[BACK]Return to imach.c CVS log [TXT] [DIR] Up to [Local Repository] / imach / src

Diff for /imach/src/imach.c between versions 1.5 and 1.118

version 1.5, 2001/05/02 17:42:45 version 1.118, 2006/03/14 18:20:07
Line 1 Line 1
      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.118  2006/03/14 18:20:07  brouard
   individuals from different ages are interviewed on their health status    (Module): varevsij Comments added explaining the second
   or degree of  disability. At least a second wave of interviews    table of variances if popbased=1 .
   ("longitudinal") should  measure each new individual health status.    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   Health expectancies are computed from the transistions observed between    (Module): Function pstamp added
   waves and are computed for each degree of severity of disability (number    (Module): Version 0.98d
   of life states). More degrees you consider, more time is necessary to  
   reach the Maximum Likelihood of the parameters involved in the model.    Revision 1.117  2006/03/14 17:16:22  brouard
   The simplest model is the multinomial logistic model where pij is    (Module): varevsij Comments added explaining the second
   the probabibility to be observed in state j at the second wave conditional    table of variances if popbased=1 .
   to be observed in state i at the first wave. Therefore the model is:    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    (Module): Function pstamp added
   is a covariate. If you want to have a more complex model than "constant and    (Module): Version 0.98d
   age", you should modify the program where the markup  
     *Covariates have to be included here again* invites you to do it.    Revision 1.116  2006/03/06 10:29:27  brouard
   More covariates you add, less is the speed of the convergence.    (Module): Variance-covariance wrong links and
     varian-covariance of ej. is needed (Saito).
   The advantage that this computer programme claims, comes from that if the  
   delay between waves is not identical for each individual, or if some    Revision 1.115  2006/02/27 12:17:45  brouard
   individual missed an interview, the information is not rounded or lost, but    (Module): One freematrix added in mlikeli! 0.98c
   taken into account using an interpolation or extrapolation.  
   hPijx is the probability to be    Revision 1.114  2006/02/26 12:57:58  brouard
   observed in state i at age x+h conditional to the observed state i at age    (Module): Some improvements in processing parameter
   x. The delay 'h' can be split into an exact number (nh*stepm) of    filename with strsep.
   unobserved intermediate  states. This elementary transition (by month or  
   quarter trimester, semester or year) is model as a multinomial logistic.    Revision 1.113  2006/02/24 14:20:24  brouard
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    (Module): Memory leaks checks with valgrind and:
   and the contribution of each individual to the likelihood is simply hPijx.    datafile was not closed, some imatrix were not freed and on matrix
     allocation too.
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.112  2006/01/30 09:55:26  brouard
      (Module): Back to gnuplot.exe instead of wgnuplot.exe
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.111  2006/01/25 20:38:18  brouard
   This software have been partly granted by Euro-REVES, a concerted action    (Module): Lots of cleaning and bugs added (Gompertz)
   from the European Union.    (Module): Comments can be added in data file. Missing date values
   It is copyrighted identically to a GNU software product, ie programme and    can be a simple dot '.'.
   software can be distributed freely for non commercial use. Latest version  
   can be accessed at http://euroreves.ined.fr/imach .    Revision 1.110  2006/01/25 00:51:50  brouard
   **********************************************************************/    (Module): Lots of cleaning and bugs added (Gompertz)
    
 #include <math.h>    Revision 1.109  2006/01/24 19:37:15  brouard
 #include <stdio.h>    (Module): Comments (lines starting with a #) are allowed in data.
 #include <stdlib.h>  
 #include <unistd.h>    Revision 1.108  2006/01/19 18:05:42  lievre
     Gnuplot problem appeared...
 #define MAXLINE 256    To be fixed
 #define FILENAMELENGTH 80  
 /*#define DEBUG*/    Revision 1.107  2006/01/19 16:20:37  brouard
 #define windows    Test existence of gnuplot in imach path
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */  
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    Revision 1.106  2006/01/19 13:24:36  brouard
     Some cleaning and links added in html output
   
     Revision 1.105  2006/01/05 20:23:19  lievre
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    *** empty log message ***
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */  
     Revision 1.104  2005/09/30 16:11:43  lievre
 #define NINTERVMAX 8    (Module): sump fixed, loop imx fixed, and simplifications.
