Diff for /imach/src/imach.c between versions 1.22 and 1.124

version 1.22, 2002/02/22 17:54:20 version 1.124, 2006/03/22 17:13:53
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolate Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.124  2006/03/22 17:13:53  lievre
      Parameters are printed with %lf instead of %f (more numbers after the comma).
   This program computes Healthy Life Expectancies from    The log-likelihood is printed in the log file
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a  
   first survey ("cross") where individuals from different ages are    Revision 1.123  2006/03/20 10:52:43  brouard
   interviewed on their health status or degree of disability (in the    * imach.c (Module): <title> changed, corresponds to .htm file
   case of a health survey which is our main interest) -2- at least a    name. <head> headers where missing.
   second wave of interviews ("longitudinal") which measure each change  
   (if any) in individual health status.  Health expectancies are    * imach.c (Module): Weights can have a decimal point as for
   computed from the time spent in each health state according to a    English (a comma might work with a correct LC_NUMERIC environment,
   model. More health states you consider, more time is necessary to reach the    otherwise the weight is truncated).
   Maximum Likelihood of the parameters involved in the model.  The    Modification of warning when the covariates values are not 0 or
   simplest model is the multinomial logistic model where pij is the    1.
   probabibility to be observed in state j at the second wave    Version 0.98g
   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    Revision 1.122  2006/03/20 09:45:41  brouard
   'age' is age and 'sex' is a covariate. If you want to have a more    (Module): Weights can have a decimal point as for
   complex model than "constant and age", you should modify the program    English (a comma might work with a correct LC_NUMERIC environment,
   where the markup *Covariates have to be included here again* invites    otherwise the weight is truncated).
   you to do it.  More covariates you add, slower the    Modification of warning when the covariates values are not 0 or
   convergence.    1.
     Version 0.98g
   The advantage of this computer programme, compared to a simple  
   multinomial logistic model, is clear when the delay between waves is not    Revision 1.121  2006/03/16 17:45:01  lievre
   identical for each individual. Also, if a individual missed an    * imach.c (Module): Comments concerning covariates added
   intermediate interview, the information is lost, but taken into  
   account using an interpolation or extrapolation.      * imach.c (Module): refinements in the computation of lli if
     status=-2 in order to have more reliable computation if stepm is
   hPijx is the probability to be observed in state i at age x+h    not 1 month. Version 0.98f
   conditional to the observed state i at age x. The delay 'h' can be  
   split into an exact number (nh*stepm) of unobserved intermediate    Revision 1.120  2006/03/16 15:10:38  lievre
   states. This elementary transition (by month or quarter trimester,    (Module): refinements in the computation of lli if
   semester or year) is model as a multinomial logistic.  The hPx    status=-2 in order to have more reliable computation if stepm is
   matrix is simply the matrix product of nh*stepm elementary matrices    not 1 month. Version 0.98f
   and the contribution of each individual to the likelihood is simply  
   hPijx.    Revision 1.119  2006/03/15 17:42:26  brouard
     (Module): Bug if status = -2, the loglikelihood was
   Also this programme outputs the covariance matrix of the parameters but also    computed as likelihood omitting the logarithm. Version O.98e
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.118  2006/03/14 18:20:07  brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    (Module): varevsij Comments added explaining the second
            Institut national d'études démographiques, Paris.    table of variances if popbased=1 .
   This software have been partly granted by Euro-REVES, a concerted action    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   from the European Union.    (Module): Function pstamp added
   It is copyrighted identically to a GNU software product, ie programme and    (Module): Version 0.98d
   software can be distributed freely for non commercial use. Latest version  
   can be accessed at http://euroreves.ined.fr/imach .    Revision 1.117  2006/03/14 17:16:22  brouard
   **********************************************************************/    (Module): varevsij Comments added explaining the second
      table of variances if popbased=1 .
 #include <math.h>    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
 #include <stdio.h>    (Module): Function pstamp added
 #include <stdlib.h>    (Module): Version 0.98d
 #include <unistd.h>  
     Revision 1.116  2006/03/06 10:29:27  brouard
 #define MAXLINE 256    (Module): Variance-covariance wrong links and
 #define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"    varian-covariance of ej. is needed (Saito).
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.115  2006/02/27 12:17:45  brouard
 #define windows    (Module): One freematrix added in mlikeli! 0.98c
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Revision 1.114  2006/02/26 12:57:58  brouard
     (Module): Some improvements in processing parameter
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    filename with strsep.
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     Revision 1.113  2006/02/24 14:20:24  brouard
 #define NINTERVMAX 8    (Module): Memory leaks checks with valgrind and:
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    datafile was not closed, some imatrix were not freed and on matrix
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    allocation too.
 #define NCOVMAX 8 /* Maximum number of covariates */  
 #define MAXN 20000    Revision 1.112  2006/01/30 09:55:26  brouard
 #define YEARM 12. /* Number of months per year */    (Module): Back to gnuplot.exe instead of wgnuplot.exe
 #define AGESUP 130  
 #define AGEBASE 40    Revision 1.111  2006/01/25 20:38:18  brouard
     (Module): Lots of cleaning and bugs added (Gompertz)
     (Module): Comments can be added in data file. Missing date values
 int erreur; /* Error number */    can be a simple dot '.'.
 int nvar;  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Revision 1.110  2006/01/25 00:51:50  brouard
 int npar=NPARMAX;    (Module): Lots of cleaning and bugs added (Gompertz)
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Revision 1.109  2006/01/24 19:37:15  brouard
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    (Module): Comments (lines starting with a #) are allowed in data.
 int popbased=0;  
     Revision 1.108  2006/01/19 18:05:42  lievre
 int *wav; /* Number of waves for this individuual 0 is possible */    Gnuplot problem appeared...
 int maxwav; /* Maxim number of waves */    To be fixed
 int jmin, jmax; /* min, max spacing between 2 waves */  
 int mle, weightopt;    Revision 1.107  2006/01/19 16:20:37  brouard
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    Test existence of gnuplot in imach path
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double jmean; /* Mean space between 2 waves */    Revision 1.106  2006/01/19 13:24:36  brouard
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Some cleaning and links added in html output
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    Revision 1.105  2006/01/05 20:23:19  lievre
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;    *** empty log message ***
 FILE *ficreseij;  
   char filerese[FILENAMELENGTH];    Revision 1.104  2005/09/30 16:11:43  lievre
  FILE  *ficresvij;    (Module): sump fixed, loop imx fixed, and simplifications.
   char fileresv[FILENAMELENGTH];    (Module): If the status is missing at the last wave but we know
  FILE  *ficresvpl;    that the person is alive, then we can code his/her status as -2
   char fileresvpl[FILENAMELENGTH];    (instead of missing=-1 in earlier versions) and his/her
     contributions to the likelihood is 1 - Prob of dying from last
 #define NR_END 1    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 #define FREE_ARG char*    the healthy state at last known wave). Version is 0.98
 #define FTOL 1.0e-10  
     Revision 1.103  2005/09/30 15:54:49  lievre
 #define NRANSI    (Module): sump fixed, loop imx fixed, and simplifications.
 #define ITMAX 200  
     Revision 1.102  2004/09/15 17:31:30  brouard
 #define TOL 2.0e-4    Add the possibility to read data file including tab characters.
   
 #define CGOLD 0.3819660    Revision 1.101  2004/09/15 10:38:38  brouard
 #define ZEPS 1.0e-10    Fix on curr_time
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     Revision 1.100  2004/07/12 18:29:06  brouard
 #define GOLD 1.618034    Add version for Mac OS X. Just define UNIX in Makefile
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.99  2004/06/05 08:57:40  brouard
     *** empty log message ***
 static double maxarg1,maxarg2;  
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Revision 1.98  2004/05/16 15:05:56  brouard
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    New version 0.97 . First attempt to estimate force of mortality
      directly from the data i.e. without the need of knowing the health
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    state at each age, but using a Gompertz model: log u =a + b*age .
 #define rint(a) floor(a+0.5)    This is the basic analysis of mortality and should be done before any
     other analysis, in order to test if the mortality estimated from the
 static double sqrarg;    cross-longitudinal survey is different from the mortality estimated
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    from other sources like vital statistic data.
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}  
     The same imach parameter file can be used but the option for mle should be -3.
 int imx;  
 int stepm;    Agnès, who wrote this part of the code, tried to keep most of the
 /* Stepm, step in month: minimum step interpolation*/    former routines in order to include the new code within the former code.
   
 int m,nb;    The output is very simple: only an estimate of the intercept and of
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    the slope with 95% confident intervals.
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;  
 double **pmmij, ***probs, ***mobaverage;    Current limitations:
 double dateintmean=0;    A) Even if you enter covariates, i.e. with the
     model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 double *weight;    B) There is no computation of Life Expectancy nor Life Table.
 int **s; /* Status */  
 double *agedc, **covar, idx;    Revision 1.97  2004/02/20 13:25:42  lievre
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Version 0.96d. Population forecasting command line is (temporarily)
     suppressed.
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */  
 double ftolhess; /* Tolerance for computing hessian */    Revision 1.96  2003/07/15 15:38:55  brouard
     * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 /**************** split *************************/    rewritten within the same printf. Workaround: many printfs.
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )  
 {    Revision 1.95  2003/07/08 07:54:34  brouard
    char *s;                             /* pointer */    * imach.c (Repository):
    int  l1, l2;                         /* length counters */    (Repository): Using imachwizard code to output a more meaningful covariance
     matrix (cov(a12,c31) instead of numbers.
    l1 = strlen( path );                 /* length of path */  
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    Revision 1.94  2003/06/27 13:00:02  brouard
 #ifdef windows    Just cleaning
    s = strrchr( path, '\\' );           /* find last / */  
 #else    Revision 1.93  2003/06/25 16:33:55  brouard
    s = strrchr( path, '/' );            /* find last / */    (Module): On windows (cygwin) function asctime_r doesn't
 #endif    exist so I changed back to asctime which exists.
    if ( s == NULL ) {                   /* no directory, so use current */    (Module): Version 0.96b
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );    Revision 1.92  2003/06/25 16:30:45  brouard
     (Module): On windows (cygwin) function asctime_r doesn't
       if ( getwd( dirc ) == NULL ) {    exist so I changed back to asctime which exists.
 #else  
       extern char       *getcwd( );    Revision 1.91  2003/06/25 15:30:29  brouard
     * imach.c (Repository): Duplicated warning errors corrected.
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    (Repository): Elapsed time after each iteration is now output. It
 #endif    helps to forecast when convergence will be reached. Elapsed time
          return( GLOCK_ERROR_GETCWD );    is stamped in powell.  We created a new html file for the graphs
       }    concerning matrix of covariance. It has extension -cov.htm.
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */    Revision 1.90  2003/06/24 12:34:15  brouard
       s++;                              /* after this, the filename */    (Module): Some bugs corrected for windows. Also, when
       l2 = strlen( s );                 /* length of filename */    mle=-1 a template is output in file "or"mypar.txt with the design
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    of the covariance matrix to be input.
       strcpy( name, s );                /* save file name */  
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    Revision 1.89  2003/06/24 12:30:52  brouard
       dirc[l1-l2] = 0;                  /* add zero */    (Module): Some bugs corrected for windows. Also, when
    }    mle=-1 a template is output in file "or"mypar.txt with the design
    l1 = strlen( dirc );                 /* length of directory */    of the covariance matrix to be input.
 #ifdef windows  
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    Revision 1.88  2003/06/23 17:54:56  brouard
 #else    * 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.
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }  
 #endif    Revision 1.87  2003/06/18 12:26:01  brouard
    s = strrchr( name, '.' );            /* find last / */    Version 0.96
    s++;  
    strcpy(ext,s);                       /* save extension */    Revision 1.86  2003/06/17 20:04:08  brouard
    l1= strlen( name);    (Module): Change position of html and gnuplot routines and added
    l2= strlen( s)+1;    routine fileappend.
    strncpy( finame, name, l1-l2);  
    finame[l1-l2]= 0;    Revision 1.85  2003/06/17 13:12:43  brouard
    return( 0 );                         /* we're done */    * imach.c (Repository): Check when date of death was earlier that
 }    current date of interview. It may happen when the death was just
     prior to the death. In this case, dh was negative and likelihood
     was wrong (infinity). We still send an "Error" but patch by
 /******************************************/    assuming that the date of death was just one stepm after the
     interview.
 void replace(char *s, char*t)    (Repository): Because some people have very long ID (first column)
 {    we changed int to long in num[] and we added a new lvector for
   int i;    memory allocation. But we also truncated to 8 characters (left
   int lg=20;    truncation)
   i=0;    (Repository): No more line truncation errors.
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Revision 1.84  2003/06/13 21:44:43  brouard
     (s[i] = t[i]);    * imach.c (Repository): Replace "freqsummary" at a correct
     if (t[i]== '\\') s[i]='/';    place. It differs from routine "prevalence" which may be called
   }    many times. Probs is memory consuming and must be used with
 }    parcimony.
     Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 int nbocc(char *s, char occ)  
 {    Revision 1.83  2003/06/10 13:39:11  lievre
   int i,j=0;    *** empty log message ***
   int lg=20;  
   i=0;    Revision 1.82  2003/06/05 15:57:20  brouard
   lg=strlen(s);    Add log in  imach.c and  fullversion number is now printed.
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;  */
   }  /*
   return j;     Interpolated Markov Chain
 }  
     Short summary of the programme:
 void cutv(char *u,char *v, char*t, char occ)    
 {    This program computes Healthy Life Expectancies from
   int i,lg,j,p=0;    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   i=0;    first survey ("cross") where individuals from different ages are
   for(j=0; j<=strlen(t)-1; j++) {    interviewed on their health status or degree of disability (in the
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    case of a health survey which is our main interest) -2- at least a
   }    second wave of interviews ("longitudinal") which measure each change
     (if any) in individual health status.  Health expectancies are
   lg=strlen(t);    computed from the time spent in each health state according to a
   for(j=0; j<p; j++) {    model. More health states you consider, more time is necessary to reach the
     (u[j] = t[j]);    Maximum Likelihood of the parameters involved in the model.  The
   }    simplest model is the multinomial logistic model where pij is the
      u[p]='\0';    probability to be observed in state j at the second wave
     conditional to be observed in state i at the first wave. Therefore
    for(j=0; j<= lg; j++) {    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
     if (j>=(p+1))(v[j-p-1] = t[j]);    'age' is age and 'sex' is a covariate. If you want to have a more
   }    complex model than "constant and age", you should modify the program
 }    where the markup *Covariates have to be included here again* invites
     you to do it.  More covariates you add, slower the
 /********************** nrerror ********************/    convergence.
   
 void nrerror(char error_text[])    The advantage of this computer programme, compared to a simple
 {    multinomial logistic model, is clear when the delay between waves is not
   fprintf(stderr,"ERREUR ...\n");    identical for each individual. Also, if a individual missed an
   fprintf(stderr,"%s\n",error_text);    intermediate interview, the information is lost, but taken into
   exit(1);    account using an interpolation or extrapolation.  
 }  
 /*********************** vector *******************/    hPijx is the probability to be observed in state i at age x+h
 double *vector(int nl, int nh)    conditional to the observed state i at age x. The delay 'h' can be
 {    split into an exact number (nh*stepm) of unobserved intermediate
   double *v;    states. This elementary transition (by month, quarter,
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    semester or year) is modelled as a multinomial logistic.  The hPx
   if (!v) nrerror("allocation failure in vector");    matrix is simply the matrix product of nh*stepm elementary matrices
   return v-nl+NR_END;    and the contribution of each individual to the likelihood is simply
 }    hPijx.
   
 /************************ free vector ******************/    Also this programme outputs the covariance matrix of the parameters but also
 void free_vector(double*v, int nl, int nh)    of the life expectancies. It also computes the period (stable) prevalence. 
 {    
   free((FREE_ARG)(v+nl-NR_END));    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 }             Institut national d'études démographiques, Paris.
     This software have been partly granted by Euro-REVES, a concerted action
 /************************ivector *******************************/    from the European Union.
 int *ivector(long nl,long nh)    It is copyrighted identically to a GNU software product, ie programme and
 {    software can be distributed freely for non commercial use. Latest version
   int *v;    can be accessed at http://euroreves.ined.fr/imach .
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  
   if (!v) nrerror("allocation failure in ivector");    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   return v-nl+NR_END;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 }    
     **********************************************************************/
 /******************free ivector **************************/  /*
 void free_ivector(int *v, long nl, long nh)    main
 {    read parameterfile
   free((FREE_ARG)(v+nl-NR_END));    read datafile
 }    concatwav
     freqsummary
 /******************* imatrix *******************************/    if (mle >= 1)
 int **imatrix(long nrl, long nrh, long ncl, long nch)      mlikeli
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    print results files
 {    if mle==1 
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;       computes hessian
   int **m;    read end of parameter file: agemin, agemax, bage, fage, estepm
          begin-prev-date,...
   /* allocate pointers to rows */    open gnuplot file
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    open html file
   if (!m) nrerror("allocation failure 1 in matrix()");    period (stable) prevalence
   m += NR_END;     for age prevalim()
   m -= nrl;    h Pij x
      variance of p varprob
      forecasting if prevfcast==1 prevforecast call prevalence()
   /* allocate rows and set pointers to them */    health expectancies
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    Variance-covariance of DFLE
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    prevalence()
   m[nrl] += NR_END;     movingaverage()
   m[nrl] -= ncl;    varevsij() 
      if popbased==1 varevsij(,popbased)
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    total life expectancies
      Variance of period (stable) prevalence
   /* return pointer to array of pointers to rows */   end
   return m;  */
 }  
   
 /****************** free_imatrix *************************/  
 void free_imatrix(m,nrl,nrh,ncl,nch)   
       int **m;  #include <math.h>
       long nch,ncl,nrh,nrl;  #include <stdio.h>
      /* free an int matrix allocated by imatrix() */  #include <stdlib.h>
 {  #include <string.h>
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  #include <unistd.h>
   free((FREE_ARG) (m+nrl-NR_END));  
 }  #include <limits.h>
   #include <sys/types.h>
 /******************* matrix *******************************/  #include <sys/stat.h>
 double **matrix(long nrl, long nrh, long ncl, long nch)  #include <errno.h>
 {  extern int errno;
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;  /* #include <sys/time.h> */
   #include <time.h>
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #include "timeval.h"
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  /* #include <libintl.h> */
   m -= nrl;  /* #define _(String) gettext (String) */
   
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #define MAXLINE 256
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  
   m[nrl] += NR_END;  #define GNUPLOTPROGRAM "gnuplot"
   m[nrl] -= ncl;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   #define FILENAMELENGTH 132
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 }  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
 /*************************free matrix ************************/  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 {  
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define NINTERVMAX 8
   free((FREE_ARG)(m+nrl-NR_END));  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
 }  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   #define NCOVMAX 8 /* Maximum number of covariates */
 /******************* ma3x *******************************/  #define MAXN 20000
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  #define YEARM 12. /* Number of months per year */
 {  #define AGESUP 130
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  #define AGEBASE 40
   double ***m;  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   #ifdef UNIX
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #define DIRSEPARATOR '/'
   if (!m) nrerror("allocation failure 1 in matrix()");  #define CHARSEPARATOR "/"
   m += NR_END;  #define ODIRSEPARATOR '\\'
   m -= nrl;  #else
   #define DIRSEPARATOR '\\'
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #define CHARSEPARATOR "\\"
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define ODIRSEPARATOR '/'
   m[nrl] += NR_END;  #endif
   m[nrl] -= ncl;  
   /* $Id$ */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  /* $State$ */
   
