Diff for /imach/src/imach.c between versions 1.11 and 1.116

version 1.11, 2001/05/17 16:07:14 version 1.116, 2006/03/06 10:29:27
Line 1 Line 1
      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.116  2006/03/06 10:29:27  brouard
   individuals from different ages are interviewed on their health status    (Module): Variance-covariance wrong links and
   or degree of  disability. At least a second wave of interviews    varian-covariance of ej. is needed (Saito).
   ("longitudinal") should  measure each new individual health status.  
   Health expectancies are computed from the transistions observed between    Revision 1.115  2006/02/27 12:17:45  brouard
   waves and are computed for each degree of severity of disability (number    (Module): One freematrix added in mlikeli! 0.98c
   of life states). More degrees you consider, more time is necessary to  
   reach the Maximum Likelihood of the parameters involved in the model.    Revision 1.114  2006/02/26 12:57:58  brouard
   The simplest model is the multinomial logistic model where pij is    (Module): Some improvements in processing parameter
   the probabibility to be observed in state j at the second wave conditional    filename with strsep.
   to be observed in state i at the first wave. Therefore the model is:  
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    Revision 1.113  2006/02/24 14:20:24  brouard
   is a covariate. If you want to have a more complex model than "constant and    (Module): Memory leaks checks with valgrind and:
   age", you should modify the program where the markup    datafile was not closed, some imatrix were not freed and on matrix
     *Covariates have to be included here again* invites you to do it.    allocation too.
   More covariates you add, less is the speed of the convergence.  
     Revision 1.112  2006/01/30 09:55:26  brouard
   The advantage that this computer programme claims, comes from that if the    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   delay between waves is not identical for each individual, or if some  
   individual missed an interview, the information is not rounded or lost, but    Revision 1.111  2006/01/25 20:38:18  brouard
   taken into account using an interpolation or extrapolation.    (Module): Lots of cleaning and bugs added (Gompertz)
   hPijx is the probability to be    (Module): Comments can be added in data file. Missing date values
   observed in state i at age x+h conditional to the observed state i at age    can be a simple dot '.'.
   x. The delay 'h' can be split into an exact number (nh*stepm) of  
   unobserved intermediate  states. This elementary transition (by month or    Revision 1.110  2006/01/25 00:51:50  brouard
   quarter trimester, semester or year) is model as a multinomial logistic.    (Module): Lots of cleaning and bugs added (Gompertz)
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices  
   and the contribution of each individual to the likelihood is simply hPijx.    Revision 1.109  2006/01/24 19:37:15  brouard
     (Module): Comments (lines starting with a #) are allowed in data.
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.108  2006/01/19 18:05:42  lievre
      Gnuplot problem appeared...
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    To be fixed
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.107  2006/01/19 16:20:37  brouard
   from the European Union.    Test existence of gnuplot in imach path
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.106  2006/01/19 13:24:36  brouard
   can be accessed at http://euroreves.ined.fr/imach .    Some cleaning and links added in html output
   **********************************************************************/  
      Revision 1.105  2006/01/05 20:23:19  lievre
 #include <math.h>    *** empty log message ***
 #include <stdio.h>  
 #include <stdlib.h>    Revision 1.104  2005/09/30 16:11:43  lievre
 #include <unistd.h>    (Module): sump fixed, loop imx fixed, and simplifications.
     (Module): If the status is missing at the last wave but we know
 #define MAXLINE 256    that the person is alive, then we can code his/her status as -2
 #define FILENAMELENGTH 80    (instead of missing=-1 in earlier versions) and his/her
 /*#define DEBUG*/    contributions to the likelihood is 1 - Prob of dying from last
 #define windows    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    the healthy state at last known wave). Version is 0.98
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */  
     Revision 1.103  2005/09/30 15:54:49  lievre
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    (Module): sump fixed, loop imx fixed, and simplifications.
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     Revision 1.102  2004/09/15 17:31:30  brouard
 #define NINTERVMAX 8    Add the possibility to read data file including tab characters.
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */  
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    Revision 1.101  2004/09/15 10:38:38  brouard
 #define NCOVMAX 8 /* Maximum number of covariates */    Fix on curr_time
 #define MAXN 20000  
 #define YEARM 12. /* Number of months per year */    Revision 1.100  2004/07/12 18:29:06  brouard
 #define AGESUP 130    Add version for Mac OS X. Just define UNIX in Makefile
 #define AGEBASE 40  
     Revision 1.99  2004/06/05 08:57:40  brouard
     *** empty log message ***
 int nvar;  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Revision 1.98  2004/05/16 15:05:56  brouard
 int npar=NPARMAX;    New version 0.97 . First attempt to estimate force of mortality
 int nlstate=2; /* Number of live states */    directly from the data i.e. without the need of knowing the health
 int ndeath=1; /* Number of dead states */    state at each age, but using a Gompertz model: log u =a + b*age .
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    This is the basic analysis of mortality and should be done before any
     other analysis, in order to test if the mortality estimated from the
 int *wav; /* Number of waves for this individuual 0 is possible */    cross-longitudinal survey is different from the mortality estimated
 int maxwav; /* Maxim number of waves */    from other sources like vital statistic data.
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    The same imach parameter file can be used but the option for mle should be -3.
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    Agnès, who wrote this part of the code, tried to keep most of the
 double jmean; /* Mean space between 2 waves */    former routines in order to include the new code within the former code.
 double **oldm, **newm, **savm; /* Working pointers to matrices */  
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    The output is very simple: only an estimate of the intercept and of
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;    the slope with 95% confident intervals.
 FILE *ficgp, *fichtm;  
 FILE *ficreseij;    Current limitations:
   char filerese[FILENAMELENGTH];    A) Even if you enter covariates, i.e. with the
  FILE  *ficresvij;    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   char fileresv[FILENAMELENGTH];    B) There is no computation of Life Expectancy nor Life Table.
  FILE  *ficresvpl;  
   char fileresvpl[FILENAMELENGTH];    Revision 1.97  2004/02/20 13:25:42  lievre
     Version 0.96d. Population forecasting command line is (temporarily)
 #define NR_END 1    suppressed.
 #define FREE_ARG char*  
 #define FTOL 1.0e-10    Revision 1.96  2003/07/15 15:38:55  brouard
     * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 #define NRANSI    rewritten within the same printf. Workaround: many printfs.
 #define ITMAX 200  
     Revision 1.95  2003/07/08 07:54:34  brouard
 #define TOL 2.0e-4    * imach.c (Repository):
     (Repository): Using imachwizard code to output a more meaningful covariance
 #define CGOLD 0.3819660    matrix (cov(a12,c31) instead of numbers.
 #define ZEPS 1.0e-10  
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    Revision 1.94  2003/06/27 13:00:02  brouard
     Just cleaning
 #define GOLD 1.618034  
 #define GLIMIT 100.0    Revision 1.93  2003/06/25 16:33:55  brouard
 #define TINY 1.0e-20    (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
 static double maxarg1,maxarg2;    (Module): Version 0.96b
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))  
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    Revision 1.92  2003/06/25 16:30:45  brouard
      (Module): On windows (cygwin) function asctime_r doesn't
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    exist so I changed back to asctime which exists.
 #define rint(a) floor(a+0.5)  
     Revision 1.91  2003/06/25 15:30:29  brouard
 static double sqrarg;    * imach.c (Repository): Duplicated warning errors corrected.
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    (Repository): Elapsed time after each iteration is now output. It
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    helps to forecast when convergence will be reached. Elapsed time
     is stamped in powell.  We created a new html file for the graphs
 int imx;    concerning matrix of covariance. It has extension -cov.htm.
 int stepm;  
 /* Stepm, step in month: minimum step interpolation*/    Revision 1.90  2003/06/24 12:34:15  brouard
     (Module): Some bugs corrected for windows. Also, when
 int m,nb;    mle=-1 a template is output in file "or"mypar.txt with the design
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    of the covariance matrix to be input.
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij;    Revision 1.89  2003/06/24 12:30:52  brouard
     (Module): Some bugs corrected for windows. Also, when
 double *weight;    mle=-1 a template is output in file "or"mypar.txt with the design
 int **s; /* Status */    of the covariance matrix to be input.
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Revision 1.88  2003/06/23 17:54:56  brouard
     * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    Revision 1.87  2003/06/18 12:26:01  brouard
     Version 0.96
 /**************** split *************************/  
 static  int split( char *path, char *dirc, char *name )    Revision 1.86  2003/06/17 20:04:08  brouard
 {    (Module): Change position of html and gnuplot routines and added
    char *s;                             /* pointer */    routine fileappend.
    int  l1, l2;                         /* length counters */  
     Revision 1.85  2003/06/17 13:12:43  brouard
    l1 = strlen( path );                 /* length of path */    * imach.c (Repository): Check when date of death was earlier that
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    current date of interview. It may happen when the death was just
    s = strrchr( path, '\\' );           /* find last / */    prior to the death. In this case, dh was negative and likelihood
    if ( s == NULL ) {                   /* no directory, so use current */    was wrong (infinity). We still send an "Error" but patch by
 #if     defined(__bsd__)                /* get current working directory */    assuming that the date of death was just one stepm after the
       extern char       *getwd( );    interview.
     (Repository): Because some people have very long ID (first column)
       if ( getwd( dirc ) == NULL ) {    we changed int to long in num[] and we added a new lvector for
 #else    memory allocation. But we also truncated to 8 characters (left
       extern char       *getcwd( );    truncation)
     (Repository): No more line truncation errors.
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {  
 #endif    Revision 1.84  2003/06/13 21:44:43  brouard
          return( GLOCK_ERROR_GETCWD );    * imach.c (Repository): Replace "freqsummary" at a correct
       }    place. It differs from routine "prevalence" which may be called
       strcpy( name, path );             /* we've got it */    many times. Probs is memory consuming and must be used with
    } else {                             /* strip direcotry from path */    parcimony.
       s++;                              /* after this, the filename */    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.83  2003/06/10 13:39:11  lievre
       strcpy( name, s );                /* save file name */    *** empty log message ***
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */    Revision 1.82  2003/06/05 15:57:20  brouard
    }    Add log in  imach.c and  fullversion number is now printed.
    l1 = strlen( dirc );                 /* length of directory */  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  */
    return( 0 );                         /* we're done */  /*
 }     Interpolated Markov Chain
   
     Short summary of the programme:
 /******************************************/    
     This program computes Healthy Life Expectancies from
 void replace(char *s, char*t)    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 {    first survey ("cross") where individuals from different ages are
   int i;    interviewed on their health status or degree of disability (in the
   int lg=20;    case of a health survey which is our main interest) -2- at least a
   i=0;    second wave of interviews ("longitudinal") which measure each change
   lg=strlen(t);    (if any) in individual health status.  Health expectancies are
   for(i=0; i<= lg; i++) {    computed from the time spent in each health state according to a
     (s[i] = t[i]);    model. More health states you consider, more time is necessary to reach the
     if (t[i]== '\\') s[i]='/';    Maximum Likelihood of the parameters involved in the model.  The
   }    simplest model is the multinomial logistic model where pij is the
 }    probability to be observed in state j at the second wave
     conditional to be observed in state i at the first wave. Therefore
 int nbocc(char *s, char occ)    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
   int i,j=0;    complex model than "constant and age", you should modify the program
   int lg=20;    where the markup *Covariates have to be included here again* invites
   i=0;    you to do it.  More covariates you add, slower the
   lg=strlen(s);    convergence.
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;    The advantage of this computer programme, compared to a simple
   }    multinomial logistic model, is clear when the delay between waves is not
   return j;    identical for each individual. Also, if a individual missed an
 }    intermediate interview, the information is lost, but taken into
     account using an interpolation or extrapolation.  
 void cutv(char *u,char *v, char*t, char occ)  
 {    hPijx is the probability to be observed in state i at age x+h
   int i,lg,j,p=0;    conditional to the observed state i at age x. The delay 'h' can be
   i=0;    split into an exact number (nh*stepm) of unobserved intermediate
   for(j=0; j<=strlen(t)-1; j++) {    states. This elementary transition (by month, quarter,
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    semester or year) is modelled as a multinomial logistic.  The hPx
   }    matrix is simply the matrix product of nh*stepm elementary matrices
     and the contribution of each individual to the likelihood is simply
   lg=strlen(t);    hPijx.
   for(j=0; j<p; j++) {  
     (u[j] = t[j]);    Also this programme outputs the covariance matrix of the parameters but also
   }    of the life expectancies. It also computes the stable prevalence. 
      u[p]='\0';    
     Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
    for(j=0; j<= lg; j++) {             Institut national d'études démographiques, Paris.
     if (j>=(p+1))(v[j-p-1] = t[j]);    This software have been partly granted by Euro-REVES, a concerted action
   }    from the European Union.
 }    It is copyrighted identically to a GNU software product, ie programme and
     software can be distributed freely for non commercial use. Latest version
 /********************** nrerror ********************/    can be accessed at http://euroreves.ined.fr/imach .
   
 void nrerror(char error_text[])    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 {    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   fprintf(stderr,"ERREUR ...\n");    
   fprintf(stderr,"%s\n",error_text);    **********************************************************************/
   exit(1);  /*
 }    main
 /*********************** vector *******************/    read parameterfile
 double *vector(int nl, int nh)    read datafile
 {    concatwav
   double *v;    freqsummary
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    if (mle >= 1)
   if (!v) nrerror("allocation failure in vector");      mlikeli
   return v-nl+NR_END;    print results files
 }    if mle==1 
        computes hessian
 /************************ free vector ******************/    read end of parameter file: agemin, agemax, bage, fage, estepm
 void free_vector(double*v, int nl, int nh)        begin-prev-date,...
 {    open gnuplot file
   free((FREE_ARG)(v+nl-NR_END));    open html file
 }    stable prevalence
      for age prevalim()
 /************************ivector *******************************/    h Pij x
 int *ivector(long nl,long nh)    variance of p varprob
 {    forecasting if prevfcast==1 prevforecast call prevalence()
   int *v;    health expectancies
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    Variance-covariance of DFLE
   if (!v) nrerror("allocation failure in ivector");    prevalence()
   return v-nl+NR_END;     movingaverage()
 }    varevsij() 
     if popbased==1 varevsij(,popbased)
 /******************free ivector **************************/    total life expectancies
 void free_ivector(int *v, long nl, long nh)    Variance of stable prevalence
 {   end
   free((FREE_ARG)(v+nl-NR_END));  */
 }  
   
 /******************* imatrix *******************************/  
 int **imatrix(long nrl, long nrh, long ncl, long nch)   
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  #include <math.h>
 {  #include <stdio.h>
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  #include <stdlib.h>
   int **m;  #include <string.h>
    #include <unistd.h>
   /* allocate pointers to rows */  
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  #include <limits.h>
   if (!m) nrerror("allocation failure 1 in matrix()");  #include <sys/types.h>
   m += NR_END;  #include <sys/stat.h>
   m -= nrl;  #include <errno.h>
    extern int errno;
    
   /* allocate rows and set pointers to them */  /* #include <sys/time.h> */
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  #include <time.h>
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #include "timeval.h"
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  /* #include <libintl.h> */
    /* #define _(String) gettext (String) */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  
    #define MAXLINE 256
   /* return pointer to array of pointers to rows */  
   return m;  #define GNUPLOTPROGRAM "gnuplot"
 }  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   #define FILENAMELENGTH 132
 /****************** free_imatrix *************************/  
 void free_imatrix(m,nrl,nrh,ncl,nch)  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
       int **m;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
       long nch,ncl,nrh,nrl;  
      /* free an int matrix allocated by imatrix() */  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 {  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));  #define NINTERVMAX 8
 }  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 /******************* matrix *******************************/  #define NCOVMAX 8 /* Maximum number of covariates */
 double **matrix(long nrl, long nrh, long ncl, long nch)  #define MAXN 20000
 {  #define YEARM 12. /* Number of months per year */
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  #define AGESUP 130
   double **m;  #define AGEBASE 40
   #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #ifdef UNIX
   if (!m) nrerror("allocation failure 1 in matrix()");  #define DIRSEPARATOR '/'
   m += NR_END;  #define CHARSEPARATOR "/"
   m -= nrl;  #define ODIRSEPARATOR '\\'
   #else
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #define DIRSEPARATOR '\\'
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define CHARSEPARATOR "\\"
   m[nrl] += NR_END;  #define ODIRSEPARATOR '/'
   m[nrl] -= ncl;  #endif
   