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    (Module): If the status is missing at the last wave but we know
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */    that the person is alive, then we can code his/her status as -2
 #define NCOVMAX 8 /* Maximum number of covariates */    (instead of missing=-1 in earlier versions) and his/her
 #define MAXN 20000    contributions to the likelihood is 1 - Prob of dying from last
 #define YEARM 12. /* Number of months per year */    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 #define AGESUP 130    the healthy state at last known wave). Version is 0.98
 #define AGEBASE 40  
     Revision 1.103  2005/09/30 15:54:49  lievre
     (Module): sump fixed, loop imx fixed, and simplifications.
 int nvar;  
 static int cptcov;    Revision 1.102  2004/09/15 17:31:30  brouard
 int cptcovn;    Add the possibility to read data file including tab characters.
 int npar=NPARMAX;  
 int nlstate=2; /* Number of live states */    Revision 1.101  2004/09/15 10:38:38  brouard
 int ndeath=1; /* Number of dead states */    Fix on curr_time
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */  
     Revision 1.100  2004/07/12 18:29:06  brouard
 int *wav; /* Number of waves for this individuual 0 is possible */    Add version for Mac OS X. Just define UNIX in Makefile
 int maxwav; /* Maxim number of waves */  
 int mle, weightopt;    Revision 1.99  2004/06/05 08:57:40  brouard
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    *** empty log message ***
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Revision 1.98  2004/05/16 15:05:56  brouard
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    New version 0.97 . First attempt to estimate force of mortality
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest;    directly from the data i.e. without the need of knowing the health
 FILE *ficgp, *fichtm;    state at each age, but using a Gompertz model: log u =a + b*age .
 FILE *ficreseij;    This is the basic analysis of mortality and should be done before any
   char filerese[FILENAMELENGTH];    other analysis, in order to test if the mortality estimated from the
  FILE  *ficresvij;    cross-longitudinal survey is different from the mortality estimated
   char fileresv[FILENAMELENGTH];    from other sources like vital statistic data.
  FILE  *ficresvpl;  
   char fileresvpl[FILENAMELENGTH];    The same imach parameter file can be used but the option for mle should be -3.
   
     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.
   
 #define NR_END 1    The output is very simple: only an estimate of the intercept and of
 #define FREE_ARG char*    the slope with 95% confident intervals.
 #define FTOL 1.0e-10  
     Current limitations:
 #define NRANSI    A) Even if you enter covariates, i.e. with the
 #define ITMAX 200    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
     B) There is no computation of Life Expectancy nor Life Table.
 #define TOL 2.0e-4  
     Revision 1.97  2004/02/20 13:25:42  lievre
 #define CGOLD 0.3819660    Version 0.96d. Population forecasting command line is (temporarily)
 #define ZEPS 1.0e-10    suppressed.
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     Revision 1.96  2003/07/15 15:38:55  brouard
 #define GOLD 1.618034    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 #define GLIMIT 100.0    rewritten within the same printf. Workaround: many printfs.
 #define TINY 1.0e-20  
     Revision 1.95  2003/07/08 07:54:34  brouard
 static double maxarg1,maxarg2;    * imach.c (Repository):
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    (Repository): Using imachwizard code to output a more meaningful covariance
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    matrix (cov(a12,c31) instead of numbers.
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Revision 1.94  2003/06/27 13:00:02  brouard
 #define rint(a) floor(a+0.5)    Just cleaning
   
 static double sqrarg;    Revision 1.93  2003/06/25 16:33:55  brouard
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    (Module): On windows (cygwin) function asctime_r doesn't
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    exist so I changed back to asctime which exists.
     (Module): Version 0.96b
 int imx;  
 int stepm;    Revision 1.92  2003/06/25 16:30:45  brouard
 /* Stepm, step in month: minimum step interpolation*/    (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
 int m,nb;  
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax;    Revision 1.91  2003/06/25 15:30:29  brouard
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    * imach.c (Repository): Duplicated warning errors corrected.
 double **pmmij;    (Repository): Elapsed time after each iteration is now output. It
     helps to forecast when convergence will be reached. Elapsed time
 double *weight;    is stamped in powell.  We created a new html file for the graphs
 int **s; /* Status */    concerning matrix of covariance. It has extension -cov.htm.
