Diff for /imach/src/imach.c between versions 1.7 and 1.116

version 1.7, 2001/05/02 17:50:24 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;  
 static int cptcov;    Revision 1.98  2004/05/16 15:05:56  brouard
 int cptcovn, cptcovage=0, cptcoveff=0;    New version 0.97 . First attempt to estimate force of mortality
 int npar=NPARMAX;    directly from the data i.e. without the need of knowing the health
 int nlstate=2; /* Number of live states */    state at each age, but using a Gompertz model: log u =a + b*age .
 int ndeath=1; /* Number of dead states */    This is the basic analysis of mortality and should be done before any
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    other analysis, in order to test if the mortality estimated from the
     cross-longitudinal survey is different from the mortality estimated
 int *wav; /* Number of waves for this individuual 0 is possible */    from other sources like vital statistic data.
 int maxwav; /* Maxim number of 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 **oldm, **newm, **savm; /* Working pointers to matrices */    former routines in order to include the new code within the former code.
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;    The output is very simple: only an estimate of the intercept and of
 FILE *ficgp, *fichtm;    the slope with 95% confident intervals.
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Current limitations:
  FILE  *ficresvij;    A) Even if you enter covariates, i.e. with the
   char fileresv[FILENAMELENGTH];    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
  FILE  *ficresvpl;    B) There is no computation of Life Expectancy nor Life Table.
   char fileresvpl[FILENAMELENGTH];  
     Revision 1.97  2004/02/20 13:25:42  lievre
 #define NR_END 1    Version 0.96d. Population forecasting command line is (temporarily)
 #define FREE_ARG char*    suppressed.
 #define FTOL 1.0e-10  
     Revision 1.96  2003/07/15 15:38:55  brouard
 #define NRANSI    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 #define ITMAX 200    rewritten within the same printf. Workaround: many printfs.
   
 #define TOL 2.0e-4    Revision 1.95  2003/07/08 07:54:34  brouard
     * imach.c (Repository):
 #define CGOLD 0.3819660    (Repository): Using imachwizard code to output a more meaningful covariance
 #define ZEPS 1.0e-10    matrix (cov(a12,c31) instead of numbers.
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     Revision 1.94  2003/06/27 13:00:02  brouard
 #define GOLD 1.618034    Just cleaning
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.93  2003/06/25 16:33:55  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
 static double maxarg1,maxarg2;    exist so I changed back to asctime which exists.
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    (Module): Version 0.96b
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Revision 1.92  2003/06/25 16:30:45  brouard
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    (Module): On windows (cygwin) function asctime_r doesn't
 #define rint(a) floor(a+0.5)    exist so I changed back to asctime which exists.
   
 static double sqrarg;    Revision 1.91  2003/06/25 15:30:29  brouard
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    * imach.c (Repository): Duplicated warning errors corrected.
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    (Repository): Elapsed time after each iteration is now output. It
     helps to forecast when convergence will be reached. Elapsed time
 int imx;    is stamped in powell.  We created a new html file for the graphs
 int stepm;    concerning matrix of covariance. It has extension -cov.htm.
 /* Stepm, step in month: minimum step interpolation*/  
     Revision 1.90  2003/06/24 12:34:15  brouard
 int m,nb;    (Module): Some bugs corrected for windows. Also, when
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    mle=-1 a template is output in file "or"mypar.txt with the design
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    of the covariance matrix to be input.
 double **pmmij;  
     Revision 1.89  2003/06/24 12:30:52  brouard
 double *weight;    (Module): Some bugs corrected for windows. Also, when
 int **s; /* Status */    mle=-1 a template is output in file "or"mypar.txt with the design
 double *agedc, **covar, idx;    of the covariance matrix to be input.
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     Revision 1.88  2003/06/23 17:54:56  brouard
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    * 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 ftolhess; /* Tolerance for computing hessian */  
     Revision 1.87  2003/06/18 12:26:01  brouard
 /**************** split *************************/    Version 0.96
 static  int split( char *path, char *dirc, char *name )  
 {    Revision 1.86  2003/06/17 20:04:08  brouard
    char *s;                             /* pointer */    (Module): Change position of html and gnuplot routines and added
    int  l1, l2;                         /* length counters */    routine fileappend.
   
    l1 = strlen( path );                 /* length of path */    Revision 1.85  2003/06/17 13:12:43  brouard
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    * imach.c (Repository): Check when date of death was earlier that
    s = strrchr( path, '\\' );           /* find last / */    current date of interview. It may happen when the death was just
    if ( s == NULL ) {                   /* no directory, so use current */    prior to the death. In this case, dh was negative and likelihood
 #if     defined(__bsd__)                /* get current working directory */    was wrong (infinity). We still send an "Error" but patch by
       extern char       *getwd( );    assuming that the date of death was just one stepm after the
     interview.
       if ( getwd( dirc ) == NULL ) {    (Repository): Because some people have very long ID (first column)
 #else    we changed int to long in num[] and we added a new lvector for
       extern char       *getcwd( );    memory allocation. But we also truncated to 8 characters (left
     truncation)
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    (Repository): No more line truncation errors.
 #endif  
          return( GLOCK_ERROR_GETCWD );    Revision 1.84  2003/06/13 21:44:43  brouard
       }    * imach.c (Repository): Replace "freqsummary" at a correct
       strcpy( name, path );             /* we've got it */    place. It differs from routine "prevalence" which may be called
    } else {                             /* strip direcotry from path */    many times. Probs is memory consuming and must be used with
       s++;                              /* after this, the filename */    parcimony.
       l2 = strlen( s );                 /* length of filename */    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  
       strcpy( name, s );                /* save file name */    Revision 1.83  2003/06/10 13:39:11  lievre
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    *** empty log message ***
       dirc[l1-l2] = 0;                  /* add zero */  
    }    Revision 1.82  2003/06/05 15:57:20  brouard
    l1 = strlen( dirc );                 /* length of directory */    Add log in  imach.c and  fullversion number is now printed.
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }  
    return( 0 );                         /* we're done */  */
 }  /*
      Interpolated Markov Chain
   
 /******************************************/    Short summary of the programme:
     
 void replace(char *s, char*t)    This program computes Healthy Life Expectancies from
 {    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   int i;    first survey ("cross") where individuals from different ages are
   int lg=20;    interviewed on their health status or degree of disability (in the
   i=0;    case of a health survey which is our main interest) -2- at least a
   lg=strlen(t);    second wave of interviews ("longitudinal") which measure each change
   for(i=0; i<= lg; i++) {    (if any) in individual health status.  Health expectancies are
     (s[i] = t[i]);    computed from the time spent in each health state according to a
     if (t[i]== '\\') s[i]='/';    model. More health states you consider, more time is necessary to reach the
   }    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
 int nbocc(char *s, char occ)    conditional to be observed in state i at the first wave. Therefore
 {    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   int i,j=0;    'age' is age and 'sex' is a covariate. If you want to have a more
   int lg=20;    complex model than "constant and age", you should modify the program
   i=0;    where the markup *Covariates have to be included here again* invites
   lg=strlen(s);    you to do it.  More covariates you add, slower the
   for(i=0; i<= lg; i++) {    convergence.
   if  (s[i] == occ ) j++;  
   }    The advantage of this computer programme, compared to a simple
   return j;    multinomial logistic model, is clear when the delay between waves is not
 }    identical for each individual. Also, if a individual missed an
     intermediate interview, the information is lost, but taken into
 void cutv(char *u,char *v, char*t, char occ)    account using an interpolation or extrapolation.  
 {  
   int i,lg,j,p=0;    hPijx is the probability to be observed in state i at age x+h
   i=0;    conditional to the observed state i at age x. The delay 'h' can be
   for(j=0; j<=strlen(t)-1; j++) {    split into an exact number (nh*stepm) of unobserved intermediate
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    states. This elementary transition (by month, quarter,
   }    semester or year) is modelled as a multinomial logistic.  The hPx
     matrix is simply the matrix product of nh*stepm elementary matrices
   lg=strlen(t);    and the contribution of each individual to the likelihood is simply
   for(j=0; j<p; j++) {    hPijx.
     (u[j] = t[j]);  
   }    Also this programme outputs the covariance matrix of the parameters but also
      u[p]='\0';    of the life expectancies. It also computes the stable prevalence. 
     
    for(j=0; j<= lg; j++) {    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
     if (j>=(p+1))(v[j-p-1] = t[j]);             Institut national d'études démographiques, Paris.
   }    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
 /********************** nrerror ********************/    software can be distributed freely for non commercial use. Latest version
     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
   fprintf(stderr,"ERREUR ...\n");    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   fprintf(stderr,"%s\n",error_text);    
   exit(1);    **********************************************************************/
 }  /*
 /*********************** vector *******************/    main
 double *vector(int nl, int nh)    read parameterfile
 {    read datafile
   double *v;    concatwav
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    freqsummary
   if (!v) nrerror("allocation failure in vector");    if (mle >= 1)
   return v-nl+NR_END;      mlikeli
 }    print results files
     if mle==1 
 /************************ free vector ******************/       computes hessian
 void free_vector(double*v, int nl, int nh)    read end of parameter file: agemin, agemax, bage, fage, estepm
 {        begin-prev-date,...
   free((FREE_ARG)(v+nl-NR_END));    open gnuplot file
 }    open html file
     stable prevalence
 /************************ivector *******************************/     for age prevalim()
 int *ivector(long nl,long nh)    h Pij x
 {    variance of p varprob
   int *v;    forecasting if prevfcast==1 prevforecast call prevalence()
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    health expectancies
   if (!v) nrerror("allocation failure in ivector");    Variance-covariance of DFLE
   return v-nl+NR_END;    prevalence()
 }     movingaverage()
     varevsij() 
 /******************free ivector **************************/    if popbased==1 varevsij(,popbased)
 void free_ivector(int *v, long nl, long nh)    total life expectancies
 {    Variance of stable prevalence
   free((FREE_ARG)(v+nl-NR_END));   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>
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  #include <stdio.h>
   int **m;  #include <stdlib.h>
    #include <string.h>
   /* allocate pointers to rows */  #include <unistd.h>
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  #include <limits.h>
   m += NR_END;  #include <sys/types.h>
   m -= nrl;  #include <sys/stat.h>
    #include <errno.h>
    extern int errno;
   /* allocate rows and set pointers to them */  
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  /* #include <sys/time.h> */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #include <time.h>
   m[nrl] += NR_END;  #include "timeval.h"
   m[nrl] -= ncl;  
    /* #include <libintl.h> */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  /* #define _(String) gettext (String) */
    
   /* return pointer to array of pointers to rows */  #define MAXLINE 256
   return m;  
 }  #define GNUPLOTPROGRAM "gnuplot"
   /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 /****************** free_imatrix *************************/  #define FILENAMELENGTH 132
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
       long nch,ncl,nrh,nrl;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
      /* free an int matrix allocated by imatrix() */  
 {  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   free((FREE_ARG) (m+nrl-NR_END));  
 }  #define NINTERVMAX 8
   #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 /******************* matrix *******************************/  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
 double **matrix(long nrl, long nrh, long ncl, long nch)  #define NCOVMAX 8 /* Maximum number of covariates */
 {  #define MAXN 20000
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  #define YEARM 12. /* Number of months per year */
   double **m;  #define AGESUP 130
   #define AGEBASE 40
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   if (!m) nrerror("allocation failure 1 in matrix()");  #ifdef UNIX
   m += NR_END;  #define DIRSEPARATOR '/'
   m -= nrl;  #define CHARSEPARATOR "/"
   #define ODIRSEPARATOR '\\'
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #else
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define DIRSEPARATOR '\\'
   m[nrl] += NR_END;  #define CHARSEPARATOR "\\"
   m[nrl] -= ncl;  #define ODIRSEPARATOR '/'
   #endif
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;  /* $Id$ */
 }  /* $State$ */
   
 /*************************free matrix ************************/  char version[]="Imach version 0.98c, February 2006, INED-EUROREVES ";
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  char fullversion[]="$Revision$ $Date$"; 
 {  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  int nvar;
   free((FREE_ARG)(m+nrl-NR_END));  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
 }  int npar=NPARMAX;
   int nlstate=2; /* Number of live states */
 /******************* ma3x *******************************/  int ndeath=1; /* Number of dead states */
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 {  int popbased=0;
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  
   double ***m;  int *wav; /* Number of waves for this individuual 0 is possible */
   int maxwav; /* Maxim number of waves */
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  int jmin, jmax; /* min, max spacing between 2 waves */
   if (!m) nrerror("allocation failure 1 in matrix()");  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
   m += NR_END;  int gipmx, gsw; /* Global variables on the number of contributions 
   m -= nrl;                     to the likelihood and the sum of weights (done by funcone)*/
   int mle, weightopt;
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   m[nrl] += NR_END;  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   m[nrl] -= ncl;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   double jmean; /* Mean space between 2 waves */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  double **oldm, **newm, **savm; /* Working pointers to matrices */
   double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  FILE *ficlog, *ficrespow;
   m[nrl][ncl] += NR_END;  int globpr; /* Global variable for printing or not */
   m[nrl][ncl] -= nll;  double fretone; /* Only one call to likelihood */
   for (j=ncl+1; j<=nch; j++)  long ipmx; /* Number of contributions */
     m[nrl][j]=m[nrl][j-1]+nlay;  double sw; /* Sum of weights */
    char filerespow[FILENAMELENGTH];
   for (i=nrl+1; i<=nrh; i++) {  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  FILE *ficresilk;
     for (j=ncl+1; j<=nch; j++)  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
       m[i][j]=m[i][j-1]+nlay;  FILE *ficresprobmorprev;
   }  FILE *fichtm, *fichtmcov; /* Html File */
   return m;  FILE *ficreseij;
 }  char filerese[FILENAMELENGTH];
   FILE  *ficresvij;
 /*************************free ma3x ************************/  char fileresv[FILENAMELENGTH];
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  FILE  *ficresvpl;
 {  char fileresvpl[FILENAMELENGTH];
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  char title[MAXLINE];
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   free((FREE_ARG)(m+nrl-NR_END));  char optionfilext[10], optionfilefiname[FILENAMELENGTH], plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
 }  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   char command[FILENAMELENGTH];
 /***************** f1dim *************************/  int  outcmd=0;
 extern int ncom;  
 extern double *pcom,*xicom;  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 extern double (*nrfunc)(double []);  
    char filelog[FILENAMELENGTH]; /* Log file */
 double f1dim(double x)  char filerest[FILENAMELENGTH];
 {  char fileregp[FILENAMELENGTH];
   int j;  char popfile[FILENAMELENGTH];
   double f;  
   double *xt;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
    