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  /* $Id$ */
   return m;  /* $State$ */
 }  
   char version[]="Imach version 0.98c, February 2006, INED-EUROREVES ";
 /*************************free matrix ************************/  char fullversion[]="$Revision$ $Date$"; 
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 {  int nvar;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   free((FREE_ARG)(m+nrl-NR_END));  int npar=NPARMAX;
 }  int nlstate=2; /* Number of live states */
   int ndeath=1; /* Number of dead states */
 /******************* ma3x *******************************/  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  int popbased=0;
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  int *wav; /* Number of waves for this individuual 0 is possible */
   double ***m;  int maxwav; /* Maxim number of waves */
   int jmin, jmax; /* min, max spacing between 2 waves */
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
   if (!m) nrerror("allocation failure 1 in matrix()");  int gipmx, gsw; /* Global variables on the number of contributions 
   m += NR_END;                     to the likelihood and the sum of weights (done by funcone)*/
   m -= nrl;  int mle, weightopt;
   int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  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;
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  FILE *ficlog, *ficrespow;
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  int globpr; /* Global variable for printing or not */
   m[nrl][ncl] += NR_END;  double fretone; /* Only one call to likelihood */
   m[nrl][ncl] -= nll;  long ipmx; /* Number of contributions */
   for (j=ncl+1; j<=nch; j++)  double sw; /* Sum of weights */
     m[nrl][j]=m[nrl][j-1]+nlay;  char filerespow[FILENAMELENGTH];
    char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   for (i=nrl+1; i<=nrh; i++) {  FILE *ficresilk;
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
     for (j=ncl+1; j<=nch; j++)  FILE *ficresprobmorprev;
       m[i][j]=m[i][j-1]+nlay;  FILE *fichtm, *fichtmcov; /* Html File */
   }  FILE *ficreseij;
   return m;  char filerese[FILENAMELENGTH];
 }  FILE  *ficresvij;
   char fileresv[FILENAMELENGTH];
 /*************************free ma3x ************************/  FILE  *ficresvpl;
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  char fileresvpl[FILENAMELENGTH];
 {  char title[MAXLINE];
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   free((FREE_ARG)(m+nrl-NR_END));  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
 }  char command[FILENAMELENGTH];
   int  outcmd=0;
 /***************** f1dim *************************/  
 extern int ncom;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);  char filelog[FILENAMELENGTH]; /* Log file */
    char filerest[FILENAMELENGTH];
 double f1dim(double x)  char fileregp[FILENAMELENGTH];
 {  char popfile[FILENAMELENGTH];
   int j;  
   double f;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   double *xt;  
    struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   xt=vector(1,ncom);  struct timezone tzp;
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  extern int gettimeofday();
   f=(*nrfunc)(xt);  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   free_vector(xt,1,ncom);  long time_value;
   return f;  extern long time();
 }  char strcurr[80], strfor[80];
   
 /*****************brent *************************/  char *endptr;
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  long lval;
 {  
   int iter;  #define NR_END 1
   double a,b,d,etemp;  #define FREE_ARG char*
   double fu,fv,fw,fx;  #define FTOL 1.0e-10
   double ftemp;  
   double p,q,r,tol1,tol2,u,v,w,x,xm;  #define NRANSI 
   double e=0.0;  #define ITMAX 200 
    
   a=(ax < cx ? ax : cx);  #define TOL 2.0e-4 
   b=(ax > cx ? ax : cx);  
   x=w=v=bx;  #define CGOLD 0.3819660 
   fw=fv=fx=(*f)(x);  #define ZEPS 1.0e-10 
   for (iter=1;iter<=ITMAX;iter++) {  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
     xm=0.5*(a+b);  
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  #define GOLD 1.618034 
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  #define GLIMIT 100.0 
     printf(".");fflush(stdout);  #define TINY 1.0e-20 
 #ifdef DEBUG  
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  static double maxarg1,maxarg2;
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
 #endif  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){    
       *xmin=x;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
       return fx;  #define rint(a) floor(a+0.5)
     }  
     ftemp=fu;  static double sqrarg;
     if (fabs(e) > tol1) {  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
       r=(x-w)*(fx-fv);  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       q=(x-v)*(fx-fw);  int agegomp= AGEGOMP;
       p=(x-v)*q-(x-w)*r;  
       q=2.0*(q-r);  int imx; 
       if (q > 0.0) p = -p;  int stepm=1;
       q=fabs(q);  /* Stepm, step in month: minimum step interpolation*/
       etemp=e;  
       e=d;  int estepm;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  
       else {  int m,nb;
         d=p/q;  long *num;
         u=x+d;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
         if (u-a < tol2 || b-u < tol2)  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
           d=SIGN(tol1,xm-x);  double **pmmij, ***probs;
       }  double *ageexmed,*agecens;
     } else {  double dateintmean=0;
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }  double *weight;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  int **s; /* Status */
     fu=(*f)(u);  double *agedc, **covar, idx;
     if (fu <= fx) {  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
       if (u >= x) a=x; else b=x;  double *lsurv, *lpop, *tpop;
       SHFT(v,w,x,u)  
         SHFT(fv,fw,fx,fu)  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
         } else {  double ftolhess; /* Tolerance for computing hessian */
           if (u < x) a=u; else b=u;  
           if (fu <= fw || w == x) {  /**************** split *************************/
             v=w;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
             w=u;  {
             fv=fw;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
             fw=fu;       the name of the file (name), its extension only (ext) and its first part of the name (finame)
           } else if (fu <= fv || v == x || v == w) {    */ 
             v=u;    char  *ss;                            /* pointer */
             fv=fu;    int   l1, l2;                         /* length counters */
           }  
         }    l1 = strlen(path );                   /* length of path */
   }    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   nrerror("Too many iterations in brent");    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   *xmin=x;    if ( ss == NULL ) {                   /* no directory, so determine current directory */
   return fx;      strcpy( name, path );               /* we got the fullname name because no directory */
 }      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
         printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 /****************** mnbrak ***********************/      /* get current working directory */
       /*    extern  char* getcwd ( char *buf , int len);*/
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
             double (*func)(double))        return( GLOCK_ERROR_GETCWD );
 {      }
   double ulim,u,r,q, dum;      /* got dirc from getcwd*/
   double fu;      printf(" DIRC = %s \n",dirc);
      } else {                              /* strip direcotry from path */
   *fa=(*func)(*ax);      ss++;                               /* after this, the filename */
   *fb=(*func)(*bx);      l2 = strlen( ss );                  /* length of filename */
   if (*fb > *fa) {      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     SHFT(dum,*ax,*bx,dum)      strcpy( name, ss );         /* save file name */
       SHFT(dum,*fb,*fa,dum)      strncpy( dirc, path, l1 - l2 );     /* now the directory */
       }      dirc[l1-l2] = 0;                    /* add zero */
   *cx=(*bx)+GOLD*(*bx-*ax);      printf(" DIRC2 = %s \n",dirc);
   *fc=(*func)(*cx);    }
   while (*fb > *fc) {    /* We add a separator at the end of dirc if not exists */
     r=(*bx-*ax)*(*fb-*fc);    l1 = strlen( dirc );                  /* length of directory */
     q=(*bx-*cx)*(*fb-*fa);    if( dirc[l1-1] != DIRSEPARATOR ){
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/      dirc[l1] =  DIRSEPARATOR;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));      dirc[l1+1] = 0; 
     ulim=(*bx)+GLIMIT*(*cx-*bx);      printf(" DIRC3 = %s \n",dirc);
     if ((*bx-u)*(u-*cx) > 0.0) {    }
       fu=(*func)(u);    ss = strrchr( name, '.' );            /* find last / */
     } else if ((*cx-u)*(u-ulim) > 0.0) {    if (ss >0){
       fu=(*func)(u);      ss++;
       if (fu < *fc) {      strcpy(ext,ss);                     /* save extension */
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))      l1= strlen( name);
           SHFT(*fb,*fc,fu,(*func)(u))      l2= strlen(ss)+1;
           }      strncpy( finame, name, l1-l2);
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {      finame[l1-l2]= 0;
       u=ulim;    }
       fu=(*func)(u);  
     } else {    return( 0 );                          /* we're done */
       u=(*cx)+GOLD*(*cx-*bx);  }
       fu=(*func)(u);  
     }  
     SHFT(*ax,*bx,*cx,u)  /******************************************/
       SHFT(*fa,*fb,*fc,fu)  
       }  void replace_back_to_slash(char *s, char*t)
 }  {
     int i;
 /*************** linmin ************************/    int lg=0;
     i=0;
 int ncom;    lg=strlen(t);
 double *pcom,*xicom;    for(i=0; i<= lg; i++) {
 double (*nrfunc)(double []);      (s[i] = t[i]);
        if (t[i]== '\\') s[i]='/';
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    }
 {  }
   double brent(double ax, double bx, double cx,  
                double (*f)(double), double tol, double *xmin);  int nbocc(char *s, char occ)
   double f1dim(double x);  {
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    int i,j=0;
               double *fc, double (*func)(double));    int lg=20;
   int j;    i=0;
   double xx,xmin,bx,ax;    lg=strlen(s);
   double fx,fb,fa;    for(i=0; i<= lg; i++) {
      if  (s[i] == occ ) j++;
   ncom=n;    }
   pcom=vector(1,n);    return j;
   xicom=vector(1,n);  }
   nrfunc=func;  
   for (j=1;j<=n;j++) {  void cutv(char *u,char *v, char*t, char occ)
     pcom[j]=p[j];  {
     xicom[j]=xi[j];    /* 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')
   ax=0.0;       gives u="abcedf" and v="ghi2j" */
   xx=1.0;    int i,lg,j,p=0;
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    i=0;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    for(j=0; j<=strlen(t)-1; j++) {
 #ifdef DEBUG      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    }
 #endif  
   for (j=1;j<=n;j++) {    lg=strlen(t);
     xi[j] *= xmin;    for(j=0; j<p; j++) {
     p[j] += xi[j];      (u[j] = t[j]);
   }    }
   free_vector(xicom,1,n);       u[p]='\0';
   free_vector(pcom,1,n);  
 }     for(j=0; j<= lg; j++) {
       if (j>=(p+1))(v[j-p-1] = t[j]);
 /*************** powell ************************/    }
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  }
             double (*func)(double []))  
 {  /********************** nrerror ********************/
   void linmin(double p[], double xi[], int n, double *fret,  
               double (*func)(double []));  void nrerror(char error_text[])
   int i,ibig,j;  {
   double del,t,*pt,*ptt,*xit;    fprintf(stderr,"ERREUR ...\n");
   double fp,fptt;    fprintf(stderr,"%s\n",error_text);
   double *xits;    exit(EXIT_FAILURE);
   pt=vector(1,n);  }
   ptt=vector(1,n);  /*********************** vector *******************/
   xit=vector(1,n);  double *vector(int nl, int nh)
   xits=vector(1,n);  {
   *fret=(*func)(p);    double *v;
   for (j=1;j<=n;j++) pt[j]=p[j];    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
   for (*iter=1;;++(*iter)) {    if (!v) nrerror("allocation failure in vector");
     fp=(*fret);    return v-nl+NR_END;
     ibig=0;  }
     del=0.0;  
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  /************************ free vector ******************/
     for (i=1;i<=n;i++)  void free_vector(double*v, int nl, int nh)
       printf(" %d %.12f",i, p[i]);  {
     printf("\n");    free((FREE_ARG)(v+nl-NR_END));
     for (i=1;i<=n;i++) {  }
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  
       fptt=(*fret);  /************************ivector *******************************/
 #ifdef DEBUG  int *ivector(long nl,long nh)
       printf("fret=%lf \n",*fret);  {
 #endif    int *v;
       printf("%d",i);fflush(stdout);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       linmin(p,xit,n,fret,func);    if (!v) nrerror("allocation failure in ivector");
       if (fabs(fptt-(*fret)) > del) {    return v-nl+NR_END;
         del=fabs(fptt-(*fret));  }
         ibig=i;  
       }  /******************free ivector **************************/
 #ifdef DEBUG  void free_ivector(int *v, long nl, long nh)
       printf("%d %.12e",i,(*fret));  {
       for (j=1;j<=n;j++) {    free((FREE_ARG)(v+nl-NR_END));
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  }
         printf(" x(%d)=%.12e",j,xit[j]);  
       }  /************************lvector *******************************/
       for(j=1;j<=n;j++)  long *lvector(long nl,long nh)
         printf(" p=%.12e",p[j]);  {
       printf("\n");    long *v;
 #endif    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     }    if (!v) nrerror("allocation failure in ivector");
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    return v-nl+NR_END;
 #ifdef DEBUG  }
       int k[2],l;  
       k[0]=1;  /******************free lvector **************************/
       k[1]=-1;  void free_lvector(long *v, long nl, long nh)
       printf("Max: %.12e",(*func)(p));  {
       for (j=1;j<=n;j++)    free((FREE_ARG)(v+nl-NR_END));
         printf(" %.12e",p[j]);  }
       printf("\n");  
       for(l=0;l<=1;l++) {  /******************* imatrix *******************************/
         for (j=1;j<=n;j++) {  int **imatrix(long nrl, long nrh, long ncl, long nch) 
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  { 
         }    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    int **m; 
       }    
 #endif    /* allocate pointers to rows */ 
     m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     if (!m) nrerror("allocation failure 1 in matrix()"); 
       free_vector(xit,1,n);    m += NR_END; 
       free_vector(xits,1,n);    m -= nrl; 
       free_vector(ptt,1,n);    
       free_vector(pt,1,n);    
       return;    /* allocate rows and set pointers to them */ 
     }    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
     for (j=1;j<=n;j++) {    m[nrl] += NR_END; 
       ptt[j]=2.0*p[j]-pt[j];    m[nrl] -= ncl; 
       xit[j]=p[j]-pt[j];    
       pt[j]=p[j];    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     }    
     fptt=(*func)(ptt);    /* return pointer to array of pointers to rows */ 
     if (fptt < fp) {    return m; 
       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);  /****************** free_imatrix *************************/
         for (j=1;j<=n;j++) {  void free_imatrix(m,nrl,nrh,ncl,nch)
           xi[j][ibig]=xi[j][n];        int **m;
           xi[j][n]=xit[j];        long nch,ncl,nrh,nrl; 
         }       /* free an int matrix allocated by imatrix() */ 
 #ifdef DEBUG  { 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
         for(j=1;j<=n;j++)    free((FREE_ARG) (m+nrl-NR_END)); 
           printf(" %.12e",xit[j]);  } 
         printf("\n");  
 #endif  /******************* matrix *******************************/
       }  double **matrix(long nrl, long nrh, long ncl, long nch)
     }  {
   }    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
 }    double **m;
   
 /**** Prevalence limit ****************/    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     if (!m) nrerror("allocation failure 1 in matrix()");
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    m += NR_END;
 {    m -= nrl;
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  
      matrix by transitions matrix until convergence is reached */    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   int i, ii,j,k;    m[nrl] += NR_END;
   double min, max, maxmin, maxmax,sumnew=0.;    m[nrl] -= ncl;
   double **matprod2();  
   double **out, cov[NCOVMAX], **pmij();    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   double **newm;    return m;
   double agefin, delaymax=50 ; /* Max number of years to converge */    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
      */
   for (ii=1;ii<=nlstate+ndeath;ii++)  }
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  /*************************free matrix ************************/
     }  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   {
    cov[1]=1.;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
      free((FREE_ARG)(m+nrl-NR_END));
  /* 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;  /******************* ma3x *******************************/
     /* Covariates have to be included here again */  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
      cov[2]=agefin;  {
      long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       for (k=1; k<=cptcovn;k++) {    double ***m;
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       }    if (!m) nrerror("allocation failure 1 in matrix()");
       for (k=1; k<=cptcovage;k++)    m += NR_END;
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    m -= nrl;
       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]]];    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    m[nrl] += NR_END;
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    m[nrl] -= ncl;
   
