ficrespop);        }
 }  
       } /* End theta */
 /***********************************************/  
 /**************** Main Program *****************/      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
 /***********************************************/  
       for(h=0; h<=nhstepm; h++) /* veij */
 int main(int argc, char *argv[])        for(j=1; j<=nlstate;j++)
 {          for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;  
   double agedeb, agefin,hf;      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;        for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
   double fret;    
   double **xi,tmp,delta;  
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   double dum; /* Dummy variable */      for(i=1;i<=nlstate;i++)
   double ***p3mat;        for(j=1;j<=nlstate;j++)
   int *indx;          vareij[i][j][(int)age] =0.;
   char line[MAXLINE], linepar[MAXLINE];  
   char title[MAXLINE];      for(h=0;h<=nhstepm;h++){
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];        for(k=0;k<=nhstepm;k++){
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
            matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];          for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
   char filerest[FILENAMELENGTH];              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
   char fileregp[FILENAMELENGTH];        }
   char popfile[FILENAMELENGTH];      }
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    
   int firstobs=1, lastobs=10;      /* pptj */
   int sdeb, sfin; /* Status at beginning and end */      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
   int c,  h , cpt,l;      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
   int ju,jl, mi;      for(j=nlstate+1;j<=nlstate+ndeath;j++)
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;        for(i=nlstate+1;i<=nlstate+ndeath;i++)
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;          varppt[j][i]=doldmp[j][i];
   int mobilav=0,popforecast=0;      /* end ppptj */
   int hstepm, nhstepm;      /*  x centered again */
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
   double bage, fage, age, agelim, agebase;   
   double ftolpl=FTOL;      if (popbased==1) {
   double **prlim;        if(mobilav ==0){
   double *severity;          for(i=1; i<=nlstate;i++)
   double ***param; /* Matrix of parameters */            prlim[i][i]=probs[(int)age][i][ij];
   double  *p;        }else{ /* mobilav */ 
   double **matcov; /* Matrix of covariance */          for(i=1; i<=nlstate;i++)
   double ***delti3; /* Scale */            prlim[i][i]=mobaverage[(int)age][i][ij];
   double *delti; /* Scale */        }
   double ***eij, ***vareij;      }
   double **varpl; /* Variances of prevalence limits by age */               
   double *epj, vepp;      /* This for computing probability of death (h=1 means
   double kk1, kk2;         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;         as a weighted average of prlim.
        */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
   char version[80]="Imach version 0.8a, May 2002, INED-EUROREVES ";        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   char *alph[]={"a","a","b","c","d","e"}, str[4];          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   char z[1]="c", occ;  
 #include <sys/time.h>      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
 #include <time.h>      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
          for(i=1; i<=nlstate;i++){
   /* long total_usecs;          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   struct timeval start_time, end_time;        }
        } 
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      fprintf(ficresprobmorprev,"\n");
   getcwd(pathcd, size);  
       fprintf(ficresvij,"%.0f ",age );
   printf("\n%s",version);      for(i=1; i<=nlstate;i++)
   if(argc <=1){        for(j=1; j<=nlstate;j++){
     printf("\nEnter the parameter file name: ");          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
     scanf("%s",pathtot);        }
   }      fprintf(ficresvij,"\n");
   else{      free_matrix(gp,0,nhstepm,1,nlstate);
     strcpy(pathtot,argv[1]);      free_matrix(gm,0,nhstepm,1,nlstate);
   }      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
   /*cygwin_split_path(pathtot,path,optionfile);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    } /* End age */
   /* cutv(path,optionfile,pathtot,'\\');*/    free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   chdir(path);    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
   replace(pathc,path);    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
 /*-------- arguments in the command line --------*/  /*   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); */
   strcpy(fileres,"r");  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
   strcat(fileres, optionfilefiname);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
   strcat(fileres,".txt");    /* Other files have txt extension */    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));
   /*---------arguments file --------*/    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    /*  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);
     printf("Problem with optionfile %s\n",optionfile);  */
     goto end;  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
   }    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
   strcpy(filereso,"o");    free_vector(xp,1,npar);
   strcat(filereso,fileres);    free_matrix(doldm,1,nlstate,1,nlstate);
   if((ficparo=fopen(filereso,"w"))==NULL) {    free_matrix(dnewm,1,nlstate,1,npar);
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    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);
   /* Reads comments: lines beginning with '#' */    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   while((c=getc(ficpar))=='#' && c!= EOF){    fclose(ficresprobmorprev);
     ungetc(c,ficpar);    fflush(ficgp);
     fgets(line, MAXLINE, ficpar);    fflush(fichtm); 
     puts(line);  }  /* end varevsij */
     fputs(line,ficparo);  
   }  /************ Variance of prevlim ******************/
   ungetc(c,ficpar);  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)
   {
   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);    /* Variance of prevalence limit */
   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);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   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);    double **newm;
 while((c=getc(ficpar))=='#' && c!= EOF){    double **dnewm,**doldm;
     ungetc(c,ficpar);    int i, j, nhstepm, hstepm;
     fgets(line, MAXLINE, ficpar);    int k, cptcode;
     puts(line);    double *xp;
     fputs(line,ficparo);    double *gp, *gm;
   }    double **gradg, **trgradg;
   ungetc(c,ficpar);    double age,agelim;
      int theta;
         
   covar=matrix(0,NCOVMAX,1,n);    fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
   cptcovn=0;    fprintf(ficresvpl,"# Age");
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
   ncovmodel=2+cptcovn;    fprintf(ficresvpl,"\n");
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  
      xp=vector(1,npar);
   /* Read guess parameters */    dnewm=matrix(1,nlstate,1,npar);
   /* Reads comments: lines beginning with '#' */    doldm=matrix(1,nlstate,1,nlstate);
   while((c=getc(ficpar))=='#' && c!= EOF){    
     ungetc(c,ficpar);    hstepm=1*YEARM; /* Every year of age */
     fgets(line, MAXLINE, ficpar);    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     puts(line);    agelim = AGESUP;
     fputs(line,ficparo);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   }      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   ungetc(c,ficpar);      if (stepm >= YEARM) hstepm=1;
        nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      gradg=matrix(1,npar,1,nlstate);
     for(i=1; i <=nlstate; i++)      gp=vector(1,nlstate);
     for(j=1; j <=nlstate+ndeath-1; j++){      gm=vector(1,nlstate);
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       fprintf(ficparo,"%1d%1d",i1,j1);      for(theta=1; theta <=npar; theta++){
       printf("%1d%1d",i,j);        for(i=1; i<=npar; i++){ /* Computes gradient */
       for(k=1; k<=ncovmodel;k++){          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         fscanf(ficpar," %lf",&param[i][j][k]);        }
         printf(" %lf",param[i][j][k]);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         fprintf(ficparo," %lf",param[i][j][k]);        for(i=1;i<=nlstate;i++)
       }          gp[i] = prlim[i][i];
       fscanf(ficpar,"\n");      
       printf("\n");        for(i=1; i<=npar; i++) /* Computes gradient */
       fprintf(ficparo,"\n");          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
          for(i=1;i<=nlstate;i++)
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;          gm[i] = prlim[i][i];
   
