Diff for /imach/src/imach.c between versions 1.7 and 1.122

version 1.7, 2001/05/02 17:50:24 version 1.122, 2006/03/20 09:45:41
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      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.122  2006/03/20 09:45:41  brouard
   individuals from different ages are interviewed on their health status    (Module): Weights can have a decimal point as for
   or degree of  disability. At least a second wave of interviews    English (a comma might work with a correct LC_NUMERIC environment,
   ("longitudinal") should  measure each new individual health status.    otherwise the weight is truncated).
   Health expectancies are computed from the transistions observed between    Modification of warning when the covariates values are not 0 or
   waves and are computed for each degree of severity of disability (number    1.
   of life states). More degrees you consider, more time is necessary to    Version 0.98g
   reach the Maximum Likelihood of the parameters involved in the model.  
   The simplest model is the multinomial logistic model where pij is    Revision 1.121  2006/03/16 17:45:01  lievre
   the probabibility to be observed in state j at the second wave conditional    * imach.c (Module): Comments concerning covariates added
   to be observed in state i at the first wave. Therefore the model is:  
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    * imach.c (Module): refinements in the computation of lli if
   is a covariate. If you want to have a more complex model than "constant and    status=-2 in order to have more reliable computation if stepm is
   age", you should modify the program where the markup    not 1 month. Version 0.98f
     *Covariates have to be included here again* invites you to do it.  
   More covariates you add, less is the speed of the convergence.    Revision 1.120  2006/03/16 15:10:38  lievre
     (Module): refinements in the computation of lli if
   The advantage that this computer programme claims, comes from that if the    status=-2 in order to have more reliable computation if stepm is
   delay between waves is not identical for each individual, or if some    not 1 month. Version 0.98f
   individual missed an interview, the information is not rounded or lost, but  
   taken into account using an interpolation or extrapolation.    Revision 1.119  2006/03/15 17:42:26  brouard
   hPijx is the probability to be    (Module): Bug if status = -2, the loglikelihood was
   observed in state i at age x+h conditional to the observed state i at age    computed as likelihood omitting the logarithm. Version O.98e
   x. The delay 'h' can be split into an exact number (nh*stepm) of  
   unobserved intermediate  states. This elementary transition (by month or    Revision 1.118  2006/03/14 18:20:07  brouard
   quarter trimester, semester or year) is model as a multinomial logistic.    (Module): varevsij Comments added explaining the second
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    table of variances if popbased=1 .
   and the contribution of each individual to the likelihood is simply hPijx.    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
     (Module): Function pstamp added
   Also this programme outputs the covariance matrix of the parameters but also    (Module): Version 0.98d
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.117  2006/03/14 17:16:22  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 1.116  2006/03/06 10:29:27  brouard
   **********************************************************************/    (Module): Variance-covariance wrong links and
      varian-covariance of ej. is needed (Saito).
 #include <math.h>  
 #include <stdio.h>    Revision 1.115  2006/02/27 12:17:45  brouard
 #include <stdlib.h>    (Module): One freematrix added in mlikeli! 0.98c
 #include <unistd.h>  
     Revision 1.114  2006/02/26 12:57:58  brouard
 #define MAXLINE 256    (Module): Some improvements in processing parameter
 #define FILENAMELENGTH 80    filename with strsep.
 /*#define DEBUG*/  
 #define windows    Revision 1.113  2006/02/24 14:20:24  brouard
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    (Module): Memory leaks checks with valgrind and:
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    datafile was not closed, some imatrix were not freed and on matrix
     allocation too.
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */  
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    Revision 1.112  2006/01/30 09:55:26  brouard
     (Module): Back to gnuplot.exe instead of wgnuplot.exe
 #define NINTERVMAX 8  
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    Revision 1.111  2006/01/25 20:38:18  brouard
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    (Module): Lots of cleaning and bugs added (Gompertz)
 #define NCOVMAX 8 /* Maximum number of covariates */    (Module): Comments can be added in data file. Missing date values
 #define MAXN 20000    can be a simple dot '.'.
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Revision 1.110  2006/01/25 00:51:50  brouard
 #define AGEBASE 40    (Module): Lots of cleaning and bugs added (Gompertz)
   
     Revision 1.109  2006/01/24 19:37:15  brouard
 int nvar;    (Module): Comments (lines starting with a #) are allowed in data.
 static int cptcov;  
 int cptcovn, cptcovage=0, cptcoveff=0;    Revision 1.108  2006/01/19 18:05:42  lievre
 int npar=NPARMAX;    Gnuplot problem appeared...
 int nlstate=2; /* Number of live states */    To be fixed
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Revision 1.107  2006/01/19 16:20:37  brouard
     Test existence of gnuplot in imach path
 int *wav; /* Number of waves for this individuual 0 is possible */  
 int maxwav; /* Maxim number of waves */    Revision 1.106  2006/01/19 13:24:36  brouard
 int mle, weightopt;    Some cleaning and links added in html output
 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 */    Revision 1.105  2006/01/05 20:23:19  lievre
 double **oldm, **newm, **savm; /* Working pointers to matrices */    *** empty log message ***
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;    Revision 1.104  2005/09/30 16:11:43  lievre
 FILE *ficgp, *fichtm;    (Module): sump fixed, loop imx fixed, and simplifications.
 FILE *ficreseij;    (Module): If the status is missing at the last wave but we know
   char filerese[FILENAMELENGTH];    that the person is alive, then we can code his/her status as -2
  FILE  *ficresvij;    (instead of missing=-1 in earlier versions) and his/her
   char fileresv[FILENAMELENGTH];    contributions to the likelihood is 1 - Prob of dying from last
  FILE  *ficresvpl;    health status (= 1-p13= p11+p12 in the easiest case of somebody in
   char fileresvpl[FILENAMELENGTH];    the healthy state at last known wave). Version is 0.98
   
 #define NR_END 1    Revision 1.103  2005/09/30 15:54:49  lievre
 #define FREE_ARG char*    (Module): sump fixed, loop imx fixed, and simplifications.
 #define FTOL 1.0e-10  
     Revision 1.102  2004/09/15 17:31:30  brouard
 #define NRANSI    Add the possibility to read data file including tab characters.
 #define ITMAX 200  
     Revision 1.101  2004/09/15 10:38:38  brouard
 #define TOL 2.0e-4    Fix on curr_time
   
 #define CGOLD 0.3819660    Revision 1.100  2004/07/12 18:29:06  brouard
 #define ZEPS 1.0e-10    Add version for Mac OS X. Just define UNIX in Makefile
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     Revision 1.99  2004/06/05 08:57:40  brouard
 #define GOLD 1.618034    *** empty log message ***
 #define GLIMIT 100.0  
 #define TINY 1.0e-20    Revision 1.98  2004/05/16 15:05:56  brouard
     New version 0.97 . First attempt to estimate force of mortality
 static double maxarg1,maxarg2;    directly from the data i.e. without the need of knowing the health
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    state at each age, but using a Gompertz model: log u =a + b*age .
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    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
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    cross-longitudinal survey is different from the mortality estimated
 #define rint(a) floor(a+0.5)    from other sources like vital statistic data.
   
 static double sqrarg;    The same imach parameter file can be used but the option for mle should be -3.
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)  
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    Agnès, who wrote this part of the code, tried to keep most of the
     former routines in order to include the new code within the former code.
 int imx;  
 int stepm;    The output is very simple: only an estimate of the intercept and of
 /* Stepm, step in month: minimum step interpolation*/    the slope with 95% confident intervals.
   
 int m,nb;    Current limitations:
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    A) Even if you enter covariates, i.e. with the
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 double **pmmij;    B) There is no computation of Life Expectancy nor Life Table.
   
 double *weight;    Revision 1.97  2004/02/20 13:25:42  lievre
 int **s; /* Status */    Version 0.96d. Population forecasting command line is (temporarily)
 double *agedc, **covar, idx;    suppressed.
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     Revision 1.96  2003/07/15 15:38:55  brouard
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 double ftolhess; /* Tolerance for computing hessian */    rewritten within the same printf. Workaround: many printfs.
   
 /**************** split *************************/    Revision 1.95  2003/07/08 07:54:34  brouard
 static  int split( char *path, char *dirc, char *name )    * imach.c (Repository):
 {    (Repository): Using imachwizard code to output a more meaningful covariance
    char *s;                             /* pointer */    matrix (cov(a12,c31) instead of numbers.
    int  l1, l2;                         /* length counters */  
     Revision 1.94  2003/06/27 13:00:02  brouard
    l1 = strlen( path );                 /* length of path */    Just cleaning
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
    s = strrchr( path, '\\' );           /* find last / */    Revision 1.93  2003/06/25 16:33:55  brouard
    if ( s == NULL ) {                   /* no directory, so use current */    (Module): On windows (cygwin) function asctime_r doesn't
 #if     defined(__bsd__)                /* get current working directory */    exist so I changed back to asctime which exists.
       extern char       *getwd( );    (Module): Version 0.96b
   
       if ( getwd( dirc ) == NULL ) {    Revision 1.92  2003/06/25 16:30:45  brouard
 #else    (Module): On windows (cygwin) function asctime_r doesn't
       extern char       *getcwd( );    exist so I changed back to asctime which exists.
   
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Revision 1.91  2003/06/25 15:30:29  brouard
 #endif    * imach.c (Repository): Duplicated warning errors corrected.
          return( GLOCK_ERROR_GETCWD );    (Repository): Elapsed time after each iteration is now output. It
       }    helps to forecast when convergence will be reached. Elapsed time
       strcpy( name, path );             /* we've got it */    is stamped in powell.  We created a new html file for the graphs
    } else {                             /* strip direcotry from path */    concerning matrix of covariance. It has extension -cov.htm.
       s++;                              /* after this, the filename */  
       l2 = strlen( s );                 /* length of filename */    Revision 1.90  2003/06/24 12:34:15  brouard
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    (Module): Some bugs corrected for windows. Also, when
       strcpy( name, s );                /* save file name */    mle=-1 a template is output in file "or"mypar.txt with the design
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    of the covariance matrix to be input.
       dirc[l1-l2] = 0;                  /* add zero */  
    }    Revision 1.89  2003/06/24 12:30:52  brouard
    l1 = strlen( dirc );                 /* length of directory */    (Module): Some bugs corrected for windows. Also, when
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    mle=-1 a template is output in file "or"mypar.txt with the design
    return( 0 );                         /* we're done */    of the covariance matrix to be input.
 }  
     Revision 1.88  2003/06/23 17:54:56  brouard
     * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
 /******************************************/  
     Revision 1.87  2003/06/18 12:26:01  brouard
 void replace(char *s, char*t)    Version 0.96
 {  
   int i;    Revision 1.86  2003/06/17 20:04:08  brouard
   int lg=20;    (Module): Change position of html and gnuplot routines and added
   i=0;    routine fileappend.
   lg=strlen(t);  
   for(i=0; i<= lg; i++) {    Revision 1.85  2003/06/17 13:12:43  brouard
     (s[i] = t[i]);    * imach.c (Repository): Check when date of death was earlier that
     if (t[i]== '\\') s[i]='/';    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
 int nbocc(char *s, char occ)    interview.
 {    (Repository): Because some people have very long ID (first column)
   int i,j=0;    we changed int to long in num[] and we added a new lvector for
   int lg=20;    memory allocation. But we also truncated to 8 characters (left
   i=0;    truncation)
   lg=strlen(s);    (Repository): No more line truncation errors.
   for(i=0; i<= lg; i++) {  
   if  (s[i] == occ ) j++;    Revision 1.84  2003/06/13 21:44:43  brouard
   }    * imach.c (Repository): Replace "freqsummary" at a correct
   return j;    place. It differs from routine "prevalence" which may be called
 }    many times. Probs is memory consuming and must be used with
     parcimony.
 void cutv(char *u,char *v, char*t, char occ)    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 {  
   int i,lg,j,p=0;    Revision 1.83  2003/06/10 13:39:11  lievre
   i=0;    *** empty log message ***
   for(j=0; j<=strlen(t)-1; j++) {  
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    Revision 1.82  2003/06/05 15:57:20  brouard
   }    Add log in  imach.c and  fullversion number is now printed.
   
   lg=strlen(t);  */
   for(j=0; j<p; j++) {  /*
     (u[j] = t[j]);     Interpolated Markov Chain
   }  
      u[p]='\0';    Short summary of the programme:
     
    for(j=0; j<= lg; j++) {    This program computes Healthy Life Expectancies from
     if (j>=(p+1))(v[j-p-1] = t[j]);    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   }    first survey ("cross") where individuals from different ages are
 }    interviewed on their health status or degree of disability (in the
     case of a health survey which is our main interest) -2- at least a
 /********************** nrerror ********************/    second wave of interviews ("longitudinal") which measure each change
     (if any) in individual health status.  Health expectancies are
 void nrerror(char error_text[])    computed from the time spent in each health state according to a
 {    model. More health states you consider, more time is necessary to reach the
   fprintf(stderr,"ERREUR ...\n");    Maximum Likelihood of the parameters involved in the model.  The
   fprintf(stderr,"%s\n",error_text);    simplest model is the multinomial logistic model where pij is the
   exit(1);    probability to be observed in state j at the second wave
 }    conditional to be observed in state i at the first wave. Therefore
 /*********************** vector *******************/    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
 double *vector(int nl, int nh)    '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
   double *v;    where the markup *Covariates have to be included here again* invites
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    you to do it.  More covariates you add, slower the
   if (!v) nrerror("allocation failure in vector");    convergence.
   return v-nl+NR_END;  
 }    The advantage of this computer programme, compared to a simple
     multinomial logistic model, is clear when the delay between waves is not
 /************************ free vector ******************/    identical for each individual. Also, if a individual missed an
 void free_vector(double*v, int nl, int nh)    intermediate interview, the information is lost, but taken into
 {    account using an interpolation or extrapolation.  
   free((FREE_ARG)(v+nl-NR_END));  
 }    hPijx is the probability to be observed in state i at age x+h
     conditional to the observed state i at age x. The delay 'h' can be
 /************************ivector *******************************/    split into an exact number (nh*stepm) of unobserved intermediate
 int *ivector(long nl,long nh)    states. This elementary transition (by month, quarter,
 {    semester or year) is modelled as a multinomial logistic.  The hPx
   int *v;    matrix is simply the matrix product of nh*stepm elementary matrices
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    and the contribution of each individual to the likelihood is simply
   if (!v) nrerror("allocation failure in ivector");    hPijx.
   return v-nl+NR_END;  
 }    Also this programme outputs the covariance matrix of the parameters but also
     of the life expectancies. It also computes the period (stable) prevalence. 
 /******************free ivector **************************/    
 void free_ivector(int *v, long nl, long nh)    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 {             Institut national d'études démographiques, Paris.
   free((FREE_ARG)(v+nl-NR_END));    This software have been partly granted by Euro-REVES, a concerted action
 }    from the European Union.
     It is copyrighted identically to a GNU software product, ie programme and
 /******************* imatrix *******************************/    software can be distributed freely for non commercial use. Latest version
 int **imatrix(long nrl, long nrh, long ncl, long nch)    can be accessed at http://euroreves.ined.fr/imach .
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  
 {    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   int **m;    
      **********************************************************************/
   /* allocate pointers to rows */  /*
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));    main
   if (!m) nrerror("allocation failure 1 in matrix()");    read parameterfile
   m += NR_END;    read datafile
   m -= nrl;    concatwav
      freqsummary
      if (mle >= 1)
   /* allocate rows and set pointers to them */      mlikeli
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));    print results files
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");    if mle==1 
   m[nrl] += NR_END;       computes hessian
   m[nrl] -= ncl;    read end of parameter file: agemin, agemax, bage, fage, estepm
          begin-prev-date,...
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;    open gnuplot file
      open html file
   /* return pointer to array of pointers to rows */    period (stable) prevalence
   return m;     for age prevalim()
 }    h Pij x
     variance of p varprob
 /****************** free_imatrix *************************/    forecasting if prevfcast==1 prevforecast call prevalence()
 void free_imatrix(m,nrl,nrh,ncl,nch)    health expectancies
       int **m;    Variance-covariance of DFLE
       long nch,ncl,nrh,nrl;    prevalence()
      /* free an int matrix allocated by imatrix() */     movingaverage()
 {    varevsij() 
   free((FREE_ARG) (m[nrl]+ncl-NR_END));    if popbased==1 varevsij(,popbased)
   free((FREE_ARG) (m+nrl-NR_END));    total life expectancies
 }    Variance of period (stable) prevalence
    end
 /******************* matrix *******************************/  */
 double **matrix(long nrl, long nrh, long ncl, long nch)  
 {  
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;   
   #include <math.h>
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #include <stdio.h>
   if (!m) nrerror("allocation failure 1 in matrix()");  #include <stdlib.h>
   m += NR_END;  #include <string.h>
   m -= nrl;  #include <unistd.h>
   