   xt=vector(1,ncom);  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  struct timezone tzp;
   f=(*nrfunc)(xt);  extern int gettimeofday();
   free_vector(xt,1,ncom);  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   return f;  long time_value;
 }  extern long time();
   char strcurr[80], strfor[80];
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  char *endptr;
 {  long lval;
   int iter;  
   double a,b,d,etemp;  #define NR_END 1
   double fu,fv,fw,fx;  #define FREE_ARG char*
   double ftemp;  #define FTOL 1.0e-10
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;  #define NRANSI 
    #define ITMAX 200 
   a=(ax < cx ? ax : cx);  
   b=(ax > cx ? ax : cx);  #define TOL 2.0e-4 
   x=w=v=bx;  
   fw=fv=fx=(*f)(x);  #define CGOLD 0.3819660 
   for (iter=1;iter<=ITMAX;iter++) {  #define ZEPS 1.0e-10 
     xm=0.5*(a+b);  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  #define GOLD 1.618034 
     printf(".");fflush(stdout);  #define GLIMIT 100.0 
 #ifdef DEBUG  #define TINY 1.0e-20 
     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);  
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  static double maxarg1,maxarg2;
 #endif  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       *xmin=x;    
       return fx;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
     }  #define rint(a) floor(a+0.5)
     ftemp=fu;  
     if (fabs(e) > tol1) {  static double sqrarg;
       r=(x-w)*(fx-fv);  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
       q=(x-v)*(fx-fw);  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       p=(x-v)*q-(x-w)*r;  int agegomp= AGEGOMP;
       q=2.0*(q-r);  
       if (q > 0.0) p = -p;  int imx; 
       q=fabs(q);  int stepm=1;
       etemp=e;  /* Stepm, step in month: minimum step interpolation*/
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  int estepm;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       else {  
         d=p/q;  int m,nb;
         u=x+d;  long *num;
         if (u-a < tol2 || b-u < tol2)  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
           d=SIGN(tol1,xm-x);  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
       }  double **pmmij, ***probs;
     } else {  double *ageexmed,*agecens;
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  double dateintmean=0;
     }  
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  double *weight;
     fu=(*f)(u);  int **s; /* Status */
     if (fu <= fx) {  double *agedc, **covar, idx;
       if (u >= x) a=x; else b=x;  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
       SHFT(v,w,x,u)  double *lsurv, *lpop, *tpop;
         SHFT(fv,fw,fx,fu)  
         } else {  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
           if (u < x) a=u; else b=u;  double ftolhess; /* Tolerance for computing hessian */
           if (fu <= fw || w == x) {  
             v=w;  /**************** split *************************/
             w=u;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
             fv=fw;  {
             fw=fu;    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
           } else if (fu <= fv || v == x || v == w) {       the name of the file (name), its extension only (ext) and its first part of the name (finame)
             v=u;    */ 
             fv=fu;    char  *ss;                            /* pointer */
           }    int   l1, l2;                         /* length counters */
         }  
   }    l1 = strlen(path );                   /* length of path */
   nrerror("Too many iterations in brent");    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   *xmin=x;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
   return fx;    if ( ss == NULL ) {                   /* no directory, so determine current directory */
 }      strcpy( name, path );               /* we got the fullname name because no directory */
       /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 /****************** mnbrak ***********************/        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
       /* get current working directory */
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,      /*    extern  char* getcwd ( char *buf , int len);*/
             double (*func)(double))      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 {        return( GLOCK_ERROR_GETCWD );
   double ulim,u,r,q, dum;      }
   double fu;      /* got dirc from getcwd*/
        printf(" DIRC = %s \n",dirc);
   *fa=(*func)(*ax);    } else {                              /* strip direcotry from path */
   *fb=(*func)(*bx);      ss++;                               /* after this, the filename */
   if (*fb > *fa) {      l2 = strlen( ss );                  /* length of filename */
     SHFT(dum,*ax,*bx,dum)      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
       SHFT(dum,*fb,*fa,dum)      strcpy( name, ss );         /* save file name */
       }      strncpy( dirc, path, l1 - l2 );     /* now the directory */
   *cx=(*bx)+GOLD*(*bx-*ax);      dirc[l1-l2] = 0;                    /* add zero */
   *fc=(*func)(*cx);      printf(" DIRC2 = %s \n",dirc);
   while (*fb > *fc) {    }
     r=(*bx-*ax)*(*fb-*fc);    /* We add a separator at the end of dirc if not exists */
     q=(*bx-*cx)*(*fb-*fa);    l1 = strlen( dirc );                  /* length of directory */
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/    if( dirc[l1-1] != DIRSEPARATOR ){
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));      dirc[l1] =  DIRSEPARATOR;
     ulim=(*bx)+GLIMIT*(*cx-*bx);      dirc[l1+1] = 0; 
     if ((*bx-u)*(u-*cx) > 0.0) {      printf(" DIRC3 = %s \n",dirc);
       fu=(*func)(u);    }
     } else if ((*cx-u)*(u-ulim) > 0.0) {    ss = strrchr( name, '.' );            /* find last / */
       fu=(*func)(u);    if (ss >0){
       if (fu < *fc) {      ss++;
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))      strcpy(ext,ss);                     /* save extension */
           SHFT(*fb,*fc,fu,(*func)(u))      l1= strlen( name);
           }      l2= strlen(ss)+1;
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {      strncpy( finame, name, l1-l2);
       u=ulim;      finame[l1-l2]= 0;
       fu=(*func)(u);    }
     } else {  
       u=(*cx)+GOLD*(*cx-*bx);    return( 0 );                          /* we're done */
       fu=(*func)(u);  }
     }  
     SHFT(*ax,*bx,*cx,u)  
       SHFT(*fa,*fb,*fc,fu)  /******************************************/
       }  
 }  void replace_back_to_slash(char *s, char*t)
   {
 /*************** linmin ************************/    int i;
     int lg=0;
 int ncom;    i=0;
 double *pcom,*xicom;    lg=strlen(t);
 double (*nrfunc)(double []);    for(i=0; i<= lg; i++) {
        (s[i] = t[i]);
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))      if (t[i]== '\\') s[i]='/';
 {    }
   double brent(double ax, double bx, double cx,  }
                double (*f)(double), double tol, double *xmin);  
   double f1dim(double x);  int nbocc(char *s, char occ)
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  {
               double *fc, double (*func)(double));    int i,j=0;
   int j;    int lg=20;
   double xx,xmin,bx,ax;    i=0;
   double fx,fb,fa;    lg=strlen(s);
      for(i=0; i<= lg; i++) {
   ncom=n;    if  (s[i] == occ ) j++;
   pcom=vector(1,n);    }
   xicom=vector(1,n);    return j;
   nrfunc=func;  }
   for (j=1;j<=n;j++) {  
     pcom[j]=p[j];  void cutv(char *u,char *v, char*t, char occ)
     xicom[j]=xi[j];  {
   }    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
   ax=0.0;       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
   xx=1.0;       gives u="abcedf" and v="ghi2j" */
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    int i,lg,j,p=0;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    i=0;
 #ifdef DEBUG    for(j=0; j<=strlen(t)-1; j++) {
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 #endif    }
   for (j=1;j<=n;j++) {  
     xi[j] *= xmin;    lg=strlen(t);
     p[j] += xi[j];    for(j=0; j<p; j++) {
   }      (u[j] = t[j]);
   free_vector(xicom,1,n);    }
   free_vector(pcom,1,n);       u[p]='\0';
 }  
      for(j=0; j<= lg; j++) {
 /*************** powell ************************/      if (j>=(p+1))(v[j-p-1] = t[j]);
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    }
             double (*func)(double []))  }
 {  
   void linmin(double p[], double xi[], int n, double *fret,  /********************** nrerror ********************/
               double (*func)(double []));  
   int i,ibig,j;  void nrerror(char error_text[])
   double del,t,*pt,*ptt,*xit;  {
   double fp,fptt;    fprintf(stderr,"ERREUR ...\n");
   double *xits;    fprintf(stderr,"%s\n",error_text);
   pt=vector(1,n);    exit(EXIT_FAILURE);
   ptt=vector(1,n);  }
   xit=vector(1,n);  /*********************** vector *******************/
   xits=vector(1,n);  double *vector(int nl, int nh)
   *fret=(*func)(p);  {
   for (j=1;j<=n;j++) pt[j]=p[j];    double *v;
   for (*iter=1;;++(*iter)) {    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
     fp=(*fret);    if (!v) nrerror("allocation failure in vector");
     ibig=0;    return v-nl+NR_END;
     del=0.0;  }
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  
     for (i=1;i<=n;i++)  /************************ free vector ******************/
       printf(" %d %.12f",i, p[i]);  void free_vector(double*v, int nl, int nh)
     printf("\n");  {
     for (i=1;i<=n;i++) {    free((FREE_ARG)(v+nl-NR_END));
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  }
       fptt=(*fret);  
 #ifdef DEBUG  /************************ivector *******************************/
       printf("fret=%lf \n",*fret);  int *ivector(long nl,long nh)
 #endif  {
       printf("%d",i);fflush(stdout);    int *v;
       linmin(p,xit,n,fret,func);    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       if (fabs(fptt-(*fret)) > del) {    if (!v) nrerror("allocation failure in ivector");
         del=fabs(fptt-(*fret));    return v-nl+NR_END;
         ibig=i;  }
       }  
 #ifdef DEBUG  /******************free ivector **************************/
       printf("%d %.12e",i,(*fret));  void free_ivector(int *v, long nl, long nh)
       for (j=1;j<=n;j++) {  {
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    free((FREE_ARG)(v+nl-NR_END));
         printf(" x(%d)=%.12e",j,xit[j]);  }
       }  
       for(j=1;j<=n;j++)  /************************lvector *******************************/
         printf(" p=%.12e",p[j]);  long *lvector(long nl,long nh)
       printf("\n");  {
 #endif    long *v;
     }    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    if (!v) nrerror("allocation failure in ivector");
 #ifdef DEBUG    return v-nl+NR_END;
       int k[2],l;  }
       k[0]=1;  
       k[1]=-1;  /******************free lvector **************************/
       printf("Max: %.12e",(*func)(p));  void free_lvector(long *v, long nl, long nh)
       for (j=1;j<=n;j++)  {
         printf(" %.12e",p[j]);    free((FREE_ARG)(v+nl-NR_END));
       printf("\n");  }
       for(l=0;l<=1;l++) {  
         for (j=1;j<=n;j++) {  /******************* imatrix *******************************/
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  int **imatrix(long nrl, long nrh, long ncl, long nch) 
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
         }  { 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       }    int **m; 
 #endif    
     /* allocate pointers to rows */ 
     m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       free_vector(xit,1,n);    if (!m) nrerror("allocation failure 1 in matrix()"); 
       free_vector(xits,1,n);    m += NR_END; 
       free_vector(ptt,1,n);    m -= nrl; 
       free_vector(pt,1,n);    
       return;    
     }    /* allocate rows and set pointers to them */ 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
     for (j=1;j<=n;j++) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       ptt[j]=2.0*p[j]-pt[j];    m[nrl] += NR_END; 
       xit[j]=p[j]-pt[j];    m[nrl] -= ncl; 
       pt[j]=p[j];    
     }    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
     fptt=(*func)(ptt);    
     if (fptt < fp) {    /* return pointer to array of pointers to rows */ 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    return m; 
       if (t < 0.0) {  } 
         linmin(p,xit,n,fret,func);  
         for (j=1;j<=n;j++) {  /****************** free_imatrix *************************/
           xi[j][ibig]=xi[j][n];  void free_imatrix(m,nrl,nrh,ncl,nch)
           xi[j][n]=xit[j];        int **m;
         }        long nch,ncl,nrh,nrl; 
 #ifdef DEBUG       /* free an int matrix allocated by imatrix() */ 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  { 
         for(j=1;j<=n;j++)    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
           printf(" %.12e",xit[j]);    free((FREE_ARG) (m+nrl-NR_END)); 
         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*)));
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    if (!m) nrerror("allocation failure 1 in matrix()");
 {    m += NR_END;
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    m -= nrl;
      matrix by transitions matrix until convergence is reached */  
     m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   int i, ii,j,k;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   double min, max, maxmin, maxmax,sumnew=0.;    m[nrl] += NR_END;
   double **matprod2();    m[nrl] -= ncl;
   double **out, cov[NCOVMAX], **pmij();  
   double **newm;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   double agefin, delaymax=50 ; /* Max number of years to converge */    return m;
     /* 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));
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    free((FREE_ARG)(m+nrl-NR_END));
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  }
     newm=savm;  
     /* Covariates have to be included here again */  /******************* ma3x *******************************/
      cov[2]=agefin;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
    {
       for (k=1; k<=cptcovn;k++) {    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    double ***m;
         /*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*)));
       for (k=1; k<=cptcovage;k++)    if (!m) nrerror("allocation failure 1 in matrix()");
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    m += NR_END;
       for (k=1; k<=cptcovprod;k++)    m -= nrl;
         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)));
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     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; 
                  /*printf("%d %d",kk,Tage[kk]);*/        fu=(*func)(u); 
               }      } else { 
               /*cov[4]=covar[1][i]*cov[2];scanf("%d", i);*/        u=(*cx)+GOLD*(*cx-*bx); 
               /*cov[3]=pow(cov[2],2)/1000.;*/        fu=(*func)(u); 
       } 
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,      SHFT(*ax,*bx,*cx,u) 
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));        SHFT(*fa,*fb,*fc,fu) 
           savm=oldm;        } 
           oldm=newm;  } 
   