   p=param[1][1];        for(i=1;i<=nlstate;i++)
            gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
   /* Reads comments: lines beginning with '#' */      } /* End theta */
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);      trgradg =matrix(1,nlstate,1,npar);
     fgets(line, MAXLINE, ficpar);  
     puts(line);      for(j=1; j<=nlstate;j++)
     fputs(line,ficparo);        for(theta=1; theta <=npar; theta++)
   }          trgradg[j][theta]=gradg[theta][j];
   ungetc(c,ficpar);  
       for(i=1;i<=nlstate;i++)
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        varpl[i][(int)age] =0.;
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   for(i=1; i <=nlstate; i++){      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
     for(j=1; j <=nlstate+ndeath-1; j++){      for(i=1;i<=nlstate;i++)
       fscanf(ficpar,"%1d%1d",&i1,&j1);        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
       printf("%1d%1d",i,j);  
       fprintf(ficparo,"%1d%1d",i1,j1);      fprintf(ficresvpl,"%.0f ",age );
       for(k=1; k<=ncovmodel;k++){      for(i=1; i<=nlstate;i++)
         fscanf(ficpar,"%le",&delti3[i][j][k]);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
         printf(" %le",delti3[i][j][k]);      fprintf(ficresvpl,"\n");
         fprintf(ficparo," %le",delti3[i][j][k]);      free_vector(gp,1,nlstate);
       }      free_vector(gm,1,nlstate);
       fscanf(ficpar,"\n");      free_matrix(gradg,1,npar,1,nlstate);
       printf("\n");      free_matrix(trgradg,1,nlstate,1,npar);
       fprintf(ficparo,"\n");    } /* End age */
     }  
   }    free_vector(xp,1,npar);
   delti=delti3[1][1];    free_matrix(doldm,1,nlstate,1,npar);
      free_matrix(dnewm,1,nlstate,1,nlstate);
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){  }
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);  /************ Variance of one-step probabilities  ******************/
     puts(line);  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)
     fputs(line,ficparo);  {
   }    int i, j=0,  i1, k1, l1, t, tj;
   ungetc(c,ficpar);    int k2, l2, j1,  z1;
      int k=0,l, cptcode;
   matcov=matrix(1,npar,1,npar);    int first=1, first1;
   for(i=1; i <=npar; i++){    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     fscanf(ficpar,"%s",&str);    double **dnewm,**doldm;
     printf("%s",str);    double *xp;
     fprintf(ficparo,"%s",str);    double *gp, *gm;
     for(j=1; j <=i; j++){    double **gradg, **trgradg;
       fscanf(ficpar," %le",&matcov[i][j]);    double **mu;
       printf(" %.5le",matcov[i][j]);    double age,agelim, cov[NCOVMAX];
       fprintf(ficparo," %.5le",matcov[i][j]);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     }    int theta;
     fscanf(ficpar,"\n");    char fileresprob[FILENAMELENGTH];
     printf("\n");    char fileresprobcov[FILENAMELENGTH];
     fprintf(ficparo,"\n");    char fileresprobcor[FILENAMELENGTH];
   }  
   for(i=1; i <=npar; i++)    double ***varpij;
     for(j=i+1;j<=npar;j++)  
       matcov[i][j]=matcov[j][i];    strcpy(fileresprob,"prob"); 
        strcat(fileresprob,fileres);
   printf("\n");    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     /*-------- Rewriting paramater file ----------*/    }
      strcpy(rfileres,"r");    /* "Rparameterfile */    strcpy(fileresprobcov,"probcov"); 
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/    strcat(fileresprobcov,fileres);
      strcat(rfileres,".");    /* */    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
      strcat(rfileres,optionfilext);    /* Other files have txt extension */      printf("Problem with resultfile: %s\n", fileresprobcov);
     if((ficres =fopen(rfileres,"w"))==NULL) {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
       printf("Problem writing new parameter file: %s\n", fileres);goto end;    }
     }    strcpy(fileresprobcor,"probcor"); 
     fprintf(ficres,"#%s\n",version);    strcat(fileresprobcor,fileres);
        if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
     /*-------- data file ----------*/      printf("Problem with resultfile: %s\n", fileresprobcor);
     if((fic=fopen(datafile,"r"))==NULL)    {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
       printf("Problem with datafile: %s\n", datafile);goto end;    }
     }    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     n= lastobs;    printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     severity = vector(1,maxwav);    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     outcome=imatrix(1,maxwav+1,1,n);    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     num=ivector(1,n);    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     moisnais=vector(1,n);    
     annais=vector(1,n);    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     moisdc=vector(1,n);    fprintf(ficresprob,"# Age");
     andc=vector(1,n);    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     agedc=vector(1,n);    fprintf(ficresprobcov,"# Age");
     cod=ivector(1,n);    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     weight=vector(1,n);    fprintf(ficresprobcov,"# 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);    for(i=1; i<=nlstate;i++)
     s=imatrix(1,maxwav+1,1,n);      for(j=1; j<=(nlstate+ndeath);j++){
     adl=imatrix(1,maxwav+1,1,n);            fprintf(ficresprob," p%1d-%1d (SE)",i,j);
     tab=ivector(1,NCOVMAX);        fprintf(ficresprobcov," p%1d-%1d ",i,j);
     ncodemax=ivector(1,8);        fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
     i=1;   /* fprintf(ficresprob,"\n");
     while (fgets(line, MAXLINE, fic) != NULL)    {    fprintf(ficresprobcov,"\n");
       if ((i >= firstobs) && (i <=lastobs)) {    fprintf(ficresprobcor,"\n");
           */
         for (j=maxwav;j>=1;j--){   xp=vector(1,npar);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           strcpy(line,stra);    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
         }    first=1;
            fprintf(ficgp,"\n# Routine varprob");
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(fichtm,"\n");
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
         for (j=ncovcol;j>=1;j--){  and drawn. It helps understanding how is the covariance between two incidences.\
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
         }    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
         num[i]=atol(stra);  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
          would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){  standard deviations wide on each axis. <br>\
           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;}*/   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>\
         i=i+1;  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;
     /* printf("ii=%d", ij);    tj=cptcoveff;
        scanf("%d",i);*/    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
   imx=i-1; /* Number of individuals */    j1=0;
     for(t=1; t<=tj;t++){
   /* for (i=1; i<=imx; i++){      for(i1=1; i1<=ncodemax[t];i1++){ 
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;        j1++;
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;        if  (cptcovn>0) {
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;          fprintf(ficresprob, "\n#********** Variable "); 
     }*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
    /*  for (i=1; i<=imx; i++){          fprintf(ficresprob, "**********\n#\n");
      if (s[4][i]==9)  s[4][i]=-1;          fprintf(ficresprobcov, "\n#********** Variable "); 
      printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
            fprintf(ficresprobcov, "**********\n#\n");
            
