Diff for /imach/src/imach.c between versions 1.38 and 1.109

version 1.38, 2002/04/03 12:19:36 version 1.109, 2006/01/24 19:37:15
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.109  2006/01/24 19:37:15  brouard
      (Module): Comments (lines starting with a #) are allowed in data.
   This program computes Healthy Life Expectancies from  
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    Revision 1.108  2006/01/19 18:05:42  lievre
   first survey ("cross") where individuals from different ages are    Gnuplot problem appeared...
   interviewed on their health status or degree of disability (in the    To be fixed
   case of a health survey which is our main interest) -2- at least a  
   second wave of interviews ("longitudinal") which measure each change    Revision 1.107  2006/01/19 16:20:37  brouard
   (if any) in individual health status.  Health expectancies are    Test existence of gnuplot in imach path
   computed from the time spent in each health state according to a  
   model. More health states you consider, more time is necessary to reach the    Revision 1.106  2006/01/19 13:24:36  brouard
   Maximum Likelihood of the parameters involved in the model.  The    Some cleaning and links added in html output
   simplest model is the multinomial logistic model where pij is the  
   probabibility to be observed in state j at the second wave    Revision 1.105  2006/01/05 20:23:19  lievre
   conditional to be observed in state i at the first wave. Therefore    *** empty log message ***
   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 1.104  2005/09/30 16:11:43  lievre
   complex model than "constant and age", you should modify the program    (Module): sump fixed, loop imx fixed, and simplifications.
   where the markup *Covariates have to be included here again* invites    (Module): If the status is missing at the last wave but we know
   you to do it.  More covariates you add, slower the    that the person is alive, then we can code his/her status as -2
   convergence.    (instead of missing=-1 in earlier versions) and his/her
     contributions to the likelihood is 1 - Prob of dying from last
   The advantage of this computer programme, compared to a simple    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   multinomial logistic model, is clear when the delay between waves is not    the healthy state at last known wave). Version is 0.98
   identical for each individual. Also, if a individual missed an  
   intermediate interview, the information is lost, but taken into    Revision 1.103  2005/09/30 15:54:49  lievre
   account using an interpolation or extrapolation.      (Module): sump fixed, loop imx fixed, and simplifications.
   
   hPijx is the probability to be observed in state i at age x+h    Revision 1.102  2004/09/15 17:31:30  brouard
   conditional to the observed state i at age x. The delay 'h' can be    Add the possibility to read data file including tab characters.
   split into an exact number (nh*stepm) of unobserved intermediate  
   states. This elementary transition (by month or quarter trimester,    Revision 1.101  2004/09/15 10:38:38  brouard
   semester or year) is model as a multinomial logistic.  The hPx    Fix on curr_time
   matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply    Revision 1.100  2004/07/12 18:29:06  brouard
   hPijx.    Add version for Mac OS X. Just define UNIX in Makefile
   
   Also this programme outputs the covariance matrix of the parameters but also    Revision 1.99  2004/06/05 08:57:40  brouard
   of the life expectancies. It also computes the prevalence limits.    *** empty log message ***
    
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    Revision 1.98  2004/05/16 15:05:56  brouard
            Institut national d'études démographiques, Paris.    New version 0.97 . First attempt to estimate force of mortality
   This software have been partly granted by Euro-REVES, a concerted action    directly from the data i.e. without the need of knowing the health
   from the European Union.    state at each age, but using a Gompertz model: log u =a + b*age .
   It is copyrighted identically to a GNU software product, ie programme and    This is the basic analysis of mortality and should be done before any
   software can be distributed freely for non commercial use. Latest version    other analysis, in order to test if the mortality estimated from the
   can be accessed at http://euroreves.ined.fr/imach .    cross-longitudinal survey is different from the mortality estimated
   **********************************************************************/    from other sources like vital statistic data.
    
 #include <math.h>    The same imach parameter file can be used but the option for mle should be -3.
 #include <stdio.h>  
 #include <stdlib.h>    Agnès, who wrote this part of the code, tried to keep most of the
 #include <unistd.h>    former routines in order to include the new code within the former code.
   
 #define MAXLINE 256    The output is very simple: only an estimate of the intercept and of
 #define GNUPLOTPROGRAM "wgnuplot"    the slope with 95% confident intervals.
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  
 #define FILENAMELENGTH 80    Current limitations:
 /*#define DEBUG*/    A) Even if you enter covariates, i.e. with the
 #define windows    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    B) There is no computation of Life Expectancy nor Life Table.
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.97  2004/02/20 13:25:42  lievre
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    Version 0.96d. Population forecasting command line is (temporarily)
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    suppressed.
   
 #define NINTERVMAX 8    Revision 1.96  2003/07/15 15:38:55  brouard
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    rewritten within the same printf. Workaround: many printfs.
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    Revision 1.95  2003/07/08 07:54:34  brouard
 #define YEARM 12. /* Number of months per year */    * imach.c (Repository):
 #define AGESUP 130    (Repository): Using imachwizard code to output a more meaningful covariance
 #define AGEBASE 40    matrix (cov(a12,c31) instead of numbers.
   
     Revision 1.94  2003/06/27 13:00:02  brouard
 int erreur; /* Error number */    Just cleaning
 int nvar;  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Revision 1.93  2003/06/25 16:33:55  brouard
 int npar=NPARMAX;    (Module): On windows (cygwin) function asctime_r doesn't
 int nlstate=2; /* Number of live states */    exist so I changed back to asctime which exists.
 int ndeath=1; /* Number of dead states */    (Module): Version 0.96b
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
 int popbased=0;    Revision 1.92  2003/06/25 16:30:45  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
 int *wav; /* Number of waves for this individuual 0 is possible */    exist so I changed back to asctime which exists.
 int maxwav; /* Maxim number of waves */  
 int jmin, jmax; /* min, max spacing between 2 waves */    Revision 1.91  2003/06/25 15:30:29  brouard
 int mle, weightopt;    * imach.c (Repository): Duplicated warning errors corrected.
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    (Repository): Elapsed time after each iteration is now output. It
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    helps to forecast when convergence will be reached. Elapsed time
 double jmean; /* Mean space between 2 waves */    is stamped in powell.  We created a new html file for the graphs
 double **oldm, **newm, **savm; /* Working pointers to matrices */    concerning matrix of covariance. It has extension -cov.htm.
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;    Revision 1.90  2003/06/24 12:34:15  brouard
 FILE *ficgp,*ficresprob,*ficpop;    (Module): Some bugs corrected for windows. Also, when
 FILE *ficreseij;    mle=-1 a template is output in file "or"mypar.txt with the design
   char filerese[FILENAMELENGTH];    of the covariance matrix to be input.
  FILE  *ficresvij;  
   char fileresv[FILENAMELENGTH];    Revision 1.89  2003/06/24 12:30:52  brouard
  FILE  *ficresvpl;    (Module): Some bugs corrected for windows. Also, when
   char fileresvpl[FILENAMELENGTH];    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
 #define NR_END 1  
 #define FREE_ARG char*    Revision 1.88  2003/06/23 17:54:56  brouard
 #define FTOL 1.0e-10    * 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.
   
 #define NRANSI    Revision 1.87  2003/06/18 12:26:01  brouard
 #define ITMAX 200    Version 0.96
   
 #define TOL 2.0e-4    Revision 1.86  2003/06/17 20:04:08  brouard
     (Module): Change position of html and gnuplot routines and added
 #define CGOLD 0.3819660    routine fileappend.
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Revision 1.85  2003/06/17 13:12:43  brouard
     * imach.c (Repository): Check when date of death was earlier that
 #define GOLD 1.618034    current date of interview. It may happen when the death was just
 #define GLIMIT 100.0    prior to the death. In this case, dh was negative and likelihood
 #define TINY 1.0e-20    was wrong (infinity). We still send an "Error" but patch by
     assuming that the date of death was just one stepm after the
 static double maxarg1,maxarg2;    interview.
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    (Repository): Because some people have very long ID (first column)
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    we changed int to long in num[] and we added a new lvector for
      memory allocation. But we also truncated to 8 characters (left
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    truncation)
 #define rint(a) floor(a+0.5)    (Repository): No more line truncation errors.
   
 static double sqrarg;    Revision 1.84  2003/06/13 21:44:43  brouard
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    * imach.c (Repository): Replace "freqsummary" at a correct
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    place. It differs from routine "prevalence" which may be called
     many times. Probs is memory consuming and must be used with
 int imx;    parcimony.
 int stepm;    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 /* Stepm, step in month: minimum step interpolation*/  
     Revision 1.83  2003/06/10 13:39:11  lievre
 int estepm;    *** empty log message ***
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/  
     Revision 1.82  2003/06/05 15:57:20  brouard
 int m,nb;    Add log in  imach.c and  fullversion number is now printed.
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  */
 double **pmmij, ***probs, ***mobaverage;  /*
 double dateintmean=0;     Interpolated Markov Chain
   
 double *weight;    Short summary of the programme:
 int **s; /* Status */    
 double *agedc, **covar, idx;    This program computes Healthy Life Expectancies from
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
     first survey ("cross") where individuals from different ages are
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    interviewed on their health status or degree of disability (in the
 double ftolhess; /* Tolerance for computing hessian */    case of a health survey which is our main interest) -2- at least a
     second wave of interviews ("longitudinal") which measure each change
 /**************** split *************************/    (if any) in individual health status.  Health expectancies are
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    computed from the time spent in each health state according to a
 {    model. More health states you consider, more time is necessary to reach the
    char *s;                             /* pointer */    Maximum Likelihood of the parameters involved in the model.  The
    int  l1, l2;                         /* length counters */    simplest model is the multinomial logistic model where pij is the
     probability to be observed in state j at the second wave
    l1 = strlen( path );                 /* length of path */    conditional to be observed in state i at the first wave. Therefore
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 #ifdef windows    'age' is age and 'sex' is a covariate. If you want to have a more
    s = strrchr( path, '\\' );           /* find last / */    complex model than "constant and age", you should modify the program
 #else    where the markup *Covariates have to be included here again* invites
    s = strrchr( path, '/' );            /* find last / */    you to do it.  More covariates you add, slower the
 #endif    convergence.
    if ( s == NULL ) {                   /* no directory, so use current */  
 #if     defined(__bsd__)                /* get current working directory */    The advantage of this computer programme, compared to a simple
       extern char       *getwd( );    multinomial logistic model, is clear when the delay between waves is not
     identical for each individual. Also, if a individual missed an
       if ( getwd( dirc ) == NULL ) {    intermediate interview, the information is lost, but taken into
 #else    account using an interpolation or extrapolation.  
       extern char       *getcwd( );  
     hPijx is the probability to be observed in state i at age x+h
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    conditional to the observed state i at age x. The delay 'h' can be
 #endif    split into an exact number (nh*stepm) of unobserved intermediate
          return( GLOCK_ERROR_GETCWD );    states. This elementary transition (by month, quarter,
       }    semester or year) is modelled as a multinomial logistic.  The hPx
       strcpy( name, path );             /* we've got it */    matrix is simply the matrix product of nh*stepm elementary matrices
    } else {                             /* strip direcotry from path */    and the contribution of each individual to the likelihood is simply
       s++;                              /* after this, the filename */    hPijx.
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    Also this programme outputs the covariance matrix of the parameters but also
       strcpy( name, s );                /* save file name */    of the life expectancies. It also computes the stable prevalence. 
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    
       dirc[l1-l2] = 0;                  /* add zero */    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
    }             Institut national d'études démographiques, Paris.
    l1 = strlen( dirc );                 /* length of directory */    This software have been partly granted by Euro-REVES, a concerted action
 #ifdef windows    from the European Union.
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    It is copyrighted identically to a GNU software product, ie programme and
 #else    software can be distributed freely for non commercial use. Latest version
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    can be accessed at http://euroreves.ined.fr/imach .
 #endif  
    s = strrchr( name, '.' );            /* find last / */    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
    s++;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
    strcpy(ext,s);                       /* save extension */    
    l1= strlen( name);    **********************************************************************/
    l2= strlen( s)+1;  /*
    strncpy( finame, name, l1-l2);    main
    finame[l1-l2]= 0;    read parameterfile
    return( 0 );                         /* we're done */    read datafile
 }    concatwav
     freqsummary
     if (mle >= 1)
 /******************************************/      mlikeli
     print results files
 void replace(char *s, char*t)    if mle==1 
 {       computes hessian
   int i;    read end of parameter file: agemin, agemax, bage, fage, estepm
   int lg=20;        begin-prev-date,...
   i=0;    open gnuplot file
   lg=strlen(t);    open html file
   for(i=0; i<= lg; i++) {    stable prevalence
     (s[i] = t[i]);     for age prevalim()
     if (t[i]== '\\') s[i]='/';    h Pij x
   }    variance of p varprob
 }    forecasting if prevfcast==1 prevforecast call prevalence()
     health expectancies
 int nbocc(char *s, char occ)    Variance-covariance of DFLE
 {    prevalence()
   int i,j=0;     movingaverage()
   int lg=20;    varevsij() 
   i=0;    if popbased==1 varevsij(,popbased)
   lg=strlen(s);    total life expectancies
   for(i=0; i<= lg; i++) {    Variance of stable prevalence
   if  (s[i] == occ ) j++;   end
   }  */
   return j;  
 }  
   
 void cutv(char *u,char *v, char*t, char occ)   
 {  #include <math.h>
   int i,lg,j,p=0;  #include <stdio.h>
   i=0;  #include <stdlib.h>
   for(j=0; j<=strlen(t)-1; j++) {  #include <string.h>
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  #include <unistd.h>
   }  
   #include <limits.h>
   lg=strlen(t);  #include <sys/types.h>
   for(j=0; j<p; j++) {  #include <sys/stat.h>
     (u[j] = t[j]);  #include <errno.h>
   }  extern int errno;
      u[p]='\0';  
   /* #include <sys/time.h> */
    for(j=0; j<= lg; j++) {  #include <time.h>
     if (j>=(p+1))(v[j-p-1] = t[j]);  #include "timeval.h"
   }  
 }  /* #include <libintl.h> */
   /* #define _(String) gettext (String) */
 /********************** nrerror ********************/  
   #define MAXLINE 256
 void nrerror(char error_text[])  
 {  #define GNUPLOTPROGRAM "gnuplot"
   fprintf(stderr,"ERREUR ...\n");  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   fprintf(stderr,"%s\n",error_text);  #define FILENAMELENGTH 132
   exit(1);  
 }  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 /*********************** vector *******************/  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 double *vector(int nl, int nh)  
 {  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   double *v;  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));  
   if (!v) nrerror("allocation failure in vector");  #define NINTERVMAX 8
   return v-nl+NR_END;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 }  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   #define NCOVMAX 8 /* Maximum number of covariates */
 /************************ free vector ******************/  #define MAXN 20000
 void free_vector(double*v, int nl, int nh)  #define YEARM 12. /* Number of months per year */
 {  #define AGESUP 130
   free((FREE_ARG)(v+nl-NR_END));  #define AGEBASE 40
 }  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   #ifdef UNIX
 /************************ivector *******************************/  #define DIRSEPARATOR '/'
 int *ivector(long nl,long nh)  #define CHARSEPARATOR "/"
 {  #define ODIRSEPARATOR '\\'
   int *v;  #else
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  #define DIRSEPARATOR '\\'
   if (!v) nrerror("allocation failure in ivector");  #define CHARSEPARATOR "\\"
   return v-nl+NR_END;  #define ODIRSEPARATOR '/'
 }  #endif
   
 /******************free ivector **************************/  /* $Id$ */
 void free_ivector(int *v, long nl, long nh)  /* $State$ */
 {  
   free((FREE_ARG)(v+nl-NR_END));  char version[]="Imach version 0.98a, January 2006, INED-EUROREVES ";
 }  char fullversion[]="$Revision$ $Date$"; 
   int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 /******************* imatrix *******************************/  int nvar;
 int **imatrix(long nrl, long nrh, long ncl, long nch)  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  int npar=NPARMAX;
 {  int nlstate=2; /* Number of live states */
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  int ndeath=1; /* Number of dead states */
   int **m;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
    int popbased=0;
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  int *wav; /* Number of waves for this individuual 0 is possible */
   if (!m) nrerror("allocation failure 1 in matrix()");  int maxwav; /* Maxim number of waves */
   m += NR_END;  int jmin, jmax; /* min, max spacing between 2 waves */
   m -= nrl;  int gipmx, gsw; /* Global variables on the number of contributions 
                       to the likelihood and the sum of weights (done by funcone)*/
    int mle, weightopt;
   /* allocate rows and set pointers to them */  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   m[nrl] += NR_END;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   m[nrl] -= ncl;  double jmean; /* Mean space between 2 waves */
    double **oldm, **newm, **savm; /* Working pointers to matrices */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
    FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   /* return pointer to array of pointers to rows */  FILE *ficlog, *ficrespow;
   return m;  int globpr; /* Global variable for printing or not */
 }  double fretone; /* Only one call to likelihood */
   long ipmx; /* Number of contributions */
 /****************** free_imatrix *************************/  double sw; /* Sum of weights */
 void free_imatrix(m,nrl,nrh,ncl,nch)  char filerespow[FILENAMELENGTH];
       int **m;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
       long nch,ncl,nrh,nrl;  FILE *ficresilk;
      /* free an int matrix allocated by imatrix() */  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 {  FILE *ficresprobmorprev;
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  FILE *fichtm, *fichtmcov; /* Html File */
   free((FREE_ARG) (m+nrl-NR_END));  FILE *ficreseij;
 }  char filerese[FILENAMELENGTH];
   FILE  *ficresvij;
 /******************* matrix *******************************/  char fileresv[FILENAMELENGTH];
 double **matrix(long nrl, long nrh, long ncl, long nch)  FILE  *ficresvpl;
 {  char fileresvpl[FILENAMELENGTH];
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  char title[MAXLINE];
   double **m;  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH];
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   if (!m) nrerror("allocation failure 1 in matrix()");  char command[FILENAMELENGTH];
   m += NR_END;  int  outcmd=0;
   m -= nrl;  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  char filelog[FILENAMELENGTH]; /* Log file */
   m[nrl] += NR_END;  char filerest[FILENAMELENGTH];
   m[nrl] -= ncl;  char fileregp[FILENAMELENGTH];
   char popfile[FILENAMELENGTH];
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 }  
   struct timeval start_time, end_time, curr_time, last_time, forecast_time;
 /*************************free matrix ************************/  struct timezone tzp;
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  extern int gettimeofday();
 {  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  long time_value;
   free((FREE_ARG)(m+nrl-NR_END));  extern long time();
 }  char strcurr[80], strfor[80];
   