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  char fullversion[]="$Revision$ $Date$"; 
   m[nrl][ncl] += NR_END;  char strstart[80];
   m[nrl][ncl] -= nll;  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   for (j=ncl+1; j<=nch; j++)  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
     m[nrl][j]=m[nrl][j-1]+nlay;  int nvar;
    int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   for (i=nrl+1; i<=nrh; i++) {  int npar=NPARMAX;
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  int nlstate=2; /* Number of live states */
     for (j=ncl+1; j<=nch; j++)  int ndeath=1; /* Number of dead states */
       m[i][j]=m[i][j-1]+nlay;  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   }  int popbased=0;
   return m;  
 }  int *wav; /* Number of waves for this individuual 0 is possible */
   int maxwav; /* Maxim number of waves */
 /*************************free ma3x ************************/  int jmin, jmax; /* min, max spacing between 2 waves */
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
 {  int gipmx, gsw; /* Global variables on the number of contributions 
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));                     to the likelihood and the sum of weights (done by funcone)*/
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  int mle, weightopt;
   free((FREE_ARG)(m+nrl-NR_END));  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 */
   int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 /***************** f1dim *************************/             * wave mi and wave mi+1 is not an exact multiple of stepm. */
 extern int ncom;  double jmean; /* Mean space between 2 waves */
 extern double *pcom,*xicom;  double **oldm, **newm, **savm; /* Working pointers to matrices */
 extern double (*nrfunc)(double []);  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
    FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 double f1dim(double x)  FILE *ficlog, *ficrespow;
 {  int globpr; /* Global variable for printing or not */
   int j;  double fretone; /* Only one call to likelihood */
   double f;  long ipmx; /* Number of contributions */
   double *xt;  double sw; /* Sum of weights */
    char filerespow[FILENAMELENGTH];
   xt=vector(1,ncom);  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  FILE *ficresilk;
   f=(*nrfunc)(xt);  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   free_vector(xt,1,ncom);  FILE *ficresprobmorprev;
   return f;  FILE *fichtm, *fichtmcov; /* Html File */
 }  FILE *ficreseij;
   char filerese[FILENAMELENGTH];
 /*****************brent *************************/  FILE *ficresstdeij;
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  char fileresstde[FILENAMELENGTH];
 {  FILE *ficrescveij;
   int iter;  char filerescve[FILENAMELENGTH];
   double a,b,d,etemp;  FILE  *ficresvij;
   double fu,fv,fw,fx;  char fileresv[FILENAMELENGTH];
   double ftemp;  FILE  *ficresvpl;
   double p,q,r,tol1,tol2,u,v,w,x,xm;  char fileresvpl[FILENAMELENGTH];
   double e=0.0;  char title[MAXLINE];
    char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   a=(ax < cx ? ax : cx);  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   b=(ax > cx ? ax : cx);  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   x=w=v=bx;  char command[FILENAMELENGTH];
   fw=fv=fx=(*f)(x);  int  outcmd=0;
   for (iter=1;iter<=ITMAX;iter++) {  
     xm=0.5*(a+b);  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  char filelog[FILENAMELENGTH]; /* Log file */
     printf(".");fflush(stdout);  char filerest[FILENAMELENGTH];
 #ifdef DEBUG  char fileregp[FILENAMELENGTH];
     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);  char popfile[FILENAMELENGTH];
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  
 #endif  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  
       *xmin=x;  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
       return fx;  struct timezone tzp;
     }  extern int gettimeofday();
     ftemp=fu;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
     if (fabs(e) > tol1) {  long time_value;
       r=(x-w)*(fx-fv);  extern long time();
       q=(x-v)*(fx-fw);  char strcurr[80], strfor[80];
       p=(x-v)*q-(x-w)*r;  
       q=2.0*(q-r);  char *endptr;
       if (q > 0.0) p = -p;  long lval;
       q=fabs(q);  double dval;
       etemp=e;  
       e=d;  #define NR_END 1
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  #define FREE_ARG char*
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  #define FTOL 1.0e-10
       else {  
         d=p/q;  #define NRANSI 
         u=x+d;  #define ITMAX 200 
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);  #define TOL 2.0e-4 
       }  
     } else {  #define CGOLD 0.3819660 
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  #define ZEPS 1.0e-10 
     }  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  
     fu=(*f)(u);  #define GOLD 1.618034 
     if (fu <= fx) {  #define GLIMIT 100.0 
       if (u >= x) a=x; else b=x;  #define TINY 1.0e-20 
       SHFT(v,w,x,u)  
         SHFT(fv,fw,fx,fu)  static double maxarg1,maxarg2;
         } else {  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
           if (u < x) a=u; else b=u;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
           if (fu <= fw || w == x) {    
             v=w;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
             w=u;  #define rint(a) floor(a+0.5)
             fv=fw;  
             fw=fu;  static double sqrarg;
           } else if (fu <= fv || v == x || v == w) {  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
             v=u;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
             fv=fu;  int agegomp= AGEGOMP;
           }  
         }  int imx; 
   }  int stepm=1;
   nrerror("Too many iterations in brent");  /* Stepm, step in month: minimum step interpolation*/
   *xmin=x;  
   return fx;  int estepm;
 }  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
   
 /****************** mnbrak ***********************/  int m,nb;
   long *num;
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
             double (*func)(double))  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
 {  double **pmmij, ***probs;
   double ulim,u,r,q, dum;  double *ageexmed,*agecens;
   double fu;  double dateintmean=0;
    
   *fa=(*func)(*ax);  double *weight;
   *fb=(*func)(*bx);  int **s; /* Status */
   if (*fb > *fa) {  double *agedc, **covar, idx;
     SHFT(dum,*ax,*bx,dum)  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
       SHFT(dum,*fb,*fa,dum)  double *lsurv, *lpop, *tpop;
       }  
   *cx=(*bx)+GOLD*(*bx-*ax);  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
   *fc=(*func)(*cx);  double ftolhess; /* Tolerance for computing hessian */
   while (*fb > *fc) {  
     r=(*bx-*ax)*(*fb-*fc);  /**************** split *************************/
     q=(*bx-*cx)*(*fb-*fa);  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  {
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
     ulim=(*bx)+GLIMIT*(*cx-*bx);       the name of the file (name), its extension only (ext) and its first part of the name (finame)
     if ((*bx-u)*(u-*cx) > 0.0) {    */ 
       fu=(*func)(u);    char  *ss;                            /* pointer */
     } else if ((*cx-u)*(u-ulim) > 0.0) {    int   l1, l2;                         /* length counters */
       fu=(*func)(u);  
       if (fu < *fc) {    l1 = strlen(path );                   /* length of path */
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
           SHFT(*fb,*fc,fu,(*func)(u))    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
           }    if ( ss == NULL ) {                   /* no directory, so determine current directory */
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {      strcpy( name, path );               /* we got the fullname name because no directory */
       u=ulim;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
       fu=(*func)(u);        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     } else {      /* get current working directory */
       u=(*cx)+GOLD*(*cx-*bx);      /*    extern  char* getcwd ( char *buf , int len);*/
       fu=(*func)(u);      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
     }        return( GLOCK_ERROR_GETCWD );
     SHFT(*ax,*bx,*cx,u)      }
       SHFT(*fa,*fb,*fc,fu)      /* got dirc from getcwd*/
       }      printf(" DIRC = %s \n",dirc);
 }    } else {                              /* strip direcotry from path */
       ss++;                               /* after this, the filename */
 /*************** linmin ************************/      l2 = strlen( ss );                  /* length of filename */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 int ncom;      strcpy( name, ss );         /* save file name */
 double *pcom,*xicom;      strncpy( dirc, path, l1 - l2 );     /* now the directory */
 double (*nrfunc)(double []);      dirc[l1-l2] = 0;                    /* add zero */
        printf(" DIRC2 = %s \n",dirc);
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    }
 {    /* We add a separator at the end of dirc if not exists */
   double brent(double ax, double bx, double cx,    l1 = strlen( dirc );                  /* length of directory */
                double (*f)(double), double tol, double *xmin);    if( dirc[l1-1] != DIRSEPARATOR ){
   double f1dim(double x);      dirc[l1] =  DIRSEPARATOR;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,      dirc[l1+1] = 0; 
               double *fc, double (*func)(double));      printf(" DIRC3 = %s \n",dirc);
   int j;    }
   double xx,xmin,bx,ax;    ss = strrchr( name, '.' );            /* find last / */
   double fx,fb,fa;    if (ss >0){
        ss++;
   ncom=n;      strcpy(ext,ss);                     /* save extension */
   pcom=vector(1,n);      l1= strlen( name);
   xicom=vector(1,n);      l2= strlen(ss)+1;
   nrfunc=func;      strncpy( finame, name, l1-l2);
   for (j=1;j<=n;j++) {      finame[l1-l2]= 0;
     pcom[j]=p[j];    }
     xicom[j]=xi[j];  
   }    return( 0 );                          /* we're done */
   ax=0.0;  }
   xx=1.0;  
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);  
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);  /******************************************/
 #ifdef DEBUG  
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  void replace_back_to_slash(char *s, char*t)
 #endif  {
   for (j=1;j<=n;j++) {    int i;
     xi[j] *= xmin;    int lg=0;
     p[j] += xi[j];    i=0;
   }    lg=strlen(t);
   free_vector(xicom,1,n);    for(i=0; i<= lg; i++) {
   free_vector(pcom,1,n);      (s[i] = t[i]);
 }      if (t[i]== '\\') s[i]='/';
     }
 /*************** powell ************************/  }
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  
             double (*func)(double []))  int nbocc(char *s, char occ)
 {  {
   void linmin(double p[], double xi[], int n, double *fret,    int i,j=0;
               double (*func)(double []));    int lg=20;
   int i,ibig,j;    i=0;
   double del,t,*pt,*ptt,*xit;    lg=strlen(s);
   double fp,fptt;    for(i=0; i<= lg; i++) {
   double *xits;    if  (s[i] == occ ) j++;
   pt=vector(1,n);    }
   ptt=vector(1,n);    return j;
   xit=vector(1,n);  }
   xits=vector(1,n);  
   *fret=(*func)(p);  void cutv(char *u,char *v, char*t, char occ)
   for (j=1;j<=n;j++) pt[j]=p[j];  {
   for (*iter=1;;++(*iter)) {    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
     fp=(*fret);       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
     ibig=0;       gives u="abcedf" and v="ghi2j" */
     del=0.0;    int i,lg,j,p=0;
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    i=0;
     for (i=1;i<=n;i++)    for(j=0; j<=strlen(t)-1; j++) {
       printf(" %d %.12f",i, p[i]);      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
     printf("\n");    }
     for (i=1;i<=n;i++) {  
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    lg=strlen(t);
       fptt=(*fret);    for(j=0; j<p; j++) {
 #ifdef DEBUG      (u[j] = t[j]);
       printf("fret=%lf \n",*fret);    }
 #endif       u[p]='\0';
       printf("%d",i);fflush(stdout);  
       linmin(p,xit,n,fret,func);     for(j=0; j<= lg; j++) {
       if (fabs(fptt-(*fret)) > del) {      if (j>=(p+1))(v[j-p-1] = t[j]);
         del=fabs(fptt-(*fret));    }
         ibig=i;  }
       }  
 #ifdef DEBUG  /********************** nrerror ********************/
       printf("%d %.12e",i,(*fret));  
       for (j=1;j<=n;j++) {  void nrerror(char error_text[])
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  {
         printf(" x(%d)=%.12e",j,xit[j]);    fprintf(stderr,"ERREUR ...\n");
       }    fprintf(stderr,"%s\n",error_text);
       for(j=1;j<=n;j++)    exit(EXIT_FAILURE);
         printf(" p=%.12e",p[j]);  }
       printf("\n");  /*********************** vector *******************/
 #endif  double *vector(int nl, int nh)
     }  {
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    double *v;
 #ifdef DEBUG    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
       int k[2],l;    if (!v) nrerror("allocation failure in vector");
       k[0]=1;    return v-nl+NR_END;
       k[1]=-1;  }
       printf("Max: %.12e",(*func)(p));  
       for (j=1;j<=n;j++)  /************************ free vector ******************/
         printf(" %.12e",p[j]);  void free_vector(double*v, int nl, int nh)
       printf("\n");  {
       for(l=0;l<=1;l++) {    free((FREE_ARG)(v+nl-NR_END));
         for (j=1;j<=n;j++) {  }
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  /************************ivector *******************************/
         }  int *ivector(long nl,long nh)
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  {
       }    int *v;
 #endif    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     if (!v) nrerror("allocation failure in ivector");
     return v-nl+NR_END;
       free_vector(xit,1,n);  }
       free_vector(xits,1,n);  
       free_vector(ptt,1,n);  /******************free ivector **************************/
       free_vector(pt,1,n);  void free_ivector(int *v, long nl, long nh)
       return;  {
     }    free((FREE_ARG)(v+nl-NR_END));
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  }
     for (j=1;j<=n;j++) {  
       ptt[j]=2.0*p[j]-pt[j];  /************************lvector *******************************/
       xit[j]=p[j]-pt[j];  long *lvector(long nl,long nh)
       pt[j]=p[j];  {
     }    long *v;
     fptt=(*func)(ptt);    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
     if (fptt < fp) {    if (!v) nrerror("allocation failure in ivector");
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    return v-nl+NR_END;
       if (t < 0.0) {  }
         linmin(p,xit,n,fret,func);  
         for (j=1;j<=n;j++) {  /******************free lvector **************************/
           xi[j][ibig]=xi[j][n];  void free_lvector(long *v, long nl, long nh)
           xi[j][n]=xit[j];  {
         }    free((FREE_ARG)(v+nl-NR_END));
 #ifdef DEBUG  }
         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++)  /******************* imatrix *******************************/
           printf(" %.12e",xit[j]);  int **imatrix(long nrl, long nrh, long ncl, long nch) 
         printf("\n");       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 #endif  { 
       }    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     }    int **m; 
   }    
 }    /* allocate pointers to rows */ 
     m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
 /**** Prevalence limit ****************/    if (!m) nrerror("allocation failure 1 in matrix()"); 
     m += NR_END; 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    m -= nrl; 
 {    
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit    
      matrix by transitions matrix until convergence is reached */    /* allocate rows and set pointers to them */ 
     m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
   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 pointer to array of pointers to rows */ 
   for (ii=1;ii<=nlstate+ndeath;ii++)    return m; 
     for (j=1;j<=nlstate+ndeath;j++){  } 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);  
     }  /****************** free_imatrix *************************/
   void free_imatrix(m,nrl,nrh,ncl,nch)
    cov[1]=1.;        int **m;
          long nch,ncl,nrh,nrl; 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */       /* free an int matrix allocated by imatrix() */ 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  { 
     newm=savm;    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     /* Covariates have to be included here again */    free((FREE_ARG) (m+nrl-NR_END)); 
      cov[2]=agefin;  } 
    
       for (k=1; k<=cptcovn;k++) {  /******************* matrix *******************************/
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  double **matrix(long nrl, long nrh, long ncl, long nch)
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  {
       }    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
       for (k=1; k<=cptcovage;k++)    double **m;
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];  
       for (k=1; k<=cptcovprod;k++)    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    m -= nrl;
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  
     m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
     savm=oldm;    m[nrl] -= ncl;
     oldm=newm;  
     maxmax=0.;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     for(j=1;j<=nlstate;j++){    return m;
       min=1.;    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       max=0.;     */
       for(i=1; i<=nlstate; i++) {  }
         sumnew=0;  
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  /*************************free matrix ************************/
         prlim[i][j]= newm[i][j]/(1-sumnew);  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
         max=FMAX(max,prlim[i][j]);  {
         min=FMIN(min,prlim[i][j]);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       }    free((FREE_ARG)(m+nrl-NR_END));
       maxmin=max-min;  }
       maxmax=FMAX(maxmax,maxmin);  
     }  /******************* ma3x *******************************/
     if(maxmax < ftolpl){  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       return prlim;  {
     }    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
   }    double ***m;
 }  
     m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
 /*************** transition probabilities ***************/    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    m -= nrl;
 {  
   double s1, s2;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
   /*double t34;*/    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
   int i,j,j1, nc, ii, jj;    m[nrl] += NR_END;
     m[nrl] -= ncl;
     for(i=1; i<= nlstate; i++){  
     for(j=1; j<i;j++){    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  
         /*s2 += param[i][j][nc]*cov[nc];*/    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    m[nrl][ncl] += NR_END;
       }    m[nrl][ncl] -= nll;
       ps[i][j]=s2;    for (j=ncl+1; j<=nch; j++) 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/      m[nrl][j]=m[nrl][j-1]+nlay;
     }    
     for(j=i+1; j<=nlstate+ndeath;j++){    for (i=nrl+1; i<=nrh; i++) {
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];      for (j=ncl+1; j<=nch; j++) 
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/        m[i][j]=m[i][j-1]+nlay;
       }    }
       ps[i][j]=s2;    return m; 
     }    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
   }             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
     /*ps[3][2]=1;*/    */
   }
   for(i=1; i<= nlstate; i++){  
      s1=0;  /*************************free ma3x ************************/
     for(j=1; j<i; j++)  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       s1+=exp(ps[i][j]);  {
     for(j=i+1; j<=nlstate+ndeath; j++)    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       s1+=exp(ps[i][j]);    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     ps[i][i]=1./(s1+1.);    free((FREE_ARG)(m+nrl-NR_END));
     for(j=1; j<i; j++)  }
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     for(j=i+1; j<=nlstate+ndeath; j++)  /*************** function subdirf ***********/
       ps[i][j]= exp(ps[i][j])*ps[i][i];  char *subdirf(char fileres[])
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  {
   } /* end i */    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    strcat(tmpout,"/"); /* Add to the right */
     for(jj=1; jj<= nlstate+ndeath; jj++){    strcat(tmpout,fileres);
       ps[ii][jj]=0;    return tmpout;
       ps[ii][ii]=1;  }
     }  
   }  /*************** function subdirf2 ***********/
   char *subdirf2(char fileres[], char *preop)
   {
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    
     for(jj=1; jj<= nlstate+ndeath; jj++){    /* Caution optionfilefiname is hidden */
      printf("%lf ",ps[ii][jj]);    strcpy(tmpout,optionfilefiname);
    }    strcat(tmpout,"/");
     printf("\n ");    strcat(tmpout,preop);
     }    strcat(tmpout,fileres);
     printf("\n ");printf("%lf ",cov[2]);*/    return tmpout;
 /*  }
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  
   goto end;*/  /*************** function subdirf3 ***********/
     return ps;  char *subdirf3(char fileres[], char *preop, char *preop2)
 }  {
     
 /**************** Product of 2 matrices ******************/    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    strcat(tmpout,"/");
 {    strcat(tmpout,preop);
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    strcat(tmpout,preop2);
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    strcat(tmpout,fileres);
   /* in, b, out are matrice of pointers which should have been initialized    return tmpout;
      before: only the contents of out is modified. The function returns  }
      a pointer to pointers identical to out */  
   long i, j, k;  /***************** f1dim *************************/
   for(i=nrl; i<= nrh; i++)  extern int ncom; 
     for(k=ncolol; k<=ncoloh; k++)  extern double *pcom,*xicom;
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  extern double (*nrfunc)(double []); 
         out[i][k] +=in[i][j]*b[j][k];   
   double f1dim(double x) 
   return out;  { 
 }    int j; 
     double f;
     double *xt; 
 /************* Higher Matrix Product ***************/   
     xt=vector(1,ncom); 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
 {    f=(*nrfunc)(xt); 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month    free_vector(xt,1,ncom); 
      duration (i.e. until    return f; 
      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  
      (typically every 2 years instead of every month which is too big).  /*****************brent *************************/
      Model is determined by parameters x and covariates have to be  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
      included manually here.  { 
     int iter; 
      */    double a,b,d,etemp;
     double fu,fv,fw,fx;
   int i, j, d, h, k;    double ftemp;
   double **out, cov[NCOVMAX];    double p,q,r,tol1,tol2,u,v,w,x,xm; 
   double **newm;    double e=0.0; 
    