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #include <limits.h>
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #include <sys/types.h>
   m[nrl] += NR_END;  #include <sys/stat.h>
   m[nrl] -= ncl;  #include <errno.h>
   extern int errno;
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  
   return m;  /* #include <sys/time.h> */
 }  #include <time.h>
   #include "timeval.h"
 /*************************free matrix ************************/  
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  /* #include <libintl.h> */
 {  /* #define _(String) gettext (String) */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));  #define MAXLINE 256
 }  
   #define GNUPLOTPROGRAM "gnuplot"
 /******************* ma3x *******************************/  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  #define FILENAMELENGTH 132
 {  
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   double ***m;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   if (!m) nrerror("allocation failure 1 in matrix()");  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   m += NR_END;  
   m -= nrl;  #define NINTERVMAX 8
   #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define NCOVMAX 8 /* Maximum number of covariates */
   m[nrl] += NR_END;  #define MAXN 20000
   m[nrl] -= ncl;  #define YEARM 12. /* Number of months per year */
   #define AGESUP 130
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #define AGEBASE 40
   #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  #ifdef UNIX
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  #define DIRSEPARATOR '/'
   m[nrl][ncl] += NR_END;  #define CHARSEPARATOR "/"
   m[nrl][ncl] -= nll;  #define ODIRSEPARATOR '\\'
   for (j=ncl+1; j<=nch; j++)  #else
     m[nrl][j]=m[nrl][j-1]+nlay;  #define DIRSEPARATOR '\\'
    #define CHARSEPARATOR "\\"
   for (i=nrl+1; i<=nrh; i++) {  #define ODIRSEPARATOR '/'
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  #endif
     for (j=ncl+1; j<=nch; j++)  
       m[i][j]=m[i][j-1]+nlay;  /* $Id$ */
   }  /* $State$ */
   return m;  
 }  char version[]="Imach version 0.98g, March 2006, INED-EUROREVES-Institut de longevite ";
   char fullversion[]="$Revision$ $Date$"; 
 /*************************free ma3x ************************/  char strstart[80];
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 {  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  int nvar;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   free((FREE_ARG)(m+nrl-NR_END));  int npar=NPARMAX;
 }  int nlstate=2; /* Number of live states */
   int ndeath=1; /* Number of dead states */
 /***************** f1dim *************************/  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
 extern int ncom;  int popbased=0;
 extern double *pcom,*xicom;  
 extern double (*nrfunc)(double []);  int *wav; /* Number of waves for this individuual 0 is possible */
    int maxwav; /* Maxim number of waves */
 double f1dim(double x)  int jmin, jmax; /* min, max spacing between 2 waves */
 {  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
   int j;  int gipmx, gsw; /* Global variables on the number of contributions 
   double f;                     to the likelihood and the sum of weights (done by funcone)*/
   double *xt;  int mle, weightopt;
    int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   xt=vector(1,ncom);  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   f=(*nrfunc)(xt);             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   free_vector(xt,1,ncom);  double jmean; /* Mean space between 2 waves */
   return f;  double **oldm, **newm, **savm; /* Working pointers to matrices */
 }  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
 /*****************brent *************************/  FILE *ficlog, *ficrespow;
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  int globpr; /* Global variable for printing or not */
 {  double fretone; /* Only one call to likelihood */
   int iter;  long ipmx; /* Number of contributions */
   double a,b,d,etemp;  double sw; /* Sum of weights */
   double fu,fv,fw,fx;  char filerespow[FILENAMELENGTH];
   double ftemp;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   double p,q,r,tol1,tol2,u,v,w,x,xm;  FILE *ficresilk;
   double e=0.0;  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
    FILE *ficresprobmorprev;
   a=(ax < cx ? ax : cx);  FILE *fichtm, *fichtmcov; /* Html File */
   b=(ax > cx ? ax : cx);  FILE *ficreseij;
   x=w=v=bx;  char filerese[FILENAMELENGTH];
   fw=fv=fx=(*f)(x);  FILE *ficresstdeij;
   for (iter=1;iter<=ITMAX;iter++) {  char fileresstde[FILENAMELENGTH];
     xm=0.5*(a+b);  FILE *ficrescveij;
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  char filerescve[FILENAMELENGTH];
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  FILE  *ficresvij;
     printf(".");fflush(stdout);  char fileresv[FILENAMELENGTH];
 #ifdef DEBUG  FILE  *ficresvpl;
     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 fileresvpl[FILENAMELENGTH];
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  char title[MAXLINE];
 #endif  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
       *xmin=x;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
       return fx;  char command[FILENAMELENGTH];
     }  int  outcmd=0;
     ftemp=fu;  
     if (fabs(e) > tol1) {  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
       r=(x-w)*(fx-fv);  
       q=(x-v)*(fx-fw);  char filelog[FILENAMELENGTH]; /* Log file */
       p=(x-v)*q-(x-w)*r;  char filerest[FILENAMELENGTH];
       q=2.0*(q-r);  char fileregp[FILENAMELENGTH];
       if (q > 0.0) p = -p;  char popfile[FILENAMELENGTH];
       q=fabs(q);  
       etemp=e;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
       e=d;  
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  struct timezone tzp;
       else {  extern int gettimeofday();
         d=p/q;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
         u=x+d;  long time_value;
         if (u-a < tol2 || b-u < tol2)  extern long time();
           d=SIGN(tol1,xm-x);  char strcurr[80], strfor[80];
       }  
     } else {  char *endptr;
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  long lval;
     }  double dval;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  
     fu=(*f)(u);  #define NR_END 1
     if (fu <= fx) {  #define FREE_ARG char*
       if (u >= x) a=x; else b=x;  #define FTOL 1.0e-10
       SHFT(v,w,x,u)  
         SHFT(fv,fw,fx,fu)  #define NRANSI 
         } else {  #define ITMAX 200 
           if (u < x) a=u; else b=u;  
           if (fu <= fw || w == x) {  #define TOL 2.0e-4 
             v=w;  
             w=u;  #define CGOLD 0.3819660 
             fv=fw;  #define ZEPS 1.0e-10 
             fw=fu;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
           } else if (fu <= fv || v == x || v == w) {  
             v=u;  #define GOLD 1.618034 
             fv=fu;  #define GLIMIT 100.0 
           }  #define TINY 1.0e-20 
         }  
   }  static double maxarg1,maxarg2;
   nrerror("Too many iterations in brent");  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   *xmin=x;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   return fx;    
 }  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   #define rint(a) floor(a+0.5)
 /****************** mnbrak ***********************/  
   static double sqrarg;
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
             double (*func)(double))  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 {  int agegomp= AGEGOMP;
   double ulim,u,r,q, dum;  
   double fu;  int imx; 
    int stepm=1;
   *fa=(*func)(*ax);  /* Stepm, step in month: minimum step interpolation*/
   *fb=(*func)(*bx);  
   if (*fb > *fa) {  int estepm;
     SHFT(dum,*ax,*bx,dum)  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
       SHFT(dum,*fb,*fa,dum)  
       }  int m,nb;
   *cx=(*bx)+GOLD*(*bx-*ax);  long *num;
   *fc=(*func)(*cx);  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
   while (*fb > *fc) {  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
     r=(*bx-*ax)*(*fb-*fc);  double **pmmij, ***probs;
     q=(*bx-*cx)*(*fb-*fa);  double *ageexmed,*agecens;
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/  double dateintmean=0;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));  
     ulim=(*bx)+GLIMIT*(*cx-*bx);  double *weight;
     if ((*bx-u)*(u-*cx) > 0.0) {  int **s; /* Status */
       fu=(*func)(u);  double *agedc, **covar, idx;
     } else if ((*cx-u)*(u-ulim) > 0.0) {  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
       fu=(*func)(u);  double *lsurv, *lpop, *tpop;
       if (fu < *fc) {  
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
           SHFT(*fb,*fc,fu,(*func)(u))  double ftolhess; /* Tolerance for computing hessian */
           }  
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {  /**************** split *************************/
       u=ulim;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
       fu=(*func)(u);  {
     } else {    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
       u=(*cx)+GOLD*(*cx-*bx);       the name of the file (name), its extension only (ext) and its first part of the name (finame)
       fu=(*func)(u);    */ 
     }    char  *ss;                            /* pointer */
     SHFT(*ax,*bx,*cx,u)    int   l1, l2;                         /* length counters */
       SHFT(*fa,*fb,*fc,fu)  
       }    l1 = strlen(path );                   /* length of path */
 }    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     ss= strrchr( path, DIRSEPARATOR );            /* find last / */
 /*************** linmin ************************/    if ( ss == NULL ) {                   /* no directory, so determine current directory */
       strcpy( name, path );               /* we got the fullname name because no directory */
 int ncom;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
 double *pcom,*xicom;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
 double (*nrfunc)(double []);      /* get current working directory */
        /*    extern  char* getcwd ( char *buf , int len);*/
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
 {        return( GLOCK_ERROR_GETCWD );
   double brent(double ax, double bx, double cx,      }
                double (*f)(double), double tol, double *xmin);      /* got dirc from getcwd*/
   double f1dim(double x);      printf(" DIRC = %s \n",dirc);
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    } else {                              /* strip direcotry from path */
               double *fc, double (*func)(double));      ss++;                               /* after this, the filename */
   int j;      l2 = strlen( ss );                  /* length of filename */
   double xx,xmin,bx,ax;      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
   double fx,fb,fa;      strcpy( name, ss );         /* save file name */
        strncpy( dirc, path, l1 - l2 );     /* now the directory */
   ncom=n;      dirc[l1-l2] = 0;                    /* add zero */
   pcom=vector(1,n);      printf(" DIRC2 = %s \n",dirc);
   xicom=vector(1,n);    }
   nrfunc=func;    /* We add a separator at the end of dirc if not exists */
   for (j=1;j<=n;j++) {    l1 = strlen( dirc );                  /* length of directory */
     pcom[j]=p[j];    if( dirc[l1-1] != DIRSEPARATOR ){
     xicom[j]=xi[j];      dirc[l1] =  DIRSEPARATOR;
   }      dirc[l1+1] = 0; 
   ax=0.0;      printf(" DIRC3 = %s \n",dirc);
   xx=1.0;    }
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    ss = strrchr( name, '.' );            /* find last / */
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    if (ss >0){
 #ifdef DEBUG      ss++;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);      strcpy(ext,ss);                     /* save extension */
 #endif      l1= strlen( name);
   for (j=1;j<=n;j++) {      l2= strlen(ss)+1;
     xi[j] *= xmin;      strncpy( finame, name, l1-l2);
     p[j] += xi[j];      finame[l1-l2]= 0;
   }    }
   free_vector(xicom,1,n);  
   free_vector(pcom,1,n);    return( 0 );                          /* we're done */
 }  }
   
 /*************** powell ************************/  
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  /******************************************/
             double (*func)(double []))  
 {  void replace_back_to_slash(char *s, char*t)
   void linmin(double p[], double xi[], int n, double *fret,  {
               double (*func)(double []));    int i;
   int i,ibig,j;    int lg=0;
   double del,t,*pt,*ptt,*xit;    i=0;
   double fp,fptt;    lg=strlen(t);
   double *xits;    for(i=0; i<= lg; i++) {
   pt=vector(1,n);      (s[i] = t[i]);
   ptt=vector(1,n);      if (t[i]== '\\') s[i]='/';
   xit=vector(1,n);    }
   xits=vector(1,n);  }
   *fret=(*func)(p);  
   for (j=1;j<=n;j++) pt[j]=p[j];  int nbocc(char *s, char occ)
   for (*iter=1;;++(*iter)) {  {
     fp=(*fret);    int i,j=0;
     ibig=0;    int lg=20;
     del=0.0;    i=0;
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    lg=strlen(s);
     for (i=1;i<=n;i++)    for(i=0; i<= lg; i++) {
       printf(" %d %.12f",i, p[i]);    if  (s[i] == occ ) j++;
     printf("\n");    }
     for (i=1;i<=n;i++) {    return j;
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  }
       fptt=(*fret);  
 #ifdef DEBUG  void cutv(char *u,char *v, char*t, char occ)
       printf("fret=%lf \n",*fret);  {
 #endif    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
       printf("%d",i);fflush(stdout);       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
       linmin(p,xit,n,fret,func);       gives u="abcedf" and v="ghi2j" */
       if (fabs(fptt-(*fret)) > del) {    int i,lg,j,p=0;
         del=fabs(fptt-(*fret));    i=0;
         ibig=i;    for(j=0; j<=strlen(t)-1; j++) {
       }      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 #ifdef DEBUG    }
       printf("%d %.12e",i,(*fret));  
       for (j=1;j<=n;j++) {    lg=strlen(t);
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    for(j=0; j<p; j++) {
         printf(" x(%d)=%.12e",j,xit[j]);      (u[j] = t[j]);
       }    }
       for(j=1;j<=n;j++)       u[p]='\0';
         printf(" p=%.12e",p[j]);  
       printf("\n");     for(j=0; j<= lg; j++) {
 #endif      if (j>=(p+1))(v[j-p-1] = t[j]);
     }    }
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  }
 #ifdef DEBUG  
       int k[2],l;  /********************** nrerror ********************/
       k[0]=1;  
       k[1]=-1;  void nrerror(char error_text[])
       printf("Max: %.12e",(*func)(p));  {
       for (j=1;j<=n;j++)    fprintf(stderr,"ERREUR ...\n");
         printf(" %.12e",p[j]);    fprintf(stderr,"%s\n",error_text);
       printf("\n");    exit(EXIT_FAILURE);
       for(l=0;l<=1;l++) {  }
         for (j=1;j<=n;j++) {  /*********************** vector *******************/
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  double *vector(int nl, int nh)
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  {
         }    double *v;
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
       }    if (!v) nrerror("allocation failure in vector");
 #endif    return v-nl+NR_END;
   }
   
       free_vector(xit,1,n);  /************************ free vector ******************/
       free_vector(xits,1,n);  void free_vector(double*v, int nl, int nh)
       free_vector(ptt,1,n);  {
       free_vector(pt,1,n);    free((FREE_ARG)(v+nl-NR_END));
       return;  }
     }  
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  /************************ivector *******************************/
     for (j=1;j<=n;j++) {  int *ivector(long nl,long nh)
       ptt[j]=2.0*p[j]-pt[j];  {
       xit[j]=p[j]-pt[j];    int *v;
       pt[j]=p[j];    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     }    if (!v) nrerror("allocation failure in ivector");
     fptt=(*func)(ptt);    return v-nl+NR_END;
     if (fptt < fp) {  }
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  
       if (t < 0.0) {  /******************free ivector **************************/
         linmin(p,xit,n,fret,func);  void free_ivector(int *v, long nl, long nh)
         for (j=1;j<=n;j++) {  {
           xi[j][ibig]=xi[j][n];    free((FREE_ARG)(v+nl-NR_END));
           xi[j][n]=xit[j];  }
         }  
 #ifdef DEBUG  /************************lvector *******************************/
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);  long *lvector(long nl,long nh)
         for(j=1;j<=n;j++)  {
           printf(" %.12e",xit[j]);    long *v;
         printf("\n");    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
 #endif    if (!v) nrerror("allocation failure in ivector");
       }    return v-nl+NR_END;
     }  }
   }  
 }  /******************free lvector **************************/
   void free_lvector(long *v, long nl, long nh)
 /**** Prevalence limit ****************/  {
     free((FREE_ARG)(v+nl-NR_END));
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)  }
 {  
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  /******************* imatrix *******************************/
      matrix by transitions matrix until convergence is reached */  int **imatrix(long nrl, long nrh, long ncl, long nch) 
        /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
   int i, ii,j,k;  { 
   double min, max, maxmin, maxmax,sumnew=0.;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
   double **matprod2();    int **m; 
   double **out, cov[NCOVMAX], **pmij();    
   double **newm;    /* allocate pointers to rows */ 
   double agefin, delaymax=50 ; /* Max number of years to converge */    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
     if (!m) nrerror("allocation failure 1 in matrix()"); 
   for (ii=1;ii<=nlstate+ndeath;ii++)    m += NR_END; 
     for (j=1;j<=nlstate+ndeath;j++){    m -= nrl; 
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    
     }    
     /* allocate rows and set pointers to them */ 
    cov[1]=1.;    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
      if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    m[nrl] += NR_END; 
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    m[nrl] -= ncl; 
     newm=savm;    
     /* Covariates have to be included here again */    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
      cov[2]=agefin;    
      /* return pointer to array of pointers to rows */ 
       for (k=1; k<=cptcovn;k++) {    return m; 
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  } 
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  
       }  /****************** free_imatrix *************************/
       for (k=1; k<=cptcovage;k++)  void free_imatrix(m,nrl,nrh,ncl,nch)
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        int **m;
       for (k=1; k<=cptcovprod;k++)        long nch,ncl,nrh,nrl; 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];       /* free an int matrix allocated by imatrix() */ 
   { 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     free((FREE_ARG) (m+nrl-NR_END)); 
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/  } 
   