   /* Calculation of the number of parameter from char model*/          fprintf(ficgp, "\n#********** Variable "); 
   Tvar=ivector(1,15);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   Tprod=ivector(1,15);          fprintf(ficgp, "**********\n#\n");
   Tvaraff=ivector(1,15);          
   Tvard=imatrix(1,15,1,2);          
   Tage=ivector(1,15);                fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
              for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
   if (strlen(model) >1){          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     j=0, j1=0, k1=1, k2=1;          
     j=nbocc(model,'+');          fprintf(ficresprobcor, "\n#********** Variable ");    
     j1=nbocc(model,'*');          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     cptcovn=j+1;          fprintf(ficresprobcor, "**********\n#");    
     cptcovprod=j1;        }
            
     strcpy(modelsav,model);        for (age=bage; age<=fage; age ++){ 
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){          cov[2]=age;
       printf("Error. Non available option model=%s ",model);          for (k=1; k<=cptcovn;k++) {
       goto end;            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
     }          }
              for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     for(i=(j+1); i>=1;i--){          for (k=1; k<=cptcovprod;k++)
       cutv(stra,strb,modelsav,'+');            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);          
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
       /*scanf("%d",i);*/          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       if (strchr(strb,'*')) {          gp=vector(1,(nlstate)*(nlstate+ndeath));
         cutv(strd,strc,strb,'*');          gm=vector(1,(nlstate)*(nlstate+ndeath));
         if (strcmp(strc,"age")==0) {      
           cptcovprod--;          for(theta=1; theta <=npar; theta++){
           cutv(strb,stre,strd,'V');            for(i=1; i<=npar; i++)
           Tvar[i]=atoi(stre);              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
           cptcovage++;            
             Tage[cptcovage]=i;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
             /*printf("stre=%s ", stre);*/            
         }            k=0;
         else if (strcmp(strd,"age")==0) {            for(i=1; i<= (nlstate); i++){
           cptcovprod--;              for(j=1; j<=(nlstate+ndeath);j++){
           cutv(strb,stre,strc,'V');                k=k+1;
           Tvar[i]=atoi(stre);                gp[k]=pmmij[i][j];
           cptcovage++;              }
           Tage[cptcovage]=i;            }
         }            
         else {            for(i=1; i<=npar; i++)
           cutv(strb,stre,strc,'V');              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
           Tvar[i]=ncovcol+k1;      
           cutv(strb,strc,strd,'V');            pmij(pmmij,cov,ncovmodel,xp,nlstate);
           Tprod[k1]=i;            k=0;
           Tvard[k1][1]=atoi(strc);            for(i=1; i<=(nlstate); i++){
           Tvard[k1][2]=atoi(stre);              for(j=1; j<=(nlstate+ndeath);j++){
           Tvar[cptcovn+k2]=Tvard[k1][1];                k=k+1;
           Tvar[cptcovn+k2+1]=Tvard[k1][2];                gm[k]=pmmij[i][j];
           for (k=1; k<=lastobs;k++)              }
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];            }
           k1++;       
           k2=k2+2;            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
         }              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
       }          }
       else {  
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
        /*  scanf("%d",i);*/            for(theta=1; theta <=npar; theta++)
       cutv(strd,strc,strb,'V');              trgradg[j][theta]=gradg[theta][j];
       Tvar[i]=atoi(strc);          
       }          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
       strcpy(modelsav,stra);            matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
         scanf("%d",i);*/          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
     }          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
 }          free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
    