   /*************** linmin ************************/
       } /* end mult */  
      int ncom; 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  double *pcom,*xicom;
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  double (*nrfunc)(double []); 
       ipmx +=1;   
       sw += weight[i];  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  { 
     } /* end of wave */    double brent(double ax, double bx, double cx, 
   } /* end of individual */                 double (*f)(double), double tol, double *xmin); 
     double f1dim(double x); 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */                double *fc, double (*func)(double)); 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    int j; 
   return -l;    double xx,xmin,bx,ax; 
 }    double fx,fb,fa;
    
     ncom=n; 
 /*********** Maximum Likelihood Estimation ***************/    pcom=vector(1,n); 
     xicom=vector(1,n); 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    nrfunc=func; 
 {    for (j=1;j<=n;j++) { 
   int i,j, iter;      pcom[j]=p[j]; 
   double **xi,*delti;      xicom[j]=xi[j]; 
   double fret;    } 
   xi=matrix(1,npar,1,npar);    ax=0.0; 
   for (i=1;i<=npar;i++)    xx=1.0; 
     for (j=1;j<=npar;j++)    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
       xi[i][j]=(i==j ? 1.0 : 0.0);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   printf("Powell\n");  #ifdef DEBUG
   powell(p,xi,npar,ftol,&iter,&fret,func);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
     fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  #endif
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));    for (j=1;j<=n;j++) { 
       xi[j] *= xmin; 
 }      p[j] += xi[j]; 
     } 
 /**** Computes Hessian and covariance matrix ***/    free_vector(xicom,1,n); 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    free_vector(pcom,1,n); 
 {  } 
   double  **a,**y,*x,pd;  
   double **hess;  char *asc_diff_time(long time_sec, char ascdiff[])
   int i, j,jk;  {
   int *indx;    long sec_left, days, hours, minutes;
     days = (time_sec) / (60*60*24);
   double hessii(double p[], double delta, int theta, double delti[]);    sec_left = (time_sec) % (60*60*24);
   double hessij(double p[], double delti[], int i, int j);    hours = (sec_left) / (60*60) ;
   void lubksb(double **a, int npar, int *indx, double b[]) ;    sec_left = (sec_left) %(60*60);
   void ludcmp(double **a, int npar, int *indx, double *d) ;    minutes = (sec_left) /60;
     sec_left = (sec_left) % (60);
     sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   hess=matrix(1,npar,1,npar);    return ascdiff;
   }
   printf("\nCalculation of the hessian matrix. Wait...\n");  
   for (i=1;i<=npar;i++){  /*************** powell ************************/
     printf("%d",i);fflush(stdout);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
     hess[i][i]=hessii(p,ftolhess,i,delti);              double (*func)(double [])) 
     /*printf(" %f ",p[i]);*/  { 
   }    void linmin(double p[], double xi[], int n, double *fret, 
                 double (*func)(double [])); 
   for (i=1;i<=npar;i++) {    int i,ibig,j; 
     for (j=1;j<=npar;j++)  {    double del,t,*pt,*ptt,*xit;
       if (j>i) {    double fp,fptt;
         printf(".%d%d",i,j);fflush(stdout);    double *xits;
         hess[i][j]=hessij(p,delti,i,j);    int niterf, itmp;
         hess[j][i]=hess[i][j];  
       }    pt=vector(1,n); 
     }    ptt=vector(1,n); 
   }    xit=vector(1,n); 
   printf("\n");    xits=vector(1,n); 
     *fret=(*func)(p); 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    for (j=1;j<=n;j++) pt[j]=p[j]; 
      for (*iter=1;;++(*iter)) { 
   a=matrix(1,npar,1,npar);      fp=(*fret); 
   y=matrix(1,npar,1,npar);      ibig=0; 
   x=vector(1,npar);      del=0.0; 
   indx=ivector(1,npar);      last_time=curr_time;
   for (i=1;i<=npar;i++)      (void) gettimeofday(&curr_time,&tzp);
     for (j=1;j<=npar;j++) a[i][j]=hess[i][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);
   ludcmp(a,npar,indx,&pd);      /*    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);
       fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
   for (j=1;j<=npar;j++) {      */
     for (i=1;i<=npar;i++) x[i]=0;     for (i=1;i<=n;i++) {
     x[j]=1;        printf(" %d %.12f",i, p[i]);
     lubksb(a,npar,indx,x);        fprintf(ficlog," %d %.12lf",i, p[i]);
     for (i=1;i<=npar;i++){        fprintf(ficrespow," %.12lf", p[i]);
       matcov[i][j]=x[i];      }
     }      printf("\n");
   }      fprintf(ficlog,"\n");
       fprintf(ficrespow,"\n");fflush(ficrespow);
   printf("\n#Hessian matrix#\n");      if(*iter <=3){
   for (i=1;i<=npar;i++) {        tm = *localtime(&curr_time.tv_sec);
     for (j=1;j<=npar;j++) {        strcpy(strcurr,asctime(&tm));
       printf("%.3e ",hess[i][j]);  /*       asctime_r(&tm,strcurr); */
     }        forecast_time=curr_time; 
     printf("\n");        itmp = strlen(strcurr);
   }        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
           strcurr[itmp-1]='\0';
   /* Recompute Inverse */        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   for (i=1;i<=npar;i++)        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];        for(niterf=10;niterf<=30;niterf+=10){
   ludcmp(a,npar,indx,&pd);          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
           tmf = *localtime(&forecast_time.tv_sec);
   /*  printf("\n#Hessian matrix recomputed#\n");  /*      asctime_r(&tmf,strfor); */
           strcpy(strfor,asctime(&tmf));
   for (j=1;j<=npar;j++) {          itmp = strlen(strfor);
     for (i=1;i<=npar;i++) x[i]=0;          if(strfor[itmp-1]=='\n')
     x[j]=1;          strfor[itmp-1]='\0';
     lubksb(a,npar,indx,x);          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);
     for (i=1;i<=npar;i++){          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);
       y[i][j]=x[i];        }
       printf("%.3e ",y[i][j]);      }
     }      for (i=1;i<=n;i++) { 
     printf("\n");        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   }        fptt=(*fret); 
   */  #ifdef DEBUG
         printf("fret=%lf \n",*fret);
   free_matrix(a,1,npar,1,npar);        fprintf(ficlog,"fret=%lf \n",*fret);
   free_matrix(y,1,npar,1,npar);  #endif
   free_vector(x,1,npar);        printf("%d",i);fflush(stdout);
   free_ivector(indx,1,npar);        fprintf(ficlog,"%d",i);fflush(ficlog);
   free_matrix(hess,1,npar,1,npar);        linmin(p,xit,n,fret,func); 
         if (fabs(fptt-(*fret)) > del) { 
           del=fabs(fptt-(*fret)); 
 }          ibig=i; 
         } 
 /*************** hessian matrix ****************/  #ifdef DEBUG
 double hessii( double x[], double delta, int theta, double delti[])        printf("%d %.12e",i,(*fret));
 {        fprintf(ficlog,"%d %.12e",i,(*fret));
   int i;        for (j=1;j<=n;j++) {
   int l=1, lmax=20;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   double k1,k2;          printf(" x(%d)=%.12e",j,xit[j]);
   double p2[NPARMAX+1];          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   double res;        }
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        for(j=1;j<=n;j++) {
   double fx;          printf(" p=%.12e",p[j]);
   int k=0,kmax=10;          fprintf(ficlog," p=%.12e",p[j]);
   double l1;        }
         printf("\n");
   fx=func(x);        fprintf(ficlog,"\n");
   for (i=1;i<=npar;i++) p2[i]=x[i];  #endif
   for(l=0 ; l <=lmax; l++){      } 
     l1=pow(10,l);      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     delts=delt;  #ifdef DEBUG
     for(k=1 ; k <kmax; k=k+1){        int k[2],l;
       delt = delta*(l1*k);        k[0]=1;
       p2[theta]=x[theta] +delt;        k[1]=-1;
       k1=func(p2)-fx;        printf("Max: %.12e",(*func)(p));
       p2[theta]=x[theta]-delt;        fprintf(ficlog,"Max: %.12e",(*func)(p));
       k2=func(p2)-fx;        for (j=1;j<=n;j++) {
       /*res= (k1-2.0*fx+k2)/delt/delt; */          printf(" %.12e",p[j]);
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          fprintf(ficlog," %.12e",p[j]);
              }
 #ifdef DEBUG        printf("\n");
       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,"\n");
 #endif        for(l=0;l<=1;l++) {
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */          for (j=1;j<=n;j++) {
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
         k=kmax;            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/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          }
         k=kmax; l=lmax*10.;          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)));
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){        }
         delts=delt;  #endif
       }  
     }  
   }        free_vector(xit,1,n); 
   delti[theta]=delts;        free_vector(xits,1,n); 
   return res;        free_vector(ptt,1,n); 
          free_vector(pt,1,n); 
 }        return; 
       } 
 double hessij( double x[], double delti[], int thetai,int thetaj)      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
 {      for (j=1;j<=n;j++) { 
   int i;        ptt[j]=2.0*p[j]-pt[j]; 
   int l=1, l1, lmax=20;        xit[j]=p[j]-pt[j]; 
   double k1,k2,k3,k4,res,fx;        pt[j]=p[j]; 
   double p2[NPARMAX+1];      } 
   int k;      fptt=(*func)(ptt); 
       if (fptt < fp) { 
   fx=func(x);        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
   for (k=1; k<=2; k++) {        if (t < 0.0) { 
     for (i=1;i<=npar;i++) p2[i]=x[i];          linmin(p,xit,n,fret,func); 
     p2[thetai]=x[thetai]+delti[thetai]/k;          for (j=1;j<=n;j++) { 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;            xi[j][ibig]=xi[j][n]; 
     k1=func(p2)-fx;            xi[j][n]=xit[j]; 
            }
     p2[thetai]=x[thetai]+delti[thetai]/k;  #ifdef DEBUG
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     k2=func(p2)-fx;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
            for(j=1;j<=n;j++){
     p2[thetai]=x[thetai]-delti[thetai]/k;            printf(" %.12e",xit[j]);
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;            fprintf(ficlog," %.12e",xit[j]);
     k3=func(p2)-fx;          }
            printf("\n");
     p2[thetai]=x[thetai]-delti[thetai]/k;          fprintf(ficlog,"\n");
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  #endif
     k4=func(p2)-fx;        }
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */      } 
 #ifdef DEBUG    } 
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);  } 
 #endif  
   }  /**** Prevalence limit (stable prevalence)  ****************/
   return res;  
 }  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   {
 /************** Inverse of matrix **************/    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
 void ludcmp(double **a, int n, int *indx, double *d)       matrix by transitions matrix until convergence is reached */
 {  
   int i,imax,j,k;    int i, ii,j,k;
   double big,dum,sum,temp;    double min, max, maxmin, maxmax,sumnew=0.;
   double *vv;    double **matprod2();
      double **out, cov[NCOVMAX], **pmij();
   vv=vector(1,n);    double **newm;
   *d=1.0;    double agefin, delaymax=50 ; /* Max number of years to converge */
   for (i=1;i<=n;i++) {  
     big=0.0;    for (ii=1;ii<=nlstate+ndeath;ii++)
     for (j=1;j<=n;j++)      for (j=1;j<=nlstate+ndeath;j++){
       if ((temp=fabs(a[i][j])) > big) big=temp;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");      }
     vv[i]=1.0/big;  
   }     cov[1]=1.;
   for (j=1;j<=n;j++) {   
     for (i=1;i<j;i++) {   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       sum=a[i][j];    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];      newm=savm;
       a[i][j]=sum;      /* Covariates have to be included here again */
     }       cov[2]=agefin;
     big=0.0;    
     for (i=j;i<=n;i++) {        for (k=1; k<=cptcovn;k++) {
       sum=a[i][j];          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       for (k=1;k<j;k++)          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
         sum -= a[i][k]*a[k][j];        }
       a[i][j]=sum;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       if ( (dum=vv[i]*fabs(sum)) >= big) {        for (k=1; k<=cptcovprod;k++)
         big=dum;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
         imax=i;  
       }        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     }        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     if (j != imax) {        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
       for (k=1;k<=n;k++) {      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
         dum=a[imax][k];  
         a[imax][k]=a[j][k];      savm=oldm;
         a[j][k]=dum;      oldm=newm;
       }      maxmax=0.;
       *d = -(*d);      for(j=1;j<=nlstate;j++){
       vv[imax]=vv[j];        min=1.;
     }        max=0.;
     indx[j]=imax;        for(i=1; i<=nlstate; i++) {
     if (a[j][j] == 0.0) a[j][j]=TINY;          sumnew=0;
     if (j != n) {          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       dum=1.0/(a[j][j]);          prlim[i][j]= newm[i][j]/(1-sumnew);
       for (i=j+1;i<=n;i++) a[i][j] *= dum;          max=FMAX(max,prlim[i][j]);
     }          min=FMIN(min,prlim[i][j]);
   }        }
   free_vector(vv,1,n);  /* Doesn't work */        maxmin=max-min;
 ;        maxmax=FMAX(maxmax,maxmin);
 }      }
       if(maxmax < ftolpl){
 void lubksb(double **a, int n, int *indx, double b[])        return prlim;
 {      }
   int i,ii=0,ip,j;    }
   double sum;  }
    
   for (i=1;i<=n;i++) {  /*************** transition probabilities ***************/ 
     ip=indx[i];  
     sum=b[ip];  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
     b[ip]=b[i];  {
     if (ii)    double s1, s2;
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    /*double t34;*/
     else if (sum) ii=i;    int i,j,j1, nc, ii, jj;
     b[i]=sum;  
   }      for(i=1; i<= nlstate; i++){
   for (i=n;i>=1;i--) {        for(j=1; j<i;j++){
     sum=b[i];          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];            /*s2 += param[i][j][nc]*cov[nc];*/
     b[i]=sum/a[i][i];            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); */
 }          }
           ps[i][j]=s2;
 /************ Frequencies ********************/  /*      printf("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 */        for(j=i+1; j<=nlstate+ndeath;j++){
            for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   double ***freq; /* Frequencies */  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
   double *pp;          }
   double pos;          ps[i][j]=s2;
   FILE *ficresp;        }
   char fileresp[FILENAMELENGTH];      }
       /*ps[3][2]=1;*/
   pp=vector(1,nlstate);      
       for(i=1; i<= nlstate; i++){
   strcpy(fileresp,"p");        s1=0;
   strcat(fileresp,fileres);        for(j=1; j<i; j++)
   if((ficresp=fopen(fileresp,"w"))==NULL) {          s1+=exp(ps[i][j]);
     printf("Problem with prevalence resultfile: %s\n", fileresp);        for(j=i+1; j<=nlstate+ndeath; j++)
     exit(0);          s1+=exp(ps[i][j]);
   }        ps[i][i]=1./(s1+1.);
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        for(j=1; j<i; j++)
   j1=0;          ps[i][j]= exp(ps[i][j])*ps[i][i];
         for(j=i+1; j<=nlstate+ndeath; j++)
   j=cptcoveff;          ps[i][j]= exp(ps[i][j])*ps[i][i];
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       } /* end i */
   for(k1=1; k1<=j;k1++){      
    for(i1=1; i1<=ncodemax[k1];i1++){      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
        j1++;        for(jj=1; jj<= nlstate+ndeath; jj++){
           ps[ii][jj]=0;
         for (i=-1; i<=nlstate+ndeath; i++)            ps[ii][ii]=1;
          for (jk=-1; jk<=nlstate+ndeath; jk++)          }
            for(m=agemin; m <= agemax+3; m++)      }
              freq[i][jk][m]=0;      
          