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  /******************* matrix *******************************/
   double **matrix(long nrl, long nrh, long ncl, long nch)
     savm=oldm;  {
     oldm=newm;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
     maxmax=0.;    double **m;
     for(j=1;j<=nlstate;j++){  
       min=1.;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       max=0.;    if (!m) nrerror("allocation failure 1 in matrix()");
       for(i=1; i<=nlstate; i++) {    m += NR_END;
         sumnew=0;    m -= nrl;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  
         prlim[i][j]= newm[i][j]/(1-sumnew);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
         max=FMAX(max,prlim[i][j]);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
         min=FMIN(min,prlim[i][j]);    m[nrl] += NR_END;
       }    m[nrl] -= ncl;
       maxmin=max-min;  
       maxmax=FMAX(maxmax,maxmin);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     }    return m;
     if(maxmax < ftolpl){    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
       return prlim;     */
     }  }
   }  
 }  /*************************free matrix ************************/
   void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
 /*************** transition probabilities **********/  {
     free((FREE_ARG)(m[nrl]+ncl-NR_END));
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    free((FREE_ARG)(m+nrl-NR_END));
 {  }
   double s1, s2;  
   /*double t34;*/  /******************* ma3x *******************************/
   int i,j,j1, nc, ii, jj;  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   {
     for(i=1; i<= nlstate; i++){    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     for(j=1; j<i;j++){    double ***m;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){  
         /*s2 += param[i][j][nc]*cov[nc];*/    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    if (!m) nrerror("allocation failure 1 in matrix()");
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    m += NR_END;
       }    m -= nrl;
       ps[i][j]=s2;  
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     for(j=i+1; j<=nlstate+ndeath;j++){    m[nrl] += NR_END;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    m[nrl] -= ncl;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];  
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
       }  
       ps[i][j]=s2;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     }    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
   }    m[nrl][ncl] += NR_END;
   for(i=1; i<= nlstate; i++){    m[nrl][ncl] -= nll;
      s1=0;    for (j=ncl+1; j<=nch; j++) 
     for(j=1; j<i; j++)      m[nrl][j]=m[nrl][j-1]+nlay;
       s1+=exp(ps[i][j]);    
     for(j=i+1; j<=nlstate+ndeath; j++)    for (i=nrl+1; i<=nrh; i++) {
       s1+=exp(ps[i][j]);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
     ps[i][i]=1./(s1+1.);      for (j=ncl+1; j<=nch; j++) 
     for(j=1; j<i; j++)        m[i][j]=m[i][j-1]+nlay;
       ps[i][j]= exp(ps[i][j])*ps[i][i];    }
     for(j=i+1; j<=nlstate+ndeath; j++)    return m; 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   } /* end i */    */
   }
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  
     for(jj=1; jj<= nlstate+ndeath; jj++){  /*************************free ma3x ************************/
       ps[ii][jj]=0;  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
       ps[ii][ii]=1;  {
     }    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
   }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
     free((FREE_ARG)(m+nrl-NR_END));
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  }
     for(jj=1; jj<= nlstate+ndeath; jj++){  
      printf("%lf ",ps[ii][jj]);  /*************** function subdirf ***********/
    }  char *subdirf(char fileres[])
     printf("\n ");  {
     }    /* Caution optionfilefiname is hidden */
     printf("\n ");printf("%lf ",cov[2]);*/    strcpy(tmpout,optionfilefiname);
 /*    strcat(tmpout,"/"); /* Add to the right */
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    strcat(tmpout,fileres);
   goto end;*/    return tmpout;
     return ps;  }
 }  
   /*************** function subdirf2 ***********/
 /**************** Product of 2 matrices ******************/  char *subdirf2(char fileres[], char *preop)
   {
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    
 {    /* Caution optionfilefiname is hidden */
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    strcpy(tmpout,optionfilefiname);
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */    strcat(tmpout,"/");
   /* in, b, out are matrice of pointers which should have been initialized    strcat(tmpout,preop);
      before: only the contents of out is modified. The function returns    strcat(tmpout,fileres);
      a pointer to pointers identical to out */    return tmpout;
   long i, j, k;  }
   for(i=nrl; i<= nrh; i++)  
     for(k=ncolol; k<=ncoloh; k++)  /*************** function subdirf3 ***********/
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  char *subdirf3(char fileres[], char *preop, char *preop2)
         out[i][k] +=in[i][j]*b[j][k];  {
     
   return out;    /* Caution optionfilefiname is hidden */
 }    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/");
     strcat(tmpout,preop);
 /************* Higher Matrix Product ***************/    strcat(tmpout,preop2);
     strcat(tmpout,fileres);
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    return tmpout;
 {  }
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  
      duration (i.e. until  /***************** f1dim *************************/
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  extern int ncom; 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  extern double *pcom,*xicom;
      (typically every 2 years instead of every month which is too big).  extern double (*nrfunc)(double []); 
      Model is determined by parameters x and covariates have to be   
      included manually here.  double f1dim(double x) 
   { 
      */    int j; 
     double f;
   int i, j, d, h, k;    double *xt; 
   double **out, cov[NCOVMAX];   
   double **newm;    xt=vector(1,ncom); 
     for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   /* Hstepm could be zero and should return the unit matrix */    f=(*nrfunc)(xt); 
   for (i=1;i<=nlstate+ndeath;i++)    free_vector(xt,1,ncom); 
     for (j=1;j<=nlstate+ndeath;j++){    return f; 
       oldm[i][j]=(i==j ? 1.0 : 0.0);  } 
       po[i][j][0]=(i==j ? 1.0 : 0.0);  
     }  /*****************brent *************************/
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   for(h=1; h <=nhstepm; h++){  { 
     for(d=1; d <=hstepm; d++){    int iter; 
       newm=savm;    double a,b,d,etemp;
       /* Covariates have to be included here again */    double fu,fv,fw,fx;
       cov[1]=1.;    double ftemp;
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;    double p,q,r,tol1,tol2,u,v,w,x,xm; 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    double e=0.0; 
 for (k=1; k<=cptcovage;k++)   
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    a=(ax < cx ? ax : cx); 
    for (k=1; k<=cptcovprod;k++)    b=(ax > cx ? ax : cx); 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    x=w=v=bx; 
     fw=fv=fx=(*f)(x); 
     for (iter=1;iter<=ITMAX;iter++) { 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      xm=0.5*(a+b); 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
                    pmij(pmmij,cov,ncovmodel,x,nlstate));      printf(".");fflush(stdout);
       savm=oldm;      fprintf(ficlog,".");fflush(ficlog);
       oldm=newm;  #ifdef DEBUG
     }      printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);
     for(i=1; i<=nlstate+ndeath; i++)      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(j=1;j<=nlstate+ndeath;j++) {      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
         po[i][j][h]=newm[i][j];  #endif
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
          */        *xmin=x; 
       }        return fx; 
   } /* end h */      } 
   return po;      ftemp=fu;
 }      if (fabs(e) > tol1) { 
         r=(x-w)*(fx-fv); 
         q=(x-v)*(fx-fw); 
 /*************** log-likelihood *************/        p=(x-v)*q-(x-w)*r; 
 double func( double *x)        q=2.0*(q-r); 
 {        if (q > 0.0) p = -p; 
   int i, ii, j, k, mi, d, kk;        q=fabs(q); 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];        etemp=e; 
   double **out;        e=d; 
   double sw; /* Sum of weights */        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
   double lli; /* Individual log likelihood */          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   long ipmx;        else { 
   /*extern weight */          d=p/q; 
   /* We are differentiating ll according to initial status */          u=x+d; 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/          if (u-a < tol2 || b-u < tol2) 
   /*for(i=1;i<imx;i++)            d=SIGN(tol1,xm-x); 
 printf(" %d\n",s[4][i]);        } 
   */      } else { 
   cov[1]=1.;        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       } 
   for(k=1; k<=nlstate; k++) ll[k]=0.;      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){      fu=(*f)(u); 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      if (fu <= fx) { 
        for(mi=1; mi<= wav[i]-1; mi++){        if (u >= x) a=x; else b=x; 
       for (ii=1;ii<=nlstate+ndeath;ii++)        SHFT(v,w,x,u) 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);          SHFT(fv,fw,fx,fu) 
             for(d=0; d<dh[mi][i]; d++){          } else { 
               newm=savm;            if (u < x) a=u; else b=u; 
               cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;            if (fu <= fw || w == x) { 
               for (kk=1; kk<=cptcovage;kk++) {              v=w; 
                  cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];              w=u; 
                  /*printf("%d %d",kk,Tage[kk]);*/              fv=fw; 
               }              fw=fu; 
               /*cov[4]=covar[1][i]*cov[2];scanf("%d", i);*/            } else if (fu <= fv || v == x || v == w) { 
               /*cov[3]=pow(cov[2],2)/1000.;*/              v=u; 
               fv=fu; 
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,            } 
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));          } 
           savm=oldm;    } 
           oldm=newm;    nrerror("Too many iterations in brent"); 
     *xmin=x; 
     return fx; 
       } /* end mult */  } 
      
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);  /****************** mnbrak ***********************/
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/  
       ipmx +=1;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       sw += weight[i];              double (*func)(double)) 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;  { 
     } /* end of wave */    double ulim,u,r,q, dum;
   } /* end of individual */    double fu; 
    
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    *fa=(*func)(*ax); 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */    *fb=(*func)(*bx); 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */    if (*fb > *fa) { 
   return -l;      SHFT(dum,*ax,*bx,dum) 
 }        SHFT(dum,*fb,*fa,dum) 
         } 
     *cx=(*bx)+GOLD*(*bx-*ax); 
 /*********** Maximum Likelihood Estimation ***************/    *fc=(*func)(*cx); 
     while (*fb > *fc) { 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))      r=(*bx-*ax)*(*fb-*fc); 
 {      q=(*bx-*cx)*(*fb-*fa); 
   int i,j, iter;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   double **xi,*delti;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   double fret;      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   xi=matrix(1,npar,1,npar);      if ((*bx-u)*(u-*cx) > 0.0) { 
   for (i=1;i<=npar;i++)        fu=(*func)(u); 
     for (j=1;j<=npar;j++)      } else if ((*cx-u)*(u-ulim) > 0.0) { 
       xi[i][j]=(i==j ? 1.0 : 0.0);        fu=(*func)(u); 
   printf("Powell\n");        if (fu < *fc) { 
   powell(p,xi,npar,ftol,&iter,&fret,func);          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
             SHFT(*fb,*fc,fu,(*func)(u)) 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));            } 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
         u=ulim; 
 }        fu=(*func)(u); 
       } else { 
 /**** Computes Hessian and covariance matrix ***/        u=(*cx)+GOLD*(*cx-*bx); 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))        fu=(*func)(u); 
 {      } 
   double  **a,**y,*x,pd;      SHFT(*ax,*bx,*cx,u) 
   double **hess;        SHFT(*fa,*fb,*fc,fu) 
   int i, j,jk;        } 
   int *indx;  } 
   
   double hessii(double p[], double delta, int theta, double delti[]);  /*************** linmin ************************/
   double hessij(double p[], double delti[], int i, int j);  
   void lubksb(double **a, int npar, int *indx, double b[]) ;  int ncom; 
   void ludcmp(double **a, int npar, int *indx, double *d) ;  double *pcom,*xicom;
   double (*nrfunc)(double []); 
    
   hess=matrix(1,npar,1,npar);  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   { 
   printf("\nCalculation of the hessian matrix. Wait...\n");    double brent(double ax, double bx, double cx, 
   for (i=1;i<=npar;i++){                 double (*f)(double), double tol, double *xmin); 
     printf("%d",i);fflush(stdout);    double f1dim(double x); 
     hess[i][i]=hessii(p,ftolhess,i,delti);    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
     /*printf(" %f ",p[i]);*/                double *fc, double (*func)(double)); 
   }    int j; 
     double xx,xmin,bx,ax; 
   for (i=1;i<=npar;i++) {    double fx,fb,fa;
     for (j=1;j<=npar;j++)  {   
       if (j>i) {    ncom=n; 
         printf(".%d%d",i,j);fflush(stdout);    pcom=vector(1,n); 
         hess[i][j]=hessij(p,delti,i,j);    xicom=vector(1,n); 
         hess[j][i]=hess[i][j];    nrfunc=func; 
       }    for (j=1;j<=n;j++) { 
     }      pcom[j]=p[j]; 
   }      xicom[j]=xi[j]; 
   printf("\n");    } 
     ax=0.0; 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    xx=1.0; 
      mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
   a=matrix(1,npar,1,npar);    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   y=matrix(1,npar,1,npar);  #ifdef DEBUG
   x=vector(1,npar);    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   indx=ivector(1,npar);    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   for (i=1;i<=npar;i++)  #endif
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    for (j=1;j<=n;j++) { 
   ludcmp(a,npar,indx,&pd);      xi[j] *= xmin; 
       p[j] += xi[j]; 
   for (j=1;j<=npar;j++) {    } 
     for (i=1;i<=npar;i++) x[i]=0;    free_vector(xicom,1,n); 
     x[j]=1;    free_vector(pcom,1,n); 
     lubksb(a,npar,indx,x);  } 
     for (i=1;i<=npar;i++){  
       matcov[i][j]=x[i];  char *asc_diff_time(long time_sec, char ascdiff[])
     }  {
   }    long sec_left, days, hours, minutes;
     days = (time_sec) / (60*60*24);
   printf("\n#Hessian matrix#\n");    sec_left = (time_sec) % (60*60*24);
   for (i=1;i<=npar;i++) {    hours = (sec_left) / (60*60) ;
     for (j=1;j<=npar;j++) {    sec_left = (sec_left) %(60*60);
       printf("%.3e ",hess[i][j]);    minutes = (sec_left) /60;
     }    sec_left = (sec_left) % (60);
     printf("\n");    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   }    return ascdiff;
   }
   /* Recompute Inverse */  
   for (i=1;i<=npar;i++)  /*************** powell ************************/
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   ludcmp(a,npar,indx,&pd);              double (*func)(double [])) 
   { 
   /*  printf("\n#Hessian matrix recomputed#\n");    void linmin(double p[], double xi[], int n, double *fret, 
                 double (*func)(double [])); 
   for (j=1;j<=npar;j++) {    int i,ibig,j; 
     for (i=1;i<=npar;i++) x[i]=0;    double del,t,*pt,*ptt,*xit;
     x[j]=1;    double fp,fptt;
     lubksb(a,npar,indx,x);    double *xits;
     for (i=1;i<=npar;i++){    int niterf, itmp;
       y[i][j]=x[i];  
       printf("%.3e ",y[i][j]);    pt=vector(1,n); 
     }    ptt=vector(1,n); 
     printf("\n");    xit=vector(1,n); 
   }    xits=vector(1,n); 
   */    *fret=(*func)(p); 
     for (j=1;j<=n;j++) pt[j]=p[j]; 
   free_matrix(a,1,npar,1,npar);    for (*iter=1;;++(*iter)) { 
   free_matrix(y,1,npar,1,npar);      fp=(*fret); 
   free_vector(x,1,npar);      ibig=0; 
   free_ivector(indx,1,npar);      del=0.0; 
   free_matrix(hess,1,npar,1,npar);      last_time=curr_time;
       (void) gettimeofday(&curr_time,&tzp);
       printf("\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);fflush(stdout);
 }      /*    fprintf(ficlog,"\nPowell iter=%d -2*LL=%.12f %ld sec. %ld sec.",*iter,*fret, curr_time.tv_sec-last_time.tv_sec, curr_time.tv_sec-start_time.tv_sec);
       fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
 /*************** hessian matrix ****************/      */
 double hessii( double x[], double delta, int theta, double delti[])     for (i=1;i<=n;i++) {
 {        printf(" %d %.12f",i, p[i]);
   int i;        fprintf(ficlog," %d %.12lf",i, p[i]);
   int l=1, lmax=20;        fprintf(ficrespow," %.12lf", p[i]);
   double k1,k2;      }
   double p2[NPARMAX+1];      printf("\n");
   double res;      fprintf(ficlog,"\n");
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;      fprintf(ficrespow,"\n");fflush(ficrespow);
   double fx;      if(*iter <=3){
   int k=0,kmax=10;        tm = *localtime(&curr_time.tv_sec);
   double l1;        strcpy(strcurr,asctime(&tm));
   /*       asctime_r(&tm,strcurr); */
   fx=func(x);        forecast_time=curr_time; 
   for (i=1;i<=npar;i++) p2[i]=x[i];        itmp = strlen(strcurr);
   for(l=0 ; l <=lmax; l++){        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
     l1=pow(10,l);          strcurr[itmp-1]='\0';
     delts=delt;        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     for(k=1 ; k <kmax; k=k+1){        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       delt = delta*(l1*k);        for(niterf=10;niterf<=30;niterf+=10){
       p2[theta]=x[theta] +delt;          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
       k1=func(p2)-fx;          tmf = *localtime(&forecast_time.tv_sec);
       p2[theta]=x[theta]-delt;  /*      asctime_r(&tmf,strfor); */
       k2=func(p2)-fx;          strcpy(strfor,asctime(&tmf));
       /*res= (k1-2.0*fx+k2)/delt/delt; */          itmp = strlen(strfor);
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          if(strfor[itmp-1]=='\n')
                strfor[itmp-1]='\0';
 #ifdef DEBUG          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);
       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,"   - 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);
 #endif        }
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */      }
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){      for (i=1;i<=n;i++) { 
         k=kmax;        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       }        fptt=(*fret); 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */  #ifdef DEBUG
         k=kmax; l=lmax*10.;        printf("fret=%lf \n",*fret);
       }        fprintf(ficlog,"fret=%lf \n",*fret);
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  #endif
         delts=delt;        printf("%d",i);fflush(stdout);
       }        fprintf(ficlog,"%d",i);fflush(ficlog);
     }        linmin(p,xit,n,fret,func); 
   }        if (fabs(fptt-(*fret)) > del) { 
   delti[theta]=delts;          del=fabs(fptt-(*fret)); 
   return res;          ibig=i; 
          } 
 }  #ifdef DEBUG
         printf("%d %.12e",i,(*fret));
 double hessij( double x[], double delti[], int thetai,int thetaj)        fprintf(ficlog,"%d %.12e",i,(*fret));
 {        for (j=1;j<=n;j++) {
   int i;          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   int l=1, l1, lmax=20;          printf(" x(%d)=%.12e",j,xit[j]);
   double k1,k2,k3,k4,res,fx;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
   double p2[NPARMAX+1];        }
   int k;        for(j=1;j<=n;j++) {
           printf(" p=%.12e",p[j]);
   fx=func(x);          fprintf(ficlog," p=%.12e",p[j]);
   for (k=1; k<=2; k++) {        }
     for (i=1;i<=npar;i++) p2[i]=x[i];        printf("\n");
     p2[thetai]=x[thetai]+delti[thetai]/k;        fprintf(ficlog,"\n");
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  #endif
     k1=func(p2)-fx;      } 
        if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
     p2[thetai]=x[thetai]+delti[thetai]/k;  #ifdef DEBUG
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        int k[2],l;
     k2=func(p2)-fx;        k[0]=1;
          k[1]=-1;
     p2[thetai]=x[thetai]-delti[thetai]/k;        printf("Max: %.12e",(*func)(p));
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        fprintf(ficlog,"Max: %.12e",(*func)(p));
     k3=func(p2)-fx;        for (j=1;j<=n;j++) {
            printf(" %.12e",p[j]);
     p2[thetai]=x[thetai]-delti[thetai]/k;          fprintf(ficlog," %.12e",p[j]);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;        }
     k4=func(p2)-fx;        printf("\n");
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */        fprintf(ficlog,"\n");
 #ifdef DEBUG        for(l=0;l<=1;l++) {
     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);          for (j=1;j<=n;j++) {
 #endif            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]);
   return res;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
 }          }
           printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 /************** Inverse of matrix **************/          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 void ludcmp(double **a, int n, int *indx, double *d)        }
 {  #endif
   int i,imax,j,k;  
   double big,dum,sum,temp;  
   double *vv;        free_vector(xit,1,n); 
          free_vector(xits,1,n); 
   vv=vector(1,n);        free_vector(ptt,1,n); 
   *d=1.0;        free_vector(pt,1,n); 
   for (i=1;i<=n;i++) {        return; 
     big=0.0;      } 
     for (j=1;j<=n;j++)      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       if ((temp=fabs(a[i][j])) > big) big=temp;      for (j=1;j<=n;j++) { 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");        ptt[j]=2.0*p[j]-pt[j]; 
     vv[i]=1.0/big;        xit[j]=p[j]-pt[j]; 
   }        pt[j]=p[j]; 
   for (j=1;j<=n;j++) {      } 
     for (i=1;i<j;i++) {      fptt=(*func)(ptt); 
       sum=a[i][j];      if (fptt < fp) { 
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       a[i][j]=sum;        if (t < 0.0) { 
     }          linmin(p,xit,n,fret,func); 
     big=0.0;          for (j=1;j<=n;j++) { 
     for (i=j;i<=n;i++) {            xi[j][ibig]=xi[j][n]; 
       sum=a[i][j];            xi[j][n]=xit[j]; 
       for (k=1;k<j;k++)          }
         sum -= a[i][k]*a[k][j];  #ifdef DEBUG
       a[i][j]=sum;          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       if ( (dum=vv[i]*fabs(sum)) >= big) {          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
         big=dum;          for(j=1;j<=n;j++){
         imax=i;            printf(" %.12e",xit[j]);
       }            fprintf(ficlog," %.12e",xit[j]);
     }          }
     if (j != imax) {          printf("\n");
       for (k=1;k<=n;k++) {          fprintf(ficlog,"\n");
         dum=a[imax][k];  #endif
         a[imax][k]=a[j][k];        }
         a[j][k]=dum;      } 
       }    } 
       *d = -(*d);  } 
       vv[imax]=vv[j];  
     }  /**** Prevalence limit (stable or period prevalence)  ****************/
     indx[j]=imax;  
     if (a[j][j] == 0.0) a[j][j]=TINY;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
     if (j != n) {  {
       dum=1.0/(a[j][j]);    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       for (i=j+1;i<=n;i++) a[i][j] *= dum;       matrix by transitions matrix until convergence is reached */
     }  
   }    int i, ii,j,k;
   free_vector(vv,1,n);  /* Doesn't work */    double min, max, maxmin, maxmax,sumnew=0.;
 ;    double **matprod2();
 }    double **out, cov[NCOVMAX], **pmij();
     double **newm;
 void lubksb(double **a, int n, int *indx, double b[])    double agefin, delaymax=50 ; /* Max number of years to converge */
 {  
   int i,ii=0,ip,j;    for (ii=1;ii<=nlstate+ndeath;ii++)
   double sum;      for (j=1;j<=nlstate+ndeath;j++){
          oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   for (i=1;i<=n;i++) {      }
     ip=indx[i];  
     sum=b[ip];     cov[1]=1.;
     b[ip]=b[i];   
     if (ii)   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
     else if (sum) ii=i;      newm=savm;
     b[i]=sum;      /* Covariates have to be included here again */
   }       cov[2]=agefin;
   for (i=n;i>=1;i--) {    
     sum=b[i];        for (k=1; k<=cptcovn;k++) {
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     b[i]=sum/a[i][i];          /*      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 (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         for (k=1; k<=cptcovprod;k++)
 /************ Frequencies ********************/          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)  
 {  /* Some frequencies */        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
          /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   double ***freq; /* Frequencies */      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
   double *pp;  
   double pos;      savm=oldm;
   FILE *ficresp;      oldm=newm;
   char fileresp[FILENAMELENGTH];      maxmax=0.;
       for(j=1;j<=nlstate;j++){
   pp=vector(1,nlstate);        min=1.;
         max=0.;
   strcpy(fileresp,"p");        for(i=1; i<=nlstate; i++) {
   strcat(fileresp,fileres);          sumnew=0;
   if((ficresp=fopen(fileresp,"w"))==NULL) {          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
     printf("Problem with prevalence resultfile: %s\n", fileresp);          prlim[i][j]= newm[i][j]/(1-sumnew);
     exit(0);          max=FMAX(max,prlim[i][j]);
   }          min=FMIN(min,prlim[i][j]);
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        }
   j1=0;        maxmin=max-min;
         maxmax=FMAX(maxmax,maxmin);
   j=cptcoveff;      }
   if (cptcovn<1) {j=1;ncodemax[1]=1;}      if(maxmax < ftolpl){
         return prlim;
   for(k1=1; k1<=j;k1++){      }
    for(i1=1; i1<=ncodemax[k1];i1++){    }
        j1++;  }
   