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   
     savm=oldm;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     oldm=newm;    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     maxmax=0.;    m[nrl][ncl] += NR_END;
     for(j=1;j<=nlstate;j++){    m[nrl][ncl] -= nll;
       min=1.;    for (j=ncl+1; j<=nch; j++) 
       max=0.;      m[nrl][j]=m[nrl][j-1]+nlay;
       for(i=1; i<=nlstate; i++) {    
         sumnew=0;    for (i=nrl+1; i<=nrh; i++) {
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
         prlim[i][j]= newm[i][j]/(1-sumnew);      for (j=ncl+1; j<=nch; j++) 
         max=FMAX(max,prlim[i][j]);        m[i][j]=m[i][j-1]+nlay;
         min=FMIN(min,prlim[i][j]);    }
       }    return m; 
       maxmin=max-min;    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       maxmax=FMAX(maxmax,maxmin);             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     }    */
     if(maxmax < ftolpl){  }
       return prlim;  
     }  /*************************free ma3x ************************/
   }  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
 }  {
     free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
 /*************** transition probabilities **********/    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  }
 {  
   double s1, s2;  /*************** function subdirf ***********/
   /*double t34;*/  char *subdirf(char fileres[])
   int i,j,j1, nc, ii, jj;  {
     /* Caution optionfilefiname is hidden */
     for(i=1; i<= nlstate; i++){    strcpy(tmpout,optionfilefiname);
     for(j=1; j<i;j++){    strcat(tmpout,"/"); /* Add to the right */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    strcat(tmpout,fileres);
         /*s2 += param[i][j][nc]*cov[nc];*/    return tmpout;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  }
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  
       }  /*************** function subdirf2 ***********/
       ps[i][j]=s2;  char *subdirf2(char fileres[], char *preop)
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  {
     }    
     for(j=i+1; j<=nlstate+ndeath;j++){    /* Caution optionfilefiname is hidden */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    strcpy(tmpout,optionfilefiname);
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    strcat(tmpout,"/");
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    strcat(tmpout,preop);
       }    strcat(tmpout,fileres);
       ps[i][j]=s2;    return tmpout;
     }  }
   }  
   for(i=1; i<= nlstate; i++){  /*************** function subdirf3 ***********/
      s1=0;  char *subdirf3(char fileres[], char *preop, char *preop2)
     for(j=1; j<i; j++)  {
       s1+=exp(ps[i][j]);    
     for(j=i+1; j<=nlstate+ndeath; j++)    /* Caution optionfilefiname is hidden */
       s1+=exp(ps[i][j]);    strcpy(tmpout,optionfilefiname);
     ps[i][i]=1./(s1+1.);    strcat(tmpout,"/");
     for(j=1; j<i; j++)    strcat(tmpout,preop);
       ps[i][j]= exp(ps[i][j])*ps[i][i];    strcat(tmpout,preop2);
     for(j=i+1; j<=nlstate+ndeath; j++)    strcat(tmpout,fileres);
       ps[i][j]= exp(ps[i][j])*ps[i][i];    return tmpout;
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  }
   } /* end i */  
   /***************** f1dim *************************/
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  extern int ncom; 
     for(jj=1; jj<= nlstate+ndeath; jj++){  extern double *pcom,*xicom;
       ps[ii][jj]=0;  extern double (*nrfunc)(double []); 
       ps[ii][ii]=1;   
     }  double f1dim(double x) 
   }  { 
     int j; 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    double f;
     for(jj=1; jj<= nlstate+ndeath; jj++){    double *xt; 
      printf("%lf ",ps[ii][jj]);   
    }    xt=vector(1,ncom); 
     printf("\n ");    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     }    f=(*nrfunc)(xt); 
     printf("\n ");printf("%lf ",cov[2]);*/    free_vector(xt,1,ncom); 
 /*    return f; 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  } 
   goto end;*/  
     return ps;  /*****************brent *************************/
 }  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   { 
 /**************** Product of 2 matrices ******************/    int iter; 
     double a,b,d,etemp;
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    double fu,fv,fw,fx;
 {    double ftemp;
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    double p,q,r,tol1,tol2,u,v,w,x,xm; 
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    double e=0.0; 
   /* in, b, out are matrice of pointers which should have been initialized   
      before: only the contents of out is modified. The function returns    a=(ax < cx ? ax : cx); 
      a pointer to pointers identical to out */    b=(ax > cx ? ax : cx); 
   long i, j, k;    x=w=v=bx; 
   for(i=nrl; i<= nrh; i++)    fw=fv=fx=(*f)(x); 
     for(k=ncolol; k<=ncoloh; k++)    for (iter=1;iter<=ITMAX;iter++) { 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)      xm=0.5*(a+b); 
         out[i][k] +=in[i][j]*b[j][k];      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   return out;      printf(".");fflush(stdout);
 }      fprintf(ficlog,".");fflush(ficlog);
   #ifdef DEBUG
       printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
 /************* Higher Matrix Product ***************/      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)))) { */
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )  #endif
 {      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month        *xmin=x; 
      duration (i.e. until        return fx; 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.      } 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step      ftemp=fu;
      (typically every 2 years instead of every month which is too big).      if (fabs(e) > tol1) { 
      Model is determined by parameters x and covariates have to be        r=(x-w)*(fx-fv); 
      included manually here.        q=(x-v)*(fx-fw); 
         p=(x-v)*q-(x-w)*r; 
      */        q=2.0*(q-r); 
         if (q > 0.0) p = -p; 
   int i, j, d, h, k;        q=fabs(q); 
   double **out, cov[NCOVMAX];        etemp=e; 
   double **newm;        e=d; 
         if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   /* Hstepm could be zero and should return the unit matrix */          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   for (i=1;i<=nlstate+ndeath;i++)        else { 
     for (j=1;j<=nlstate+ndeath;j++){          d=p/q; 
       oldm[i][j]=(i==j ? 1.0 : 0.0);          u=x+d; 
       po[i][j][0]=(i==j ? 1.0 : 0.0);          if (u-a < tol2 || b-u < tol2) 
     }            d=SIGN(tol1,xm-x); 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */        } 
   for(h=1; h <=nhstepm; h++){      } else { 
     for(d=1; d <=hstepm; d++){        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       newm=savm;      } 
       /* Covariates have to be included here again */      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       cov[1]=1.;      fu=(*f)(u); 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      if (fu <= fx) { 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];        if (u >= x) a=x; else b=x; 
 for (k=1; k<=cptcovage;k++)        SHFT(v,w,x,u) 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];          SHFT(fv,fw,fx,fu) 
    for (k=1; k<=cptcovprod;k++)          } else { 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];            if (u < x) a=u; else b=u; 
             if (fu <= fw || w == x) { 
               v=w; 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/              w=u; 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/              fv=fw; 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,              fw=fu; 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));            } else if (fu <= fv || v == x || v == w) { 
       savm=oldm;              v=u; 
       oldm=newm;              fv=fu; 
     }            } 
     for(i=1; i<=nlstate+ndeath; i++)          } 
       for(j=1;j<=nlstate+ndeath;j++) {    } 
         po[i][j][h]=newm[i][j];    nrerror("Too many iterations in brent"); 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    *xmin=x; 
          */    return fx; 
       }  } 
   } /* end h */  
   return po;  /****************** mnbrak ***********************/
 }  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
               double (*func)(double)) 
 /*************** log-likelihood *************/  { 
 double func( double *x)    double ulim,u,r,q, dum;
 {    double fu; 
   int i, ii, j, k, mi, d, kk;   
   double l, ll[NLSTATEMAX], cov[NCOVMAX];    *fa=(*func)(*ax); 
   double **out;    *fb=(*func)(*bx); 
   double sw; /* Sum of weights */    if (*fb > *fa) { 
   double lli; /* Individual log likelihood */      SHFT(dum,*ax,*bx,dum) 
   long ipmx;        SHFT(dum,*fb,*fa,dum) 
   /*extern weight */        } 
   /* We are differentiating ll according to initial status */    *cx=(*bx)+GOLD*(*bx-*ax); 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/    *fc=(*func)(*cx); 
   /*for(i=1;i<imx;i++)    while (*fb > *fc) { 
     printf(" %d\n",s[4][i]);      r=(*bx-*ax)*(*fb-*fc); 
   */      q=(*bx-*cx)*(*fb-*fa); 
   cov[1]=1.;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   for(k=1; k<=nlstate; k++) ll[k]=0.;      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      if ((*bx-u)*(u-*cx) > 0.0) { 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];        fu=(*func)(u); 
     for(mi=1; mi<= wav[i]-1; mi++){      } else if ((*cx-u)*(u-ulim) > 0.0) { 
       for (ii=1;ii<=nlstate+ndeath;ii++)        fu=(*func)(u); 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        if (fu < *fc) { 
       for(d=0; d<dh[mi][i]; d++){          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
         newm=savm;            SHFT(*fb,*fc,fu,(*func)(u)) 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;            } 
         for (kk=1; kk<=cptcovage;kk++) {      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        u=ulim; 
         }        fu=(*func)(u); 
              } else { 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        u=(*cx)+GOLD*(*cx-*bx); 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        fu=(*func)(u); 
         savm=oldm;      } 
         oldm=newm;      SHFT(*ax,*bx,*cx,u) 
                SHFT(*fa,*fb,*fc,fu) 
                } 
       } /* end mult */  } 
        
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  /*************** linmin ************************/
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  
       ipmx +=1;  int ncom; 
       sw += weight[i];  double *pcom,*xicom;
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  double (*nrfunc)(double []); 
     } /* end of wave */   
   } /* end of individual */  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   { 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    double brent(double ax, double bx, double cx, 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */                 double (*f)(double), double tol, double *xmin); 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    double f1dim(double x); 
   return -l;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
 }                double *fc, double (*func)(double)); 
     int j; 
     double xx,xmin,bx,ax; 
 /*********** Maximum Likelihood Estimation ***************/    double fx,fb,fa;
    
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    ncom=n; 
 {    pcom=vector(1,n); 
   int i,j, iter;    xicom=vector(1,n); 
   double **xi,*delti;    nrfunc=func; 
   double fret;    for (j=1;j<=n;j++) { 
   xi=matrix(1,npar,1,npar);      pcom[j]=p[j]; 
   for (i=1;i<=npar;i++)      xicom[j]=xi[j]; 
     for (j=1;j<=npar;j++)    } 
       xi[i][j]=(i==j ? 1.0 : 0.0);    ax=0.0; 
   printf("Powell\n");    xx=1.0; 
   powell(p,xi,npar,ftol,&iter,&fret,func);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  #ifdef DEBUG
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 }  #endif
     for (j=1;j<=n;j++) { 
 /**** Computes Hessian and covariance matrix ***/      xi[j] *= xmin; 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))      p[j] += xi[j]; 
 {    } 
   double  **a,**y,*x,pd;    free_vector(xicom,1,n); 
   double **hess;    free_vector(pcom,1,n); 
   int i, j,jk;  } 
   int *indx;  
   char *asc_diff_time(long time_sec, char ascdiff[])
   double hessii(double p[], double delta, int theta, double delti[]);  {
   double hessij(double p[], double delti[], int i, int j);    long sec_left, days, hours, minutes;
   void lubksb(double **a, int npar, int *indx, double b[]) ;    days = (time_sec) / (60*60*24);
   void ludcmp(double **a, int npar, int *indx, double *d) ;    sec_left = (time_sec) % (60*60*24);
     hours = (sec_left) / (60*60) ;
     sec_left = (sec_left) %(60*60);
   hess=matrix(1,npar,1,npar);    minutes = (sec_left) /60;
     sec_left = (sec_left) % (60);
   printf("\nCalculation of the hessian matrix. Wait...\n");    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   for (i=1;i<=npar;i++){    return ascdiff;
     printf("%d",i);fflush(stdout);  }
     hess[i][i]=hessii(p,ftolhess,i,delti);  
     /*printf(" %f ",p[i]);*/  /*************** powell ************************/
   }  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
               double (*func)(double [])) 
   for (i=1;i<=npar;i++) {  { 
     for (j=1;j<=npar;j++)  {    void linmin(double p[], double xi[], int n, double *fret, 
       if (j>i) {                double (*func)(double [])); 
         printf(".%d%d",i,j);fflush(stdout);    int i,ibig,j; 
         hess[i][j]=hessij(p,delti,i,j);    double del,t,*pt,*ptt,*xit;
         hess[j][i]=hess[i][j];    double fp,fptt;
       }    double *xits;
     }    int niterf, itmp;
   }  
   printf("\n");    pt=vector(1,n); 
     ptt=vector(1,n); 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    xit=vector(1,n); 
      xits=vector(1,n); 
   a=matrix(1,npar,1,npar);    *fret=(*func)(p); 
   y=matrix(1,npar,1,npar);    for (j=1;j<=n;j++) pt[j]=p[j]; 
   x=vector(1,npar);    for (*iter=1;;++(*iter)) { 
   indx=ivector(1,npar);      fp=(*fret); 
   for (i=1;i<=npar;i++)      ibig=0; 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];      del=0.0; 
   ludcmp(a,npar,indx,&pd);      last_time=curr_time;
       (void) gettimeofday(&curr_time,&tzp);
   for (j=1;j<=npar;j++) {      printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
     for (i=1;i<=npar;i++) x[i]=0;      /*    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);
     x[j]=1;      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
     lubksb(a,npar,indx,x);      */
     for (i=1;i<=npar;i++){     for (i=1;i<=n;i++) {
       matcov[i][j]=x[i];        printf(" %d %.12f",i, p[i]);
     }        fprintf(ficlog," %d %.12lf",i, p[i]);
   }        fprintf(ficrespow," %.12lf", p[i]);
       }
   printf("\n#Hessian matrix#\n");      printf("\n");
   for (i=1;i<=npar;i++) {      fprintf(ficlog,"\n");
     for (j=1;j<=npar;j++) {      fprintf(ficrespow,"\n");fflush(ficrespow);
       printf("%.3e ",hess[i][j]);      if(*iter <=3){
     }        tm = *localtime(&curr_time.tv_sec);
     printf("\n");        strcpy(strcurr,asctime(&tm));
   }  /*       asctime_r(&tm,strcurr); */
         forecast_time=curr_time; 
   /* Recompute Inverse */        itmp = strlen(strcurr);
   for (i=1;i<=npar;i++)        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];          strcurr[itmp-1]='\0';
   ludcmp(a,npar,indx,&pd);        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   /*  printf("\n#Hessian matrix recomputed#\n");        for(niterf=10;niterf<=30;niterf+=10){
           forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
   for (j=1;j<=npar;j++) {          tmf = *localtime(&forecast_time.tv_sec);
     for (i=1;i<=npar;i++) x[i]=0;  /*      asctime_r(&tmf,strfor); */
     x[j]=1;          strcpy(strfor,asctime(&tmf));
     lubksb(a,npar,indx,x);          itmp = strlen(strfor);
     for (i=1;i<=npar;i++){          if(strfor[itmp-1]=='\n')
       y[i][j]=x[i];          strfor[itmp-1]='\0';
       printf("%.3e ",y[i][j]);          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("\n");        }
   }      }
   */      for (i=1;i<=n;i++) { 
         for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   free_matrix(a,1,npar,1,npar);        fptt=(*fret); 
   free_matrix(y,1,npar,1,npar);  #ifdef DEBUG
   free_vector(x,1,npar);        printf("fret=%lf \n",*fret);
   free_ivector(indx,1,npar);        fprintf(ficlog,"fret=%lf \n",*fret);
   free_matrix(hess,1,npar,1,npar);  #endif
         printf("%d",i);fflush(stdout);
         fprintf(ficlog,"%d",i);fflush(ficlog);
 }        linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
 /*************** hessian matrix ****************/          del=fabs(fptt-(*fret)); 
 double hessii( double x[], double delta, int theta, double delti[])          ibig=i; 
 {        } 
   int i;  #ifdef DEBUG
   int l=1, lmax=20;        printf("%d %.12e",i,(*fret));
   double k1,k2;        fprintf(ficlog,"%d %.12e",i,(*fret));
   double p2[NPARMAX+1];        for (j=1;j<=n;j++) {
   double res;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;          printf(" x(%d)=%.12e",j,xit[j]);
   double fx;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   int k=0,kmax=10;        }
   double l1;        for(j=1;j<=n;j++) {
           printf(" p=%.12e",p[j]);
   fx=func(x);          fprintf(ficlog," p=%.12e",p[j]);
   for (i=1;i<=npar;i++) p2[i]=x[i];        }
   for(l=0 ; l <=lmax; l++){        printf("\n");
     l1=pow(10,l);        fprintf(ficlog,"\n");
     delts=delt;  #endif
     for(k=1 ; k <kmax; k=k+1){      } 
       delt = delta*(l1*k);      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
       p2[theta]=x[theta] +delt;  #ifdef DEBUG
       k1=func(p2)-fx;        int k[2],l;
       p2[theta]=x[theta]-delt;        k[0]=1;
       k2=func(p2)-fx;        k[1]=-1;
       /*res= (k1-2.0*fx+k2)/delt/delt; */        printf("Max: %.12e",(*func)(p));
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        fprintf(ficlog,"Max: %.12e",(*func)(p));
              for (j=1;j<=n;j++) {
 #ifdef DEBUG          printf(" %.12e",p[j]);
       printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);          fprintf(ficlog," %.12e",p[j]);
 #endif        }
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */        printf("\n");
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){        fprintf(ficlog,"\n");
         k=kmax;        for(l=0;l<=1;l++) {
       }          for (j=1;j<=n;j++) {
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
         k=kmax; l=lmax*10.;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       }            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          }
         delts=delt;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       }          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     }        }
   }  #endif
   delti[theta]=delts;  
   return res;  
          free_vector(xit,1,n); 
 }        free_vector(xits,1,n); 
         free_vector(ptt,1,n); 
 double hessij( double x[], double delti[], int thetai,int thetaj)        free_vector(pt,1,n); 
 {        return; 
   int i;      } 
   int l=1, l1, lmax=20;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   double k1,k2,k3,k4,res,fx;      for (j=1;j<=n;j++) { 
   double p2[NPARMAX+1];        ptt[j]=2.0*p[j]-pt[j]; 
   int k;        xit[j]=p[j]-pt[j]; 
         pt[j]=p[j]; 
   fx=func(x);      } 
   for (k=1; k<=2; k++) {      fptt=(*func)(ptt); 
     for (i=1;i<=npar;i++) p2[i]=x[i];      if (fptt < fp) { 
     p2[thetai]=x[thetai]+delti[thetai]/k;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        if (t < 0.0) { 
     k1=func(p2)-fx;          linmin(p,xit,n,fret,func); 
            for (j=1;j<=n;j++) { 
     p2[thetai]=x[thetai]+delti[thetai]/k;            xi[j][ibig]=xi[j][n]; 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;            xi[j][n]=xit[j]; 
     k2=func(p2)-fx;          }
    #ifdef DEBUG
     p2[thetai]=x[thetai]-delti[thetai]/k;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     k3=func(p2)-fx;          for(j=1;j<=n;j++){
              printf(" %.12e",xit[j]);
     p2[thetai]=x[thetai]-delti[thetai]/k;            fprintf(ficlog," %.12e",xit[j]);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          }
     k4=func(p2)-fx;          printf("\n");
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          fprintf(ficlog,"\n");
 #ifdef DEBUG  #endif
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);        }
 #endif      } 
   }    } 
   return res;  } 
 }  
   /**** Prevalence limit (stable prevalence)  ****************/
 /************** Inverse of matrix **************/  
 void ludcmp(double **a, int n, int *indx, double *d)  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
 {  {
   int i,imax,j,k;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
   double big,dum,sum,temp;       matrix by transitions matrix until convergence is reached */
   double *vv;  
      int i, ii,j,k;
   vv=vector(1,n);    double min, max, maxmin, maxmax,sumnew=0.;
   *d=1.0;    double **matprod2();
   for (i=1;i<=n;i++) {    double **out, cov[NCOVMAX], **pmij();
     big=0.0;    double **newm;
     for (j=1;j<=n;j++)    double agefin, delaymax=50 ; /* Max number of years to converge */
       if ((temp=fabs(a[i][j])) > big) big=temp;  
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    for (ii=1;ii<=nlstate+ndeath;ii++)
     vv[i]=1.0/big;      for (j=1;j<=nlstate+ndeath;j++){
   }        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (j=1;j<=n;j++) {      }
     for (i=1;i<j;i++) {  
       sum=a[i][j];     cov[1]=1.;
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];   
       a[i][j]=sum;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     }    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     big=0.0;      newm=savm;
     for (i=j;i<=n;i++) {      /* Covariates have to be included here again */
       sum=a[i][j];       cov[2]=agefin;
       for (k=1;k<j;k++)    
         sum -= a[i][k]*a[k][j];        for (k=1; k<=cptcovn;k++) {
       a[i][j]=sum;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       if ( (dum=vv[i]*fabs(sum)) >= big) {          /*      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]]);*/
         big=dum;        }
         imax=i;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       }        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]]];
     if (j != imax) {  
       for (k=1;k<=n;k++) {        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
         dum=a[imax][k];        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
         a[imax][k]=a[j][k];        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
         a[j][k]=dum;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
       }  
       *d = -(*d);      savm=oldm;
       vv[imax]=vv[j];      oldm=newm;
     }      maxmax=0.;
     indx[j]=imax;      for(j=1;j<=nlstate;j++){
     if (a[j][j] == 0.0) a[j][j]=TINY;        min=1.;
     if (j != n) {        max=0.;
       dum=1.0/(a[j][j]);        for(i=1; i<=nlstate; i++) {
       for (i=j+1;i<=n;i++) a[i][j] *= dum;          sumnew=0;
     }          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   }          prlim[i][j]= newm[i][j]/(1-sumnew);
   free_vector(vv,1,n);  /* Doesn't work */          max=FMAX(max,prlim[i][j]);
 ;          min=FMIN(min,prlim[i][j]);
 }        }
         maxmin=max-min;
 void lubksb(double **a, int n, int *indx, double b[])        maxmax=FMAX(maxmax,maxmin);
 {      }
   int i,ii=0,ip,j;      if(maxmax < ftolpl){
   double sum;        return prlim;
        }
   for (i=1;i<=n;i++) {    }
     ip=indx[i];  }
     sum=b[ip];  
     b[ip]=b[i];  /*************** transition probabilities ***************/ 
     if (ii)  
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     else if (sum) ii=i;  {
     b[i]=sum;    double s1, s2;
   }    /*double t34;*/
   for (i=n;i>=1;i--) {    int i,j,j1, nc, ii, jj;
     sum=b[i];  
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];      for(i=1; i<= nlstate; i++){
     b[i]=sum/a[i][i];        for(j=1; j<i;j++){
   }          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
 }            /*s2 += param[i][j][nc]*cov[nc];*/
             s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
 /************ Frequencies ********************/  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)          }
 {  /* Some frequencies */          ps[i][j]=s2;
    /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;        }
   double ***freq; /* Frequencies */        for(j=i+1; j<=nlstate+ndeath;j++){
   double *pp;          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   double pos;            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   FILE *ficresp;  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
   char fileresp[FILENAMELENGTH];          }
           ps[i][j]=s2;
   pp=vector(1,nlstate);        }
       }
   strcpy(fileresp,"p");      /*ps[3][2]=1;*/
   strcat(fileresp,fileres);      
   if((ficresp=fopen(fileresp,"w"))==NULL) {      for(i=1; i<= nlstate; i++){
     printf("Problem with prevalence resultfile: %s\n", fileresp);        s1=0;
     exit(0);        for(j=1; j<i; j++)
   }          s1+=exp(ps[i][j]);
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        for(j=i+1; j<=nlstate+ndeath; j++)
   j1=0;          s1+=exp(ps[i][j]);
         ps[i][i]=1./(s1+1.);
   j=cptcoveff;        for(j=1; j<i; j++)
   if (cptcovn<1) {j=1;ncodemax[1]=1;}          ps[i][j]= exp(ps[i][j])*ps[i][i];
         for(j=i+1; j<=nlstate+ndeath; j++)
   for(k1=1; k1<=j;k1++){          ps[i][j]= exp(ps[i][j])*ps[i][i];
    for(i1=1; i1<=ncodemax[k1];i1++){        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
        j1++;      } /* end i */
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);      
          scanf("%d", i);*/      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
         for (i=-1; i<=nlstate+ndeath; i++)          for(jj=1; jj<= nlstate+ndeath; jj++){
          for (jk=-1; jk<=nlstate+ndeath; jk++)            ps[ii][jj]=0;
            for(m=agemin; m <= agemax+3; m++)          ps[ii][ii]=1;
              freq[i][jk][m]=0;        }
              }
        for (i=1; i<=imx; i++) {      
          bool=1;  
          if  (cptcovn>0) {  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
            for (z1=1; z1<=cptcoveff; z1++)  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])  /*         printf("ddd %lf ",ps[ii][jj]); */
                bool=0;  /*       } */
          }  /*       printf("\n "); */
           if (bool==1) {  /*        } */
            for(m=firstpass; m<=lastpass-1; m++){  /*        printf("\n ");printf("%lf ",cov[2]); */
              if(agev[m][i]==0) agev[m][i]=agemax+1;         /*
              if(agev[m][i]==1) agev[m][i]=agemax+2;        for(i=1; i<= npar; i++) printf("%f ",x[i]);
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        goto end;*/
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];      return ps;
            }  }
          }  
        }  /**************** Product of 2 matrices ******************/
         if  (cptcovn>0) {  
          fprintf(ficresp, "\n#********** Variable ");  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  {
        fprintf(ficresp, "**********\n#");    /* 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(...) */
        for(i=1; i<=nlstate;i++)    /* in, b, out are matrice of pointers which should have been initialized 
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);       before: only the contents of out is modified. The function returns
        fprintf(ficresp, "\n");       a pointer to pointers identical to out */
            long i, j, k;
   for(i=(int)agemin; i <= (int)agemax+3; i++){    for(i=nrl; i<= nrh; i++)
     if(i==(int)agemax+3)      for(k=ncolol; k<=ncoloh; k++)
       printf("Total");        for(j=ncl,out[i][k]=0.; j<=nch; j++)
     else          out[i][k] +=in[i][j]*b[j][k];
       printf("Age %d", i);  
     for(jk=1; jk <=nlstate ; jk++){    return out;
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  }
         pp[jk] += freq[jk][m][i];  
     }  
     for(jk=1; jk <=nlstate ; jk++){  /************* Higher Matrix Product ***************/
       for(m=-1, pos=0; m <=0 ; m++)  
         pos += freq[jk][m][i];  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
       if(pp[jk]>=1.e-10)  {
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);    /* Computes the transition matrix starting at age 'age' over 
       else       'nhstepm*hstepm*stepm' months (i.e. until
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
     }       nhstepm*hstepm matrices. 
     for(jk=1; jk <=nlstate ; jk++){       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)       (typically every 2 years instead of every month which is too big 
         pp[jk] += freq[jk][m][i];       for the memory).
     }       Model is determined by parameters x and covariates have to be 
     for(jk=1,pos=0; jk <=nlstate ; jk++)       included manually here. 
       pos += pp[jk];  
     for(jk=1; jk <=nlstate ; jk++){       */
       if(pos>=1.e-5)  
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    int i, j, d, h, k;
       else    double **out, cov[NCOVMAX];
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);    double **newm;
       if( i <= (int) agemax){  
         if(pos>=1.e-5)    /* Hstepm could be zero and should return the unit matrix */
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    for (i=1;i<=nlstate+ndeath;i++)
       else      for (j=1;j<=nlstate+ndeath;j++){
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        oldm[i][j]=(i==j ? 1.0 : 0.0);
       }        po[i][j][0]=(i==j ? 1.0 : 0.0);
     }      }
     for(jk=-1; jk <=nlstate+ndeath; jk++)    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       for(m=-1; m <=nlstate+ndeath; m++)    for(h=1; h <=nhstepm; h++){
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);      for(d=1; d <=hstepm; d++){
     if(i <= (int) agemax)        newm=savm;
       fprintf(ficresp,"\n");        /* Covariates have to be included here again */
     printf("\n");        cov[1]=1.;
     }        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];
   fclose(ficresp);        for (k=1; k<=cptcovprod;k++)
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   free_vector(pp,1,nlstate);  
   