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);          pmij(pmmij,cov,ncovmodel,x,nlstate);
   printf("cptcovprod=%d ", cptcovprod);          
   scanf("%d ",i);*/          k=0;
     fclose(fic);          for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
     /*  if(mle==1){*/              k=k+1;
     if (weightopt != 1) { /* Maximisation without weights*/              mu[k][(int) age]=pmmij[i][j];
       for(i=1;i<=n;i++) weight[i]=1.0;            }
     }          }
     /*-calculation of age at interview from date of interview and age at death -*/          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
     agev=matrix(1,maxwav,1,imx);            for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
     for (i=1; i<=imx; i++) {  
       for(m=2; (m<= maxwav); m++) {          /*printf("\n%d ",(int)age);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
          anint[m][i]=9999;            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
          s[m][i]=-1;            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
        }            }*/
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;  
       }          fprintf(ficresprob,"\n%d ",(int)age);
     }          fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
     for (i=1; i<=imx; i++)  {  
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
       for(m=1; (m<= maxwav); m++){            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
         if(s[m][i] >0){          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
           if (s[m][i] >= nlstate+1) {            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             if(agedc[i]>0)            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
               if(moisdc[i]!=99 && andc[i]!=9999)          }
                 agev[m][i]=agedc[i];          i=0;
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/          for (k=1; k<=(nlstate);k++){
            else {            for (l=1; l<=(nlstate+ndeath);l++){ 
               if (andc[i]!=9999){              i=i++;
               printf("Warning negative age at death: %d line:%d\n",num[i],i);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               agev[m][i]=-1;              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               }              for (j=1; j<=i;j++){
             }                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
           }                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
           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)          }/* end of loop for state */
               agev[m][i]=1;        } /* end of loop for age */
             else if(agev[m][i] <agemin){  
               agemin=agev[m][i];        /* Confidence intervalle of pij  */
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/        /*
             }          fprintf(ficgp,"\nset noparametric;unset label");
             else if(agev[m][i] >agemax){          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
               agemax=agev[m][i];          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/          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);
             /*agev[m][i]=anint[m][i]-annais[i];*/          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
             /*   agev[m][i] = age[i]+2*m;*/          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
           }        */
           else { /* =9 */  
             agev[m][i]=1;        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
             s[m][i]=-1;        first1=1;
           }        for (k2=1; k2<=(nlstate);k2++){
         }          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
         else /*= 0 Unknown */            if(l2==k2) continue;
           agev[m][i]=1;            j=(k2-1)*(nlstate+ndeath)+l2;
       }            for (k1=1; k1<=(nlstate);k1++){
                  for (l1=1; l1<=(nlstate+ndeath);l1++){ 
     }                if(l1==k1) continue;
     for (i=1; i<=imx; i++)  {                i=(k1-1)*(nlstate+ndeath)+l1;
       for(m=1; (m<= maxwav); m++){                if(i<=j) continue;
         if (s[m][i] > (nlstate+ndeath)) {                for (age=bage; age<=fage; age ++){ 
           printf("Error: Wrong value in nlstate or ndeath\n");                    if ((int)age %5==0){
           goto end;                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
         }                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
       }                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
     }                    mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);                    c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
     free_vector(severity,1,maxwav);                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     free_imatrix(outcome,1,maxwav+1,1,n);                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
     free_vector(moisnais,1,n);                    /* Eigen vectors */
     free_vector(annais,1,n);                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
     /* free_matrix(mint,1,maxwav,1,n);                    /*v21=sqrt(1.-v11*v11); *//* error */
        free_matrix(anint,1,maxwav,1,n);*/                    v21=(lc1-v1)/cv12*v11;
     free_vector(moisdc,1,n);                    v12=-v21;
     free_vector(andc,1,n);                    v22=v11;
                     tnalp=v21/v11;
                        if(first1==1){
     wav=ivector(1,imx);                      first1=0;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);                      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);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);                    }
                        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);
     /* Concatenates waves */                    /*printf(fignu*/
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
       Tcode=ivector(1,100);                      first=0;
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);                      fprintf(ficgp,"\nset parametric;unset label");
       ncodemax[1]=1;                      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);
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                            fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
    codtab=imatrix(1,100,1,10);   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
    h=0;  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
    m=pow(2,cptcoveff);                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                                subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
    for(k=1;k<=cptcoveff; k++){                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
      for(i=1; i <=(m/pow(2,k));i++){                      fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
        for(j=1; j <= ncodemax[k]; j++){                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
            h++;                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;                      fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
          }                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
        }                    }else{
      }                      first=0;
    }                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
       codtab[1][2]=1;codtab[2][2]=2; */                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
    /* for(i=1; i <=m ;i++){                      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",\
       for(k=1; k <=cptcovn; k++){                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
       }                    }/* if first */
       printf("\n");                  } /* age mod 5 */
       }                } /* end loop age */
       scanf("%d",i);*/                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                    first=1;
    /* Calculates basic frequencies. Computes observed prevalence at single age              } /*l12 */
        and prints on file fileres'p'. */            } /* k12 */
           } /*l1 */
            }/* k1 */
          } /* loop covariates */
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    }
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    free_vector(xp,1,npar);
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    fclose(ficresprob);
          fclose(ficresprobcov);
     /* For Powell, parameters are in a vector p[] starting at p[1]    fclose(ficresprobcor);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */    fflush(ficgp);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    fflush(fichtmcov);
   }
     if(mle==1){  
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);  
     }  /******************* Printing html file ***********/
      void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
     /*--------- results files --------------*/                    int lastpass, int stepm, int weightopt, char model[],\
     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);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                      int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
    jk=1;                    double jprev2, double mprev2,double anprev2){
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    int jj1, k1, i1, cpt;
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");  
    for(i=1,jk=1; i <=nlstate; i++){     fprintf(fichtm,"<ul><li><h4>Result files (first order: no variance)</h4>\n \
      for(k=1; k <=(nlstate+ndeath); k++){   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
        if (k != i)             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
          {     fprintf(fichtm,"\
            printf("%d%d ",i,k);   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
            fprintf(ficres,"%1d%1d ",i,k);             stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
            for(j=1; j <=ncovmodel; j++){     fprintf(fichtm,"\
              printf("%f ",p[jk]);   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              fprintf(ficres,"%f ",p[jk]);             subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
              jk++;     fprintf(fichtm,"\
            }   - Life expectancies by age and initial health status (estepm=%2d months): \
            printf("\n");     <a href=\"%s\">%s</a> <br>\n</li>",
            fprintf(ficres,"\n");             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
          }  
      }  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
    }  
  if(mle==1){   m=cptcoveff;
     /* Computing hessian and covariance matrix */   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
     ftolhess=ftol; /* Usually correct */  
     hesscov(matcov, p, npar, delti, ftolhess, func);   jj1=0;
  }   for(k1=1; k1<=m;k1++){
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");     for(i1=1; i1<=ncodemax[k1];i1++){
     printf("# Scales (for hessian or gradient estimation)\n");       jj1++;
      for(i=1,jk=1; i <=nlstate; i++){       if (cptcovn > 0) {
       for(j=1; j <=nlstate+ndeath; j++){         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
         if (j!=i) {         for (cpt=1; cpt<=cptcoveff;cpt++) 
           fprintf(ficres,"%1d%1d",i,j);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
           printf("%1d%1d",i,j);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
           for(k=1; k<=ncovmodel;k++){       }
             printf(" %.5e",delti[jk]);       /* Pij */
             fprintf(ficres," %.5e",delti[jk]);       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> \
             jk++;  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
           }       /* Quasi-incidences */
           printf("\n");       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
           fprintf(ficres,"\n");   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
         }  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
       }         /* Stable prevalence in each health state */
      }         for(cpt=1; cpt<nlstate;cpt++){
               fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
     k=1;  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
     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");         }
     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(cpt=1; cpt<=nlstate;cpt++) {
     for(i=1;i<=npar;i++){          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
       /*  if (k>nlstate) k=1;  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
       i1=(i-1)/(ncovmodel*nlstate)+1;       }
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);     } /* end i1 */
       printf("%s%d%d",alph[k],i1,tab[i]);*/   }/* End k1 */
       fprintf(ficres,"%3d",i);   fprintf(fichtm,"</ul>");
       printf("%3d",i);  
       for(j=1; j<=i;j++){  
         fprintf(ficres," %.5e",matcov[i][j]);   fprintf(fichtm,"\
         printf(" %.5e",matcov[i][j]);  \n<br><li><h4> Result files (second order: variances)</h4>\n\
       }   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
       fprintf(ficres,"\n");  
       printf("\n");   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
       k++;           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
     }   fprintf(fichtm,"\
       - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
     while((c=getc(ficpar))=='#' && c!= EOF){           subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
       ungetc(c,ficpar);  
       fgets(line, MAXLINE, ficpar);   fprintf(fichtm,"\
       puts(line);   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
       fputs(line,ficparo);           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
     }   fprintf(fichtm,"\
     ungetc(c,ficpar);   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
     estepm=0;           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);   fprintf(fichtm,"\
     if (estepm==0 || estepm < stepm) estepm=stepm;   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
     if (fage <= 2) {           subdirf2(fileres,"t"),subdirf2(fileres,"t"));
       bage = ageminpar;   fprintf(fichtm,"\
       fage = agemaxpar;   - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
     }           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");  /*  if(popforecast==1) fprintf(fichtm,"\n */
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
    /*      <br>",fileres,fileres,fileres,fileres); */
     while((c=getc(ficpar))=='#' && c!= EOF){  /*  else  */
     ungetc(c,ficpar);  /*    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); */
     fgets(line, MAXLINE, ficpar);   fflush(fichtm);
     puts(line);   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
     fputs(line,ficparo);  
   }   m=cptcoveff;
   ungetc(c,ficpar);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
    
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);   jj1=0;
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);   for(k1=1; k1<=m;k1++){
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);     for(i1=1; i1<=ncodemax[k1];i1++){
             jj1++;
   while((c=getc(ficpar))=='#' && c!= EOF){       if (cptcovn > 0) {
     ungetc(c,ficpar);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
     fgets(line, MAXLINE, ficpar);         for (cpt=1; cpt<=cptcoveff;cpt++) 
     puts(line);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     fputs(line,ficparo);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   }       }
   ungetc(c,ficpar);       for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
    dateprev1=anprev1+mprev1/12.+jprev1/365.;  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
    dateprev2=anprev2+mprev2/12.+jprev2/365.;       }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   fscanf(ficpar,"pop_based=%d\n",&popbased);  health expectancies in states (1) and (2): %s%d.png<br>\
   fprintf(ficparo,"pop_based=%d\n",popbased);    <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
   fprintf(ficres,"pop_based=%d\n",popbased);       } /* end i1 */
     }/* End k1 */
   while((c=getc(ficpar))=='#' && c!= EOF){   fprintf(fichtm,"</ul>");
     ungetc(c,ficpar);   fflush(fichtm);
     fgets(line, MAXLINE, ficpar);  }
     puts(line);  
     fputs(line,ficparo);  /******************* Gnuplot file **************/
   }  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   ungetc(c,ficpar);  
     char dirfileres[132],optfileres[132];
   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);    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
 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);    int ng;
 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);  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
 while((c=getc(ficpar))=='#' && c!= EOF){  /*   } */
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    /*#ifdef windows */
     puts(line);    fprintf(ficgp,"cd \"%s\" \n",pathc);
     fputs(line,ficparo);      /*#endif */
   }    m=pow(2,cptcoveff);
   ungetc(c,ficpar);  
     strcpy(dirfileres,optionfilefiname);
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);    strcpy(optfileres,"vpl");
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);   /* 1eme*/
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);    for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);       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);
 /*------------ gnuplot -------------*/       fprintf(ficgp,"set xlabel \"Age\" \n\
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);  set ylabel \"Probability\" \n\
    set ter png small\n\
 /*------------ free_vector  -------------*/  set size 0.65,0.65\n\
  chdir(path);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
    