         for (i=-1; i<=nlstate+ndeath; i++)    /*************** transition probabilities ***************/ 
          for (jk=-1; jk<=nlstate+ndeath; jk++)    
            for(m=agemin; m <= agemax+3; m++)  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
              freq[i][jk][m]=0;  {
            double s1, s2;
        for (i=1; i<=imx; i++) {    /*double t34;*/
          bool=1;    int i,j,j1, nc, ii, jj;
          if  (cptcovn>0) {  
            for (z1=1; z1<=cptcoveff; z1++)      for(i=1; i<= nlstate; i++){
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) bool=0;        for(j=1; j<i;j++){
          }          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
           if (bool==1) {            /*s2 += param[i][j][nc]*cov[nc];*/
            for(m=firstpass; m<=lastpass-1; m++){            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
              if(agev[m][i]==0) agev[m][i]=agemax+1;  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
              if(agev[m][i]==1) agev[m][i]=agemax+2;          }
              freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];          ps[i][j]=s2;
              freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
            }        }
          }        for(j=i+1; j<=nlstate+ndeath;j++){
        }          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
         if  (cptcovn>0) {            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
          fprintf(ficresp, "\n#********** Variable ");  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);          }
        }          ps[i][j]=s2;
        fprintf(ficresp, "**********\n#");        }
        for(i=1; i<=nlstate;i++)      }
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);      /*ps[3][2]=1;*/
        fprintf(ficresp, "\n");      
              for(i=1; i<= nlstate; i++){
   for(i=(int)agemin; i <= (int)agemax+3; i++){        s1=0;
     if(i==(int)agemax+3)        for(j=1; j<i; j++)
       printf("Total");          s1+=exp(ps[i][j]);
     else        for(j=i+1; j<=nlstate+ndeath; j++)
       printf("Age %d", i);          s1+=exp(ps[i][j]);
     for(jk=1; jk <=nlstate ; jk++){        ps[i][i]=1./(s1+1.);
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        for(j=1; j<i; j++)
         pp[jk] += freq[jk][m][i];          ps[i][j]= exp(ps[i][j])*ps[i][i];
     }        for(j=i+1; j<=nlstate+ndeath; j++)
     for(jk=1; jk <=nlstate ; jk++){          ps[i][j]= exp(ps[i][j])*ps[i][i];
       for(m=-1, pos=0; m <=0 ; m++)        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
         pos += freq[jk][m][i];      } /* end i */
       if(pp[jk]>=1.e-10)      
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       else        for(jj=1; jj<= nlstate+ndeath; jj++){
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          ps[ii][jj]=0;
     }          ps[ii][ii]=1;
     for(jk=1; jk <=nlstate ; jk++){        }
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)      }
         pp[jk] += freq[jk][m][i];      
     }  
     for(jk=1,pos=0; jk <=nlstate ; jk++)  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
       pos += pp[jk];  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
     for(jk=1; jk <=nlstate ; jk++){  /*         printf("ddd %lf ",ps[ii][jj]); */
       if(pos>=1.e-5)  /*       } */
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  /*       printf("\n "); */
       else  /*        } */
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  /*        printf("\n ");printf("%lf ",cov[2]); */
       if( i <= (int) agemax){         /*
         if(pos>=1.e-5)        for(i=1; i<= npar; i++) printf("%f ",x[i]);
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        goto end;*/
       else      return ps;
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);  }
       }  
     }  /**************** Product of 2 matrices ******************/
     for(jk=-1; jk <=nlstate+ndeath; jk++)  
       for(m=-1; m <=nlstate+ndeath; m++)  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);  {
     if(i <= (int) agemax)    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       fprintf(ficresp,"\n");       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
     printf("\n");    /* in, b, out are matrice of pointers which should have been initialized 
     }       before: only the contents of out is modified. The function returns
     }       a pointer to pointers identical to out */
  }    long i, j, k;
      for(i=nrl; i<= nrh; i++)
   fclose(ficresp);      for(k=ncolol; k<=ncoloh; k++)
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);        for(j=ncl,out[i][k]=0.; j<=nch; j++)
   free_vector(pp,1,nlstate);          out[i][k] +=in[i][j]*b[j][k];
   
 }  /* End of Freq */    return out;
   }
 /************* Waves Concatenation ***************/  
   