 /******************* ma3x *******************************/  char *endptr;
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  long lval;
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  #define NR_END 1
   double ***m;  #define FREE_ARG char*
   #define FTOL 1.0e-10
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  #define NRANSI 
   m += NR_END;  #define ITMAX 200 
   m -= nrl;  
   #define TOL 2.0e-4 
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define CGOLD 0.3819660 
   m[nrl] += NR_END;  #define ZEPS 1.0e-10 
   m[nrl] -= ncl;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #define GOLD 1.618034 
   #define GLIMIT 100.0 
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  #define TINY 1.0e-20 
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  
   m[nrl][ncl] += NR_END;  static double maxarg1,maxarg2;
   m[nrl][ncl] -= nll;  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   for (j=ncl+1; j<=nch; j++)  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     m[nrl][j]=m[nrl][j-1]+nlay;    
    #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   for (i=nrl+1; i<=nrh; i++) {  #define rint(a) floor(a+0.5)
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  
     for (j=ncl+1; j<=nch; j++)  static double sqrarg;
       m[i][j]=m[i][j-1]+nlay;  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
   }  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
   return m;  int agegomp= AGEGOMP;
 }  
   int imx; 
 /*************************free ma3x ************************/  int stepm=1;
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  /* Stepm, step in month: minimum step interpolation*/
 {  
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  int estepm;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   free((FREE_ARG)(m+nrl-NR_END));  
 }  int m,nb;
   long *num;
 /***************** f1dim *************************/  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
 extern int ncom;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 extern double *pcom,*xicom;  double **pmmij, ***probs;
 extern double (*nrfunc)(double []);  double *ageexmed,*agecens;
    double dateintmean=0;
 double f1dim(double x)  
 {  double *weight;
   int j;  int **s; /* Status */
   double f;  double *agedc, **covar, idx;
   double *xt;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
    double *lsurv, *lpop, *tpop;
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   f=(*nrfunc)(xt);  double ftolhess; /* Tolerance for computing hessian */
   free_vector(xt,1,ncom);  
   return f;  /**************** split *************************/
 }  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   {
 /*****************brent *************************/    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)       the name of the file (name), its extension only (ext) and its first part of the name (finame)
 {    */ 
   int iter;    char  *ss;                            /* pointer */
   double a,b,d,etemp;    int   l1, l2;                         /* length counters */
   double fu,fv,fw,fx;  
   double ftemp;    l1 = strlen(path );                   /* length of path */
   double p,q,r,tol1,tol2,u,v,w,x,xm;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   double e=0.0;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
      if ( ss == NULL ) {                   /* no directory, so determine current directory */
   a=(ax < cx ? ax : cx);      strcpy( name, path );               /* we got the fullname name because no directory */
   b=(ax > cx ? ax : cx);      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   x=w=v=bx;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   fw=fv=fx=(*f)(x);      /* get current working directory */
   for (iter=1;iter<=ITMAX;iter++) {      /*    extern  char* getcwd ( char *buf , int len);*/
     xm=0.5*(a+b);      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);        return( GLOCK_ERROR_GETCWD );
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/      }
     printf(".");fflush(stdout);      /* got dirc from getcwd*/
 #ifdef DEBUG      printf(" DIRC = %s \n",dirc);
     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);    } else {                              /* strip direcotry from path */
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */      ss++;                               /* after this, the filename */
 #endif      l2 = strlen( ss );                  /* length of filename */
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       *xmin=x;      strcpy( name, ss );         /* save file name */
       return fx;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
     }      dirc[l1-l2] = 0;                    /* add zero */
     ftemp=fu;      printf(" DIRC2 = %s \n",dirc);
     if (fabs(e) > tol1) {    }
       r=(x-w)*(fx-fv);    /* We add a separator at the end of dirc if not exists */
       q=(x-v)*(fx-fw);    l1 = strlen( dirc );                  /* length of directory */
       p=(x-v)*q-(x-w)*r;    if( dirc[l1-1] != DIRSEPARATOR ){
       q=2.0*(q-r);      dirc[l1] =  DIRSEPARATOR;
       if (q > 0.0) p = -p;      dirc[l1+1] = 0; 
       q=fabs(q);      printf(" DIRC3 = %s \n",dirc);
       etemp=e;    }
       e=d;    ss = strrchr( name, '.' );            /* find last / */
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))    if (ss >0){
         d=CGOLD*(e=(x >= xm ? a-x : b-x));      ss++;
       else {      strcpy(ext,ss);                     /* save extension */
         d=p/q;      l1= strlen( name);
         u=x+d;      l2= strlen(ss)+1;
         if (u-a < tol2 || b-u < tol2)      strncpy( finame, name, l1-l2);
           d=SIGN(tol1,xm-x);      finame[l1-l2]= 0;
       }    }
     } else {  
       d=CGOLD*(e=(x >= xm ? a-x : b-x));    return( 0 );                          /* we're done */
     }  }
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  
     fu=(*f)(u);  
     if (fu <= fx) {  /******************************************/
       if (u >= x) a=x; else b=x;  
       SHFT(v,w,x,u)  void replace_back_to_slash(char *s, char*t)
         SHFT(fv,fw,fx,fu)  {
         } else {    int i;
           if (u < x) a=u; else b=u;    int lg=0;
           if (fu <= fw || w == x) {    i=0;
             v=w;    lg=strlen(t);
             w=u;    for(i=0; i<= lg; i++) {
             fv=fw;      (s[i] = t[i]);
             fw=fu;      if (t[i]== '\\') s[i]='/';
           } else if (fu <= fv || v == x || v == w) {    }
             v=u;  }
             fv=fu;  
           }  int nbocc(char *s, char occ)
         }  {
   }    int i,j=0;
   nrerror("Too many iterations in brent");    int lg=20;
   *xmin=x;    i=0;
   return fx;    lg=strlen(s);
 }    for(i=0; i<= lg; i++) {
     if  (s[i] == occ ) j++;
 /****************** mnbrak ***********************/    }
     return j;
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  }
             double (*func)(double))  
 {  void cutv(char *u,char *v, char*t, char occ)
   double ulim,u,r,q, dum;  {
   double fu;    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
         and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
   *fa=(*func)(*ax);       gives u="abcedf" and v="ghi2j" */
   *fb=(*func)(*bx);    int i,lg,j,p=0;
   if (*fb > *fa) {    i=0;
     SHFT(dum,*ax,*bx,dum)    for(j=0; j<=strlen(t)-1; j++) {
       SHFT(dum,*fb,*fa,dum)      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
       }    }
   *cx=(*bx)+GOLD*(*bx-*ax);  
   *fc=(*func)(*cx);    lg=strlen(t);
   while (*fb > *fc) {    for(j=0; j<p; j++) {
     r=(*bx-*ax)*(*fb-*fc);      (u[j] = t[j]);
     q=(*bx-*cx)*(*fb-*fa);    }
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/       u[p]='\0';
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  
     ulim=(*bx)+GLIMIT*(*cx-*bx);     for(j=0; j<= lg; j++) {
     if ((*bx-u)*(u-*cx) > 0.0) {      if (j>=(p+1))(v[j-p-1] = t[j]);
       fu=(*func)(u);    }
     } else if ((*cx-u)*(u-ulim) > 0.0) {  }
       fu=(*func)(u);  
       if (fu < *fc) {  /********************** nrerror ********************/
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))  void nrerror(char error_text[])
           }  {
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    fprintf(stderr,"ERREUR ...\n");
       u=ulim;    fprintf(stderr,"%s\n",error_text);
       fu=(*func)(u);    exit(EXIT_FAILURE);
     } else {  }
       u=(*cx)+GOLD*(*cx-*bx);  /*********************** vector *******************/
       fu=(*func)(u);  double *vector(int nl, int nh)
     }  {
     SHFT(*ax,*bx,*cx,u)    double *v;
       SHFT(*fa,*fb,*fc,fu)    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
       }    if (!v) nrerror("allocation failure in vector");
 }    return v-nl+NR_END;
   }
 /*************** linmin ************************/  
   /************************ free vector ******************/
 int ncom;  void free_vector(double*v, int nl, int nh)
 double *pcom,*xicom;  {
 double (*nrfunc)(double []);    free((FREE_ARG)(v+nl-NR_END));
    }
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  
 {  /************************ivector *******************************/
   double brent(double ax, double bx, double cx,  int *ivector(long nl,long nh)
                double (*f)(double), double tol, double *xmin);  {
   double f1dim(double x);    int *v;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
               double *fc, double (*func)(double));    if (!v) nrerror("allocation failure in ivector");
   int j;    return v-nl+NR_END;
   double xx,xmin,bx,ax;  }
   double fx,fb,fa;  
    /******************free ivector **************************/
   ncom=n;  void free_ivector(int *v, long nl, long nh)
   pcom=vector(1,n);  {
   xicom=vector(1,n);    free((FREE_ARG)(v+nl-NR_END));
   nrfunc=func;  }
   for (j=1;j<=n;j++) {  
     pcom[j]=p[j];  /************************lvector *******************************/
     xicom[j]=xi[j];  long *lvector(long nl,long nh)
   }  {
   ax=0.0;    long *v;
   xx=1.0;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    if (!v) nrerror("allocation failure in ivector");
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    return v-nl+NR_END;
 #ifdef DEBUG  }
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  
 #endif  /******************free lvector **************************/
   for (j=1;j<=n;j++) {  void free_lvector(long *v, long nl, long nh)
     xi[j] *= xmin;  {
     p[j] += xi[j];    free((FREE_ARG)(v+nl-NR_END));
   }  }
   free_vector(xicom,1,n);  
   free_vector(pcom,1,n);  /******************* imatrix *******************************/
 }  int **imatrix(long nrl, long nrh, long ncl, long nch) 
        /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 /*************** powell ************************/  { 
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
             double (*func)(double []))    int **m; 
 {    
   void linmin(double p[], double xi[], int n, double *fret,    /* allocate pointers to rows */ 
               double (*func)(double []));    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
   int i,ibig,j;    if (!m) nrerror("allocation failure 1 in matrix()"); 
   double del,t,*pt,*ptt,*xit;    m += NR_END; 
   double fp,fptt;    m -= nrl; 
   double *xits;    
   pt=vector(1,n);    
   ptt=vector(1,n);    /* allocate rows and set pointers to them */ 
   xit=vector(1,n);    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   xits=vector(1,n);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
   *fret=(*func)(p);    m[nrl] += NR_END; 
   for (j=1;j<=n;j++) pt[j]=p[j];    m[nrl] -= ncl; 
   for (*iter=1;;++(*iter)) {    
     fp=(*fret);    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     ibig=0;    
     del=0.0;    /* return pointer to array of pointers to rows */ 
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    return m; 
     for (i=1;i<=n;i++)  } 
       printf(" %d %.12f",i, p[i]);  
     printf("\n");  /****************** free_imatrix *************************/
     for (i=1;i<=n;i++) {  void free_imatrix(m,nrl,nrh,ncl,nch)
       for (j=1;j<=n;j++) xit[j]=xi[j][i];        int **m;
       fptt=(*fret);        long nch,ncl,nrh,nrl; 
 #ifdef DEBUG       /* free an int matrix allocated by imatrix() */ 
       printf("fret=%lf \n",*fret);  { 
 #endif    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
       printf("%d",i);fflush(stdout);    free((FREE_ARG) (m+nrl-NR_END)); 
       linmin(p,xit,n,fret,func);  } 
       if (fabs(fptt-(*fret)) > del) {  
         del=fabs(fptt-(*fret));  /******************* matrix *******************************/
         ibig=i;  double **matrix(long nrl, long nrh, long ncl, long nch)
       }  {
 #ifdef DEBUG    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       printf("%d %.12e",i,(*fret));    double **m;
       for (j=1;j<=n;j++) {  
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
         printf(" x(%d)=%.12e",j,xit[j]);    if (!m) nrerror("allocation failure 1 in matrix()");
       }    m += NR_END;
       for(j=1;j<=n;j++)    m -= nrl;
         printf(" p=%.12e",p[j]);  
       printf("\n");    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 #endif    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     }    m[nrl] += NR_END;
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    m[nrl] -= ncl;
 #ifdef DEBUG  
       int k[2],l;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       k[0]=1;    return m;
       k[1]=-1;    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       printf("Max: %.12e",(*func)(p));     */
       for (j=1;j<=n;j++)  }
         printf(" %.12e",p[j]);  
       printf("\n");  /*************************free matrix ************************/
       for(l=0;l<=1;l++) {  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
         for (j=1;j<=n;j++) {  {
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    free((FREE_ARG)(m[nrl]+ncl-NR_END));
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    free((FREE_ARG)(m+nrl-NR_END));
         }  }
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  
       }  /******************* ma3x *******************************/
 #endif  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   {
     long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       free_vector(xit,1,n);    double ***m;
       free_vector(xits,1,n);  
       free_vector(ptt,1,n);    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       free_vector(pt,1,n);    if (!m) nrerror("allocation failure 1 in matrix()");
       return;    m += NR_END;
     }    m -= nrl;
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  
     for (j=1;j<=n;j++) {    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       ptt[j]=2.0*p[j]-pt[j];    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       xit[j]=p[j]-pt[j];    m[nrl] += NR_END;
       pt[j]=p[j];    m[nrl] -= ncl;
     }  
     fptt=(*func)(ptt);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     if (fptt < fp) {  
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       if (t < 0.0) {    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
         linmin(p,xit,n,fret,func);    m[nrl][ncl] += NR_END;
         for (j=1;j<=n;j++) {    m[nrl][ncl] -= nll;
           xi[j][ibig]=xi[j][n];    for (j=ncl+1; j<=nch; j++) 
           xi[j][n]=xit[j];      m[nrl][j]=m[nrl][j-1]+nlay;
         }    
 #ifdef DEBUG    for (i=nrl+1; i<=nrh; i++) {
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
         for(j=1;j<=n;j++)      for (j=ncl+1; j<=nch; j++) 
           printf(" %.12e",xit[j]);        m[i][j]=m[i][j-1]+nlay;
         printf("\n");    }
 #endif    return m; 
       }    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     }             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   }    */
 }  }
   
 /**** Prevalence limit ****************/  /*************************free ma3x ************************/
   void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  {
 {    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    free((FREE_ARG)(m[nrl]+ncl-NR_END));
      matrix by transitions matrix until convergence is reached */    free((FREE_ARG)(m+nrl-NR_END));
   }
   int i, ii,j,k;  
   double min, max, maxmin, maxmax,sumnew=0.;  /*************** function subdirf ***********/
   double **matprod2();  char *subdirf(char fileres[])
   double **out, cov[NCOVMAX], **pmij();  {
   double **newm;    /* Caution optionfilefiname is hidden */
   double agefin, delaymax=50 ; /* Max number of years to converge */    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/"); /* Add to the right */
   for (ii=1;ii<=nlstate+ndeath;ii++)    strcat(tmpout,fileres);
     for (j=1;j<=nlstate+ndeath;j++){    return tmpout;
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  }
     }  
   /*************** function subdirf2 ***********/
    cov[1]=1.;  char *subdirf2(char fileres[], char *preop)
    {
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    /* Caution optionfilefiname is hidden */
     newm=savm;    strcpy(tmpout,optionfilefiname);
     /* Covariates have to be included here again */    strcat(tmpout,"/");
      cov[2]=agefin;    strcat(tmpout,preop);
      strcat(tmpout,fileres);
       for (k=1; k<=cptcovn;k++) {    return tmpout;
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  }
         /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/  
       }  /*************** function subdirf3 ***********/
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  char *subdirf3(char fileres[], char *preop, char *preop2)
       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]]];    
     /* Caution optionfilefiname is hidden */
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    strcpy(tmpout,optionfilefiname);
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    strcat(tmpout,"/");
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/    strcat(tmpout,preop);
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    strcat(tmpout,preop2);
     strcat(tmpout,fileres);
     savm=oldm;    return tmpout;
     oldm=newm;  }
     maxmax=0.;  
     for(j=1;j<=nlstate;j++){  /***************** f1dim *************************/
       min=1.;  extern int ncom; 
       max=0.;  extern double *pcom,*xicom;
       for(i=1; i<=nlstate; i++) {  extern double (*nrfunc)(double []); 
         sumnew=0;   
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  double f1dim(double x) 
         prlim[i][j]= newm[i][j]/(1-sumnew);  { 
         max=FMAX(max,prlim[i][j]);    int j; 
         min=FMIN(min,prlim[i][j]);    double f;
       }    double *xt; 
       maxmin=max-min;   
       maxmax=FMAX(maxmax,maxmin);    xt=vector(1,ncom); 
     }    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     if(maxmax < ftolpl){    f=(*nrfunc)(xt); 
       return prlim;    free_vector(xt,1,ncom); 
     }    return f; 
   }  } 
 }  
   /*****************brent *************************/
 /*************** transition probabilities ***************/  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   { 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    int iter; 
 {    double a,b,d,etemp;
   double s1, s2;    double fu,fv,fw,fx;
   /*double t34;*/    double ftemp;
   int i,j,j1, nc, ii, jj;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     double e=0.0; 
     for(i=1; i<= nlstate; i++){   
     for(j=1; j<i;j++){    a=(ax < cx ? ax : cx); 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    b=(ax > cx ? ax : cx); 
         /*s2 += param[i][j][nc]*cov[nc];*/    x=w=v=bx; 
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    fw=fv=fx=(*f)(x); 
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    for (iter=1;iter<=ITMAX;iter++) { 
       }      xm=0.5*(a+b); 
       ps[i][j]=s2;      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     }      printf(".");fflush(stdout);
     for(j=i+1; j<=nlstate+ndeath;j++){      fprintf(ficlog,".");fflush(ficlog);
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  #ifdef DEBUG
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/      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)))) { */
       ps[i][j]=s2;  #endif
     }      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   }        *xmin=x; 
     /*ps[3][2]=1;*/        return fx; 
       } 
   for(i=1; i<= nlstate; i++){      ftemp=fu;
      s1=0;      if (fabs(e) > tol1) { 
     for(j=1; j<i; j++)        r=(x-w)*(fx-fv); 
       s1+=exp(ps[i][j]);        q=(x-v)*(fx-fw); 
     for(j=i+1; j<=nlstate+ndeath; j++)        p=(x-v)*q-(x-w)*r; 
       s1+=exp(ps[i][j]);        q=2.0*(q-r); 
     ps[i][i]=1./(s1+1.);        if (q > 0.0) p = -p; 
     for(j=1; j<i; j++)        q=fabs(q); 
       ps[i][j]= exp(ps[i][j])*ps[i][i];        etemp=e; 
     for(j=i+1; j<=nlstate+ndeath; j++)        e=d; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   } /* end i */        else { 
           d=p/q; 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){          u=x+d; 
     for(jj=1; jj<= nlstate+ndeath; jj++){          if (u-a < tol2 || b-u < tol2) 
       ps[ii][jj]=0;            d=SIGN(tol1,xm-x); 
       ps[ii][ii]=1;        } 
     }      } else { 
   }        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       } 
       u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){      fu=(*f)(u); 
     for(jj=1; jj<= nlstate+ndeath; jj++){      if (fu <= fx) { 
      printf("%lf ",ps[ii][jj]);        if (u >= x) a=x; else b=x; 
    }        SHFT(v,w,x,u) 
     printf("\n ");          SHFT(fv,fw,fx,fu) 
     }          } else { 
     printf("\n ");printf("%lf ",cov[2]);*/            if (u < x) a=u; else b=u; 
 /*            if (fu <= fw || w == x) { 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);              v=w; 
   goto end;*/              w=u; 
     return ps;              fv=fw; 
 }              fw=fu; 
             } else if (fu <= fv || v == x || v == w) { 
 /**************** Product of 2 matrices ******************/              v=u; 
               fv=fu; 
 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    } 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    nrerror("Too many iterations in brent"); 
   /* in, b, out are matrice of pointers which should have been initialized    *xmin=x; 
      before: only the contents of out is modified. The function returns    return fx; 
      a pointer to pointers identical to out */  } 
   long i, j, k;  
   for(i=nrl; i<= nrh; i++)  /****************** mnbrak ***********************/
     for(k=ncolol; k<=ncoloh; k++)  
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
         out[i][k] +=in[i][j]*b[j][k];              double (*func)(double)) 
   { 
   return out;    double ulim,u,r,q, dum;
 }    double fu; 
    