   /* Hstepm could be zero and should return the unit matrix */    a=(ax < cx ? ax : cx); 
   for (i=1;i<=nlstate+ndeath;i++)    b=(ax > cx ? ax : cx); 
     for (j=1;j<=nlstate+ndeath;j++){    x=w=v=bx; 
       oldm[i][j]=(i==j ? 1.0 : 0.0);    fw=fv=fx=(*f)(x); 
       po[i][j][0]=(i==j ? 1.0 : 0.0);    for (iter=1;iter<=ITMAX;iter++) { 
     }      xm=0.5*(a+b); 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
   for(h=1; h <=nhstepm; h++){      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
     for(d=1; d <=hstepm; d++){      printf(".");fflush(stdout);
       newm=savm;      fprintf(ficlog,".");fflush(ficlog);
       /* Covariates have to be included here again */  #ifdef DEBUG
       cov[1]=1.;      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);
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;      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);
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       for (k=1; k<=cptcovage;k++)  #endif
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       for (k=1; k<=cptcovprod;k++)        *xmin=x; 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];        return fx; 
       } 
       ftemp=fu;
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      if (fabs(e) > tol1) { 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        r=(x-w)*(fx-fv); 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,        q=(x-v)*(fx-fw); 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        p=(x-v)*q-(x-w)*r; 
       savm=oldm;        q=2.0*(q-r); 
       oldm=newm;        if (q > 0.0) p = -p; 
     }        q=fabs(q); 
     for(i=1; i<=nlstate+ndeath; i++)        etemp=e; 
       for(j=1;j<=nlstate+ndeath;j++) {        e=d; 
         po[i][j][h]=newm[i][j];        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
          */        else { 
       }          d=p/q; 
   } /* end h */          u=x+d; 
   return po;          if (u-a < tol2 || b-u < tol2) 
 }            d=SIGN(tol1,xm-x); 
         } 
       } else { 
 /*************** log-likelihood *************/        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
 double func( double *x)      } 
 {      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   int i, ii, j, k, mi, d, kk;      fu=(*f)(u); 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      if (fu <= fx) { 
   double **out;        if (u >= x) a=x; else b=x; 
   double sw; /* Sum of weights */        SHFT(v,w,x,u) 
   double lli; /* Individual log likelihood */          SHFT(fv,fw,fx,fu) 
   long ipmx;          } else { 
   /*extern weight */            if (u < x) a=u; else b=u; 
   /* We are differentiating ll according to initial status */            if (fu <= fw || w == x) { 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/              v=w; 
   /*for(i=1;i<imx;i++)              w=u; 
     printf(" %d\n",s[4][i]);              fv=fw; 
   */              fw=fu; 
   cov[1]=1.;            } else if (fu <= fv || v == x || v == w) { 
               v=u; 
   for(k=1; k<=nlstate; k++) ll[k]=0.;              fv=fu; 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){            } 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];          } 
     for(mi=1; mi<= wav[i]-1; mi++){    } 
       for (ii=1;ii<=nlstate+ndeath;ii++)    nrerror("Too many iterations in brent"); 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);    *xmin=x; 
       for(d=0; d<dh[mi][i]; d++){    return fx; 
         newm=savm;  } 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  
         for (kk=1; kk<=cptcovage;kk++) {  /****************** mnbrak ***********************/
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  
         }  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
                      double (*func)(double)) 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  { 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));    double ulim,u,r,q, dum;
         savm=oldm;    double fu; 
         oldm=newm;   
            *fa=(*func)(*ax); 
            *fb=(*func)(*bx); 
       } /* end mult */    if (*fb > *fa) { 
            SHFT(dum,*ax,*bx,dum) 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        SHFT(dum,*fb,*fa,dum) 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        } 
       ipmx +=1;    *cx=(*bx)+GOLD*(*bx-*ax); 
       sw += weight[i];    *fc=(*func)(*cx); 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    while (*fb > *fc) { 
     } /* end of wave */      r=(*bx-*ax)*(*fb-*fc); 
   } /* end of individual */      q=(*bx-*cx)*(*fb-*fa); 
       u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      if ((*bx-u)*(u-*cx) > 0.0) { 
   return -l;        fu=(*func)(u); 
 }      } else if ((*cx-u)*(u-ulim) > 0.0) { 
         fu=(*func)(u); 
         if (fu < *fc) { 
 /*********** Maximum Likelihood Estimation ***************/          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
             SHFT(*fb,*fc,fu,(*func)(u)) 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))            } 
 {      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   int i,j, iter;        u=ulim; 
   double **xi,*delti;        fu=(*func)(u); 
   double fret;      } else { 
   xi=matrix(1,npar,1,npar);        u=(*cx)+GOLD*(*cx-*bx); 
   for (i=1;i<=npar;i++)        fu=(*func)(u); 
     for (j=1;j<=npar;j++)      } 
       xi[i][j]=(i==j ? 1.0 : 0.0);      SHFT(*ax,*bx,*cx,u) 
   printf("Powell\n");        SHFT(*fa,*fb,*fc,fu) 
   powell(p,xi,npar,ftol,&iter,&fret,func);        } 
   } 
    printf("\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));  /*************** linmin ************************/
   
 }  int ncom; 
   double *pcom,*xicom;
 /**** Computes Hessian and covariance matrix ***/  double (*nrfunc)(double []); 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))   
 {  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   double  **a,**y,*x,pd;  { 
   double **hess;    double brent(double ax, double bx, double cx, 
   int i, j,jk;                 double (*f)(double), double tol, double *xmin); 
   int *indx;    double f1dim(double x); 
     void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   double hessii(double p[], double delta, int theta, double delti[]);                double *fc, double (*func)(double)); 
   double hessij(double p[], double delti[], int i, int j);    int j; 
   void lubksb(double **a, int npar, int *indx, double b[]) ;    double xx,xmin,bx,ax; 
   void ludcmp(double **a, int npar, int *indx, double *d) ;    double fx,fb,fa;
    
   hess=matrix(1,npar,1,npar);    ncom=n; 
     pcom=vector(1,n); 
   printf("\nCalculation of the hessian matrix. Wait...\n");    xicom=vector(1,n); 
   for (i=1;i<=npar;i++){    nrfunc=func; 
     printf("%d",i);fflush(stdout);    for (j=1;j<=n;j++) { 
     hess[i][i]=hessii(p,ftolhess,i,delti);      pcom[j]=p[j]; 
     /*printf(" %f ",p[i]);*/      xicom[j]=xi[j]; 
     /*printf(" %lf ",hess[i][i]);*/    } 
   }    ax=0.0; 
      xx=1.0; 
   for (i=1;i<=npar;i++) {    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
     for (j=1;j<=npar;j++)  {    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       if (j>i) {  #ifdef DEBUG
         printf(".%d%d",i,j);fflush(stdout);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         hess[i][j]=hessij(p,delti,i,j);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
         hess[j][i]=hess[i][j];      #endif
         /*printf(" %lf ",hess[i][j]);*/    for (j=1;j<=n;j++) { 
       }      xi[j] *= xmin; 
     }      p[j] += xi[j]; 
   }    } 
   printf("\n");    free_vector(xicom,1,n); 
     free_vector(pcom,1,n); 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");  } 
    
   a=matrix(1,npar,1,npar);  char *asc_diff_time(long time_sec, char ascdiff[])
   y=matrix(1,npar,1,npar);  {
   x=vector(1,npar);    long sec_left, days, hours, minutes;
   indx=ivector(1,npar);    days = (time_sec) / (60*60*24);
   for (i=1;i<=npar;i++)    sec_left = (time_sec) % (60*60*24);
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    hours = (sec_left) / (60*60) ;
   ludcmp(a,npar,indx,&pd);    sec_left = (sec_left) %(60*60);
     minutes = (sec_left) /60;
   for (j=1;j<=npar;j++) {    sec_left = (sec_left) % (60);
     for (i=1;i<=npar;i++) x[i]=0;    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
     x[j]=1;    return ascdiff;
     lubksb(a,npar,indx,x);  }
     for (i=1;i<=npar;i++){  
       matcov[i][j]=x[i];  /*************** powell ************************/
     }  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   }              double (*func)(double [])) 
   { 
   printf("\n#Hessian matrix#\n");    void linmin(double p[], double xi[], int n, double *fret, 
   for (i=1;i<=npar;i++) {                double (*func)(double [])); 
     for (j=1;j<=npar;j++) {    int i,ibig,j; 
       printf("%.3e ",hess[i][j]);    double del,t,*pt,*ptt,*xit;
     }    double fp,fptt;
     printf("\n");    double *xits;
   }    int niterf, itmp;
   
   /* Recompute Inverse */    pt=vector(1,n); 
   for (i=1;i<=npar;i++)    ptt=vector(1,n); 
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    xit=vector(1,n); 
   ludcmp(a,npar,indx,&pd);    xits=vector(1,n); 
     *fret=(*func)(p); 
   /*  printf("\n#Hessian matrix recomputed#\n");    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for (*iter=1;;++(*iter)) { 
   for (j=1;j<=npar;j++) {      fp=(*fret); 
     for (i=1;i<=npar;i++) x[i]=0;      ibig=0; 
     x[j]=1;      del=0.0; 
     lubksb(a,npar,indx,x);      last_time=curr_time;
     for (i=1;i<=npar;i++){      (void) gettimeofday(&curr_time,&tzp);
       y[i][j]=x[i];      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);
       printf("%.3e ",y[i][j]);      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); fflush(ficlog);
     }  /*     fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec); */
     printf("\n");     for (i=1;i<=n;i++) {
   }        printf(" %d %.12f",i, p[i]);
   */        fprintf(ficlog," %d %.12lf",i, p[i]);
         fprintf(ficrespow," %.12lf", p[i]);
   free_matrix(a,1,npar,1,npar);      }
   free_matrix(y,1,npar,1,npar);      printf("\n");
   free_vector(x,1,npar);      fprintf(ficlog,"\n");
   free_ivector(indx,1,npar);      fprintf(ficrespow,"\n");fflush(ficrespow);
   free_matrix(hess,1,npar,1,npar);      if(*iter <=3){
         tm = *localtime(&curr_time.tv_sec);
         strcpy(strcurr,asctime(&tm));
 }  /*       asctime_r(&tm,strcurr); */
         forecast_time=curr_time; 
 /*************** hessian matrix ****************/        itmp = strlen(strcurr);
 double hessii( double x[], double delta, int theta, double delti[])        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
 {          strcurr[itmp-1]='\0';
   int i;        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   int l=1, lmax=20;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   double k1,k2;        for(niterf=10;niterf<=30;niterf+=10){
   double p2[NPARMAX+1];          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
   double res;          tmf = *localtime(&forecast_time.tv_sec);
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;  /*      asctime_r(&tmf,strfor); */
   double fx;          strcpy(strfor,asctime(&tmf));
   int k=0,kmax=10;          itmp = strlen(strfor);
   double l1;          if(strfor[itmp-1]=='\n')
           strfor[itmp-1]='\0';
   fx=func(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++) p2[i]=x[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);
   for(l=0 ; l <=lmax; l++){        }
     l1=pow(10,l);      }
     delts=delt;      for (i=1;i<=n;i++) { 
     for(k=1 ; k <kmax; k=k+1){        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       delt = delta*(l1*k);        fptt=(*fret); 
       p2[theta]=x[theta] +delt;  #ifdef DEBUG
       k1=func(p2)-fx;        printf("fret=%lf \n",*fret);
       p2[theta]=x[theta]-delt;        fprintf(ficlog,"fret=%lf \n",*fret);
       k2=func(p2)-fx;  #endif
       /*res= (k1-2.0*fx+k2)/delt/delt; */        printf("%d",i);fflush(stdout);
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        fprintf(ficlog,"%d",i);fflush(ficlog);
              linmin(p,xit,n,fret,func); 
 #ifdef DEBUG        if (fabs(fptt-(*fret)) > del) { 
       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);          del=fabs(fptt-(*fret)); 
 #endif          ibig=i; 
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */        } 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){  #ifdef DEBUG
         k=kmax;        printf("%d %.12e",i,(*fret));
       }        fprintf(ficlog,"%d %.12e",i,(*fret));
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */        for (j=1;j<=n;j++) {
         k=kmax; l=lmax*10.;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
       }          printf(" x(%d)=%.12e",j,xit[j]);
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         delts=delt;        }
       }        for(j=1;j<=n;j++) {
     }          printf(" p=%.12e",p[j]);
   }          fprintf(ficlog," p=%.12e",p[j]);
   delti[theta]=delts;        }
   return res;        printf("\n");
          fprintf(ficlog,"\n");
 }  #endif
       } 
 double hessij( double x[], double delti[], int thetai,int thetaj)      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
 {  #ifdef DEBUG
   int i;        int k[2],l;
   int l=1, l1, lmax=20;        k[0]=1;
   double k1,k2,k3,k4,res,fx;        k[1]=-1;
   double p2[NPARMAX+1];        printf("Max: %.12e",(*func)(p));
   int k;        fprintf(ficlog,"Max: %.12e",(*func)(p));
         for (j=1;j<=n;j++) {
   fx=func(x);          printf(" %.12e",p[j]);
   for (k=1; k<=2; k++) {          fprintf(ficlog," %.12e",p[j]);
     for (i=1;i<=npar;i++) p2[i]=x[i];        }
     p2[thetai]=x[thetai]+delti[thetai]/k;        printf("\n");
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        fprintf(ficlog,"\n");
     k1=func(p2)-fx;        for(l=0;l<=1;l++) {
            for (j=1;j<=n;j++) {
     p2[thetai]=x[thetai]+delti[thetai]/k;            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     k2=func(p2)-fx;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
            }
     p2[thetai]=x[thetai]-delti[thetai]/k;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     k3=func(p2)-fx;        }
    #endif
     p2[thetai]=x[thetai]-delti[thetai]/k;  
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;  
     k4=func(p2)-fx;        free_vector(xit,1,n); 
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        free_vector(xits,1,n); 
 #ifdef DEBUG        free_vector(ptt,1,n); 
     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);        free_vector(pt,1,n); 
 #endif        return; 
   }      } 
   return res;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
 }      for (j=1;j<=n;j++) { 
         ptt[j]=2.0*p[j]-pt[j]; 
 /************** Inverse of matrix **************/        xit[j]=p[j]-pt[j]; 
 void ludcmp(double **a, int n, int *indx, double *d)        pt[j]=p[j]; 
 {      } 
   int i,imax,j,k;      fptt=(*func)(ptt); 
   double big,dum,sum,temp;      if (fptt < fp) { 
   double *vv;        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
          if (t < 0.0) { 
   vv=vector(1,n);          linmin(p,xit,n,fret,func); 
   *d=1.0;          for (j=1;j<=n;j++) { 
   for (i=1;i<=n;i++) {            xi[j][ibig]=xi[j][n]; 
     big=0.0;            xi[j][n]=xit[j]; 
     for (j=1;j<=n;j++)          }
       if ((temp=fabs(a[i][j])) > big) big=temp;  #ifdef DEBUG
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     vv[i]=1.0/big;          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++){
   for (j=1;j<=n;j++) {            printf(" %.12e",xit[j]);
     for (i=1;i<j;i++) {            fprintf(ficlog," %.12e",xit[j]);
       sum=a[i][j];          }
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];          printf("\n");
       a[i][j]=sum;          fprintf(ficlog,"\n");
     }  #endif
     big=0.0;        }
     for (i=j;i<=n;i++) {      } 
       sum=a[i][j];    } 
       for (k=1;k<j;k++)  } 
         sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;  /**** Prevalence limit (stable or period prevalence)  ****************/
       if ( (dum=vv[i]*fabs(sum)) >= big) {  
         big=dum;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
         imax=i;  {
       }    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     }       matrix by transitions matrix until convergence is reached */
     if (j != imax) {  
       for (k=1;k<=n;k++) {    int i, ii,j,k;
         dum=a[imax][k];    double min, max, maxmin, maxmax,sumnew=0.;
         a[imax][k]=a[j][k];    double **matprod2();
         a[j][k]=dum;    double **out, cov[NCOVMAX], **pmij();
       }    double **newm;
       *d = -(*d);    double agefin, delaymax=50 ; /* Max number of years to converge */
       vv[imax]=vv[j];  
     }    for (ii=1;ii<=nlstate+ndeath;ii++)
     indx[j]=imax;      for (j=1;j<=nlstate+ndeath;j++){
     if (a[j][j] == 0.0) a[j][j]=TINY;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     if (j != n) {      }
       dum=1.0/(a[j][j]);  
       for (i=j+1;i<=n;i++) a[i][j] *= dum;     cov[1]=1.;
     }   
   }   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   free_vector(vv,1,n);  /* Doesn't work */    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
 ;      newm=savm;
 }      /* Covariates have to be included here again */
        cov[2]=agefin;
 void lubksb(double **a, int n, int *indx, double b[])    
 {        for (k=1; k<=cptcovn;k++) {
   int i,ii=0,ip,j;          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   double sum;          /*      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]]);*/
          }
   for (i=1;i<=n;i++) {        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     ip=indx[i];        for (k=1; k<=cptcovprod;k++)
     sum=b[ip];          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
     b[ip]=b[i];  
     if (ii)        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     else if (sum) ii=i;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     b[i]=sum;      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   }  
   for (i=n;i>=1;i--) {      savm=oldm;
     sum=b[i];      oldm=newm;
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];      maxmax=0.;
     b[i]=sum/a[i][i];      for(j=1;j<=nlstate;j++){
   }        min=1.;
 }        max=0.;
         for(i=1; i<=nlstate; i++) {
 /************ Frequencies ********************/          sumnew=0;
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2)          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
 {  /* Some frequencies */          prlim[i][j]= newm[i][j]/(1-sumnew);
            max=FMAX(max,prlim[i][j]);
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          min=FMIN(min,prlim[i][j]);
   double ***freq; /* Frequencies */        }
   double *pp;        maxmin=max-min;
   double pos, k2, dateintsum=0,k2cpt=0;        maxmax=FMAX(maxmax,maxmin);
   FILE *ficresp;      }
   char fileresp[FILENAMELENGTH];      if(maxmax < ftolpl){
         return prlim;
   pp=vector(1,nlstate);      }
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    }
   strcpy(fileresp,"p");  }
   strcat(fileresp,fileres);  
   if((ficresp=fopen(fileresp,"w"))==NULL) {  /*************** transition probabilities ***************/ 
     printf("Problem with prevalence resultfile: %s\n", fileresp);  
     exit(0);  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   }  {
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    double s1, s2;
   j1=0;    /*double t34;*/
     int i,j,j1, nc, ii, jj;
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      for(i=1; i<= nlstate; i++){
         for(j=1; j<i;j++){
   for(k1=1; k1<=j;k1++){          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
    for(i1=1; i1<=ncodemax[k1];i1++){            /*s2 += param[i][j][nc]*cov[nc];*/
        j1++;            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
          scanf("%d", i);*/          }
         for (i=-1; i<=nlstate+ndeath; i++)            ps[i][j]=s2;
          for (jk=-1; jk<=nlstate+ndeath; jk++)    /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
            for(m=agemin; m <= agemax+3; m++)        }
              freq[i][jk][m]=0;        for(j=i+1; j<=nlstate+ndeath;j++){
           for (nc=1, s2=0.;nc <=ncovmodel; nc++){
         dateintsum=0;            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
         k2cpt=0;  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
        for (i=1; i<=imx; i++) {          }
          bool=1;          ps[i][j]=s2;
          if  (cptcovn>0) {        }
            for (z1=1; z1<=cptcoveff; z1++)      }
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      /*ps[3][2]=1;*/
                bool=0;      
          }      for(i=1; i<= nlstate; i++){
          if (bool==1) {        s1=0;
            for(m=firstpass; m<=lastpass; m++){        for(j=1; j<i; j++)
              k2=anint[m][i]+(mint[m][i]/12.);          s1+=exp(ps[i][j]);
              if ((k2>=dateprev1) && (k2<=dateprev2)) {        for(j=i+1; j<=nlstate+ndeath; j++)
                if(agev[m][i]==0) agev[m][i]=agemax+1;          s1+=exp(ps[i][j]);
                if(agev[m][i]==1) agev[m][i]=agemax+2;        ps[i][i]=1./(s1+1.);
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];        for(j=1; j<i; j++)
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];          ps[i][j]= exp(ps[i][j])*ps[i][i];
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {        for(j=i+1; j<=nlstate+ndeath; j++)
                  dateintsum=dateintsum+k2;          ps[i][j]= exp(ps[i][j])*ps[i][i];
                  k2cpt++;        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
                }      } /* end i */
       