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)  /************* Higher Matrix Product ***************/
 {  
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
      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    /* Computes the transition matrix starting at age 'age' over 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]       'nhstepm*hstepm*stepm' months (i.e. until
      and mw[mi+1][i]. dh depends on stepm.       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
      */       nhstepm*hstepm matrices. 
        Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
   int i, mi, m;       (typically every 2 years instead of every month which is too big 
   int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;       for the memory).
 float sum=0.;       Model is determined by parameters x and covariates have to be 
        included manually here. 
   for(i=1; i<=imx; i++){  
     mi=0;       */
     m=firstpass;  
     while(s[m][i] <= nlstate){    int i, j, d, h, k;
       if(s[m][i]>=1)    double **out, cov[NCOVMAX];
         mw[++mi][i]=m;    double **newm;
       if(m >=lastpass)  
         break;    /* Hstepm could be zero and should return the unit matrix */
       else    for (i=1;i<=nlstate+ndeath;i++)
         m++;      for (j=1;j<=nlstate+ndeath;j++){
     }/* end while */        oldm[i][j]=(i==j ? 1.0 : 0.0);
     if (s[m][i] > nlstate){        po[i][j][0]=(i==j ? 1.0 : 0.0);
       mi++;     /* Death is another wave */      }
       /* if(mi==0)  never been interviewed correctly before death */    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
          /* Only death is a correct wave */    for(h=1; h <=nhstepm; h++){
       mw[mi][i]=m;      for(d=1; d <=hstepm; d++){
     }        newm=savm;
         /* Covariates have to be included here again */
     wav[i]=mi;        cov[1]=1.;
     if(mi==0)        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
   }        for (k=1; k<=cptcovage;k++)
           cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
   for(i=1; i<=imx; i++){        for (k=1; k<=cptcovprod;k++)
     for(mi=1; mi<wav[i];mi++){          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       if (stepm <=0)  
         dh[mi][i]=1;  
       else{        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
         if (s[mw[mi+1][i]][i] > nlstate) {        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
           if(j=0) j=1;  /* Survives at least one month after exam */                     pmij(pmmij,cov,ncovmodel,x,nlstate));
         }        savm=oldm;
         else{        oldm=newm;
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));      }
           k=k+1;      for(i=1; i<=nlstate+ndeath; i++)
           if (j >= jmax) jmax=j;        for(j=1;j<=nlstate+ndeath;j++) {
           else if (j <= jmin)jmin=j;          po[i][j][h]=newm[i][j];
           sum=sum+j;          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
         }           */
         jk= j/stepm;        }
         jl= j -jk*stepm;    } /* end h */
         ju= j -(jk+1)*stepm;    return po;
         if(jl <= -ju)  }
           dh[mi][i]=jk;  
         else  
           dh[mi][i]=jk+1;  /*************** log-likelihood *************/
         if(dh[mi][i]==0)  double func( double *x)
           dh[mi][i]=1; /* At least one step */  {
       }    int i, ii, j, k, mi, d, kk;
     }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   }    double **out;
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);    double sw; /* Sum of weights */
 }    double lli; /* Individual log likelihood */
 /*********** Tricode ****************************/    int s1, s2;
 void tricode(int *Tvar, int **nbcode, int imx)    double bbh, survp;
 {    long ipmx;
   int Ndum[20],ij=1, k, j, i;    /*extern weight */
   int cptcode=0;    /* We are differentiating ll according to initial status */
   cptcoveff=0;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
      /*for(i=1;i<imx;i++) 
   for (k=0; k<19; k++) Ndum[k]=0;      printf(" %d\n",s[4][i]);
   for (k=1; k<=7; k++) ncodemax[k]=0;    */
     cov[1]=1.;
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {  
     for (i=1; i<=imx; i++) {    for(k=1; k<=nlstate; k++) ll[k]=0.;
       ij=(int)(covar[Tvar[j]][i]);  
       Ndum[ij]++;    if(mle==1){
       if (ij > cptcode) cptcode=ij;      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++){
     /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/          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++){
     for (i=1; i<=ncodemax[j]; i++) {            newm=savm;
       for (k=0; k<=19; k++) {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         if (Ndum[k] != 0) {            for (kk=1; kk<=cptcovage;kk++) {
           nbcode[Tvar[j]][ij]=k;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           /*   printf("ij=%d ",nbcode[Tvar[2]][1]);*/            }
           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 */
   }          
  for (i=1; i<=10; i++) {          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       ij=Tvar[i];          /* But now since version 0.9 we anticipate for bias at large stepm.
       Ndum[ij]++;           * 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 
  ij=1;           * the nearest (and in case of equal distance, to the lowest) interval but now
  for (i=1; i<=cptcovn; i++) {           * we keep into memory the bias bh[mi][i] and also the previous matrix product
    if((Ndum[i]!=0) && (i<=ncov)){           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
      Tvaraff[i]=ij;           * probability in order to take into account the bias as a fraction of the way
    ij++;           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
    }           * -stepm/2 to stepm/2 .
  }           * For stepm=1 the results are the same as for previous versions of Imach.
             * For stepm > 1 the results are less biased than in previous versions. 
  for (j=1; j<=(cptcovn+2*cptcovprod); j++) {           */
    if ((Tvar[j]>= cptcoveff) && (Tvar[j] <=ncov)) cptcoveff=Tvar[j];          s1=s[mw[mi][i]][i];
    /*printf("j=%d %d\n",j,Tvar[j]);*/          s2=s[mw[mi+1][i]][i];
  }          bbh=(double)bh[mi][i]/(double)stepm; 
            /* bias bh is positive if real duration
  /* printf("cptcoveff=%d Tvaraff=%d %d\n",cptcoveff, Tvaraff[1],Tvaraff[2]);           * is higher than the multiple of stepm and negative otherwise.
     scanf("%d",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]));*/
           if( s2 > nlstate){ 
 /*********** Health Expectancies ****************/            /* 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 
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)               die between last step unit time and current  step unit time, 
 {               which is also equal to probability to die before dh 
   /* Health expectancies */               minus probability to die before dh-stepm . 
   int i, j, nhstepm, hstepm, h;               In version up to 0.92 likelihood was computed
   double age, agelim,hf;          as if date of death was unknown. Death was treated as any other
   double ***p3mat;          health state: the date of the interview describes the actual state
            and not the date of a change in health state. The former idea was
   fprintf(ficreseij,"# Health expectancies\n");          to consider that at each interview the state was recorded
   fprintf(ficreseij,"# Age");          (healthy, disable or death) and IMaCh was corrected; but when we
   for(i=1; i<=nlstate;i++)          introduced the exact date of death then we should have modified
     for(j=1; j<=nlstate;j++)          the contribution of an exact death to the likelihood. This new
       fprintf(ficreseij," %1d-%1d",i,j);          contribution is smaller and very dependent of the step unit
   fprintf(ficreseij,"\n");          stepm. It is no more the probability to die between last interview
           and month of death but the probability to survive from last
   hstepm=1*YEARM; /*  Every j years of age (in month) */          interview up to one month before death multiplied by the
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          probability to die within a month. Thanks to Chris
           Jackson for correcting this bug.  Former versions increased
   agelim=AGESUP;          mortality artificially. The bad side is that we add another loop
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          which slows down the processing. The difference can be up to 10%
     /* nhstepm age range expressed in number of stepm */          lower mortality.
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);            */
     /* Typically if 20 years = 20*12/6=40 stepm */            lli=log(out[s1][s2] - savm[s1][s2]);
     if (stepm >= YEARM) hstepm=1;  
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */  
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          } else if  (s2==-2) {
     /* Computed by stepm unit matrices, product of hstepm matrices, stored            for (j=1,survp=0. ; j<=nlstate; j++) 
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);              /*survp += out[s1][j]; */
             lli= log(survp);
           }
     for(i=1; i<=nlstate;i++)          
       for(j=1; j<=nlstate;j++)          else if  (s2==-4) { 
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){            for (j=3,survp=0. ; j<=nlstate; j++)  
           eij[i][j][(int)age] +=p3mat[i][j][h];              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
         }            lli= log(survp); 
              } 
     hf=1;  
     if (stepm >= YEARM) hf=stepm/YEARM;          else if  (s2==-5) { 
     fprintf(ficreseij,"%.0f",age );            for (j=1,survp=0. ; j<=2; j++)  
     for(i=1; i<=nlstate;i++)              survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
       for(j=1; j<=nlstate;j++){            lli= log(survp); 
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);          } 
       }          
     fprintf(ficreseij,"\n");          else{
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   }            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
 }          } 
           /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
 /************ Variance ******************/          /*if(lli ==000.0)*/
 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)          /*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); */
 {          ipmx +=1;
   /* Variance of health expectancies */          sw += weight[i];
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   double **newm;        } /* end of wave */
   double **dnewm,**doldm;      } /* end of individual */
   int i, j, nhstepm, hstepm, h;    }  else if(mle==2){
   int k, cptcode;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
    double *xp;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double **gp, **gm;        for(mi=1; mi<= wav[i]-1; mi++){
   double ***gradg, ***trgradg;          for (ii=1;ii<=nlstate+ndeath;ii++)
   double ***p3mat;            for (j=1;j<=nlstate+ndeath;j++){
   double age,agelim;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   int theta;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
    fprintf(ficresvij,"# Covariances of life expectancies\n");          for(d=0; d<=dh[mi][i]; d++){
   fprintf(ficresvij,"# Age");            newm=savm;
   for(i=1; i<=nlstate;i++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for(j=1; j<=nlstate;j++)            for (kk=1; kk<=cptcovage;kk++) {
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   fprintf(ficresvij,"\n");            }
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   xp=vector(1,npar);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   dnewm=matrix(1,nlstate,1,npar);            savm=oldm;
   doldm=matrix(1,nlstate,1,nlstate);            oldm=newm;
            } /* end mult */
   hstepm=1*YEARM; /* Every year of age */        
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */          s1=s[mw[mi][i]][i];
   agelim = AGESUP;          s2=s[mw[mi+1][i]][i];
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          bbh=(double)bh[mi][i]/(double)stepm; 
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
     if (stepm >= YEARM) hstepm=1;          ipmx +=1;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          sw += weight[i];
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);        } /* end of wave */
     gp=matrix(0,nhstepm,1,nlstate);      } /* end of individual */
     gm=matrix(0,nhstepm,1,nlstate);    }  else if(mle==3){  /* exponential inter-extrapolation */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for(theta=1; theta <=npar; theta++){        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(i=1; i<=npar; i++){ /* Computes gradient */        for(mi=1; mi<= wav[i]-1; mi++){
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          for (ii=1;ii<=nlstate+ndeath;ii++)
       }            for (j=1;j<=nlstate+ndeath;j++){
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
       for(j=1; j<= nlstate; j++){            }
         for(h=0; h<=nhstepm; h++){          for(d=0; d<dh[mi][i]; d++){
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)            newm=savm;
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         }            for (kk=1; kk<=cptcovage;kk++) {
       }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
                }
       for(i=1; i<=npar; i++) /* Computes gradient */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         xp[i] = x[i] - (i==theta ?delti[theta]:0);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              savm=oldm;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);            oldm=newm;
       for(j=1; j<= nlstate; j++){          } /* end mult */
         for(h=0; h<=nhstepm; h++){        
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)          s1=s[mw[mi][i]][i];
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];          s2=s[mw[mi+1][i]][i];
         }          bbh=(double)bh[mi][i]/(double)stepm; 
       }          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 */
       for(j=1; j<= nlstate; j++)          ipmx +=1;
         for(h=0; h<=nhstepm; h++){          sw += weight[i];
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         }        } /* end of wave */
     } /* End theta */      } /* end of individual */
     }else if (mle==4){  /* ml=4 no inter-extrapolation */
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     for(h=0; h<=nhstepm; h++)        for(mi=1; mi<= wav[i]-1; mi++){
       for(j=1; j<=nlstate;j++)          for (ii=1;ii<=nlstate+ndeath;ii++)
         for(theta=1; theta <=npar; theta++)            for (j=1;j<=nlstate+ndeath;j++){
           trgradg[h][j][theta]=gradg[h][theta][j];              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
               savm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(i=1;i<=nlstate;i++)            }
       for(j=1;j<=nlstate;j++)          for(d=0; d<dh[mi][i]; d++){
         vareij[i][j][(int)age] =0.;            newm=savm;
     for(h=0;h<=nhstepm;h++){            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       for(k=0;k<=nhstepm;k++){            for (kk=1; kk<=cptcovage;kk++) {
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);            }
         for(i=1;i<=nlstate;i++)          
           for(j=1;j<=nlstate;j++)            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
             vareij[i][j][(int)age] += doldm[i][j];                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       }            savm=oldm;
     }            oldm=newm;
     h=1;          } /* end mult */
     if (stepm >= YEARM) h=stepm/YEARM;        
     fprintf(ficresvij,"%.0f ",age );          s1=s[mw[mi][i]][i];
     for(i=1; i<=nlstate;i++)          s2=s[mw[mi+1][i]][i];
       for(j=1; j<=nlstate;j++){          if( s2 > nlstate){ 
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);            lli=log(out[s1][s2] - savm[s1][s2]);
       }          }else{
     fprintf(ficresvij,"\n");            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     free_matrix(gp,0,nhstepm,1,nlstate);          }
     free_matrix(gm,0,nhstepm,1,nlstate);          ipmx +=1;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);          sw += weight[i];
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
   } /* End age */        } /* end of wave */
        } /* end of individual */
   free_vector(xp,1,npar);    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   free_matrix(doldm,1,nlstate,1,npar);      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   free_matrix(dnewm,1,nlstate,1,nlstate);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         for(mi=1; mi<= wav[i]-1; mi++){
 }          for (ii=1;ii<=nlstate+ndeath;ii++)
             for (j=1;j<=nlstate+ndeath;j++){
 /************ Variance of prevlim ******************/              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 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)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 {            }
   /* Variance of prevalence limit */          for(d=0; d<dh[mi][i]; d++){
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/            newm=savm;
   double **newm;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   double **dnewm,**doldm;            for (kk=1; kk<=cptcovage;kk++) {
   int i, j, nhstepm, hstepm;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   int k, cptcode;            }
   double *xp;          
   double *gp, *gm;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   double **gradg, **trgradg;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   double age,agelim;            savm=oldm;
   int theta;            oldm=newm;
              } /* end mult */
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");        
   fprintf(ficresvpl,"# Age");          s1=s[mw[mi][i]][i];
   for(i=1; i<=nlstate;i++)          s2=s[mw[mi+1][i]][i];
       fprintf(ficresvpl," %1d-%1d",i,i);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
   fprintf(ficresvpl,"\n");          ipmx +=1;
           sw += weight[i];
   xp=vector(1,npar);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   dnewm=matrix(1,nlstate,1,npar);          /*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]);*/
   doldm=matrix(1,nlstate,1,nlstate);        } /* end of wave */
        } /* end of individual */
   hstepm=1*YEARM; /* Every year of age */    } /* End of if */
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   agelim = AGESUP;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    return -l;
     if (stepm >= YEARM) hstepm=1;  }
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  
     gradg=matrix(1,npar,1,nlstate);  /*************** log-likelihood *************/
     gp=vector(1,nlstate);  double funcone( double *x)
     gm=vector(1,nlstate);  {
     /* Same as likeli but slower because of a lot of printf and if */
     for(theta=1; theta <=npar; theta++){    int i, ii, j, k, mi, d, kk;
       for(i=1; i<=npar; i++){ /* Computes gradient */    double l, ll[NLSTATEMAX], cov[NCOVMAX];
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    double **out;
       }    double lli; /* Individual log likelihood */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    double llt;
       for(i=1;i<=nlstate;i++)    int s1, s2;
         gp[i] = prlim[i][i];    double bbh, survp;
        /*extern weight */
       for(i=1; i<=npar; i++) /* Computes gradient */    /* We are differentiating ll according to initial status */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    /*for(i=1;i<imx;i++) 
       for(i=1;i<=nlstate;i++)      printf(" %d\n",s[4][i]);
         gm[i] = prlim[i][i];    */
     cov[1]=1.;
       for(i=1;i<=nlstate;i++)  
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    for(k=1; k<=nlstate; k++) ll[k]=0.;
     } /* End theta */  
     for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     trgradg =matrix(1,nlstate,1,npar);      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){
     for(j=1; j<=nlstate;j++)        for (ii=1;ii<=nlstate+ndeath;ii++)
       for(theta=1; theta <=npar; theta++)          for (j=1;j<=nlstate+ndeath;j++){
         trgradg[j][theta]=gradg[theta][j];            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
             savm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(i=1;i<=nlstate;i++)          }
       varpl[i][(int)age] =0.;        for(d=0; d<dh[mi][i]; d++){
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          newm=savm;
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     for(i=1;i<=nlstate;i++)          for (kk=1; kk<=cptcovage;kk++) {
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           }
     fprintf(ficresvpl,"%.0f ",age );          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     for(i=1; i<=nlstate;i++)                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));          savm=oldm;
     fprintf(ficresvpl,"\n");          oldm=newm;
     free_vector(gp,1,nlstate);        } /* end mult */
     free_vector(gm,1,nlstate);        
     free_matrix(gradg,1,npar,1,nlstate);        s1=s[mw[mi][i]][i];
     free_matrix(trgradg,1,nlstate,1,npar);        s2=s[mw[mi+1][i]][i];
   } /* End age */        bbh=(double)bh[mi][i]/(double)stepm; 
         /* bias is positive if real duration
   free_vector(xp,1,npar);         * is higher than the multiple of stepm and negative otherwise.
   free_matrix(doldm,1,nlstate,1,npar);         */
   free_matrix(dnewm,1,nlstate,1,nlstate);        if( s2 > nlstate && (mle <5) ){  /* Jackson */
           lli=log(out[s1][s2] - savm[s1][s2]);
 }        } else if  (s2==-2) {
           for (j=1,survp=0. ; j<=nlstate; j++) 
             survp += (1.+bbh)*out[s1][j]- bbh*savm[s1][j];
           lli= log(survp);
 /***********************************************/        }else if (mle==1){
 /**************** Main Program *****************/          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 /***********************************************/        } else if(mle==2){
           lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
 /*int main(int argc, char *argv[])*/        } else if(mle==3){  /* exponential inter-extrapolation */
 int main()          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 */
   int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
   double agedeb, agefin,hf;          lli=log(out[s1][s2]); /* Original formula */
   double agemin=1.e20, agemax=-1.e20;        } /* End of if */
         ipmx +=1;
   double fret;        sw += weight[i];
   double **xi,tmp,delta;        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]); */
   double dum; /* Dummy variable */        if(globpr){
   double ***p3mat;          fprintf(ficresilk,"%9d %6d %2d %2d %1d %1d %3d %11.6f %8.4f\
   int *indx;   %11.6f %11.6f %11.6f ", \
   char line[MAXLINE], linepar[MAXLINE];                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   char title[MAXLINE];                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];            llt +=ll[k]*gipmx/gsw;
   char filerest[FILENAMELENGTH];            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   char fileregp[FILENAMELENGTH];          }
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];          fprintf(ficresilk," %10.6f\n", -llt);
   int firstobs=1, lastobs=10;        }
   int sdeb, sfin; /* Status at beginning and end */      } /* end of wave */
   int c,  h , cpt,l;    } /* end of individual */
   int ju,jl, mi;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
      if(globpr==0){ /* First time we count the contributions and weights */
   int hstepm, nhstepm;      gipmx=ipmx;
   double bage, fage, age, agelim, agebase;      gsw=sw;
   double ftolpl=FTOL;    }
   double **prlim;    return -l;
   double *severity;  }
   double ***param; /* Matrix of parameters */  
   double  *p;  
   double **matcov; /* Matrix of covariance */  /*************** function likelione ***********/
   double ***delti3; /* Scale */  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   double *delti; /* Scale */  {
   double ***eij, ***vareij;    /* This routine should help understanding what is done with 
   double **varpl; /* Variances of prevalence limits by age */       the selection of individuals/waves and
   double *epj, vepp;       to check the exact contribution to the likelihood.
   char version[80]="Imach version 62c, May 1999, INED-EUROREVES ";       Plotting could be done.
   char *alph[]={"a","a","b","c","d","e"}, str[4];     */
     int k;
   char z[1]="c", occ;  
 #include <sys/time.h>    if(*globpri !=0){ /* Just counts and sums, no printings */
 #include <time.h>      strcpy(fileresilk,"ilk"); 
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      strcat(fileresilk,fileres);
   /* long total_usecs;      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   struct timeval start_time, end_time;        printf("Problem with resultfile: %s\n", fileresilk);
          fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */      }
       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 ");
   printf("\nIMACH, Version 0.64a");      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   printf("\nEnter the parameter file name: ");      for(k=1; k<=nlstate; k++) 
         fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
 #ifdef windows      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
   scanf("%s",pathtot);    }
   getcwd(pathcd, size);  
   /*cygwin_split_path(pathtot,path,optionfile);    *fretone=(*funcone)(p);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    if(*globpri !=0){
   /* cutv(path,optionfile,pathtot,'\\');*/      fclose(ficresilk);
       fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
 split(pathtot, path,optionfile);      fflush(fichtm); 
   chdir(path);    } 
   replace(pathc,path);    return;
 #endif  }
 #ifdef unix  
   scanf("%s",optionfile);  
 #endif  /*********** Maximum Likelihood Estimation ***************/
   
 /*-------- arguments in the command line --------*/  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   {
   strcpy(fileres,"r");    int i,j, iter;
   strcat(fileres, optionfile);    double **xi;
     double fret;
   /*---------arguments file --------*/    double fretone; /* Only one call to likelihood */
     /*  char filerespow[FILENAMELENGTH];*/
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    xi=matrix(1,npar,1,npar);
     printf("Problem with optionfile %s\n",optionfile);    for (i=1;i<=npar;i++)
     goto end;      for (j=1;j<=npar;j++)
   }        xi[i][j]=(i==j ? 1.0 : 0.0);
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
   strcpy(filereso,"o");    strcpy(filerespow,"pow"); 
   strcat(filereso,fileres);    strcat(filerespow,fileres);
   if((ficparo=fopen(filereso,"w"))==NULL) {    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      printf("Problem with resultfile: %s\n", filerespow);
   }      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
     }
   /* Reads comments: lines beginning with '#' */    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   while((c=getc(ficpar))=='#' && c!= EOF){    for (i=1;i<=nlstate;i++)
     ungetc(c,ficpar);      for(j=1;j<=nlstate+ndeath;j++)
     fgets(line, MAXLINE, ficpar);        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
     puts(line);    fprintf(ficrespow,"\n");
     fputs(line,ficparo);  
   }    powell(p,xi,npar,ftol,&iter,&fret,func);
   ungetc(c,ficpar);  
     free_matrix(xi,1,npar,1,npar);
   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);    fclose(ficrespow);
   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);    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   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);    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
     fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   covar=matrix(0,NCOVMAX,1,n);      
   if (strlen(model)<=1) cptcovn=0;  }
   else {  
     j=0;  /**** Computes Hessian and covariance matrix ***/
     j=nbocc(model,'+');  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     cptcovn=j+1;  {
   }    double  **a,**y,*x,pd;
     double **hess;
   ncovmodel=2+cptcovn;    int i, j,jk;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    int *indx;
    
   /* Read guess parameters */    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   /* Reads comments: lines beginning with '#' */    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   while((c=getc(ficpar))=='#' && c!= EOF){    void lubksb(double **a, int npar, int *indx, double b[]) ;
     ungetc(c,ficpar);    void ludcmp(double **a, int npar, int *indx, double *d) ;
     fgets(line, MAXLINE, ficpar);    double gompertz(double p[]);
     puts(line);    hess=matrix(1,npar,1,npar);
     fputs(line,ficparo);  
   }    printf("\nCalculation of the hessian matrix. Wait...\n");
   ungetc(c,ficpar);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
      for (i=1;i<=npar;i++){
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      printf("%d",i);fflush(stdout);
     for(i=1; i <=nlstate; i++)      fprintf(ficlog,"%d",i);fflush(ficlog);
     for(j=1; j <=nlstate+ndeath-1; j++){     
       fscanf(ficpar,"%1d%1d",&i1,&j1);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
       fprintf(ficparo,"%1d%1d",i1,j1);      
       printf("%1d%1d",i,j);      /*  printf(" %f ",p[i]);
       for(k=1; k<=ncovmodel;k++){          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
         fscanf(ficpar," %lf",&param[i][j][k]);    }
         printf(" %lf",param[i][j][k]);    
         fprintf(ficparo," %lf",param[i][j][k]);    for (i=1;i<=npar;i++) {
       }      for (j=1;j<=npar;j++)  {
       fscanf(ficpar,"\n");        if (j>i) { 
       printf("\n");          printf(".%d%d",i,j);fflush(stdout);
       fprintf(ficparo,"\n");          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     }          hess[i][j]=hessij(p,delti,i,j,func,npar);
            