 }  /* End of Freq */        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
 /************* Waves Concatenation ***************/        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                      pmij(pmmij,cov,ncovmodel,x,nlstate));
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)        savm=oldm;
 {        oldm=newm;
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.      }
      Death is a valid wave (if date is known).      for(i=1; i<=nlstate+ndeath; i++)
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i        for(j=1;j<=nlstate+ndeath;j++) {
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          po[i][j][h]=newm[i][j];
      and mw[mi+1][i]. dh depends on stepm.          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
      */           */
         }
   int i, mi, m;    } /* end h */
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    return po;
      double sum=0., jmean=0.;*/  }
   
   int j, k=0,jk, ju, jl;  
   double sum=0.;  /*************** log-likelihood *************/
   jmin=1e+5;  double func( double *x)
   jmax=-1;  {
   jmean=0.;    int i, ii, j, k, mi, d, kk;
   for(i=1; i<=imx; i++){    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     mi=0;    double **out;
     m=firstpass;    double sw; /* Sum of weights */
     while(s[m][i] <= nlstate){    double lli; /* Individual log likelihood */
       if(s[m][i]>=1)    int s1, s2;
         mw[++mi][i]=m;    double bbh, survp;
       if(m >=lastpass)    long ipmx;
         break;    /*extern weight */
       else    /* We are differentiating ll according to initial status */
         m++;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     }/* end while */    /*for(i=1;i<imx;i++) 
     if (s[m][i] > nlstate){      printf(" %d\n",s[4][i]);
       mi++;     /* Death is another wave */    */
       /* if(mi==0)  never been interviewed correctly before death */    cov[1]=1.;
          /* Only death is a correct wave */  
       mw[mi][i]=m;    for(k=1; k<=nlstate; k++) ll[k]=0.;
     }  
     if(mle==1){
     wav[i]=mi;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     if(mi==0)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        for(mi=1; mi<= wav[i]-1; mi++){
   }          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
   for(i=1; i<=imx; i++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(mi=1; mi<wav[i];mi++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       if (stepm <=0)            }
         dh[mi][i]=1;          for(d=0; d<dh[mi][i]; d++){
       else{            newm=savm;
         if (s[mw[mi+1][i]][i] > nlstate) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           if (agedc[i] < 2*AGESUP) {            for (kk=1; kk<=cptcovage;kk++) {
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           if(j==0) j=1;  /* Survives at least one month after exam */            }
           k=k+1;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           if (j >= jmax) jmax=j;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           if (j <= jmin) jmin=j;            savm=oldm;
           sum=sum+j;            oldm=newm;
           if (j<0) printf("j=%d num=%d ",j,i);          } /* end mult */
           }        
         }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
         else{          /* But now since version 0.9 we anticipate for bias at large stepm.
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));           * If stepm is larger than one month (smallest stepm) and if the exact delay 
           k=k+1;           * (in months) between two waves is not a multiple of stepm, we rounded to 
           if (j >= jmax) jmax=j;           * the nearest (and in case of equal distance, to the lowest) interval but now
           else if (j <= jmin)jmin=j;           * we keep into memory the bias bh[mi][i] and also the previous matrix product
           sum=sum+j;           * (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
         jk= j/stepm;           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
         jl= j -jk*stepm;           * -stepm/2 to stepm/2 .
         ju= j -(jk+1)*stepm;           * For stepm=1 the results are the same as for previous versions of Imach.
         if(jl <= -ju)           * For stepm > 1 the results are less biased than in previous versions. 
           dh[mi][i]=jk;           */
         else          s1=s[mw[mi][i]][i];
           dh[mi][i]=jk+1;          s2=s[mw[mi+1][i]][i];
         if(dh[mi][i]==0)          bbh=(double)bh[mi][i]/(double)stepm; 
           dh[mi][i]=1; /* At least one step */          /* bias bh is positive if real duration
       }           * is higher than the multiple of stepm and negative otherwise.
     }           */
   }          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
   jmean=sum/k;          if( s2 > nlstate){ 
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);            /* i.e. if s2 is a death state and if the date of death is known 
 }               then the contribution to the likelihood is the probability to 
 /*********** Tricode ****************************/               die between last step unit time and current  step unit time, 
 void tricode(int *Tvar, int **nbcode, int imx)               which is also equal to probability to die before dh 
 {               minus probability to die before dh-stepm . 
   int Ndum[20],ij=1, k, j, i;               In version up to 0.92 likelihood was computed
   int cptcode=0;          as if date of death was unknown. Death was treated as any other
   cptcoveff=0;          health state: the date of the interview describes the actual state
            and not the date of a change in health state. The former idea was
   for (k=0; k<19; k++) Ndum[k]=0;          to consider that at each interview the state was recorded
   for (k=1; k<=7; k++) ncodemax[k]=0;          (healthy, disable or death) and IMaCh was corrected; but when we
           introduced the exact date of death then we should have modified
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          the contribution of an exact death to the likelihood. This new
     for (i=1; i<=imx; i++) {          contribution is smaller and very dependent of the step unit
       ij=(int)(covar[Tvar[j]][i]);          stepm. It is no more the probability to die between last interview
       Ndum[ij]++;          and month of death but the probability to survive from last
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          interview up to one month before death multiplied by the
       if (ij > cptcode) cptcode=ij;          probability to die within a month. Thanks to Chris
     }          Jackson for correcting this bug.  Former versions increased
           mortality artificially. The bad side is that we add another loop
     for (i=0; i<=cptcode; i++) {          which slows down the processing. The difference can be up to 10%
       if(Ndum[i]!=0) ncodemax[j]++;          lower mortality.
     }            */
     ij=1;            lli=log(out[s1][s2] - savm[s1][s2]);
   
   
     for (i=1; i<=ncodemax[j]; i++) {          } else if  (s2==-2) {
       for (k=0; k<=19; k++) {            for (j=1,survp=0. ; j<=nlstate; j++) 
         if (Ndum[k] != 0) {              survp += out[s1][j];
           nbcode[Tvar[j]][ij]=k;            lli= survp;
           ij++;          }
         }          
         if (ij > ncodemax[j]) break;          else if  (s2==-4) {
       }              for (j=3,survp=0. ; j<=nlstate; j++) 
     }              survp += out[s1][j];
   }              lli= survp;
           }
  for (k=0; k<19; k++) Ndum[k]=0;          
           else if  (s2==-5) {
  for (i=1; i<=ncovmodel; i++) {            for (j=1,survp=0. ; j<=2; j++) 
       ij=Tvar[i];              survp += out[s1][j];
       Ndum[ij]++;            lli= survp;
     }          }
   