              }      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
            }        for(jj=1; jj<= nlstate+ndeath; jj++){
          }          ps[ii][jj]=0;
        }          ps[ii][ii]=1;
         if  (cptcovn>0) {        }
          fprintf(ficresp, "\n#********** Variable ");      }
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);      
        fprintf(ficresp, "**********\n#");  
         }  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
        for(i=1; i<=nlstate;i++)  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);  /*         printf("ddd %lf ",ps[ii][jj]); */
        fprintf(ficresp, "\n");  /*       } */
          /*       printf("\n "); */
   for(i=(int)agemin; i <= (int)agemax+3; i++){  /*        } */
     if(i==(int)agemax+3)  /*        printf("\n ");printf("%lf ",cov[2]); */
       printf("Total");         /*
     else        for(i=1; i<= npar; i++) printf("%f ",x[i]);
       printf("Age %d", i);        goto end;*/
     for(jk=1; jk <=nlstate ; jk++){      return ps;
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  }
         pp[jk] += freq[jk][m][i];  
     }  /**************** Product of 2 matrices ******************/
     for(jk=1; jk <=nlstate ; jk++){  
       for(m=-1, pos=0; m <=0 ; m++)  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
         pos += freq[jk][m][i];  {
       if(pp[jk]>=1.e-10)    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
       else    /* in, b, out are matrice of pointers which should have been initialized 
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);       before: only the contents of out is modified. The function returns
     }       a pointer to pointers identical to out */
     long i, j, k;
      for(jk=1; jk <=nlstate ; jk++){    for(i=nrl; i<= nrh; i++)
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)      for(k=ncolol; k<=ncoloh; k++)
         pp[jk] += freq[jk][m][i];        for(j=ncl,out[i][k]=0.; j<=nch; j++)
      }          out[i][k] +=in[i][j]*b[j][k];
   
     for(jk=1,pos=0; jk <=nlstate ; jk++)    return out;
       pos += pp[jk];  }
     for(jk=1; jk <=nlstate ; jk++){  
       if(pos>=1.e-5)  
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  /************* Higher Matrix Product ***************/
       else  
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
       if( i <= (int) agemax){  {
         if(pos>=1.e-5){    /* Computes the transition matrix starting at age 'age' over 
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);       'nhstepm*hstepm*stepm' months (i.e. until
           probs[i][jk][j1]= pp[jk]/pos;       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
           /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/       nhstepm*hstepm matrices. 
         }       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
       else       (typically every 2 years instead of every month which is too big 
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);       for the memory).
       }       Model is determined by parameters x and covariates have to be 
     }       included manually here. 
     for(jk=-1; jk <=nlstate+ndeath; jk++)  
       for(m=-1; m <=nlstate+ndeath; m++)       */
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  
     if(i <= (int) agemax)    int i, j, d, h, k;
       fprintf(ficresp,"\n");    double **out, cov[NCOVMAX];
     printf("\n");    double **newm;
     }  
     }    /* Hstepm could be zero and should return the unit matrix */
  }    for (i=1;i<=nlstate+ndeath;i++)
   dateintmean=dateintsum/k2cpt;      for (j=1;j<=nlstate+ndeath;j++){
          oldm[i][j]=(i==j ? 1.0 : 0.0);
   fclose(ficresp);        po[i][j][0]=(i==j ? 1.0 : 0.0);
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      }
   free_vector(pp,1,nlstate);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
     for(h=1; h <=nhstepm; h++){
   /* End of Freq */      for(d=1; d <=hstepm; d++){
 }        newm=savm;
         /* Covariates have to be included here again */
 /************ Prevalence ********************/        cov[1]=1.;
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
 {  /* Some frequencies */        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
          for (k=1; k<=cptcovage;k++)
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   double ***freq; /* Frequencies */        for (k=1; k<=cptcovprod;k++)
   double *pp;          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
   double pos, k2;  
   
   pp=vector(1,nlstate);        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        /*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, 
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);                     pmij(pmmij,cov,ncovmodel,x,nlstate));
   j1=0;        savm=oldm;
          oldm=newm;
   j=cptcoveff;      }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      for(i=1; i<=nlstate+ndeath; i++)
          for(j=1;j<=nlstate+ndeath;j++) {
  for(k1=1; k1<=j;k1++){          po[i][j][h]=newm[i][j];
     for(i1=1; i1<=ncodemax[k1];i1++){          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
       j1++;           */
          }
       for (i=-1; i<=nlstate+ndeath; i++)      } /* end h */
         for (jk=-1; jk<=nlstate+ndeath; jk++)      return po;
           for(m=agemin; m <= agemax+3; m++)  }
             freq[i][jk][m]=0;  
        
       for (i=1; i<=imx; i++) {  /*************** log-likelihood *************/
         bool=1;  double func( double *x)
         if  (cptcovn>0) {  {
           for (z1=1; z1<=cptcoveff; z1++)    int i, ii, j, k, mi, d, kk;
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])    double l, ll[NLSTATEMAX], cov[NCOVMAX];
               bool=0;    double **out;
         }    double sw; /* Sum of weights */
         if (bool==1) {    double lli; /* Individual log likelihood */
           for(m=firstpass; m<=lastpass; m++){    int s1, s2;
             k2=anint[m][i]+(mint[m][i]/12.);    double bbh, survp;
             if ((k2>=dateprev1) && (k2<=dateprev2)) {    long ipmx;
               if(agev[m][i]==0) agev[m][i]=agemax+1;    /*extern weight */
               if(agev[m][i]==1) agev[m][i]=agemax+2;    /* We are differentiating ll according to initial status */
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];      /*for(i=1;i<imx;i++) 
             }      printf(" %d\n",s[4][i]);
           }    */
         }    cov[1]=1.;
       }  
          for(k=1; k<=nlstate; k++) ll[k]=0.;
         for(i=(int)agemin; i <= (int)agemax+3; i++){  
           for(jk=1; jk <=nlstate ; jk++){    if(mle==1){
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
               pp[jk] += freq[jk][m][i];        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           }        for(mi=1; mi<= wav[i]-1; mi++){
           for(jk=1; jk <=nlstate ; jk++){          for (ii=1;ii<=nlstate+ndeath;ii++)
             for(m=-1, pos=0; m <=0 ; m++)            for (j=1;j<=nlstate+ndeath;j++){
             pos += freq[jk][m][i];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
                    }
          for(jk=1; jk <=nlstate ; jk++){          for(d=0; d<dh[mi][i]; d++){
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)            newm=savm;
              pp[jk] += freq[jk][m][i];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
          }            for (kk=1; kk<=cptcovage;kk++) {
                        cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
          for(jk=1; jk <=nlstate ; jk++){                                   1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
            if( i <= (int) agemax){            savm=oldm;
              if(pos>=1.e-5){            oldm=newm;
                probs[i][jk][j1]= pp[jk]/pos;          } /* end mult */
              }        
            }          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
          }          /* But now since version 0.9 we anticipate for bias at large stepm.
                     * If stepm is larger than one month (smallest stepm) and if the exact delay 
         }           * (in months) between two waves is not a multiple of stepm, we rounded to 
     }           * the nearest (and in case of equal distance, to the lowest) interval but now
   }           * 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
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
   free_vector(pp,1,nlstate);           * -stepm/2 to stepm/2 .
             * For stepm=1 the results are the same as for previous versions of Imach.
 }  /* End of Freq */           * For stepm > 1 the results are less biased than in previous versions. 
            */
 /************* Waves Concatenation ***************/          s1=s[mw[mi][i]][i];
           s2=s[mw[mi+1][i]][i];
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          bbh=(double)bh[mi][i]/(double)stepm; 
 {          /* bias bh is positive if real duration
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.           * is higher than the multiple of stepm and negative otherwise.
      Death is a valid wave (if date is known).           */
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          if( s2 > nlstate){ 
      and mw[mi+1][i]. dh depends on stepm.            /* i.e. if s2 is a death state and if the date of death is known 
      */               then the contribution to the likelihood is the probability to 
                die between last step unit time and current  step unit time, 
   int i, mi, m;               which is also equal to probability to die before dh 
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;               minus probability to die before dh-stepm . 
      double sum=0., jmean=0.;*/               In version up to 0.92 likelihood was computed
           as if date of death was unknown. Death was treated as any other
   int j, k=0,jk, ju, jl;          health state: the date of the interview describes the actual state
   double sum=0.;          and not the date of a change in health state. The former idea was
   jmin=1e+5;          to consider that at each interview the state was recorded
   jmax=-1;          (healthy, disable or death) and IMaCh was corrected; but when we
   jmean=0.;          introduced the exact date of death then we should have modified
   for(i=1; i<=imx; i++){          the contribution of an exact death to the likelihood. This new
     mi=0;          contribution is smaller and very dependent of the step unit
     m=firstpass;          stepm. It is no more the probability to die between last interview
     while(s[m][i] <= nlstate){          and month of death but the probability to survive from last
       if(s[m][i]>=1)          interview up to one month before death multiplied by the
         mw[++mi][i]=m;          probability to die within a month. Thanks to Chris
       if(m >=lastpass)          Jackson for correcting this bug.  Former versions increased
         break;          mortality artificially. The bad side is that we add another loop
       else          which slows down the processing. The difference can be up to 10%
         m++;          lower mortality.
     }/* end while */            */
     if (s[m][i] > nlstate){            lli=log(out[s1][s2] - savm[s1][s2]);
       mi++;     /* Death is another wave */  
       /* if(mi==0)  never been interviewed correctly before death */  
          /* Only death is a correct wave */          } else if  (s2==-2) {
       mw[mi][i]=m;            for (j=1,survp=0. ; j<=nlstate; j++) 
     }              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
             /*survp += out[s1][j]; */
     wav[i]=mi;            lli= log(survp);
     if(mi==0)          }
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          
   }          else if  (s2==-4) { 
             for (j=3,survp=0. ; j<=nlstate; j++)  
   for(i=1; i<=imx; i++){              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     for(mi=1; mi<wav[i];mi++){            lli= log(survp); 
       if (stepm <=0)          } 
         dh[mi][i]=1;  
       else{          else if  (s2==-5) { 
         if (s[mw[mi+1][i]][i] > nlstate) {            for (j=1,survp=0. ; j<=2; j++)  
           if (agedc[i] < 2*AGESUP) {              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);            lli= log(survp); 
           if(j==0) j=1;  /* Survives at least one month after exam */          } 
           k=k+1;          
           if (j >= jmax) jmax=j;          else{
           if (j <= jmin) jmin=j;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
           sum=sum+j;            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
           /* if (j<10) printf("j=%d num=%d ",j,i); */          } 
           }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
         }          /*if(lli ==000.0)*/
         else{          /*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); */
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));          ipmx +=1;
           k=k+1;          sw += weight[i];
           if (j >= jmax) jmax=j;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           else if (j <= jmin)jmin=j;        } /* end of wave */
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */      } /* end of individual */
           sum=sum+j;    }  else if(mle==2){
         }      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         jk= j/stepm;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         jl= j -jk*stepm;        for(mi=1; mi<= wav[i]-1; mi++){
         ju= j -(jk+1)*stepm;          for (ii=1;ii<=nlstate+ndeath;ii++)
         if(jl <= -ju)            for (j=1;j<=nlstate+ndeath;j++){
           dh[mi][i]=jk;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         else              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           dh[mi][i]=jk+1;            }
         if(dh[mi][i]==0)          for(d=0; d<=dh[mi][i]; d++){
           dh[mi][i]=1; /* At least one step */            newm=savm;
       }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     }            for (kk=1; kk<=cptcovage;kk++) {
   }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   jmean=sum/k;            }
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
  }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
 /*********** Tricode ****************************/            savm=oldm;
 void tricode(int *Tvar, int **nbcode, int imx)            oldm=newm;
 {          } /* end mult */
   int Ndum[20],ij=1, k, j, i;        
   int cptcode=0;          s1=s[mw[mi][i]][i];
   cptcoveff=0;          s2=s[mw[mi+1][i]][i];
            bbh=(double)bh[mi][i]/(double)stepm; 
   for (k=0; k<19; k++) Ndum[k]=0;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
   for (k=1; k<=7; k++) ncodemax[k]=0;          ipmx +=1;
           sw += weight[i];
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for (i=1; i<=imx; i++) {        } /* end of wave */
       ij=(int)(covar[Tvar[j]][i]);      } /* end of individual */
       Ndum[ij]++;    }  else if(mle==3){  /* exponential inter-extrapolation */
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       if (ij > cptcode) cptcode=ij;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     }        for(mi=1; mi<= wav[i]-1; mi++){
           for (ii=1;ii<=nlstate+ndeath;ii++)
     for (i=0; i<=cptcode; i++) {            for (j=1;j<=nlstate+ndeath;j++){
       if(Ndum[i]!=0) ncodemax[j]++;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     ij=1;            }
           for(d=0; d<dh[mi][i]; d++){
             newm=savm;
     for (i=1; i<=ncodemax[j]; i++) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for (k=0; k<=19; k++) {            for (kk=1; kk<=cptcovage;kk++) {
         if (Ndum[k] != 0) {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           nbcode[Tvar[j]][ij]=k;            }
           ij++;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         }                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         if (ij > ncodemax[j]) break;            savm=oldm;
       }              oldm=newm;
     }          } /* end mult */
   }          
           s1=s[mw[mi][i]][i];
  for (k=0; k<19; k++) Ndum[k]=0;          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
  for (i=1; i<=ncovmodel-2; i++) {          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 */
       ij=Tvar[i];          ipmx +=1;
       Ndum[ij]++;          sw += weight[i];
     }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
  ij=1;      } /* end of individual */
  for (i=1; i<=10; i++) {    }else if (mle==4){  /* ml=4 no inter-extrapolation */
    if((Ndum[i]!=0) && (i<=ncov)){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
      Tvaraff[ij]=i;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
      ij++;        for(mi=1; mi<= wav[i]-1; mi++){
    }          for (ii=1;ii<=nlstate+ndeath;ii++)
  }            for (j=1;j<=nlstate+ndeath;j++){
                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     cptcoveff=ij-1;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 }            }
           for(d=0; d<dh[mi][i]; d++){
 /*********** Health Expectancies ****************/            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)            for (kk=1; kk<=cptcovage;kk++) {
 {              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   /* Health expectancies */            }
   int i, j, nhstepm, hstepm, h;          
   double age, agelim,hf;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double ***p3mat;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              savm=oldm;
   fprintf(ficreseij,"# Health expectancies\n");            oldm=newm;
   fprintf(ficreseij,"# Age");          } /* end mult */
   for(i=1; i<=nlstate;i++)        
     for(j=1; j<=nlstate;j++)          s1=s[mw[mi][i]][i];
       fprintf(ficreseij," %1d-%1d",i,j);          s2=s[mw[mi+1][i]][i];
   fprintf(ficreseij,"\n");          if( s2 > nlstate){ 
             lli=log(out[s1][s2] - savm[s1][s2]);
   hstepm=1*YEARM; /*  Every j years of age (in month) */          }else{
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
           }
   agelim=AGESUP;          ipmx +=1;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          sw += weight[i];
     /* nhstepm age range expressed in number of stepm */          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);  /*      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]); */
     /* Typically if 20 years = 20*12/6=40 stepm */        } /* end of wave */
     if (stepm >= YEARM) hstepm=1;      } /* end of individual */
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     /* Computed by stepm unit matrices, product of hstepm matrices, stored        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        for(mi=1; mi<= wav[i]-1; mi++){
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
               oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(i=1; i<=nlstate;i++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(j=1; j<=nlstate;j++)            }
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){          for(d=0; d<dh[mi][i]; d++){
           eij[i][j][(int)age] +=p3mat[i][j][h];            newm=savm;
         }            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
                for (kk=1; kk<=cptcovage;kk++) {
     hf=1;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     if (stepm >= YEARM) hf=stepm/YEARM;            }
     fprintf(ficreseij,"%.0f",age );          
     for(i=1; i<=nlstate;i++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for(j=1; j<=nlstate;j++){                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);            savm=oldm;
       }            oldm=newm;
     fprintf(ficreseij,"\n");          } /* end mult */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        
   }          s1=s[mw[mi][i]][i];
 }          s2=s[mw[mi+1][i]][i];
           lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
 /************ Variance ******************/          ipmx +=1;
 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)          sw += weight[i];
 {          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /* Variance of health expectancies */          /*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]);*/
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        } /* end of wave */
   double **newm;      } /* end of individual */
   double **dnewm,**doldm;    } /* End of if */
   int i, j, nhstepm, hstepm, h;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   int k, cptcode;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   double *xp;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   double **gp, **gm;    return -l;
   double ***gradg, ***trgradg;  }
   double ***p3mat;  
   double age,agelim;  /*************** log-likelihood *************/
   int theta;  double funcone( double *x)
   {
    fprintf(ficresvij,"# Covariances of life expectancies\n");    /* Same as likeli but slower because of a lot of printf and if */
   fprintf(ficresvij,"# Age");    int i, ii, j, k, mi, d, kk;
   for(i=1; i<=nlstate;i++)    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     for(j=1; j<=nlstate;j++)    double **out;
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);    double lli; /* Individual log likelihood */
   fprintf(ficresvij,"\n");    double llt;
     int s1, s2;
   xp=vector(1,npar);    double bbh, survp;
   dnewm=matrix(1,nlstate,1,npar);    /*extern weight */
   doldm=matrix(1,nlstate,1,nlstate);    /* We are differentiating ll according to initial status */
      /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   hstepm=1*YEARM; /* Every year of age */    /*for(i=1;i<imx;i++) 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      printf(" %d\n",s[4][i]);
   agelim = AGESUP;    */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    cov[1]=1.;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  
     if (stepm >= YEARM) hstepm=1;    for(k=1; k<=nlstate; k++) ll[k]=0.;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     gp=matrix(0,nhstepm,1,nlstate);      for(mi=1; mi<= wav[i]-1; mi++){
     gm=matrix(0,nhstepm,1,nlstate);        for (ii=1;ii<=nlstate+ndeath;ii++)
           for (j=1;j<=nlstate+ndeath;j++){
     for(theta=1; theta <=npar; theta++){            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(i=1; i<=npar; i++){ /* Computes gradient */            savm[ii][j]=(ii==j ? 1.0 : 0.0);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          }
       }        for(d=0; d<dh[mi][i]; d++){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            newm=savm;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           for (kk=1; kk<=cptcovage;kk++) {
       if (popbased==1) {            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         for(i=1; i<=nlstate;i++)          }
           prlim[i][i]=probs[(int)age][i][ij];          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       }                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
                savm=oldm;
       for(j=1; j<= nlstate; j++){          oldm=newm;
         for(h=0; h<=nhstepm; h++){        } /* end mult */
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)        
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];        s1=s[mw[mi][i]][i];
         }        s2=s[mw[mi+1][i]][i];
       }        bbh=(double)bh[mi][i]/(double)stepm; 
            /* bias is positive if real duration
       for(i=1; i<=npar; i++) /* Computes gradient */         * is higher than the multiple of stepm and negative otherwise.
         xp[i] = x[i] - (i==theta ?delti[theta]:0);         */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          if( s2 > nlstate && (mle <5) ){  /* Jackson */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          lli=log(out[s1][s2] - savm[s1][s2]);
         } else if  (s2==-2) {
       if (popbased==1) {          for (j=1,survp=0. ; j<=nlstate; j++) 
         for(i=1; i<=nlstate;i++)            survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           prlim[i][i]=probs[(int)age][i][ij];          lli= log(survp);
       }        }else if (mle==1){
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       for(j=1; j<= nlstate; j++){        } else if(mle==2){
         for(h=0; h<=nhstepm; h++){          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        } else if(mle==3){  /* exponential inter-extrapolation */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          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 */
         }        } else if (mle==4){  /* mle=4 no inter-extrapolation */
       }          lli=log(out[s1][s2]); /* Original formula */
         } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
       for(j=1; j<= nlstate; j++)          lli=log(out[s1][s2]); /* Original formula */
         for(h=0; h<=nhstepm; h++){        } /* End of if */
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];        ipmx +=1;
         }        sw += weight[i];
     } /* End theta */        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]); */
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);        if(globpr){
           fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
     for(h=0; h<=nhstepm; h++)   %11.6f %11.6f %11.6f ", \
       for(j=1; j<=nlstate;j++)                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
         for(theta=1; theta <=npar; theta++)                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
           trgradg[h][j][theta]=gradg[h][theta][j];          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
             llt +=ll[k]*gipmx/gsw;
     for(i=1;i<=nlstate;i++)            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
       for(j=1;j<=nlstate;j++)          }
         vareij[i][j][(int)age] =0.;          fprintf(ficresilk," %10.6f\n", -llt);
     for(h=0;h<=nhstepm;h++){        }
       for(k=0;k<=nhstepm;k++){      } /* end of wave */
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    } /* end of individual */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    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 */
             vareij[i][j][(int)age] += doldm[i][j];    if(globpr==0){ /* First time we count the contributions and weights */
       }      gipmx=ipmx;
     }      gsw=sw;
     h=1;    }
     if (stepm >= YEARM) h=stepm/YEARM;    return -l;
     fprintf(ficresvij,"%.0f ",age );  }
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){  
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);  /*************** function likelione ***********/
       }  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
     fprintf(ficresvij,"\n");  {
     free_matrix(gp,0,nhstepm,1,nlstate);    /* This routine should help understanding what is done with 
     free_matrix(gm,0,nhstepm,1,nlstate);       the selection of individuals/waves and
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);       to check the exact contribution to the likelihood.
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);       Plotting could be done.
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     */
   } /* End age */    int k;
    