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab;    Revision 1.90  2003/06/24 12:34:15  brouard
     (Module): Some bugs corrected for windows. Also, when
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    mle=-1 a template is output in file "or"mypar.txt with the design
 double ftolhess; /* Tolerance for computing hessian */    of the covariance matrix to be input.
   
     Revision 1.89  2003/06/24 12:30:52  brouard
 static  int split( char *path, char *dirc, char *name )    (Module): Some bugs corrected for windows. Also, when
 {    mle=-1 a template is output in file "or"mypar.txt with the design
    char *s;                             /* pointer */    of the covariance matrix to be input.
    int  l1, l2;                         /* length counters */  
     Revision 1.88  2003/06/23 17:54:56  brouard
    l1 = strlen( path );                 /* length of path */    * imach.c (Repository): Create a sub-directory where all the secondary files are. Only imach, htm, gp and r(imach) are on the main directory. Correct time and other things.
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );  
    s = strrchr( path, '\\' );           /* find last / */    Revision 1.87  2003/06/18 12:26:01  brouard
    if ( s == NULL ) {                   /* no directory, so use current */    Version 0.96
 #if     defined(__bsd__)                /* get current working directory */  
       extern char       *getwd( );    Revision 1.86  2003/06/17 20:04:08  brouard
     (Module): Change position of html and gnuplot routines and added
       if ( getwd( dirc ) == NULL ) {    routine fileappend.
 #else  
       extern char       *getcwd( );    Revision 1.85  2003/06/17 13:12:43  brouard
     * imach.c (Repository): Check when date of death was earlier that
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    current date of interview. It may happen when the death was just
 #endif    prior to the death. In this case, dh was negative and likelihood
          return( GLOCK_ERROR_GETCWD );    was wrong (infinity). We still send an "Error" but patch by
       }    assuming that the date of death was just one stepm after the
       strcpy( name, path );             /* we've got it */    interview.
    } else {                             /* strip direcotry from path */    (Repository): Because some people have very long ID (first column)
       s++;                              /* after this, the filename */    we changed int to long in num[] and we added a new lvector for
       l2 = strlen( s );                 /* length of filename */    memory allocation. But we also truncated to 8 characters (left
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    truncation)
       strcpy( name, s );                /* save file name */    (Repository): No more line truncation errors.
       strncpy( dirc, path, l1 - l2 );   /* now the directory */  
       dirc[l1-l2] = 0;                  /* add zero */    Revision 1.84  2003/06/13 21:44:43  brouard
    }    * imach.c (Repository): Replace "freqsummary" at a correct
    l1 = strlen( dirc );                 /* length of directory */    place. It differs from routine "prevalence" which may be called
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    many times. Probs is memory consuming and must be used with
    return( 0 );                         /* we're done */    parcimony.
 }    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
   
     Revision 1.83  2003/06/10 13:39:11  lievre
 /******************************************/    *** empty log message ***
   
 void replace(char *s, char*t)    Revision 1.82  2003/06/05 15:57:20  brouard
 {    Add log in  imach.c and  fullversion number is now printed.
   int i;  
   int lg=20;  */
   i=0;  /*
   lg=strlen(t);     Interpolated Markov Chain
   for(i=0; i<= lg; i++) {  
     (s[i] = t[i]);    Short summary of the programme:
     if (t[i]== '\\') s[i]='/';    
   }    This program computes Healthy Life Expectancies from
 }    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
     first survey ("cross") where individuals from different ages are
 int nbocc(char *s, char occ)    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
   int i,j=0;    second wave of interviews ("longitudinal") which measure each change
   int lg=20;    (if any) in individual health status.  Health expectancies are
   i=0;    computed from the time spent in each health state according to a
   lg=strlen(s);    model. More health states you consider, more time is necessary to reach the
   for(i=0; i<= lg; i++) {    Maximum Likelihood of the parameters involved in the model.  The
   if  (s[i] == occ ) j++;    simplest model is the multinomial logistic model where pij is the
   }    probability to be observed in state j at the second wave
   return j;    conditional to be observed in state i at the first wave. Therefore
 }    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
     'age' is age and 'sex' is a covariate. If you want to have a more
 void cutv(char *u,char *v, char*t, char occ)    complex model than "constant and age", you should modify the program
 {    where the markup *Covariates have to be included here again* invites
   int i,lg,j,p;    you to do it.  More covariates you add, slower the
   i=0;    convergence.