  free_ivector(wav,1,imx);       for (i=1; i<= nlstate ; i ++) {
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);           else fprintf(ficgp," \%%*lf (\%%*lf)");
  free_ivector(num,1,n);       }
  free_vector(agedc,1,n);       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);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/       for (i=1; i<= nlstate ; i ++) {
  fclose(ficparo);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
  fclose(ficres);         else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
 /*--------- index.htm --------*/       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
         }  
   /*--------------- Prevalence limit --------------*/       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
       }
   strcpy(filerespl,"pl");    }
   strcat(filerespl,fileres);    /*2 eme*/
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    for (k1=1; k1<= m ; k1 ++) { 
   }      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
   fprintf(ficrespl,"#Prevalence limit\n");      
   fprintf(ficrespl,"#Age ");      for (i=1; i<= nlstate+1 ; i ++) {
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);        k=2*i;
   fprintf(ficrespl,"\n");        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
          for (j=1; j<= nlstate+1 ; j ++) {
   prlim=matrix(1,nlstate,1,nlstate);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          else fprintf(ficgp," \%%*lf (\%%*lf)");
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        }   
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
   k=0;        for (j=1; j<= nlstate+1 ; j ++) {
   agebase=ageminpar;          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
   agelim=agemaxpar;          else fprintf(ficgp," \%%*lf (\%%*lf)");
   ftolpl=1.e-10;        }   
   i1=cptcoveff;        fprintf(ficgp,"\" t\"\" w l 0,");
   if (cptcovn < 1){i1=1;}        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
   for(cptcov=1;cptcov<=i1;cptcov++){          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){          else fprintf(ficgp," \%%*lf (\%%*lf)");
         k=k+1;        }   
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/        if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         fprintf(ficrespl,"\n#******");        else fprintf(ficgp,"\" t\"\" w l 0,");
         for(j=1;j<=cptcoveff;j++)      }
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    }
         fprintf(ficrespl,"******\n");    
            /*3eme*/
         for (age=agebase; age<=agelim; age++){    
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    for (k1=1; k1<= m ; k1 ++) { 
           fprintf(ficrespl,"%.0f",age );      for (cpt=1; cpt<= nlstate ; cpt ++) {
           for(i=1; i<=nlstate;i++)        k=2+nlstate*(2*cpt-2);
           fprintf(ficrespl," %.5f", prlim[i][i]);        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
           fprintf(ficrespl,"\n");        fprintf(ficgp,"set ter png small\n\
         }  set size 0.65,0.65\n\
       }  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
     }        /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
   fclose(ficrespl);          for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   /*------------- h Pij x at various ages ------------*/          fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
            for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);          fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {          
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;        */
   }        for (i=1; i< nlstate ; i ++) {
   printf("Computing pij: result on file '%s' \n", filerespij);          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);
            
   stepsize=(int) (stepm+YEARM-1)/YEARM;        } 
   /*if (stepm<=24) stepsize=2;*/      }
     }
   agelim=AGESUP;    
   hstepm=stepsize*YEARM; /* Every year of age */    /* CV preval stable (period) */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    for (k1=1; k1<= m ; k1 ++) { 
        for (cpt=1; cpt<=nlstate ; cpt ++) {
   k=0;        k=3;
   for(cptcov=1;cptcov<=i1;cptcov++){        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
       k=k+1;  set ter png small\nset size 0.65,0.65\n\
         fprintf(ficrespij,"\n#****** ");  unset log y\n\
         for(j=1;j<=cptcoveff;j++)  plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        
         fprintf(ficrespij,"******\n");        for (i=1; i< nlstate ; i ++)
                  fprintf(ficgp,"+$%d",k+i+1);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */        fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        l=3+(nlstate+ndeath)*cpt;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
           oldm=oldms;savm=savms;        for (i=1; i< nlstate ; i ++) {
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            l=3+(nlstate+ndeath)*cpt;
           fprintf(ficrespij,"# Age");          fprintf(ficgp,"+$%d",l+i+1);
           for(i=1; i<=nlstate;i++)        }
             for(j=1; j<=nlstate+ndeath;j++)        fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
               fprintf(ficrespij," %1d-%1d",i,j);      } 
           fprintf(ficrespij,"\n");    }  
            for (h=0; h<=nhstepm; h++){    
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    /* proba elementaires */
             for(i=1; i<=nlstate;i++)    for(i=1,jk=1; i <=nlstate; i++){
               for(j=1; j<=nlstate+ndeath;j++)      for(k=1; k <=(nlstate+ndeath); k++){
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);        if (k != i) {
             fprintf(ficrespij,"\n");          for(j=1; j <=ncovmodel; j++){
              }            fprintf(ficgp,"p%d=%f ",jk,p[jk]);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            jk++; 
           fprintf(ficrespij,"\n");            fprintf(ficgp,"\n");
         }          }
     }        }
   }      }
      }
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);  
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
   fclose(ficrespij);       for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
   /*---------- Forecasting ------------------*/           fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
   if((stepm == 1) && (strcmp(model,".")==0)){         else
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);           fprintf(ficgp,"\nset title \"Probability\"\n");
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);         fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
   }         i=1;
   else{         for(k2=1; k2<=nlstate; k2++) {
     erreur=108;           k3=i;
     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(k=1; k<=(nlstate+ndeath); k++) {
   }             if (k != k2){
                 if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
   /*---------- Health expectancies and variances ------------*/               else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
   strcpy(filerest,"t");               ij=1;
   strcat(filerest,fileres);               for(j=3; j <=ncovmodel; j++) {
   if((ficrest=fopen(filerest,"w"))==NULL) {                 if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;                   fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   }                   ij++;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);                 }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   strcpy(filerese,"e");               }
   strcat(filerese,fileres);               fprintf(ficgp,")/(1");
   if((ficreseij=fopen(filerese,"w"))==NULL) {               
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);               for(k1=1; k1 <=nlstate; k1++){   
   }                 fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);                 ij=1;
                  for(j=3; j <=ncovmodel; j++){
  strcpy(fileresv,"v");                   if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
   strcat(fileresv,fileres);                     fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {                     ij++;
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);                   }
   }                   else
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);                     fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
   calagedate=-1;                 }
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);                 fprintf(ficgp,")");
                }
   k=0;               fprintf(ficgp,") t \"p%d%d\" ", k2,k);
   for(cptcov=1;cptcov<=i1;cptcov++){               if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){               i=i+ncovmodel;
       k=k+1;             }
       fprintf(ficrest,"\n#****** ");           } /* end k */
       for(j=1;j<=cptcoveff;j++)         } /* end k2 */
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       } /* end jk */
       fprintf(ficrest,"******\n");     } /* end ng */
      fflush(ficgp); 
       fprintf(ficreseij,"\n#****** ");  }  /* end gnuplot */
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficreseij,"******\n");  /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
       fprintf(ficresvij,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)    int i, cpt, cptcod;
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    int modcovmax =1;
       fprintf(ficresvij,"******\n");    int mobilavrange, mob;
     double age;
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;    modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);                               a covariate has 2 modalities */
      if (cptcovn<1) modcovmax=1; /* At least 1 pass */
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;    if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);      if(mobilav==1) mobilavrange=5; /* default */
          else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
          for (i=1; i<=nlstate;i++)
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");          for (cptcod=1;cptcod<=modcovmax;cptcod++)
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);            mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       fprintf(ficrest,"\n");      /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
       epj=vector(1,nlstate+1);         we use a 5 terms etc. until the borders are no more concerned. 
       for(age=bage; age <=fage ;age++){      */ 
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      for (mob=3;mob <=mobilavrange;mob=mob+2){
         if (popbased==1) {        for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for(i=1; i<=nlstate;i++)          for (i=1; i<=nlstate;i++){
             prlim[i][i]=probs[(int)age][i][k];            for (cptcod=1;cptcod<=modcovmax;cptcod++){
         }              mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                        for (cpt=1;cpt<=(mob-1)/2;cpt++){
         fprintf(ficrest," %4.0f",age);                  mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){                  mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
           for(i=1, epj[j]=0.;i <=nlstate;i++) {                }
             epj[j] += prlim[i][i]*eij[i][j][(int)age];              mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/            }
           }          }
           epj[nlstate+1] +=epj[j];        }/* end age */
         }      }/* end mob */
     }else return -1;
         for(i=1, vepp=0.;i <=nlstate;i++)    return 0;
           for(j=1;j <=nlstate;j++)  }/* End movingaverage */
             vepp += vareij[i][j][(int)age];  
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));  
         for(j=1;j <=nlstate;j++){  /************** Forecasting ******************/
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));  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 
         fprintf(ficrest,"\n");       agemin, agemax range of age
       }       dateprev1 dateprev2 range of dates during which prevalence is computed
     }       anproj2 year of en of projection (same day and month as proj1).
   }    */
 free_matrix(mint,1,maxwav,1,n);    int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);    int *popage;
     free_vector(weight,1,n);    double agec; /* generic age */
   fclose(ficreseij);    double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
   fclose(ficresvij);    double *popeffectif,*popcount;
   fclose(ficrest);    double ***p3mat;
   fclose(ficpar);    double ***mobaverage;
   free_vector(epj,1,nlstate+1);    char fileresf[FILENAMELENGTH];
    