     *fa=(*func)(*ax); 
 /************* Higher Matrix Product ***************/    *fb=(*func)(*bx); 
     if (*fb > *fa) { 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      SHFT(dum,*ax,*bx,dum) 
 {        SHFT(dum,*fb,*fa,dum) 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month        } 
      duration (i.e. until    *cx=(*bx)+GOLD*(*bx-*ax); 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.    *fc=(*func)(*cx); 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step    while (*fb > *fc) { 
      (typically every 2 years instead of every month which is too big).      r=(*bx-*ax)*(*fb-*fc); 
      Model is determined by parameters x and covariates have to be      q=(*bx-*cx)*(*fb-*fa); 
      included manually here.      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
      */      ulim=(*bx)+GLIMIT*(*cx-*bx); 
       if ((*bx-u)*(u-*cx) > 0.0) { 
   int i, j, d, h, k;        fu=(*func)(u); 
   double **out, cov[NCOVMAX];      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   double **newm;        fu=(*func)(u); 
         if (fu < *fc) { 
   /* Hstepm could be zero and should return the unit matrix */          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   for (i=1;i<=nlstate+ndeath;i++)            SHFT(*fb,*fc,fu,(*func)(u)) 
     for (j=1;j<=nlstate+ndeath;j++){            } 
       oldm[i][j]=(i==j ? 1.0 : 0.0);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
       po[i][j][0]=(i==j ? 1.0 : 0.0);        u=ulim; 
     }        fu=(*func)(u); 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      } else { 
   for(h=1; h <=nhstepm; h++){        u=(*cx)+GOLD*(*cx-*bx); 
     for(d=1; d <=hstepm; d++){        fu=(*func)(u); 
       newm=savm;      } 
       /* Covariates have to be included here again */      SHFT(*ax,*bx,*cx,u) 
       cov[1]=1.;        SHFT(*fa,*fb,*fc,fu) 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;        } 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  } 
       for (k=1; k<=cptcovage;k++)  
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  /*************** linmin ************************/
       for (k=1; k<=cptcovprod;k++)  
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];  int ncom; 
   double *pcom,*xicom;
   double (*nrfunc)(double []); 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/   
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  { 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));    double brent(double ax, double bx, double cx, 
       savm=oldm;                 double (*f)(double), double tol, double *xmin); 
       oldm=newm;    double f1dim(double x); 
     }    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     for(i=1; i<=nlstate+ndeath; i++)                double *fc, double (*func)(double)); 
       for(j=1;j<=nlstate+ndeath;j++) {    int j; 
         po[i][j][h]=newm[i][j];    double xx,xmin,bx,ax; 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    double fx,fb,fa;
          */   
       }    ncom=n; 
   } /* end h */    pcom=vector(1,n); 
   return po;    xicom=vector(1,n); 
 }    nrfunc=func; 
     for (j=1;j<=n;j++) { 
       pcom[j]=p[j]; 
 /*************** log-likelihood *************/      xicom[j]=xi[j]; 
 double func( double *x)    } 
 {    ax=0.0; 
   int i, ii, j, k, mi, d, kk;    xx=1.0; 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   double **out;    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   double sw; /* Sum of weights */  #ifdef DEBUG
   double lli; /* Individual log likelihood */    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   long ipmx;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   /*extern weight */  #endif
   /* We are differentiating ll according to initial status */    for (j=1;j<=n;j++) { 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/      xi[j] *= xmin; 
   /*for(i=1;i<imx;i++)      p[j] += xi[j]; 
     printf(" %d\n",s[4][i]);    } 
   */    free_vector(xicom,1,n); 
   cov[1]=1.;    free_vector(pcom,1,n); 
   } 
   for(k=1; k<=nlstate; k++) ll[k]=0.;  
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){  char *asc_diff_time(long time_sec, char ascdiff[])
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];  {
     for(mi=1; mi<= wav[i]-1; mi++){    long sec_left, days, hours, minutes;
       for (ii=1;ii<=nlstate+ndeath;ii++)    days = (time_sec) / (60*60*24);
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    sec_left = (time_sec) % (60*60*24);
       for(d=0; d<dh[mi][i]; d++){    hours = (sec_left) / (60*60) ;
         newm=savm;    sec_left = (sec_left) %(60*60);
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    minutes = (sec_left) /60;
         for (kk=1; kk<=cptcovage;kk++) {    sec_left = (sec_left) % (60);
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
         }    return ascdiff;
          }
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  /*************** powell ************************/
         savm=oldm;  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
         oldm=newm;              double (*func)(double [])) 
          { 
            void linmin(double p[], double xi[], int n, double *fret, 
       } /* end mult */                double (*func)(double [])); 
          int i,ibig,j; 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    double del,t,*pt,*ptt,*xit;
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    double fp,fptt;
       ipmx +=1;    double *xits;
       sw += weight[i];    int niterf, itmp;
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  
     } /* end of wave */    pt=vector(1,n); 
   } /* end of individual */    ptt=vector(1,n); 
     xit=vector(1,n); 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    xits=vector(1,n); 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    *fret=(*func)(p); 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    for (j=1;j<=n;j++) pt[j]=p[j]; 
   return -l;    for (*iter=1;;++(*iter)) { 
 }      fp=(*fret); 
       ibig=0; 
       del=0.0; 
 /*********** Maximum Likelihood Estimation ***************/      last_time=curr_time;
       (void) gettimeofday(&curr_time,&tzp);
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))      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);
   int i,j, iter;      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
   double **xi,*delti;      */
   double fret;     for (i=1;i<=n;i++) {
   xi=matrix(1,npar,1,npar);        printf(" %d %.12f",i, p[i]);
   for (i=1;i<=npar;i++)        fprintf(ficlog," %d %.12lf",i, p[i]);
     for (j=1;j<=npar;j++)        fprintf(ficrespow," %.12lf", p[i]);
       xi[i][j]=(i==j ? 1.0 : 0.0);      }
   printf("Powell\n");      printf("\n");
   powell(p,xi,npar,ftol,&iter,&fret,func);      fprintf(ficlog,"\n");
       fprintf(ficrespow,"\n");fflush(ficrespow);
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));      if(*iter <=3){
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));        tm = *localtime(&curr_time.tv_sec);
         strcpy(strcurr,asctime(&tm));
 }  /*       asctime_r(&tm,strcurr); */
         forecast_time=curr_time; 
 /**** Computes Hessian and covariance matrix ***/        itmp = strlen(strcurr);
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
 {          strcurr[itmp-1]='\0';
   double  **a,**y,*x,pd;        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   double **hess;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   int i, j,jk;        for(niterf=10;niterf<=30;niterf+=10){
   int *indx;          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
           tmf = *localtime(&forecast_time.tv_sec);
   double hessii(double p[], double delta, int theta, double delti[]);  /*      asctime_r(&tmf,strfor); */
   double hessij(double p[], double delti[], int i, int j);          strcpy(strfor,asctime(&tmf));
   void lubksb(double **a, int npar, int *indx, double b[]) ;          itmp = strlen(strfor);
   void ludcmp(double **a, int npar, int *indx, double *d) ;          if(strfor[itmp-1]=='\n')
           strfor[itmp-1]='\0';
   hess=matrix(1,npar,1,npar);          printf("   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
           fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
   printf("\nCalculation of the hessian matrix. Wait...\n");        }
   for (i=1;i<=npar;i++){      }
     printf("%d",i);fflush(stdout);      for (i=1;i<=n;i++) { 
     hess[i][i]=hessii(p,ftolhess,i,delti);        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
     /*printf(" %f ",p[i]);*/        fptt=(*fret); 
     /*printf(" %lf ",hess[i][i]);*/  #ifdef DEBUG
   }        printf("fret=%lf \n",*fret);
          fprintf(ficlog,"fret=%lf \n",*fret);
   for (i=1;i<=npar;i++) {  #endif
     for (j=1;j<=npar;j++)  {        printf("%d",i);fflush(stdout);
       if (j>i) {        fprintf(ficlog,"%d",i);fflush(ficlog);
         printf(".%d%d",i,j);fflush(stdout);        linmin(p,xit,n,fret,func); 
         hess[i][j]=hessij(p,delti,i,j);        if (fabs(fptt-(*fret)) > del) { 
         hess[j][i]=hess[i][j];              del=fabs(fptt-(*fret)); 
         /*printf(" %lf ",hess[i][j]);*/          ibig=i; 
       }        } 
     }  #ifdef DEBUG
   }        printf("%d %.12e",i,(*fret));
   printf("\n");        fprintf(ficlog,"%d %.12e",i,(*fret));
         for (j=1;j<=n;j++) {
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
            printf(" x(%d)=%.12e",j,xit[j]);
   a=matrix(1,npar,1,npar);          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   y=matrix(1,npar,1,npar);        }
   x=vector(1,npar);        for(j=1;j<=n;j++) {
   indx=ivector(1,npar);          printf(" p=%.12e",p[j]);
   for (i=1;i<=npar;i++)          fprintf(ficlog," p=%.12e",p[j]);
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];        }
   ludcmp(a,npar,indx,&pd);        printf("\n");
         fprintf(ficlog,"\n");
   for (j=1;j<=npar;j++) {  #endif
     for (i=1;i<=npar;i++) x[i]=0;      } 
     x[j]=1;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     lubksb(a,npar,indx,x);  #ifdef DEBUG
     for (i=1;i<=npar;i++){        int k[2],l;
       matcov[i][j]=x[i];        k[0]=1;
     }        k[1]=-1;
   }        printf("Max: %.12e",(*func)(p));
         fprintf(ficlog,"Max: %.12e",(*func)(p));
   printf("\n#Hessian matrix#\n");        for (j=1;j<=n;j++) {
   for (i=1;i<=npar;i++) {          printf(" %.12e",p[j]);
     for (j=1;j<=npar;j++) {          fprintf(ficlog," %.12e",p[j]);
       printf("%.3e ",hess[i][j]);        }
     }        printf("\n");
     printf("\n");        fprintf(ficlog,"\n");
   }        for(l=0;l<=1;l++) {
           for (j=1;j<=n;j++) {
   /* Recompute Inverse */            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   for (i=1;i<=npar;i++)            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   ludcmp(a,npar,indx,&pd);          }
           printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
   /*  printf("\n#Hessian matrix recomputed#\n");          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
         }
   for (j=1;j<=npar;j++) {  #endif
     for (i=1;i<=npar;i++) x[i]=0;  
     x[j]=1;  
     lubksb(a,npar,indx,x);        free_vector(xit,1,n); 
     for (i=1;i<=npar;i++){        free_vector(xits,1,n); 
       y[i][j]=x[i];        free_vector(ptt,1,n); 
       printf("%.3e ",y[i][j]);        free_vector(pt,1,n); 
     }        return; 
     printf("\n");      } 
   }      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   */      for (j=1;j<=n;j++) { 
         ptt[j]=2.0*p[j]-pt[j]; 
   free_matrix(a,1,npar,1,npar);        xit[j]=p[j]-pt[j]; 
   free_matrix(y,1,npar,1,npar);        pt[j]=p[j]; 
   free_vector(x,1,npar);      } 
   free_ivector(indx,1,npar);      fptt=(*func)(ptt); 
   free_matrix(hess,1,npar,1,npar);      if (fptt < fp) { 
         t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
         if (t < 0.0) { 
 }          linmin(p,xit,n,fret,func); 
           for (j=1;j<=n;j++) { 
 /*************** hessian matrix ****************/            xi[j][ibig]=xi[j][n]; 
 double hessii( double x[], double delta, int theta, double delti[])            xi[j][n]=xit[j]; 
 {          }
   int i;  #ifdef DEBUG
   int l=1, lmax=20;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   double k1,k2;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   double p2[NPARMAX+1];          for(j=1;j<=n;j++){
   double res;            printf(" %.12e",xit[j]);
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;            fprintf(ficlog," %.12e",xit[j]);
   double fx;          }
   int k=0,kmax=10;          printf("\n");
   double l1;          fprintf(ficlog,"\n");
   #endif
   fx=func(x);        }
   for (i=1;i<=npar;i++) p2[i]=x[i];      } 
   for(l=0 ; l <=lmax; l++){    } 
     l1=pow(10,l);  } 
     delts=delt;  
     for(k=1 ; k <kmax; k=k+1){  /**** Prevalence limit (stable prevalence)  ****************/
       delt = delta*(l1*k);  
       p2[theta]=x[theta] +delt;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
       k1=func(p2)-fx;  {
       p2[theta]=x[theta]-delt;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       k2=func(p2)-fx;       matrix by transitions matrix until convergence is reached */
       /*res= (k1-2.0*fx+k2)/delt/delt; */  
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */    int i, ii,j,k;
          double min, max, maxmin, maxmax,sumnew=0.;
 #ifdef DEBUG    double **matprod2();
       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);    double **out, cov[NCOVMAX], **pmij();
 #endif    double **newm;
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */    double agefin, delaymax=50 ; /* Max number of years to converge */
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  
         k=kmax;    for (ii=1;ii<=nlstate+ndeath;ii++)
       }      for (j=1;j<=nlstate+ndeath;j++){
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         k=kmax; l=lmax*10.;      }
       }  
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){     cov[1]=1.;
         delts=delt;   
       }   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     }    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   }      newm=savm;
   delti[theta]=delts;      /* Covariates have to be included here again */
   return res;       cov[2]=agefin;
      
 }        for (k=1; k<=cptcovn;k++) {
           cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
 double hessij( double x[], double delti[], int thetai,int thetaj)          /*      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]]);*/
 {        }
   int i;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   int l=1, l1, lmax=20;        for (k=1; k<=cptcovprod;k++)
   double k1,k2,k3,k4,res,fx;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   double p2[NPARMAX+1];  
   int k;        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   fx=func(x);        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   for (k=1; k<=2; k++) {      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
     for (i=1;i<=npar;i++) p2[i]=x[i];  
     p2[thetai]=x[thetai]+delti[thetai]/k;      savm=oldm;
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;      oldm=newm;
     k1=func(p2)-fx;      maxmax=0.;
        for(j=1;j<=nlstate;j++){
     p2[thetai]=x[thetai]+delti[thetai]/k;        min=1.;
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        max=0.;
     k2=func(p2)-fx;        for(i=1; i<=nlstate; i++) {
            sumnew=0;
     p2[thetai]=x[thetai]-delti[thetai]/k;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          prlim[i][j]= newm[i][j]/(1-sumnew);
     k3=func(p2)-fx;          max=FMAX(max,prlim[i][j]);
            min=FMIN(min,prlim[i][j]);
     p2[thetai]=x[thetai]-delti[thetai]/k;        }
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        maxmin=max-min;
     k4=func(p2)-fx;        maxmax=FMAX(maxmax,maxmin);
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */      }
 #ifdef DEBUG      if(maxmax < ftolpl){
     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);        return prlim;
 #endif      }
   }    }
   return res;  }
 }  
   /*************** transition probabilities ***************/ 
 /************** Inverse of matrix **************/  
 void ludcmp(double **a, int n, int *indx, double *d)  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
 {  {
   int i,imax,j,k;    double s1, s2;
   double big,dum,sum,temp;    /*double t34;*/
   double *vv;    int i,j,j1, nc, ii, jj;
    
   vv=vector(1,n);      for(i=1; i<= nlstate; i++){
   *d=1.0;        for(j=1; j<i;j++){
   for (i=1;i<=n;i++) {          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     big=0.0;            /*s2 += param[i][j][nc]*cov[nc];*/
     for (j=1;j<=n;j++)            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       if ((temp=fabs(a[i][j])) > big) big=temp;  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          }
     vv[i]=1.0/big;          ps[i][j]=s2;
   }  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
   for (j=1;j<=n;j++) {        }
     for (i=1;i<j;i++) {        for(j=i+1; j<=nlstate+ndeath;j++){
       sum=a[i][j];          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
       a[i][j]=sum;  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
     }          }
     big=0.0;          ps[i][j]=s2;
     for (i=j;i<=n;i++) {        }
       sum=a[i][j];      }
       for (k=1;k<j;k++)      /*ps[3][2]=1;*/
         sum -= a[i][k]*a[k][j];      
       a[i][j]=sum;      for(i=1; i<= nlstate; i++){
       if ( (dum=vv[i]*fabs(sum)) >= big) {        s1=0;
         big=dum;        for(j=1; j<i; j++)
         imax=i;          s1+=exp(ps[i][j]);
       }        for(j=i+1; j<=nlstate+ndeath; j++)
     }          s1+=exp(ps[i][j]);
     if (j != imax) {        ps[i][i]=1./(s1+1.);
       for (k=1;k<=n;k++) {        for(j=1; j<i; j++)
         dum=a[imax][k];          ps[i][j]= exp(ps[i][j])*ps[i][i];
         a[imax][k]=a[j][k];        for(j=i+1; j<=nlstate+ndeath; j++)
         a[j][k]=dum;          ps[i][j]= exp(ps[i][j])*ps[i][i];
       }        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       *d = -(*d);      } /* end i */
       vv[imax]=vv[j];      
     }      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     indx[j]=imax;        for(jj=1; jj<= nlstate+ndeath; jj++){
     if (a[j][j] == 0.0) a[j][j]=TINY;          ps[ii][jj]=0;
     if (j != n) {          ps[ii][ii]=1;
       dum=1.0/(a[j][j]);        }
       for (i=j+1;i<=n;i++) a[i][j] *= dum;      }
     }      
   }  
   free_vector(vv,1,n);  /* Doesn't work */  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
 ;  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
 }  /*         printf("ddd %lf ",ps[ii][jj]); */
   /*       } */
 void lubksb(double **a, int n, int *indx, double b[])  /*       printf("\n "); */
 {  /*        } */
   int i,ii=0,ip,j;  /*        printf("\n ");printf("%lf ",cov[2]); */
   double sum;         /*
          for(i=1; i<= npar; i++) printf("%f ",x[i]);
   for (i=1;i<=n;i++) {        goto end;*/
     ip=indx[i];      return ps;
     sum=b[ip];  }
     b[ip]=b[i];  
     if (ii)  /**************** Product of 2 matrices ******************/
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  
     else if (sum) ii=i;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
     b[i]=sum;  {
   }    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
   for (i=n;i>=1;i--) {       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     sum=b[i];    /* in, b, out are matrice of pointers which should have been initialized 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];       before: only the contents of out is modified. The function returns
     b[i]=sum/a[i][i];       a pointer to pointers identical to out */
   }    long i, j, k;
 }    for(i=nrl; i<= nrh; i++)
       for(k=ncolol; k<=ncoloh; k++)
 /************ Frequencies ********************/        for(j=ncl,out[i][k]=0.; j<=nch; j++)
 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)          out[i][k] +=in[i][j]*b[j][k];
 {  /* Some frequencies */  
      return out;
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;  }
   double ***freq; /* Frequencies */  
   double *pp;  
   double pos, k2, dateintsum=0,k2cpt=0;  /************* Higher Matrix Product ***************/
   FILE *ficresp;  
   char fileresp[FILENAMELENGTH];  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
    {
   pp=vector(1,nlstate);    /* Computes the transition matrix starting at age 'age' over 
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);       'nhstepm*hstepm*stepm' months (i.e. until
   strcpy(fileresp,"p");       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
   strcat(fileresp,fileres);       nhstepm*hstepm matrices. 
   if((ficresp=fopen(fileresp,"w"))==NULL) {       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
     printf("Problem with prevalence resultfile: %s\n", fileresp);       (typically every 2 years instead of every month which is too big 
     exit(0);       for the memory).
   }       Model is determined by parameters x and covariates have to be 
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);       included manually here. 
   j1=0;  
         */
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    int i, j, d, h, k;
      double **out, cov[NCOVMAX];
   for(k1=1; k1<=j;k1++){    double **newm;
     for(i1=1; i1<=ncodemax[k1];i1++){  
       j1++;    /* Hstepm could be zero and should return the unit matrix */
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);    for (i=1;i<=nlstate+ndeath;i++)
         scanf("%d", i);*/      for (j=1;j<=nlstate+ndeath;j++){
       for (i=-1; i<=nlstate+ndeath; i++)          oldm[i][j]=(i==j ? 1.0 : 0.0);
         for (jk=-1; jk<=nlstate+ndeath; jk++)          po[i][j][0]=(i==j ? 1.0 : 0.0);
           for(m=agemin; m <= agemax+3; m++)      }
             freq[i][jk][m]=0;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
          for(h=1; h <=nhstepm; h++){
       dateintsum=0;      for(d=1; d <=hstepm; d++){
       k2cpt=0;        newm=savm;
       for (i=1; i<=imx; i++) {        /* Covariates have to be included here again */
         bool=1;        cov[1]=1.;
         if  (cptcovn>0) {        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
           for (z1=1; z1<=cptcoveff; z1++)        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])        for (k=1; k<=cptcovage;k++)
               bool=0;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         }        for (k=1; k<=cptcovprod;k++)
         if (bool==1) {          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
           for(m=firstpass; m<=lastpass; m++){  
             k2=anint[m][i]+(mint[m][i]/12.);  
             if ((k2>=dateprev1) && (k2<=dateprev2)) {        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
               if(agev[m][i]==0) agev[m][i]=agemax+1;        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
               if(agev[m][i]==1) agev[m][i]=agemax+2;        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
               if (m<lastpass) {                     pmij(pmmij,cov,ncovmodel,x,nlstate));
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        savm=oldm;
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];        oldm=newm;
               }      }
                    for(i=1; i<=nlstate+ndeath; i++)
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {        for(j=1;j<=nlstate+ndeath;j++) {
                 dateintsum=dateintsum+k2;          po[i][j][h]=newm[i][j];
                 k2cpt++;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
               }           */
             }        }
           }    } /* end h */
         }    return po;
       }  }
          