  ij=1;  
  for (i=1; i<=10; i++) {          else{
    if((Ndum[i]!=0) && (i<=ncov)){            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
      Tvaraff[ij]=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 */
      ij++;          } 
    }          /*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); */
     cptcoveff=ij-1;          ipmx +=1;
 }          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 /*********** Health Expectancies ****************/        } /* end of wave */
       } /* end of individual */
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)    }  else if(mle==2){
 {      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   /* Health expectancies */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   int i, j, nhstepm, hstepm, h;        for(mi=1; mi<= wav[i]-1; mi++){
   double age, agelim,hf;          for (ii=1;ii<=nlstate+ndeath;ii++)
   double ***p3mat;            for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   fprintf(ficreseij,"# Health expectancies\n");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   fprintf(ficreseij,"# Age");            }
   for(i=1; i<=nlstate;i++)          for(d=0; d<=dh[mi][i]; d++){
     for(j=1; j<=nlstate;j++)            newm=savm;
       fprintf(ficreseij," %1d-%1d",i,j);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   fprintf(ficreseij,"\n");            for (kk=1; kk<=cptcovage;kk++) {
               cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   hstepm=1*YEARM; /*  Every j years of age (in month) */            }
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   agelim=AGESUP;            savm=oldm;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            oldm=newm;
     /* nhstepm age range expressed in number of stepm */          } /* end mult */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);        
     /* Typically if 20 years = 20*12/6=40 stepm */          s1=s[mw[mi][i]][i];
     if (stepm >= YEARM) hstepm=1;          s2=s[mw[mi+1][i]][i];
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */          bbh=(double)bh[mi][i]/(double)stepm; 
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          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 */
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          ipmx +=1;
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          sw += weight[i];
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
       } /* end of individual */
     for(i=1; i<=nlstate;i++)    }  else if(mle==3){  /* exponential inter-extrapolation */
       for(j=1; j<=nlstate;j++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           eij[i][j][(int)age] +=p3mat[i][j][h];        for(mi=1; mi<= wav[i]-1; mi++){
         }          for (ii=1;ii<=nlstate+ndeath;ii++)
                for (j=1;j<=nlstate+ndeath;j++){
     hf=1;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     if (stepm >= YEARM) hf=stepm/YEARM;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     fprintf(ficreseij,"%.0f",age );            }
     for(i=1; i<=nlstate;i++)          for(d=0; d<dh[mi][i]; d++){
       for(j=1; j<=nlstate;j++){            newm=savm;
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       }            for (kk=1; kk<=cptcovage;kk++) {
     fprintf(ficreseij,"\n");              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            }
   }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
 }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
 /************ Variance ******************/            oldm=newm;
 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)          } /* end mult */
 {        
   /* Variance of health expectancies */          s1=s[mw[mi][i]][i];
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          s2=s[mw[mi+1][i]][i];
   double **newm;          bbh=(double)bh[mi][i]/(double)stepm; 
   double **dnewm,**doldm;          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 */
   int i, j, nhstepm, hstepm, h;          ipmx +=1;
   int k, cptcode;          sw += weight[i];
    double *xp;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double **gp, **gm;        } /* end of wave */
   double ***gradg, ***trgradg;      } /* end of individual */
   double ***p3mat;    }else if (mle==4){  /* ml=4 no inter-extrapolation */
   double age,agelim;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int theta;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
    fprintf(ficresvij,"# Covariances of life expectancies\n");          for (ii=1;ii<=nlstate+ndeath;ii++)
   fprintf(ficresvij,"# Age");            for (j=1;j<=nlstate+ndeath;j++){
   for(i=1; i<=nlstate;i++)              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(j=1; j<=nlstate;j++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);            }
   fprintf(ficresvij,"\n");          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
   xp=vector(1,npar);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   dnewm=matrix(1,nlstate,1,npar);            for (kk=1; kk<=cptcovage;kk++) {
   doldm=matrix(1,nlstate,1,nlstate);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
              }
   hstepm=1*YEARM; /* Every year of age */          
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   agelim = AGESUP;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            savm=oldm;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            oldm=newm;
     if (stepm >= YEARM) hstepm=1;          } /* end mult */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          s1=s[mw[mi][i]][i];
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);          s2=s[mw[mi+1][i]][i];
     gp=matrix(0,nhstepm,1,nlstate);          if( s2 > nlstate){ 
     gm=matrix(0,nhstepm,1,nlstate);            lli=log(out[s1][s2] - savm[s1][s2]);
           }else{
     for(theta=1; theta <=npar; theta++){            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       for(i=1; i<=npar; i++){ /* Computes gradient */          }
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          ipmx +=1;
       }          sw += weight[i];
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  /*      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(j=1; j<= nlstate; j++){        } /* end of wave */
         for(h=0; h<=nhstepm; h++){      } /* end of individual */
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       }        for(mi=1; mi<= wav[i]-1; mi++){
              for (ii=1;ii<=nlstate+ndeath;ii++)
       for(i=1; i<=npar; i++) /* Computes gradient */            for (j=1;j<=nlstate+ndeath;j++){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                savm[ii][j]=(ii==j ? 1.0 : 0.0);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            }
       for(j=1; j<= nlstate; j++){          for(d=0; d<dh[mi][i]; d++){
         for(h=0; h<=nhstepm; h++){            newm=savm;
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];            for (kk=1; kk<=cptcovage;kk++) {
         }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       }            }
       for(j=1; j<= nlstate; j++)          
         for(h=0; h<=nhstepm; h++){            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         }            savm=oldm;
     } /* End theta */            oldm=newm;
           } /* end mult */
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);        
           s1=s[mw[mi][i]][i];
     for(h=0; h<=nhstepm; h++)          s2=s[mw[mi+1][i]][i];
       for(j=1; j<=nlstate;j++)          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         for(theta=1; theta <=npar; theta++)          ipmx +=1;
           trgradg[h][j][theta]=gradg[h][theta][j];          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(i=1;i<=nlstate;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]);*/
       for(j=1;j<=nlstate;j++)        } /* end of wave */
         vareij[i][j][(int)age] =0.;      } /* end of individual */
     for(h=0;h<=nhstepm;h++){    } /* End of if */
       for(k=0;k<=nhstepm;k++){    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         for(i=1;i<=nlstate;i++)    return -l;
           for(j=1;j<=nlstate;j++)  }
             vareij[i][j][(int)age] += doldm[i][j];  
       }  /*************** log-likelihood *************/
     }  double funcone( double *x)
     h=1;  {
     if (stepm >= YEARM) h=stepm/YEARM;    /* Same as likeli but slower because of a lot of printf and if */
     fprintf(ficresvij,"%.0f ",age );    int i, ii, j, k, mi, d, kk;
     for(i=1; i<=nlstate;i++)    double l, ll[NLSTATEMAX], cov[NCOVMAX];
       for(j=1; j<=nlstate;j++){    double **out;
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    double lli; /* Individual log likelihood */
       }    double llt;
     fprintf(ficresvij,"\n");    int s1, s2;
     free_matrix(gp,0,nhstepm,1,nlstate);    double bbh, survp;
     free_matrix(gm,0,nhstepm,1,nlstate);    /*extern weight */
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    /* We are differentiating ll according to initial status */
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /*for(i=1;i<imx;i++) 
   } /* End age */      printf(" %d\n",s[4][i]);
      */
   free_vector(xp,1,npar);    cov[1]=1.;
   free_matrix(doldm,1,nlstate,1,npar);  
   free_matrix(dnewm,1,nlstate,1,nlstate);    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
 }    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
 /************ Variance of prevlim ******************/      for(mi=1; mi<= wav[i]-1; mi++){
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)        for (ii=1;ii<=nlstate+ndeath;ii++)
 {          for (j=1;j<=nlstate+ndeath;j++){
   /* Variance of prevalence limit */            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            savm[ii][j]=(ii==j ? 1.0 : 0.0);
   double **newm;          }
   double **dnewm,**doldm;        for(d=0; d<dh[mi][i]; d++){
   int i, j, nhstepm, hstepm;          newm=savm;
   int k, cptcode;          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double *xp;          for (kk=1; kk<=cptcovage;kk++) {
   double *gp, *gm;            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double **gradg, **trgradg;          }
   double age,agelim;          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int theta;                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              savm=oldm;
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");          oldm=newm;
   fprintf(ficresvpl,"# Age");        } /* end mult */
   for(i=1; i<=nlstate;i++)        
       fprintf(ficresvpl," %1d-%1d",i,i);        s1=s[mw[mi][i]][i];
   fprintf(ficresvpl,"\n");        s2=s[mw[mi+1][i]][i];
         bbh=(double)bh[mi][i]/(double)stepm; 
   xp=vector(1,npar);        /* bias is positive if real duration
   dnewm=matrix(1,nlstate,1,npar);         * is higher than the multiple of stepm and negative otherwise.
   doldm=matrix(1,nlstate,1,nlstate);         */
          if( s2 > nlstate && (mle <5) ){  /* Jackson */
   hstepm=1*YEARM; /* Every year of age */          lli=log(out[s1][s2] - savm[s1][s2]);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        } else if (mle==1){
   agelim = AGESUP;          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        } else if(mle==2){
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
     if (stepm >= YEARM) hstepm=1;        } else if(mle==3){  /* exponential inter-extrapolation */
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          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 */
     gradg=matrix(1,npar,1,nlstate);        } else if (mle==4){  /* mle=4 no inter-extrapolation */
     gp=vector(1,nlstate);          lli=log(out[s1][s2]); /* Original formula */
     gm=vector(1,nlstate);        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
           lli=log(out[s1][s2]); /* Original formula */
     for(theta=1; theta <=npar; theta++){        } /* End of if */
       for(i=1; i<=npar; i++){ /* Computes gradient */        ipmx +=1;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        sw += weight[i];
       }        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  /*       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(i=1;i<=nlstate;i++)        if(globpr){
         gp[i] = prlim[i][i];          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
       %10.6f %10.6f %10.6f ", \
       for(i=1; i<=npar; i++) /* Computes gradient */                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
         xp[i] = x[i] - (i==theta ?delti[theta]:0);                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
       for(i=1;i<=nlstate;i++)            llt +=ll[k]*gipmx/gsw;
         gm[i] = prlim[i][i];            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           }
       for(i=1;i<=nlstate;i++)          fprintf(ficresilk," %10.6f\n", -llt);
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        }
     } /* End theta */      } /* end of wave */
     } /* end of individual */
     trgradg =matrix(1,nlstate,1,npar);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     for(j=1; j<=nlstate;j++)    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
       for(theta=1; theta <=npar; theta++)    if(globpr==0){ /* First time we count the contributions and weights */
         trgradg[j][theta]=gradg[theta][j];      gipmx=ipmx;
       gsw=sw;
     for(i=1;i<=nlstate;i++)    }
       varpl[i][(int)age] =0.;    return -l;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);  }
     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 */  /*************** function likelione ***********/
   void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
     fprintf(ficresvpl,"%.0f ",age );  {
     for(i=1; i<=nlstate;i++)    /* This routine should help understanding what is done with 
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));       the selection of individuals/waves and
     fprintf(ficresvpl,"\n");       to check the exact contribution to the likelihood.
     free_vector(gp,1,nlstate);       Plotting could be done.
     free_vector(gm,1,nlstate);     */
     free_matrix(gradg,1,npar,1,nlstate);    int k;
     free_matrix(trgradg,1,nlstate,1,npar);  
   } /* End age */    if(*globpri !=0){ /* Just counts and sums, no printings */
       strcpy(fileresilk,"ilk"); 
   free_vector(xp,1,npar);      strcat(fileresilk,fileres);
   free_matrix(doldm,1,nlstate,1,npar);      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   free_matrix(dnewm,1,nlstate,1,nlstate);        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");
       fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
       /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
 /***********************************************/      for(k=1; k<=nlstate; k++) 
 /**************** Main Program *****************/        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
 /***********************************************/      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     }
 /*int main(int argc, char *argv[])*/  
 int main()    *fretone=(*funcone)(p);
 {    if(*globpri !=0){
       fclose(ficresilk);
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   double agedeb, agefin,hf;      fflush(fichtm); 
   double agemin=1.e20, agemax=-1.e20;    } 
     return;
   double fret;  }
   double **xi,tmp,delta;  
   
   double dum; /* Dummy variable */  /*********** Maximum Likelihood Estimation ***************/
   double ***p3mat;  
   int *indx;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   char line[MAXLINE], linepar[MAXLINE];  {
   char title[MAXLINE];    int i,j, iter;
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];    double **xi;
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];    double fret;
   char filerest[FILENAMELENGTH];    double fretone; /* Only one call to likelihood */
   char fileregp[FILENAMELENGTH];    /*  char filerespow[FILENAMELENGTH];*/
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    xi=matrix(1,npar,1,npar);
   int firstobs=1, lastobs=10;    for (i=1;i<=npar;i++)
   int sdeb, sfin; /* Status at beginning and end */      for (j=1;j<=npar;j++)
   int c,  h , cpt,l;        xi[i][j]=(i==j ? 1.0 : 0.0);
   int ju,jl, mi;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    strcpy(filerespow,"pow"); 
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    strcat(filerespow,fileres);
      if((ficrespow=fopen(filerespow,"w"))==NULL) {
   int hstepm, nhstepm;      printf("Problem with resultfile: %s\n", filerespow);
   double bage, fage, age, agelim, agebase;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   double ftolpl=FTOL;    }
   double **prlim;    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   double *severity;    for (i=1;i<=nlstate;i++)
   double ***param; /* Matrix of parameters */      for(j=1;j<=nlstate+ndeath;j++)
   double  *p;        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   double **matcov; /* Matrix of covariance */    fprintf(ficrespow,"\n");
   double ***delti3; /* Scale */  
   double *delti; /* Scale */    powell(p,xi,npar,ftol,&iter,&fret,func);
   double ***eij, ***vareij;  
   double **varpl; /* Variances of prevalence limits by age */    free_matrix(xi,1,npar,1,npar);
   double *epj, vepp;    fclose(ficrespow);
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   char *alph[]={"a","a","b","c","d","e"}, str[4];    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   char z[1]="c", occ;  
 #include <sys/time.h>  }
 #include <time.h>  
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  /**** Computes Hessian and covariance matrix ***/
   /* long total_usecs;  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   struct timeval start_time, end_time;  {
      double  **a,**y,*x,pd;
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    double **hess;
     int i, j,jk;
     int *indx;
   printf("\nIMACH, Version 0.64b");  
   printf("\nEnter the parameter file name: ");    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
 #ifdef windows    void lubksb(double **a, int npar, int *indx, double b[]) ;
   scanf("%s",pathtot);    void ludcmp(double **a, int npar, int *indx, double *d) ;
   getcwd(pathcd, size);    double gompertz(double p[]);
   /*cygwin_split_path(pathtot,path,optionfile);    hess=matrix(1,npar,1,npar);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/  
   /* cutv(path,optionfile,pathtot,'\\');*/    printf("\nCalculation of the hessian matrix. Wait...\n");
     fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
 split(pathtot, path,optionfile);    for (i=1;i<=npar;i++){
   chdir(path);      printf("%d",i);fflush(stdout);
   replace(pathc,path);      fprintf(ficlog,"%d",i);fflush(ficlog);
 #endif     
 #ifdef unix       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
   scanf("%s",optionfile);      
 #endif      /*  printf(" %f ",p[i]);
           printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
 /*-------- arguments in the command line --------*/    }
     
   strcpy(fileres,"r");    for (i=1;i<=npar;i++) {
   strcat(fileres, optionfile);      for (j=1;j<=npar;j++)  {
         if (j>i) { 
   /*---------arguments file --------*/          printf(".%d%d",i,j);fflush(stdout);
           fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {          hess[i][j]=hessij(p,delti,i,j,func,npar);
     printf("Problem with optionfile %s\n",optionfile);          
     goto end;          hess[j][i]=hess[i][j];    
   }          /*printf(" %lf ",hess[i][j]);*/
         }
   strcpy(filereso,"o");      }
   strcat(filereso,fileres);    }
   if((ficparo=fopen(filereso,"w"))==NULL) {    printf("\n");
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    fprintf(ficlog,"\n");
   }  
     printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   /* Reads comments: lines beginning with '#' */    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   while((c=getc(ficpar))=='#' && c!= EOF){    
     ungetc(c,ficpar);    a=matrix(1,npar,1,npar);
     fgets(line, MAXLINE, ficpar);    y=matrix(1,npar,1,npar);
     puts(line);    x=vector(1,npar);
     fputs(line,ficparo);    indx=ivector(1,npar);
   }    for (i=1;i<=npar;i++)
   ungetc(c,ficpar);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     ludcmp(a,npar,indx,&pd);
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);  
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);    for (j=1;j<=npar;j++) {
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
   covar=matrix(0,NCOVMAX,1,n);      lubksb(a,npar,indx,x);
   cptcovn=0;      for (i=1;i<=npar;i++){ 
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;        matcov[i][j]=x[i];
       }
   ncovmodel=2+cptcovn;    }
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  
      printf("\n#Hessian matrix#\n");
   /* Read guess parameters */    fprintf(ficlog,"\n#Hessian matrix#\n");
   /* Reads comments: lines beginning with '#' */    for (i=1;i<=npar;i++) { 
   while((c=getc(ficpar))=='#' && c!= EOF){      for (j=1;j<=npar;j++) { 
     ungetc(c,ficpar);        printf("%.3e ",hess[i][j]);
     fgets(line, MAXLINE, ficpar);        fprintf(ficlog,"%.3e ",hess[i][j]);
     puts(line);      }
     fputs(line,ficparo);      printf("\n");
   }      fprintf(ficlog,"\n");
   ungetc(c,ficpar);    }
    
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    /* Recompute Inverse */
     for(i=1; i <=nlstate; i++)    for (i=1;i<=npar;i++)
     for(j=1; j <=nlstate+ndeath-1; j++){      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
       fscanf(ficpar,"%1d%1d",&i1,&j1);    ludcmp(a,npar,indx,&pd);
       fprintf(ficparo,"%1d%1d",i1,j1);  
       printf("%1d%1d",i,j);    /*  printf("\n#Hessian matrix recomputed#\n");
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar," %lf",&param[i][j][k]);    for (j=1;j<=npar;j++) {
         printf(" %lf",param[i][j][k]);      for (i=1;i<=npar;i++) x[i]=0;
         fprintf(ficparo," %lf",param[i][j][k]);      x[j]=1;
       }      lubksb(a,npar,indx,x);
       fscanf(ficpar,"\n");      for (i=1;i<=npar;i++){ 
       printf("\n");        y[i][j]=x[i];
       fprintf(ficparo,"\n");        printf("%.3e ",y[i][j]);
     }        fprintf(ficlog,"%.3e ",y[i][j]);
        }
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;      printf("\n");
   p=param[1][1];      fprintf(ficlog,"\n");
      }
   /* Reads comments: lines beginning with '#' */    */
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    free_matrix(a,1,npar,1,npar);
     fgets(line, MAXLINE, ficpar);    free_matrix(y,1,npar,1,npar);
     puts(line);    free_vector(x,1,npar);
     fputs(line,ficparo);    free_ivector(indx,1,npar);
   }    free_matrix(hess,1,npar,1,npar);
   ungetc(c,ficpar);  
   