   free_vector(xp,1,npar);    if(*globpri !=0){ /* Just counts and sums, no printings */
   free_matrix(doldm,1,nlstate,1,npar);      strcpy(fileresilk,"ilk"); 
   free_matrix(dnewm,1,nlstate,1,nlstate);      strcat(fileresilk,fileres);
       if((ficresilk=fopen(fileresilk,"w"))==NULL) {
 }        printf("Problem with resultfile: %s\n", fileresilk);
         fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
 /************ 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)      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
 {      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
   /* Variance of prevalence limit */      /*  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 **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/      for(k=1; k<=nlstate; k++) 
   double **newm;        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
   double **dnewm,**doldm;      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   int i, j, nhstepm, hstepm;    }
   int k, cptcode;  
   double *xp;    *fretone=(*funcone)(p);
   double *gp, *gm;    if(*globpri !=0){
   double **gradg, **trgradg;      fclose(ficresilk);
   double age,agelim;      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   int theta;      fflush(fichtm); 
        } 
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    return;
   fprintf(ficresvpl,"# Age");  }
   for(i=1; i<=nlstate;i++)  
       fprintf(ficresvpl," %1d-%1d",i,i);  
   fprintf(ficresvpl,"\n");  /*********** Maximum Likelihood Estimation ***************/
   
   xp=vector(1,npar);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   dnewm=matrix(1,nlstate,1,npar);  {
   doldm=matrix(1,nlstate,1,nlstate);    int i,j, iter;
      double **xi;
   hstepm=1*YEARM; /* Every year of age */    double fret;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    double fretone; /* Only one call to likelihood */
   agelim = AGESUP;    /*  char filerespow[FILENAMELENGTH];*/
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    xi=matrix(1,npar,1,npar);
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    for (i=1;i<=npar;i++)
     if (stepm >= YEARM) hstepm=1;      for (j=1;j<=npar;j++)
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        xi[i][j]=(i==j ? 1.0 : 0.0);
     gradg=matrix(1,npar,1,nlstate);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     gp=vector(1,nlstate);    strcpy(filerespow,"pow"); 
     gm=vector(1,nlstate);    strcat(filerespow,fileres);
     if((ficrespow=fopen(filerespow,"w"))==NULL) {
     for(theta=1; theta <=npar; theta++){      printf("Problem with resultfile: %s\n", filerespow);
       for(i=1; i<=npar; i++){ /* Computes gradient */      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    }
       }    fprintf(ficrespow,"# Powell\n# iter -2*LL");
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    for (i=1;i<=nlstate;i++)
       for(i=1;i<=nlstate;i++)      for(j=1;j<=nlstate+ndeath;j++)
         gp[i] = prlim[i][i];        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
        fprintf(ficrespow,"\n");
       for(i=1; i<=npar; i++) /* Computes gradient */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    powell(p,xi,npar,ftol,&iter,&fret,func);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);  
       for(i=1;i<=nlstate;i++)    free_matrix(xi,1,npar,1,npar);
         gm[i] = prlim[i][i];    fclose(ficrespow);
     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
       for(i=1;i<=nlstate;i++)    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     } /* End theta */  
   }
     trgradg =matrix(1,nlstate,1,npar);  
   /**** Computes Hessian and covariance matrix ***/
     for(j=1; j<=nlstate;j++)  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
       for(theta=1; theta <=npar; theta++)  {
         trgradg[j][theta]=gradg[theta][j];    double  **a,**y,*x,pd;
     double **hess;
     for(i=1;i<=nlstate;i++)    int i, j,jk;
       varpl[i][(int)age] =0.;    int *indx;
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);  
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     for(i=1;i<=nlstate;i++)    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    void lubksb(double **a, int npar, int *indx, double b[]) ;
     void ludcmp(double **a, int npar, int *indx, double *d) ;
     fprintf(ficresvpl,"%.0f ",age );    double gompertz(double p[]);
     for(i=1; i<=nlstate;i++)    hess=matrix(1,npar,1,npar);
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));  
     fprintf(ficresvpl,"\n");    printf("\nCalculation of the hessian matrix. Wait...\n");
     free_vector(gp,1,nlstate);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
     free_vector(gm,1,nlstate);    for (i=1;i<=npar;i++){
     free_matrix(gradg,1,npar,1,nlstate);      printf("%d",i);fflush(stdout);
     free_matrix(trgradg,1,nlstate,1,npar);      fprintf(ficlog,"%d",i);fflush(ficlog);
   } /* End age */     
        hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
   free_vector(xp,1,npar);      
   free_matrix(doldm,1,nlstate,1,npar);      /*  printf(" %f ",p[i]);
   free_matrix(dnewm,1,nlstate,1,nlstate);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     }
 }    
     for (i=1;i<=npar;i++) {
 /************ Variance of one-step probabilities  ******************/      for (j=1;j<=npar;j++)  {
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)        if (j>i) { 
 {          printf(".%d%d",i,j);fflush(stdout);
   int i, j;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   int k=0, cptcode;          hess[i][j]=hessij(p,delti,i,j,func,npar);
   double **dnewm,**doldm;          
   double *xp;          hess[j][i]=hess[i][j];    
   double *gp, *gm;          /*printf(" %lf ",hess[i][j]);*/
   double **gradg, **trgradg;        }
   double age,agelim, cov[NCOVMAX];      }
   int theta;    }
   char fileresprob[FILENAMELENGTH];    printf("\n");
     fprintf(ficlog,"\n");
   strcpy(fileresprob,"prob");  
   strcat(fileresprob,fileres);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     printf("Problem with resultfile: %s\n", fileresprob);    
   }    a=matrix(1,npar,1,npar);
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);    y=matrix(1,npar,1,npar);
      x=vector(1,npar);
     indx=ivector(1,npar);
   xp=vector(1,npar);    for (i=1;i<=npar;i++)
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    ludcmp(a,npar,indx,&pd);
    
   cov[1]=1;    for (j=1;j<=npar;j++) {
   for (age=bage; age<=fage; age ++){      for (i=1;i<=npar;i++) x[i]=0;
     cov[2]=age;      x[j]=1;
     gradg=matrix(1,npar,1,9);      lubksb(a,npar,indx,x);
     trgradg=matrix(1,9,1,npar);      for (i=1;i<=npar;i++){ 
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        matcov[i][j]=x[i];
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      }
        }
     for(theta=1; theta <=npar; theta++){  
       for(i=1; i<=npar; i++)    printf("\n#Hessian matrix#\n");
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    fprintf(ficlog,"\n#Hessian matrix#\n");
          for (i=1;i<=npar;i++) { 
       pmij(pmmij,cov,ncovmodel,xp,nlstate);      for (j=1;j<=npar;j++) { 
            printf("%.3e ",hess[i][j]);
       k=0;        fprintf(ficlog,"%.3e ",hess[i][j]);
       for(i=1; i<= (nlstate+ndeath); i++){      }
         for(j=1; j<=(nlstate+ndeath);j++){      printf("\n");
            k=k+1;      fprintf(ficlog,"\n");
           gp[k]=pmmij[i][j];    }
         }  
       }    /* Recompute Inverse */
     for (i=1;i<=npar;i++)
       for(i=1; i<=npar; i++)      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    ludcmp(a,npar,indx,&pd);
      
     /*  printf("\n#Hessian matrix recomputed#\n");
       pmij(pmmij,cov,ncovmodel,xp,nlstate);  
       k=0;    for (j=1;j<=npar;j++) {
       for(i=1; i<=(nlstate+ndeath); i++){      for (i=1;i<=npar;i++) x[i]=0;
         for(j=1; j<=(nlstate+ndeath);j++){      x[j]=1;
           k=k+1;      lubksb(a,npar,indx,x);
           gm[k]=pmmij[i][j];      for (i=1;i<=npar;i++){ 
         }        y[i][j]=x[i];
       }        printf("%.3e ",y[i][j]);
              fprintf(ficlog,"%.3e ",y[i][j]);
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)      }
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];        printf("\n");
     }      fprintf(ficlog,"\n");
     }
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    */
       for(theta=1; theta <=npar; theta++)  
       trgradg[j][theta]=gradg[theta][j];    free_matrix(a,1,npar,1,npar);
      free_matrix(y,1,npar,1,npar);
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);    free_vector(x,1,npar);
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);    free_ivector(indx,1,npar);
     free_matrix(hess,1,npar,1,npar);
      pmij(pmmij,cov,ncovmodel,x,nlstate);  
   
      k=0;  }
      for(i=1; i<=(nlstate+ndeath); i++){  
        for(j=1; j<=(nlstate+ndeath);j++){  /*************** hessian matrix ****************/
          k=k+1;  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
          gm[k]=pmmij[i][j];  {
         }    int i;
      }    int l=1, lmax=20;
          double k1,k2;
      /*printf("\n%d ",(int)age);    double p2[NPARMAX+1];
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    double res;
            double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     double fx;
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));    int k=0,kmax=10;
      }*/    double l1;
   
   fprintf(ficresprob,"\n%d ",(int)age);    fx=func(x);
     for (i=1;i<=npar;i++) p2[i]=x[i];
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){    for(l=0 ; l <=lmax; l++){
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);      l1=pow(10,l);
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);      delts=delt;
   }      for(k=1 ; k <kmax; k=k+1){
         delt = delta*(l1*k);
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));        p2[theta]=x[theta] +delt;
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));        k1=func(p2)-fx;
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        p2[theta]=x[theta]-delt;
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);        k2=func(p2)-fx;
 }        /*res= (k1-2.0*fx+k2)/delt/delt; */
  free_vector(xp,1,npar);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
 fclose(ficresprob);        
  exit(0);  #ifdef DEBUG
 }        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
 /***********************************************/  #endif
 /**************** Main Program *****************/        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
 /***********************************************/        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
           k=kmax;
 int main(int argc, char *argv[])        }
 {        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           k=kmax; l=lmax*10.;
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;        }
   double agedeb, agefin,hf;        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   double agemin=1.e20, agemax=-1.e20;          delts=delt;
         }
   double fret;      }
   double **xi,tmp,delta;    }
     delti[theta]=delts;
   double dum; /* Dummy variable */    return res; 
   double ***p3mat;    
   int *indx;  }
   char line[MAXLINE], linepar[MAXLINE];  
   char title[MAXLINE];  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];  {
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];    int i;
      int l=1, l1, lmax=20;
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];;    double k1,k2,k3,k4,res,fx;
     double p2[NPARMAX+1];
   char filerest[FILENAMELENGTH];    int k;
   char fileregp[FILENAMELENGTH];  
   char popfile[FILENAMELENGTH];    fx=func(x);
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    for (k=1; k<=2; k++) {
   int firstobs=1, lastobs=10;      for (i=1;i<=npar;i++) p2[i]=x[i];
   int sdeb, sfin; /* Status at beginning and end */      p2[thetai]=x[thetai]+delti[thetai]/k;
   int c,  h , cpt,l;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   int ju,jl, mi;      k1=func(p2)-fx;
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;      p2[thetai]=x[thetai]+delti[thetai]/k;
   int mobilav=0,popforecast=0;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   int hstepm, nhstepm;      k2=func(p2)-fx;
   int *popage;/*boolprev=0 if date and zero if wave*/    
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;      p2[thetai]=x[thetai]-delti[thetai]/k;
       p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   double bage, fage, age, agelim, agebase;      k3=func(p2)-fx;
   double ftolpl=FTOL;    
   double **prlim;      p2[thetai]=x[thetai]-delti[thetai]/k;
   double *severity;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   double ***param; /* Matrix of parameters */      k4=func(p2)-fx;
   double  *p;      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   double **matcov; /* Matrix of covariance */  #ifdef DEBUG
   double ***delti3; /* Scale */      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);
   double *delti; /* Scale */      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);
   double ***eij, ***vareij;  #endif
   double **varpl; /* Variances of prevalence limits by age */    }
   double *epj, vepp;    return res;
   double kk1, kk2;  }
   double *popeffectif,*popcount;  
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;  /************** Inverse of matrix **************/
   double yp,yp1,yp2;  void ludcmp(double **a, int n, int *indx, double *d) 
   { 
   char version[80]="Imach version 0.7, February 2002, INED-EUROREVES ";    int i,imax,j,k; 
   char *alph[]={"a","a","b","c","d","e"}, str[4];    double big,dum,sum,temp; 
     double *vv; 
    
   char z[1]="c", occ;    vv=vector(1,n); 
 #include <sys/time.h>    *d=1.0; 
 #include <time.h>    for (i=1;i<=n;i++) { 
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      big=0.0; 
        for (j=1;j<=n;j++) 
   /* long total_usecs;        if ((temp=fabs(a[i][j])) > big) big=temp; 
   struct timeval start_time, end_time;      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
        vv[i]=1.0/big; 
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    } 
     for (j=1;j<=n;j++) { 
       for (i=1;i<j;i++) { 
   printf("\n%s",version);        sum=a[i][j]; 
   if(argc <=1){        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
     printf("\nEnter the parameter file name: ");        a[i][j]=sum; 
     scanf("%s",pathtot);      } 
   }      big=0.0; 
   else{      for (i=j;i<=n;i++) { 
     strcpy(pathtot,argv[1]);        sum=a[i][j]; 
   }        for (k=1;k<j;k++) 
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/          sum -= a[i][k]*a[k][j]; 
   /*cygwin_split_path(pathtot,path,optionfile);        a[i][j]=sum; 
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   /* cutv(path,optionfile,pathtot,'\\');*/          big=dum; 
           imax=i; 
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);        } 
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);      } 
   chdir(path);      if (j != imax) { 
   replace(pathc,path);        for (k=1;k<=n;k++) { 
           dum=a[imax][k]; 
 /*-------- arguments in the command line --------*/          a[imax][k]=a[j][k]; 
           a[j][k]=dum; 
   strcpy(fileres,"r");        } 
   strcat(fileres, optionfilefiname);        *d = -(*d); 
   strcat(fileres,".txt");    /* Other files have txt extension */        vv[imax]=vv[j]; 
       } 
   /*---------arguments file --------*/      indx[j]=imax; 
       if (a[j][j] == 0.0) a[j][j]=TINY; 
   if((ficpar=fopen(optionfile,"r"))==NULL)    {      if (j != n) { 
     printf("Problem with optionfile %s\n",optionfile);        dum=1.0/(a[j][j]); 
     goto end;        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   }      } 
     } 
   strcpy(filereso,"o");    free_vector(vv,1,n);  /* Doesn't work */
   strcat(filereso,fileres);  ;
   if((ficparo=fopen(filereso,"w"))==NULL) {  } 
     printf("Problem with Output resultfile: %s\n", filereso);goto end;  
   }  void lubksb(double **a, int n, int *indx, double b[]) 
   { 
   /* Reads comments: lines beginning with '#' */    int i,ii=0,ip,j; 
   while((c=getc(ficpar))=='#' && c!= EOF){    double sum; 
     ungetc(c,ficpar);   
     fgets(line, MAXLINE, ficpar);    for (i=1;i<=n;i++) { 
     puts(line);      ip=indx[i]; 
     fputs(line,ficparo);      sum=b[ip]; 
   }      b[ip]=b[i]; 
   ungetc(c,ficpar);      if (ii) 
         for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   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);      else if (sum) ii=i; 
   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);      b[i]=sum; 
   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);    } 
 while((c=getc(ficpar))=='#' && c!= EOF){    for (i=n;i>=1;i--) { 
     ungetc(c,ficpar);      sum=b[i]; 
     fgets(line, MAXLINE, ficpar);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     puts(line);      b[i]=sum/a[i][i]; 
     fputs(line,ficparo);    } 
   }  } 
   ungetc(c,ficpar);  
    void pstamp(FILE *fichier)
      {
   covar=matrix(0,NCOVMAX,1,n);    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   cptcovn=0;  }
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;  
   /************ Frequencies ********************/
   ncovmodel=2+cptcovn;  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[])
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */  {  /* Some frequencies */
      