   /*------- Variance limit prevalence------*/      agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
   strcpy(fileresvpl,"vpl");   
   strcat(fileresvpl,fileres);    strcpy(fileresf,"f"); 
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    strcat(fileresf,fileres);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    if((ficresf=fopen(fileresf,"w"))==NULL) {
     exit(0);      printf("Problem with forecast resultfile: %s\n", fileresf);
   }      fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
   k=0;    fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    if (cptcoveff==0) ncodemax[cptcoveff]=1;
       k=k+1;  
       fprintf(ficresvpl,"\n#****** ");    if (mobilav!=0) {
       for(j=1;j<=cptcoveff;j++)      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
       fprintf(ficresvpl,"******\n");        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
              printf(" Error in movingaverage mobilav=%d\n",mobilav);
       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);  
     }    stepsize=(int) (stepm+YEARM-1)/YEARM;
  }    if (stepm<=12) stepsize=1;
     if(estepm < stepm){
   fclose(ficresvpl);      printf ("Problem %d lower than %d\n",estepm, stepm);
     }
   /*---------- End : free ----------------*/    else  hstepm=estepm;   
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  
      hstepm=hstepm/stepm; 
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);                                 fractional in yp1 */
      anprojmean=yp;
      yp2=modf((yp1*12),&yp);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    mprojmean=yp;
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    yp1=modf((yp2*30.5),&yp);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    jprojmean=yp;
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    if(jprojmean==0) jprojmean=1;
      if(mprojmean==0) jprojmean=1;
   free_matrix(matcov,1,npar,1,npar);  
   free_vector(delti,1,npar);    i1=cptcoveff;
   free_matrix(agev,1,maxwav,1,imx);    if (cptcovn < 1){i1=1;}
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
   if(erreur >0)    
     printf("End of Imach with error or warning %d\n",erreur);    fprintf(ficresf,"#****** Routine prevforecast **\n");
   else   printf("End of Imach\n");  
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */  /*            if (h==(int)(YEARM*yearp)){ */
      for(cptcov=1, k=0;cptcov<=i1;cptcov++){
   /* 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);*/      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
   /*printf("Total time was %d uSec.\n", total_usecs);*/        k=k+1;
   /*------ End -----------*/        fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
  end:        }
   /* chdir(pathcd);*/        fprintf(ficresf,"******\n");
  /*system("wgnuplot graph.plt");*/        fprintf(ficresf,"# Covariate valuofcovar yearproj age");
  /*system("../gp37mgw/wgnuplot graph.plt");*/        for(j=1; j<=nlstate+ndeath;j++){ 
  /*system("cd ../gp37mgw");*/          for(i=1; i<=nlstate;i++)              
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/            fprintf(ficresf," p%d%d",i,j);
  strcpy(plotcmd,GNUPLOTPROGRAM);          fprintf(ficresf," p.%d",j);
  strcat(plotcmd," ");        }
  strcat(plotcmd,optionfilegnuplot);        for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
  system(plotcmd);          fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
  /*#ifdef windows*/  
   while (z[0] != 'q') {          for (agec=fage; agec>=(ageminpar-1); agec--){ 
     /* chdir(path); */            nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");            nhstepm = nhstepm/hstepm; 
     scanf("%s",z);            p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     if (z[0] == 'c') system("./imach");            oldm=oldms;savm=savms;
     else if (z[0] == 'e') system(optionfilehtm);            hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
     else if (z[0] == 'g') system(plotcmd);          
     else if (z[0] == 'q') exit(0);            for (h=0; h<=nhstepm; h++){
   }              if (h*hstepm/YEARM*stepm ==yearp) {
   /*#endif */                fprintf(ficresf,"\n");
 }                for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE]; 
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
   
     char *alph[]={"a","a","b","c","d","e"}, str[4];
   
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char strstart[80], *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       scanf("%s",pathtot);
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("pathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: ");
     fprintf(ficlog,"pathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
    
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     /* Read guess parameters */
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     for(i=1; i <=nlstate; i++){
       j=0;
       for(jj=1; jj <=nlstate+ndeath; jj++){
         if(jj==i) continue;
         j++;
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1 != i) && (j1 != j)){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);
         }
         fprintf(ficparo,"%1d%1d",i1,j1);
         if(mle==1)
           printf("%1d%1d",i,j);
         fprintf(ficlog,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar," %lf",&param[i][j][k]);
           if(mle==1){
             printf(" %lf",param[i][j][k]);
             fprintf(ficlog," %lf",param[i][j][k]);
           }
           else
             fprintf(ficlog," %lf",param[i][j][k]);
           fprintf(ficparo," %lf",param[i][j][k]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
     }  
     fflush(ficlog);
   