        for (i=1; i<=imx; i++) {  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
          bool=1;  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
          if  (cptcovn>0) {  /*         printf("ddd %lf ",ps[ii][jj]); */
            for (z1=1; z1<=cptcoveff; z1++)  /*       } */
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) bool=0;  /*       printf("\n "); */
          }  /*        } */
           if (bool==1) {  /*        printf("\n ");printf("%lf ",cov[2]); */
            for(m=firstpass; m<=lastpass-1; m++){         /*
              if(agev[m][i]==0) agev[m][i]=agemax+1;        for(i=1; i<= npar; i++) printf("%f ",x[i]);
              if(agev[m][i]==1) agev[m][i]=agemax+2;        goto end;*/
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];      return ps;
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];  }
            }  
          }  /**************** Product of 2 matrices ******************/
        }  
         if  (cptcovn>0) {  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
          fprintf(ficresp, "\n#********** Variable ");  {
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    /* 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(...) */
        fprintf(ficresp, "**********\n#");    /* in, b, out are matrice of pointers which should have been initialized 
        for(i=1; i<=nlstate;i++)       before: only the contents of out is modified. The function returns
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);       a pointer to pointers identical to out */
        fprintf(ficresp, "\n");    long i, j, k;
            for(i=nrl; i<= nrh; i++)
   for(i=(int)agemin; i <= (int)agemax+3; i++){      for(k=ncolol; k<=ncoloh; k++)
     if(i==(int)agemax+3)        for(j=ncl,out[i][k]=0.; j<=nch; j++)
       printf("Total");          out[i][k] +=in[i][j]*b[j][k];
     else  
       printf("Age %d", i);    return out;
     for(jk=1; jk <=nlstate ; jk++){  }
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  
         pp[jk] += freq[jk][m][i];  
     }  /************* Higher Matrix Product ***************/
     for(jk=1; jk <=nlstate ; jk++){  
       for(m=-1, pos=0; m <=0 ; m++)  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
         pos += freq[jk][m][i];  {
       if(pp[jk]>=1.e-10)    /* Computes the transition matrix starting at age 'age' over 
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);       'nhstepm*hstepm*stepm' months (i.e. until
       else       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);       nhstepm*hstepm matrices. 
     }       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
     for(jk=1; jk <=nlstate ; jk++){       (typically every 2 years instead of every month which is too big 
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)       for the memory).
         pp[jk] += freq[jk][m][i];       Model is determined by parameters x and covariates have to be 
     }       included manually here. 
     for(jk=1,pos=0; jk <=nlstate ; jk++)  
       pos += pp[jk];       */
     for(jk=1; jk <=nlstate ; jk++){  
       if(pos>=1.e-5)    int i, j, d, h, k;
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    double **out, cov[NCOVMAX];
       else    double **newm;
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  
       if( i <= (int) agemax){    /* Hstepm could be zero and should return the unit matrix */
         if(pos>=1.e-5)    for (i=1;i<=nlstate+ndeath;i++)
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);      for (j=1;j<=nlstate+ndeath;j++){
       else        oldm[i][j]=(i==j ? 1.0 : 0.0);
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        po[i][j][0]=(i==j ? 1.0 : 0.0);
       }      }
     }    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(jk=-1; jk <=nlstate+ndeath; jk++)    for(h=1; h <=nhstepm; h++){
       for(m=-1; m <=nlstate+ndeath; m++)      for(d=1; d <=hstepm; d++){
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        newm=savm;
     if(i <= (int) agemax)        /* Covariates have to be included here again */
       fprintf(ficresp,"\n");        cov[1]=1.;
     printf("\n");        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];
          for (k=1; k<=cptcovprod;k++)
   fclose(ficresp);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  
   free_vector(pp,1,nlstate);  
         /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
 }  /* End of Freq */        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
 /************* Waves Concatenation ***************/                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         savm=oldm;
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)        oldm=newm;
 {      }
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.      for(i=1; i<=nlstate+ndeath; i++)
      Death is a valid wave (if date is known).        for(j=1;j<=nlstate+ndeath;j++) {
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          po[i][j][h]=newm[i][j];
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
      and mw[mi+1][i]. dh depends on stepm.           */
      */        }
     } /* end h */
   int i, mi, m;    return po;
   int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  }
 float sum=0.;  
   
   for(i=1; i<=imx; i++){  /*************** log-likelihood *************/
     mi=0;  double func( double *x)
     m=firstpass;  {
     while(s[m][i] <= nlstate){    int i, ii, j, k, mi, d, kk;
       if(s[m][i]>=1)    double l, ll[NLSTATEMAX], cov[NCOVMAX];
         mw[++mi][i]=m;    double **out;
       if(m >=lastpass)    double sw; /* Sum of weights */
         break;    double lli; /* Individual log likelihood */
       else    int s1, s2;
         m++;    double bbh, survp;
     }/* end while */    long ipmx;
     if (s[m][i] > nlstate){    /*extern weight */
       mi++;     /* Death is another wave */    /* We are differentiating ll according to initial status */
       /* if(mi==0)  never been interviewed correctly before death */    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
          /* Only death is a correct wave */    /*for(i=1;i<imx;i++) 
       mw[mi][i]=m;      printf(" %d\n",s[4][i]);
     }    */
     cov[1]=1.;
     wav[i]=mi;  
     if(mi==0)    for(k=1; k<=nlstate; k++) ll[k]=0.;
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);  
   }    if(mle==1){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   for(i=1; i<=imx; i++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     for(mi=1; mi<wav[i];mi++){        for(mi=1; mi<= wav[i]-1; mi++){
       if (stepm <=0)          for (ii=1;ii<=nlstate+ndeath;ii++)
         dh[mi][i]=1;            for (j=1;j<=nlstate+ndeath;j++){
       else{              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         if (s[mw[mi+1][i]][i] > nlstate) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);            }
           if(j=0) j=1;  /* Survives at least one month after exam */          for(d=0; d<dh[mi][i]; d++){
         }            newm=savm;
         else{            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));            for (kk=1; kk<=cptcovage;kk++) {
           k=k+1;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           if (j >= jmax) jmax=j;            }
           else if (j <= jmin)jmin=j;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           sum=sum+j;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         }            savm=oldm;
         jk= j/stepm;            oldm=newm;
         jl= j -jk*stepm;          } /* end mult */
         ju= j -(jk+1)*stepm;        
         if(jl <= -ju)          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
           dh[mi][i]=jk;          /* But now since version 0.9 we anticipate for bias at large stepm.
         else           * If stepm is larger than one month (smallest stepm) and if the exact delay 
           dh[mi][i]=jk+1;           * (in months) between two waves is not a multiple of stepm, we rounded to 
         if(dh[mi][i]==0)           * the nearest (and in case of equal distance, to the lowest) interval but now
           dh[mi][i]=1; /* At least one step */           * we keep into memory the bias bh[mi][i] and also the previous matrix product
       }           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
     }           * probability in order to take into account the bias as a fraction of the way
   }           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);           * -stepm/2 to stepm/2 .
 }           * For stepm=1 the results are the same as for previous versions of Imach.
 /*********** Tricode ****************************/           * For stepm > 1 the results are less biased than in previous versions. 
 void tricode(int *Tvar, int **nbcode, int imx)           */
 {          s1=s[mw[mi][i]][i];
   int Ndum[20],ij=1, k, j, i;          s2=s[mw[mi+1][i]][i];
   int cptcode=0;          bbh=(double)bh[mi][i]/(double)stepm; 
   cptcoveff=0;          /* bias bh is positive if real duration
             * is higher than the multiple of stepm and negative otherwise.
   for (k=0; k<19; k++) Ndum[k]=0;           */
   for (k=1; k<=7; k++) ncodemax[k]=0;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
           if( s2 > nlstate){ 
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {            /* i.e. if s2 is a death state and if the date of death is known 
     for (i=1; i<=imx; i++) {               then the contribution to the likelihood is the probability to 
       ij=(int)(covar[Tvar[j]][i]);               die between last step unit time and current  step unit time, 
       Ndum[ij]++;               which is also equal to probability to die before dh 
       if (ij > cptcode) cptcode=ij;               minus probability to die before dh-stepm . 
     }               In version up to 0.92 likelihood was computed
           as if date of death was unknown. Death was treated as any other
     /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/          health state: the date of the interview describes the actual state
     for (i=0; i<=cptcode; i++) {          and not the date of a change in health state. The former idea was
       if(Ndum[i]!=0) ncodemax[j]++;          to consider that at each interview the state was recorded
     }          (healthy, disable or death) and IMaCh was corrected; but when we
     ij=1;          introduced the exact date of death then we should have modified
           the contribution of an exact death to the likelihood. This new
     for (i=1; i<=ncodemax[j]; i++) {          contribution is smaller and very dependent of the step unit
       for (k=0; k<=19; k++) {          stepm. It is no more the probability to die between last interview
         if (Ndum[k] != 0) {          and month of death but the probability to survive from last
           nbcode[Tvar[j]][ij]=k;          interview up to one month before death multiplied by the
           /*   printf("ij=%d ",nbcode[Tvar[2]][1]);*/          probability to die within a month. Thanks to Chris
           ij++;          Jackson for correcting this bug.  Former versions increased
         }          mortality artificially. The bad side is that we add another loop
         if (ij > ncodemax[j]) break;          which slows down the processing. The difference can be up to 10%
       }            lower mortality.
     }            */
   }              lli=log(out[s1][s2] - savm[s1][s2]);
  for (i=1; i<=10; i++) {  
       ij=Tvar[i];  
       Ndum[ij]++;          } else if  (s2==-2) {
     }            for (j=1,survp=0. ; j<=nlstate; j++) 
  ij=1;              survp += out[s1][j];
  for (i=1; i<=cptcovn; i++) {            lli= survp;
    if((Ndum[i]!=0) && (i<=ncov)){          }
      Tvaraff[i]=ij;          
    ij++;          else if  (s2==-4) {
    }            for (j=3,survp=0. ; j<=nlstate; j++) 
  }              survp += out[s1][j];
              lli= survp;
  for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          }
    if ((Tvar[j]>= cptcoveff) && (Tvar[j] <=ncov)) cptcoveff=Tvar[j];          
    /*printf("j=%d %d\n",j,Tvar[j]);*/          else if  (s2==-5) {
  }            for (j=1,survp=0. ; j<=2; j++) 
                survp += out[s1][j];
  /* printf("cptcoveff=%d Tvaraff=%d %d\n",cptcoveff, Tvaraff[1],Tvaraff[2]);            lli= survp;
     scanf("%d",i);*/          }
 }  
   