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);  }
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */  
   for(i=1; i <=nlstate; i++){  /*************** hessian matrix ****************/
     for(j=1; j <=nlstate+ndeath-1; j++){  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
       fscanf(ficpar,"%1d%1d",&i1,&j1);  {
       printf("%1d%1d",i,j);    int i;
       fprintf(ficparo,"%1d%1d",i1,j1);    int l=1, lmax=20;
       for(k=1; k<=ncovmodel;k++){    double k1,k2;
         fscanf(ficpar,"%le",&delti3[i][j][k]);    double p2[NPARMAX+1];
         printf(" %le",delti3[i][j][k]);    double res;
         fprintf(ficparo," %le",delti3[i][j][k]);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
       }    double fx;
       fscanf(ficpar,"\n");    int k=0,kmax=10;
       printf("\n");    double l1;
       fprintf(ficparo,"\n");  
     }    fx=func(x);
   }    for (i=1;i<=npar;i++) p2[i]=x[i];
   delti=delti3[1][1];    for(l=0 ; l <=lmax; l++){
        l1=pow(10,l);
   /* Reads comments: lines beginning with '#' */      delts=delt;
   while((c=getc(ficpar))=='#' && c!= EOF){      for(k=1 ; k <kmax; k=k+1){
     ungetc(c,ficpar);        delt = delta*(l1*k);
     fgets(line, MAXLINE, ficpar);        p2[theta]=x[theta] +delt;
     puts(line);        k1=func(p2)-fx;
     fputs(line,ficparo);        p2[theta]=x[theta]-delt;
   }        k2=func(p2)-fx;
   ungetc(c,ficpar);        /*res= (k1-2.0*fx+k2)/delt/delt; */
          res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   matcov=matrix(1,npar,1,npar);        
   for(i=1; i <=npar; i++){  #ifdef DEBUG
     fscanf(ficpar,"%s",&str);        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
     printf("%s",str);        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);
     fprintf(ficparo,"%s",str);  #endif
     for(j=1; j <=i; j++){        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
       fscanf(ficpar," %le",&matcov[i][j]);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
       printf(" %.5le",matcov[i][j]);          k=kmax;
       fprintf(ficparo," %.5le",matcov[i][j]);        }
     }        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
     fscanf(ficpar,"\n");          k=kmax; l=lmax*10.;
     printf("\n");        }
     fprintf(ficparo,"\n");        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   }          delts=delt;
   for(i=1; i <=npar; i++)        }
     for(j=i+1;j<=npar;j++)      }
       matcov[i][j]=matcov[j][i];    }
        delti[theta]=delts;
   printf("\n");    return res; 
     
   }
     /*-------- data file ----------*/  
     if((ficres =fopen(fileres,"w"))==NULL) {  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
       printf("Problem with resultfile: %s\n", fileres);goto end;  {
     }    int i;
     fprintf(ficres,"#%s\n",version);    int l=1, l1, lmax=20;
        double k1,k2,k3,k4,res,fx;
     if((fic=fopen(datafile,"r"))==NULL)    {    double p2[NPARMAX+1];
       printf("Problem with datafile: %s\n", datafile);goto end;    int k;
     }  
     fx=func(x);
     n= lastobs;    for (k=1; k<=2; k++) {
     severity = vector(1,maxwav);      for (i=1;i<=npar;i++) p2[i]=x[i];
     outcome=imatrix(1,maxwav+1,1,n);      p2[thetai]=x[thetai]+delti[thetai]/k;
     num=ivector(1,n);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     moisnais=vector(1,n);      k1=func(p2)-fx;
     annais=vector(1,n);    
     moisdc=vector(1,n);      p2[thetai]=x[thetai]+delti[thetai]/k;
     andc=vector(1,n);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     agedc=vector(1,n);      k2=func(p2)-fx;
     cod=ivector(1,n);    
     weight=vector(1,n);      p2[thetai]=x[thetai]-delti[thetai]/k;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     mint=matrix(1,maxwav,1,n);      k3=func(p2)-fx;
     anint=matrix(1,maxwav,1,n);    
     s=imatrix(1,maxwav+1,1,n);      p2[thetai]=x[thetai]-delti[thetai]/k;
     adl=imatrix(1,maxwav+1,1,n);          p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     tab=ivector(1,NCOVMAX);      k4=func(p2)-fx;
     ncodemax=ivector(1,8);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   #ifdef DEBUG
     i=1;      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);
     while (fgets(line, MAXLINE, fic) != NULL)    {      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);
       if ((i >= firstobs) && (i <=lastobs)) {  #endif
            }
         for (j=maxwav;j>=1;j--){    return res;
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);  }
           strcpy(line,stra);  
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  /************** Inverse of matrix **************/
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  void ludcmp(double **a, int n, int *indx, double *d) 
         }  { 
            int i,imax,j,k; 
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);    double big,dum,sum,temp; 
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    double *vv; 
    
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);    vv=vector(1,n); 
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    *d=1.0; 
     for (i=1;i<=n;i++) { 
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      big=0.0; 
         for (j=ncov;j>=1;j--){      for (j=1;j<=n;j++) 
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);        if ((temp=fabs(a[i][j])) > big) big=temp; 
         }      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
         num[i]=atol(stra);      vv[i]=1.0/big; 
     } 
         /*printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/    for (j=1;j<=n;j++) { 
       for (i=1;i<j;i++) { 
         i=i+1;        sum=a[i][j]; 
       }        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     }        a[i][j]=sum; 
       } 
     /*scanf("%d",i);*/      big=0.0; 
   imx=i-1; /* Number of individuals */      for (i=j;i<=n;i++) { 
         sum=a[i][j]; 
   /* Calculation of the number of parameter from char model*/        for (k=1;k<j;k++) 
   Tvar=ivector(1,15);          sum -= a[i][k]*a[k][j]; 
   Tprod=ivector(1,15);        a[i][j]=sum; 
   Tvaraff=ivector(1,15);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   Tvard=imatrix(1,15,1,2);          big=dum; 
   Tage=ivector(1,15);                imax=i; 
            } 
   if (strlen(model) >1){      } 
     j=0, j1=0, k1=1, k2=1;      if (j != imax) { 
     j=nbocc(model,'+');        for (k=1;k<=n;k++) { 
     j1=nbocc(model,'*');          dum=a[imax][k]; 
     cptcovn=j+1;          a[imax][k]=a[j][k]; 
     cptcovprod=j1;          a[j][k]=dum; 
            } 
            *d = -(*d); 
     strcpy(modelsav,model);        vv[imax]=vv[j]; 
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){      } 
       printf("Error. Non available option model=%s ",model);      indx[j]=imax; 
       goto end;      if (a[j][j] == 0.0) a[j][j]=TINY; 
     }      if (j != n) { 
            dum=1.0/(a[j][j]); 
     for(i=(j+1); i>=1;i--){        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
       cutv(stra,strb,modelsav,'+');      } 
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    } 
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    free_vector(vv,1,n);  /* Doesn't work */
       /*scanf("%d",i);*/  ;
       if (strchr(strb,'*')) {  } 
         cutv(strd,strc,strb,'*');  
         if (strcmp(strc,"age")==0) {  void lubksb(double **a, int n, int *indx, double b[]) 
           cptcovprod--;  { 
           cutv(strb,stre,strd,'V');    int i,ii=0,ip,j; 
           Tvar[i]=atoi(stre);    double sum; 
           cptcovage++;   
             Tage[cptcovage]=i;    for (i=1;i<=n;i++) { 
             /*printf("stre=%s ", stre);*/      ip=indx[i]; 
         }      sum=b[ip]; 
         else if (strcmp(strd,"age")==0) {      b[ip]=b[i]; 
           cptcovprod--;      if (ii) 
           cutv(strb,stre,strc,'V');        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
           Tvar[i]=atoi(stre);      else if (sum) ii=i; 
           cptcovage++;      b[i]=sum; 
           Tage[cptcovage]=i;    } 
         }    for (i=n;i>=1;i--) { 
         else {      sum=b[i]; 
           cutv(strb,stre,strc,'V');      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
           Tvar[i]=ncov+k1;      b[i]=sum/a[i][i]; 
           cutv(strb,strc,strd,'V');    } 
           Tprod[k1]=i;  } 
           Tvard[k1][1]=atoi(strc);  
           Tvard[k1][2]=atoi(stre);  /************ Frequencies ********************/
           Tvar[cptcovn+k2]=Tvard[k1][1];  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[])
           Tvar[cptcovn+k2+1]=Tvard[k1][2];  {  /* Some frequencies */
           for (k=1; k<=lastobs;k++)    
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
           k1++;    int first;
           k2=k2+2;    double ***freq; /* Frequencies */
         }    double *pp, **prop;
       }    double pos,posprop, k2, dateintsum=0,k2cpt=0;
       else {    FILE *ficresp;
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/    char fileresp[FILENAMELENGTH];
        /*  scanf("%d",i);*/    
       cutv(strd,strc,strb,'V');    pp=vector(1,nlstate);
       Tvar[i]=atoi(strc);    prop=matrix(1,nlstate,iagemin,iagemax+3);
       }    strcpy(fileresp,"p");
       strcpy(modelsav,stra);      strcat(fileresp,fileres);
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    if((ficresp=fopen(fileresp,"w"))==NULL) {
         scanf("%d",i);*/      printf("Problem with prevalence resultfile: %s\n", fileresp);
     }      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
 }      exit(0);
      }
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
   printf("cptcovprod=%d ", cptcovprod);    j1=0;
   scanf("%d ",i);*/    
     fclose(fic);    j=cptcoveff;
     if (cptcovn<1) {j=1;ncodemax[1]=1;}
     /*  if(mle==1){*/  
     if (weightopt != 1) { /* Maximisation without weights*/    first=1;
       for(i=1;i<=n;i++) weight[i]=1.0;  
     }    for(k1=1; k1<=j;k1++){
     /*-calculation of age at interview from date of interview and age at death -*/      for(i1=1; i1<=ncodemax[k1];i1++){
     agev=matrix(1,maxwav,1,imx);        j1++;
            /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     for (i=1; i<=imx; i++)  {          scanf("%d", i);*/
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);        for (i=-5; i<=nlstate+ndeath; i++)  
       for(m=1; (m<= maxwav); m++){          for (jk=-5; jk<=nlstate+ndeath; jk++)  
         if(s[m][i] >0){            for(m=iagemin; m <= iagemax+3; m++)
           if (s[m][i] == nlstate+1) {              freq[i][jk][m]=0;
             if(agedc[i]>0)  
               if(moisdc[i]!=99 && andc[i]!=9999)      for (i=1; i<=nlstate; i++)  
               agev[m][i]=agedc[i];        for(m=iagemin; m <= iagemax+3; m++)
             else {          prop[i][m]=0;
               if (andc[i]!=9999){        
               printf("Warning negative age at death: %d line:%d\n",num[i],i);        dateintsum=0;
               agev[m][i]=-1;        k2cpt=0;
               }        for (i=1; i<=imx; i++) {
             }          bool=1;
           }          if  (cptcovn>0) {
           else if(s[m][i] !=9){ /* Should no more exist */            for (z1=1; z1<=cptcoveff; z1++) 
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
             if(mint[m][i]==99 || anint[m][i]==9999)                bool=0;
               agev[m][i]=1;          }
             else if(agev[m][i] <agemin){          if (bool==1){
               agemin=agev[m][i];            for(m=firstpass; m<=lastpass; m++){
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/              k2=anint[m][i]+(mint[m][i]/12.);
             }              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
             else if(agev[m][i] >agemax){                if(agev[m][i]==0) agev[m][i]=iagemax+1;
               agemax=agev[m][i];                if(agev[m][i]==1) agev[m][i]=iagemax+2;
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
             }                if (m<lastpass) {
             /*agev[m][i]=anint[m][i]-annais[i];*/                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
             /*   agev[m][i] = age[i]+2*m;*/                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
           }                }
           else { /* =9 */                
             agev[m][i]=1;                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
             s[m][i]=-1;                  dateintsum=dateintsum+k2;
           }                  k2cpt++;
         }                }
         else /*= 0 Unknown */                /*}*/
           agev[m][i]=1;            }
       }          }
            }
     }         
     for (i=1; i<=imx; i++)  {        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       for(m=1; (m<= maxwav); m++){  fprintf(ficresp, "#Local time at start: %s", strstart);
         if (s[m][i] > (nlstate+ndeath)) {        if  (cptcovn>0) {
           printf("Error: Wrong value in nlstate or ndeath\n");            fprintf(ficresp, "\n#********** Variable "); 
           goto end;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         }          fprintf(ficresp, "**********\n#");
       }        }
     }        for(i=1; i<=nlstate;i++) 
           fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);        fprintf(ficresp, "\n");
         
     free_vector(severity,1,maxwav);        for(i=iagemin; i <= iagemax+3; i++){
     free_imatrix(outcome,1,maxwav+1,1,n);          if(i==iagemax+3){
     free_vector(moisnais,1,n);            fprintf(ficlog,"Total");
     free_vector(annais,1,n);          }else{
     free_matrix(mint,1,maxwav,1,n);            if(first==1){
     free_matrix(anint,1,maxwav,1,n);              first=0;
     free_vector(moisdc,1,n);              printf("See log file for details...\n");
     free_vector(andc,1,n);            }
             fprintf(ficlog,"Age %d", i);
              }
     wav=ivector(1,imx);          for(jk=1; jk <=nlstate ; jk++){
     dh=imatrix(1,lastpass-firstpass+1,1,imx);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     mw=imatrix(1,lastpass-firstpass+1,1,imx);              pp[jk] += freq[jk][m][i]; 
              }
     /* Concatenates waves */          for(jk=1; jk <=nlstate ; jk++){
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);            for(m=-1, pos=0; m <=0 ; m++)
               pos += freq[jk][m][i];
             if(pp[jk]>=1.e-10){
       Tcode=ivector(1,100);              if(first==1){
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
       ncodemax[1]=1;              }
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                  }else{
    codtab=imatrix(1,100,1,10);              if(first==1)
    h=0;                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
    m=pow(2,cptcoveff);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
              }
    for(k=1;k<=cptcoveff; k++){          }
      for(i=1; i <=(m/pow(2,k));i++){  
        for(j=1; j <= ncodemax[k]; j++){          for(jk=1; jk <=nlstate ; jk++){
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
            h++;              pp[jk] += freq[jk][m][i];
            if (h>m) h=1;codtab[h][k]=j;          }       
          }          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
        }            pos += pp[jk];
      }            posprop += prop[jk][i];
    }          }
           for(jk=1; jk <=nlstate ; jk++){
             if(pos>=1.e-5){
    /*for(i=1; i <=m ;i++){              if(first==1)
      for(k=1; k <=cptcovn; k++){                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
      }            }else{
      printf("\n");              if(first==1)
    }                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
    scanf("%d",i);*/              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
                }
    /* Calculates basic frequencies. Computes observed prevalence at single age            if( i <= iagemax){
        and prints on file fileres'p'. */              if(pos>=1.e-5){
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                 /*probs[i][jk][j1]= pp[jk]/pos;*/
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              }
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              else
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     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] */          for(jk=-1; jk <=nlstate+ndeath; jk++)
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */            for(m=-1; m <=nlstate+ndeath; m++)
               if(freq[jk][m][i] !=0 ) {
     if(mle==1){              if(first==1)
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
     }                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
                  }
     /*--------- results files --------------*/          if(i <= iagemax)
     fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);            fprintf(ficresp,"\n");
              if(first==1)
    jk=1;            printf("Others in log...\n");
    fprintf(ficres,"# Parameters\n");          fprintf(ficlog,"\n");
    printf("# Parameters\n");        }
    for(i=1,jk=1; i <=nlstate; i++){      }
      for(k=1; k <=(nlstate+ndeath); k++){    }
        if (k != i)    dateintmean=dateintsum/k2cpt; 
          {   
            printf("%d%d ",i,k);    fclose(ficresp);
            fprintf(ficres,"%1d%1d ",i,k);    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
            for(j=1; j <=ncovmodel; j++){    free_vector(pp,1,nlstate);
              printf("%f ",p[jk]);    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
              fprintf(ficres,"%f ",p[jk]);    /* End of Freq */
              jk++;  }
            }  
            printf("\n");  /************ Prevalence ********************/
            fprintf(ficres,"\n");  void prevalence(double ***probs, double agemin, double agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, int firstpass, int lastpass)
          }  {  
      }    /* 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).
  if(mle==1){       We still use firstpass and lastpass as another selection.
     /* Computing hessian and covariance matrix */    */
     ftolhess=ftol; /* Usually correct */   
     hesscov(matcov, p, npar, delti, ftolhess, func);    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
  }    double ***freq; /* Frequencies */
     fprintf(ficres,"# Scales\n");    double *pp, **prop;
     printf("# Scales\n");    double pos,posprop; 
      for(i=1,jk=1; i <=nlstate; i++){    double  y2; /* in fractional years */
       for(j=1; j <=nlstate+ndeath; j++){    int iagemin, iagemax;
         if (j!=i) {  
           fprintf(ficres,"%1d%1d",i,j);    iagemin= (int) agemin;
           printf("%1d%1d",i,j);    iagemax= (int) agemax;
           for(k=1; k<=ncovmodel;k++){    /*pp=vector(1,nlstate);*/
             printf(" %.5e",delti[jk]);    prop=matrix(1,nlstate,iagemin,iagemax+3); 
             fprintf(ficres," %.5e",delti[jk]);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
             jk++;    j1=0;
           }    
           printf("\n");    j=cptcoveff;
           fprintf(ficres,"\n");    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         }    
       }    for(k1=1; k1<=j;k1++){
       }      for(i1=1; i1<=ncodemax[k1];i1++){
            j1++;
     k=1;        
     fprintf(ficres,"# Covariance\n");        for (i=1; i<=nlstate; i++)  
     printf("# Covariance\n");          for(m=iagemin; m <= iagemax+3; m++)
     for(i=1;i<=npar;i++){            prop[i][m]=0.0;
       /*  if (k>nlstate) k=1;       
       i1=(i-1)/(ncovmodel*nlstate)+1;        for (i=1; i<=imx; i++) { /* Each individual */
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);          bool=1;
       printf("%s%d%d",alph[k],i1,tab[i]);*/          if  (cptcovn>0) {
       fprintf(ficres,"%3d",i);            for (z1=1; z1<=cptcoveff; z1++) 
       printf("%3d",i);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       for(j=1; j<=i;j++){                bool=0;
         fprintf(ficres," %.5e",matcov[i][j]);          } 
         printf(" %.5e",matcov[i][j]);          if (bool==1) { 
       }            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
       fprintf(ficres,"\n");              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
       printf("\n");              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
       k++;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     }                if(agev[m][i]==1) agev[m][i]=iagemax+2;
                    if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
     while((c=getc(ficpar))=='#' && c!= EOF){                if (s[m][i]>0 && s[m][i]<=nlstate) { 
       ungetc(c,ficpar);                  /*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]]);*/
       fgets(line, MAXLINE, ficpar);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
       puts(line);                  prop[s[m][i]][iagemax+3] += weight[i]; 
       fputs(line,ficparo);                } 
     }              }
     ungetc(c,ficpar);            } /* end selection of waves */
            }
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);        }
            for(i=iagemin; i <= iagemax+3; i++){  
     if (fage <= 2) {          
       bage = agemin;          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
       fage = agemax;            posprop += prop[jk][i]; 
     }          } 
   