   for(j=0; j<=strlen(t)-1; j++) {  
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    The advantage of this computer programme, compared to a simple
   }    multinomial logistic model, is clear when the delay between waves is not
     identical for each individual. Also, if a individual missed an
   lg=strlen(t);    intermediate interview, the information is lost, but taken into
   for(j=0; j<p; j++) {    account using an interpolation or extrapolation.  
     (u[j] = t[j]);  
     u[p]='\0';    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
     split into an exact number (nh*stepm) of unobserved intermediate
    for(j=0; j<= lg; j++) {    states. This elementary transition (by month, quarter,
     if (j>=(p+1))(v[j-p-1] = t[j]);    semester or year) is modelled as a multinomial logistic.  The hPx
   }    matrix is simply the matrix product of nh*stepm elementary matrices
 }    and the contribution of each individual to the likelihood is simply
     hPijx.
 /********************** nrerror ********************/  
     Also this programme outputs the covariance matrix of the parameters but also
 void nrerror(char error_text[])    of the life expectancies. It also computes the period (stable) prevalence. 
 {    
   fprintf(stderr,"ERREUR ...\n");    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   fprintf(stderr,"%s\n",error_text);             Institut national d'études démographiques, Paris.
   exit(1);    This software have been partly granted by Euro-REVES, a concerted action
 }    from the European Union.
 /*********************** vector *******************/    It is copyrighted identically to a GNU software product, ie programme and
 double *vector(int nl, int nh)    software can be distributed freely for non commercial use. Latest version
 {    can be accessed at http://euroreves.ined.fr/imach .
   double *v;  
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
   if (!v) nrerror("allocation failure in vector");    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   return v-nl+NR_END;    
 }    **********************************************************************/
   /*
 /************************ free vector ******************/    main
 void free_vector(double*v, int nl, int nh)    read parameterfile
 {    read datafile
   free((FREE_ARG)(v+nl-NR_END));    concatwav
 }    freqsummary
     if (mle >= 1)
 /************************ivector *******************************/      mlikeli
 int *ivector(long nl,long nh)    print results files
 {    if mle==1 
   int *v;       computes hessian
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));    read end of parameter file: agemin, agemax, bage, fage, estepm
   if (!v) nrerror("allocation failure in ivector");        begin-prev-date,...
   return v-nl+NR_END;    open gnuplot file
 }    open html file
     period (stable) prevalence
 /******************free ivector **************************/     for age prevalim()
 void free_ivector(int *v, long nl, long nh)    h Pij x
 {    variance of p varprob
   free((FREE_ARG)(v+nl-NR_END));    forecasting if prevfcast==1 prevforecast call prevalence()
 }    health expectancies
     Variance-covariance of DFLE
 /******************* imatrix *******************************/    prevalence()
 int **imatrix(long nrl, long nrh, long ncl, long nch)     movingaverage()
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */    varevsij() 
 {    if popbased==1 varevsij(,popbased)
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;    total life expectancies
   int **m;    Variance of period (stable) prevalence
     end
   /* allocate pointers to rows */  */
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  
   m -= nrl;   
    #include <math.h>
    #include <stdio.h>
   /* allocate rows and set pointers to them */  #include <stdlib.h>
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  #include <string.h>
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #include <unistd.h>
   m[nrl] += NR_END;  
   m[nrl] -= ncl;  #include <limits.h>
    #include <sys/types.h>
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  #include <sys/stat.h>
    #include <errno.h>
   /* return pointer to array of pointers to rows */  extern int errno;
   return m;  
 }  /* #include <sys/time.h> */
   #include <time.h>
 /****************** free_imatrix *************************/  #include "timeval.h"
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;  /* #include <libintl.h> */
       long nch,ncl,nrh,nrl;  /* #define _(String) gettext (String) */