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     p=param[1][1];
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     /* delti=vector(1,npar); *//* Scale of each paramater (output from hesscov) */
     for(i=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath-1; j++){
         fscanf(ficpar,"%1d%1d",&i1,&j1);
         if ((i1-i)*(j1-j)!=0){
           printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
           exit(1);
         }
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i1,j1);
         fprintf(ficlog,"%1d%1d",i1,j1);
         for(k=1; k<=ncovmodel;k++){
           fscanf(ficpar,"%le",&delti3[i][j][k]);
           printf(" %le",delti3[i][j][k]);
           fprintf(ficparo," %le",delti3[i][j][k]);
           fprintf(ficlog," %le",delti3[i][j][k]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
         fprintf(ficlog,"\n");
       }
     }
     fflush(ficlog);
   
     delti=delti3[1][1];
   
   
     /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
     /* Reads comments: lines beginning with '#' */
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
     
     matcov=matrix(1,npar,1,npar);
     for(i=1; i <=npar; i++){
       fscanf(ficpar,"%s",&str);
       if(mle==1)
         printf("%s",str);
       fprintf(ficlog,"%s",str);
       fprintf(ficparo,"%s",str);
       for(j=1; j <=i; j++){
         fscanf(ficpar," %le",&matcov[i][j]);
         if(mle==1){
           printf(" %.5le",matcov[i][j]);
         }
         fprintf(ficlog," %.5le",matcov[i][j]);
         fprintf(ficparo," %.5le",matcov[i][j]);
       }
       fscanf(ficpar,"\n");
       numlinepar++;
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       fprintf(ficparo,"\n");
     }
     for(i=1; i <=npar; i++)
       for(j=i+1;j<=npar;j++)
         matcov[i][j]=matcov[j][i];
      
     if(mle==1)
       printf("\n");
     fprintf(ficlog,"\n");
   
     fflush(ficlog);
   
     /*-------- Rewriting paramater file ----------*/
     strcpy(rfileres,"r");    /* "Rparameterfile */
     strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
     strcat(rfileres,".");    /* */
     strcat(rfileres,optionfilext);    /* Other files have txt extension */
     if((ficres =fopen(rfileres,"w"))==NULL) {
       printf("Problem writing new parameter file: %s\n", fileres);goto end;
       fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
     }
     fprintf(ficres,"#%s\n",version);
       
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     while (fgets(line, MAXLINE, fic) != NULL)    {
       if ((i >= firstobs) && (i <=lastobs)) {
           
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb); 
           strcpy(line,stra);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);
   
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);
         } 
         lstra=strlen(stra);
         if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
           stratrunc = &(stra[lstra-9]);
           num[i]=atol(stratrunc);
         }
         else
           num[i]=atol(stra);
           
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
           printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
   
         i=i+1;
       }
     }
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
    for (i=1; i<=imx; i++)
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameter from char model*/
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);
     fclose(fic);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a
                                    month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     strcat(optionfilegnuplot,".gp");
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);
     printf("\n");
     globpr=1; /* to print the contributions */
     likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
     printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
     for (k=1; k<=npar;k++)
       printf(" %d %8.5f",k,p[k]);
     printf("\n");
     if(mle>=1){ /* Could be 1 or 2 */
       mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
     }
       
     /*--------- results files --------------*/
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
     
   
     fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           printf("%d%d ",i,k);
           fprintf(ficlog,"%d%d ",i,k);
           fprintf(ficres,"%1d%1d ",i,k);
           for(j=1; j <=ncovmodel; j++){
             printf("%f ",p[jk]);
             fprintf(ficlog,"%f ",p[jk]);
             fprintf(ficres,"%f ",p[jk]);
             jk++; 
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
     if(mle!=0){
       /* Computing hessian and covariance matrix */
       ftolhess=ftol; /* Usually correct */
       hesscov(matcov, p, npar, delti, ftolhess, func);
     }
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
     for(i=1,jk=1; i <=nlstate; i++){
       for(j=1; j <=nlstate+ndeath; j++){
         if (j!=i) {
           fprintf(ficres,"%1d%1d",i,j);
           printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             printf(" %.5e",delti[jk]);
             fprintf(ficlog," %.5e",delti[jk]);
             fprintf(ficres," %.5e",delti[jk]);
             jk++;
           }
           printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficres,"\n");
         }
       }
     }
      
     fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     if(mle>=1)
       printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
     fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
   
   
   /* Just to have a covariance matrix which will be more understandable
      even is we still don't want to manage dictionary of variables
   */
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               if(mle>=1)
                 printf("#%1d%1d%d",i,j,k);
               fprintf(ficlog,"#%1d%1d%d",i,j,k);
               fprintf(ficres,"#%1d%1d%d",i,j,k);
             }else{
               if(mle>=1)
                 printf("%1d%1d%d",i,j,k);
               fprintf(ficlog,"%1d%1d%d",i,j,k);
               fprintf(ficres,"%1d%1d%d",i,j,k);
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         if(mle>=1)
                           printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         if(mle>=1)
                           printf(" %.5e",matcov[jj][ll]); 
                         fprintf(ficlog," %.5e",matcov[jj][ll]); 
                         fprintf(ficres," %.5e",matcov[jj][ll]); 
                       }
                     }else{
                       if(itimes==1){
                         if(mle>=1)
                           printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         if(mle>=1)
                           printf(" %.5e",matcov[jj][ll]); 
                         fprintf(ficlog," %.5e",matcov[jj][ll]); 
                         fprintf(ficres," %.5e",matcov[jj][ll]); 
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             if(mle>=1)
               printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
     fflush(ficlog);
     fflush(ficres);
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     estepm=0;
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
     if (estepm==0 || estepm < stepm) estepm=stepm;
     if (fage <= 2) {
       bage = ageminpar;
       fage = agemaxpar;
     }
      
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
     
     fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
     fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
     fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
      
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
    
   
     dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
     dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
   
     fscanf(ficpar,"pop_based=%d\n",&popbased);
     fprintf(ficparo,"pop_based=%d\n",popbased);   
     fprintf(ficres,"pop_based=%d\n",popbased);   
     
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
     fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
     /* day and month of proj2 are not used but only year anproj2.*/
   
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       puts(line);
       fputs(line,ficparo);
     }
     ungetc(c,ficpar);
   
     /*  fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);
     fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);
     fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);*/
   
     /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
     /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
   
     replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
     printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
   
     printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                  model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                  jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
    
     /*------------ free_vector  -------------*/
     /*  chdir(path); */
    
     free_ivector(wav,1,imx);
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
     free_lvector(num,1,n);
     free_vector(agedc,1,n);
     /*free_matrix(covar,0,NCOVMAX,1,n);*/
     /*free_matrix(covar,1,NCOVMAX,1,n);*/
     fclose(ficparo);
     fclose(ficres);
   