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;          hess[j][i]=hess[i][j];    
   p=param[1][1];          /*printf(" %lf ",hess[i][j]);*/
          }
   /* Reads comments: lines beginning with '#' */      }
   while((c=getc(ficpar))=='#' && c!= EOF){    }
     ungetc(c,ficpar);    printf("\n");
     fgets(line, MAXLINE, ficpar);    fprintf(ficlog,"\n");
     puts(line);  
     fputs(line,ficparo);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   }    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   ungetc(c,ficpar);    
     a=matrix(1,npar,1,npar);
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    y=matrix(1,npar,1,npar);
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */    x=vector(1,npar);
   for(i=1; i <=nlstate; i++){    indx=ivector(1,npar);
     for(j=1; j <=nlstate+ndeath-1; j++){    for (i=1;i<=npar;i++)
       fscanf(ficpar,"%1d%1d",&i1,&j1);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
       printf("%1d%1d",i,j);    ludcmp(a,npar,indx,&pd);
       fprintf(ficparo,"%1d%1d",i1,j1);  
       for(k=1; k<=ncovmodel;k++){    for (j=1;j<=npar;j++) {
         fscanf(ficpar,"%le",&delti3[i][j][k]);      for (i=1;i<=npar;i++) x[i]=0;
         printf(" %le",delti3[i][j][k]);      x[j]=1;
         fprintf(ficparo," %le",delti3[i][j][k]);      lubksb(a,npar,indx,x);
       }      for (i=1;i<=npar;i++){ 
       fscanf(ficpar,"\n");        matcov[i][j]=x[i];
       printf("\n");      }
       fprintf(ficparo,"\n");    }
     }  
   }    printf("\n#Hessian matrix#\n");
   delti=delti3[1][1];    fprintf(ficlog,"\n#Hessian matrix#\n");
      for (i=1;i<=npar;i++) { 
   /* Reads comments: lines beginning with '#' */      for (j=1;j<=npar;j++) { 
   while((c=getc(ficpar))=='#' && c!= EOF){        printf("%.3e ",hess[i][j]);
     ungetc(c,ficpar);        fprintf(ficlog,"%.3e ",hess[i][j]);
     fgets(line, MAXLINE, ficpar);      }
     puts(line);      printf("\n");
     fputs(line,ficparo);      fprintf(ficlog,"\n");
   }    }
   ungetc(c,ficpar);  
      /* Recompute Inverse */
   matcov=matrix(1,npar,1,npar);    for (i=1;i<=npar;i++)
   for(i=1; i <=npar; i++){      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     fscanf(ficpar,"%s",&str);    ludcmp(a,npar,indx,&pd);
     printf("%s",str);  
     fprintf(ficparo,"%s",str);    /*  printf("\n#Hessian matrix recomputed#\n");
     for(j=1; j <=i; j++){  
       fscanf(ficpar," %le",&matcov[i][j]);    for (j=1;j<=npar;j++) {
       printf(" %.5le",matcov[i][j]);      for (i=1;i<=npar;i++) x[i]=0;
       fprintf(ficparo," %.5le",matcov[i][j]);      x[j]=1;
     }      lubksb(a,npar,indx,x);
     fscanf(ficpar,"\n");      for (i=1;i<=npar;i++){ 
     printf("\n");        y[i][j]=x[i];
     fprintf(ficparo,"\n");        printf("%.3e ",y[i][j]);
   }        fprintf(ficlog,"%.3e ",y[i][j]);
   for(i=1; i <=npar; i++)      }
     for(j=i+1;j<=npar;j++)      printf("\n");
       matcov[i][j]=matcov[j][i];      fprintf(ficlog,"\n");
        }
   printf("\n");    */
   
     free_matrix(a,1,npar,1,npar);
     /*-------- data file ----------*/    free_matrix(y,1,npar,1,npar);
     if((ficres =fopen(fileres,"w"))==NULL) {    free_vector(x,1,npar);
       printf("Problem with resultfile: %s\n", fileres);goto end;    free_ivector(indx,1,npar);
     }    free_matrix(hess,1,npar,1,npar);
     fprintf(ficres,"#%s\n",version);  
      
     if((fic=fopen(datafile,"r"))==NULL)    {  }
       printf("Problem with datafile: %s\n", datafile);goto end;  
     }  /*************** hessian matrix ****************/
   double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
     n= lastobs;  {
     severity = vector(1,maxwav);    int i;
     outcome=imatrix(1,maxwav+1,1,n);    int l=1, lmax=20;
     num=ivector(1,n);    double k1,k2;
     moisnais=vector(1,n);    double p2[NPARMAX+1];
     annais=vector(1,n);    double res;
     moisdc=vector(1,n);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     andc=vector(1,n);    double fx;
     agedc=vector(1,n);    int k=0,kmax=10;
     cod=ivector(1,n);    double l1;
     weight=vector(1,n);  
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    fx=func(x);
     mint=matrix(1,maxwav,1,n);    for (i=1;i<=npar;i++) p2[i]=x[i];
     anint=matrix(1,maxwav,1,n);    for(l=0 ; l <=lmax; l++){
     s=imatrix(1,maxwav+1,1,n);      l1=pow(10,l);
     adl=imatrix(1,maxwav+1,1,n);          delts=delt;
     tab=ivector(1,NCOVMAX);      for(k=1 ; k <kmax; k=k+1){
     ncodemax=ivector(1,8);        delt = delta*(l1*k);
         p2[theta]=x[theta] +delt;
     i=1;        k1=func(p2)-fx;
     while (fgets(line, MAXLINE, fic) != NULL)    {        p2[theta]=x[theta]-delt;
       if ((i >= firstobs) && (i <=lastobs)) {        k2=func(p2)-fx;
                /*res= (k1-2.0*fx+k2)/delt/delt; */
         for (j=maxwav;j>=1;j--){        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);        
           strcpy(line,stra);  #ifdef DEBUG
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        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);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         }  #endif
                /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);          k=kmax;
         }
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);          k=kmax; l=lmax*10.;
         }
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
         for (j=ncov;j>=1;j--){          delts=delt;
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);        }
         }      }
         num[i]=atol(stra);    }
     delti[theta]=delts;
         /*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]));*/    return res; 
     
         i=i+1;  }
       }  
     }  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   {
     /*scanf("%d",i);*/    int i;
   imx=i-1; /* Number of individuals */    int l=1, l1, lmax=20;
     double k1,k2,k3,k4,res,fx;
   /* Calculation of the number of parameter from char model*/    double p2[NPARMAX+1];
   Tvar=ivector(1,15);    int k;
   Tprod=ivector(1,15);  
   Tvaraff=ivector(1,15);    fx=func(x);
   Tvard=imatrix(1,15,1,2);    for (k=1; k<=2; k++) {
   Tage=ivector(1,15);            for (i=1;i<=npar;i++) p2[i]=x[i];
          p2[thetai]=x[thetai]+delti[thetai]/k;
   if (strlen(model) >1){      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
     j=0, j1=0, k1=1, k2=1;      k1=func(p2)-fx;
     j=nbocc(model,'+');    
     j1=nbocc(model,'*');      p2[thetai]=x[thetai]+delti[thetai]/k;
     cptcovn=j+1;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     cptcovprod=j1;      k2=func(p2)-fx;
        
     strcpy(modelsav,model);      p2[thetai]=x[thetai]-delti[thetai]/k;
    if (j==0) {      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       if (j1==0){      k3=func(p2)-fx;
         cutv(stra,strb,modelsav,'V');    
         Tvar[1]=atoi(strb);      p2[thetai]=x[thetai]-delti[thetai]/k;
       }      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       else if (j1==1) {      k4=func(p2)-fx;
         cutv(stra,strb,modelsav,'*');      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
         Tage[1]=1; cptcovage++;  #ifdef DEBUG
         if (strcmp(stra,"age")==0) {      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);
           cptcovprod--;      fprintf(ficlog,"%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
           cutv(strd,strc,strb,'V');  #endif
           Tvar[1]=atoi(strc);    }
         }    return res;
         else if (strcmp(strb,"age")==0) {  }
           cptcovprod--;  
           cutv(strd,strc,stra,'V');  /************** Inverse of matrix **************/
           Tvar[1]=atoi(strc);  void ludcmp(double **a, int n, int *indx, double *d) 
         }  { 
         else {    int i,imax,j,k; 
           cutv(strd,strc,strb,'V');    double big,dum,sum,temp; 
           cutv(stre,strd,stra,'V');    double *vv; 
           Tvar[1]=ncov+1;   
           for (k=1; k<=lastobs;k++)    vv=vector(1,n); 
               covar[ncov+1][k]=covar[atoi(strc)][k]*covar[atoi(strd)][k];    *d=1.0; 
         }    for (i=1;i<=n;i++) { 
         /*printf("%s %s %s\n", stra,strb,modelsav);      big=0.0; 
 printf("%d ",Tvar[1]);      for (j=1;j<=n;j++) 
 scanf("%d",i);*/        if ((temp=fabs(a[i][j])) > big) big=temp; 
       }      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     }      vv[i]=1.0/big; 
    else {    } 
       for(i=j; i>=1;i--){    for (j=1;j<=n;j++) { 
         cutv(stra,strb,modelsav,'+');      for (i=1;i<j;i++) { 
         /*printf("%s %s %s\n", stra,strb,modelsav);        sum=a[i][j]; 
           scanf("%d",i);*/        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
         if (strchr(strb,'*')) {        a[i][j]=sum; 
           cutv(strd,strc,strb,'*');      } 
           if (strcmp(strc,"age")==0) {      big=0.0; 
             cptcovprod--;      for (i=j;i<=n;i++) { 
             cutv(strb,stre,strd,'V');        sum=a[i][j]; 
             Tvar[i+1]=atoi(stre);        for (k=1;k<j;k++) 
             cptcovage++;          sum -= a[i][k]*a[k][j]; 
             Tage[cptcovage]=i+1;        a[i][j]=sum; 
             printf("stre=%s ", stre);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           }          big=dum; 
           else if (strcmp(strd,"age")==0) {          imax=i; 
             cptcovprod--;        } 
             cutv(strb,stre,strc,'V');      } 
             Tvar[i+1]=atoi(stre);      if (j != imax) { 
             cptcovage++;        for (k=1;k<=n;k++) { 
             Tage[cptcovage]=i+1;          dum=a[imax][k]; 
           }          a[imax][k]=a[j][k]; 
           else {          a[j][k]=dum; 
             cutv(strb,stre,strc,'V');        } 
             Tvar[i+1]=ncov+k1;        *d = -(*d); 
             cutv(strb,strc,strd,'V');        vv[imax]=vv[j]; 
             Tprod[k1]=i+1;      } 
             Tvard[k1][1]=atoi(strc);      indx[j]=imax; 
             Tvard[k1][2]=atoi(stre);      if (a[j][j] == 0.0) a[j][j]=TINY; 
             Tvar[cptcovn+k2]=Tvard[k1][1];      if (j != n) { 
             Tvar[cptcovn+k2+1]=Tvard[k1][2];        dum=1.0/(a[j][j]); 
             for (k=1; k<=lastobs;k++)        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
               covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];      } 
             k1++;    } 
             k2=k2+2;    free_vector(vv,1,n);  /* Doesn't work */
           }  ;
         }  } 
         else {  
           cutv(strd,strc,strb,'V');  void lubksb(double **a, int n, int *indx, double b[]) 
           /* printf("%s %s %s", strd,strc,strb);*/  { 
           Tvar[i+1]=atoi(strc);    int i,ii=0,ip,j; 
         }    double sum; 
         strcpy(modelsav,stra);     
       }    for (i=1;i<=n;i++) { 
       cutv(strd,strc,stra,'V');      ip=indx[i]; 
       Tvar[1]=atoi(strc);      sum=b[ip]; 
     }      b[ip]=b[i]; 
   }      if (ii) 
   /* for (i=1; i<=5; i++)        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
      printf("i=%d %d ",i,Tvar[i]);*/      else if (sum) ii=i; 
   /* printf("tvar=%d %d cptcovage=%d %d",Tvar[1],Tvar[2],cptcovage,Tage[1]);*/      b[i]=sum; 
  /*printf("cptcovprod=%d ", cptcovprod);*/    } 
   /*  scanf("%d ",i);*/    for (i=n;i>=1;i--) { 
     fclose(fic);      sum=b[i]; 
       for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
     /*  if(mle==1){*/      b[i]=sum/a[i][i]; 
     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 -*/  void pstamp(FILE *fichier)
     agev=matrix(1,maxwav,1,imx);  {
        fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
     for (i=1; i<=imx; i++)  {  }
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);  
       for(m=1; (m<= maxwav); m++){  /************ Frequencies ********************/
         if(s[m][i] >0){  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[])
           if (s[m][i] == nlstate+1) {  {  /* Some frequencies */
             if(agedc[i]>0)    
               if(moisdc[i]!=99 && andc[i]!=9999)    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
               agev[m][i]=agedc[i];    int first;
             else{    double ***freq; /* Frequencies */
               printf("Warning negative age at death: %d line:%d\n",num[i],i);    double *pp, **prop;
               agev[m][i]=-1;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
             }    char fileresp[FILENAMELENGTH];
           }    
           else if(s[m][i] !=9){ /* Should no more exist */    pp=vector(1,nlstate);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    prop=matrix(1,nlstate,iagemin,iagemax+3);
             if(mint[m][i]==99 || anint[m][i]==9999)    strcpy(fileresp,"p");
               agev[m][i]=1;    strcat(fileresp,fileres);
             else if(agev[m][i] <agemin){    if((ficresp=fopen(fileresp,"w"))==NULL) {
               agemin=agev[m][i];      printf("Problem with prevalence resultfile: %s\n", fileresp);
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
             }      exit(0);
             else if(agev[m][i] >agemax){    }
               agemax=agev[m][i];    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/    j1=0;
             }    
             /*agev[m][i]=anint[m][i]-annais[i];*/    j=cptcoveff;
             /*   agev[m][i] = age[i]+2*m;*/    if (cptcovn<1) {j=1;ncodemax[1]=1;}
           }  
           else { /* =9 */    first=1;
             agev[m][i]=1;  
             s[m][i]=-1;    for(k1=1; k1<=j;k1++){
           }      for(i1=1; i1<=ncodemax[k1];i1++){
         }        j1++;
         else /*= 0 Unknown */        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
           agev[m][i]=1;          scanf("%d", i);*/
       }        for (i=-5; i<=nlstate+ndeath; i++)  
              for (jk=-5; jk<=nlstate+ndeath; jk++)  
     }            for(m=iagemin; m <= iagemax+3; m++)
     for (i=1; i<=imx; i++)  {              freq[i][jk][m]=0;
       for(m=1; (m<= maxwav); m++){  
         if (s[m][i] > (nlstate+ndeath)) {      for (i=1; i<=nlstate; i++)  
           printf("Error: Wrong value in nlstate or ndeath\n");          for(m=iagemin; m <= iagemax+3; m++)
           goto end;          prop[i][m]=0;
         }        
       }        dateintsum=0;
     }        k2cpt=0;
         for (i=1; i<=imx; i++) {
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);          bool=1;
           if  (cptcovn>0) {
     free_vector(severity,1,maxwav);            for (z1=1; z1<=cptcoveff; z1++) 
     free_imatrix(outcome,1,maxwav+1,1,n);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     free_vector(moisnais,1,n);                bool=0;
     free_vector(annais,1,n);          }
     free_matrix(mint,1,maxwav,1,n);          if (bool==1){
     free_matrix(anint,1,maxwav,1,n);            for(m=firstpass; m<=lastpass; m++){
     free_vector(moisdc,1,n);              k2=anint[m][i]+(mint[m][i]/12.);
     free_vector(andc,1,n);              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                 if(agev[m][i]==0) agev[m][i]=iagemax+1;
                    if(agev[m][i]==1) agev[m][i]=iagemax+2;
     wav=ivector(1,imx);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     dh=imatrix(1,lastpass-firstpass+1,1,imx);                if (m<lastpass) {
     mw=imatrix(1,lastpass-firstpass+1,1,imx);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
                      freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
     /* Concatenates waves */                }
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);                
                 if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                   dateintsum=dateintsum+k2;
       Tcode=ivector(1,100);                  k2cpt++;
       nbcode=imatrix(1,nvar,1,8);                }
       ncodemax[1]=1;                /*}*/
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);            }
                }
    codtab=imatrix(1,100,1,10);        }
    h=0;         
    m=pow(2,cptcoveff);        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
          pstamp(ficresp);
    for(k=1;k<=cptcoveff; k++){        if  (cptcovn>0) {
      for(i=1; i <=(m/pow(2,k));i++){          fprintf(ficresp, "\n#********** Variable "); 
        for(j=1; j <= ncodemax[k]; j++){          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){          fprintf(ficresp, "**********\n#");
            h++;        }
            if (h>m) h=1;codtab[h][k]=j;        for(i=1; i<=nlstate;i++) 
          }          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
        }        fprintf(ficresp, "\n");
      }        
    }        for(i=iagemin; i <= iagemax+3; i++){
           if(i==iagemax+3){
             fprintf(ficlog,"Total");
    /*for(i=1; i <=m ;i++){          }else{
      for(k=1; k <=cptcovn; k++){            if(first==1){
        printf("i=%d k=%d %d %d",i,k,codtab[i][k], cptcoveff);              first=0;
      }              printf("See log file for details...\n");
      printf("\n");            }
    }            fprintf(ficlog,"Age %d", i);
    scanf("%d",i);*/          }
              for(jk=1; jk <=nlstate ; jk++){
    /* Calculates basic frequencies. Computes observed prevalence at single age            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
        and prints on file fileres'p'. */              pp[jk] += freq[jk][m][i]; 
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);          }
           for(jk=1; jk <=nlstate ; jk++){
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            for(m=-1, pos=0; m <=0 ; m++)
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              pos += freq[jk][m][i];
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            if(pp[jk]>=1.e-10){
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              if(first==1){
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
                  }
     /* For Powell, parameters are in a vector p[] starting at p[1]              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */            }else{
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */              if(first==1)
                 printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     if(mle==1){              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);            }
     }          }
      