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);  
   /*************** log-likelihood *************/
       if  (cptcovn>0) {  double func( double *x)
         fprintf(ficresp, "\n#********** Variable ");  {
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    int i, ii, j, k, mi, d, kk;
         fprintf(ficresp, "**********\n#");    double l, ll[NLSTATEMAX], cov[NCOVMAX];
       }    double **out;
       for(i=1; i<=nlstate;i++)    double sw; /* Sum of weights */
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    double lli; /* Individual log likelihood */
       fprintf(ficresp, "\n");    int s1, s2;
          double bbh, survp;
       for(i=(int)agemin; i <= (int)agemax+3; i++){    long ipmx;
         if(i==(int)agemax+3)    /*extern weight */
           printf("Total");    /* We are differentiating ll according to initial status */
         else    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
           printf("Age %d", i);    /*for(i=1;i<imx;i++) 
         for(jk=1; jk <=nlstate ; jk++){      printf(" %d\n",s[4][i]);
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    */
             pp[jk] += freq[jk][m][i];    cov[1]=1.;
         }  
         for(jk=1; jk <=nlstate ; jk++){    for(k=1; k<=nlstate; k++) ll[k]=0.;
           for(m=-1, pos=0; m <=0 ; m++)  
             pos += freq[jk][m][i];    if(mle==1){
           if(pp[jk]>=1.e-10)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           else        for(mi=1; mi<= wav[i]-1; mi++){
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          for (ii=1;ii<=nlstate+ndeath;ii++)
         }            for (j=1;j<=nlstate+ndeath;j++){
               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=0, pp[jk]=0; m <=nlstate+ndeath; m++)            }
             pp[jk] += freq[jk][m][i];          for(d=0; d<dh[mi][i]; d++){
         }            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         for(jk=1,pos=0; jk <=nlstate ; jk++)            for (kk=1; kk<=cptcovage;kk++) {
           pos += pp[jk];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         for(jk=1; jk <=nlstate ; jk++){            }
           if(pos>=1.e-5)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           else            savm=oldm;
             printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);            oldm=newm;
           if( i <= (int) agemax){          } /* end mult */
             if(pos>=1.e-5){        
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
               probs[i][jk][j1]= pp[jk]/pos;          /* But now since version 0.9 we anticipate for bias at large stepm.
               /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/           * If stepm is larger than one month (smallest stepm) and if the exact delay 
             }           * (in months) between two waves is not a multiple of stepm, we rounded to 
             else           * the nearest (and in case of equal distance, to the lowest) interval but now
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);           * we keep into memory the bias bh[mi][i] and also the previous matrix product
           }           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
         }           * probability in order to take into account the bias as a fraction of the way
                   * from savm to out if bh is negative or even beyond if bh is positive. bh varies
         for(jk=-1; jk <=nlstate+ndeath; jk++)           * -stepm/2 to stepm/2 .
           for(m=-1; m <=nlstate+ndeath; m++)           * For stepm=1 the results are the same as for previous versions of Imach.
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);           * For stepm > 1 the results are less biased than in previous versions. 
         if(i <= (int) agemax)           */
           fprintf(ficresp,"\n");          s1=s[mw[mi][i]][i];
         printf("\n");          s2=s[mw[mi+1][i]][i];
       }          bbh=(double)bh[mi][i]/(double)stepm; 
     }          /* bias bh is positive if real duration
   }           * is higher than the multiple of stepm and negative otherwise.
   dateintmean=dateintsum/k2cpt;           */
            /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   fclose(ficresp);          if( s2 > nlstate){ 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);            /* i.e. if s2 is a death state and if the date of death is known 
   free_vector(pp,1,nlstate);               then the contribution to the likelihood is the probability to 
                 die between last step unit time and current  step unit time, 
   /* End of Freq */               which is also equal to probability to die before dh 
 }               minus probability to die before dh-stepm . 
                In version up to 0.92 likelihood was computed
 /************ Prevalence ********************/          as if date of death was unknown. Death was treated as any other
 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)          health state: the date of the interview describes the actual state
 {  /* Some frequencies */          and not the date of a change in health state. The former idea was
            to consider that at each interview the state was recorded
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          (healthy, disable or death) and IMaCh was corrected; but when we
   double ***freq; /* Frequencies */          introduced the exact date of death then we should have modified
   double *pp;          the contribution of an exact death to the likelihood. This new
   double pos, k2;          contribution is smaller and very dependent of the step unit
           stepm. It is no more the probability to die between last interview
   pp=vector(1,nlstate);          and month of death but the probability to survive from last
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);          interview up to one month before death multiplied by the
            probability to die within a month. Thanks to Chris
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);          Jackson for correcting this bug.  Former versions increased
   j1=0;          mortality artificially. The bad side is that we add another loop
            which slows down the processing. The difference can be up to 10%
   j=cptcoveff;          lower mortality.
   if (cptcovn<1) {j=1;ncodemax[1]=1;}            */
              lli=log(out[s1][s2] - savm[s1][s2]);
  for(k1=1; k1<=j;k1++){  
     for(i1=1; i1<=ncodemax[k1];i1++){  
       j1++;          } else if  (s2==-2) {
              for (j=1,survp=0. ; j<=nlstate; j++) 
       for (i=-1; i<=nlstate+ndeath; i++)                survp += out[s1][j];
         for (jk=-1; jk<=nlstate+ndeath; jk++)              lli= survp;
           for(m=agemin; m <= agemax+3; m++)          }
             freq[i][jk][m]=0;          
                else if  (s2==-4) {
       for (i=1; i<=imx; i++) {            for (j=3,survp=0. ; j<=nlstate; j++) 
         bool=1;              survp += out[s1][j];
         if  (cptcovn>0) {            lli= survp;
           for (z1=1; z1<=cptcoveff; z1++)          }
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          
               bool=0;          else if  (s2==-5) {
         }            for (j=1,survp=0. ; j<=2; j++) 
         if (bool==1) {              survp += out[s1][j];
           for(m=firstpass; m<=lastpass; m++){            lli= survp;
             k2=anint[m][i]+(mint[m][i]/12.);          }
             if ((k2>=dateprev1) && (k2<=dateprev2)) {  
               if(agev[m][i]==0) agev[m][i]=agemax+1;  
               if(agev[m][i]==1) agev[m][i]=agemax+2;          else{
               if (m<lastpass) freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
               /* freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[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 */
             }          } 
           }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         }          /*if(lli ==000.0)*/
       }          /*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(i=(int)agemin; i <= (int)agemax+3; i++){          ipmx +=1;
           for(jk=1; jk <=nlstate ; jk++){          sw += weight[i];
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
               pp[jk] += freq[jk][m][i];        } /* end of wave */
           }      } /* end of individual */
           for(jk=1; jk <=nlstate ; jk++){    }  else if(mle==2){
             for(m=-1, pos=0; m <=0 ; m++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             pos += freq[jk][m][i];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         }        for(mi=1; mi<= wav[i]-1; mi++){
                  for (ii=1;ii<=nlstate+ndeath;ii++)
          for(jk=1; jk <=nlstate ; jk++){            for (j=1;j<=nlstate+ndeath;j++){
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
              pp[jk] += freq[jk][m][i];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
          }            }
                    for(d=0; d<=dh[mi][i]; d++){
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
          for(jk=1; jk <=nlstate ; jk++){                      for (kk=1; kk<=cptcovage;kk++) {
            if( i <= (int) agemax){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
              if(pos>=1.e-5){            }
                probs[i][jk][j1]= pp[jk]/pos;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
              }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
            }            savm=oldm;
          }            oldm=newm;
                    } /* end mult */
         }        
     }          s1=s[mw[mi][i]][i];
   }          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 */
   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 */
 /************* Waves Concatenation ***************/    }  else if(mle==3){  /* exponential inter-extrapolation */
       for (i=1,ipmx=0, sw=0.; i<=imx; 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 (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 {        for(mi=1; mi<= wav[i]-1; mi++){
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.          for (ii=1;ii<=nlstate+ndeath;ii++)
      Death is a valid wave (if date is known).            for (j=1;j<=nlstate+ndeath;j++){
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]              savm[ii][j]=(ii==j ? 1.0 : 0.0);
      and mw[mi+1][i]. dh depends on stepm.            }
      */          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
   int i, mi, m;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;            for (kk=1; kk<=cptcovage;kk++) {
      double sum=0., jmean=0.;*/              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
   int j, k=0,jk, ju, jl;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double sum=0.;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   jmin=1e+5;            savm=oldm;
   jmax=-1;            oldm=newm;
   jmean=0.;          } /* end mult */
   for(i=1; i<=imx; i++){        
     mi=0;          s1=s[mw[mi][i]][i];
     m=firstpass;          s2=s[mw[mi+1][i]][i];
     while(s[m][i] <= nlstate){          bbh=(double)bh[mi][i]/(double)stepm; 
       if(s[m][i]>=1)          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 */
         mw[++mi][i]=m;          ipmx +=1;
       if(m >=lastpass)          sw += weight[i];
         break;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       else        } /* end of wave */
         m++;      } /* end of individual */
     }/* end while */    }else if (mle==4){  /* ml=4 no inter-extrapolation */
     if (s[m][i] > nlstate){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       mi++;     /* Death is another wave */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       /* if(mi==0)  never been interviewed correctly before death */        for(mi=1; mi<= wav[i]-1; mi++){
          /* Only death is a correct wave */          for (ii=1;ii<=nlstate+ndeath;ii++)
       mw[mi][i]=m;            for (j=1;j<=nlstate+ndeath;j++){
     }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
     wav[i]=mi;            }
     if(mi==0)          for(d=0; d<dh[mi][i]; d++){
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);            newm=savm;
   }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
   for(i=1; i<=imx; i++){              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     for(mi=1; mi<wav[i];mi++){            }
       if (stepm <=0)          
         dh[mi][i]=1;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       else{                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         if (s[mw[mi+1][i]][i] > nlstate) {            savm=oldm;
           if (agedc[i] < 2*AGESUP) {            oldm=newm;
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          } /* end mult */
           if(j==0) j=1;  /* Survives at least one month after exam */        
           k=k+1;          s1=s[mw[mi][i]][i];
           if (j >= jmax) jmax=j;          s2=s[mw[mi+1][i]][i];
           if (j <= jmin) jmin=j;          if( s2 > nlstate){ 
           sum=sum+j;            lli=log(out[s1][s2] - savm[s1][s2]);
           /*if (j<0) printf("j=%d num=%d \n",j,i); */          }else{
           }            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         }          }
         else{          ipmx +=1;
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          sw += weight[i];
           k=k+1;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           if (j >= jmax) jmax=j;  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
           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;    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
         }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         jk= j/stepm;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         jl= j -jk*stepm;        for(mi=1; mi<= wav[i]-1; mi++){
         ju= j -(jk+1)*stepm;          for (ii=1;ii<=nlstate+ndeath;ii++)
         if(jl <= -ju)            for (j=1;j<=nlstate+ndeath;j++){
           dh[mi][i]=jk;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         else              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           dh[mi][i]=jk+1;            }
         if(dh[mi][i]==0)          for(d=0; d<dh[mi][i]; d++){
           dh[mi][i]=1; /* At least one step */            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];
   jmean=sum/k;            }
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);          
  }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 /*********** Tricode ****************************/                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 void tricode(int *Tvar, int **nbcode, int imx)            savm=oldm;
 {            oldm=newm;
   int Ndum[20],ij=1, k, j, i;          } /* end mult */
   int cptcode=0;        
   cptcoveff=0;          s1=s[mw[mi][i]][i];
            s2=s[mw[mi+1][i]][i];
   for (k=0; k<19; k++) Ndum[k]=0;          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   for (k=1; k<=7; k++) ncodemax[k]=0;          ipmx +=1;
           sw += weight[i];
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for (i=1; i<=imx; i++) {          /*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]);*/
       ij=(int)(covar[Tvar[j]][i]);        } /* end of wave */
       Ndum[ij]++;      } /* end of individual */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/    } /* End of if */
       if (ij > cptcode) cptcode=ij;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     }    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     for (i=0; i<=cptcode; i++) {    return -l;
       if(Ndum[i]!=0) ncodemax[j]++;  }
     }  
     ij=1;  /*************** log-likelihood *************/
   double funcone( double *x)
   {
     for (i=1; i<=ncodemax[j]; i++) {    /* Same as likeli but slower because of a lot of printf and if */
       for (k=0; k<=19; k++) {    int i, ii, j, k, mi, d, kk;
         if (Ndum[k] != 0) {    double l, ll[NLSTATEMAX], cov[NCOVMAX];
           nbcode[Tvar[j]][ij]=k;    double **out;
           /*     printf("nbcodeaaaaaaaaaaa=%d Tvar[j]=%d ij=%d j=%d",nbcode[Tvar[j]][ij],Tvar[j],ij,j);*/    double lli; /* Individual log likelihood */
           ij++;    double llt;
         }    int s1, s2;
         if (ij > ncodemax[j]) break;    double bbh, survp;
       }      /*extern weight */
     }    /* We are differentiating ll according to initial status */
   }      /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     /*for(i=1;i<imx;i++) 
  for (k=0; k<19; k++) Ndum[k]=0;      printf(" %d\n",s[4][i]);
     */
  for (i=1; i<=ncovmodel-2; i++) {    cov[1]=1.;
       ij=Tvar[i];  
       Ndum[ij]++;    for(k=1; k<=nlstate; k++) ll[k]=0.;
     }  
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
  ij=1;      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
  for (i=1; i<=10; i++) {      for(mi=1; mi<= wav[i]-1; mi++){
    if((Ndum[i]!=0) && (i<=ncovcol)){        for (ii=1;ii<=nlstate+ndeath;ii++)
      Tvaraff[ij]=i;          for (j=1;j<=nlstate+ndeath;j++){
      ij++;            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
    }            savm[ii][j]=(ii==j ? 1.0 : 0.0);
  }          }
          for(d=0; d<dh[mi][i]; d++){
     cptcoveff=ij-1;          newm=savm;
 }          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for (kk=1; kk<=cptcovage;kk++) {
 /*********** Health Expectancies ****************/            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           }
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm)          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 {                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   /* Health expectancies */          savm=oldm;
   int i, j, nhstepm, hstepm, h, nstepm;          oldm=newm;
   double age, agelim, hf;        } /* end mult */
   double ***p3mat;        
          s1=s[mw[mi][i]][i];
   fprintf(ficreseij,"# Health expectancies\n");        s2=s[mw[mi+1][i]][i];
   fprintf(ficreseij,"# Age");        bbh=(double)bh[mi][i]/(double)stepm; 
   for(i=1; i<=nlstate;i++)        /* bias is positive if real duration
     for(j=1; j<=nlstate;j++)         * is higher than the multiple of stepm and negative otherwise.
       fprintf(ficreseij," %1d-%1d",i,j);         */
   fprintf(ficreseij,"\n");        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           lli=log(out[s1][s2] - savm[s1][s2]);
   if(estepm < stepm){        } else if (mle==1){
     printf ("Problem %d lower than %d\n",estepm, stepm);          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   }        } else if(mle==2){
   else  hstepm=estepm;            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 */
   /* We compute the life expectancy from trapezoids spaced every estepm months        } else if(mle==3){  /* exponential inter-extrapolation */
    * This is mainly to measure the difference between two models: for example          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 */
    * if stepm=24 months pijx are given only every 2 years and by summing them        } else if (mle==4){  /* mle=4 no inter-extrapolation */
    * we are calculating an estimate of the Life Expectancy assuming a linear          lli=log(out[s1][s2]); /* Original formula */
    * progression inbetween and thus overestimating or underestimating according        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
    * to the curvature of the survival function. If, for the same date, we          lli=log(out[s1][s2]); /* Original formula */
    * estimate the model with stepm=1 month, we can keep estepm to 24 months        } /* End of if */
    * to compare the new estimate of Life expectancy with the same linear        ipmx +=1;
    * hypothesis. A more precise result, taking into account a more precise        sw += weight[i];
    * curvature will be obtained if estepm is as small as stepm. */        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]); */
   /* For example we decided to compute the life expectancy with the smallest unit */        if(globpr){
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
      nhstepm is the number of hstepm from age to agelim   %10.6f %10.6f %10.6f ", \
      nstepm is the number of stepm from age to agelin.                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
      Look at hpijx to understand the reason of that which relies in memory size                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
      and note for a fixed period like estepm months */          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the            llt +=ll[k]*gipmx/gsw;
      survival function given by stepm (the optimization length). Unfortunately it            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
      means that if the survival funtion is printed only each two years of age and if          }
      you sum them up and add 1 year (area under the trapezoids) you won't get the same          fprintf(ficresilk," %10.6f\n", -llt);
      results. So we changed our mind and took the option of the best precision.        }
   */      } /* end of wave */
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    } /* end of individual */
     for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   agelim=AGESUP;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     /* nhstepm age range expressed in number of stepm */    if(globpr==0){ /* First time we count the contributions and weights */
     nstepm=(int) rint((agelim-age)*YEARM/stepm);      gipmx=ipmx;
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */      gsw=sw;
     /* if (stepm >= YEARM) hstepm=1;*/    }
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    return -l;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  }
     /* Computed by stepm unit matrices, product of hstepm matrices, stored  
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */  
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);    /*************** function likelione ***********/
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
     for(i=1; i<=nlstate;i++)  {
       for(j=1; j<=nlstate;j++)    /* This routine should help understanding what is done with 
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){       the selection of individuals/waves and
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;       to check the exact contribution to the likelihood.
           /* 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]);*/       Plotting could be done.
         }     */
     fprintf(ficreseij,"%3.0f",age );    int k;
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){    if(*globpri !=0){ /* Just counts and sums, no printings */
         fprintf(ficreseij," %9.4f", eij[i][j][(int)age]);      strcpy(fileresilk,"ilk"); 
       }      strcat(fileresilk,fileres);
     fprintf(ficreseij,"\n");      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        printf("Problem with resultfile: %s\n", fileresilk);
   }        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
 }      }
       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");
 /************ Variance ******************/      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
 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)      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
 {      for(k=1; k<=nlstate; k++) 
   /* Variance of health expectancies */        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   double **newm;    }
   double **dnewm,**doldm;  
   int i, j, nhstepm, hstepm, h, nstepm ;    *fretone=(*funcone)(p);
   int k, cptcode;    if(*globpri !=0){
   double *xp;      fclose(ficresilk);
   double **gp, **gm;      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   double ***gradg, ***trgradg;      fflush(fichtm); 
   double ***p3mat;    } 
   double age,agelim, hf;    return;
   int theta;  }
   
    fprintf(ficresvij,"# Covariances of life expectancies\n");  
   fprintf(ficresvij,"# Age");  /*********** Maximum Likelihood Estimation ***************/
   for(i=1; i<=nlstate;i++)  
     for(j=1; j<=nlstate;j++)  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);  {
   fprintf(ficresvij,"\n");    int i,j, iter;
     double **xi;
   xp=vector(1,npar);    double fret;
   dnewm=matrix(1,nlstate,1,npar);    double fretone; /* Only one call to likelihood */
   doldm=matrix(1,nlstate,1,nlstate);    /*  char filerespow[FILENAMELENGTH];*/
      xi=matrix(1,npar,1,npar);
   if(estepm < stepm){    for (i=1;i<=npar;i++)
     printf ("Problem %d lower than %d\n",estepm, stepm);      for (j=1;j<=npar;j++)
   }        xi[i][j]=(i==j ? 1.0 : 0.0);
   else  hstepm=estepm;      printf("Powell\n");  fprintf(ficlog,"Powell\n");
   /* For example we decided to compute the life expectancy with the smallest unit */    strcpy(filerespow,"pow"); 
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.    strcat(filerespow,fileres);
      nhstepm is the number of hstepm from age to agelim    if((ficrespow=fopen(filerespow,"w"))==NULL) {
      nstepm is the number of stepm from age to agelin.      printf("Problem with resultfile: %s\n", filerespow);
      Look at hpijx to understand the reason of that which relies in memory size      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
      and note for a fixed period like k years */    }
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    fprintf(ficrespow,"# Powell\n# iter -2*LL");
      survival function given by stepm (the optimization length). Unfortunately it    for (i=1;i<=nlstate;i++)
      means that if the survival funtion is printed only each two years of age and if      for(j=1;j<=nlstate+ndeath;j++)
      you sum them up and add 1 year (area under the trapezoids) you won't get the same        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
      results. So we changed our mind and took the option of the best precision.    fprintf(ficrespow,"\n");
   */  
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    powell(p,xi,npar,ftol,&iter,&fret,func);
   agelim = AGESUP;  
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    fclose(ficrespow);
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);  
     gp=matrix(0,nhstepm,1,nlstate);  }
     gm=matrix(0,nhstepm,1,nlstate);  
   /**** Computes Hessian and covariance matrix ***/
     for(theta=1; theta <=npar; theta++){  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
       for(i=1; i<=npar; i++){ /* Computes gradient */  {
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    double  **a,**y,*x,pd;
       }    double **hess;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);      int i, j,jk;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    int *indx;
   
       if (popbased==1) {    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
         for(i=1; i<=nlstate;i++)    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
           prlim[i][i]=probs[(int)age][i][ij];    void lubksb(double **a, int npar, int *indx, double b[]) ;
       }    void ludcmp(double **a, int npar, int *indx, double *d) ;
      double gompertz(double p[]);
       for(j=1; j<= nlstate; j++){    hess=matrix(1,npar,1,npar);
         for(h=0; h<=nhstepm; h++){  
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    printf("\nCalculation of the hessian matrix. Wait...\n");
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         }    for (i=1;i<=npar;i++){
       }      printf("%d",i);fflush(stdout);
          fprintf(ficlog,"%d",i);fflush(ficlog);
       for(i=1; i<=npar; i++) /* Computes gradient */     
         xp[i] = x[i] - (i==theta ?delti[theta]:0);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      /*  printf(" %f ",p[i]);
            printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
       if (popbased==1) {    }
         for(i=1; i<=nlstate;i++)    
           prlim[i][i]=probs[(int)age][i][ij];    for (i=1;i<=npar;i++) {
       }      for (j=1;j<=npar;j++)  {
         if (j>i) { 
       for(j=1; j<= nlstate; j++){          printf(".%d%d",i,j);fflush(stdout);
         for(h=0; h<=nhstepm; h++){          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          hess[i][j]=hessij(p,delti,i,j,func,npar);
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          
         }          hess[j][i]=hess[i][j];    
       }          /*printf(" %lf ",hess[i][j]);*/
         }
       for(j=1; j<= nlstate; j++)      }
         for(h=0; h<=nhstepm; h++){    }
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    printf("\n");
         }    fprintf(ficlog,"\n");
     } /* End theta */  
     printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     
     for(h=0; h<=nhstepm; h++)    a=matrix(1,npar,1,npar);
       for(j=1; j<=nlstate;j++)    y=matrix(1,npar,1,npar);
         for(theta=1; theta <=npar; theta++)    x=vector(1,npar);
           trgradg[h][j][theta]=gradg[h][theta][j];    indx=ivector(1,npar);
     for (i=1;i<=npar;i++)
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     for(i=1;i<=nlstate;i++)    ludcmp(a,npar,indx,&pd);
       for(j=1;j<=nlstate;j++)  
         vareij[i][j][(int)age] =0.;    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
     for(h=0;h<=nhstepm;h++){      x[j]=1;
       for(k=0;k<=nhstepm;k++){      lubksb(a,npar,indx,x);
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      for (i=1;i<=npar;i++){ 
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        matcov[i][j]=x[i];
         for(i=1;i<=nlstate;i++)      }
           for(j=1;j<=nlstate;j++)    }
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;  
       }    printf("\n#Hessian matrix#\n");
     }    fprintf(ficlog,"\n#Hessian matrix#\n");
     for (i=1;i<=npar;i++) { 
     fprintf(ficresvij,"%.0f ",age );      for (j=1;j<=npar;j++) { 
     for(i=1; i<=nlstate;i++)        printf("%.3e ",hess[i][j]);
       for(j=1; j<=nlstate;j++){        fprintf(ficlog,"%.3e ",hess[i][j]);
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);      }
       }      printf("\n");
     fprintf(ficresvij,"\n");      fprintf(ficlog,"\n");
     free_matrix(gp,0,nhstepm,1,nlstate);    }
     free_matrix(gm,0,nhstepm,1,nlstate);  
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    /* Recompute Inverse */
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    for (i=1;i<=npar;i++)
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   } /* End age */    ludcmp(a,npar,indx,&pd);
    