   /* Read guess parameters */    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   /* Reads comments: lines beginning with '#' */    int first;
   while((c=getc(ficpar))=='#' && c!= EOF){    double ***freq; /* Frequencies */
     ungetc(c,ficpar);    double *pp, **prop;
     fgets(line, MAXLINE, ficpar);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     puts(line);    char fileresp[FILENAMELENGTH];
     fputs(line,ficparo);    
   }    pp=vector(1,nlstate);
   ungetc(c,ficpar);    prop=matrix(1,nlstate,iagemin,iagemax+3);
      strcpy(fileresp,"p");
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    strcat(fileresp,fileres);
     for(i=1; i <=nlstate; i++)    if((ficresp=fopen(fileresp,"w"))==NULL) {
     for(j=1; j <=nlstate+ndeath-1; j++){      printf("Problem with prevalence resultfile: %s\n", fileresp);
       fscanf(ficpar,"%1d%1d",&i1,&j1);      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficparo,"%1d%1d",i1,j1);      exit(0);
       printf("%1d%1d",i,j);    }
       for(k=1; k<=ncovmodel;k++){    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
         fscanf(ficpar," %lf",&param[i][j][k]);    j1=0;
         printf(" %lf",param[i][j][k]);    
         fprintf(ficparo," %lf",param[i][j][k]);    j=cptcoveff;
       }    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       fscanf(ficpar,"\n");  
       printf("\n");    first=1;
       fprintf(ficparo,"\n");  
     }    for(k1=1; k1<=j;k1++){
        for(i1=1; i1<=ncodemax[k1];i1++){
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;        j1++;
         /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
   p=param[1][1];          scanf("%d", i);*/
          for (i=-5; i<=nlstate+ndeath; i++)  
   /* Reads comments: lines beginning with '#' */          for (jk=-5; jk<=nlstate+ndeath; jk++)  
   while((c=getc(ficpar))=='#' && c!= EOF){            for(m=iagemin; m <= iagemax+3; m++)
     ungetc(c,ficpar);              freq[i][jk][m]=0;
     fgets(line, MAXLINE, ficpar);  
     puts(line);      for (i=1; i<=nlstate; i++)  
     fputs(line,ficparo);        for(m=iagemin; m <= iagemax+3; m++)
   }          prop[i][m]=0;
   ungetc(c,ficpar);        
         dateintsum=0;
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        k2cpt=0;
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */        for (i=1; i<=imx; i++) {
   for(i=1; i <=nlstate; i++){          bool=1;
     for(j=1; j <=nlstate+ndeath-1; j++){          if  (cptcovn>0) {
       fscanf(ficpar,"%1d%1d",&i1,&j1);            for (z1=1; z1<=cptcoveff; z1++) 
       printf("%1d%1d",i,j);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       fprintf(ficparo,"%1d%1d",i1,j1);                bool=0;
       for(k=1; k<=ncovmodel;k++){          }
         fscanf(ficpar,"%le",&delti3[i][j][k]);          if (bool==1){
         printf(" %le",delti3[i][j][k]);            for(m=firstpass; m<=lastpass; m++){
         fprintf(ficparo," %le",delti3[i][j][k]);              k2=anint[m][i]+(mint[m][i]/12.);
       }              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
       fscanf(ficpar,"\n");                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       printf("\n");                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       fprintf(ficparo,"\n");                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     }                if (m<lastpass) {
   }                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
   delti=delti3[1][1];                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
                  }
   /* Reads comments: lines beginning with '#' */                
   while((c=getc(ficpar))=='#' && c!= EOF){                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
     ungetc(c,ficpar);                  dateintsum=dateintsum+k2;
     fgets(line, MAXLINE, ficpar);                  k2cpt++;
     puts(line);                }
     fputs(line,ficparo);                /*}*/
   }            }
   ungetc(c,ficpar);          }
          }
   matcov=matrix(1,npar,1,npar);         
   for(i=1; i <=npar; i++){        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
     fscanf(ficpar,"%s",&str);        pstamp(ficresp);
     printf("%s",str);        if  (cptcovn>0) {
     fprintf(ficparo,"%s",str);          fprintf(ficresp, "\n#********** Variable "); 
     for(j=1; j <=i; j++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       fscanf(ficpar," %le",&matcov[i][j]);          fprintf(ficresp, "**********\n#");
       printf(" %.5le",matcov[i][j]);        }
       fprintf(ficparo," %.5le",matcov[i][j]);        for(i=1; i<=nlstate;i++) 
     }          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     fscanf(ficpar,"\n");        fprintf(ficresp, "\n");
     printf("\n");        
     fprintf(ficparo,"\n");        for(i=iagemin; i <= iagemax+3; i++){
   }          if(i==iagemax+3){
   for(i=1; i <=npar; i++)            fprintf(ficlog,"Total");
     for(j=i+1;j<=npar;j++)            fprintf(fichtm,"<br>Total<br>");
       matcov[i][j]=matcov[j][i];          }else{
                if(first==1){
   printf("\n");              first=0;
               printf("See log file for details...\n");
             }
     /*-------- data file ----------*/            fprintf(ficlog,"Age %d", i);
     if((ficres =fopen(fileres,"w"))==NULL) {          }
       printf("Problem with resultfile: %s\n", fileres);goto end;          for(jk=1; jk <=nlstate ; jk++){
     }            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     fprintf(ficres,"#%s\n",version);              pp[jk] += freq[jk][m][i]; 
              }
     if((fic=fopen(datafile,"r"))==NULL)    {          for(jk=1; jk <=nlstate ; jk++){
       printf("Problem with datafile: %s\n", datafile);goto end;            for(m=-1, pos=0; m <=0 ; m++)
     }              pos += freq[jk][m][i];
             if(pp[jk]>=1.e-10){
     n= lastobs;              if(first==1){
     severity = vector(1,maxwav);              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     outcome=imatrix(1,maxwav+1,1,n);              }
     num=ivector(1,n);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     moisnais=vector(1,n);            }else{
     annais=vector(1,n);              if(first==1)
     moisdc=vector(1,n);                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     andc=vector(1,n);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     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 */          for(jk=1; jk <=nlstate ; jk++){
     mint=matrix(1,maxwav,1,n);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     anint=matrix(1,maxwav,1,n);              pp[jk] += freq[jk][m][i];
     s=imatrix(1,maxwav+1,1,n);          }       
     adl=imatrix(1,maxwav+1,1,n);              for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
     tab=ivector(1,NCOVMAX);            pos += pp[jk];
     ncodemax=ivector(1,8);            posprop += prop[jk][i];
           }
     i=1;          for(jk=1; jk <=nlstate ; jk++){
     while (fgets(line, MAXLINE, fic) != NULL)    {            if(pos>=1.e-5){
       if ((i >= firstobs) && (i <=lastobs)) {              if(first==1)
                        printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
         for (j=maxwav;j>=1;j--){              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);            }else{
           strcpy(line,stra);              if(first==1)
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
         }            }
                    if( i <= iagemax){
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);              if(pos>=1.e-5){
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                 /*probs[i][jk][j1]= pp[jk]/pos;*/
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);              }
               else
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
         for (j=ncov;j>=1;j--){            }
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);          }
         }          
         num[i]=atol(stra);          for(jk=-1; jk <=nlstate+ndeath; jk++)
                    for(m=-1; m <=nlstate+ndeath; m++)
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){              if(freq[jk][m][i] !=0 ) {
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/              if(first==1)
                 printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
         i=i+1;                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
       }              }
     }          if(i <= iagemax)
     /* printf("ii=%d", ij);            fprintf(ficresp,"\n");
        scanf("%d",i);*/          if(first==1)
   imx=i-1; /* Number of individuals */            printf("Others in log...\n");
           fprintf(ficlog,"\n");
   /* 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;    dateintmean=dateintsum/k2cpt; 
     }   
     fclose(ficresp);
     for (i=1; i<=imx; i++)    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     if (covar[1][i]==0) 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]));*/    free_vector(pp,1,nlstate);
     free_matrix(prop,1,nlstate,iagemin, iagemax+3);
   /* Calculation of the number of parameter from char model*/    /* End of Freq */
   Tvar=ivector(1,15);  }
   Tprod=ivector(1,15);  
   Tvaraff=ivector(1,15);  /************ Prevalence ********************/
   Tvard=imatrix(1,15,1,2);  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)
   Tage=ivector(1,15);        {  
        /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
   if (strlen(model) >1){       in each health status at the date of interview (if between dateprev1 and dateprev2).
     j=0, j1=0, k1=1, k2=1;       We still use firstpass and lastpass as another selection.
     j=nbocc(model,'+');    */
     j1=nbocc(model,'*');   
     cptcovn=j+1;    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     cptcovprod=j1;    double ***freq; /* Frequencies */
        double *pp, **prop;
        double pos,posprop; 
     strcpy(modelsav,model);    double  y2; /* in fractional years */
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){    int iagemin, iagemax;
       printf("Error. Non available option model=%s ",model);  
       goto end;    iagemin= (int) agemin;
     }    iagemax= (int) agemax;
        /*pp=vector(1,nlstate);*/
     for(i=(j+1); i>=1;i--){    prop=matrix(1,nlstate,iagemin,iagemax+3); 
       cutv(stra,strb,modelsav,'+');    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);    j1=0;
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/    
       /*scanf("%d",i);*/    j=cptcoveff;
       if (strchr(strb,'*')) {    if (cptcovn<1) {j=1;ncodemax[1]=1;}
         cutv(strd,strc,strb,'*');    
         if (strcmp(strc,"age")==0) {    for(k1=1; k1<=j;k1++){
           cptcovprod--;      for(i1=1; i1<=ncodemax[k1];i1++){
           cutv(strb,stre,strd,'V');        j1++;
           Tvar[i]=atoi(stre);        
           cptcovage++;        for (i=1; i<=nlstate; i++)  
             Tage[cptcovage]=i;          for(m=iagemin; m <= iagemax+3; m++)
             /*printf("stre=%s ", stre);*/            prop[i][m]=0.0;
         }       
         else if (strcmp(strd,"age")==0) {        for (i=1; i<=imx; i++) { /* Each individual */
           cptcovprod--;          bool=1;
           cutv(strb,stre,strc,'V');          if  (cptcovn>0) {
           Tvar[i]=atoi(stre);            for (z1=1; z1<=cptcoveff; z1++) 
           cptcovage++;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
           Tage[cptcovage]=i;                bool=0;
         }          } 
         else {          if (bool==1) { 
           cutv(strb,stre,strc,'V');            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
           Tvar[i]=ncov+k1;              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
           cutv(strb,strc,strd,'V');              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
           Tprod[k1]=i;                if(agev[m][i]==0) agev[m][i]=iagemax+1;
           Tvard[k1][1]=atoi(strc);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
           Tvard[k1][2]=atoi(stre);                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); 
           Tvar[cptcovn+k2]=Tvard[k1][1];                if (s[m][i]>0 && s[m][i]<=nlstate) { 
           Tvar[cptcovn+k2+1]=Tvard[k1][2];                  /*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]]);*/
           for (k=1; k<=lastobs;k++)                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];                  prop[s[m][i]][iagemax+3] += weight[i]; 
           k1++;                } 
           k2=k2+2;              }
         }            } /* end selection of waves */
       }          }
       else {        }
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/        for(i=iagemin; i <= iagemax+3; i++){  
        /*  scanf("%d",i);*/          
       cutv(strd,strc,strb,'V');          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
       Tvar[i]=atoi(strc);            posprop += prop[jk][i]; 
       }          } 
       strcpy(modelsav,stra);    
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);          for(jk=1; jk <=nlstate ; jk++){     
         scanf("%d",i);*/            if( i <=  iagemax){ 
     }              if(posprop>=1.e-5){ 
 }                probs[i][jk][j1]= prop[jk][i]/posprop;
                } 
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);            } 
   printf("cptcovprod=%d ", cptcovprod);          }/* end jk */ 
   scanf("%d ",i);*/        }/* end i */ 
     fclose(fic);      } /* end i1 */
     } /* end k1 */
     /*  if(mle==1){*/    
     if (weightopt != 1) { /* Maximisation without weights*/    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
       for(i=1;i<=n;i++) weight[i]=1.0;    /*free_vector(pp,1,nlstate);*/
     }    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
     /*-calculation of age at interview from date of interview and age at death -*/  }  /* End of prevalence */
     agev=matrix(1,maxwav,1,imx);  
   /************* Waves Concatenation ***************/
    for (i=1; i<=imx; i++)  
      for(m=2; (m<= maxwav); m++)  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)
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){  {
          anint[m][i]=9999;    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
          s[m][i]=-1;       Death is a valid wave (if date is known).
        }       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
           dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
     for (i=1; i<=imx; i++)  {       and mw[mi+1][i]. dh depends on stepm.
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);       */
       for(m=1; (m<= maxwav); m++){  
         if(s[m][i] >0){    int i, mi, m;
           if (s[m][i] == nlstate+1) {    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
             if(agedc[i]>0)       double sum=0., jmean=0.;*/
               if(moisdc[i]!=99 && andc[i]!=9999)    int first;
               agev[m][i]=agedc[i];    int j, k=0,jk, ju, jl;
             else {    double sum=0.;
               if (andc[i]!=9999){    first=0;
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    jmin=1e+5;
               agev[m][i]=-1;    jmax=-1;
               }    jmean=0.;
             }    for(i=1; i<=imx; i++){
           }      mi=0;
           else if(s[m][i] !=9){ /* Should no more exist */      m=firstpass;
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);      while(s[m][i] <= nlstate){
             if(mint[m][i]==99 || anint[m][i]==9999)        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
               agev[m][i]=1;          mw[++mi][i]=m;
             else if(agev[m][i] <agemin){        if(m >=lastpass)
               agemin=agev[m][i];          break;
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/        else
             }          m++;
             else if(agev[m][i] >agemax){      }/* end while */
               agemax=agev[m][i];      if (s[m][i] > nlstate){
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/        mi++;     /* Death is another wave */
             }        /* if(mi==0)  never been interviewed correctly before death */
             /*agev[m][i]=anint[m][i]-annais[i];*/           /* Only death is a correct wave */
             /*   agev[m][i] = age[i]+2*m;*/        mw[mi][i]=m;
           }      }
           else { /* =9 */  
             agev[m][i]=1;      wav[i]=mi;
             s[m][i]=-1;      if(mi==0){
           }        nbwarn++;
         }        if(first==0){
         else /*= 0 Unknown */          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
           agev[m][i]=1;          first=1;
       }        }
            if(first==1){
     }          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
     for (i=1; i<=imx; i++)  {        }
       for(m=1; (m<= maxwav); m++){      } /* end mi==0 */
         if (s[m][i] > (nlstate+ndeath)) {    } /* End individuals */
           printf("Error: Wrong value in nlstate or ndeath\n");    
           goto end;    for(i=1; i<=imx; i++){
         }      for(mi=1; mi<wav[i];mi++){
       }        if (stepm <=0)
     }          dh[mi][i]=1;
         else{
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
             if (agedc[i] < 2*AGESUP) {
     free_vector(severity,1,maxwav);              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     free_imatrix(outcome,1,maxwav+1,1,n);              if(j==0) j=1;  /* Survives at least one month after exam */
     free_vector(moisnais,1,n);              else if(j<0){
     free_vector(annais,1,n);                nberr++;
     /* free_matrix(mint,1,maxwav,1,n);                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]);
        free_matrix(anint,1,maxwav,1,n);*/                j=1; /* Temporary Dangerous patch */
     free_vector(moisdc,1,n);                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);
     free_vector(andc,1,n);                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(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);
                  }
     wav=ivector(1,imx);              k=k+1;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);              if (j >= jmax){
     mw=imatrix(1,lastpass-firstpass+1,1,imx);                jmax=j;
                    ijmax=i;
     /* Concatenates waves */              }
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);              if (j <= jmin){
                 jmin=j;
                 ijmin=i;
       Tcode=ivector(1,100);              }
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);              sum=sum+j;
       ncodemax[1]=1;              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
                  }
    codtab=imatrix(1,100,1,10);          }
    h=0;          else{
    m=pow(2,cptcoveff);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
    /*        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]); */
    for(k=1;k<=cptcoveff; k++){  
      for(i=1; i <=(m/pow(2,k));i++){            k=k+1;
        for(j=1; j <= ncodemax[k]; j++){            if (j >= jmax) {
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){              jmax=j;
            h++;              ijmax=i;
            if (h>m) h=1;codtab[h][k]=j;            }
          }            else if (j <= jmin){
        }              jmin=j;
      }              ijmin=i;
    }            }
             /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
    /*for(i=1; i <=m ;i++){            if(j<0){
      for(k=1; k <=cptcovn; k++){              nberr++;
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
      }              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
      printf("\n");            }
    }            sum=sum+j;
    scanf("%d",i);*/          }
              jk= j/stepm;
    /* Calculates basic frequencies. Computes observed prevalence at single age          jl= j -jk*stepm;
        and prints on file fileres'p'. */          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;
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              bh[mi][i]=0;
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            }else{ /* We want a negative bias in order to only have interpolation ie
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    * at the price of an extra matrix product in likelihood */
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              dh[mi][i]=jk+1;
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */              bh[mi][i]=ju;
                  }
     /* For Powell, parameters are in a vector p[] starting at p[1]          }else{
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */            if(jl <= -ju){
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */              dh[mi][i]=jk;
               bh[mi][i]=jl;       /* bias is positive if real duration
     if(mle==1){                                   * is higher than the multiple of stepm and negative otherwise.
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);                                   */
     }            }
                else{
     /*--------- results files --------------*/              dh[mi][i]=jk+1;
     fprintf(ficres,"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);              bh[mi][i]=ju;
              }
             if(dh[mi][i]==0){
    jk=1;              dh[mi][i]=1; /* At least one step */
    fprintf(ficres,"# Parameters\n");              bh[mi][i]=ju; /* At least one step */
    printf("# Parameters\n");              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
    for(i=1,jk=1; i <=nlstate; i++){            }
      for(k=1; k <=(nlstate+ndeath); k++){          } /* end if mle */
        if (k != i)        }
          {      } /* end wave */
            printf("%d%d ",i,k);    }
            fprintf(ficres,"%1d%1d ",i,k);    jmean=sum/k;
            for(j=1; j <=ncovmodel; j++){    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);
              printf("%f ",p[jk]);    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
              fprintf(ficres,"%f ",p[jk]);   }
              jk++;  
            }  /*********** Tricode ****************************/
            printf("\n");  void tricode(int *Tvar, int **nbcode, int imx)
            fprintf(ficres,"\n");  {
          }    
      }    int Ndum[20],ij=1, k, j, i, maxncov=19;
    }    int cptcode=0;
  if(mle==1){    cptcoveff=0; 
     /* Computing hessian and covariance matrix */   
     ftolhess=ftol; /* Usually correct */    for (k=0; k<maxncov; k++) Ndum[k]=0;
     hesscov(matcov, p, npar, delti, ftolhess, func);    for (k=1; k<=7; k++) ncodemax[k]=0;
  }  
     fprintf(ficres,"# Scales\n");    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
     printf("# Scales\n");      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
      for(i=1,jk=1; i <=nlstate; i++){                                 modality*/ 
       for(j=1; j <=nlstate+ndeath; j++){        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
         if (j!=i) {        Ndum[ij]++; /*store the modality */
           fprintf(ficres,"%1d%1d",i,j);        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
           printf("%1d%1d",i,j);        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
           for(k=1; k<=ncovmodel;k++){                                         Tvar[j]. If V=sex and male is 0 and 
             printf(" %.5e",delti[jk]);                                         female is 1, then  cptcode=1.*/
             fprintf(ficres," %.5e",delti[jk]);      }
             jk++;  
           }      for (i=0; i<=cptcode; i++) {
           printf("\n");        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 */
           fprintf(ficres,"\n");      }
         }  
       }      ij=1; 
      }      for (i=1; i<=ncodemax[j]; i++) {
            for (k=0; k<= maxncov; k++) {
     k=1;          if (Ndum[k] != 0) {
     fprintf(ficres,"# Covariance\n");            nbcode[Tvar[j]][ij]=k; 
     printf("# Covariance\n");            /* 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; */
     for(i=1;i<=npar;i++){            
       /*  if (k>nlstate) k=1;            ij++;
       i1=(i-1)/(ncovmodel*nlstate)+1;          }
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);          if (ij > ncodemax[j]) break; 
       printf("%s%d%d",alph[k],i1,tab[i]);*/        }  
       fprintf(ficres,"%3d",i);      } 
       printf("%3d",i);    }  
       for(j=1; j<=i;j++){  
         fprintf(ficres," %.5e",matcov[i][j]);   for (k=0; k< maxncov; k++) Ndum[k]=0;
         printf(" %.5e",matcov[i][j]);  
       }   for (i=1; i<=ncovmodel-2; i++) { 
       fprintf(ficres,"\n");     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
       printf("\n");     ij=Tvar[i];
       k++;     Ndum[ij]++;
     }   }
      
     while((c=getc(ficpar))=='#' && c!= EOF){   ij=1;
       ungetc(c,ficpar);   for (i=1; i<= maxncov; i++) {
       fgets(line, MAXLINE, ficpar);     if((Ndum[i]!=0) && (i<=ncovcol)){
       puts(line);       Tvaraff[ij]=i; /*For printing */
       fputs(line,ficparo);       ij++;
     }     }
     ungetc(c,ficpar);   }
     