 /*********** Health Expectancies ****************/          else{
             lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)            /*  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 */
 {          } 
   /* Health expectancies */          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   int i, j, nhstepm, hstepm, h;          /*if(lli ==000.0)*/
   double age, agelim,hf;          /*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); */
   double ***p3mat;          ipmx +=1;
            sw += weight[i];
   fprintf(ficreseij,"# Health expectancies\n");          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   fprintf(ficreseij,"# Age");        } /* end of wave */
   for(i=1; i<=nlstate;i++)      } /* end of individual */
     for(j=1; j<=nlstate;j++)    }  else if(mle==2){
       fprintf(ficreseij," %1d-%1d",i,j);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   fprintf(ficreseij,"\n");        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
   hstepm=1*YEARM; /*  Every j years of age (in month) */          for (ii=1;ii<=nlstate+ndeath;ii++)
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   agelim=AGESUP;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            }
     /* nhstepm age range expressed in number of stepm */          for(d=0; d<=dh[mi][i]; d++){
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);            newm=savm;
     /* Typically if 20 years = 20*12/6=40 stepm */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     if (stepm >= YEARM) hstepm=1;            for (kk=1; kk<=cptcovage;kk++) {
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            }
     /* Computed by stepm unit matrices, product of hstepm matrices, stored            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);              savm=oldm;
             oldm=newm;
           } /* end mult */
     for(i=1; i<=nlstate;i++)        
       for(j=1; j<=nlstate;j++)          s1=s[mw[mi][i]][i];
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){          s2=s[mw[mi+1][i]][i];
           eij[i][j][(int)age] +=p3mat[i][j][h];          bbh=(double)bh[mi][i]/(double)stepm; 
         }          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
              ipmx +=1;
     hf=1;          sw += weight[i];
     if (stepm >= YEARM) hf=stepm/YEARM;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     fprintf(ficreseij,"%.0f",age );        } /* end of wave */
     for(i=1; i<=nlstate;i++)      } /* end of individual */
       for(j=1; j<=nlstate;j++){    }  else if(mle==3){  /* exponential inter-extrapolation */
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     fprintf(ficreseij,"\n");        for(mi=1; mi<= wav[i]-1; mi++){
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for (ii=1;ii<=nlstate+ndeath;ii++)
   }            for (j=1;j<=nlstate+ndeath;j++){
 }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
 /************ Variance ******************/            }
 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)          for(d=0; d<dh[mi][i]; d++){
 {            newm=savm;
   /* Variance of health expectancies */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            for (kk=1; kk<=cptcovage;kk++) {
   double **newm;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   double **dnewm,**doldm;            }
   int i, j, nhstepm, hstepm, h;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   int k, cptcode;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
    double *xp;            savm=oldm;
   double **gp, **gm;            oldm=newm;
   double ***gradg, ***trgradg;          } /* end mult */
   double ***p3mat;        
   double age,agelim;          s1=s[mw[mi][i]][i];
   int theta;          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
    fprintf(ficresvij,"# Covariances of life expectancies\n");          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
   fprintf(ficresvij,"# Age");          ipmx +=1;
   for(i=1; i<=nlstate;i++)          sw += weight[i];
     for(j=1; j<=nlstate;j++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);        } /* end of wave */
   fprintf(ficresvij,"\n");      } /* end of individual */
     }else if (mle==4){  /* ml=4 no inter-extrapolation */
   xp=vector(1,npar);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   dnewm=matrix(1,nlstate,1,npar);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   doldm=matrix(1,nlstate,1,nlstate);        for(mi=1; mi<= wav[i]-1; mi++){
            for (ii=1;ii<=nlstate+ndeath;ii++)
   hstepm=1*YEARM; /* Every year of age */            for (j=1;j<=nlstate+ndeath;j++){
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   agelim = AGESUP;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            }
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          for(d=0; d<dh[mi][i]; d++){
     if (stepm >= YEARM) hstepm=1;            newm=savm;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            for (kk=1; kk<=cptcovage;kk++) {
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     gp=matrix(0,nhstepm,1,nlstate);            }
     gm=matrix(0,nhstepm,1,nlstate);          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for(theta=1; theta <=npar; theta++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       for(i=1; i<=npar; i++){ /* Computes gradient */            savm=oldm;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);            oldm=newm;
       }          } /* end mult */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          s1=s[mw[mi][i]][i];
       for(j=1; j<= nlstate; j++){          s2=s[mw[mi+1][i]][i];
         for(h=0; h<=nhstepm; h++){          if( s2 > nlstate){ 
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)            lli=log(out[s1][s2] - savm[s1][s2]);
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];          }else{
         }            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       }          }
              ipmx +=1;
       for(i=1; i<=npar; i++) /* Computes gradient */          sw += weight[i];
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, 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]); */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        } /* end of wave */
       for(j=1; j<= nlstate; j++){      } /* end of individual */
         for(h=0; h<=nhstepm; h++){    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         }        for(mi=1; mi<= wav[i]-1; mi++){
       }          for (ii=1;ii<=nlstate+ndeath;ii++)
       for(j=1; j<= nlstate; j++)            for (j=1;j<=nlstate+ndeath;j++){
         for(h=0; h<=nhstepm; h++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         }            }
     } /* End theta */          for(d=0; d<dh[mi][i]; d++){
             newm=savm;
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
     for(h=0; h<=nhstepm; h++)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       for(j=1; j<=nlstate;j++)            }
         for(theta=1; theta <=npar; theta++)          
           trgradg[h][j][theta]=gradg[h][theta][j];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     for(i=1;i<=nlstate;i++)            savm=oldm;
       for(j=1;j<=nlstate;j++)            oldm=newm;
         vareij[i][j][(int)age] =0.;          } /* end mult */
     for(h=0;h<=nhstepm;h++){        
       for(k=0;k<=nhstepm;k++){          s1=s[mw[mi][i]][i];
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);          s2=s[mw[mi+1][i]][i];
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
         for(i=1;i<=nlstate;i++)          ipmx +=1;
           for(j=1;j<=nlstate;j++)          sw += weight[i];
             vareij[i][j][(int)age] += doldm[i][j];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       }          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
     }        } /* end of wave */
     h=1;      } /* end of individual */
     if (stepm >= YEARM) h=stepm/YEARM;    } /* End of if */
     fprintf(ficresvij,"%.0f ",age );    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
     for(i=1; i<=nlstate;i++)    /* 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 */
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    return -l;
       }  }
     fprintf(ficresvij,"\n");  
     free_matrix(gp,0,nhstepm,1,nlstate);  /*************** log-likelihood *************/
     free_matrix(gm,0,nhstepm,1,nlstate);  double funcone( double *x)
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);  {
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    /* Same as likeli but slower because of a lot of printf and if */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int i, ii, j, k, mi, d, kk;
   } /* End age */    double l, ll[NLSTATEMAX], cov[NCOVMAX];
      double **out;
   free_vector(xp,1,npar);    double lli; /* Individual log likelihood */
   free_matrix(doldm,1,nlstate,1,npar);    double llt;
   free_matrix(dnewm,1,nlstate,1,nlstate);    int s1, s2;
     double bbh, survp;
 }    /*extern weight */
     /* We are differentiating ll according to initial status */
 /************ Variance of prevlim ******************/    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)    /*for(i=1;i<imx;i++) 
 {      printf(" %d\n",s[4][i]);
   /* Variance of prevalence limit */    */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    cov[1]=1.;
   double **newm;  
   double **dnewm,**doldm;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   int i, j, nhstepm, hstepm;  
   int k, cptcode;    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double *xp;      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double *gp, *gm;      for(mi=1; mi<= wav[i]-1; mi++){
   double **gradg, **trgradg;        for (ii=1;ii<=nlstate+ndeath;ii++)
   double age,agelim;          for (j=1;j<=nlstate+ndeath;j++){
   int theta;            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
                savm[ii][j]=(ii==j ? 1.0 : 0.0);
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");          }
   fprintf(ficresvpl,"# Age");        for(d=0; d<dh[mi][i]; d++){
   for(i=1; i<=nlstate;i++)          newm=savm;
       fprintf(ficresvpl," %1d-%1d",i,i);          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   fprintf(ficresvpl,"\n");          for (kk=1; kk<=cptcovage;kk++) {
             cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   xp=vector(1,npar);          }
   dnewm=matrix(1,nlstate,1,npar);          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   doldm=matrix(1,nlstate,1,nlstate);                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
            savm=oldm;
   hstepm=1*YEARM; /* Every year of age */          oldm=newm;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */        } /* end mult */
   agelim = AGESUP;        
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        s1=s[mw[mi][i]][i];
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        s2=s[mw[mi+1][i]][i];
     if (stepm >= YEARM) hstepm=1;        bbh=(double)bh[mi][i]/(double)stepm; 
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        /* bias is positive if real duration
     gradg=matrix(1,npar,1,nlstate);         * is higher than the multiple of stepm and negative otherwise.
     gp=vector(1,nlstate);         */
     gm=vector(1,nlstate);        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           lli=log(out[s1][s2] - savm[s1][s2]);
     for(theta=1; theta <=npar; theta++){        } else if (mle==1){
       for(i=1; i<=npar; i++){ /* Computes gradient */          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        } else if(mle==2){
       }          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 */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        } else if(mle==3){  /* exponential inter-extrapolation */
       for(i=1;i<=nlstate;i++)          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 */
         gp[i] = prlim[i][i];        } else if (mle==4){  /* mle=4 no inter-extrapolation */
              lli=log(out[s1][s2]); /* Original formula */
       for(i=1; i<=npar; i++) /* Computes gradient */        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);          lli=log(out[s1][s2]); /* Original formula */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);        } /* End of if */
       for(i=1;i<=nlstate;i++)        ipmx +=1;
         gm[i] = prlim[i][i];        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]); */
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];        if(globpr){
     } /* End theta */          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
    %10.6f %10.6f %10.6f ", \
     trgradg =matrix(1,nlstate,1,npar);                  num[i],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(j=1; j<=nlstate;j++)          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
       for(theta=1; theta <=npar; theta++)            llt +=ll[k]*gipmx/gsw;
         trgradg[j][theta]=gradg[theta][j];            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
           }
     for(i=1;i<=nlstate;i++)          fprintf(ficresilk," %10.6f\n", -llt);
       varpl[i][(int)age] =0.;        }
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      } /* end of wave */
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    } /* end of individual */
     for(i=1;i<=nlstate;i++)    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     fprintf(ficresvpl,"%.0f ",age );    if(globpr==0){ /* First time we count the contributions and weights */
     for(i=1; i<=nlstate;i++)      gipmx=ipmx;
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));      gsw=sw;
     fprintf(ficresvpl,"\n");    }
     free_vector(gp,1,nlstate);    return -l;
     free_vector(gm,1,nlstate);  }
     free_matrix(gradg,1,npar,1,nlstate);  
     free_matrix(trgradg,1,nlstate,1,npar);  
   } /* End age */  /*************** function likelione ***********/
   void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   free_vector(xp,1,npar);  {
   free_matrix(doldm,1,nlstate,1,npar);    /* This routine should help understanding what is done with 
   free_matrix(dnewm,1,nlstate,1,nlstate);       the selection of individuals/waves and
        to check the exact contribution to the likelihood.
 }       Plotting could be done.
      */
     int k;
   
 /***********************************************/    if(*globpri !=0){ /* Just counts and sums, no printings */
 /**************** Main Program *****************/      strcpy(fileresilk,"ilk"); 
 /***********************************************/      strcat(fileresilk,fileres);
       if((ficresilk=fopen(fileresilk,"w"))==NULL) {
 /*int main(int argc, char *argv[])*/        printf("Problem with resultfile: %s\n", fileresilk);
 int main()        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");
   int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   double agedeb, agefin,hf;      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   double agemin=1.e20, agemax=-1.e20;      for(k=1; k<=nlstate; k++) 
         fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   double fret;      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   double **xi,tmp,delta;    }
   
   double dum; /* Dummy variable */    *fretone=(*funcone)(p);
   double ***p3mat;    if(*globpri !=0){
   int *indx;      fclose(ficresilk);
   char line[MAXLINE], linepar[MAXLINE];      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   char title[MAXLINE];      fflush(fichtm); 
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];    } 
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];    return;
   char filerest[FILENAMELENGTH];  }
   char fileregp[FILENAMELENGTH];  
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];  
   int firstobs=1, lastobs=10;  /*********** Maximum Likelihood Estimation ***************/
   int sdeb, sfin; /* Status at beginning and end */  
   int c,  h , cpt,l;  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   int ju,jl, mi;  {
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    int i,j, iter;
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    double **xi;
      double fret;
   int hstepm, nhstepm;    double fretone; /* Only one call to likelihood */
   double bage, fage, age, agelim, agebase;    /*  char filerespow[FILENAMELENGTH];*/
   double ftolpl=FTOL;    xi=matrix(1,npar,1,npar);
   double **prlim;    for (i=1;i<=npar;i++)
   double *severity;      for (j=1;j<=npar;j++)
   double ***param; /* Matrix of parameters */        xi[i][j]=(i==j ? 1.0 : 0.0);
   double  *p;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   double **matcov; /* Matrix of covariance */    strcpy(filerespow,"pow"); 
   double ***delti3; /* Scale */    strcat(filerespow,fileres);
   double *delti; /* Scale */    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   double ***eij, ***vareij;      printf("Problem with resultfile: %s\n", filerespow);
   double **varpl; /* Variances of prevalence limits by age */      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   double *epj, vepp;    }
   char version[80]="Imach version 62c, May 1999, INED-EUROREVES ";    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   char *alph[]={"a","a","b","c","d","e"}, str[4];    for (i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate+ndeath;j++)
   char z[1]="c", occ;        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
 #include <sys/time.h>    fprintf(ficrespow,"\n");
 #include <time.h>  
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    powell(p,xi,npar,ftol,&iter,&fret,func);
   /* long total_usecs;  
   struct timeval start_time, end_time;    free_matrix(xi,1,npar,1,npar);
      fclose(ficrespow);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
     fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   printf("\nIMACH, Version 0.64a");  
   printf("\nEnter the parameter file name: ");  }
   
 #ifdef windows  /**** Computes Hessian and covariance matrix ***/
   scanf("%s",pathtot);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
   getcwd(pathcd, size);  {
   /*cygwin_split_path(pathtot,path,optionfile);    double  **a,**y,*x,pd;
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    double **hess;
   /* cutv(path,optionfile,pathtot,'\\');*/    int i, j,jk;
     int *indx;
 split(pathtot, path,optionfile);  
   chdir(path);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   replace(pathc,path);    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
 #endif    void lubksb(double **a, int npar, int *indx, double b[]) ;
 #ifdef unix    void ludcmp(double **a, int npar, int *indx, double *d) ;
   scanf("%s",optionfile);    double gompertz(double p[]);
 #endif    hess=matrix(1,npar,1,npar);
   
 /*-------- arguments in the command line --------*/    printf("\nCalculation of the hessian matrix. Wait...\n");
     fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   strcpy(fileres,"r");    for (i=1;i<=npar;i++){
   strcat(fileres, optionfile);      printf("%d",i);fflush(stdout);
       fprintf(ficlog,"%d",i);fflush(ficlog);
   /*---------arguments file --------*/     
        hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
   if((ficpar=fopen(optionfile,"r"))==NULL)    {      
     printf("Problem with optionfile %s\n",optionfile);      /*  printf(" %f ",p[i]);
     goto end;          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   }    }
     
   strcpy(filereso,"o");    for (i=1;i<=npar;i++) {
   strcat(filereso,fileres);      for (j=1;j<=npar;j++)  {
   if((ficparo=fopen(filereso,"w"))==NULL) {        if (j>i) { 
     printf("Problem with Output resultfile: %s\n", filereso);goto end;          printf(".%d%d",i,j);fflush(stdout);
   }          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
           hess[i][j]=hessij(p,delti,i,j,func,npar);
   /* Reads comments: lines beginning with '#' */          
   while((c=getc(ficpar))=='#' && c!= EOF){          hess[j][i]=hess[i][j];    
     ungetc(c,ficpar);          /*printf(" %lf ",hess[i][j]);*/
     fgets(line, MAXLINE, ficpar);        }
     puts(line);      }
     fputs(line,ficparo);    }
   }    printf("\n");
   ungetc(c,ficpar);    fprintf(ficlog,"\n");
   