   free_vector(xp,1,npar);    /*  printf("\n#Hessian matrix recomputed#\n");
   free_matrix(doldm,1,nlstate,1,npar);  
   free_matrix(dnewm,1,nlstate,1,nlstate);    for (j=1;j<=npar;j++) {
       for (i=1;i<=npar;i++) x[i]=0;
 }      x[j]=1;
       lubksb(a,npar,indx,x);
 /************ Variance of prevlim ******************/      for (i=1;i<=npar;i++){ 
 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)        y[i][j]=x[i];
 {        printf("%.3e ",y[i][j]);
   /* Variance of prevalence limit */        fprintf(ficlog,"%.3e ",y[i][j]);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      }
   double **newm;      printf("\n");
   double **dnewm,**doldm;      fprintf(ficlog,"\n");
   int i, j, nhstepm, hstepm;    }
   int k, cptcode;    */
   double *xp;  
   double *gp, *gm;    free_matrix(a,1,npar,1,npar);
   double **gradg, **trgradg;    free_matrix(y,1,npar,1,npar);
   double age,agelim;    free_vector(x,1,npar);
   int theta;    free_ivector(indx,1,npar);
        free_matrix(hess,1,npar,1,npar);
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");  
   fprintf(ficresvpl,"# Age");  
   for(i=1; i<=nlstate;i++)  }
       fprintf(ficresvpl," %1d-%1d",i,i);  
   fprintf(ficresvpl,"\n");  /*************** hessian matrix ****************/
   double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
   xp=vector(1,npar);  {
   dnewm=matrix(1,nlstate,1,npar);    int i;
   doldm=matrix(1,nlstate,1,nlstate);    int l=1, lmax=20;
      double k1,k2;
   hstepm=1*YEARM; /* Every year of age */    double p2[NPARMAX+1];
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    double res;
   agelim = AGESUP;    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    double fx;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    int k=0,kmax=10;
     if (stepm >= YEARM) hstepm=1;    double l1;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
     gradg=matrix(1,npar,1,nlstate);    fx=func(x);
     gp=vector(1,nlstate);    for (i=1;i<=npar;i++) p2[i]=x[i];
     gm=vector(1,nlstate);    for(l=0 ; l <=lmax; l++){
       l1=pow(10,l);
     for(theta=1; theta <=npar; theta++){      delts=delt;
       for(i=1; i<=npar; i++){ /* Computes gradient */      for(k=1 ; k <kmax; k=k+1){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        delt = delta*(l1*k);
       }        p2[theta]=x[theta] +delt;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        k1=func(p2)-fx;
       for(i=1;i<=nlstate;i++)        p2[theta]=x[theta]-delt;
         gp[i] = prlim[i][i];        k2=func(p2)-fx;
            /*res= (k1-2.0*fx+k2)/delt/delt; */
       for(i=1; i<=npar; i++) /* Computes gradient */        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  #ifdef DEBUG
       for(i=1;i<=nlstate;i++)        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         gm[i] = prlim[i][i];        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
   #endif
       for(i=1;i<=nlstate;i++)        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
     } /* End theta */          k=kmax;
         }
     trgradg =matrix(1,nlstate,1,npar);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           k=kmax; l=lmax*10.;
     for(j=1; j<=nlstate;j++)        }
       for(theta=1; theta <=npar; theta++)        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
         trgradg[j][theta]=gradg[theta][j];          delts=delt;
         }
     for(i=1;i<=nlstate;i++)      }
       varpl[i][(int)age] =0.;    }
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    delti[theta]=delts;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    return res; 
     for(i=1;i<=nlstate;i++)    
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */  }
   
     fprintf(ficresvpl,"%.0f ",age );  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
     for(i=1; i<=nlstate;i++)  {
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    int i;
     fprintf(ficresvpl,"\n");    int l=1, l1, lmax=20;
     free_vector(gp,1,nlstate);    double k1,k2,k3,k4,res,fx;
     free_vector(gm,1,nlstate);    double p2[NPARMAX+1];
     free_matrix(gradg,1,npar,1,nlstate);    int k;
     free_matrix(trgradg,1,nlstate,1,npar);  
   } /* End age */    fx=func(x);
     for (k=1; k<=2; k++) {
   free_vector(xp,1,npar);      for (i=1;i<=npar;i++) p2[i]=x[i];
   free_matrix(doldm,1,nlstate,1,npar);      p2[thetai]=x[thetai]+delti[thetai]/k;
   free_matrix(dnewm,1,nlstate,1,nlstate);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k1=func(p2)-fx;
 }    
       p2[thetai]=x[thetai]+delti[thetai]/k;
 /************ Variance of one-step probabilities  ******************/      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)      k2=func(p2)-fx;
 {    
   int i, j;      p2[thetai]=x[thetai]-delti[thetai]/k;
   int k=0, cptcode;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   double **dnewm,**doldm;      k3=func(p2)-fx;
   double *xp;    
   double *gp, *gm;      p2[thetai]=x[thetai]-delti[thetai]/k;
   double **gradg, **trgradg;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   double age,agelim, cov[NCOVMAX];      k4=func(p2)-fx;
   int theta;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   char fileresprob[FILENAMELENGTH];  #ifdef DEBUG
       printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
   strcpy(fileresprob,"prob");      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);
   strcat(fileresprob,fileres);  #endif
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    }
     printf("Problem with resultfile: %s\n", fileresprob);    return res;
   }  }
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);  
    /************** Inverse of matrix **************/
   void ludcmp(double **a, int n, int *indx, double *d) 
   xp=vector(1,npar);  { 
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    int i,imax,j,k; 
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    double big,dum,sum,temp; 
      double *vv; 
   cov[1]=1;   
   for (age=bage; age<=fage; age ++){    vv=vector(1,n); 
     cov[2]=age;    *d=1.0; 
     gradg=matrix(1,npar,1,9);    for (i=1;i<=n;i++) { 
     trgradg=matrix(1,9,1,npar);      big=0.0; 
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      for (j=1;j<=n;j++) 
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        if ((temp=fabs(a[i][j])) > big) big=temp; 
          if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     for(theta=1; theta <=npar; theta++){      vv[i]=1.0/big; 
       for(i=1; i<=npar; i++)    } 
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    for (j=1;j<=n;j++) { 
            for (i=1;i<j;i++) { 
       pmij(pmmij,cov,ncovmodel,xp,nlstate);        sum=a[i][j]; 
            for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
       k=0;        a[i][j]=sum; 
       for(i=1; i<= (nlstate+ndeath); i++){      } 
         for(j=1; j<=(nlstate+ndeath);j++){      big=0.0; 
            k=k+1;      for (i=j;i<=n;i++) { 
           gp[k]=pmmij[i][j];        sum=a[i][j]; 
         }        for (k=1;k<j;k++) 
       }          sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
       for(i=1; i<=npar; i++)        if ( (dum=vv[i]*fabs(sum)) >= big) { 
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          big=dum; 
              imax=i; 
         } 
       pmij(pmmij,cov,ncovmodel,xp,nlstate);      } 
       k=0;      if (j != imax) { 
       for(i=1; i<=(nlstate+ndeath); i++){        for (k=1;k<=n;k++) { 
         for(j=1; j<=(nlstate+ndeath);j++){          dum=a[imax][k]; 
           k=k+1;          a[imax][k]=a[j][k]; 
           gm[k]=pmmij[i][j];          a[j][k]=dum; 
         }        } 
       }        *d = -(*d); 
              vv[imax]=vv[j]; 
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)      } 
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];        indx[j]=imax; 
     }      if (a[j][j] == 0.0) a[j][j]=TINY; 
       if (j != n) { 
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)        dum=1.0/(a[j][j]); 
       for(theta=1; theta <=npar; theta++)        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       trgradg[j][theta]=gradg[theta][j];      } 
      } 
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    free_vector(vv,1,n);  /* Doesn't work */
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);  ;
   } 
      pmij(pmmij,cov,ncovmodel,x,nlstate);  
   void lubksb(double **a, int n, int *indx, double b[]) 
      k=0;  { 
      for(i=1; i<=(nlstate+ndeath); i++){    int i,ii=0,ip,j; 
        for(j=1; j<=(nlstate+ndeath);j++){    double sum; 
          k=k+1;   
          gm[k]=pmmij[i][j];    for (i=1;i<=n;i++) { 
         }      ip=indx[i]; 
      }      sum=b[ip]; 
            b[ip]=b[i]; 
      /*printf("\n%d ",(int)age);      if (ii) 
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
              else if (sum) ii=i; 
       b[i]=sum; 
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    } 
      }*/    for (i=n;i>=1;i--) { 
       sum=b[i]; 
   fprintf(ficresprob,"\n%d ",(int)age);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       b[i]=sum/a[i][i]; 
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    } 
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  } 
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);  
   }  /************ Frequencies ********************/
   void  freqsummary(char fileres[], int iagemin, int iagemax, int **s, double **agev, int nlstate, int imx, int *Tvaraff, int **nbcode, int *ncodemax,double **mint,double **anint, char strstart[])
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));  {  /* Some frequencies */
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));    
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    int first;
 }    double ***freq; /* Frequencies */
  free_vector(xp,1,npar);    double *pp, **prop;
 fclose(ficresprob);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     FILE *ficresp;
 }    char fileresp[FILENAMELENGTH];
     
 /******************* Printing html file ***********/    pp=vector(1,nlstate);
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \    prop=matrix(1,nlstate,iagemin,iagemax+3);
  int lastpass, int stepm, int weightopt, char model[],\    strcpy(fileresp,"p");
  int imx,int jmin, int jmax, double jmeanint,char optionfile[], \    strcat(fileresp,fileres);
  char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\    if((ficresp=fopen(fileresp,"w"))==NULL) {
  char version[], int popforecast, int estepm ){      printf("Problem with prevalence resultfile: %s\n", fileresp);
   int jj1, k1, i1, cpt;      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
   FILE *fichtm;      exit(0);
   /*char optionfilehtm[FILENAMELENGTH];*/    }
     freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
   strcpy(optionfilehtm,optionfile);    j1=0;
   strcat(optionfilehtm,".htm");    
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {    j=cptcoveff;
     printf("Problem with %s \n",optionfilehtm), exit(0);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   }  
     first=1;
  fprintf(fichtm,"<body> <font size=\"2\">%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    for(k1=1; k1<=j;k1++){
 \n      for(i1=1; i1<=ncodemax[k1];i1++){
 Total number of observations=%d <br>\n        j1++;
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
 <hr  size=\"2\" color=\"#EC5E5E\">          scanf("%d", i);*/
  <ul><li>Outputs files<br>\n        for (i=-5; i<=nlstate+ndeath; i++)  
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n          for (jk=-5; jk<=nlstate+ndeath; jk++)  
  - Gnuplot file name: <a href=\"%s\">%s</a><br>\n            for(m=iagemin; m <= iagemax+3; m++)
  - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n              freq[i][jk][m]=0;
  - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>\n  
  - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>\n      for (i=1; i<=nlstate; i++)  
  - 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);        for(m=iagemin; m <= iagemax+3; m++)
           prop[i][m]=0;
  fprintf(fichtm,"\n        
  - Parameter file with estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>\n        dateintsum=0;
  - Variances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n        k2cpt=0;
  - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>\n        for (i=1; i<=imx; i++) {
  - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);          bool=1;
           if  (cptcovn>0) {
  if(popforecast==1) fprintf(fichtm,"\n            for (z1=1; z1<=cptcoveff; z1++) 
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n                bool=0;
         <br>",fileres,fileres,fileres,fileres);          }
  else          if (bool==1){
    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);            for(m=firstpass; m<=lastpass; m++){
 fprintf(fichtm," <li>Graphs</li><p>");              k2=anint[m][i]+(mint[m][i]/12.);
               /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
  m=cptcoveff;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                 if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
  jj1=0;                if (m<lastpass) {
  for(k1=1; k1<=m;k1++){                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
    for(i1=1; i1<=ncodemax[k1];i1++){                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
        jj1++;                }
        if (cptcovn > 0) {                
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
          for (cpt=1; cpt<=cptcoveff;cpt++)                  dateintsum=dateintsum+k2;
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);                  k2cpt++;
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");                }
        }                /*}*/
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>            }
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);              }
        for(cpt=1; cpt<nlstate;cpt++){        }
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>         
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
        }  fprintf(ficresp, "#Local time at start: %s", strstart);
     for(cpt=1; cpt<=nlstate;cpt++) {        if  (cptcovn>0) {
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident          fprintf(ficresp, "\n#********** Variable "); 
 interval) in state (%d): v%s%d%d.gif <br>          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);            fprintf(ficresp, "**********\n#");
      }        }
      for(cpt=1; cpt<=nlstate;cpt++) {        for(i=1; i<=nlstate;i++) 
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);        fprintf(ficresp, "\n");
      }        
      fprintf(fichtm,"\n<br>- Total life expectancy by age and        for(i=iagemin; i <= iagemax+3; i++){
 health expectancies in states (1) and (2): e%s%d.gif<br>          if(i==iagemax+3){
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);            fprintf(ficlog,"Total");
 fprintf(fichtm,"\n</body>");          }else{
    }            if(first==1){
    }              first=0;
 fclose(fichtm);              printf("See log file for details...\n");
 }            }
             fprintf(ficlog,"Age %d", i);
 /******************* Gnuplot file **************/          }
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){          for(jk=1; jk <=nlstate ; jk++){
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;              pp[jk] += freq[jk][m][i]; 
           }
   strcpy(optionfilegnuplot,optionfilefiname);          for(jk=1; jk <=nlstate ; jk++){
   strcat(optionfilegnuplot,".gp.txt");            for(m=-1, pos=0; m <=0 ; m++)
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {              pos += freq[jk][m][i];
     printf("Problem with file %s",optionfilegnuplot);            if(pp[jk]>=1.e-10){
   }              if(first==1){
               printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 #ifdef windows              }
     fprintf(ficgp,"cd \"%s\" \n",pathc);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
 #endif            }else{
 m=pow(2,cptcoveff);              if(first==1)
                  printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
  /* 1eme*/              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
   for (cpt=1; cpt<= nlstate ; cpt ++) {            }
    for (k1=1; k1<= m ; k1 ++) {          }
   
 #ifdef windows          for(jk=1; jk <=nlstate ; jk++){
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
 #endif              pp[jk] += freq[jk][m][i];
 #ifdef unix          }       
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
 #endif            pos += pp[jk];
             posprop += prop[jk][i];
 for (i=1; i<= nlstate ; i ++) {          }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          for(jk=1; jk <=nlstate ; jk++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");            if(pos>=1.e-5){
 }              if(first==1)
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     for (i=1; i<= nlstate ; i ++) {              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            }else{
   else fprintf(ficgp," \%%*lf (\%%*lf)");              if(first==1)
 }                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
      for (i=1; i<= nlstate ; i ++) {            }
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            if( i <= iagemax){
   else fprintf(ficgp," \%%*lf (\%%*lf)");              if(pos>=1.e-5){
 }                  fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));                /*probs[i][jk][j1]= pp[jk]/pos;*/
 #ifdef unix                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
 fprintf(ficgp,"\nset ter gif small size 400,300");              }
 #endif              else
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
    }            }
   }          }
   /*2 eme*/          
           for(jk=-1; jk <=nlstate+ndeath; jk++)
   for (k1=1; k1<= m ; k1 ++) {            for(m=-1; m <=nlstate+ndeath; m++)
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",ageminpar,fage);              if(freq[jk][m][i] !=0 ) {
                  if(first==1)
     for (i=1; i<= nlstate+1 ; i ++) {                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
       k=2*i;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);              }
       for (j=1; j<= nlstate+1 ; j ++) {          if(i <= iagemax)
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");            fprintf(ficresp,"\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");          if(first==1)
 }              printf("Others in log...\n");
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          fprintf(ficlog,"\n");
       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 ++) {    }
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    dateintmean=dateintsum/k2cpt; 
         else fprintf(ficgp," \%%*lf (\%%*lf)");   
 }      fclose(ficresp);
       fprintf(ficgp,"\" t\"\" w l 0,");    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    free_vector(pp,1,nlstate);
       for (j=1; j<= nlstate+1 ; j ++) {    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    /* End of Freq */
   else fprintf(ficgp," \%%*lf (\%%*lf)");  }
 }    
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");  /************ Prevalence ********************/
       else fprintf(ficgp,"\" t\"\" w l 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(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   }       in each health status at the date of interview (if between dateprev1 and dateprev2).
         We still use firstpass and lastpass as another selection.
   /*3eme*/    */
    
   for (k1=1; k1<= m ; k1 ++) {    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     for (cpt=1; cpt<= nlstate ; cpt ++) {    double ***freq; /* Frequencies */
       k=2+nlstate*(cpt-1);    double *pp, **prop;
       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);    double pos,posprop; 
       for (i=1; i< nlstate ; i ++) {    double  y2; /* in fractional years */
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);    int iagemin, iagemax;
       }  
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    iagemin= (int) agemin;
     }    iagemax= (int) agemax;
     }    /*pp=vector(1,nlstate);*/
      prop=matrix(1,nlstate,iagemin,iagemax+3); 
   /* CV preval stat */    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     for (k1=1; k1<= m ; k1 ++) {    j1=0;
     for (cpt=1; cpt<nlstate ; cpt ++) {    
       k=3;    j=cptcoveff;
       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);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     
       for (i=1; i< nlstate ; i ++)    for(k1=1; k1<=j;k1++){
         fprintf(ficgp,"+$%d",k+i+1);      for(i1=1; i1<=ncodemax[k1];i1++){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);        j1++;
              
       l=3+(nlstate+ndeath)*cpt;        for (i=1; i<=nlstate; i++)  
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);          for(m=iagemin; m <= iagemax+3; m++)
       for (i=1; i< nlstate ; i ++) {            prop[i][m]=0.0;
         l=3+(nlstate+ndeath)*cpt;       
         fprintf(ficgp,"+$%d",l+i+1);        for (i=1; i<=imx; i++) { /* Each individual */
       }          bool=1;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            if  (cptcovn>0) {
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            for (z1=1; z1<=cptcoveff; z1++) 
     }              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
   }                  bool=0;
            } 
   /* proba elementaires */          if (bool==1) { 
    for(i=1,jk=1; i <=nlstate; i++){            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     for(k=1; k <=(nlstate+ndeath); k++){              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
       if (k != i) {              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
         for(j=1; j <=ncovmodel; j++){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
                        if(agev[m][i]==1) agev[m][i]=iagemax+2;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);                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); 
           jk++;                if (s[m][i]>0 && s[m][i]<=nlstate) { 
           fprintf(ficgp,"\n");                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
         }                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
       }                  prop[s[m][i]][iagemax+3] += weight[i]; 
     }                } 
     }              }
             } /* end selection of waves */
     for(jk=1; jk <=m; jk++) {          }
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);        }
    i=1;        for(i=iagemin; i <= iagemax+3; i++){  
    for(k2=1; k2<=nlstate; k2++) {          
      k3=i;          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
      for(k=1; k<=(nlstate+ndeath); k++) {            posprop += prop[jk][i]; 
        if (k != k2){          } 
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);  
 ij=1;          for(jk=1; jk <=nlstate ; jk++){     
         for(j=3; j <=ncovmodel; j++) {            if( i <=  iagemax){ 
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              if(posprop>=1.e-5){ 
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);                probs[i][jk][j1]= prop[jk][i]/posprop;
             ij++;              } 
           }            } 
           else          }/* end jk */ 
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        }/* end i */ 
         }      } /* end i1 */
           fprintf(ficgp,")/(1");    } /* end k1 */
            