   
     /*--------------- Prevalence limit  (stable prevalence) --------------*/
     
     strcpy(filerespl,"pl");
     strcat(filerespl,fileres);
     if((ficrespl=fopen(filerespl,"w"))==NULL) {
       printf("Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
       fprintf(ficlog,"Problem with stable prevalence resultfile: %s\n", filerespl);goto end;
     }
     printf("Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficlog,"Computing stable prevalence: result on file '%s' \n", filerespl);
     fprintf(ficrespl,"#Stable prevalence \n");
     fprintf(ficrespl,"#Age ");
     for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
     fprintf(ficrespl,"\n");
     
     prlim=matrix(1,nlstate,1,nlstate);
   
     agebase=ageminpar;
     agelim=agemaxpar;
     ftolpl=1.e-10;
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
         fprintf(ficrespl,"\n#******");
         printf("\n#******");
         fprintf(ficlog,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespl,"******\n");
         printf("******\n");
         fprintf(ficlog,"******\n");
           
         for (age=agebase; age<=agelim; age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           fprintf(ficrespl,"%.0f ",age );
           for(j=1;j<=cptcoveff;j++)
             fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           for(i=1; i<=nlstate;i++)
             fprintf(ficrespl," %.5f", prlim[i][i]);
           fprintf(ficrespl,"\n");
         }
       }
     }
     fclose(ficrespl);
   
     /*------------- h Pij x at various ages ------------*/
     
     strcpy(filerespij,"pij");  strcat(filerespij,fileres);
     if((ficrespij=fopen(filerespij,"w"))==NULL) {
       printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
       fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
     }
     printf("Computing pij: result on file '%s' \n", filerespij);
     fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     /*if (stepm<=24) stepsize=2;*/
   
     agelim=AGESUP;
     hstepm=stepsize*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
     /* hstepm=1;   aff par mois*/
   
     fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficrespij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrespij,"******\n");
           
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
           /*        nhstepm=nhstepm*YEARM; aff par mois*/
   
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           oldm=oldms;savm=savms;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
           for(i=1; i<=nlstate;i++)
             for(j=1; j<=nlstate+ndeath;j++)
               fprintf(ficrespij," %1d-%1d",i,j);
           fprintf(ficrespij,"\n");
           for (h=0; h<=nhstepm; h++){
             fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);
             fprintf(ficrespij,"\n");
           }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           fprintf(ficrespij,"\n");
         }
       }
     }
   
     varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax);
   
     fclose(ficrespij);
   
     probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
     for(i=1;i<=AGESUP;i++)
       for(j=1;j<=NCOVMAX;j++)
         for(k=1;k<=NCOVMAX;k++)
           probs[i][j][k]=0.;
   
     /*---------- Forecasting ------------------*/
     /*if((stepm == 1) && (strcmp(model,".")==0)){*/
     if(prevfcast==1){
       /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
   /*      }  */
   /*      else{ */
   /*        erreur=108; */
   /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
   /*      } */
     }
     
   
     /*---------- Health expectancies and variances ------------*/
   
     strcpy(filerest,"t");
     strcat(filerest,fileres);
     if((ficrest=fopen(filerest,"w"))==NULL) {
       printf("Problem with total LE resultfile: %s\n", filerest);goto end;
       fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
     }
     printf("Computing Total LEs with variances: file '%s' \n", filerest); 
     fprintf(ficlog,"Computing Total LEs with variances: file '%s' \n", filerest); 
   
   
     strcpy(filerese,"e");
     strcat(filerese,fileres);
     if((ficreseij=fopen(filerese,"w"))==NULL) {
       printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
     }
     printf("Computing Health Expectancies: result on file '%s' \n", filerese);
     fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
     strcpy(fileresv,"v");
     strcat(fileresv,fileres);
     if((ficresvij=fopen(fileresv,"w"))==NULL) {
       printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
       fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
     }
     printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
     fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
     /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
     prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
   ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
     */
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1; 
         fprintf(ficrest,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficrest,"******\n");
   
         fprintf(ficreseij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficreseij,"******\n");
   
         fprintf(ficresvij,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvij,"******\n");
   
         eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);  
    
         vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav);
         if(popbased==1){
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav);
         }
   
    
         fprintf(ficrest,"#Total LEs with variances: e.. (std) ");
         for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
         fprintf(ficrest,"\n");
   
         epj=vector(1,nlstate+1);
         for(age=bage; age <=fage ;age++){
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
           if (popbased==1) {
             if(mobilav ==0){
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=probs[(int)age][i][k];
             }else{ /* mobilav */ 
               for(i=1; i<=nlstate;i++)
                 prlim[i][i]=mobaverage[(int)age][i][k];
             }
           }
           
           fprintf(ficrest," %4.0f",age);
           for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
             for(i=1, epj[j]=0.;i <=nlstate;i++) {
               epj[j] += prlim[i][i]*eij[i][j][(int)age];
               /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
             }
             epj[nlstate+1] +=epj[j];
           }
   
           for(i=1, vepp=0.;i <=nlstate;i++)
             for(j=1;j <=nlstate;j++)
               vepp += vareij[i][j][(int)age];
           fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
           for(j=1;j <=nlstate;j++){
             fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
           }
           fprintf(ficrest,"\n");
         }
         free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
         free_vector(epj,1,nlstate+1);
       }
     }
     free_vector(weight,1,n);
     free_imatrix(Tvard,1,15,1,2);
     free_imatrix(s,1,maxwav+1,1,n);
     free_matrix(anint,1,maxwav,1,n); 
     free_matrix(mint,1,maxwav,1,n);
     free_ivector(cod,1,n);
     free_ivector(tab,1,NCOVMAX);
     fclose(ficreseij);
     fclose(ficresvij);
     fclose(ficrest);
     fclose(ficpar);
     
     /*------- Variance of stable prevalence------*/   
   
     strcpy(fileresvpl,"vpl");
     strcat(fileresvpl,fileres);
     if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
       printf("Problem with variance of stable prevalence  resultfile: %s\n", fileresvpl);
       exit(0);
     }
     printf("Computing Variance-covariance of stable prevalence: file '%s' \n", fileresvpl);
   
     for(cptcov=1,k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
         k=k+1;
         fprintf(ficresvpl,"\n#****** ");
         for(j=1;j<=cptcoveff;j++) 
           fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         fprintf(ficresvpl,"******\n");
         
         varpl=matrix(1,nlstate,(int) bage, (int) fage);
         oldm=oldms;savm=savms;
         varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);
         free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
       }
     }
   
     fclose(ficresvpl);
   
     /*---------- End : free ----------------*/
     free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
     free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
     
     free_matrix(covar,0,NCOVMAX,1,n);
     free_matrix(matcov,1,npar,1,npar);
     /*free_vector(delti,1,npar);*/
     free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
     free_matrix(agev,1,maxwav,1,imx);
     free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     free_ivector(ncodemax,1,8);
     free_ivector(Tvar,1,15);
     free_ivector(Tprod,1,15);
     free_ivector(Tvaraff,1,15);
     free_ivector(Tage,1,15);
     free_ivector(Tcode,1,100);
   
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocaltime at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
     fclose(fichtm);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
     chdir(path);
     strcpy(plotcmd,GNUPLOTPROGRAM);
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
     if((outcmd=system(plotcmd)) != 0){
       printf(" Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') system(optionfilehtm);
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   
Removed from v.1.41.2.1  
changed lines
  Added in v.1.97

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