     /*--------- results files --------------*/          for(jk=1; jk <=nlstate ; jk++){
     fprintf(ficres,"\ntitle=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate, ndeath, maxwav, mle,weightopt,model);            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
                  pp[jk] += freq[jk][m][i];
    jk=1;          }       
    fprintf(ficres,"# Parameters\n");          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
    printf("# Parameters\n");            pos += pp[jk];
    for(i=1,jk=1; i <=nlstate; i++){            posprop += prop[jk][i];
      for(k=1; k <=(nlstate+ndeath); k++){          }
        if (k != i)          for(jk=1; jk <=nlstate ; jk++){
          {            if(pos>=1.e-5){
            printf("%d%d ",i,k);              if(first==1)
            fprintf(ficres,"%1d%1d ",i,k);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
            for(j=1; j <=ncovmodel; j++){              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
              printf("%f ",p[jk]);            }else{
              fprintf(ficres,"%f ",p[jk]);              if(first==1)
              jk++;                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
            }              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
            printf("\n");            }
            fprintf(ficres,"\n");            if( i <= iagemax){
          }              if(pos>=1.e-5){
      }                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
    }                /*probs[i][jk][j1]= pp[jk]/pos;*/
  if(mle==1){                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
     /* Computing hessian and covariance matrix */              }
     ftolhess=ftol; /* Usually correct */              else
     hesscov(matcov, p, npar, delti, ftolhess, func);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
  }            }
     fprintf(ficres,"# Scales\n");          }
     printf("# Scales\n");          
      for(i=1,jk=1; i <=nlstate; i++){          for(jk=-1; jk <=nlstate+ndeath; jk++)
       for(j=1; j <=nlstate+ndeath; j++){            for(m=-1; m <=nlstate+ndeath; m++)
         if (j!=i) {              if(freq[jk][m][i] !=0 ) {
           fprintf(ficres,"%1d%1d",i,j);              if(first==1)
           printf("%1d%1d",i,j);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
           for(k=1; k<=ncovmodel;k++){                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
             printf(" %.5e",delti[jk]);              }
             fprintf(ficres," %.5e",delti[jk]);          if(i <= iagemax)
             jk++;            fprintf(ficresp,"\n");
           }          if(first==1)
           printf("\n");            printf("Others in log...\n");
           fprintf(ficres,"\n");          fprintf(ficlog,"\n");
         }        }
       }      }
       }    }
        dateintmean=dateintsum/k2cpt; 
     k=1;   
     fprintf(ficres,"# Covariance\n");    fclose(ficresp);
     printf("# Covariance\n");    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     for(i=1;i<=npar;i++){    free_vector(pp,1,nlstate);
       /*  if (k>nlstate) k=1;    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
       i1=(i-1)/(ncovmodel*nlstate)+1;    /* End of Freq */
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);  }
       printf("%s%d%d",alph[k],i1,tab[i]);*/  
       fprintf(ficres,"%3d",i);  /************ Prevalence ********************/
       printf("%3d",i);  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)
       for(j=1; j<=i;j++){  {  
         fprintf(ficres," %.5e",matcov[i][j]);    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
         printf(" %.5e",matcov[i][j]);       in each health status at the date of interview (if between dateprev1 and dateprev2).
       }       We still use firstpass and lastpass as another selection.
       fprintf(ficres,"\n");    */
       printf("\n");   
       k++;    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     }    double ***freq; /* Frequencies */
        double *pp, **prop;
     while((c=getc(ficpar))=='#' && c!= EOF){    double pos,posprop; 
       ungetc(c,ficpar);    double  y2; /* in fractional years */
       fgets(line, MAXLINE, ficpar);    int iagemin, iagemax;
       puts(line);  
       fputs(line,ficparo);    iagemin= (int) agemin;
     }    iagemax= (int) agemax;
     ungetc(c,ficpar);    /*pp=vector(1,nlstate);*/
      prop=matrix(1,nlstate,iagemin,iagemax+3); 
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
        j1=0;
     if (fage <= 2) {    
       bage = agemin;    j=cptcoveff;
       fage = agemax;    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     }    
     for(k1=1; k1<=j;k1++){
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");      for(i1=1; i1<=ncodemax[k1];i1++){
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);        j1++;
         
            for (i=1; i<=nlstate; i++)  
 /*------------ gnuplot -------------*/          for(m=iagemin; m <= iagemax+3; m++)
 chdir(pathcd);            prop[i][m]=0.0;
   if((ficgp=fopen("graph.plt","w"))==NULL) {       
     printf("Problem with file graph.gp");goto end;        for (i=1; i<=imx; i++) { /* Each individual */
   }          bool=1;
 #ifdef windows          if  (cptcovn>0) {
   fprintf(ficgp,"cd \"%s\" \n",pathc);            for (z1=1; z1<=cptcoveff; z1++) 
 #endif              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
 m=pow(2,cptcoveff);                bool=0;
            } 
  /* 1eme*/          if (bool==1) { 
   for (cpt=1; cpt<= nlstate ; cpt ++) {            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
    for (k1=1; k1<= m ; k1 ++) {              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
               if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
 #ifdef windows                if(agev[m][i]==0) agev[m][i]=iagemax+1;
     fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",agemin,fage,fileres,k1-1,k1-1);                if(agev[m][i]==1) agev[m][i]=iagemax+2;
 #endif                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); 
 #ifdef unix                if (s[m][i]>0 && s[m][i]<=nlstate) { 
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);                  /*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]]);*/
 #endif                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
                   prop[s[m][i]][iagemax+3] += weight[i]; 
 for (i=1; i<= nlstate ; i ++) {                } 
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              }
   else fprintf(ficgp," \%%*lf (\%%*lf)");            } /* end selection of waves */
 }          }
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);        }
     for (i=1; i<= nlstate ; i ++) {        for(i=iagemin; i <= iagemax+3; i++){  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          
   else fprintf(ficgp," \%%*lf (\%%*lf)");          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
 }            posprop += prop[jk][i]; 
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);          } 
      for (i=1; i<= nlstate ; i ++) {  
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");          for(jk=1; jk <=nlstate ; jk++){     
   else fprintf(ficgp," \%%*lf (\%%*lf)");            if( i <=  iagemax){ 
 }                if(posprop>=1.e-5){ 
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));                probs[i][jk][j1]= prop[jk][i]/posprop;
 #ifdef unix              } 
 fprintf(ficgp,"\nset ter gif small size 400,300");            } 
 #endif          }/* end jk */ 
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        }/* end i */ 
    }      } /* end i1 */
   }    } /* end k1 */
   /*2 eme*/    
     /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
   for (k1=1; k1<= m ; k1 ++) {    /*free_vector(pp,1,nlstate);*/
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
      }  /* End of prevalence */
     for (i=1; i<= nlstate+1 ; i ++) {  
       k=2*i;  /************* Waves Concatenation ***************/
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {  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 (j==i) fprintf(ficgp," \%%lf (\%%lf)");  {
   else fprintf(ficgp," \%%*lf (\%%*lf)");    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
 }         Death is a valid wave (if date is known).
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);       and mw[mi+1][i]. dh depends on stepm.
       for (j=1; j<= nlstate+1 ; j ++) {       */
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
         else fprintf(ficgp," \%%*lf (\%%*lf)");    int i, mi, m;
 }      /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
       fprintf(ficgp,"\" t\"\" w l 0,");       double sum=0., jmean=0.;*/
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    int first;
       for (j=1; j<= nlstate+1 ; j ++) {    int j, k=0,jk, ju, jl;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    double sum=0.;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    first=0;
 }      jmin=1e+5;
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    jmax=-1;
       else fprintf(ficgp,"\" t\"\" w l 0,");    jmean=0.;
     }    for(i=1; i<=imx; i++){
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);      mi=0;
   }      m=firstpass;
        while(s[m][i] <= nlstate){
   /*3eme*/        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
           mw[++mi][i]=m;
   for (k1=1; k1<= m ; k1 ++) {        if(m >=lastpass)
     for (cpt=1; cpt<= nlstate ; cpt ++) {          break;
       k=2+nlstate*(cpt-1);        else
       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);          m++;
       for (i=1; i< nlstate ; i ++) {      }/* end while */
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);      if (s[m][i] > nlstate){
       }        mi++;     /* Death is another wave */
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        /* if(mi==0)  never been interviewed correctly before death */
     }           /* Only death is a correct wave */
   }        mw[mi][i]=m;
        }
   /* CV preval stat */  
   for (k1=1; k1<= m ; k1 ++) {      wav[i]=mi;
     for (cpt=1; cpt<nlstate ; cpt ++) {      if(mi==0){
       k=3;        nbwarn++;
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);        if(first==0){
       for (i=1; i< nlstate ; i ++)          printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
         fprintf(ficgp,"+$%d",k+i+1);          first=1;
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);        }
              if(first==1){
       l=3+(nlstate+ndeath)*cpt;          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);        }
       for (i=1; i< nlstate ; i ++) {      } /* end mi==0 */
         l=3+(nlstate+ndeath)*cpt;    } /* End individuals */
         fprintf(ficgp,"+$%d",l+i+1);  
       }    for(i=1; i<=imx; i++){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);        for(mi=1; mi<wav[i];mi++){
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);        if (stepm <=0)
     }          dh[mi][i]=1;
   }        else{
           if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
   /* proba elementaires */            if (agedc[i] < 2*AGESUP) {
    for(i=1,jk=1; i <=nlstate; i++){              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
     for(k=1; k <=(nlstate+ndeath); k++){              if(j==0) j=1;  /* Survives at least one month after exam */
       if (k != i) {              else if(j<0){
         for(j=1; j <=ncovmodel; j++){                nberr++;
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/                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]);
           /*fprintf(ficgp,"%s",alph[1]);*/                j=1; /* Temporary Dangerous patch */
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);                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);
           jk++;                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
           fprintf(ficgp,"\n");                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);
         }              }
       }              k=k+1;
     }              if (j >= jmax){
     }                jmax=j;
                 ijmax=i;
   for(jk=1; jk <=m; jk++) {              }
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);              if (j <= jmin){
    i=1;                jmin=j;
    for(k2=1; k2<=nlstate; k2++) {                ijmin=i;
      k3=i;              }
      for(k=1; k<=(nlstate+ndeath); k++) {              sum=sum+j;
        if (k != k2){              /*if (j<0) printf("j=%d num=%d \n",j,i);*/
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
 ij=1;            }
         for(j=3; j <=ncovmodel; j++) {          }
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {          else{
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
             ij++;  /*        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]); */
           }  
           else            k=k+1;
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            if (j >= jmax) {
         }              jmax=j;
           fprintf(ficgp,")/(1");              ijmax=i;
                    }
         for(k1=1; k1 <=nlstate; k1++){              else if (j <= jmin){
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);              jmin=j;
 ij=1;              ijmin=i;
           for(j=3; j <=ncovmodel; j++){            }
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);            /*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]);*/
             ij++;            if(j<0){
           }              nberr++;
           else              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);              fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
           }            }
           fprintf(ficgp,")");            sum=sum+j;
         }          }
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);          jk= j/stepm;
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");          jl= j -jk*stepm;
         i=i+ncovmodel;          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;
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);              bh[mi][i]=0;
   }            }else{ /* We want a negative bias in order to only have interpolation ie
                        * at the price of an extra matrix product in likelihood */
   fclose(ficgp);              dh[mi][i]=jk+1;
                  bh[mi][i]=ju;
 chdir(path);            }
     free_matrix(agev,1,maxwav,1,imx);          }else{
     free_ivector(wav,1,imx);            if(jl <= -ju){
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);              dh[mi][i]=jk;
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);              bh[mi][i]=jl;       /* bias is positive if real duration
                                       * is higher than the multiple of stepm and negative otherwise.
     free_imatrix(s,1,maxwav+1,1,n);                                   */
                }
                else{
     free_ivector(num,1,n);              dh[mi][i]=jk+1;
     free_vector(agedc,1,n);              bh[mi][i]=ju;
     free_vector(weight,1,n);            }
     /*free_matrix(covar,1,NCOVMAX,1,n);*/            if(dh[mi][i]==0){
     fclose(ficparo);              dh[mi][i]=1; /* At least one step */
     fclose(ficres);              bh[mi][i]=ju; /* At least one step */
     /*  }*/              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
                }
    /*________fin mle=1_________*/          } /* end if mle */
            }
       } /* end wave */
      }
     /* No more information from the sample is required now */    jmean=sum/k;
   /* Reads comments: lines beginning with '#' */    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);
   while((c=getc(ficpar))=='#' && c!= EOF){    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);
     ungetc(c,ficpar);   }
     fgets(line, MAXLINE, ficpar);  
     puts(line);  /*********** Tricode ****************************/
     fputs(line,ficparo);  void tricode(int *Tvar, int **nbcode, int imx)
   }  {
   ungetc(c,ficpar);    
      int Ndum[20],ij=1, k, j, i, maxncov=19;
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    int cptcode=0;
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);    cptcoveff=0; 
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);   
 /*--------- index.htm --------*/    for (k=0; k<maxncov; k++) Ndum[k]=0;
     for (k=1; k<=7; k++) ncodemax[k]=0;
   if((fichtm=fopen("index.htm","w"))==NULL)    {  
     printf("Problem with index.htm \n");goto end;    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
   }      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                                  modality*/ 
  fprintf(fichtm,"<body><ul> Imach, Version 0.64a<hr> <li>Outputs files<br><br>\n        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n        Ndum[ij]++; /*store the modality */
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>                                         Tvar[j]. If V=sex and male is 0 and 
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>                                         female is 1, then  cptcode=1.*/
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>      }
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>  
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>      for (i=0; i<=cptcode; i++) {
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br><br>",fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);        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(fichtm," <li>Graphs</li>\n<p>");  
       ij=1; 
  m=cptcoveff;      for (i=1; i<=ncodemax[j]; i++) {
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}        for (k=0; k<= maxncov; k++) {
           if (Ndum[k] != 0) {
  j1=0;            nbcode[Tvar[j]][ij]=k; 
  for(k1=1; k1<=m;k1++){            /* 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(i1=1; i1<=ncodemax[k1];i1++){            
        j1++;            ij++;
        if (cptcovn > 0) {          }
          fprintf(fichtm,"<hr>************ Results for covariates");          if (ij > ncodemax[j]) break; 
          for (cpt=1; cpt<=cptcoveff;cpt++)        }  
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);      } 
          fprintf(fichtm," ************\n<hr>");    }  
        }  
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>   for (k=0; k< maxncov; k++) Ndum[k]=0;
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);      
        for(cpt=1; cpt<nlstate;cpt++){   for (i=1; i<=ncovmodel-2; i++) { 
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);     ij=Tvar[i];
        }     Ndum[ij]++;
     for(cpt=1; cpt<=nlstate;cpt++) {   }
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident  
 interval) in state (%d): v%s%d%d.gif <br>   ij=1;
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);     for (i=1; i<= maxncov; i++) {
      }     if((Ndum[i]!=0) && (i<=ncovcol)){
      for(cpt=1; cpt<=nlstate;cpt++) {       Tvaraff[ij]=i; /*For printing */
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>       ij++;
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);     }
      }   }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and   
 health expectancies in states (1) and (2): e%s%d.gif<br>   cptcoveff=ij-1; /*Number of simple covariates*/
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);  }
 fprintf(fichtm,"\n</body>");  
    }  /*********** Health Expectancies ****************/
  }  
 fclose(fichtm);  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[] )
   
   /*--------------- Prevalence limit --------------*/  {
      /* Health expectancies, no variances */
   strcpy(filerespl,"pl");    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
   strcat(filerespl,fileres);    double age, agelim, hf;
   if((ficrespl=fopen(filerespl,"w"))==NULL) {    double ***p3mat;
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    double eip;
   }  
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    pstamp(ficreseij);
   fprintf(ficrespl,"#Prevalence limit\n");    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
   fprintf(ficrespl,"#Age ");    fprintf(ficreseij,"# Age");
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);    for(i=1; i<=nlstate;i++){
   fprintf(ficrespl,"\n");      for(j=1; j<=nlstate;j++){
          fprintf(ficreseij," e%1d%1d ",i,j);
   prlim=matrix(1,nlstate,1,nlstate);      }
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      fprintf(ficreseij," e%1d. ",i);
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    }
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficreseij,"\n");
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    
   k=0;    if(estepm < stepm){
   agebase=agemin;      printf ("Problem %d lower than %d\n",estepm, stepm);
   agelim=agemax;    }
   ftolpl=1.e-10;    else  hstepm=estepm;   
   i1=cptcoveff;    /* We compute the life expectancy from trapezoids spaced every estepm months
   if (cptcovn < 1){i1=1;}     * This is mainly to measure the difference between two models: for example
      * if stepm=24 months pijx are given only every 2 years and by summing them
   for(cptcov=1;cptcov<=i1;cptcov++){     * we are calculating an estimate of the Life Expectancy assuming a linear 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){     * progression in between and thus overestimating or underestimating according
         k=k+1;     * to the curvature of the survival function. If, for the same date, we 
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/     * estimate the model with stepm=1 month, we can keep estepm to 24 months
         fprintf(ficrespl,"\n#******");     * to compare the new estimate of Life expectancy with the same linear 
         for(j=1;j<=cptcoveff;j++)     * hypothesis. A more precise result, taking into account a more precise
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);     * curvature will be obtained if estepm is as small as stepm. */
         fprintf(ficrespl,"******\n");  
            /* For example we decided to compute the life expectancy with the smallest unit */
         for (age=agebase; age<=agelim; age++){    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);       nhstepm is the number of hstepm from age to agelim 
           fprintf(ficrespl,"%.0f",age );       nstepm is the number of stepm from age to agelin. 
           for(i=1; i<=nlstate;i++)       Look at hpijx to understand the reason of that which relies in memory size
           fprintf(ficrespl," %.5f", prlim[i][i]);       and note for a fixed period like estepm months */
           fprintf(ficrespl,"\n");    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         }       survival function given by stepm (the optimization length). Unfortunately it
       }       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 
   fclose(ficrespl);       results. So we changed our mind and took the option of the best precision.
   /*------------- h Pij x at various ages ------------*/    */
      hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  
   if((ficrespij=fopen(filerespij,"w"))==NULL) {    agelim=AGESUP;
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    /* nhstepm age range expressed in number of stepm */
   }    nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   printf("Computing pij: result on file '%s' \n", filerespij);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
      /* if (stepm >= YEARM) hstepm=1;*/
   stepsize=(int) (stepm+YEARM-1)/YEARM;    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   if (stepm<=24) stepsize=2;    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   
   agelim=AGESUP;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   hstepm=stepsize*YEARM; /* Every year of age */      /* Computed by stepm unit matrices, product of hstepm matrices, stored
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
        