   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("\nInverting the hessian to get the covariance matrix. Wait...\n");
   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);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   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);    
     a=matrix(1,npar,1,npar);
   covar=matrix(0,NCOVMAX,1,n);        y=matrix(1,npar,1,npar);
   if (strlen(model)<=1) cptcovn=0;    x=vector(1,npar);
   else {    indx=ivector(1,npar);
     j=0;    for (i=1;i<=npar;i++)
     j=nbocc(model,'+');      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     cptcovn=j+1;    ludcmp(a,npar,indx,&pd);
   }  
     for (j=1;j<=npar;j++) {
   ncovmodel=2+cptcovn;      for (i=1;i<=npar;i++) x[i]=0;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */      x[j]=1;
        lubksb(a,npar,indx,x);
   /* Read guess parameters */      for (i=1;i<=npar;i++){ 
   /* Reads comments: lines beginning with '#' */        matcov[i][j]=x[i];
   while((c=getc(ficpar))=='#' && c!= EOF){      }
     ungetc(c,ficpar);    }
     fgets(line, MAXLINE, ficpar);  
     puts(line);    printf("\n#Hessian matrix#\n");
     fputs(line,ficparo);    fprintf(ficlog,"\n#Hessian matrix#\n");
   }    for (i=1;i<=npar;i++) { 
   ungetc(c,ficpar);      for (j=1;j<=npar;j++) { 
          printf("%.3e ",hess[i][j]);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        fprintf(ficlog,"%.3e ",hess[i][j]);
     for(i=1; i <=nlstate; i++)      }
     for(j=1; j <=nlstate+ndeath-1; j++){      printf("\n");
       fscanf(ficpar,"%1d%1d",&i1,&j1);      fprintf(ficlog,"\n");
       fprintf(ficparo,"%1d%1d",i1,j1);    }
       printf("%1d%1d",i,j);  
       for(k=1; k<=ncovmodel;k++){    /* Recompute Inverse */
         fscanf(ficpar," %lf",&param[i][j][k]);    for (i=1;i<=npar;i++)
         printf(" %lf",param[i][j][k]);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
         fprintf(ficparo," %lf",param[i][j][k]);    ludcmp(a,npar,indx,&pd);
       }  
       fscanf(ficpar,"\n");    /*  printf("\n#Hessian matrix recomputed#\n");
       printf("\n");  
       fprintf(ficparo,"\n");    for (j=1;j<=npar;j++) {
     }      for (i=1;i<=npar;i++) x[i]=0;
        x[j]=1;
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;      lubksb(a,npar,indx,x);
   p=param[1][1];      for (i=1;i<=npar;i++){ 
          y[i][j]=x[i];
   /* Reads comments: lines beginning with '#' */        printf("%.3e ",y[i][j]);
   while((c=getc(ficpar))=='#' && c!= EOF){        fprintf(ficlog,"%.3e ",y[i][j]);
     ungetc(c,ficpar);      }
     fgets(line, MAXLINE, ficpar);      printf("\n");
     puts(line);      fprintf(ficlog,"\n");
     fputs(line,ficparo);    }
   }    */
   ungetc(c,ficpar);  
     free_matrix(a,1,npar,1,npar);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    free_matrix(y,1,npar,1,npar);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    free_vector(x,1,npar);
   for(i=1; i <=nlstate; i++){    free_ivector(indx,1,npar);
     for(j=1; j <=nlstate+ndeath-1; j++){    free_matrix(hess,1,npar,1,npar);
       fscanf(ficpar,"%1d%1d",&i1,&j1);  
       printf("%1d%1d",i,j);  
       fprintf(ficparo,"%1d%1d",i1,j1);  }
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar,"%le",&delti3[i][j][k]);  /*************** hessian matrix ****************/
         printf(" %le",delti3[i][j][k]);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
         fprintf(ficparo," %le",delti3[i][j][k]);  {
       }    int i;
       fscanf(ficpar,"\n");    int l=1, lmax=20;
       printf("\n");    double k1,k2;
       fprintf(ficparo,"\n");    double p2[NPARMAX+1];
     }    double res;
   }    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
   delti=delti3[1][1];    double fx;
      int k=0,kmax=10;
   /* Reads comments: lines beginning with '#' */    double l1;
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    fx=func(x);
     fgets(line, MAXLINE, ficpar);    for (i=1;i<=npar;i++) p2[i]=x[i];
     puts(line);    for(l=0 ; l <=lmax; l++){
     fputs(line,ficparo);      l1=pow(10,l);
   }      delts=delt;
   ungetc(c,ficpar);      for(k=1 ; k <kmax; k=k+1){
          delt = delta*(l1*k);
   matcov=matrix(1,npar,1,npar);        p2[theta]=x[theta] +delt;
   for(i=1; i <=npar; i++){        k1=func(p2)-fx;
     fscanf(ficpar,"%s",&str);        p2[theta]=x[theta]-delt;
     printf("%s",str);        k2=func(p2)-fx;
     fprintf(ficparo,"%s",str);        /*res= (k1-2.0*fx+k2)/delt/delt; */
     for(j=1; j <=i; j++){        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
       fscanf(ficpar," %le",&matcov[i][j]);        
       printf(" %.5le",matcov[i][j]);  #ifdef DEBUG
       fprintf(ficparo," %.5le",matcov[i][j]);        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
     }        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
     fscanf(ficpar,"\n");  #endif
     printf("\n");        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
     fprintf(ficparo,"\n");        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
   }          k=kmax;
   for(i=1; i <=npar; i++)        }
     for(j=i+1;j<=npar;j++)        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
       matcov[i][j]=matcov[j][i];          k=kmax; l=lmax*10.;
            }
   printf("\n");        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           delts=delt;
         }
     /*-------- data file ----------*/      }
     if((ficres =fopen(fileres,"w"))==NULL) {    }
       printf("Problem with resultfile: %s\n", fileres);goto end;    delti[theta]=delts;
     }    return res; 
     fprintf(ficres,"#%s\n",version);    
      }
     if((fic=fopen(datafile,"r"))==NULL)    {  
       printf("Problem with datafile: %s\n", datafile);goto end;  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
     }  {
     int i;
     n= lastobs;    int l=1, l1, lmax=20;
     severity = vector(1,maxwav);    double k1,k2,k3,k4,res,fx;
     outcome=imatrix(1,maxwav+1,1,n);    double p2[NPARMAX+1];
     num=ivector(1,n);    int k;
     moisnais=vector(1,n);  
     annais=vector(1,n);    fx=func(x);
     moisdc=vector(1,n);    for (k=1; k<=2; k++) {
     andc=vector(1,n);      for (i=1;i<=npar;i++) p2[i]=x[i];
     agedc=vector(1,n);      p2[thetai]=x[thetai]+delti[thetai]/k;
     cod=ivector(1,n);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     weight=vector(1,n);      k1=func(p2)-fx;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    
     mint=matrix(1,maxwav,1,n);      p2[thetai]=x[thetai]+delti[thetai]/k;
     anint=matrix(1,maxwav,1,n);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     s=imatrix(1,maxwav+1,1,n);      k2=func(p2)-fx;
     adl=imatrix(1,maxwav+1,1,n);        
     tab=ivector(1,NCOVMAX);      p2[thetai]=x[thetai]-delti[thetai]/k;
     ncodemax=ivector(1,8);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k3=func(p2)-fx;
     i=1;    
     while (fgets(line, MAXLINE, fic) != NULL)    {      p2[thetai]=x[thetai]-delti[thetai]/k;
       if ((i >= firstobs) && (i <=lastobs)) {      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
              k4=func(p2)-fx;
         for (j=maxwav;j>=1;j--){      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);  #ifdef DEBUG
           strcpy(line,stra);      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);
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);      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);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  #endif
         }    }
            return res;
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);  }
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);  
   /************** Inverse of matrix **************/
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);  void ludcmp(double **a, int n, int *indx, double *d) 
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);  { 
     int i,imax,j,k; 
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    double big,dum,sum,temp; 
         for (j=ncov;j>=1;j--){    double *vv; 
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);   
         }    vv=vector(1,n); 
         num[i]=atol(stra);    *d=1.0; 
     for (i=1;i<=n;i++) { 
         /*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]));*/      big=0.0; 
       for (j=1;j<=n;j++) 
         i=i+1;        if ((temp=fabs(a[i][j])) > big) big=temp; 
       }      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     }      vv[i]=1.0/big; 
     } 
     /*scanf("%d",i);*/    for (j=1;j<=n;j++) { 
   imx=i-1; /* Number of individuals */      for (i=1;i<j;i++) { 
         sum=a[i][j]; 
   /* Calculation of the number of parameter from char model*/        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   Tvar=ivector(1,15);        a[i][j]=sum; 
   Tprod=ivector(1,15);      } 
   Tvaraff=ivector(1,15);      big=0.0; 
   Tvard=imatrix(1,15,1,2);      for (i=j;i<=n;i++) { 
   Tage=ivector(1,15);              sum=a[i][j]; 
            for (k=1;k<j;k++) 
   if (strlen(model) >1){          sum -= a[i][k]*a[k][j]; 
     j=0, j1=0, k1=1, k2=1;        a[i][j]=sum; 
     j=nbocc(model,'+');        if ( (dum=vv[i]*fabs(sum)) >= big) { 
     j1=nbocc(model,'*');          big=dum; 
     cptcovn=j+1;          imax=i; 
     cptcovprod=j1;        } 
          } 
     strcpy(modelsav,model);      if (j != imax) { 
    if (j==0) {        for (k=1;k<=n;k++) { 
       if (j1==0){          dum=a[imax][k]; 
         cutv(stra,strb,modelsav,'V');          a[imax][k]=a[j][k]; 
         Tvar[1]=atoi(strb);          a[j][k]=dum; 
       }        } 
       else if (j1==1) {        *d = -(*d); 
         cutv(stra,strb,modelsav,'*');        vv[imax]=vv[j]; 
         Tage[1]=1; cptcovage++;      } 
         if (strcmp(stra,"age")==0) {      indx[j]=imax; 
           cptcovprod--;      if (a[j][j] == 0.0) a[j][j]=TINY; 
           cutv(strd,strc,strb,'V');      if (j != n) { 
           Tvar[1]=atoi(strc);        dum=1.0/(a[j][j]); 
         }        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
         else if (strcmp(strb,"age")==0) {      } 
           cptcovprod--;    } 
           cutv(strd,strc,stra,'V');    free_vector(vv,1,n);  /* Doesn't work */
           Tvar[1]=atoi(strc);  ;
         }  } 
         else {  
           cutv(strd,strc,strb,'V');  void lubksb(double **a, int n, int *indx, double b[]) 
           cutv(stre,strd,stra,'V');  { 
           Tvar[1]=ncov+1;    int i,ii=0,ip,j; 
           for (k=1; k<=lastobs;k++)    double sum; 
               covar[ncov+1][k]=covar[atoi(strc)][k]*covar[atoi(strd)][k];   
         }    for (i=1;i<=n;i++) { 
         /*printf("%s %s %s\n", stra,strb,modelsav);      ip=indx[i]; 
 printf("%d ",Tvar[1]);      sum=b[ip]; 
 scanf("%d",i);*/      b[ip]=b[i]; 
       }      if (ii) 
     }        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
    else {      else if (sum) ii=i; 
       for(i=j; i>=1;i--){      b[i]=sum; 
         cutv(stra,strb,modelsav,'+');    } 
         /*printf("%s %s %s\n", stra,strb,modelsav);    for (i=n;i>=1;i--) { 
           scanf("%d",i);*/      sum=b[i]; 
         if (strchr(strb,'*')) {      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
           cutv(strd,strc,strb,'*');      b[i]=sum/a[i][i]; 
           if (strcmp(strc,"age")==0) {    } 
             cptcovprod--;  } 
             cutv(strb,stre,strd,'V');  
             Tvar[i+1]=atoi(stre);  /************ Frequencies ********************/
             cptcovage++;  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[])
             Tage[cptcovage]=i+1;  {  /* Some frequencies */
             printf("stre=%s ", stre);    
           }    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
           else if (strcmp(strd,"age")==0) {    int first;
             cptcovprod--;    double ***freq; /* Frequencies */
             cutv(strb,stre,strc,'V');    double *pp, **prop;
             Tvar[i+1]=atoi(stre);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
             cptcovage++;    FILE *ficresp;
             Tage[cptcovage]=i+1;    char fileresp[FILENAMELENGTH];
           }    
           else {    pp=vector(1,nlstate);
             cutv(strb,stre,strc,'V');    prop=matrix(1,nlstate,iagemin,iagemax+3);
             Tvar[i+1]=ncov+k1;    strcpy(fileresp,"p");
             cutv(strb,strc,strd,'V');    strcat(fileresp,fileres);
             Tprod[k1]=i+1;    if((ficresp=fopen(fileresp,"w"))==NULL) {
             Tvard[k1][1]=atoi(strc);      printf("Problem with prevalence resultfile: %s\n", fileresp);
             Tvard[k1][2]=atoi(stre);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
             Tvar[cptcovn+k2]=Tvard[k1][1];      exit(0);
             Tvar[cptcovn+k2+1]=Tvard[k1][2];    }
             for (k=1; k<=lastobs;k++)    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
               covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    j1=0;
             k1++;    
             k2=k2+2;    j=cptcoveff;
           }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         }  
         else {    first=1;
           cutv(strd,strc,strb,'V');  
           /* printf("%s %s %s", strd,strc,strb);*/    for(k1=1; k1<=j;k1++){
           Tvar[i+1]=atoi(strc);      for(i1=1; i1<=ncodemax[k1];i1++){
         }        j1++;
         strcpy(modelsav,stra);          /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
       }          scanf("%d", i);*/
       cutv(strd,strc,stra,'V');        for (i=-5; i<=nlstate+ndeath; i++)  
       Tvar[1]=atoi(strc);          for (jk=-5; jk<=nlstate+ndeath; jk++)  
     }            for(m=iagemin; m <= iagemax+3; m++)
   }              freq[i][jk][m]=0;
   /* for (i=1; i<=5; i++)  
      printf("i=%d %d ",i,Tvar[i]);*/      for (i=1; i<=nlstate; i++)  
   /* printf("tvar=%d %d cptcovage=%d %d",Tvar[1],Tvar[2],cptcovage,Tage[1]);*/        for(m=iagemin; m <= iagemax+3; m++)
  /*printf("cptcovprod=%d ", cptcovprod);*/          prop[i][m]=0;
   /*  scanf("%d ",i);*/        
     fclose(fic);        dateintsum=0;
         k2cpt=0;
     /*  if(mle==1){*/        for (i=1; i<=imx; i++) {
     if (weightopt != 1) { /* Maximisation without weights*/          bool=1;
       for(i=1;i<=n;i++) weight[i]=1.0;          if  (cptcovn>0) {
     }            for (z1=1; z1<=cptcoveff; z1++) 
     /*-calculation of age at interview from date of interview and age at death -*/              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     agev=matrix(1,maxwav,1,imx);                bool=0;
              }
     for (i=1; i<=imx; i++)  {          if (bool==1){
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);            for(m=firstpass; m<=lastpass; m++){
       for(m=1; (m<= maxwav); m++){              k2=anint[m][i]+(mint[m][i]/12.);
         if(s[m][i] >0){              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
           if (s[m][i] == nlstate+1) {                if(agev[m][i]==0) agev[m][i]=iagemax+1;
             if(agedc[i]>0)                if(agev[m][i]==1) agev[m][i]=iagemax+2;
               if(moisdc[i]!=99 && andc[i]!=9999)                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
               agev[m][i]=agedc[i];                if (m<lastpass) {
             else{                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
               printf("Warning negative age at death: %d line:%d\n",num[i],i);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
               agev[m][i]=-1;                }
             }                
           }                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
           else if(s[m][i] !=9){ /* Should no more exist */                  dateintsum=dateintsum+k2;
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);                  k2cpt++;
             if(mint[m][i]==99 || 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){        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
               agemax=agev[m][i];  fprintf(ficresp, "#Local time at start: %s", strstart);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/        if  (cptcovn>0) {
             }          fprintf(ficresp, "\n#********** Variable "); 
             /*agev[m][i]=anint[m][i]-annais[i];*/          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
             /*   agev[m][i] = age[i]+2*m;*/          fprintf(ficresp, "**********\n#");
           }        }
           else { /* =9 */        for(i=1; i<=nlstate;i++) 
             agev[m][i]=1;          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
             s[m][i]=-1;        fprintf(ficresp, "\n");
           }        
         }        for(i=iagemin; i <= iagemax+3; i++){
         else /*= 0 Unknown */          if(i==iagemax+3){
           agev[m][i]=1;            fprintf(ficlog,"Total");
       }          }else{
                if(first==1){
     }              first=0;
     for (i=1; i<=imx; i++)  {              printf("See log file for details...\n");
       for(m=1; (m<= maxwav); m++){            }
         if (s[m][i] > (nlstate+ndeath)) {            fprintf(ficlog,"Age %d", i);
           printf("Error: Wrong value in nlstate or ndeath\n");            }
           goto end;          for(jk=1; jk <=nlstate ; jk++){
         }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
       }              pp[jk] += freq[jk][m][i]; 
     }          }
           for(jk=1; jk <=nlstate ; jk++){
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);            for(m=-1, pos=0; m <=0 ; m++)
               pos += freq[jk][m][i];
     free_vector(severity,1,maxwav);            if(pp[jk]>=1.e-10){
     free_imatrix(outcome,1,maxwav+1,1,n);              if(first==1){
     free_vector(moisnais,1,n);              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     free_vector(annais,1,n);              }
     free_matrix(mint,1,maxwav,1,n);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     free_matrix(anint,1,maxwav,1,n);            }else{
     free_vector(moisdc,1,n);              if(first==1)
     free_vector(andc,1,n);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
                }
     wav=ivector(1,imx);          }
     dh=imatrix(1,lastpass-firstpass+1,1,imx);  
     mw=imatrix(1,lastpass-firstpass+1,1,imx);          for(jk=1; jk <=nlstate ; jk++){
                for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     /* Concatenates waves */              pp[jk] += freq[jk][m][i];
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);          }       
           for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
             pos += pp[jk];
       Tcode=ivector(1,100);            posprop += prop[jk][i];
       nbcode=imatrix(1,nvar,1,8);          }
       ncodemax[1]=1;          for(jk=1; jk <=nlstate ; jk++){
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);            if(pos>=1.e-5){
                    if(first==1)
    codtab=imatrix(1,100,1,10);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
    h=0;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
    m=pow(2,cptcoveff);            }else{
                if(first==1)
    for(k=1;k<=cptcoveff; k++){                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
      for(i=1; i <=(m/pow(2,k));i++){              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
        for(j=1; j <= ncodemax[k]; j++){            }
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){            if( i <= iagemax){
            h++;              if(pos>=1.e-5){
            if (h>m) h=1;codtab[h][k]=j;                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
          }                /*probs[i][jk][j1]= pp[jk]/pos;*/
        }                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
      }              }
    }              else
                 fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
             }
    /*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);          for(jk=-1; jk <=nlstate+ndeath; jk++)
      }            for(m=-1; m <=nlstate+ndeath; m++)
      printf("\n");              if(freq[jk][m][i] !=0 ) {
    }              if(first==1)
    scanf("%d",i);*/                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                    fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
    /* Calculates basic frequencies. Computes observed prevalence at single age              }
        and prints on file fileres'p'. */          if(i <= iagemax)
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);            fprintf(ficresp,"\n");
           if(first==1)
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            printf("Others in log...\n");
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */          fprintf(ficlog,"\n");
     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 */    }
        dateintmean=dateintsum/k2cpt; 
     /* 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] */    fclose(ficresp);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     free_vector(pp,1,nlstate);
     if(mle==1){    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    /* End of Freq */
     }  }
      