      /* free an int matrix allocated by imatrix() */  
 {  #define MAXLINE 256
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  
   free((FREE_ARG) (m+nrl-NR_END));  #define GNUPLOTPROGRAM "gnuplot"
 }  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   #define FILENAMELENGTH 132
 /******************* matrix *******************************/  
 double **matrix(long nrl, long nrh, long ncl, long nch)  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
 {  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  
   double **m;  #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  
   if (!m) nrerror("allocation failure 1 in matrix()");  #define NINTERVMAX 8
   m += NR_END;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   m -= nrl;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   #define NCOVMAX 8 /* Maximum number of covariates */
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #define MAXN 20000
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define YEARM 12. /* Number of months per year */
   m[nrl] += NR_END;  #define AGESUP 130
   m[nrl] -= ncl;  #define AGEBASE 40
   #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #ifdef UNIX
   return m;  #define DIRSEPARATOR '/'
 }  #define CHARSEPARATOR "/"
   #define ODIRSEPARATOR '\\'
 /*************************free matrix ************************/  #else
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  #define DIRSEPARATOR '\\'
 {  #define CHARSEPARATOR "\\"
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  #define ODIRSEPARATOR '/'
   free((FREE_ARG)(m+nrl-NR_END));  #endif
 }  
   /* $Id$ */
 /******************* ma3x *******************************/  /* $State$ */
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  
 {  char version[]="Imach version 0.98d, March 2006, INED-EUROREVES-Institut de longevite ";
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  char fullversion[]="$Revision$ $Date$"; 
   double ***m;  char strstart[80];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   if (!m) nrerror("allocation failure 1 in matrix()");  int nvar;
   m += NR_END;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   m -= nrl;  int npar=NPARMAX;
   int nlstate=2; /* Number of live states */
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  int ndeath=1; /* Number of dead states */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   m[nrl] += NR_END;  int popbased=0;
   m[nrl] -= ncl;  
   int *wav; /* Number of waves for this individuual 0 is possible */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  int maxwav; /* Maxim number of waves */
   int jmin, jmax; /* min, max spacing between 2 waves */
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  int gipmx, gsw; /* Global variables on the number of contributions 
   m[nrl][ncl] += NR_END;                     to the likelihood and the sum of weights (done by funcone)*/
   m[nrl][ncl] -= nll;  int mle, weightopt;
   for (j=ncl+1; j<=nch; j++)  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
     m[nrl][j]=m[nrl][j-1]+nlay;  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
    int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   for (i=nrl+1; i<=nrh; i++) {             * wave mi and wave mi+1 is not an exact multiple of stepm. */
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  double jmean; /* Mean space between 2 waves */
     for (j=ncl+1; j<=nch; j++)  double **oldm, **newm, **savm; /* Working pointers to matrices */
       m[i][j]=m[i][j-1]+nlay;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
   }  FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   return m;  FILE *ficlog, *ficrespow;
 }  int globpr; /* Global variable for printing or not */
   double fretone; /* Only one call to likelihood */
 /*************************free ma3x ************************/  long ipmx; /* Number of contributions */
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  double sw; /* Sum of weights */
 {  char filerespow[FILENAMELENGTH];
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  FILE *ficresilk;
   free((FREE_ARG)(m+nrl-NR_END));  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 }  FILE *ficresprobmorprev;
   FILE *fichtm, *fichtmcov; /* Html File */
 /***************** f1dim *************************/  FILE *ficreseij;
 extern int ncom;  char filerese[FILENAMELENGTH];
 extern double *pcom,*xicom;  FILE *ficresstdeij;
 extern double (*nrfunc)(double []);  char fileresstde[FILENAMELENGTH];
    FILE *ficrescveij;
 double f1dim(double x)  char filerescve[FILENAMELENGTH];