         for(k1=1; k1 <=nlstate; k1++){      /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    /*free_vector(pp,1,nlstate);*/
 ij=1;    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
           for(j=3; j <=ncovmodel; j++){  }  /* End of prevalence */
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {  
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  /************* Waves Concatenation ***************/
             ij++;  
           }  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)
           else  {
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
           }       Death is a valid wave (if date is known).
           fprintf(ficgp,")");       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
         }       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);       and mw[mi+1][i]. dh depends on stepm.
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");       */
         i=i+ncovmodel;  
        }    int i, mi, m;
      }    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
    }       double sum=0., jmean=0.;*/
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    int first;
    }    int j, k=0,jk, ju, jl;
        double sum=0.;
   fclose(ficgp);    first=0;
 }  /* end gnuplot */    jmin=1e+5;
     jmax=-1;
     jmean=0.;
 /*************** Moving average **************/    for(i=1; i<=imx; i++){
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){      mi=0;
       m=firstpass;
   int i, cpt, cptcod;      while(s[m][i] <= nlstate){
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
       for (i=1; i<=nlstate;i++)          mw[++mi][i]=m;
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)        if(m >=lastpass)
           mobaverage[(int)agedeb][i][cptcod]=0.;          break;
            else
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){          m++;
       for (i=1; i<=nlstate;i++){      }/* end while */
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){      if (s[m][i] > nlstate){
           for (cpt=0;cpt<=4;cpt++){        mi++;     /* Death is another wave */
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];        /* if(mi==0)  never been interviewed correctly before death */
           }           /* Only death is a correct wave */
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;        mw[mi][i]=m;
         }      }
       }  
     }      wav[i]=mi;
          if(mi==0){
 }        nbwarn++;
         if(first==0){
           printf("Warning! None valid information for:%ld line=%d (skipped) and may be others, see log file\n",num[i],i);
 /************** Forecasting ******************/          first=1;
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){        }
          if(first==1){
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;          fprintf(ficlog,"Warning! None valid information for:%ld line=%d (skipped)\n",num[i],i);
   int *popage;        }
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;      } /* end mi==0 */
   double *popeffectif,*popcount;    } /* End individuals */
   double ***p3mat;  
   char fileresf[FILENAMELENGTH];    for(i=1; i<=imx; i++){
       for(mi=1; mi<wav[i];mi++){
  agelim=AGESUP;        if (stepm <=0)
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;          dh[mi][i]=1;
         else{
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
              if (agedc[i] < 2*AGESUP) {
                j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   strcpy(fileresf,"f");              if(j==0) j=1;  /* Survives at least one month after exam */
   strcat(fileresf,fileres);              else if(j<0){
   if((ficresf=fopen(fileresf,"w"))==NULL) {                nberr++;
     printf("Problem with forecast resultfile: %s\n", fileresf);                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   }                j=1; /* Temporary Dangerous patch */
   printf("Computing forecasting: result on file '%s' \n", fileresf);                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. You MUST fix the contradiction between dates.\n",stepm);
                 fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
               }
   if (mobilav==1) {              k=k+1;
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              if (j >= jmax) jmax=j;
     movingaverage(agedeb, fage, ageminpar, mobaverage);              if (j <= jmin) jmin=j;
   }              sum=sum+j;
               /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   stepsize=(int) (stepm+YEARM-1)/YEARM;              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
   if (stepm<=12) stepsize=1;            }
            }
   agelim=AGESUP;          else{
              j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
   hstepm=1;  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
   hstepm=hstepm/stepm;  
   yp1=modf(dateintmean,&yp);            k=k+1;
   anprojmean=yp;            if (j >= jmax) jmax=j;
   yp2=modf((yp1*12),&yp);            else if (j <= jmin)jmin=j;
   mprojmean=yp;            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
   yp1=modf((yp2*30.5),&yp);            /*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]);*/
   jprojmean=yp;            if(j<0){
   if(jprojmean==0) jprojmean=1;              nberr++;
   if(mprojmean==0) jprojmean=1;              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
                fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);            }
              sum=sum+j;
   for(cptcov=1;cptcov<=i2;cptcov++){          }
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          jk= j/stepm;
       k=k+1;          jl= j -jk*stepm;
       fprintf(ficresf,"\n#******");          ju= j -(jk+1)*stepm;
       for(j=1;j<=cptcoveff;j++) {          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);            if(jl==0){
       }              dh[mi][i]=jk;
       fprintf(ficresf,"******\n");              bh[mi][i]=0;
       fprintf(ficresf,"# StartingAge FinalAge");            }else{ /* We want a negative bias in order to only have interpolation ie
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);                    * at the price of an extra matrix product in likelihood */
                    dh[mi][i]=jk+1;
                    bh[mi][i]=ju;
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {            }
         fprintf(ficresf,"\n");          }else{
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);              if(jl <= -ju){
               dh[mi][i]=jk;
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){              bh[mi][i]=jl;       /* bias is positive if real duration
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);                                   * is higher than the multiple of stepm and negative otherwise.
           nhstepm = nhstepm/hstepm;                                   */
                      }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            else{
           oldm=oldms;savm=savms;              dh[mi][i]=jk+1;
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                bh[mi][i]=ju;
                    }
           for (h=0; h<=nhstepm; h++){            if(dh[mi][i]==0){
             if (h==(int) (calagedate+YEARM*cpt)) {              dh[mi][i]=1; /* At least one step */
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);              bh[mi][i]=ju; /* At least one step */
             }              /*  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);*/
             for(j=1; j<=nlstate+ndeath;j++) {            }
               kk1=0.;kk2=0;          } /* end if mle */
               for(i=1; i<=nlstate;i++) {                      }
                 if (mobilav==1)      } /* end wave */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    }
                 else {    jmean=sum/k;
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
                 }    fprintf(ficlog,"Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);
                   }
               }  
               if (h==(int)(calagedate+12*cpt)){  /*********** Tricode ****************************/
                 fprintf(ficresf," %.3f", kk1);  void tricode(int *Tvar, int **nbcode, int imx)
                          {
               }    
             }    int Ndum[20],ij=1, k, j, i, maxncov=19;
           }    int cptcode=0;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    cptcoveff=0; 
         }   
       }    for (k=0; k<maxncov; k++) Ndum[k]=0;
     }    for (k=1; k<=7; k++) ncodemax[k]=0;
   }  
            for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                  modality*/ 
   fclose(ficresf);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
 }        Ndum[ij]++; /*store the modality */
 /************** Forecasting ******************/        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
 populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
                                           Tvar[j]. If V=sex and male is 0 and 
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;                                         female is 1, then  cptcode=1.*/
   int *popage;      }
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  
   double *popeffectif,*popcount;      for (i=0; i<=cptcode; i++) {
   double ***p3mat,***tabpop,***tabpopprev;        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 */
   char filerespop[FILENAMELENGTH];      }
   
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      ij=1; 
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      for (i=1; i<=ncodemax[j]; i++) {
   agelim=AGESUP;        for (k=0; k<= maxncov; k++) {
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;          if (Ndum[k] != 0) {
              nbcode[Tvar[j]][ij]=k; 
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);            /* 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; */
              
              ij++;
   strcpy(filerespop,"pop");          }
   strcat(filerespop,fileres);          if (ij > ncodemax[j]) break; 
   if((ficrespop=fopen(filerespop,"w"))==NULL) {        }  
     printf("Problem with forecast resultfile: %s\n", filerespop);      } 
   }    }  
   printf("Computing forecasting: result on file '%s' \n", filerespop);  
    for (k=0; k< maxncov; k++) Ndum[k]=0;
   if (cptcoveff==0) ncodemax[cptcoveff]=1;  
    for (i=1; i<=ncovmodel-2; i++) { 
   if (mobilav==1) {     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);     ij=Tvar[i];
     movingaverage(agedeb, fage, ageminpar, mobaverage);     Ndum[ij]++;
   }   }
   
   stepsize=(int) (stepm+YEARM-1)/YEARM;   ij=1;
   if (stepm<=12) stepsize=1;   for (i=1; i<= maxncov; i++) {
       if((Ndum[i]!=0) && (i<=ncovcol)){
   agelim=AGESUP;       Tvaraff[ij]=i; /*For printing */
         ij++;
   hstepm=1;     }
   hstepm=hstepm/stepm;   }
     
   if (popforecast==1) {   cptcoveff=ij-1; /*Number of simple covariates*/
     if((ficpop=fopen(popfile,"r"))==NULL) {  }
       printf("Problem with population file : %s\n",popfile);exit(0);  
     }  /*********** Health Expectancies ****************/
     popage=ivector(0,AGESUP);  
     popeffectif=vector(0,AGESUP);  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,char strstart[] )
     popcount=vector(0,AGESUP);  
      {
     i=1;      /* Health expectancies */
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
        double age, agelim, hf;
     imx=i;    double ***p3mat,***varhe;
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    double **dnewm,**doldm;
   }    double *xp;
     double **gp, **gm;
   for(cptcov=1;cptcov<=i2;cptcov++){    double ***gradg, ***trgradg;
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    int theta;
       k=k+1;  
       fprintf(ficrespop,"\n#******");    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
       for(j=1;j<=cptcoveff;j++) {    xp=vector(1,npar);
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    dnewm=matrix(1,nlstate*nlstate,1,npar);
       }    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
       fprintf(ficrespop,"******\n");    
       fprintf(ficrespop,"# Age");    fprintf(ficreseij,"# Local time at start: %s", strstart);
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);    fprintf(ficreseij,"# Health expectancies\n");
       if (popforecast==1)  fprintf(ficrespop," [Population]");    fprintf(ficreseij,"# Age");
          for(i=1; i<=nlstate;i++)
       for (cpt=0; cpt<=0;cpt++) {      for(j=1; j<=nlstate;j++)
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          fprintf(ficreseij," %1d-%1d (SE)",i,j);
            fprintf(ficreseij,"\n");
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    if(estepm < stepm){
           nhstepm = nhstepm/hstepm;      printf ("Problem %d lower than %d\n",estepm, stepm);
              }
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    else  hstepm=estepm;   
           oldm=oldms;savm=savms;    /* We compute the life expectancy from trapezoids spaced every estepm months
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);       * This is mainly to measure the difference between two models: for example
             * if stepm=24 months pijx are given only every 2 years and by summing them
           for (h=0; h<=nhstepm; h++){     * we are calculating an estimate of the Life Expectancy assuming a linear 
             if (h==(int) (calagedate+YEARM*cpt)) {     * progression in between and thus overestimating or underestimating according
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);     * to the curvature of the survival function. If, for the same date, we 
             }     * estimate the model with stepm=1 month, we can keep estepm to 24 months
             for(j=1; j<=nlstate+ndeath;j++) {     * to compare the new estimate of Life expectancy with the same linear 
               kk1=0.;kk2=0;     * hypothesis. A more precise result, taking into account a more precise
               for(i=1; i<=nlstate;i++) {                   * curvature will be obtained if estepm is as small as stepm. */
                 if (mobilav==1)  
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    /* For example we decided to compute the life expectancy with the smallest unit */
                 else {    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];       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
               if (h==(int)(calagedate+12*cpt)){       and note for a fixed period like estepm months */
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
                   /*fprintf(ficrespop," %.3f", kk1);       survival function given by stepm (the optimization length). Unfortunately it
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/       means that if the survival funtion is printed only each two years of age and if
               }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
             }       results. So we changed our mind and took the option of the best precision.
             for(i=1; i<=nlstate;i++){    */
               kk1=0.;    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
                 for(j=1; j<=nlstate;j++){  
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];    agelim=AGESUP;
                 }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];      /* nhstepm age range expressed in number of stepm */
             }      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
       /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)      /* if (stepm >= YEARM) hstepm=1;*/
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
           }      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
         }      gp=matrix(0,nhstepm,1,nlstate*nlstate);
       }      gm=matrix(0,nhstepm,1,nlstate*nlstate);
    
   /******/      /* Computed by stepm unit matrices, product of hstepm matrices, stored
          in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);     
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           nhstepm = nhstepm/hstepm;  
                /* Computing  Variances of health expectancies */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           oldm=oldms;savm=savms;       for(theta=1; theta <=npar; theta++){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          for(i=1; i<=npar; i++){ 
           for (h=0; h<=nhstepm; h++){          xp[i] = x[i] + (i==theta ?delti[theta]:0);
             if (h==(int) (calagedate+YEARM*cpt)) {        }
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
             }    
             for(j=1; j<=nlstate+ndeath;j++) {        cptj=0;
               kk1=0.;kk2=0;        for(j=1; j<= nlstate; j++){
               for(i=1; i<=nlstate;i++) {                        for(i=1; i<=nlstate; i++){
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];                cptj=cptj+1;
               }            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
             }            }
           }          }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        }
         }       
       }       
    }        for(i=1; i<=npar; i++) 
   }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
          hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        
         cptj=0;
   if (popforecast==1) {        for(j=1; j<= nlstate; j++){
     free_ivector(popage,0,AGESUP);          for(i=1;i<=nlstate;i++){
     free_vector(popeffectif,0,AGESUP);            cptj=cptj+1;
     free_vector(popcount,0,AGESUP);            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   }  
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            }
   fclose(ficrespop);          }
 }        }
         for(j=1; j<= nlstate*nlstate; j++)
 /***********************************************/          for(h=0; h<=nhstepm-1; h++){
 /**************** Main Program *****************/            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
 /***********************************************/          }
        } 
 int main(int argc, char *argv[])     
 {  /* End theta */
   
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   double agedeb, agefin,hf;  
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;       for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*nlstate;j++)
   double fret;          for(theta=1; theta <=npar; theta++)
   double **xi,tmp,delta;            trgradg[h][j][theta]=gradg[h][theta][j];
        
   double dum; /* Dummy variable */  
   double ***p3mat;       for(i=1;i<=nlstate*nlstate;i++)
   int *indx;        for(j=1;j<=nlstate*nlstate;j++)
   char line[MAXLINE], linepar[MAXLINE];          varhe[i][j][(int)age] =0.;
   char title[MAXLINE];  
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];       printf("%d|",(int)age);fflush(stdout);
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
         for(h=0;h<=nhstepm-1;h++){
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];        for(k=0;k<=nhstepm-1;k++){
           matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
   char filerest[FILENAMELENGTH];          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   char fileregp[FILENAMELENGTH];          for(i=1;i<=nlstate*nlstate;i++)
   char popfile[FILENAMELENGTH];            for(j=1;j<=nlstate*nlstate;j++)
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
   int firstobs=1, lastobs=10;        }
   int sdeb, sfin; /* Status at beginning and end */      }
   int c,  h , cpt,l;      /* Computing expectancies */
   int ju,jl, mi;      for(i=1; i<=nlstate;i++)
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;        for(j=1; j<=nlstate;j++)
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   int mobilav=0,popforecast=0;            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   int hstepm, nhstepm;            
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1;  /* 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]);*/
   
   double bage, fage, age, agelim, agebase;          }
   double ftolpl=FTOL;  
   double **prlim;      fprintf(ficreseij,"%3.0f",age );
   double *severity;      cptj=0;
   double ***param; /* Matrix of parameters */      for(i=1; i<=nlstate;i++)
   double  *p;        for(j=1; j<=nlstate;j++){
   double **matcov; /* Matrix of covariance */          cptj++;
   double ***delti3; /* Scale */          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   double *delti; /* Scale */        }
   double ***eij, ***vareij;      fprintf(ficreseij,"\n");
   double **varpl; /* Variances of prevalence limits by age */     
   double *epj, vepp;      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   double kk1, kk2;      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
        free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   char version[80]="Imach version 0.8b, March 2002, INED-EUROREVES ";    }
   char *alph[]={"a","a","b","c","d","e"}, str[4];    printf("\n");
     fprintf(ficlog,"\n");
   
   char z[1]="c", occ;    free_vector(xp,1,npar);
 #include <sys/time.h>    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
 #include <time.h>    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
    }
   /* long total_usecs;  
   struct timeval start_time, end_time;  /************ Variance ******************/
    void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */  {
   getcwd(pathcd, size);    /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
   printf("\n%s",version);    /* double **newm;*/
   if(argc <=1){    double **dnewm,**doldm;
     printf("\nEnter the parameter file name: ");    double **dnewmp,**doldmp;
     scanf("%s",pathtot);    int i, j, nhstepm, hstepm, h, nstepm ;
   }    int k, cptcode;
   else{    double *xp;
     strcpy(pathtot,argv[1]);    double **gp, **gm;  /* for var eij */
   }    double ***gradg, ***trgradg; /*for var eij */
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    double **gradgp, **trgradgp; /* for var p point j */
   /*cygwin_split_path(pathtot,path,optionfile);    double *gpp, *gmp; /* for var p point j */
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   /* cutv(path,optionfile,pathtot,'\\');*/    double ***p3mat;
     double age,agelim, hf;
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);    double ***mobaverage;
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    int theta;
   chdir(path);    char digit[4];
   replace(pathc,path);    char digitp[25];
   
 /*-------- arguments in the command line --------*/    char fileresprobmorprev[FILENAMELENGTH];
   