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);   cptcoveff=ij-1; /*Number of simple covariates*/
      }
     if (fage <= 2) {  
       bage = agemin;  /*********** Health Expectancies ****************/
       fage = agemax;  
     }  void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,char strstart[] )
      
     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);    /* Health expectancies, no variances */
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
      double age, agelim, hf;
     while((c=getc(ficpar))=='#' && c!= EOF){    double ***p3mat;
     ungetc(c,ficpar);    double eip;
     fgets(line, MAXLINE, ficpar);  
     puts(line);    pstamp(ficreseij);
     fputs(line,ficparo);    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
   }    fprintf(ficreseij,"# Age");
   ungetc(c,ficpar);    for(i=1; i<=nlstate;i++){
        for(j=1; j<=nlstate;j++){
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mob_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);        fprintf(ficreseij," e%1d%1d ",i,j);
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);      }
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);      fprintf(ficreseij," e%1d. ",i);
          }
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficreseij,"\n");
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    
     puts(line);    if(estepm < stepm){
     fputs(line,ficparo);      printf ("Problem %d lower than %d\n",estepm, stepm);
   }    }
   ungetc(c,ficpar);    else  hstepm=estepm;   
      /* We compute the life expectancy from trapezoids spaced every estepm months
      * This is mainly to measure the difference between two models: for example
    dateprev1=anprev1+mprev1/12.+jprev1/365.;     * if stepm=24 months pijx are given only every 2 years and by summing them
    dateprev2=anprev2+mprev2/12.+jprev2/365.;     * we are calculating an estimate of the Life Expectancy assuming a linear 
      * progression in between and thus overestimating or underestimating according
   fscanf(ficpar,"pop_based=%d\n",&popbased);     * to the curvature of the survival function. If, for the same date, we 
    fprintf(ficparo,"pop_based=%d\n",popbased);       * estimate the model with stepm=1 month, we can keep estepm to 24 months
    fprintf(ficres,"pop_based=%d\n",popbased);       * to compare the new estimate of Life expectancy with the same linear 
      * hypothesis. A more precise result, taking into account a more precise
   while((c=getc(ficpar))=='#' && c!= EOF){     * curvature will be obtained if estepm is as small as stepm. */
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);    /* For example we decided to compute the life expectancy with the smallest unit */
     puts(line);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
     fputs(line,ficparo);       nhstepm is the number of hstepm from age to agelim 
   }       nstepm is the number of stepm from age to agelin. 
   ungetc(c,ficpar);       Look at hpijx to understand the reason of that which relies in memory size
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);       and note for a fixed period like estepm months */
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);       survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);       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.
        */
     /*------------ gnuplot -------------*/    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     /*chdir(pathcd);*/  
     strcpy(optionfilegnuplot,optionfilefiname);    agelim=AGESUP;
     strcat(optionfilegnuplot,".plt");    /* nhstepm age range expressed in number of stepm */
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {    nstepm=(int) rint((agelim-age)*YEARM/stepm); 
       printf("Problem with file %s",optionfilegnuplot);goto end;    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     }    /* if (stepm >= YEARM) hstepm=1;*/
 #ifdef windows    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     fprintf(ficgp,"cd \"%s\" \n",pathc);    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 #endif  
 m=pow(2,cptcoveff);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
        /* Computed by stepm unit matrices, product of hstepm matrices, stored
  /* 1eme*/         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   for (cpt=1; cpt<= nlstate ; cpt ++) {      
    for (k1=1; k1<= m ; k1 ++) {      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       
 #ifdef windows      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);      
 #endif      printf("%d|",(int)age);fflush(stdout);
 #ifdef unix      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);      
 #endif      /* Computing expectancies */
       for(i=1; i<=nlstate;i++)
 for (i=1; i<= nlstate ; i ++) {        for(j=1; j<=nlstate;j++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
 }            
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);            /* 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]);*/
     for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          }
   else fprintf(ficgp," \%%*lf (\%%*lf)");  
 }      fprintf(ficreseij,"%3.0f",age );
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);      for(i=1; i<=nlstate;i++){
      for (i=1; i<= nlstate ; i ++) {        eip=0;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        for(j=1; j<=nlstate;j++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");          eip +=eij[i][j][(int)age];
 }            fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));        }
 #ifdef unix        fprintf(ficreseij,"%9.4f", eip );
 fprintf(ficgp,"\nset ter gif small size 400,300");      }
 #endif      fprintf(ficreseij,"\n");
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      
    }    }
   }    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   /*2 eme*/    printf("\n");
     fprintf(ficlog,"\n");
   for (k1=1; k1<= m ; k1 ++) {    
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);  }
      
     for (i=1; i<= nlstate+1 ; i ++) {  void cvevsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
       k=2*i;  
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);  {
       for (j=1; j<= nlstate+1 ; j ++) {    /* Covariances of health expectancies eij and of total life expectancies according
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");     to initial status i, ei. .
   else fprintf(ficgp," \%%*lf (\%%*lf)");    */
 }      int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    double age, agelim, hf;
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    double ***p3matp, ***p3matm, ***varhe;
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    double **dnewm,**doldm;
       for (j=1; j<= nlstate+1 ; j ++) {    double *xp, *xm;
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    double **gp, **gm;
         else fprintf(ficgp," \%%*lf (\%%*lf)");    double ***gradg, ***trgradg;
 }      int theta;
       fprintf(ficgp,"\" t\"\" w l 0,");  
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    double eip, vip;
       for (j=1; j<= nlstate+1 ; j ++) {  
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   else fprintf(ficgp," \%%*lf (\%%*lf)");    xp=vector(1,npar);
 }      xm=vector(1,npar);
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    dnewm=matrix(1,nlstate*nlstate,1,npar);
       else fprintf(ficgp,"\" t\"\" w l 0,");    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
     }    
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    pstamp(ficresstdeij);
   }    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
      fprintf(ficresstdeij,"# Age");
   /*3eme*/    for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++)
   for (k1=1; k1<= m ; k1 ++) {        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
     for (cpt=1; cpt<= nlstate ; cpt ++) {      fprintf(ficresstdeij," e%1d. ",i);
       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);    fprintf(ficresstdeij,"\n");
       for (i=1; i< nlstate ; i ++) {  
         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);    pstamp(ficrescveij);
       }    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);    fprintf(ficrescveij,"# Age");
     }    for(i=1; i<=nlstate;i++)
   }      for(j=1; j<=nlstate;j++){
          cptj= (j-1)*nlstate+i;
   /* CV preval stat */        for(i2=1; i2<=nlstate;i2++)
   for (k1=1; k1<= m ; k1 ++) {          for(j2=1; j2<=nlstate;j2++){
     for (cpt=1; cpt<nlstate ; cpt ++) {            cptj2= (j2-1)*nlstate+i2;
       k=3;            if(cptj2 <= cptj)
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
       for (i=1; i< nlstate ; i ++)          }
         fprintf(ficgp,"+$%d",k+i+1);      }
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);    fprintf(ficrescveij,"\n");
          
       l=3+(nlstate+ndeath)*cpt;    if(estepm < stepm){
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);      printf ("Problem %d lower than %d\n",estepm, stepm);
       for (i=1; i< nlstate ; i ++) {    }
         l=3+(nlstate+ndeath)*cpt;    else  hstepm=estepm;   
         fprintf(ficgp,"+$%d",l+i+1);    /* We compute the life expectancy from trapezoids spaced every estepm months
       }     * This is mainly to measure the difference between two models: for example
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);       * if stepm=24 months pijx are given only every 2 years and by summing them
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);     * we are calculating an estimate of the Life Expectancy assuming a linear 
     }     * progression in between and thus overestimating or underestimating according
   }       * to the curvature of the survival function. If, for the same date, we 
      * estimate the model with stepm=1 month, we can keep estepm to 24 months
   /* proba elementaires */     * to compare the new estimate of Life expectancy with the same linear 
    for(i=1,jk=1; i <=nlstate; i++){     * hypothesis. A more precise result, taking into account a more precise
     for(k=1; k <=(nlstate+ndeath); k++){     * curvature will be obtained if estepm is as small as stepm. */
       if (k != i) {  
         for(j=1; j <=ncovmodel; j++){    /* For example we decided to compute the life expectancy with the smallest unit */
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           /*fprintf(ficgp,"%s",alph[1]);*/       nhstepm is the number of hstepm from age to agelim 
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);       nstepm is the number of stepm from age to agelin. 
           jk++;       Look at hpijx to understand the reason of that which relies in memory size
           fprintf(ficgp,"\n");       and note for a fixed period like estepm months */
         }    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       }       survival function given by stepm (the optimization length). Unfortunately it
     }       means that if the survival funtion is printed only each two years of age and if
     }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
   for(jk=1; jk <=m; jk++) {    */
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
    i=1;  
    for(k2=1; k2<=nlstate; k2++) {    /* If stepm=6 months */
      k3=i;    /* nhstepm age range expressed in number of stepm */
      for(k=1; k<=(nlstate+ndeath); k++) {    agelim=AGESUP;
        if (k != k2){    nstepm=(int) rint((agelim-age)*YEARM/stepm); 
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
 ij=1;    /* if (stepm >= YEARM) hstepm=1;*/
         for(j=3; j <=ncovmodel; j++) {    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
           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]]]);    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             ij++;    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
           else    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);    gp=matrix(0,nhstepm,1,nlstate*nlstate);
         }    gm=matrix(0,nhstepm,1,nlstate*nlstate);
           fprintf(ficgp,")/(1");  
            for (age=bage; age<=fage; age ++){ 
         for(k1=1; k1 <=nlstate; k1++){    
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);      /* Computed by stepm unit matrices, product of hstepm matrices, stored
 ij=1;         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
           for(j=3; j <=ncovmodel; j++){   
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  
             ij++;      /* Computing  Variances of health expectancies */
           }      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
           else         decrease memory allocation */
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      for(theta=1; theta <=npar; theta++){
           }        for(i=1; i<=npar; i++){ 
           fprintf(ficgp,")");          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }          xm[i] = x[i] - (i==theta ?delti[theta]:0);
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);        }
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
         i=i+ncovmodel;        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
        }    
      }        for(j=1; j<= nlstate; j++){
    }          for(i=1; i<=nlstate; i++){
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);            for(h=0; h<=nhstepm-1; h++){
   }              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
                  gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
   fclose(ficgp);            }
   /* end gnuplot */          }
            }
 chdir(path);       
            for(ij=1; ij<= nlstate*nlstate; ij++)
     free_ivector(wav,1,imx);          for(h=0; h<=nhstepm-1; h++){
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);            }
     free_ivector(num,1,n);      }/* End theta */
     free_vector(agedc,1,n);      
     /*free_matrix(covar,1,NCOVMAX,1,n);*/      
     fclose(ficparo);      for(h=0; h<=nhstepm-1; h++)
     fclose(ficres);        for(j=1; j<=nlstate*nlstate;j++)
     /*  }*/          for(theta=1; theta <=npar; theta++)
                trgradg[h][j][theta]=gradg[h][theta][j];
    /*________fin mle=1_________*/      
      
        for(ij=1;ij<=nlstate*nlstate;ij++)
          for(ji=1;ji<=nlstate*nlstate;ji++)
     /* No more information from the sample is required now */          varhe[ij][ji][(int)age] =0.;
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){       printf("%d|",(int)age);fflush(stdout);
     ungetc(c,ficpar);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
     fgets(line, MAXLINE, ficpar);       for(h=0;h<=nhstepm-1;h++){
     puts(line);        for(k=0;k<=nhstepm-1;k++){
     fputs(line,ficparo);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
   }          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   ungetc(c,ficpar);          for(ij=1;ij<=nlstate*nlstate;ij++)
              for(ji=1;ji<=nlstate*nlstate;ji++)
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);        }
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);      }
 /*--------- index.htm --------*/      /* Computing expectancies */
       hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   strcpy(optionfilehtm,optionfile);      for(i=1; i<=nlstate;i++)
   strcat(optionfilehtm,".htm");        for(j=1; j<=nlstate;j++)
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     printf("Problem with %s \n",optionfilehtm);goto end;            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
   }            
             /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">  
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>          }
 Total number of observations=%d <br>  
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>      fprintf(ficresstdeij,"%3.0f",age );
 <hr  size=\"2\" color=\"#EC5E5E\">      for(i=1; i<=nlstate;i++){
 <li>Outputs files<br><br>\n        eip=0.;
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n        vip=0.;
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>        for(j=1; j<=nlstate;j++){
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>          eip += eij[i][j][(int)age];
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>        }
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>      }
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>      fprintf(ficresstdeij,"\n");
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);  
       fprintf(ficrescveij,"%3.0f",age );
  fprintf(fichtm," <li>Graphs</li><p>");      for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
  m=cptcoveff;          cptj= (j-1)*nlstate+i;
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}          for(i2=1; i2<=nlstate;i2++)
             for(j2=1; j2<=nlstate;j2++){
  j1=0;              cptj2= (j2-1)*nlstate+i2;
  for(k1=1; k1<=m;k1++){              if(cptj2 <= cptj)
    for(i1=1; i1<=ncodemax[k1];i1++){                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
        j1++;            }
        if (cptcovn > 0) {        }
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");      fprintf(ficrescveij,"\n");
          for (cpt=1; cpt<=cptcoveff;cpt++)     
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);    }
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
        }    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);        free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
        for(cpt=1; cpt<nlstate;cpt++){    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    printf("\n");
        }    fprintf(ficlog,"\n");
     for(cpt=1; cpt<=nlstate;cpt++) {  
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident    free_vector(xm,1,npar);
 interval) in state (%d): v%s%d%d.gif <br>    free_vector(xp,1,npar);
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      free_matrix(dnewm,1,nlstate*nlstate,1,npar);
      }    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
      for(cpt=1; cpt<=nlstate;cpt++) {    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>  }
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);  
      }  /************ Variance ******************/
      fprintf(fichtm,"\n<br>- Total life expectancy by age and  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[])
 health expectancies in states (1) and (2): e%s%d.gif<br>  {
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);    /* Variance of health expectancies */
 fprintf(fichtm,"\n</body>");    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
    }    /* double **newm;*/
  }    double **dnewm,**doldm;
 fclose(fichtm);    double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
   /*--------------- Prevalence limit --------------*/    int k, cptcode;
      double *xp;
   strcpy(filerespl,"pl");    double **gp, **gm;  /* for var eij */
   strcat(filerespl,fileres);    double ***gradg, ***trgradg; /*for var eij */
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    double **gradgp, **trgradgp; /* for var p point j */
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    double *gpp, *gmp; /* for var p point j */
   }    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    double ***p3mat;
   fprintf(ficrespl,"#Prevalence limit\n");    double age,agelim, hf;
   fprintf(ficrespl,"#Age ");    double ***mobaverage;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    int theta;
   fprintf(ficrespl,"\n");    char digit[4];
      char digitp[25];
   prlim=matrix(1,nlstate,1,nlstate);  
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    char fileresprobmorprev[FILENAMELENGTH];
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    if(popbased==1){
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      if(mobilav!=0)
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        strcpy(digitp,"-populbased-mobilav-");
   k=0;      else strcpy(digitp,"-populbased-nomobil-");
   agebase=agemin;    }
   agelim=agemax;    else 
   ftolpl=1.e-10;      strcpy(digitp,"-stablbased-");
   i1=cptcoveff;  
   if (cptcovn < 1){i1=1;}    if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   for(cptcov=1;cptcov<=i1;cptcov++){      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         k=k+1;        printf(" Error in movingaverage mobilav=%d\n",mobilav);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/      }
         fprintf(ficrespl,"\n#******");    }
         for(j=1;j<=cptcoveff;j++)  
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    strcpy(fileresprobmorprev,"prmorprev"); 
         fprintf(ficrespl,"******\n");    sprintf(digit,"%-d",ij);
            /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
         for (age=agebase; age<=agelim; age++){    strcat(fileresprobmorprev,digit); /* Tvar to be done */
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
           fprintf(ficrespl,"%.0f",age );    strcat(fileresprobmorprev,fileres);
           for(i=1; i<=nlstate;i++)    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
           fprintf(ficrespl," %.5f", prlim[i][i]);      printf("Problem with resultfile: %s\n", fileresprobmorprev);
           fprintf(ficrespl,"\n");      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
         }    }
       }    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     }   
   fclose(ficrespl);    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     pstamp(ficresprobmorprev);
   /*------------- h Pij x at various ages ------------*/    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);
      fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   if((ficrespij=fopen(filerespij,"w"))==NULL) {      fprintf(ficresprobmorprev," p.%-d SE",j);
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;      for(i=1; i<=nlstate;i++)
   }        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   printf("Computing pij: result on file '%s' \n", filerespij);    }  
      fprintf(ficresprobmorprev,"\n");
   stepsize=(int) (stepm+YEARM-1)/YEARM;    fprintf(ficgp,"\n# Routine varevsij");
   /*if (stepm<=24) stepsize=2;*/    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     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");
   agelim=AGESUP;    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   hstepm=stepsize*YEARM; /* Every year of age */  /*   } */
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
      pstamp(ficresvij);
   k=0;    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
   for(cptcov=1;cptcov<=i1;cptcov++){    if(popbased==1)
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
       k=k+1;    else
         fprintf(ficrespij,"\n#****** ");      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
         for(j=1;j<=cptcoveff;j++)    fprintf(ficresvij,"# Age");
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    for(i=1; i<=nlstate;i++)
         fprintf(ficrespij,"******\n");      for(j=1; j<=nlstate;j++)
                fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    fprintf(ficresvij,"\n");
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    xp=vector(1,npar);
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    dnewm=matrix(1,nlstate,1,npar);
           oldm=oldms;savm=savms;    doldm=matrix(1,nlstate,1,nlstate);
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);      dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
           fprintf(ficrespij,"# Age");    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           for(i=1; i<=nlstate;i++)  
             for(j=1; j<=nlstate+ndeath;j++)    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
               fprintf(ficrespij," %1d-%1d",i,j);    gpp=vector(nlstate+1,nlstate+ndeath);
           fprintf(ficrespij,"\n");    gmp=vector(nlstate+1,nlstate+ndeath);
           for (h=0; h<=nhstepm; h++){    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    
             for(i=1; i<=nlstate;i++)    if(estepm < stepm){
               for(j=1; j<=nlstate+ndeath;j++)      printf ("Problem %d lower than %d\n",estepm, stepm);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    }
             fprintf(ficrespij,"\n");    else  hstepm=estepm;   
           }    /* For example we decided to compute the life expectancy with the smallest unit */
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           fprintf(ficrespij,"\n");       nhstepm is the number of hstepm from age to agelim 
         }       nstepm is the number of stepm from age to agelin. 
     }       Look at hpijx to understand the reason of that which relies in memory size
   }       and note for a fixed period like k years */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/       survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed every two years of age and if
   fclose(ficrespij);       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.
   if(stepm == 1) {    */
   /*---------- Forecasting ------------------*/    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   /*printf("calage= %f", calagedate);*/      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
        nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
   strcpy(fileresf,"f");      gm=matrix(0,nhstepm,1,nlstate);
   strcat(fileresf,fileres);  
   if((ficresf=fopen(fileresf,"w"))==NULL) {  
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;      for(theta=1; theta <=npar; theta++){
   }        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   printf("Computing forecasting: result on file '%s' \n", fileresf);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
   free_matrix(mint,1,maxwav,1,n);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   free_matrix(anint,1,maxwav,1,n);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   free_matrix(agev,1,maxwav,1,imx);  
   /* Mobile average */        if (popbased==1) {
           if(mobilav ==0){
   if (cptcoveff==0) ncodemax[cptcoveff]=1;            for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
   if (mobilav==1) {          }else{ /* mobilav */ 
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            for(i=1; i<=nlstate;i++)
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)              prlim[i][i]=mobaverage[(int)age][i][ij];
       for (i=1; i<=nlstate;i++)          }
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)        }
           mobaverage[(int)agedeb][i][cptcod]=0.;    
            for(j=1; j<= nlstate; j++){
     for (agedeb=bage+4; agedeb<=fage; agedeb++){          for(h=0; h<=nhstepm; h++){
       for (i=1; i<=nlstate;i++){            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           for (cpt=0;cpt<=4;cpt++){          }
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];        }
           }        /* This for computing probability of death (h=1 means
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;           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];
   stepsize=(int) (stepm+YEARM-1)/YEARM;        }    
   if (stepm<=12) stepsize=1;        /* end probability of death */
   