 {  FILE  *ficresvij;
   int j;  char fileresv[FILENAMELENGTH];
   double f;  FILE  *ficresvpl;
   double *xt;  char fileresvpl[FILENAMELENGTH];
    char title[MAXLINE];
   xt=vector(1,ncom);  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   f=(*nrfunc)(xt);  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   free_vector(xt,1,ncom);  char command[FILENAMELENGTH];
   return f;  int  outcmd=0;
 }  
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  char filelog[FILENAMELENGTH]; /* Log file */
 {  char filerest[FILENAMELENGTH];
   int iter;  char fileregp[FILENAMELENGTH];
   double a,b,d,etemp;  char popfile[FILENAMELENGTH];
   double fu,fv,fw,fx;  
   double ftemp;  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
   double p,q,r,tol1,tol2,u,v,w,x,xm;  
   double e=0.0;  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
    struct timezone tzp;
   a=(ax < cx ? ax : cx);  extern int gettimeofday();
   b=(ax > cx ? ax : cx);  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   x=w=v=bx;  long time_value;
   fw=fv=fx=(*f)(x);  extern long time();
   for (iter=1;iter<=ITMAX;iter++) {  char strcurr[80], strfor[80];
     xm=0.5*(a+b);  
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  char *endptr;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  long lval;
     printf(".");fflush(stdout);  
 #ifdef DEBUG  #define NR_END 1
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  #define FREE_ARG char*
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  #define FTOL 1.0e-10
 #endif  
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  #define NRANSI 
       *xmin=x;  #define ITMAX 200 
       return fx;  
     }  #define TOL 2.0e-4 
     ftemp=fu;  
     if (fabs(e) > tol1) {  #define CGOLD 0.3819660 
       r=(x-w)*(fx-fv);  #define ZEPS 1.0e-10 
       q=(x-v)*(fx-fw);  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
       p=(x-v)*q-(x-w)*r;  
       q=2.0*(q-r);  #define GOLD 1.618034 
       if (q > 0.0) p = -p;  #define GLIMIT 100.0 
       q=fabs(q);  #define TINY 1.0e-20 
       etemp=e;  
       e=d;  static double maxarg1,maxarg2;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       else {    
         d=p/q;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
         u=x+d;  #define rint(a) floor(a+0.5)
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);  static double sqrarg;
       }  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
     } else {  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  int agegomp= AGEGOMP;
     }  
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  int imx; 
     fu=(*f)(u);  int stepm=1;
     if (fu <= fx) {  /* Stepm, step in month: minimum step interpolation*/
       if (u >= x) a=x; else b=x;  
       SHFT(v,w,x,u)  int estepm;
         SHFT(fv,fw,fx,fu)  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
         } else {  
           if (u < x) a=u; else b=u;  int m,nb;
           if (fu <= fw || w == x) {  long *num;
             v=w;  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
             w=u;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
             fv=fw;  double **pmmij, ***probs;
             fw=fu;  double *ageexmed,*agecens;
           } else if (fu <= fv || v == x || v == w) {  double dateintmean=0;
             v=u;  
             fv=fu;  double *weight;
           }  int **s; /* Status */
         }  double *agedc, **covar, idx;
   }  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
   nrerror("Too many iterations in brent");  double *lsurv, *lpop, *tpop;
   *xmin=x;  
   return fx;  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
 }  double ftolhess; /* Tolerance for computing hessian */
   
 /****************** mnbrak ***********************/  /**************** split *************************/
   static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,  {
             double (*func)(double))    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
 {       the name of the file (name), its extension only (ext) and its first part of the name (finame)
   double ulim,u,r,q, dum;    */ 
   double fu;    char  *ss;                            /* pointer */
      int   l1, l2;                         /* length counters */
   *fa=(*func)(*ax);  
   *fb=(*func)(*bx);    l1 = strlen(path );                   /* length of path */
   if (*fb > *fa) {    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
     SHFT(dum,*ax,*bx,dum)    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