     /*--------- results files --------------*/  /************ Prevalence ********************/
     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);  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)
      {  
    jk=1;    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
    fprintf(ficres,"# Parameters\n");       in each health status at the date of interview (if between dateprev1 and dateprev2).
    printf("# Parameters\n");       We still use firstpass and lastpass as another selection.
    for(i=1,jk=1; i <=nlstate; i++){    */
      for(k=1; k <=(nlstate+ndeath); k++){   
        if (k != i)    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
          {    double ***freq; /* Frequencies */
            printf("%d%d ",i,k);    double *pp, **prop;
            fprintf(ficres,"%1d%1d ",i,k);    double pos,posprop; 
            for(j=1; j <=ncovmodel; j++){    double  y2; /* in fractional years */
              printf("%f ",p[jk]);    int iagemin, iagemax;
              fprintf(ficres,"%f ",p[jk]);  
              jk++;    iagemin= (int) agemin;
            }    iagemax= (int) agemax;
            printf("\n");    /*pp=vector(1,nlstate);*/
            fprintf(ficres,"\n");    prop=matrix(1,nlstate,iagemin,iagemax+3); 
          }    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
      }    j1=0;
    }    
  if(mle==1){    j=cptcoveff;
     /* Computing hessian and covariance matrix */    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     ftolhess=ftol; /* Usually correct */    
     hesscov(matcov, p, npar, delti, ftolhess, func);    for(k1=1; k1<=j;k1++){
  }      for(i1=1; i1<=ncodemax[k1];i1++){
     fprintf(ficres,"# Scales\n");        j1++;
     printf("# Scales\n");        
      for(i=1,jk=1; i <=nlstate; i++){        for (i=1; i<=nlstate; i++)  
       for(j=1; j <=nlstate+ndeath; j++){          for(m=iagemin; m <= iagemax+3; m++)
         if (j!=i) {            prop[i][m]=0.0;
           fprintf(ficres,"%1d%1d",i,j);       
           printf("%1d%1d",i,j);        for (i=1; i<=imx; i++) { /* Each individual */
           for(k=1; k<=ncovmodel;k++){          bool=1;
             printf(" %.5e",delti[jk]);          if  (cptcovn>0) {
             fprintf(ficres," %.5e",delti[jk]);            for (z1=1; z1<=cptcoveff; z1++) 
             jk++;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
           }                bool=0;
           printf("\n");          } 
           fprintf(ficres,"\n");          if (bool==1) { 
         }            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
       }              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
       }              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                    if(agev[m][i]==0) agev[m][i]=iagemax+1;
     k=1;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
     fprintf(ficres,"# Covariance\n");                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); 
     printf("# Covariance\n");                if (s[m][i]>0 && s[m][i]<=nlstate) { 
     for(i=1;i<=npar;i++){                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
       /*  if (k>nlstate) k=1;                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
       i1=(i-1)/(ncovmodel*nlstate)+1;                  prop[s[m][i]][iagemax+3] += weight[i]; 
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);                } 
       printf("%s%d%d",alph[k],i1,tab[i]);*/              }
       fprintf(ficres,"%3d",i);            } /* end selection of waves */
       printf("%3d",i);          }
       for(j=1; j<=i;j++){        }
         fprintf(ficres," %.5e",matcov[i][j]);        for(i=iagemin; i <= iagemax+3; i++){  
         printf(" %.5e",matcov[i][j]);          
       }          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
       fprintf(ficres,"\n");            posprop += prop[jk][i]; 
       printf("\n");          } 
       k++;  
     }          for(jk=1; jk <=nlstate ; jk++){     
                if( i <=  iagemax){ 
     while((c=getc(ficpar))=='#' && c!= EOF){              if(posprop>=1.e-5){ 
       ungetc(c,ficpar);                probs[i][jk][j1]= prop[jk][i]/posprop;
       fgets(line, MAXLINE, ficpar);              } 
       puts(line);            } 
       fputs(line,ficparo);          }/* end jk */ 
     }        }/* end i */ 
     ungetc(c,ficpar);      } /* end i1 */
      } /* end k1 */
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    
        /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
     if (fage <= 2) {    /*free_vector(pp,1,nlstate);*/
       bage = agemin;    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
       fage = agemax;  }  /* End of prevalence */
     }  
   /************* Waves Concatenation ***************/
     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\n",agemin,agemax,bage,fage);  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)
   {
        /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
 /*------------ gnuplot -------------*/       Death is a valid wave (if date is known).
 chdir(pathcd);       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
   if((ficgp=fopen("graph.plt","w"))==NULL) {       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
     printf("Problem with file graph.gp");goto end;       and mw[mi+1][i]. dh depends on stepm.
   }       */
 #ifdef windows  
   fprintf(ficgp,"cd \"%s\" \n",pathc);    int i, mi, m;
 #endif    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
 m=pow(2,cptcoveff);       double sum=0., jmean=0.;*/
      int first;
  /* 1eme*/    int j, k=0,jk, ju, jl;
   for (cpt=1; cpt<= nlstate ; cpt ++) {    double sum=0.;
    for (k1=1; k1<= m ; k1 ++) {    first=0;
     jmin=1e+5;
 #ifdef windows    jmax=-1;
     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);    jmean=0.;
 #endif    for(i=1; i<=imx; i++){
 #ifdef unix      mi=0;
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);      m=firstpass;
 #endif      while(s[m][i] <= nlstate){
         if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
 for (i=1; i<= nlstate ; i ++) {          mw[++mi][i]=m;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        if(m >=lastpass)
   else fprintf(ficgp," \%%*lf (\%%*lf)");          break;
 }        else
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);          m++;
     for (i=1; i<= nlstate ; i ++) {      }/* end while */
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      if (s[m][i] > nlstate){
   else fprintf(ficgp," \%%*lf (\%%*lf)");        mi++;     /* Death is another wave */
 }        /* if(mi==0)  never been interviewed correctly before death */
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);           /* Only death is a correct wave */
      for (i=1; i<= nlstate ; i ++) {        mw[mi][i]=m;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      }
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }        wav[i]=mi;
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));      if(mi==0){
 #ifdef unix        nbwarn++;
 fprintf(ficgp,"\nset ter gif small size 400,300");        if(first==0){
 #endif          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          first=1;
    }        }
   }        if(first==1){
   /*2 eme*/          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
         }
   for (k1=1; k1<= m ; k1 ++) {      } /* end mi==0 */
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);    } /* End individuals */
      
     for (i=1; i<= nlstate+1 ; i ++) {    for(i=1; i<=imx; i++){
       k=2*i;      for(mi=1; mi<wav[i];mi++){
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);        if (stepm <=0)
       for (j=1; j<= nlstate+1 ; j ++) {          dh[mi][i]=1;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        else{
   else fprintf(ficgp," \%%*lf (\%%*lf)");          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
 }              if (agedc[i] < 2*AGESUP) {
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);              if(j==0) j=1;  /* Survives at least one month after exam */
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);              else if(j<0){
       for (j=1; j<= nlstate+1 ; j ++) {                nberr++;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");                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]);
         else fprintf(ficgp," \%%*lf (\%%*lf)");                j=1; /* Temporary Dangerous patch */
 }                  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,"\" t\"\" w l 0,");                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
       for (j=1; j<= nlstate+1 ; j ++) {              }
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");              k=k+1;
   else fprintf(ficgp," \%%*lf (\%%*lf)");              if (j >= jmax){
 }                  jmax=j;
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");                ijmax=i;
       else fprintf(ficgp,"\" t\"\" w l 0,");              }
     }              if (j <= jmin){
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);                jmin=j;
   }                ijmin=i;
                }
   /*3eme*/              sum=sum+j;
               /*if (j<0) printf("j=%d num=%d \n",j,i);*/
   for (k1=1; k1<= m ; k1 ++) {              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     for (cpt=1; cpt<= nlstate ; cpt ++) {            }
       k=2+nlstate*(cpt-1);          }
       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);          else{
       for (i=1; i< nlstate ; i ++) {            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
         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);  /*        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]); */
       }  
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);            k=k+1;
     }            if (j >= jmax) {
   }              jmax=j;
                ijmax=i;
   /* CV preval stat */            }
   for (k1=1; k1<= m ; k1 ++) {            else if (j <= jmin){
     for (cpt=1; cpt<nlstate ; cpt ++) {              jmin=j;
       k=3;              ijmin=i;
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);            }
       for (i=1; i< nlstate ; i ++)            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
         fprintf(ficgp,"+$%d",k+i+1);            /*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]);*/
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);            if(j<0){
                    nberr++;
       l=3+(nlstate+ndeath)*cpt;              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,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       for (i=1; i< nlstate ; i ++) {            }
         l=3+(nlstate+ndeath)*cpt;            sum=sum+j;
         fprintf(ficgp,"+$%d",l+i+1);          }
       }          jk= j/stepm;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);            jl= j -jk*stepm;
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);          ju= j -(jk+1)*stepm;
     }          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
   }            if(jl==0){
               dh[mi][i]=jk;
   /* proba elementaires */              bh[mi][i]=0;
    for(i=1,jk=1; i <=nlstate; i++){            }else{ /* We want a negative bias in order to only have interpolation ie
     for(k=1; k <=(nlstate+ndeath); k++){                    * at the price of an extra matrix product in likelihood */
       if (k != i) {              dh[mi][i]=jk+1;
         for(j=1; j <=ncovmodel; j++){              bh[mi][i]=ju;
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/            }
           /*fprintf(ficgp,"%s",alph[1]);*/          }else{
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);            if(jl <= -ju){
           jk++;              dh[mi][i]=jk;
           fprintf(ficgp,"\n");              bh[mi][i]=jl;       /* bias is positive if real duration
         }                                   * is higher than the multiple of stepm and negative otherwise.
       }                                   */
     }            }
     }            else{
               dh[mi][i]=jk+1;
   for(jk=1; jk <=m; jk++) {              bh[mi][i]=ju;
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);            }
    i=1;            if(dh[mi][i]==0){
    for(k2=1; k2<=nlstate; k2++) {              dh[mi][i]=1; /* At least one step */
      k3=i;              bh[mi][i]=ju; /* At least one step */
      for(k=1; k<=(nlstate+ndeath); k++) {              /*  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 (k != k2){            }
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);          } /* end if mle */
 ij=1;        }
         for(j=3; j <=ncovmodel; j++) {      } /* end wave */
           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]]]);    jmean=sum/k;
             ij++;    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(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
           else   }
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  
         }  /*********** Tricode ****************************/
           fprintf(ficgp,")/(1");  void tricode(int *Tvar, int **nbcode, int imx)
          {
         for(k1=1; k1 <=nlstate; k1++){      
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    int Ndum[20],ij=1, k, j, i, maxncov=19;
 ij=1;    int cptcode=0;
           for(j=3; j <=ncovmodel; j++){    cptcoveff=0; 
           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]]]);    for (k=0; k<maxncov; k++) Ndum[k]=0;
             ij++;    for (k=1; k<=7; k++) ncodemax[k]=0;
           }  
           else    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
           }                                 modality*/ 
           fprintf(ficgp,")");        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
         }        Ndum[ij]++; /*store the modality */
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
         i=i+ncovmodel;                                         Tvar[j]. If V=sex and male is 0 and 
        }                                         female is 1, then  cptcode=1.*/
      }      }
    }  
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);      for (i=0; i<=cptcode; i++) {
   }        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(ficgp);  
          ij=1; 
 chdir(path);      for (i=1; i<=ncodemax[j]; i++) {
     free_matrix(agev,1,maxwav,1,imx);        for (k=0; k<= maxncov; k++) {
     free_ivector(wav,1,imx);          if (Ndum[k] != 0) {
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);            nbcode[Tvar[j]][ij]=k; 
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);            /* store the modality in an array. k is a modality. If we have model=V1+V1*sex then: nbcode[1][1]=0 ; nbcode[1][2]=1; nbcode[2][1]=0 ; nbcode[2][2]=1; */
                
     free_imatrix(s,1,maxwav+1,1,n);            ij++;
              }
              if (ij > ncodemax[j]) break; 
     free_ivector(num,1,n);        }  
     free_vector(agedc,1,n);      } 
     free_vector(weight,1,n);    }  
     /*free_matrix(covar,1,NCOVMAX,1,n);*/  
     fclose(ficparo);   for (k=0; k< maxncov; k++) Ndum[k]=0;
     fclose(ficres);  
     /*  }*/   for (i=1; i<=ncovmodel-2; i++) { 
         /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
    /*________fin mle=1_________*/     ij=Tvar[i];
         Ndum[ij]++;
    }
    