   agelim=AGESUP;        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
   /*hstepm=stepsize*YEARM; *//* Every year of age */          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   hstepm=1;        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   yp1=modf(dateintmean,&yp);   
   anprojmean=yp;        if (popbased==1) {
   yp2=modf((yp1*12),&yp);          if(mobilav ==0){
   mprojmean=yp;            for(i=1; i<=nlstate;i++)
   yp1=modf((yp2*30.5),&yp);              prlim[i][i]=probs[(int)age][i][ij];
   jprojmean=yp;          }else{ /* mobilav */ 
   if(jprojmean==0) jprojmean=1;            for(i=1; i<=nlstate;i++)
   if(mprojmean==0) jprojmean=1;              prlim[i][i]=mobaverage[(int)age][i][ij];
           }
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);        }
   
   if (popforecast==1) {        for(j=1; j<= nlstate; j++){
     if((ficpop=fopen(popfile,"r"))==NULL)    {          for(h=0; h<=nhstepm; h++){
       printf("Problem with population file : %s\n",popfile);goto end;            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
     }              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
     popage=ivector(0,AGESUP);          }
     popeffectif=vector(0,AGESUP);        }
     popcount=vector(0,AGESUP);        /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
     i=1;             as a weighted average of prlim.
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)        */
       {        for(j=nlstate+1;j<=nlstate+ndeath;j++){
         i=i+1;          for(i=1,gmp[j]=0.; i<= nlstate; i++)
       }           gmp[j] += prlim[i][i]*p3mat[i][j][1];
     imx=i;        }    
            /* end probability of death */
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];  
   }        for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
   for(cptcov=1;cptcov<=i1;cptcov++){            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          }
       k=k+1;  
       fprintf(ficresf,"\n#******");        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
       for(j=1;j<=cptcoveff;j++) {          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        }
       }  
       fprintf(ficresf,"******\n");      } /* End theta */
       fprintf(ficresf,"# StartingAge FinalAge");  
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
       if (popforecast==1)  fprintf(ficresf," [Population]");  
          for(h=0; h<=nhstepm; h++) /* veij */
       for (cpt=0; cpt<4;cpt++) {        for(j=1; j<=nlstate;j++)
         fprintf(ficresf,"\n");          for(theta=1; theta <=npar; theta++)
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);              trgradg[h][j][theta]=gradg[h][theta][j];
   
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(bage-((int)calagedate %12)/12.); agedeb--){ /* If stepm=6 months */      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);        for(theta=1; theta <=npar; theta++)
         nhstepm = nhstepm/hstepm;          trgradgp[j][theta]=gradgp[theta][j];
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/    
   
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         oldm=oldms;savm=savms;      for(i=1;i<=nlstate;i++)
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          for(j=1;j<=nlstate;j++)
                  vareij[i][j][(int)age] =0.;
         for (h=0; h<=nhstepm; h++){  
           if (h==(int) (calagedate+YEARM*cpt)) {      for(h=0;h<=nhstepm;h++){
             fprintf(ficresf,"\n %.f ",agedeb+h*hstepm/YEARM*stepm);        for(k=0;k<=nhstepm;k++){
           }          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           for(j=1; j<=nlstate+ndeath;j++) {          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
             kk1=0.;kk2=0;          for(i=1;i<=nlstate;i++)
             for(i=1; i<=nlstate;i++) {                    for(j=1;j<=nlstate;j++)
               if (mobilav==1)              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
                 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];    
                 /* fprintf(ficresf," p3=%.3f p=%.3f ", p3mat[i][j][h], probs[(int)(agedeb)+1][i][cptcod]);*/      /* 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);
               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];      for(j=nlstate+1;j<=nlstate+ndeath;j++)
             }        for(i=nlstate+1;i<=nlstate+ndeath;i++)
                    varppt[j][i]=doldmp[j][i];
             if (h==(int)(calagedate+12*cpt)){      /* end ppptj */
               fprintf(ficresf," %.3f", kk1);      /*  x centered again */
                    hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
             }   
           }      if (popbased==1) {
         }        if(mobilav ==0){
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          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];
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);        }
   if (popforecast==1) {      }
     free_ivector(popage,0,AGESUP);               
     free_vector(popeffectif,0,AGESUP);      /* This for computing probability of death (h=1 means
     free_vector(popcount,0,AGESUP);         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
   }         as a weighted average of prlim.
   free_imatrix(s,1,maxwav+1,1,n);      */
   free_vector(weight,1,n);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
   fclose(ficresf);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   }/* End forecasting */          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   else{      }    
     erreur=108;      /* end probability of death */
     printf("Error %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d\n", erreur, stepm);  
   }      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   /*---------- Health expectancies and variances ------------*/        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
   strcpy(filerest,"t");          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   strcat(filerest,fileres);        }
   if((ficrest=fopen(filerest,"w"))==NULL) {      } 
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;      fprintf(ficresprobmorprev,"\n");
   }  
   printf("Computing Total LEs with variances: file '%s' \n", filerest);      fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
   strcpy(filerese,"e");          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
   strcat(filerese,fileres);        }
   if((ficreseij=fopen(filerese,"w"))==NULL) {      fprintf(ficresvij,"\n");
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);      free_matrix(gp,0,nhstepm,1,nlstate);
   }      free_matrix(gm,0,nhstepm,1,nlstate);
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
  strcpy(fileresv,"v");      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   strcat(fileresv,fileres);    } /* End age */
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    free_vector(gpp,nlstate+1,nlstate+ndeath);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    free_vector(gmp,nlstate+1,nlstate+ndeath);
   }    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    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");
   k=0;    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
   for(cptcov=1;cptcov<=i1;cptcov++){    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
       k=k+1;  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
       fprintf(ficrest,"\n#****** ");  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
       for(j=1;j<=cptcoveff;j++)    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
       fprintf(ficrest,"******\n");    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(ficreseij,"\n#****** ");    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);
       for(j=1;j<=cptcoveff;j++)    /*  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(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);  */
       fprintf(ficreseij,"******\n");  /*   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);
       fprintf(ficresvij,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)    free_vector(xp,1,npar);
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    free_matrix(doldm,1,nlstate,1,nlstate);
       fprintf(ficresvij,"******\n");    free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
       oldm=oldms;savm=savms;    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);      if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    fclose(ficresprobmorprev);
       oldm=oldms;savm=savms;    fflush(ficgp);
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    fflush(fichtm); 
        }  /* end varevsij */
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");  
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);  /************ Variance of prevlim ******************/
       fprintf(ficrest,"\n");  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[])
          {
       hf=1;    /* Variance of prevalence limit */
       if (stepm >= YEARM) hf=stepm/YEARM;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
       epj=vector(1,nlstate+1);    double **newm;
       for(age=bage; age <=fage ;age++){    double **dnewm,**doldm;
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    int i, j, nhstepm, hstepm;
         if (popbased==1) {    int k, cptcode;
           for(i=1; i<=nlstate;i++)    double *xp;
             prlim[i][i]=probs[(int)age][i][k];    double *gp, *gm;
         }    double **gradg, **trgradg;
            double age,agelim;
         fprintf(ficrest," %.0f",age);    int theta;
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    pstamp(ficresvpl);
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
           }    fprintf(ficresvpl,"# Age");
           epj[nlstate+1] +=epj[j];    for(i=1; i<=nlstate;i++)
         }        fprintf(ficresvpl," %1d-%1d",i,i);
         for(i=1, vepp=0.;i <=nlstate;i++)    fprintf(ficresvpl,"\n");
           for(j=1;j <=nlstate;j++)  
             vepp += vareij[i][j][(int)age];    xp=vector(1,npar);
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    dnewm=matrix(1,nlstate,1,npar);
         for(j=1;j <=nlstate;j++){    doldm=matrix(1,nlstate,1,nlstate);
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));    
         }    hstepm=1*YEARM; /* Every year of age */
         fprintf(ficrest,"\n");    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);
  fclose(ficreseij);      gm=vector(1,nlstate);
  fclose(ficresvij);  
   fclose(ficrest);      for(theta=1; theta <=npar; theta++){
   fclose(ficpar);        for(i=1; i<=npar; i++){ /* Computes gradient */
   free_vector(epj,1,nlstate+1);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
   /*  scanf("%d ",i); */        }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   /*------- Variance limit prevalence------*/          for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
 strcpy(fileresvpl,"vpl");      
   strcat(fileresvpl,fileres);        for(i=1; i<=npar; i++) /* Computes gradient */
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {          xp[i] = x[i] - (i==theta ?delti[theta]:0);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     exit(0);        for(i=1;i<=nlstate;i++)
   }          gm[i] = prlim[i][i];
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);  
         for(i=1;i<=nlstate;i++)
  k=0;          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
  for(cptcov=1;cptcov<=i1;cptcov++){      } /* End theta */
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){  
      k=k+1;      trgradg =matrix(1,nlstate,1,npar);
      fprintf(ficresvpl,"\n#****** ");  
      for(j=1;j<=cptcoveff;j++)      for(j=1; j<=nlstate;j++)
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);        for(theta=1; theta <=npar; theta++)
      fprintf(ficresvpl,"******\n");          trgradg[j][theta]=gradg[theta][j];
        
      varpl=matrix(1,nlstate,(int) bage, (int) fage);      for(i=1;i<=nlstate;i++)
      oldm=oldms;savm=savms;        varpl[i][(int)age] =0.;
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);      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 */
   fclose(ficresvpl);  
       fprintf(ficresvpl,"%.0f ",age );
   /*---------- End : free ----------------*/      for(i=1; i<=nlstate;i++)
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
        fprintf(ficresvpl,"\n");
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      free_vector(gp,1,nlstate);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);      free_vector(gm,1,nlstate);
        free_matrix(gradg,1,npar,1,nlstate);
        free_matrix(trgradg,1,nlstate,1,npar);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    } /* End age */
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);  
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);    free_vector(xp,1,npar);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    free_matrix(doldm,1,nlstate,1,npar);
      free_matrix(dnewm,1,nlstate,1,nlstate);
   free_matrix(matcov,1,npar,1,npar);  
   free_vector(delti,1,npar);  }
    
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);  /************ 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[])
   if(erreur >0)  {
     printf("End of Imach with error %d\n",erreur);    int i, j=0,  i1, k1, l1, t, tj;
   else   printf("End of Imach\n");    int k2, l2, j1,  z1;
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    int k=0,l, cptcode;
      int first=1, first1;
   /* 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);*/    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
   /*printf("Total time was %d uSec.\n", total_usecs);*/    double **dnewm,**doldm;
   /*------ End -----------*/    double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
  end:    double **mu;
 #ifdef windows    double age,agelim, cov[NCOVMAX];
   /* chdir(pathcd);*/    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
 #endif    int theta;
  /*system("wgnuplot graph.plt");*/    char fileresprob[FILENAMELENGTH];
  /*system("../gp37mgw/wgnuplot graph.plt");*/    char fileresprobcov[FILENAMELENGTH];
  /*system("cd ../gp37mgw");*/    char fileresprobcor[FILENAMELENGTH];
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/  
  strcpy(plotcmd,GNUPLOTPROGRAM);    double ***varpij;
  strcat(plotcmd," ");  
  strcat(plotcmd,optionfilegnuplot);    strcpy(fileresprob,"prob"); 
  system(plotcmd);    strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
 #ifdef windows      printf("Problem with resultfile: %s\n", fileresprob);
   while (z[0] != 'q') {      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     chdir(path);    }
     printf("\nType e to edit output files, c to start again, and q for exiting: ");    strcpy(fileresprobcov,"probcov"); 
     scanf("%s",z);    strcat(fileresprobcov,fileres);
     if (z[0] == 'c') system("./imach");    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
     else if (z[0] == 'e') {      printf("Problem with resultfile: %s\n", fileresprobcov);
       chdir(path);      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
       system(optionfilehtm);    }
     }    strcpy(fileresprobcor,"probcor"); 
     else if (z[0] == 'q') exit(0);    strcat(fileresprobcor,fileres);
   }    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
 #endif      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);
     pstamp(ficresprob);
     fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
     fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
     fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
     fprintf(ficresprobcov,"# Age");
     pstamp(ficresprobcor);
     fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     fprintf(ficresprobcor,"# 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,"\
    - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
      fprintf(fichtm,"\
    - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age:  ei., eij . If one or more covariate are included, specific tables for each value of the covariate are output in sequences within the same file (estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   
   
   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: <a href=\"%s%d1.png\">%s%d1.png</a><br> \
   <img src=\"%s%d1.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,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: <a href=\"%s%d2.png\">%s%d2.png</a><br> \
   <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
          /* Period (stable) prevalence in each health state */
          for(cpt=1; cpt<nlstate;cpt++){
            fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
   <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
        for(cpt=1; cpt<=nlstate;cpt++) {
           fprintf(fichtm,"\n<br>- Life expectancy by health state (%d) at initial age and its decomposition into health expectancies : <a href=\"%s%d%d.png\">%s%d%d.png</a> <br> \
   <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,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 and <b>initial health status</b> (cov(e<sup>ij</sup>,e<sup>kl</sup>)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
    fprintf(fichtm,"\
    - (a) Health expectancies by health status at initial age (e<sup>ij</sup>) and standard errors (in parentheses) (b) life expectancies and standard errors (e<sup>i.</sup>=e<sup>i1</sup>+e<sup>i2</sup>+...)(estepm=%2d months): \
      <a href=\"%s\">%s</a> <br>\n</li>",
              estepm,subdirf2(fileres,"stde"),subdirf2(fileres,"stde"));
    fprintf(fichtm,"\
    - Variances and covariances of health expectancies by age. Status (i) based health expectancies (in state j), eij are weighted by the period prevalences in each state i (if popbased=1, an additional computation is done using the cross-sectional prevalences (i.e population based) (estepm=%d months): <a href=\"%s\">%s</a><br>\n",
            estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
    fprintf(fichtm,"\
    - Total life expectancy and total health expectancies to be spent in each health state e<sup>.j</sup> with their standard errors: <a href=\"%s\">%s</a> <br>\n",
            subdirf2(fileres,"t"),subdirf2(fileres,"t"));
    fprintf(fichtm,"\
    - Standard deviation of period (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\"Period (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); */
         k=2+(nlstate+1)*(cpt-1);
         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+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* 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  *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; /* Dirty */
       }
     }
     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); /* Can be a relative path */
     if(getcwd(pathcd,MAXLINE) > 0) /* So pathcd is the full path */
       printf("Current directory %s!\n",pathcd);
     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);
       goto end;
       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 \
   It might be a problem of design; if ncovcol and the model are correct\n \
   run imach with mle=-1 to get a correct template of the parameter file.\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 while opening datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem while opening 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;
       dval=strtod(strb,&endptr); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%f' at line number %ld, \"%s\" for individual %d\nShould be a weight.  Exiting.\n",dval, i,line,linei);
         exit(1);
       }
       weight[i]=dval; 
       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 for individual %d, '%s'\n \
    Should be a value of %d(nth) covariate (0 should be the value for the reference and 1\n \
    for the alternative. IMaCh does not build design variables automatically, do it yourself.\n \
    For example, for multinomial values like 1, 2 and 3,\n \
    build V1=0 V2=0 for the reference value (1),\n \
           V1=1 V2=0 for (2) \n \
    and V1=0 V2=1 for (3). V1=1 V2=1 should not exist and the corresponding\n \
    output of IMaCh is often meaningless.\n \
    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,"<html><head>\n<title>IMaCh Cov %s</title></head>\n <body><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",\
             optionfilehtmcov,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<html><head>\n<title>IMaCh %s</title></head>\n <body><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\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\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",\
             optionfilehtm,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             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,pathcd); /* 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("%lf ",p[jk]);
               fprintf(ficlog,"%lf ",p[jk]);
               fprintf(ficres,"%lf ",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,pathcd); /* 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  (period or stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (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*/
       pstamp(ficrespij);
       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 Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: 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(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       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#****** ");
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\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, strstart);  
           cvevsij(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);
           }
   
           pstamp(ficrest);
           fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( 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(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (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>\n</body></html>",strstart, strtend);
     fclose(fichtm);
     fprintf(fichtmcov,"<br>Local time at start %s<br>Local time at end   %s<br>\n</body></html>",strstart, strtend);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
   
      printf("Before Current directory %s!\n",pathcd);
      if(chdir(pathcd) != 0)
       printf("Can't move to directory %s!\n",path);
     if(getcwd(pathcd,MAXLINE) > 0)
       printf("Current directory %s!\n",pathcd);
     /*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.1.22  
changed lines
  Added in v.1.124


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