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");          for(jk=1; jk <=nlstate ; jk++){     
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);            if( i <=  iagemax){ 
               if(posprop>=1.e-5){ 
                    probs[i][jk][j1]= prop[jk][i]/posprop;
 /*------------ gnuplot -------------*/              } 
 chdir(pathcd);            } 
   if((ficgp=fopen("graph.plt","w"))==NULL) {          }/* end jk */ 
     printf("Problem with file graph.gp");goto end;        }/* end i */ 
   }      } /* end i1 */
 #ifdef windows    } /* end k1 */
   fprintf(ficgp,"cd \"%s\" \n",pathc);    
 #endif    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
 m=pow(2,cptcoveff);    /*free_vector(pp,1,nlstate);*/
      free_matrix(prop,1,nlstate, iagemin,iagemax+3);
  /* 1eme*/  }  /* End of prevalence */
   for (cpt=1; cpt<= nlstate ; cpt ++) {  
    for (k1=1; k1<= m ; k1 ++) {  /************* Waves Concatenation ***************/
   
 #ifdef windows  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
     fprintf(ficgp,"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",agemin,fage,fileres,k1-1,k1-1);  {
 #endif    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
 #ifdef unix       Death is a valid wave (if date is known).
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
 #endif       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
        and mw[mi+1][i]. dh depends on stepm.
 for (i=1; i<= nlstate ; i ++) {       */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");    int i, mi, m;
 }    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-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);       double sum=0., jmean=0.;*/
     for (i=1; i<= nlstate ; i ++) {    int first;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    int j, k=0,jk, ju, jl;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double sum=0.;
 }    first=0;
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    jmin=1e+5;
      for (i=1; i<= nlstate ; i ++) {    jmax=-1;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    jmean=0.;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    for(i=1; i<=imx; i++){
 }        mi=0;
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      m=firstpass;
 #ifdef unix      while(s[m][i] <= nlstate){
 fprintf(ficgp,"\nset ter gif small size 400,300");        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
 #endif          mw[++mi][i]=m;
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        if(m >=lastpass)
    }          break;
   }        else
   /*2 eme*/          m++;
       }/* end while */
   for (k1=1; k1<= m ; k1 ++) {      if (s[m][i] > nlstate){
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);        mi++;     /* Death is another wave */
            /* if(mi==0)  never been interviewed correctly before death */
     for (i=1; i<= nlstate+1 ; i ++) {           /* Only death is a correct wave */
       k=2*i;        mw[mi][i]=m;
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);      }
       for (j=1; j<= nlstate+1 ; j ++) {  
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      wav[i]=mi;
   else fprintf(ficgp," \%%*lf (\%%*lf)");      if(mi==0){
 }          nbwarn++;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");        if(first==0){
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);          first=1;
       for (j=1; j<= nlstate+1 ; j ++) {        }
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        if(first==1){
         else fprintf(ficgp," \%%*lf (\%%*lf)");          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
 }          }
       fprintf(ficgp,"\" t\"\" w l 0,");      } /* end mi==0 */
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    } /* End individuals */
       for (j=1; j<= nlstate+1 ; j ++) {  
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    for(i=1; i<=imx; i++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");      for(mi=1; mi<wav[i];mi++){
 }          if (stepm <=0)
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");          dh[mi][i]=1;
       else fprintf(ficgp,"\" t\"\" w l 0,");        else{
     }          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);            if (agedc[i] < 2*AGESUP) {
   }              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
                if(j==0) j=1;  /* Survives at least one month after exam */
   /*3eme*/              else if(j<0){
                 nberr++;
   for (k1=1; k1<= m ; k1 ++) {                printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     for (cpt=1; cpt<= nlstate ; cpt ++) {                j=1; /* Temporary Dangerous patch */
       k=2+nlstate*(cpt-1);                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(ficgp,"set ter gif small size 400,300\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",agemin,fage,fileres,k1-1,k1-1,k,cpt);                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       for (i=1; i< nlstate ; i ++) {                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
         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);              }
       }              k=k+1;
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              if (j >= jmax){
     }                jmax=j;
   }                ijmax=i;
                }
   /* CV preval stat */              if (j <= jmin){
   for (k1=1; k1<= m ; k1 ++) {                jmin=j;
     for (cpt=1; cpt<nlstate ; cpt ++) {                ijmin=i;
       k=3;              }
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);              sum=sum+j;
       for (i=1; i< nlstate ; i ++)              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
         fprintf(ficgp,"+$%d",k+i+1);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);            }
                }
       l=3+(nlstate+ndeath)*cpt;          else{
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
       for (i=1; i< nlstate ; i ++) {  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
         l=3+(nlstate+ndeath)*cpt;  
         fprintf(ficgp,"+$%d",l+i+1);            k=k+1;
       }            if (j >= jmax) {
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                jmax=j;
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              ijmax=i;
     }            }
   }            else if (j <= jmin){
               jmin=j;
   /* proba elementaires */              ijmin=i;
    for(i=1,jk=1; i <=nlstate; i++){            }
     for(k=1; k <=(nlstate+ndeath); k++){            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
       if (k != i) {            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
         for(j=1; j <=ncovmodel; j++){            if(j<0){
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/              nberr++;
           /*fprintf(ficgp,"%s",alph[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(ficgp,"p%d=%f ",jk,p[jk]);              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]);
           jk++;            }
           fprintf(ficgp,"\n");            sum=sum+j;
         }          }
       }          jk= j/stepm;
     }          jl= j -jk*stepm;
     }          ju= j -(jk+1)*stepm;
           if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
   for(jk=1; jk <=m; jk++) {            if(jl==0){
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);              dh[mi][i]=jk;
    i=1;              bh[mi][i]=0;
    for(k2=1; k2<=nlstate; k2++) {            }else{ /* We want a negative bias in order to only have interpolation ie
      k3=i;                    * at the price of an extra matrix product in likelihood */
      for(k=1; k<=(nlstate+ndeath); k++) {              dh[mi][i]=jk+1;
        if (k != k2){              bh[mi][i]=ju;
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);            }
 ij=1;          }else{
         for(j=3; j <=ncovmodel; j++) {            if(jl <= -ju){
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {              dh[mi][i]=jk;
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);              bh[mi][i]=jl;       /* bias is positive if real duration
             ij++;                                   * is higher than the multiple of stepm and negative otherwise.
           }                                   */
           else            }
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            else{
         }              dh[mi][i]=jk+1;
           fprintf(ficgp,")/(1");              bh[mi][i]=ju;
                    }
         for(k1=1; k1 <=nlstate; k1++){              if(dh[mi][i]==0){
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);              dh[mi][i]=1; /* At least one step */
 ij=1;              bh[mi][i]=ju; /* At least one step */
           for(j=3; j <=ncovmodel; j++){              /*  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);*/
           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]]]);          } /* end if mle */
             ij++;        }
           }      } /* end wave */
           else    }
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    jmean=sum/k;
           }    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
           fprintf(ficgp,")");    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
         }   }
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);  
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");  /*********** Tricode ****************************/
         i=i+ncovmodel;  void tricode(int *Tvar, int **nbcode, int imx)
        }  {
      }    
    }    int Ndum[20],ij=1, k, j, i, maxncov=19;
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    int cptcode=0;
   }    cptcoveff=0; 
       
   fclose(ficgp);    for (k=0; k<maxncov; k++) Ndum[k]=0;
        for (k=1; k<=7; k++) ncodemax[k]=0;
 chdir(path);  
     free_matrix(agev,1,maxwav,1,imx);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
     free_ivector(wav,1,imx);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);                                 modality*/ 
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
            Ndum[ij]++; /*store the modality */
     free_imatrix(s,1,maxwav+1,1,n);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
            if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
                                             Tvar[j]. If V=sex and male is 0 and 
     free_ivector(num,1,n);                                         female is 1, then  cptcode=1.*/
     free_vector(agedc,1,n);      }
     free_vector(weight,1,n);  
     /*free_matrix(covar,1,NCOVMAX,1,n);*/      for (i=0; i<=cptcode; i++) {
     fclose(ficparo);        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 */
     fclose(ficres);      }
     /*  }*/  
          ij=1; 
    /*________fin mle=1_________*/      for (i=1; i<=ncodemax[j]; i++) {
            for (k=0; k<= maxncov; k++) {
           if (Ndum[k] != 0) {
              nbcode[Tvar[j]][ij]=k; 
     /* No more information from the sample is required now */            /* 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; */
   /* Reads comments: lines beginning with '#' */            
   while((c=getc(ficpar))=='#' && c!= EOF){            ij++;
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);          if (ij > ncodemax[j]) break; 
     puts(line);        }  
     fputs(line,ficparo);      } 
   }    }  
   ungetc(c,ficpar);  
     for (k=0; k< maxncov; k++) Ndum[k]=0;
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);  
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);   for (i=1; i<=ncovmodel-2; i++) { 
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
 /*--------- index.htm --------*/     ij=Tvar[i];
      Ndum[ij]++;
   strcpy(optionfilehtm,optionfile);   }
   strcat(optionfilehtm,".htm");  
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {   ij=1;
     printf("Problem with %s \n",optionfilehtm);goto end;   for (i=1; i<= maxncov; i++) {
   }     if((Ndum[i]!=0) && (i<=ncovcol)){
        Tvaraff[ij]=i; /*For printing */
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.64b </font> <hr size=\"2\" color=\"#EC5E5E\">       ij++;
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>     }
 Total number of observations=%d <br>   }
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>   
 <hr  size=\"2\" color=\"#EC5E5E\">   cptcoveff=ij-1; /*Number of simple covariates*/
 <li>Outputs files<br><br>\n  }
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n  
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>  /*********** Health Expectancies ****************/
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>  
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>  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[] )
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>  
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>  {
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>    /* Health expectancies */
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);    double age, agelim, hf;
     double ***p3mat,***varhe;
  fprintf(fichtm," <li>Graphs</li><p>");    double **dnewm,**doldm;
     double *xp;
  m=cptcoveff;    double **gp, **gm;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    double ***gradg, ***trgradg;
     int theta;
  j1=0;  
  for(k1=1; k1<=m;k1++){    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
    for(i1=1; i1<=ncodemax[k1];i1++){    xp=vector(1,npar);
        j1++;    dnewm=matrix(1,nlstate*nlstate,1,npar);
        if (cptcovn > 0) {    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    
          for (cpt=1; cpt<=cptcoveff;cpt++)    fprintf(ficreseij,"# Local time at start: %s", strstart);
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);    fprintf(ficreseij,"# Health expectancies\n");
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    fprintf(ficreseij,"# Age");
        }    for(i=1; i<=nlstate;i++)
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>      for(j=1; j<=nlstate;j++)
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);            fprintf(ficreseij," %1d-%1d (SE)",i,j);
        for(cpt=1; cpt<nlstate;cpt++){    fprintf(ficreseij,"\n");
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>  
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    if(estepm < stepm){
        }      printf ("Problem %d lower than %d\n",estepm, stepm);
     for(cpt=1; cpt<=nlstate;cpt++) {    }
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    else  hstepm=estepm;   
 interval) in state (%d): v%s%d%d.gif <br>    /* We compute the life expectancy from trapezoids spaced every estepm months
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);       * This is mainly to measure the difference between two models: for example
      }     * if stepm=24 months pijx are given only every 2 years and by summing them
      for(cpt=1; cpt<=nlstate;cpt++) {     * we are calculating an estimate of the Life Expectancy assuming a linear 
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>     * progression in between and thus overestimating or underestimating according
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);     * 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
      fprintf(fichtm,"\n<br>- Total life expectancy by age and     * to compare the new estimate of Life expectancy with the same linear 
 health expectancies in states (1) and (2): e%s%d.gif<br>     * hypothesis. A more precise result, taking into account a more precise
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);     * curvature will be obtained if estepm is as small as stepm. */
 fprintf(fichtm,"\n</body>");  
    }    /* For example we decided to compute the life expectancy with the smallest unit */
  }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
 fclose(fichtm);       nhstepm is the number of hstepm from age to agelim 
        nstepm is the number of stepm from age to agelin. 
   /*--------------- Prevalence limit --------------*/       Look at hpijx to understand the reason of that which relies in memory size
         and note for a fixed period like estepm months */
   strcpy(filerespl,"pl");    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   strcat(filerespl,fileres);       survival function given by stepm (the optimization length). Unfortunately it
   if((ficrespl=fopen(filerespl,"w"))==NULL) {       means that if the survival funtion is printed only each two years of age and if
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;       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.
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    */
   fprintf(ficrespl,"#Prevalence limit\n");    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   fprintf(ficrespl,"#Age ");  
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    agelim=AGESUP;
   fprintf(ficrespl,"\n");    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
        /* nhstepm age range expressed in number of stepm */
   prlim=matrix(1,nlstate,1,nlstate);      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      /* if (stepm >= YEARM) hstepm=1;*/
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   k=0;      gp=matrix(0,nhstepm,1,nlstate*nlstate);
   agebase=agemin;      gm=matrix(0,nhstepm,1,nlstate*nlstate);
   agelim=agemax;  
   ftolpl=1.e-10;      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   i1=cptcoveff;         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   if (cptcovn < 1){i1=1;}      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
    
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         k=k+1;  
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/      /* Computing  Variances of health expectancies */
         fprintf(ficrespl,"\n#******");  
         for(j=1;j<=cptcoveff;j++)       for(theta=1; theta <=npar; theta++){
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for(i=1; i<=npar; i++){ 
         fprintf(ficrespl,"******\n");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
                }
         for (age=agebase; age<=agelim; age++){        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    
           fprintf(ficrespl,"%.0f",age );        cptj=0;
           for(i=1; i<=nlstate;i++)        for(j=1; j<= nlstate; j++){
           fprintf(ficrespl," %.5f", prlim[i][i]);          for(i=1; i<=nlstate; i++){
           fprintf(ficrespl,"\n");            cptj=cptj+1;
         }            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
       }              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     }            }
   fclose(ficrespl);          }
   /*------------- h Pij x at various ages ------------*/        }
         