     /* No more information from the sample is required now */   ij=1;
   /* Reads comments: lines beginning with '#' */   for (i=1; i<= maxncov; i++) {
   while((c=getc(ficpar))=='#' && c!= EOF){     if((Ndum[i]!=0) && (i<=ncovcol)){
     ungetc(c,ficpar);       Tvaraff[ij]=i; /*For printing */
     fgets(line, MAXLINE, ficpar);       ij++;
     puts(line);     }
     fputs(line,ficparo);   }
   }   
   ungetc(c,ficpar);   cptcoveff=ij-1; /*Number of simple covariates*/
    }
   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);  /*********** Health Expectancies ****************/
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);  
 /*--------- index.htm --------*/  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[] )
   
   if((fichtm=fopen("index.htm","w"))==NULL)    {  {
     printf("Problem with index.htm \n");goto end;    /* Health expectancies */
   }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj;
     double age, agelim, hf;
  fprintf(fichtm,"<body><ul> Imach, Version 0.64a<hr> <li>Outputs files<br><br>\n    double ***p3mat,***varhe;
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n    double **dnewm,**doldm;
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>    double *xp;
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>    double **gp, **gm;
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>    double ***gradg, ***trgradg;
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>    int theta;
         - 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>    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>    xp=vector(1,npar);
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);    dnewm=matrix(1,nlstate*nlstate,1,npar);
     doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
  fprintf(fichtm," <li>Graphs</li>\n<p>");    
     fprintf(ficreseij,"# Local time at start: %s", strstart);
  m=cptcoveff;    fprintf(ficreseij,"# Health expectancies\n");
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    fprintf(ficreseij,"# Age");
     for(i=1; i<=nlstate;i++)
  j1=0;      for(j=1; j<=nlstate;j++)
  for(k1=1; k1<=m;k1++){        fprintf(ficreseij," %1d-%1d (SE)",i,j);
    for(i1=1; i1<=ncodemax[k1];i1++){    fprintf(ficreseij,"\n");
        j1++;  
        if (cptcovn > 0) {    if(estepm < stepm){
          fprintf(fichtm,"<hr>************ Results for covariates");      printf ("Problem %d lower than %d\n",estepm, stepm);
          for (cpt=1; cpt<=cptcoveff;cpt++)    }
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);    else  hstepm=estepm;   
          fprintf(fichtm," ************\n<hr>");    /* We compute the life expectancy from trapezoids spaced every estepm months
        }     * This is mainly to measure the difference between two models: for example
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>     * if stepm=24 months pijx are given only every 2 years and by summing them
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);         * we are calculating an estimate of the Life Expectancy assuming a linear 
        for(cpt=1; cpt<nlstate;cpt++){     * progression in between and thus overestimating or underestimating according
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>     * to the curvature of the survival function. If, for the same date, we 
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
        }     * to compare the new estimate of Life expectancy with the same linear 
     for(cpt=1; cpt<=nlstate;cpt++) {     * hypothesis. A more precise result, taking into account a more precise
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident     * curvature will be obtained if estepm is as small as stepm. */
 interval) in state (%d): v%s%d%d.gif <br>  
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      /* For example we decided to compute the life expectancy with the smallest unit */
      }    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
      for(cpt=1; cpt<=nlstate;cpt++) {       nhstepm is the number of hstepm from age to agelim 
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>       nstepm is the number of stepm from age to agelin. 
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);       Look at hpijx to understand the reason of that which relies in memory size
      }       and note for a fixed period like estepm months */
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 health expectancies in states (1) and (2): e%s%d.gif<br>       survival function given by stepm (the optimization length). Unfortunately it
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);       means that if the survival funtion is printed only each two years of age and if
 fprintf(fichtm,"\n</body>");       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.
  }    */
 fclose(fichtm);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
   /*--------------- Prevalence limit --------------*/    agelim=AGESUP;
      for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   strcpy(filerespl,"pl");      /* nhstepm age range expressed in number of stepm */
   strcat(filerespl,fileres);      nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   if((ficrespl=fopen(filerespl,"w"))==NULL) {      /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;      /* if (stepm >= YEARM) hstepm=1;*/
   }      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fprintf(ficrespl,"#Prevalence limit\n");      gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   fprintf(ficrespl,"#Age ");      gp=matrix(0,nhstepm,1,nlstate*nlstate);
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      gm=matrix(0,nhstepm,1,nlstate*nlstate);
   fprintf(ficrespl,"\n");  
        /* Computed by stepm unit matrices, product of hstepm matrices, stored
   prlim=matrix(1,nlstate,1,nlstate);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);  
   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 */      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
   k=0;      /* Computing  Variances of health expectancies */
   agebase=agemin;  
   agelim=agemax;       for(theta=1; theta <=npar; theta++){
   ftolpl=1.e-10;        for(i=1; i<=npar; i++){ 
   i1=cptcoveff;          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   if (cptcovn < 1){i1=1;}        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   for(cptcov=1;cptcov<=i1;cptcov++){    
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        cptj=0;
         k=k+1;        for(j=1; j<= nlstate; j++){
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/          for(i=1; i<=nlstate; i++){
         fprintf(ficrespl,"\n#******");            cptj=cptj+1;
         for(j=1;j<=cptcoveff;j++)            for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);              gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
         fprintf(ficrespl,"******\n");            }
                  }
         for (age=agebase; age<=agelim; age++){        }
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);       
           fprintf(ficrespl,"%.0f",age );       
           for(i=1; i<=nlstate;i++)        for(i=1; i<=npar; i++) 
           fprintf(ficrespl," %.5f", prlim[i][i]);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
           fprintf(ficrespl,"\n");        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         }        
       }        cptj=0;
     }        for(j=1; j<= nlstate; j++){
   fclose(ficrespl);          for(i=1;i<=nlstate;i++){
   /*------------- h Pij x at various ages ------------*/            cptj=cptj+1;
              for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  
   if((ficrespij=fopen(filerespij,"w"))==NULL) {              gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;            }
   }          }
   printf("Computing pij: result on file '%s' \n", filerespij);        }
          for(j=1; j<= nlstate*nlstate; j++)
   stepsize=(int) (stepm+YEARM-1)/YEARM;          for(h=0; h<=nhstepm-1; h++){
   if (stepm<=24) stepsize=2;            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   agelim=AGESUP;       } 
   hstepm=stepsize*YEARM; /* Every year of age */     
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */  /* End theta */
    
   k=0;       trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){       for(h=0; h<=nhstepm-1; h++)
       k=k+1;        for(j=1; j<=nlstate*nlstate;j++)
         fprintf(ficrespij,"\n#****** ");          for(theta=1; theta <=npar; theta++)
         for(j=1;j<=cptcoveff;j++)            trgradg[h][j][theta]=gradg[h][theta][j];
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       
         fprintf(ficrespij,"******\n");  
               for(i=1;i<=nlstate*nlstate;i++)
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */        for(j=1;j<=nlstate*nlstate;j++)
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          varhe[i][j][(int)age] =0.;
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       printf("%d|",(int)age);fflush(stdout);
           oldm=oldms;savm=savms;       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);         for(h=0;h<=nhstepm-1;h++){
           fprintf(ficrespij,"# Age");        for(k=0;k<=nhstepm-1;k++){
           for(i=1; i<=nlstate;i++)          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
             for(j=1; j<=nlstate+ndeath;j++)          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
               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] += doldm[i][j]*hf*hf;
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );        }
             for(i=1; i<=nlstate;i++)      }
               for(j=1; j<=nlstate+ndeath;j++)      /* Computing expectancies */
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);      for(i=1; i<=nlstate;i++)
             fprintf(ficrespij,"\n");        for(j=1; j<=nlstate;j++)
           }          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
           fprintf(ficrespij,"\n");            
         }  /* 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]);*/
     }  
   }          }
   
   fclose(ficrespij);      fprintf(ficreseij,"%3.0f",age );
       cptj=0;
   /*---------- Health expectancies and variances ------------*/      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
   strcpy(filerest,"t");          cptj++;
   strcat(filerest,fileres);          fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );
   if((ficrest=fopen(filerest,"w"))==NULL) {        }
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;      fprintf(ficreseij,"\n");
   }     
   printf("Computing Total LEs with variances: file '%s' \n", filerest);      free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
       free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   strcpy(filerese,"e");      free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   strcat(filerese,fileres);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if((ficreseij=fopen(filerese,"w"))==NULL) {    }
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    printf("\n");
   }    fprintf(ficlog,"\n");
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);  
     free_vector(xp,1,npar);
  strcpy(fileresv,"v");    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   strcat(fileresv,fileres);    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);  }
   }  
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);  /************ Variance ******************/
   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
   k=0;  {
   for(cptcov=1;cptcov<=i1;cptcov++){    /* Variance of health expectancies */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
       k=k+1;    /* double **newm;*/
       fprintf(ficrest,"\n#****** ");    double **dnewm,**doldm;
       for(j=1;j<=cptcoveff;j++)    double **dnewmp,**doldmp;
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    int i, j, nhstepm, hstepm, h, nstepm ;
       fprintf(ficrest,"******\n");    int k, cptcode;
     double *xp;
       fprintf(ficreseij,"\n#****** ");    double **gp, **gm;  /* for var eij */
       for(j=1;j<=cptcoveff;j++)    double ***gradg, ***trgradg; /*for var eij */
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    double **gradgp, **trgradgp; /* for var p point j */
       fprintf(ficreseij,"******\n");    double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
       fprintf(ficresvij,"\n#****** ");    double ***p3mat;
       for(j=1;j<=cptcoveff;j++)    double age,agelim, hf;
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    double ***mobaverage;
       fprintf(ficresvij,"******\n");    int theta;
     char digit[4];
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    char digitp[25];
       oldm=oldms;savm=savms;  
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);      char fileresprobmorprev[FILENAMELENGTH];
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  
       oldm=oldms;savm=savms;    if(popbased==1){
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      if(mobilav!=0)
              strcpy(digitp,"-populbased-mobilav-");
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");      else strcpy(digitp,"-populbased-nomobil-");
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    }
       fprintf(ficrest,"\n");    else 
              strcpy(digitp,"-stablbased-");
       hf=1;  
       if (stepm >= YEARM) hf=stepm/YEARM;    if (mobilav!=0) {
       epj=vector(1,nlstate+1);      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(age=bage; age <=fage ;age++){      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         fprintf(ficrest," %.0f",age);        printf(" Error in movingaverage mobilav=%d\n",mobilav);
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){      }
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    }
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];  
           }    strcpy(fileresprobmorprev,"prmorprev"); 
           epj[nlstate+1] +=epj[j];    sprintf(digit,"%-d",ij);
         }    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
         for(i=1, vepp=0.;i <=nlstate;i++)    strcat(fileresprobmorprev,digit); /* Tvar to be done */
           for(j=1;j <=nlstate;j++)    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
             vepp += vareij[i][j][(int)age];    strcat(fileresprobmorprev,fileres);
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
         for(j=1;j <=nlstate;j++){      printf("Problem with resultfile: %s\n", fileresprobmorprev);
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
         }    }
         fprintf(ficrest,"\n");    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
       }   
     }    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);
            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);
  fclose(ficreseij);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
  fclose(ficresvij);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   fclose(ficrest);      fprintf(ficresprobmorprev," p.%-d SE",j);
   fclose(ficpar);      for(i=1; i<=nlstate;i++)
   free_vector(epj,1,nlstate+1);        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   /*  scanf("%d ",i); */    }  
     fprintf(ficresprobmorprev,"\n");
   /*------- Variance limit prevalence------*/      fprintf(ficgp,"\n# Routine varevsij");
     /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
 strcpy(fileresvpl,"vpl");    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");
   strcat(fileresvpl,fileres);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  /*   } */
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     exit(0);   fprintf(ficresvij, "#Local time at start: %s", strstart);
   }    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");
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);    fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
  k=0;      for(j=1; j<=nlstate;j++)
  for(cptcov=1;cptcov<=i1;cptcov++){        fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficresvij,"\n");
      k=k+1;  
      fprintf(ficresvpl,"\n#****** ");    xp=vector(1,npar);
      for(j=1;j<=cptcoveff;j++)    dnewm=matrix(1,nlstate,1,npar);
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    doldm=matrix(1,nlstate,1,nlstate);
      fprintf(ficresvpl,"******\n");    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
          doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      varpl=matrix(1,nlstate,(int) bage, (int) fage);  
      oldm=oldms;savm=savms;    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    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*/
     
   fclose(ficresvpl);    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
   /*---------- End : free ----------------*/    }
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    else  hstepm=estepm;   
      /* For example we decided to compute the life expectancy with the smallest unit */
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);       nhstepm is the number of hstepm from age to agelim 
         nstepm is the number of stepm from age to agelin. 
         Look at hpijx to understand the reason of that which relies in memory size
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);       and note for a fixed period like k years */
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);       survival function given by stepm (the optimization length). Unfortunately it
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);       means that if the survival funtion is printed every two years of age and if
         you sum them up and add 1 year (area under the trapezoids) you won't get the same 
   free_matrix(matcov,1,npar,1,npar);       results. So we changed our mind and took the option of the best precision.
   free_vector(delti,1,npar);    */
      hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   printf("End of Imach\n");      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
        p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /* 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);*/      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
   /*printf("Total time was %d uSec.\n", total_usecs);*/      gp=matrix(0,nhstepm,1,nlstate);
   /*------ End -----------*/      gm=matrix(0,nhstepm,1,nlstate);
   
  end:  
 #ifdef windows      for(theta=1; theta <=npar; theta++){
  chdir(pathcd);        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
 #endif          xp[i] = x[i] + (i==theta ?delti[theta]:0);
  system("wgnuplot graph.plt");        }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
 #ifdef windows        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   while (z[0] != 'q') {  
     chdir(pathcd);        if (popbased==1) {
     printf("\nType e to edit output files, c to start again, and q for exiting: ");          if(mobilav ==0){
     scanf("%s",z);            for(i=1; i<=nlstate;i++)
     if (z[0] == 'c') system("./imach");              prlim[i][i]=probs[(int)age][i][ij];
     else if (z[0] == 'e') {          }else{ /* mobilav */ 
       chdir(path);            for(i=1; i<=nlstate;i++)
       system("index.htm");              prlim[i][i]=mobaverage[(int)age][i][ij];
     }          }
     else if (z[0] == 'q') exit(0);        }
   }    
 #endif        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.1.7  
changed lines
  Added in v.1.116


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