   strcpy(fileres,"r");    if(popbased==1){
   strcat(fileres, optionfilefiname);      if(mobilav!=0)
   strcat(fileres,".txt");    /* Other files have txt extension */        strcpy(digitp,"-populbased-mobilav-");
       else strcpy(digitp,"-populbased-nomobil-");
   /*---------arguments file --------*/    }
     else 
   if((ficpar=fopen(optionfile,"r"))==NULL)    {      strcpy(digitp,"-stablbased-");
     printf("Problem with optionfile %s\n",optionfile);  
     goto end;    if (mobilav!=0) {
   }      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   strcpy(filereso,"o");        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   strcat(filereso,fileres);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   if((ficparo=fopen(filereso,"w"))==NULL) {      }
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    }
   }  
     strcpy(fileresprobmorprev,"prmorprev"); 
   /* Reads comments: lines beginning with '#' */    sprintf(digit,"%-d",ij);
   while((c=getc(ficpar))=='#' && c!= EOF){    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     ungetc(c,ficpar);    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     fgets(line, MAXLINE, ficpar);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     puts(line);    strcat(fileresprobmorprev,fileres);
     fputs(line,ficparo);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   }      printf("Problem with resultfile: %s\n", fileresprobmorprev);
   ungetc(c,ficpar);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
   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);    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   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,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
 while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
     ungetc(c,ficpar);    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);
     fgets(line, MAXLINE, ficpar);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     puts(line);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     fputs(line,ficparo);      fprintf(ficresprobmorprev," p.%-d SE",j);
   }      for(i=1; i<=nlstate;i++)
   ungetc(c,ficpar);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
      }  
        fprintf(ficresprobmorprev,"\n");
   covar=matrix(0,NCOVMAX,1,n);    fprintf(ficgp,"\n# Routine varevsij");
   cptcovn=0;    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    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);
   ncovmodel=2+cptcovn;  /*   } */
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     fprintf(ficresvij, "#Local time at start: %s", strstart);
   /* Read guess parameters */    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");
   /* Reads comments: lines beginning with '#' */    fprintf(ficresvij,"# Age");
   while((c=getc(ficpar))=='#' && c!= EOF){    for(i=1; i<=nlstate;i++)
     ungetc(c,ficpar);      for(j=1; j<=nlstate;j++)
     fgets(line, MAXLINE, ficpar);        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
     puts(line);    fprintf(ficresvij,"\n");
     fputs(line,ficparo);  
   }    xp=vector(1,npar);
   ungetc(c,ficpar);    dnewm=matrix(1,nlstate,1,npar);
      doldm=matrix(1,nlstate,1,nlstate);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     for(i=1; i <=nlstate; i++)    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     for(j=1; j <=nlstate+ndeath-1; j++){  
       fscanf(ficpar,"%1d%1d",&i1,&j1);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
       fprintf(ficparo,"%1d%1d",i1,j1);    gpp=vector(nlstate+1,nlstate+ndeath);
       printf("%1d%1d",i,j);    gmp=vector(nlstate+1,nlstate+ndeath);
       for(k=1; k<=ncovmodel;k++){    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
         fscanf(ficpar," %lf",&param[i][j][k]);    
         printf(" %lf",param[i][j][k]);    if(estepm < stepm){
         fprintf(ficparo," %lf",param[i][j][k]);      printf ("Problem %d lower than %d\n",estepm, stepm);
       }    }
       fscanf(ficpar,"\n");    else  hstepm=estepm;   
       printf("\n");    /* For example we decided to compute the life expectancy with the smallest unit */
       fprintf(ficparo,"\n");    /* 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. 
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;       Look at hpijx to understand the reason of that which relies in memory size
        and note for a fixed period like k years */
   p=param[1][1];    /* 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
   /* Reads comments: lines beginning with '#' */       means that if the survival funtion is printed every two years of age and if
   while((c=getc(ficpar))=='#' && c!= EOF){       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     ungetc(c,ficpar);       results. So we changed our mind and took the option of the best precision.
     fgets(line, MAXLINE, ficpar);    */
     puts(line);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     fputs(line,ficparo);    agelim = AGESUP;
   }    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   ungetc(c,ficpar);      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   for(i=1; i <=nlstate; i++){      gp=matrix(0,nhstepm,1,nlstate);
     for(j=1; j <=nlstate+ndeath-1; j++){      gm=matrix(0,nhstepm,1,nlstate);
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       printf("%1d%1d",i,j);  
       fprintf(ficparo,"%1d%1d",i1,j1);      for(theta=1; theta <=npar; theta++){
       for(k=1; k<=ncovmodel;k++){        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
         fscanf(ficpar,"%le",&delti3[i][j][k]);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         printf(" %le",delti3[i][j][k]);        }
         fprintf(ficparo," %le",delti3[i][j][k]);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       fscanf(ficpar,"\n");  
       printf("\n");        if (popbased==1) {
       fprintf(ficparo,"\n");          if(mobilav ==0){
     }            for(i=1; i<=nlstate;i++)
   }              prlim[i][i]=probs[(int)age][i][ij];
   delti=delti3[1][1];          }else{ /* mobilav */ 
              for(i=1; i<=nlstate;i++)
   /* Reads comments: lines beginning with '#' */              prlim[i][i]=mobaverage[(int)age][i][ij];
   while((c=getc(ficpar))=='#' && c!= EOF){          }
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);    
     puts(line);        for(j=1; j<= nlstate; j++){
     fputs(line,ficparo);          for(h=0; h<=nhstepm; h++){
   }            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   ungetc(c,ficpar);              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
            }
   matcov=matrix(1,npar,1,npar);        }
   for(i=1; i <=npar; i++){        /* This for computing probability of death (h=1 means
     fscanf(ficpar,"%s",&str);           computed over hstepm matrices product = hstepm*stepm months) 
     printf("%s",str);           as a weighted average of prlim.
     fprintf(ficparo,"%s",str);        */
     for(j=1; j <=i; j++){        for(j=nlstate+1;j<=nlstate+ndeath;j++){
       fscanf(ficpar," %le",&matcov[i][j]);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
       printf(" %.5le",matcov[i][j]);            gpp[j] += prlim[i][i]*p3mat[i][j][1];
       fprintf(ficparo," %.5le",matcov[i][j]);        }    
     }        /* end probability of death */
     fscanf(ficpar,"\n");  
     printf("\n");        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
     fprintf(ficparo,"\n");          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   for(i=1; i <=npar; i++)        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     for(j=i+1;j<=npar;j++)   
       matcov[i][j]=matcov[j][i];        if (popbased==1) {
              if(mobilav ==0){
   printf("\n");            for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
     /*-------- Rewriting paramater file ----------*/            for(i=1; i<=nlstate;i++)
      strcpy(rfileres,"r");    /* "Rparameterfile */              prlim[i][i]=mobaverage[(int)age][i][ij];
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/          }
      strcat(rfileres,".");    /* */        }
      strcat(rfileres,optionfilext);    /* Other files have txt extension */  
     if((ficres =fopen(rfileres,"w"))==NULL) {        for(j=1; j<= nlstate; j++){
       printf("Problem writing new parameter file: %s\n", fileres);goto end;          for(h=0; h<=nhstepm; h++){
     }            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
     fprintf(ficres,"#%s\n",version);              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
              }
     /*-------- data file ----------*/        }
     if((fic=fopen(datafile,"r"))==NULL)    {        /* This for computing probability of death (h=1 means
       printf("Problem with datafile: %s\n", datafile);goto end;           computed over hstepm matrices product = hstepm*stepm months) 
     }           as a weighted average of prlim.
         */
     n= lastobs;        for(j=nlstate+1;j<=nlstate+ndeath;j++){
     severity = vector(1,maxwav);          for(i=1,gmp[j]=0.; i<= nlstate; i++)
     outcome=imatrix(1,maxwav+1,1,n);           gmp[j] += prlim[i][i]*p3mat[i][j][1];
     num=ivector(1,n);        }    
     moisnais=vector(1,n);        /* end probability of death */
     annais=vector(1,n);  
     moisdc=vector(1,n);        for(j=1; j<= nlstate; j++) /* vareij */
     andc=vector(1,n);          for(h=0; h<=nhstepm; h++){
     agedc=vector(1,n);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     cod=ivector(1,n);          }
     weight=vector(1,n);  
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
     mint=matrix(1,maxwav,1,n);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
     anint=matrix(1,maxwav,1,n);        }
     s=imatrix(1,maxwav+1,1,n);  
     adl=imatrix(1,maxwav+1,1,n);          } /* End theta */
     tab=ivector(1,NCOVMAX);  
     ncodemax=ivector(1,8);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
     i=1;      for(h=0; h<=nhstepm; h++) /* veij */
     while (fgets(line, MAXLINE, fic) != NULL)    {        for(j=1; j<=nlstate;j++)
       if ((i >= firstobs) && (i <=lastobs)) {          for(theta=1; theta <=npar; theta++)
                    trgradg[h][j][theta]=gradg[h][theta][j];
         for (j=maxwav;j>=1;j--){  
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
           strcpy(line,stra);        for(theta=1; theta <=npar; theta++)
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          trgradgp[j][theta]=gradgp[theta][j];
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);    
         }  
              hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);      for(i=1;i<=nlstate;i++)
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);        for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);  
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);      for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
         for (j=ncovcol;j>=1;j--){          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);          for(i=1;i<=nlstate;i++)
         }            for(j=1;j<=nlstate;j++)
         num[i]=atol(stra);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
                }
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){      }
           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;}*/    
       /* pptj */
         i=i+1;      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       }      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
     }      for(j=nlstate+1;j<=nlstate+ndeath;j++)
     /* printf("ii=%d", ij);        for(i=nlstate+1;i<=nlstate+ndeath;i++)
        scanf("%d",i);*/          varppt[j][i]=doldmp[j][i];
   imx=i-1; /* Number of individuals */      /* end ppptj */
       /*  x centered again */
   /* for (i=1; i<=imx; i++){      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
     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;      if (popbased==1) {
     }*/        if(mobilav ==0){
            for(i=1; i<=nlstate;i++)
   /* for (i=1; i<=imx; i++){            prlim[i][i]=probs[(int)age][i][ij];
      if (s[4][i]==9)  s[4][i]=-1;        }else{ /* mobilav */ 
      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(i=1; i<=nlstate;i++)
   */            prlim[i][i]=mobaverage[(int)age][i][ij];
          }
   /* Calculation of the number of parameter from char model*/      }
   Tvar=ivector(1,15);               
   Tprod=ivector(1,15);      /* This for computing probability of death (h=1 means
   Tvaraff=ivector(1,15);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
   Tvard=imatrix(1,15,1,2);         as a weighted average of prlim.
   Tage=ivector(1,15);            */
          for(j=nlstate+1;j<=nlstate+ndeath;j++){
   if (strlen(model) >1){        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
     j=0, j1=0, k1=1, k2=1;          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
     j=nbocc(model,'+');      }    
     j1=nbocc(model,'*');      /* end probability of death */
     cptcovn=j+1;  
     cptcovprod=j1;      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
          for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     strcpy(modelsav,model);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){        for(i=1; i<=nlstate;i++){
       printf("Error. Non available option model=%s ",model);          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
       goto end;        }
     }      } 
          fprintf(ficresprobmorprev,"\n");
     for(i=(j+1); i>=1;i--){  
       cutv(stra,strb,modelsav,'+');      fprintf(ficresvij,"%.0f ",age );
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);      for(i=1; i<=nlstate;i++)
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/        for(j=1; j<=nlstate;j++){
       /*scanf("%d",i);*/          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
       if (strchr(strb,'*')) {        }
         cutv(strd,strc,strb,'*');      fprintf(ficresvij,"\n");
         if (strcmp(strc,"age")==0) {      free_matrix(gp,0,nhstepm,1,nlstate);
           cptcovprod--;      free_matrix(gm,0,nhstepm,1,nlstate);
           cutv(strb,stre,strd,'V');      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
           Tvar[i]=atoi(stre);      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
           cptcovage++;      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             Tage[cptcovage]=i;    } /* End age */
             /*printf("stre=%s ", stre);*/    free_vector(gpp,nlstate+1,nlstate+ndeath);
         }    free_vector(gmp,nlstate+1,nlstate+ndeath);
         else if (strcmp(strd,"age")==0) {    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
           cptcovprod--;    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
           cutv(strb,stre,strc,'V');    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
           Tvar[i]=atoi(stre);    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
           cptcovage++;    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
           Tage[cptcovage]=i;  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
         }  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
         else {  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
           cutv(strb,stre,strc,'V');    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
           Tvar[i]=ncovcol+k1;    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
           cutv(strb,strc,strd,'V');    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
           Tprod[k1]=i;    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
           Tvard[k1][1]=atoi(strc);    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);
           Tvard[k1][2]=atoi(stre);    /*  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);
           Tvar[cptcovn+k2]=Tvard[k1][1];  */
           Tvar[cptcovn+k2+1]=Tvard[k1][2];  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
           for (k=1; k<=lastobs;k++)    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];  
           k1++;    free_vector(xp,1,npar);
           k2=k2+2;    free_matrix(doldm,1,nlstate,1,nlstate);
         }    free_matrix(dnewm,1,nlstate,1,npar);
       }    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       else {    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
        /*  scanf("%d",i);*/    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       cutv(strd,strc,strb,'V');    fclose(ficresprobmorprev);
       Tvar[i]=atoi(strc);    fflush(ficgp);
       }    fflush(fichtm); 
       strcpy(modelsav,stra);    }  /* end varevsij */
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);  
         scanf("%d",i);*/  /************ 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, char strstart[])
 }  {
      /* Variance of prevalence limit */
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
   printf("cptcovprod=%d ", cptcovprod);    double **newm;
   scanf("%d ",i);*/    double **dnewm,**doldm;
     fclose(fic);    int i, j, nhstepm, hstepm;
     int k, cptcode;
     /*  if(mle==1){*/    double *xp;
     if (weightopt != 1) { /* Maximisation without weights*/    double *gp, *gm;
       for(i=1;i<=n;i++) weight[i]=1.0;    double **gradg, **trgradg;
     }    double age,agelim;
     /*-calculation of age at interview from date of interview and age at death -*/    int theta;
     agev=matrix(1,maxwav,1,imx);    fprintf(ficresvpl, "#Local time at start: %s", strstart); 
     fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
     for (i=1; i<=imx; i++) {    fprintf(ficresvpl,"# Age");
       for(m=2; (m<= maxwav); m++) {    for(i=1; i<=nlstate;i++)
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){        fprintf(ficresvpl," %1d-%1d",i,i);
          anint[m][i]=9999;    fprintf(ficresvpl,"\n");
          s[m][i]=-1;  
        }    xp=vector(1,npar);
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;    dnewm=matrix(1,nlstate,1,npar);
       }    doldm=matrix(1,nlstate,1,nlstate);
     }    
     hstepm=1*YEARM; /* Every year of age */
     for (i=1; i<=imx; i++)  {    hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    agelim = AGESUP;
       for(m=1; (m<= maxwav); m++){    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
         if(s[m][i] >0){      nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
           if (s[m][i] >= nlstate+1) {      if (stepm >= YEARM) hstepm=1;
             if(agedc[i]>0)      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
               if(moisdc[i]!=99 && andc[i]!=9999)      gradg=matrix(1,npar,1,nlstate);
                 agev[m][i]=agedc[i];      gp=vector(1,nlstate);
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/      gm=vector(1,nlstate);
            else {  
               if (andc[i]!=9999){      for(theta=1; theta <=npar; theta++){
               printf("Warning negative age at death: %d line:%d\n",num[i],i);        for(i=1; i<=npar; i++){ /* Computes gradient */
               agev[m][i]=-1;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
               }        }
             }        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
           }        for(i=1;i<=nlstate;i++)
           else if(s[m][i] !=9){ /* Should no more exist */          gp[i] = prlim[i][i];
             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)        for(i=1; i<=npar; i++) /* Computes gradient */
               agev[m][i]=1;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
             else if(agev[m][i] <agemin){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
               agemin=agev[m][i];        for(i=1;i<=nlstate;i++)
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/          gm[i] = prlim[i][i];
             }  
             else if(agev[m][i] >agemax){        for(i=1;i<=nlstate;i++)
               agemax=agev[m][i];          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/      } /* End theta */
             }  
             /*agev[m][i]=anint[m][i]-annais[i];*/      trgradg =matrix(1,nlstate,1,npar);
             /*   agev[m][i] = age[i]+2*m;*/  
           }      for(j=1; j<=nlstate;j++)
           else { /* =9 */        for(theta=1; theta <=npar; theta++)
             agev[m][i]=1;          trgradg[j][theta]=gradg[theta][j];
             s[m][i]=-1;  
           }      for(i=1;i<=nlstate;i++)
         }        varpl[i][(int)age] =0.;
         else /*= 0 Unknown */      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
           agev[m][i]=1;      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       }      for(i=1;i<=nlstate;i++)
            varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
     }  
     for (i=1; i<=imx; i++)  {      fprintf(ficresvpl,"%.0f ",age );
       for(m=1; (m<= maxwav); m++){      for(i=1; i<=nlstate;i++)
         if (s[m][i] > (nlstate+ndeath)) {        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
           printf("Error: Wrong value in nlstate or ndeath\n");        fprintf(ficresvpl,"\n");
           goto end;      free_vector(gp,1,nlstate);
         }      free_vector(gm,1,nlstate);
       }      free_matrix(gradg,1,npar,1,nlstate);
     }      free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);  
     free_vector(xp,1,npar);
     free_vector(severity,1,maxwav);    free_matrix(doldm,1,nlstate,1,npar);
     free_imatrix(outcome,1,maxwav+1,1,n);    free_matrix(dnewm,1,nlstate,1,nlstate);
     free_vector(moisnais,1,n);  
     free_vector(annais,1,n);  }
     /* free_matrix(mint,1,maxwav,1,n);  
        free_matrix(anint,1,maxwav,1,n);*/  /************ Variance of one-step probabilities  ******************/
     free_vector(moisdc,1,n);  void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
     free_vector(andc,1,n);  {
     int i, j=0,  i1, k1, l1, t, tj;
        int k2, l2, j1,  z1;
     wav=ivector(1,imx);    int k=0,l, cptcode;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    int first=1, first1;
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
        double **dnewm,**doldm;
     /* Concatenates waves */    double *xp;
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
       Tcode=ivector(1,100);    double age,agelim, cov[NCOVMAX];
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
       ncodemax[1]=1;    int theta;
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    char fileresprob[FILENAMELENGTH];
          char fileresprobcov[FILENAMELENGTH];
    codtab=imatrix(1,100,1,10);    char fileresprobcor[FILENAMELENGTH];
    h=0;  
    m=pow(2,cptcoveff);    double ***varpij;
    
    for(k=1;k<=cptcoveff; k++){    strcpy(fileresprob,"prob"); 
      for(i=1; i <=(m/pow(2,k));i++){    strcat(fileresprob,fileres);
        for(j=1; j <= ncodemax[k]; j++){    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){      printf("Problem with resultfile: %s\n", fileresprob);
            h++;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
            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]);*/    strcpy(fileresprobcov,"probcov"); 
          }    strcat(fileresprobcov,fileres);
        }    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
      }      printf("Problem with resultfile: %s\n", fileresprobcov);
    }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);    }
       codtab[1][2]=1;codtab[2][2]=2; */    strcpy(fileresprobcor,"probcor"); 
    /* for(i=1; i <=m ;i++){    strcat(fileresprobcor,fileres);
       for(k=1; k <=cptcovn; k++){    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);      printf("Problem with resultfile: %s\n", fileresprobcor);
       }      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
       printf("\n");    }
       }    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
       scanf("%d",i);*/    fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
        printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
    /* Calculates basic frequencies. Computes observed prevalence at single age    fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
        and prints on file fileres'p'. */    printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
        fprintf(ficresprob, "#Local time at start: %s", strstart);
        fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficresprob,"# Age");
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficresprobcov, "#Local time at start: %s", strstart);
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficresprobcov,"# Age");
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    fprintf(ficresprobcor, "#Local time at start: %s", strstart);
          fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     /* For Powell, parameters are in a vector p[] starting at p[1]    fprintf(ficresprobcov,"# Age");
        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) */  
     for(i=1; i<=nlstate;i++)
     if(mle==1){      for(j=1; j<=(nlstate+ndeath);j++){
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
     }        fprintf(ficresprobcov," p%1d-%1d ",i,j);
            fprintf(ficresprobcor," p%1d-%1d ",i,j);
     /*--------- results files --------------*/      }  
     fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);   /* fprintf(ficresprob,"\n");
      fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    jk=1;   */
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");   xp=vector(1,npar);
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
    for(i=1,jk=1; i <=nlstate; i++){    doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
      for(k=1; k <=(nlstate+ndeath); k++){    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
        if (k != i)    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
          {    first=1;
            printf("%d%d ",i,k);    fprintf(ficgp,"\n# Routine varprob");
            fprintf(ficres,"%1d%1d ",i,k);    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
            for(j=1; j <=ncovmodel; j++){    fprintf(fichtm,"\n");
              printf("%f ",p[jk]);  
              fprintf(ficres,"%f ",p[jk]);    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
              jk++;    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
            }    file %s<br>\n",optionfilehtmcov);
            printf("\n");    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
            fprintf(ficres,"\n");  and drawn. It helps understanding how is the covariance between two incidences.\
          }   They are expressed in year<sup>-1</sup> in order to be less dependent of stepm.<br>\n");
      }    fprintf(fichtmcov,"\n<br> Contour plot corresponding to x'cov<sup>-1</sup>x = 4 (where x is the column vector (pij,pkl)) are drawn. \
    }  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
  if(mle==1){  would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
     /* Computing hessian and covariance matrix */  standard deviations wide on each axis. <br>\
     ftolhess=ftol; /* Usually correct */   Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
     hesscov(matcov, p, npar, delti, ftolhess, func);   and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
  }  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");  
     printf("# Scales (for hessian or gradient estimation)\n");    cov[1]=1;
      for(i=1,jk=1; i <=nlstate; i++){    tj=cptcoveff;
       for(j=1; j <=nlstate+ndeath; j++){    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
         if (j!=i) {    j1=0;
           fprintf(ficres,"%1d%1d",i,j);    for(t=1; t<=tj;t++){
           printf("%1d%1d",i,j);      for(i1=1; i1<=ncodemax[t];i1++){ 
           for(k=1; k<=ncovmodel;k++){        j1++;
             printf(" %.5e",delti[jk]);        if  (cptcovn>0) {
             fprintf(ficres," %.5e",delti[jk]);          fprintf(ficresprob, "\n#********** Variable "); 
             jk++;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           }          fprintf(ficresprob, "**********\n#\n");
           printf("\n");          fprintf(ficresprobcov, "\n#********** Variable "); 
           fprintf(ficres,"\n");          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         }          fprintf(ficresprobcov, "**********\n#\n");
       }          
      }          fprintf(ficgp, "\n#********** Variable "); 
              for (z1=1; z1<=cptcoveff; z1++) fprintf(ficgp, " V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     k=1;          fprintf(ficgp, "**********\n#\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");          
     printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");          
     for(i=1;i<=npar;i++){          fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
       /*  if (k>nlstate) k=1;          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       i1=(i-1)/(ncovmodel*nlstate)+1;          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);          
       printf("%s%d%d",alph[k],i1,tab[i]);*/          fprintf(ficresprobcor, "\n#********** Variable ");    
       fprintf(ficres,"%3d",i);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       printf("%3d",i);          fprintf(ficresprobcor, "**********\n#");    
       for(j=1; j<=i;j++){        }
         fprintf(ficres," %.5e",matcov[i][j]);        
         printf(" %.5e",matcov[i][j]);        for (age=bage; age<=fage; age ++){ 
       }          cov[2]=age;
       fprintf(ficres,"\n");          for (k=1; k<=cptcovn;k++) {
       printf("\n");            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
       k++;          }
     }          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
              for (k=1; k<=cptcovprod;k++)
     while((c=getc(ficpar))=='#' && c!= EOF){            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       ungetc(c,ficpar);          
       fgets(line, MAXLINE, ficpar);          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
       puts(line);          trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
       fputs(line,ficparo);          gp=vector(1,(nlstate)*(nlstate+ndeath));
     }          gm=vector(1,(nlstate)*(nlstate+ndeath));
     ungetc(c,ficpar);      
     estepm=0;          for(theta=1; theta <=npar; theta++){
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);            for(i=1; i<=npar; i++)
     if (estepm==0 || estepm < stepm) estepm=stepm;              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
     if (fage <= 2) {            
       bage = ageminpar;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
       fage = agemaxpar;            
     }            k=0;
                for(i=1; i<= (nlstate); i++){
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");              for(j=1; j<=(nlstate+ndeath);j++){
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                k=k+1;
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);                gp[k]=pmmij[i][j];
                }
     while((c=getc(ficpar))=='#' && c!= EOF){            }
     ungetc(c,ficpar);            
     fgets(line, MAXLINE, ficpar);            for(i=1; i<=npar; i++)
     puts(line);              xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
     fputs(line,ficparo);      
   }            pmij(pmmij,cov,ncovmodel,xp,nlstate);
   ungetc(c,ficpar);            k=0;
              for(i=1; i<=(nlstate); i++){
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);              for(j=1; j<=(nlstate+ndeath);j++){
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                k=k+1;
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);                gm[k]=pmmij[i][j];
                    }
   while((c=getc(ficpar))=='#' && c!= EOF){            }
     ungetc(c,ficpar);       
     fgets(line, MAXLINE, ficpar);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
     puts(line);              gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
     fputs(line,ficparo);          }
   }  
   ungetc(c,ficpar);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
              for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
    dateprev1=anprev1+mprev1/12.+jprev1/365.;          
    dateprev2=anprev2+mprev2/12.+jprev2/365.;          matprod2(dnewm,trgradg,1,(nlstate)*(nlstate+ndeath),1,npar,1,npar,matcov); 
           matprod2(doldm,dnewm,1,(nlstate)*(nlstate+ndeath),1,npar,1,(nlstate)*(nlstate+ndeath),gradg);
   fscanf(ficpar,"pop_based=%d\n",&popbased);          free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
   fprintf(ficparo,"pop_based=%d\n",popbased);            free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
   fprintf(ficres,"pop_based=%d\n",popbased);            free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
            free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);          pmij(pmmij,cov,ncovmodel,x,nlstate);
     fgets(line, MAXLINE, ficpar);          
     puts(line);          k=0;
     fputs(line,ficparo);          for(i=1; i<=(nlstate); i++){
   }            for(j=1; j<=(nlstate+ndeath);j++){
   ungetc(c,ficpar);              k=k+1;
               mu[k][(int) age]=pmmij[i][j];
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);            }
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);          }
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
 while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);          /*printf("\n%d ",(int)age);
     fgets(line, MAXLINE, ficpar);            for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
     puts(line);            printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     fputs(line,ficparo);            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
   }            }*/
   ungetc(c,ficpar);  
           fprintf(ficresprob,"\n%d ",(int)age);
   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(ficresprobcov,"\n%d ",(int)age);
   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(ficresprobcor,"\n%d ",(int)age);
   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 (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
 /*------------ gnuplot -------------*/            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);            fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
            }
 /*------------ free_vector  -------------*/          i=0;
  chdir(path);          for (k=1; k<=(nlstate);k++){
              for (l=1; l<=(nlstate+ndeath);l++){ 
  free_ivector(wav,1,imx);              i=i++;
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);                fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
  free_ivector(num,1,n);              for (j=1; j<=i;j++){
  free_vector(agedc,1,n);                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
  /*free_matrix(covar,1,NCOVMAX,1,n);*/                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
  fclose(ficparo);              }
  fclose(ficres);            }
           }/* end of loop for state */
 /*--------- index.htm --------*/        } /* end of loop for age */
   
   printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm);        /* Confidence intervalle of pij  */
         /*
            fprintf(ficgp,"\nset noparametric;unset label");
   /*--------------- Prevalence limit --------------*/          fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
            fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
   strcpy(filerespl,"pl");          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);
   strcat(filerespl,fileres);          fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
   if((ficrespl=fopen(filerespl,"w"))==NULL) {          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;          fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
   }        */
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);  
   fprintf(ficrespl,"#Prevalence limit\n");        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
   fprintf(ficrespl,"#Age ");        first1=1;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);        for (k2=1; k2<=(nlstate);k2++){
   fprintf(ficrespl,"\n");          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
              if(l2==k2) continue;
   prlim=matrix(1,nlstate,1,nlstate);            j=(k2-1)*(nlstate+ndeath)+l2;
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            for (k1=1; k1<=(nlstate);k1++){
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                if(l1==k1) continue;
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                i=(k1-1)*(nlstate+ndeath)+l1;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */                if(i<=j) continue;
   k=0;                for (age=bage; age<=fage; age ++){ 
   agebase=ageminpar;                  if ((int)age %5==0){
   agelim=agemaxpar;                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   ftolpl=1.e-10;                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
   i1=cptcoveff;                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
   if (cptcovn < 1){i1=1;}                    mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
   for(cptcov=1;cptcov<=i1;cptcov++){                    c12=cv12/sqrt(v1*v2);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                    /* Computing eigen value of matrix of covariance */
         k=k+1;                    lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/                    lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
         fprintf(ficrespl,"\n#******");                    /* Eigen vectors */
         for(j=1;j<=cptcoveff;j++)                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    /*v21=sqrt(1.-v11*v11); *//* error */
         fprintf(ficrespl,"******\n");                    v21=(lc1-v1)/cv12*v11;
                            v12=-v21;
         for (age=agebase; age<=agelim; age++){                    v22=v11;
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                    tnalp=v21/v11;
           fprintf(ficrespl,"%.0f",age );                    if(first1==1){
           for(i=1; i<=nlstate;i++)                      first1=0;
           fprintf(ficrespl," %.5f", prlim[i][i]);                      printf("%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tang %.3f\nOthers in log...\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
           fprintf(ficrespl,"\n");                    }
         }                    fprintf(ficlog,"%d %d%d-%d%d mu %.4e %.4e Var %.4e %.4e cor %.3f cov %.4e Eig %.3e %.3e 1stv %.3f %.3f tan %.3f\n",(int) age,k1,l1,k2,l2,mu1,mu2,v1,v2,c12,cv12,lc1,lc2,v11,v21,tnalp);
       }                    /*printf(fignu*/
     }                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
   fclose(ficrespl);                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
   /*------------- h Pij x at various ages ------------*/                      first=0;
                        fprintf(ficgp,"\nset parametric;unset label");
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);                      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((ficrespij=fopen(filerespij,"w"))==NULL) {                      fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;                      fprintf(fichtmcov,"\n<br>Ellipsoids of confidence cov(p%1d%1d,p%1d%1d) expressed in year<sup>-1</sup>\
   }   :<a href=\"%s%d%1d%1d-%1d%1d.png\">\
   printf("Computing pij: result on file '%s' \n", filerespij);  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                                subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
   stepsize=(int) (stepm+YEARM-1)/YEARM;                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   /*if (stepm<=24) stepsize=2;*/                      fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
   agelim=AGESUP;                      fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
   hstepm=stepsize*YEARM; /* Every year of age */                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                        fprintf(ficgp,"\nplot [-pi:pi] %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
   k=0;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   for(cptcov=1;cptcov<=i1;cptcov++){                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                    }else{
       k=k+1;                      first=0;
         fprintf(ficrespij,"\n#****** ");                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
         for(j=1;j<=cptcoveff;j++)                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
         fprintf(ficrespij,"******\n");                      fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                                      mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                    }/* if first */
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */                  } /* age mod 5 */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);                } /* end loop age */
           oldm=oldms;savm=savms;                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);                  first=1;
           fprintf(ficrespij,"# Age");              } /*l12 */
           for(i=1; i<=nlstate;i++)            } /* k12 */
             for(j=1; j<=nlstate+ndeath;j++)          } /*l1 */
               fprintf(ficrespij," %1d-%1d",i,j);        }/* k1 */
           fprintf(ficrespij,"\n");      } /* loop covariates */
           for (h=0; h<=nhstepm; h++){    }
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
             for(i=1; i<=nlstate;i++)    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
               for(j=1; j<=nlstate+ndeath;j++)    free_vector(xp,1,npar);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    fclose(ficresprob);
             fprintf(ficrespij,"\n");    fclose(ficresprobcov);
           }    fclose(ficresprobcor);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fflush(ficgp);
           fprintf(ficrespij,"\n");    fflush(fichtmcov);
         }  }
     }  
   }  
   /******************* Printing html file ***********/
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
   fclose(ficrespij);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
   /*---------- Forecasting ------------------*/                    double jprev2, double mprev2,double anprev2){
   if((stepm == 1) && (strcmp(model,".")==0)){    int jj1, k1, i1, cpt;
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);  
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
     free_matrix(mint,1,maxwav,1,n);     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);  </ul>");
     free_vector(weight,1,n);}     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
   else{   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
     erreur=108;             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
     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(fichtm,"\
   }   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
               stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
   /*---------- Health expectancies and variances ------------*/   - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
   strcpy(filerest,"t");     fprintf(fichtm,"\
   strcat(filerest,fileres);   - Life expectancies by age and initial health status (estepm=%2d months): \
   if((ficrest=fopen(filerest,"w"))==NULL) {     <a href=\"%s\">%s</a> <br>\n</li>",
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   }  
   printf("Computing Total LEs with variances: file '%s' \n", filerest);  fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
   strcpy(filerese,"e");   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   strcat(filerese,fileres);  
   if((ficreseij=fopen(filerese,"w"))==NULL) {   jj1=0;
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);   for(k1=1; k1<=m;k1++){
   }     for(i1=1; i1<=ncodemax[k1];i1++){
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);       jj1++;
        if (cptcovn > 0) {
  strcpy(fileresv,"v");         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   strcat(fileresv,fileres);         for (cpt=1; cpt<=cptcoveff;cpt++) 
   if((ficresvij=fopen(fileresv,"w"))==NULL) {           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   }       }
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);       /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
   k=0;  <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
   for(cptcov=1;cptcov<=i1;cptcov++){       /* Quasi-incidences */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
       k=k+1;   before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
       fprintf(ficrest,"\n#****** ");  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
       for(j=1;j<=cptcoveff;j++)         /* Stable prevalence in each health state */
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);         for(cpt=1; cpt<nlstate;cpt++){
       fprintf(ficrest,"******\n");           fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
       fprintf(ficreseij,"\n#****** ");         }
       for(j=1;j<=cptcoveff;j++)       for(cpt=1; cpt<=nlstate;cpt++) {
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);          fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
       fprintf(ficreseij,"******\n");  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
       fprintf(ficresvij,"\n#****** ");     } /* end i1 */
       for(j=1;j<=cptcoveff;j++)   }/* End k1 */
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   fprintf(fichtm,"</ul>");
       fprintf(ficresvij,"******\n");  
   
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);   fprintf(fichtm,"\
       oldm=oldms;savm=savms;  \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm);     - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;   fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
       fprintf(fichtm,"\
    - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
             subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");  
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);   fprintf(fichtm,"\
       fprintf(ficrest,"\n");   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
       epj=vector(1,nlstate+1);   fprintf(fichtm,"\
       for(age=bage; age <=fage ;age++){   - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
         if (popbased==1) {   fprintf(fichtm,"\
           for(i=1; i<=nlstate;i++)   - Health expectancies with their variances (no covariance): <a href=\"%s\">%s</a> <br>\n",
             prlim[i][i]=probs[(int)age][i][k];           subdirf2(fileres,"t"),subdirf2(fileres,"t"));
         }   fprintf(fichtm,"\
           - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
         fprintf(ficrest," %4.0f",age);           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){  
           for(i=1, epj[j]=0.;i <=nlstate;i++) {  /*  if(popforecast==1) fprintf(fichtm,"\n */
             epj[j] += prlim[i][i]*eij[i][j][(int)age];  /*  - 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 */
           epj[nlstate+1] +=epj[j];  /*      <br>",fileres,fileres,fileres,fileres); */
         }  /*  else  */
         for(i=1, vepp=0.;i <=nlstate;i++)  /*    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); */
           for(j=1;j <=nlstate;j++)   fflush(fichtm);
             vepp += vareij[i][j][(int)age];   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));  
         for(j=1;j <=nlstate;j++){   m=cptcoveff;
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
         }  
         fprintf(ficrest,"\n");   jj1=0;
       }   for(k1=1; k1<=m;k1++){
     }     for(i1=1; i1<=ncodemax[k1];i1++){
   }       jj1++;
        if (cptcovn > 0) {
   fclose(ficreseij);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   fclose(ficresvij);         for (cpt=1; cpt<=cptcoveff;cpt++) 
   fclose(ficrest);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   fclose(ficpar);         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   free_vector(epj,1,nlstate+1);       }
         for(cpt=1; cpt<=nlstate;cpt++) {
   /*------- Variance limit prevalence------*/           fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   strcpy(fileresvpl,"vpl");  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
   strcat(fileresvpl,fileres);       }
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);  health expectancies in states (1) and (2): %s%d.png<br>\
     exit(0);  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
   }     } /* end i1 */
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);   }/* End k1 */
    fprintf(fichtm,"</ul>");
   k=0;   fflush(fichtm);
   for(cptcov=1;cptcov<=i1;cptcov++){  }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
       k=k+1;  /******************* Gnuplot file **************/
       fprintf(ficresvpl,"\n#****** ");  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
       for(j=1;j<=cptcoveff;j++)  
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    char dirfileres[132],optfileres[132];
       fprintf(ficresvpl,"******\n");    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
          int ng;
       varpl=matrix(1,nlstate,(int) bage, (int) fage);  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
       oldm=oldms;savm=savms;  /*     printf("Problem with file %s",optionfilegnuplot); */
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
     }  /*   } */
  }  
     /*#ifdef windows */
   fclose(ficresvpl);    fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   /*---------- End : free ----------------*/    m=pow(2,cptcoveff);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  
      strcpy(dirfileres,optionfilefiname);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    strcpy(optfileres,"vpl");
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);   /* 1eme*/
      for (cpt=1; cpt<= nlstate ; cpt ++) {
       for (k1=1; k1<= m ; k1 ++) {
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);       fprintf(ficgp,"set xlabel \"Age\" \n\
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);  set ylabel \"Probability\" \n\
    set ter png small\n\
   free_matrix(matcov,1,npar,1,npar);  set size 0.65,0.65\n\
   free_vector(delti,1,npar);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   free_matrix(agev,1,maxwav,1,imx);  
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);       for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   if(erreur >0)         else fprintf(ficgp," \%%*lf (\%%*lf)");
     printf("End of Imach with error or warning %d\n",erreur);       }
   else   printf("End of Imach\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);
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */       for (i=1; i<= nlstate ; i ++) {
           if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   /* 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);*/         else fprintf(ficgp," \%%*lf (\%%*lf)");
   /*printf("Total time was %d uSec.\n", total_usecs);*/       } 
   /*------ End -----------*/       fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
  end:         else fprintf(ficgp," \%%*lf (\%%*lf)");
 #ifdef windows       }  
   /* chdir(pathcd);*/       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
 #endif     }
  /*system("wgnuplot graph.plt");*/    }
  /*system("../gp37mgw/wgnuplot graph.plt");*/    /*2 eme*/
  /*system("cd ../gp37mgw");*/    
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    for (k1=1; k1<= m ; k1 ++) { 
  strcpy(plotcmd,GNUPLOTPROGRAM);      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
  strcat(plotcmd," ");      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
  strcat(plotcmd,optionfilegnuplot);      
  system(plotcmd);      for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
 #ifdef windows        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
   while (z[0] != 'q') {        for (j=1; j<= nlstate+1 ; j ++) {
     /* chdir(path); */          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");          else fprintf(ficgp," \%%*lf (\%%*lf)");
     scanf("%s",z);        }   
     if (z[0] == 'c') system("./imach");        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
     else if (z[0] == 'e') system(optionfilehtm);        else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
     else if (z[0] == 'g') system(plotcmd);        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
     else if (z[0] == 'q') exit(0);        for (j=1; j<= nlstate+1 ; j ++) {
   }          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
 #endif          else fprintf(ficgp," \%%*lf (\%%*lf)");
 }        }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         k=2+nlstate*(2*cpt-2);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           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) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);
           
         } 
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            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);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i]==1 & wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i]==0 & wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         if (wav[i]>1 & agecens[i]>15) {
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   /***********************************************/
   /**************** 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 linei;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
   
     char ca[32], cb[32], cc[32];
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     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], pathimach[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;
     int agemortsup;
     float  sumlpop=0.;
     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;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     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 argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%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: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,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 */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     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);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* 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);
   
       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);
   
       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 parameter 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);
     }    /* End of mle != -3 */
   
     /*-------- 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;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) ||((i >= firstobs) && (i <=lastobs)))    {
       linei=linei+1;
       printf("IIIII= %d linei=%d\n",i,linei);
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
           if(line[j] == '\t')
             line[j] = ' ';
         }
         for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10);j--){;};line[j+1]=0;  /* Trims blanks at end of line */
         if(line[0]=='#'){
           fprintf(ficlog,"Comment line\n%s\n",line);
           printf("Comment line\n%s\n",line);
           continue;
         }
         for (j=maxwav;j>=1;j--){
           cutv(stra, strb,line,' '); 
           errno=0;
           lval=strtol(strb,&endptr,10); 
           /*      if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%d' at line number %d %s for individual %d\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n",lval, i,line,linei,j,maxwav);
             exit(1);
           }
           s[j][i]=lval;
   
           strcpy(line,stra);
           cutv(stra, strb,line,'/');
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%d'.at line number %ld %s for individual %d\nShould be a year of exam at wave %d.  Exiting.\n",lval, i,line,linei,j);
             exit(1);
           }
           anint[j][i]=(double)(lval); 
   
           strcpy(line,stra);
           cutv(stra, strb,line,' ');
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a month of exam at wave %d.  Exiting.\n",lval, i,line, linei,j);
             exit(1);
           }
           mint[j][i]=(double)(lval); 
           strcpy(line,stra);
         }
           
         cutv(stra, strb,line,'/'); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a year of death.  Exiting.\n",lval, i,line,linei);
           exit(1);
         }
         andc[i]=(double)(lval); 
         strcpy(line,stra);
   
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a month of death.  Exiting.\n",lval,i,line, linei);
           exit(1);
         }
         moisdc[i]=(double)(lval); 
   
         strcpy(line,stra);
         cutv(stra, strb,line,'/'); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a year of birth.  Exiting.\n",lval, i,line, linei);
           exit(1);
         }
         annais[i]=(double)(lval);
   
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a month of birth.  Exiting.\n",lval,i,line,linei);
           exit(1);
         }
         moisnais[i]=(double)(lval); 
         strcpy(line,stra);
   
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight.  Exiting.\n",lval, i,line,linei);
           exit(1);
         }
         weight[i]=(double)(lval); 
         strcpy(line,stra);
   
         for (j=ncovcol;j>=1;j--){
           cutv(stra, strb,line,' '); 
           errno=0;
           lval=strtol(strb,&endptr,10); 
           if( strb[0]=='\0' || (*endptr != '\0')){
             printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, i,line,linei);
             exit(1);
           }
           if(lval <0 || lval >1){
             printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self).  Exiting.\n",lval,i,line,linei,j);
             exit(1);
           }
           covar[j][i]=(double)(lval);
           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);
         printf ("num [i] %ld %d\n",i, num[i]);fflush(stdout);
         /*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;
     } /* End loop reading  data */
     /* 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 parameters 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 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           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); 
   
     agegomp=(int)agemin;
     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);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     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 */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     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,strstart);
   
     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*/
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM);
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (j=1; j<=lastpass; j++)
           if (s[j][i]>nlstate) {
             dcwave[i]=j;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];agecens[i]=1.; 
           if (ageexmed[i]>1 & wav[i]>0) agecens[i]=agev[mw[j][i]][i];
           cens[i]=1;
           
           if (ageexmed[i]<1) cens[i]=-1;
           if (agedc[i]< AGESUP & agedc[i]>1 & dcwave[i]>firstpass & dcwave[i]<=lastpass) cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
   
       p[1]=0.1; p[2]=0.1;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
     strcpy(filerespow,"pow-mort"); 
     strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }
     fprintf(ficrespow,"# Powell\n# iter -2*LL");
     /*  for (i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate+ndeath;j++)
         if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     */
     fprintf(ficrespow,"\n");
   
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM,delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
   lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
      
        for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
      
         for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
   
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
   
    tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
          }
      
      
          printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
   
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
   
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
     } /* Endof if mle==-3 */
   
     else{ /* For mle >=1 */
     
       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.*/
       
       
       
       /*  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, "#Local time at start: %s", strstart);
       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, "#Local time at start: %s", strstart);
       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,strstart);
   
       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, strstart);  
    
           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, strstart);
           if(popbased==1){
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
           }
   
           fprintf(ficrest, "#Local time at start: %s", strstart);
           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,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
       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);
   
       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\nLocal time 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);
   #ifndef UNIX
     /*  strcpy(plotcmd,"\""); */
   #endif
     strcpy(plotcmd,pathimach);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     strcat(plotcmd,GNUPLOTPROGRAM);
   #ifndef UNIX
     strcat(plotcmd,".exe");
     /*  strcat(plotcmd,"\"");*/
   #endif
     if(stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
     }
   
   #ifndef UNIX
     strcpy(plotcmd,"\"");
   #endif
     strcat(plotcmd,pathimach);
     strcat(plotcmd,GNUPLOTPROGRAM);
   #ifndef UNIX
     strcat(plotcmd,".exe");
     strcat(plotcmd,"\"");
   #endif
     strcat(plotcmd," ");
     strcat(plotcmd,optionfilegnuplot);
     printf("Starting graphs with: %s",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n 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') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.38  
changed lines
  Added in v.1.109


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