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);       
   if((ficrespij=fopen(filerespij,"w"))==NULL) {        for(i=1; i<=npar; i++) 
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   }        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   printf("Computing pij: result on file '%s' \n", filerespij);        
          cptj=0;
   stepsize=(int) (stepm+YEARM-1)/YEARM;        for(j=1; j<= nlstate; j++){
   if (stepm<=24) stepsize=2;          for(i=1;i<=nlstate;i++){
             cptj=cptj+1;
   agelim=AGESUP;            for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   hstepm=stepsize*YEARM; /* Every year of age */  
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
              }
   k=0;          }
   for(cptcov=1;cptcov<=i1;cptcov++){        }
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        for(j=1; j<= nlstate*nlstate; j++)
       k=k+1;          for(h=0; h<=nhstepm-1; h++){
         fprintf(ficrespij,"\n#****** ");            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
         for(j=1;j<=cptcoveff;j++)          }
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       } 
         fprintf(ficrespij,"******\n");     
          /* End theta */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */  
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       for(h=0; h<=nhstepm-1; h++)
           oldm=oldms;savm=savms;        for(j=1; j<=nlstate*nlstate;j++)
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);            for(theta=1; theta <=npar; theta++)
           fprintf(ficrespij,"# Age");            trgradg[h][j][theta]=gradg[h][theta][j];
           for(i=1; i<=nlstate;i++)       
             for(j=1; j<=nlstate+ndeath;j++)  
               fprintf(ficrespij," %1d-%1d",i,j);       for(i=1;i<=nlstate*nlstate;i++)
           fprintf(ficrespij,"\n");        for(j=1;j<=nlstate*nlstate;j++)
           for (h=0; h<=nhstepm; h++){          varhe[i][j][(int)age] =0.;
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );  
             for(i=1; i<=nlstate;i++)       printf("%d|",(int)age);fflush(stdout);
               for(j=1; j<=nlstate+ndeath;j++)       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);       for(h=0;h<=nhstepm-1;h++){
             fprintf(ficrespij,"\n");        for(k=0;k<=nhstepm-1;k++){
           }          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
           fprintf(ficrespij,"\n");          for(i=1;i<=nlstate*nlstate;i++)
         }            for(j=1;j<=nlstate*nlstate;j++)
     }              varhe[i][j][(int)age] += doldm[i][j]*hf*hf;
   }        }
       }
   fclose(ficrespij);      /* Computing expectancies */
       for(i=1; i<=nlstate;i++)
   /*---------- Health expectancies and variances ------------*/        for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   strcpy(filerest,"t");            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
   strcat(filerest,fileres);            
   if((ficrest=fopen(filerest,"w"))==NULL) {  /* 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]);*/
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;  
   }          }
   printf("Computing Total LEs with variances: file '%s' \n", filerest);  
       fprintf(ficreseij,"%3.0f",age );
       cptj=0;
   strcpy(filerese,"e");      for(i=1; i<=nlstate;i++)
   strcat(filerese,fileres);        for(j=1; j<=nlstate;j++){
   if((ficreseij=fopen(filerese,"w"))==NULL) {          cptj++;
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   }        }
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      fprintf(ficreseij,"\n");
      
  strcpy(fileresv,"v");      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   strcat(fileresv,fileres);      free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   }      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    }
     printf("\n");
   k=0;    fprintf(ficlog,"\n");
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    free_vector(xp,1,npar);
       k=k+1;    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
       fprintf(ficrest,"\n#****** ");    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
       for(j=1;j<=cptcoveff;j++)    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  }
       fprintf(ficrest,"******\n");  
   /************ Variance ******************/
       fprintf(ficreseij,"\n#****** ");  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[])
       for(j=1;j<=cptcoveff;j++)  {
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    /* Variance of health expectancies */
       fprintf(ficreseij,"******\n");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
       fprintf(ficresvij,"\n#****** ");    double **dnewm,**doldm;
       for(j=1;j<=cptcoveff;j++)    double **dnewmp,**doldmp;
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    int i, j, nhstepm, hstepm, h, nstepm ;
       fprintf(ficresvij,"******\n");    int k, cptcode;
     double *xp;
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    double **gp, **gm;  /* for var eij */
       oldm=oldms;savm=savms;    double ***gradg, ***trgradg; /*for var eij */
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);      double **gradgp, **trgradgp; /* for var p point j */
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    double *gpp, *gmp; /* for var p point j */
       oldm=oldms;savm=savms;    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    double ***p3mat;
          double age,agelim, hf;
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    double ***mobaverage;
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    int theta;
       fprintf(ficrest,"\n");    char digit[4];
            char digitp[25];
       hf=1;  
       if (stepm >= YEARM) hf=stepm/YEARM;    char fileresprobmorprev[FILENAMELENGTH];
       epj=vector(1,nlstate+1);  
       for(age=bage; age <=fage ;age++){    if(popbased==1){
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);      if(mobilav!=0)
         fprintf(ficrest," %.0f",age);        strcpy(digitp,"-populbased-mobilav-");
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){      else strcpy(digitp,"-populbased-nomobil-");
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    }
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];    else 
           }      strcpy(digitp,"-stablbased-");
           epj[nlstate+1] +=epj[j];  
         }    if (mobilav!=0) {
         for(i=1, vepp=0.;i <=nlstate;i++)      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
           for(j=1;j <=nlstate;j++)      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
             vepp += vareij[i][j][(int)age];        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));        printf(" Error in movingaverage mobilav=%d\n",mobilav);
         for(j=1;j <=nlstate;j++){      }
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));    }
         }  
         fprintf(ficrest,"\n");    strcpy(fileresprobmorprev,"prmorprev"); 
       }    sprintf(digit,"%-d",ij);
     }    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   }    strcat(fileresprobmorprev,digit); /* Tvar to be done */
            strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
  fclose(ficreseij);    strcat(fileresprobmorprev,fileres);
  fclose(ficresvij);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   fclose(ficrest);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
   fclose(ficpar);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   free_vector(epj,1,nlstate+1);    }
   /*  scanf("%d ",i); */    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    
   /*------- Variance limit prevalence------*/      fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     fprintf(ficresprobmorprev, "#Local time at start: %s", strstart);
 strcpy(fileresvpl,"vpl");    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);
   strcat(fileresvpl,fileres);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);      fprintf(ficresprobmorprev," p.%-d SE",j);
     exit(0);      for(i=1; i<=nlstate;i++)
   }        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    }  
     fprintf(ficresprobmorprev,"\n");
  k=0;    fprintf(ficgp,"\n# Routine varevsij");
  for(cptcov=1;cptcov<=i1;cptcov++){    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    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");
      k=k+1;    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
      fprintf(ficresvpl,"\n#****** ");  /*   } */
      for(j=1;j<=cptcoveff;j++)    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);   fprintf(ficresvij, "#Local time at start: %s", strstart);
      fprintf(ficresvpl,"******\n");    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");
          fprintf(ficresvij,"# Age");
      varpl=matrix(1,nlstate,(int) bage, (int) fage);    for(i=1; i<=nlstate;i++)
      oldm=oldms;savm=savms;      for(j=1; j<=nlstate;j++)
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
    }    fprintf(ficresvij,"\n");
  }  
     xp=vector(1,npar);
   fclose(ficresvpl);    dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
   /*---------- End : free ----------------*/    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
    
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    gpp=vector(nlstate+1,nlstate+ndeath);
      gmp=vector(nlstate+1,nlstate+ndeath);
      trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    if(estepm < stepm){
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);      printf ("Problem %d lower than %d\n",estepm, stepm);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    }
      else  hstepm=estepm;   
   free_matrix(matcov,1,npar,1,npar);    /* For example we decided to compute the life expectancy with the smallest unit */
   free_vector(delti,1,npar);    /* 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 
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);       nstepm is the number of stepm from age to agelin. 
        Look at hpijx to understand the reason of that which relies in memory size
   printf("End of Imach\n");       and note for a fixed period like k years */
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         survival function given by stepm (the optimization length). Unfortunately it
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/       means that if the survival funtion is printed every two years of age and if
   /*printf("Total time was %d uSec.\n", total_usecs);*/       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   /*------ End -----------*/       results. So we changed our mind and took the option of the best precision.
     */
  end:    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
 #ifdef windows    agelim = AGESUP;
  chdir(pathcd);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
 #endif      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
  /*system("wgnuplot graph.plt");*/      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
  /*system("../gp37mgw/wgnuplot graph.plt");*/      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
  /*system("cd ../gp37mgw");*/      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
  system("..\\gp37mgw\\wgnuplot graph.plt");      gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
 #ifdef windows  
   while (z[0] != 'q') {  
     chdir(pathcd);      for(theta=1; theta <=npar; theta++){
     printf("\nType e to edit output files, c to start again, and q for exiting: ");        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
     scanf("%s",z);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     if (z[0] == 'c') system("./imach");        }
     else if (z[0] == 'e') {        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       chdir(path);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       system(optionfilehtm);  
     }        if (popbased==1) {
     else if (z[0] == 'q') exit(0);          if(mobilav ==0){
   }            for(i=1; i<=nlstate;i++)
 #endif              prlim[i][i]=probs[(int)age][i][ij];
 }          }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
     
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
   
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       } /* End theta */
   
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
       for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       }
     
       /* pptj */
       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++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   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); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
     free_vector(xp,1,npar);
     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);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
   }  /* end varevsij */
   
   /************ 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 */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     double **newm;
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
     int k, cptcode;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim;
     int theta;
     fprintf(ficresvpl, "#Local time at start: %s", strstart); 
     fprintf(ficresvpl,"# Standard deviation of stable prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       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 */
   
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
     int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
     int k=0,l, cptcode;
     int first=1, first1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age,agelim, cov[NCOVMAX];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
   
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     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);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("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");
     fprintf(ficresprob,"# Age");
     fprintf(ficresprobcov, "#Local time at start: %s", strstart);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     fprintf(ficresprobcor, "#Local time at start: %s", strstart);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcov,"# Age");
   
   
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprob," p%1d-%1d (SE)",i,j);
         fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
       }  
    /* fprintf(ficresprob,"\n");
     fprintf(ficresprobcov,"\n");
     fprintf(ficresprobcor,"\n");
    */
    xp=vector(1,npar);
     dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
     varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
     first=1;
     fprintf(ficgp,"\n# Routine varprob");
     fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
     fprintf(fichtm,"\n");
   
     fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
     file %s<br>\n",optionfilehtmcov);
     fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
   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 \
   would have been (1/(var pij), 0 , 0, 1/(var pkl)), and the confidence interval would be 2 \
   standard deviations wide on each axis. <br>\
    Now, if both incidences are correlated (usual case) we diagonalised the inverse of the covariance matrix\
    and made the appropriate rotation to look at the uncorrelated principal directions.<br>\
   To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
   
     cov[1]=1;
     tj=cptcoveff;
     if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     j1=0;
     for(t=1; t<=tj;t++){
       for(i1=1; i1<=ncodemax[t];i1++){ 
         j1++;
         if  (cptcovn>0) {
           fprintf(ficresprob, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprob, "**********\n#\n");
           fprintf(ficresprobcov, "\n#********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           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]]);
           fprintf(ficgp, "**********\n#\n");
           
           
           fprintf(fichtmcov, "\n<hr  size=\"2\" color=\"#EC5E5E\">********** Variable "); 
           for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
           
           fprintf(ficresprobcor, "\n#********** Variable ");    
           for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           fprintf(ficresprobcor, "**********\n#");    
         }
         
         for (age=bage; age<=fage; age ++){ 
           cov[2]=age;
           for (k=1; k<=cptcovn;k++) {
             cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
           }
           for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
           for (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]]];
           
           gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
           trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
           gp=vector(1,(nlstate)*(nlstate+ndeath));
           gm=vector(1,(nlstate)*(nlstate+ndeath));
       
           for(theta=1; theta <=npar; theta++){
             for(i=1; i<=npar; i++)
               xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
             
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             
             k=0;
             for(i=1; i<= (nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gp[k]=pmmij[i][j];
               }
             }
             
             for(i=1; i<=npar; i++)
               xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
       
             pmij(pmmij,cov,ncovmodel,xp,nlstate);
             k=0;
             for(i=1; i<=(nlstate); i++){
               for(j=1; j<=(nlstate+ndeath);j++){
                 k=k+1;
                 gm[k]=pmmij[i][j];
               }
             }
        
             for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
               gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
           }
   
           for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
             for(theta=1; theta <=npar; theta++)
               trgradg[j][theta]=gradg[theta][j];
           
           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);
           free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
           free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   
           pmij(pmmij,cov,ncovmodel,x,nlstate);
           
           k=0;
           for(i=1; i<=(nlstate); i++){
             for(j=1; j<=(nlstate+ndeath);j++){
               k=k+1;
               mu[k][(int) age]=pmmij[i][j];
             }
           }
           for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
               varpij[i][j][(int)age] = doldm[i][j];
   
           /*printf("\n%d ",(int)age);
             for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
             }*/
   
           fprintf(ficresprob,"\n%d ",(int)age);
           fprintf(ficresprobcov,"\n%d ",(int)age);
           fprintf(ficresprobcor,"\n%d ",(int)age);
   
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
             fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
             fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
           }
           i=0;
           for (k=1; k<=(nlstate);k++){
             for (l=1; l<=(nlstate+ndeath);l++){ 
               i=i++;
               fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
               fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
               for (j=1; j<=i;j++){
                 fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
                 fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
               }
             }
           }/* end of loop for state */
         } /* end of loop for age */
   
         /* Confidence intervalle of pij  */
         /*
           fprintf(ficgp,"\nset noparametric;unset label");
           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");
           fprintf(fichtm,"\n<br>Probability with  confidence intervals expressed in year<sup>-1</sup> :<a href=\"pijgr%s.png\">pijgr%s.png</A>, ",optionfilefiname,optionfilefiname);
           fprintf(fichtm,"\n<br><img src=\"pijgr%s.png\"> ",optionfilefiname);
           fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
           fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
         */
   
         /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
         first1=1;
         for (k2=1; k2<=(nlstate);k2++){
           for (l2=1; l2<=(nlstate+ndeath);l2++){ 
             if(l2==k2) continue;
             j=(k2-1)*(nlstate+ndeath)+l2;
             for (k1=1; k1<=(nlstate);k1++){
               for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                 if(l1==k1) continue;
                 i=(k1-1)*(nlstate+ndeath)+l1;
                 if(i<=j) continue;
                 for (age=bage; age<=fage; age ++){ 
                   if ((int)age %5==0){
                     v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
                     v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
                     mu1=mu[i][(int) age]/stepm*YEARM ;
                     mu2=mu[j][(int) age]/stepm*YEARM;
                     c12=cv12/sqrt(v1*v2);
                     /* Computing eigen value of matrix of covariance */
                     lc1=((v1+v2)+sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     lc2=((v1+v2)-sqrt((v1+v2)*(v1+v2) - 4*(v1*v2-cv12*cv12)))/2.;
                     /* Eigen vectors */
                     v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
                     /*v21=sqrt(1.-v11*v11); *//* error */
                     v21=(lc1-v1)/cv12*v11;
                     v12=-v21;
                     v22=v11;
                     tnalp=v21/v11;
                     if(first1==1){
                       first1=0;
                       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(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) */
                     /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
                     if(first==1){
                       first=0;
                       fprintf(ficgp,"\nset parametric;unset label");
                       fprintf(ficgp,"\nset log y;set log x; set xlabel \"p%1d%1d (year-1)\";set ylabel \"p%1d%1d (year-1)\"",k1,l1,k2,l2);
                       fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65");
                       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\">\
   %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
                               subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br><img src=\"%s%d%1d%1d-%1d%1d.png\"> ",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(fichtmcov,"\n<br> Correlation at age %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\"",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       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",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }else{
                       first=0;
                       fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
                       fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
                       fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
                       fprintf(ficgp,"\nreplot %11.3e+ %.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)), %11.3e +%.3f*(%11.3e*%11.3e*cos(t)+%11.3e*%11.3e*sin(t)) not",\
                               mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
                               mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
                     }/* if first */
                   } /* age mod 5 */
                 } /* end loop age */
                 fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
                 first=1;
               } /*l12 */
             } /* k12 */
           } /*l1 */
         }/* k1 */
       } /* loop covariates */
     }
     free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
     free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
     free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
     free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
     free_vector(xp,1,npar);
     fclose(ficresprob);
     fclose(ficresprobcov);
     fclose(ficresprobcor);
     fflush(ficgp);
     fflush(fichtmcov);
   }
   
   
   /******************* Printing html file ***********/
   void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
                     double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   
      fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
      <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
   </ul>");
      fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
    - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
              jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
      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,"\
    - Stable prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - Life expectancies by age and initial health status (estepm=%2d months) WRONG LINK (to be made): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"le"),subdirf2(fileres,"le"));
      fprintf(fichtm,"\
    - Health expectancies by age and initial health status with standard errors (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
      fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age and initial health status (estepm=%2d months) TO BE MADE: \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"vch"),subdirf2(fileres,"vch"));
   
   
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        /* Pij */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i, %d (stepm) months before: %s%d1.png<br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1);     
        /* Quasi-incidences */
        fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
    before but expressed in per year i.e. quasi incidences if stepm is small and probabilities too: %s%d2.png<br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Stable prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): %s%d%d.png <br> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
        }
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
   
   
    fprintf(fichtm,"\
   \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
    - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
   
    fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            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(fichtm,"\
    - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Life and health expectancies with their standard errors: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of stable prevalences: <a href=\"%s\">%s</a> <br>\n",\
            subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
   
   /*  if(popforecast==1) fprintf(fichtm,"\n */
   /*  - 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 */
   /*      <br>",fileres,fileres,fileres,fileres); */
   /*  else  */
   /*    fprintf(fichtm,"\n No population forecast: popforecast = %d (instead of 1) or stepm = %d (instead of 1) or model=%s (instead of .)<br><br></li>\n",popforecast, stepm, model); */
    fflush(fichtm);
    fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
   
    m=cptcoveff;
    if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   
    jj1=0;
    for(k1=1; k1<=m;k1++){
      for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
        if (cptcovn > 0) {
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
          for (cpt=1; cpt<=cptcoveff;cpt++) 
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
        }
        for(cpt=1; cpt<=nlstate;cpt++) {
          fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
        }
        fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   health expectancies in states (1) and (2): %s%d.png<br>\
   <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
    }/* End k1 */
    fprintf(fichtm,"</ul>");
    fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplot(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;
   /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
   /*     printf("Problem with file %s",optionfilegnuplot); */
   /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
     m=pow(2,cptcoveff);
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
    /* 1eme*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {
      for (k1=1; k1<= m ; k1 ++) {
        fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
        fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
        fprintf(ficgp,"set xlabel \"Age\" \n\
   set ylabel \"Probability\" \n\
   set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }
        fprintf(ficgp,"\" t\"Stable prevalence\" w l 0,\"%s\" every :::%d::%d u 1:($2+1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1);
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
        for (i=1; i<= nlstate ; i ++) {
          if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
          else fprintf(ficgp," \%%*lf (\%%*lf)");
        }  
        fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
      }
     }
     /*2 eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
       fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
       for (i=1; i<= nlstate+1 ; i ++) {
         k=2*i;
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%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== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
         else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           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) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           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, month, year,iout;
     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];
     char dummy[]="                         ";
     /*  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]; 
     char **bp, *tok, *val; /* pathtot */
     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: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Un peu sale */
       }
     }
     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;
       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)||(line[j]==13);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, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
           exit(1);
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           exit(1);
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         exit(1);
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
         exit(1);
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       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, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);
           exit(1);
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\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,linei, i,line,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);
       /*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 */
     fclose(fic);
     /* 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);*/
   
       /*  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 (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    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;
           }else 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]=0.0268; p[NDIM]=0.083;
       /*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(prlim,1,nlstate,1,nlstate);
       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);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     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);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",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.1.11  
changed lines
  Added in v.1.116


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