   k=0;      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
   for(cptcov=1;cptcov<=i1;cptcov++){      
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       k=k+1;      
         fprintf(ficrespij,"\n#****** ");      printf("%d|",(int)age);fflush(stdout);
         for(j=1;j<=cptcoveff;j++)      fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      
         fprintf(ficrespij,"******\n");      /* Computing expectancies */
              for(i=1; i<=nlstate;i++)
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */        for(j=1; j<=nlstate;j++)
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            
           oldm=oldms;savm=savms;            /* 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]);*/
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
           fprintf(ficrespij,"# Age");          }
           for(i=1; i<=nlstate;i++)  
             for(j=1; j<=nlstate+ndeath;j++)      fprintf(ficreseij,"%3.0f",age );
               fprintf(ficrespij," %1d-%1d",i,j);      for(i=1; i<=nlstate;i++){
           fprintf(ficrespij,"\n");        eip=0;
           for (h=0; h<=nhstepm; h++){        for(j=1; j<=nlstate;j++){
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );          eip +=eij[i][j][(int)age];
             for(i=1; i<=nlstate;i++)          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
               for(j=1; j<=nlstate+ndeath;j++)        }
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);        fprintf(ficreseij,"%9.4f", eip );
             fprintf(ficrespij,"\n");      }
           }      fprintf(ficreseij,"\n");
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      
           fprintf(ficrespij,"\n");    }
         }    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     }    printf("\n");
   }    fprintf(ficlog,"\n");
     
   fclose(ficrespij);  }
   
   /*---------- Health expectancies and variances ------------*/  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[] )
   
   strcpy(filerest,"t");  {
   strcat(filerest,fileres);    /* Covariances of health expectancies eij and of total life expectancies according
   if((ficrest=fopen(filerest,"w"))==NULL) {     to initial status i, ei. .
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    */
   }    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    double age, agelim, hf;
     double ***p3matp, ***p3matm, ***varhe;
     double **dnewm,**doldm;
   strcpy(filerese,"e");    double *xp, *xm;
   strcat(filerese,fileres);    double **gp, **gm;
   if((ficreseij=fopen(filerese,"w"))==NULL) {    double ***gradg, ***trgradg;
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    int theta;
   }  
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    double eip, vip;
   
  strcpy(fileresv,"v");    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   strcat(fileresv,fileres);    xp=vector(1,npar);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    xm=vector(1,npar);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    dnewm=matrix(1,nlstate*nlstate,1,npar);
   }    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    
     pstamp(ficresstdeij);
   k=0;    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
   for(cptcov=1;cptcov<=i1;cptcov++){    fprintf(ficresstdeij,"# Age");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    for(i=1; i<=nlstate;i++){
       k=k+1;      for(j=1; j<=nlstate;j++)
       fprintf(ficrest,"\n#****** ");        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
       for(j=1;j<=cptcoveff;j++)      fprintf(ficresstdeij," e%1d. ",i);
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    }
       fprintf(ficrest,"******\n");    fprintf(ficresstdeij,"\n");
   
       fprintf(ficreseij,"\n#****** ");    pstamp(ficrescveij);
       for(j=1;j<=cptcoveff;j++)    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    fprintf(ficrescveij,"# Age");
       fprintf(ficreseij,"******\n");    for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){
       fprintf(ficresvij,"\n#****** ");        cptj= (j-1)*nlstate+i;
       for(j=1;j<=cptcoveff;j++)        for(i2=1; i2<=nlstate;i2++)
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);          for(j2=1; j2<=nlstate;j2++){
       fprintf(ficresvij,"******\n");            cptj2= (j2-1)*nlstate+i2;
             if(cptj2 <= cptj)
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
       oldm=oldms;savm=savms;          }
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);        }
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    fprintf(ficrescveij,"\n");
       oldm=oldms;savm=savms;    
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    if(estepm < stepm){
            printf ("Problem %d lower than %d\n",estepm, stepm);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    }
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    else  hstepm=estepm;   
       fprintf(ficrest,"\n");    /* We compute the life expectancy from trapezoids spaced every estepm months
             * This is mainly to measure the difference between two models: for example
       hf=1;     * if stepm=24 months pijx are given only every 2 years and by summing them
       if (stepm >= YEARM) hf=stepm/YEARM;     * we are calculating an estimate of the Life Expectancy assuming a linear 
       epj=vector(1,nlstate+1);     * progression in between and thus overestimating or underestimating according
       for(age=bage; age <=fage ;age++){     * to the curvature of the survival function. If, for the same date, we 
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
         fprintf(ficrest," %.0f",age);     * to compare the new estimate of Life expectancy with the same linear 
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){     * hypothesis. A more precise result, taking into account a more precise
           for(i=1, epj[j]=0.;i <=nlstate;i++) {     * curvature will be obtained if estepm is as small as stepm. */
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];  
           }    /* For example we decided to compute the life expectancy with the smallest unit */
           epj[nlstate+1] +=epj[j];    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         }       nhstepm is the number of hstepm from age to agelim 
         for(i=1, vepp=0.;i <=nlstate;i++)       nstepm is the number of stepm from age to agelin. 
           for(j=1;j <=nlstate;j++)       Look at hpijx to understand the reason of that which relies in memory size
             vepp += vareij[i][j][(int)age];       and note for a fixed period like estepm months */
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
         for(j=1;j <=nlstate;j++){       survival function given by stepm (the optimization length). Unfortunately it
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));       means that if the survival funtion is printed only each two years of age and if
         }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         fprintf(ficrest,"\n");       results. So we changed our mind and took the option of the best precision.
       }    */
     }    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   }  
            /* If stepm=6 months */
  fclose(ficreseij);    /* nhstepm age range expressed in number of stepm */
  fclose(ficresvij);    agelim=AGESUP;
   fclose(ficrest);    nstepm=(int) rint((agelim-age)*YEARM/stepm); 
   fclose(ficpar);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   free_vector(epj,1,nlstate+1);    /* if (stepm >= YEARM) hstepm=1;*/
   /*  scanf("%d ",i); */    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     
   /*------- Variance limit prevalence------*/      p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 strcpy(fileresvpl,"vpl");    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
   strcat(fileresvpl,fileres);    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    gp=matrix(0,nhstepm,1,nlstate*nlstate);
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    gm=matrix(0,nhstepm,1,nlstate*nlstate);
     exit(0);  
   }    for (age=bage; age<=fage; age ++){ 
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);  
       /* Computed by stepm unit matrices, product of hstepm matrices, stored
  k=0;         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
  for(cptcov=1;cptcov<=i1;cptcov++){   
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
      k=k+1;  
      fprintf(ficresvpl,"\n#****** ");      /* Computing  Variances of health expectancies */
      for(j=1;j<=cptcoveff;j++)      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);         decrease memory allocation */
      fprintf(ficresvpl,"******\n");      for(theta=1; theta <=npar; theta++){
              for(i=1; i<=npar; i++){ 
      varpl=matrix(1,nlstate,(int) bage, (int) fage);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
      oldm=oldms;savm=savms;          xm[i] = x[i] - (i==theta ?delti[theta]:0);
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);        }
    }        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
  }        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     
   fclose(ficresvpl);        for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
   /*---------- End : free ----------------*/            for(h=0; h<=nhstepm-1; h++){
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);              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.;
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);            }
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);          }
          }
         
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);        for(ij=1; ij<= nlstate*nlstate; ij++)
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);          for(h=0; h<=nhstepm-1; h++){
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);          }
        }/* End theta */
   free_matrix(matcov,1,npar,1,npar);      
   free_vector(delti,1,npar);      
        for(h=0; h<=nhstepm-1; h++)
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);        for(j=1; j<=nlstate*nlstate;j++)
           for(theta=1; theta <=npar; theta++)
   printf("End of Imach\n");            trgradg[h][j][theta]=gradg[h][theta][j];
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */      
    
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/       for(ij=1;ij<=nlstate*nlstate;ij++)
   /*printf("Total time was %d uSec.\n", total_usecs);*/        for(ji=1;ji<=nlstate*nlstate;ji++)
   /*------ End -----------*/          varhe[ij][ji][(int)age] =0.;
   
  end:       printf("%d|",(int)age);fflush(stdout);
 #ifdef windows       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
  chdir(pathcd);       for(h=0;h<=nhstepm-1;h++){
 #endif        for(k=0;k<=nhstepm-1;k++){
  system("wgnuplot graph.plt");          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]);
 #ifdef windows          for(ij=1;ij<=nlstate*nlstate;ij++)
   while (z[0] != 'q') {            for(ji=1;ji<=nlstate*nlstate;ji++)
     chdir(pathcd);              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
     printf("\nType e to edit output files, c to start again, and q for exiting: ");        }
     scanf("%s",z);      }
     if (z[0] == 'c') system("./imach");      /* Computing expectancies */
     else if (z[0] == 'e') {      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       chdir(path);      for(i=1; i<=nlstate;i++)
       system("index.htm");        for(j=1; j<=nlstate;j++)
     }          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
     else if (z[0] == 'q') exit(0);            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
   }            
 #endif            /* 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(ficresstdeij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
         eip=0.;
         vip=0.;
         for(j=1; j<=nlstate;j++){
           eip += eij[i][j][(int)age];
           for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
             vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
           fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
         }
         fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
       }
       fprintf(ficresstdeij,"\n");
   
       fprintf(ficrescveij,"%3.0f",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           cptj= (j-1)*nlstate+i;
           for(i2=1; i2<=nlstate;i2++)
             for(j2=1; j2<=nlstate;j2++){
               cptj2= (j2-1)*nlstate+i2;
               if(cptj2 <= cptj)
                 fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             }
         }
       fprintf(ficrescveij,"\n");
      
     }
     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
     free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
     free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
     free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     printf("\n");
     fprintf(ficlog,"\n");
   
     free_vector(xm,1,npar);
     free_vector(xp,1,npar);
     free_matrix(dnewm,1,nlstate*nlstate,1,npar);
     free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
     free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
   }
   
   /************ Variance ******************/
   void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
   {
     /* Variance of health expectancies */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
     /* double **newm;*/
     double **dnewm,**doldm;
     double **dnewmp,**doldmp;
     int i, j, nhstepm, hstepm, h, nstepm ;
     int k, cptcode;
     double *xp;
     double **gp, **gm;  /* for var eij */
     double ***gradg, ***trgradg; /*for var eij */
     double **gradgp, **trgradgp; /* for var p point j */
     double *gpp, *gmp; /* for var p point j */
     double **varppt; /* for var p point j nlstate to nlstate+ndeath */
     double ***p3mat;
     double age,agelim, hf;
     double ***mobaverage;
     int theta;
     char digit[4];
     char digitp[25];
   
     char fileresprobmorprev[FILENAMELENGTH];
   
     if(popbased==1){
       if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
       else strcpy(digitp,"-populbased-nomobil-");
     }
     else 
       strcpy(digitp,"-stablbased-");
   
     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);
       }
     }
   
     strcpy(fileresprobmorprev,"prmorprev"); 
     sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
     strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
     strcat(fileresprobmorprev,fileres);
     if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobmorprev);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
     }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
    
     fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     pstamp(ficresprobmorprev);
     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);
     for(j=nlstate+1; j<=(nlstate+ndeath);j++){
       fprintf(ficresprobmorprev," p.%-d SE",j);
       for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }  
     fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
     /* 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");
     fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   /*   } */
     varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     pstamp(ficresvij);
     fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
     if(popbased==1)
       fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
     else
       fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
     fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++)
         fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
     fprintf(ficresvij,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   
     gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
     gpp=vector(nlstate+1,nlstate+ndeath);
     gmp=vector(nlstate+1,nlstate+ndeath);
     trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
     /* For example we decided to compute the life expectancy with the smallest unit */
     /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
        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
        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
        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.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       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 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
       gm=matrix(0,nhstepm,1,nlstate);
   
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
     
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gp[h][j]=0.;i<=nlstate;i++)
               gp[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gpp[j]=0.; i<= nlstate; i++)
             gpp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(i=1; i<=npar; i++) /* Computes gradient x - delta */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
    
         if (popbased==1) {
           if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=probs[(int)age][i][ij];
           }else{ /* mobilav */ 
             for(i=1; i<=nlstate;i++)
               prlim[i][i]=mobaverage[(int)age][i][ij];
           }
         }
   
         for(j=1; j<= nlstate; j++){
           for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
               gm[h][j] += prlim[i][i]*p3mat[i][j][h];
           }
         }
         /* This for computing probability of death (h=1 means
            computed over hstepm matrices product = hstepm*stepm months) 
            as a weighted average of prlim.
         */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
           for(i=1,gmp[j]=0.; i<= nlstate; i++)
            gmp[j] += prlim[i][i]*p3mat[i][j][1];
         }    
         /* end probability of death */
   
         for(j=1; j<= nlstate; j++) /* vareij */
           for(h=0; h<=nhstepm; h++){
             gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
           }
   
         for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
           gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
         }
   
       } /* End theta */
   
       trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
   
       for(h=0; h<=nhstepm; h++) /* veij */
         for(j=1; j<=nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
   
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
         for(theta=1; theta <=npar; theta++)
           trgradgp[j][theta]=gradgp[theta][j];
     
   
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         for(j=1;j<=nlstate;j++)
           vareij[i][j][(int)age] =0.;
   
       for(h=0;h<=nhstepm;h++){
         for(k=0;k<=nhstepm;k++){
           matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
           matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
             for(j=1;j<=nlstate;j++)
               vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
       }
     
       /* pptj */
       matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
       matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
       for(j=nlstate+1;j<=nlstate+ndeath;j++)
         for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
       /* end ppptj */
       /*  x centered again */
       hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
       prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
    
       if (popbased==1) {
         if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=probs[(int)age][i][ij];
         }else{ /* mobilav */ 
           for(i=1; i<=nlstate;i++)
             prlim[i][i]=mobaverage[(int)age][i][ij];
         }
       }
                
       /* This for computing probability of death (h=1 means
          computed over hstepm (estepm) matrices product = hstepm*stepm months) 
          as a weighted average of prlim.
       */
       for(j=nlstate+1;j<=nlstate+ndeath;j++){
         for(i=1,gmp[j]=0.;i<= nlstate; i++) 
           gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
       }    
       /* end probability of death */
   
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
       for(j=nlstate+1; j<=(nlstate+ndeath);j++){
         fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
         for(i=1; i<=nlstate;i++){
           fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
         }
       } 
       fprintf(ficresprobmorprev,"\n");
   
       fprintf(ficresvij,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++){
           fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
         }
       fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
       free_matrix(gm,0,nhstepm,1,nlstate);
       free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
       free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     } /* End age */
     free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
     free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
     free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
     /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
     fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
   /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
   /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
     fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
     fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months and then divided by estepm and multiplied by %.0f in order to have the probability to die over a year <br> <img src=\"varmuptjgr%s%s.png\"> <br>\n", stepm,YEARM,digitp,digit);
   */
   /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
     fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,nlstate);
     free_matrix(dnewm,1,nlstate,1,npar);
     free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
     free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficresprobmorprev);
     fflush(ficgp);
     fflush(fichtm); 
   }  /* end varevsij */
   
   /************ Variance of prevlim ******************/
   void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, char strstart[])
   {
     /* Variance of prevalence limit */
     /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
     double **newm;
     double **dnewm,**doldm;
     int i, j, nhstepm, hstepm;
     int k, cptcode;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double age,agelim;
     int theta;
     
     pstamp(ficresvpl);
     fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     fprintf(ficresvpl,"# Age");
     for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
   
     xp=vector(1,npar);
     dnewm=matrix(1,nlstate,1,npar);
     doldm=matrix(1,nlstate,1,nlstate);
     
     hstepm=1*YEARM; /* Every year of age */
     hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */ 
     agelim = AGESUP;
     for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
       if (stepm >= YEARM) hstepm=1;
       nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       gradg=matrix(1,npar,1,nlstate);
       gp=vector(1,nlstate);
       gm=vector(1,nlstate);
   
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gp[i] = prlim[i][i];
       
         for(i=1; i<=npar; i++) /* Computes gradient */
           xp[i] = x[i] - (i==theta ?delti[theta]:0);
         prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
           gm[i] = prlim[i][i];
   
         for(i=1;i<=nlstate;i++)
           gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
       } /* End theta */
   
       trgradg =matrix(1,nlstate,1,npar);
   
       for(j=1; j<=nlstate;j++)
         for(theta=1; theta <=npar; theta++)
           trgradg[j][theta]=gradg[theta][j];
   
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
       matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
         varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   
       fprintf(ficresvpl,"%.0f ",age );
       for(i=1; i<=nlstate;i++)
         fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
       fprintf(ficresvpl,"\n");
       free_vector(gp,1,nlstate);
       free_vector(gm,1,nlstate);
       free_matrix(gradg,1,npar,1,nlstate);
       free_matrix(trgradg,1,nlstate,1,npar);
     } /* End age */
   
     free_vector(xp,1,npar);
     free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
   
   }
   
   /************ Variance of one-step probabilities  ******************/
   void varprob(char optionfilefiname[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax, char strstart[])
   {
     int i, j=0,  i1, k1, l1, t, tj;
     int k2, l2, j1,  z1;
     int k=0,l, cptcode;
     int first=1, first1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
     double **dnewm,**doldm;
     double *xp;
     double *gp, *gm;
     double **gradg, **trgradg;
     double **mu;
     double age,agelim, cov[NCOVMAX];
     double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
     char fileresprobcov[FILENAMELENGTH];
     char fileresprobcor[FILENAMELENGTH];
   
     double ***varpij;
   
     strcpy(fileresprob,"prob"); 
     strcat(fileresprob,fileres);
     if((ficresprob=fopen(fileresprob,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprob);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
     }
     strcpy(fileresprobcov,"probcov"); 
     strcat(fileresprobcov,fileres);
     if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcov);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
     }
     strcpy(fileresprobcor,"probcor"); 
     strcat(fileresprobcor,fileres);
     if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
       printf("Problem with resultfile: %s\n", fileresprobcor);
       fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
     }
     printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     fprintf(ficlog,"Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
     printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     fprintf(ficlog,"Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);
     printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
     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);
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem 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,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - 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",\
             fileres,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("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,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>",strstart, strtend);
     fclose(fichtm);
     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.1.7  
changed lines
  Added in v.1.122


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