       SHFT(dum,*fb,*fa,dum)    if ( ss == NULL ) {                   /* no directory, so determine current directory */
       }      strcpy( name, path );               /* we got the fullname name because no directory */
   *cx=(*bx)+GOLD*(*bx-*ax);      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   *fc=(*func)(*cx);        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
   while (*fb > *fc) {      /* get current working directory */
     r=(*bx-*ax)*(*fb-*fc);      /*    extern  char* getcwd ( char *buf , int len);*/
     q=(*bx-*cx)*(*fb-*fa);      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/        return( GLOCK_ERROR_GETCWD );
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));      }
     ulim=(*bx)+GLIMIT*(*cx-*bx);      /* got dirc from getcwd*/
     if ((*bx-u)*(u-*cx) > 0.0) {      printf(" DIRC = %s \n",dirc);
       fu=(*func)(u);    } else {                              /* strip direcotry from path */
     } else if ((*cx-u)*(u-ulim) > 0.0) {      ss++;                               /* after this, the filename */
       fu=(*func)(u);      l2 = strlen( ss );                  /* length of filename */
       if (fu < *fc) {      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))      strcpy( name, ss );         /* save file name */
           SHFT(*fb,*fc,fu,(*func)(u))      strncpy( dirc, path, l1 - l2 );     /* now the directory */
           }      dirc[l1-l2] = 0;                    /* add zero */
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {      printf(" DIRC2 = %s \n",dirc);
       u=ulim;    }
       fu=(*func)(u);    /* We add a separator at the end of dirc if not exists */
     } else {    l1 = strlen( dirc );                  /* length of directory */
       u=(*cx)+GOLD*(*cx-*bx);    if( dirc[l1-1] != DIRSEPARATOR ){
       fu=(*func)(u);      dirc[l1] =  DIRSEPARATOR;
     }      dirc[l1+1] = 0; 
     SHFT(*ax,*bx,*cx,u)      printf(" DIRC3 = %s \n",dirc);
       SHFT(*fa,*fb,*fc,fu)    }
       }    ss = strrchr( name, '.' );            /* find last / */
 }    if (ss >0){
       ss++;
 /*************** linmin ************************/      strcpy(ext,ss);                     /* save extension */
       l1= strlen( name);
 int ncom;      l2= strlen(ss)+1;
 double *pcom,*xicom;      strncpy( finame, name, l1-l2);
 double (*nrfunc)(double []);      finame[l1-l2]= 0;
      }
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  
 {    return( 0 );                          /* we're done */
   double brent(double ax, double bx, double cx,  }
                double (*f)(double), double tol, double *xmin);  
   double f1dim(double x);  
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  /******************************************/
               double *fc, double (*func)(double));  
   int j;  void replace_back_to_slash(char *s, char*t)
   double xx,xmin,bx,ax;  {
   double fx,fb,fa;    int i;
      int lg=0;
   ncom=n;    i=0;
   pcom=vector(1,n);    lg=strlen(t);
   xicom=vector(1,n);    for(i=0; i<= lg; i++) {
   nrfunc=func;      (s[i] = t[i]);
   for (j=1;j<=n;j++) {      if (t[i]== '\\') s[i]='/';
     pcom[j]=p[j];    }
     xicom[j]=xi[j];  }
   }  
   ax=0.0;  int nbocc(char *s, char occ)
   xx=1.0;  {
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    int i,j=0;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    int lg=20;
 #ifdef DEBUG    i=0;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);    lg=strlen(s);
 #endif    for(i=0; i<= lg; i++) {
   for (j=1;j<=n;j++) {    if  (s[i] == occ ) j++;
     xi[j] *= xmin;    }
     p[j] += xi[j];    return j;
   }  }
   free_vector(xicom,1,n);  
   free_vector(pcom,1,n);  void cutv(char *u,char *v, char*t, char occ)
 }  {
     /* cuts string t into u and v where u ends before first occurence of char 'occ' 
 /*************** powell ************************/       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,       gives u="abcedf" and v="ghi2j" */
             double (*func)(double []))    int i,lg,j,p=0;
 {    i=0;
   void linmin(double p[], double xi[], int n, double *fret,    for(j=0; j<=strlen(t)-1; j++) {
               double (*func)(double []));      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   int i,ibig,j;    }
   double del,t,*pt,*ptt,*xit;  
   double fp,fptt;    lg=strlen(t);
   double *xits;    for(j=0; j<p; j++) {
   pt=vector(1,n);      (u[j] = t[j]);
   ptt=vector(1,n);    }
   xit=vector(1,n);       u[p]='\0';
   xits=vector(1,n);  
   *fret=(*func)(p);     for(j=0; j<= lg; j++) {
   for (j=1;j<=n;j++) pt[j]=p[j];      if (j>=(p+1))(v[j-p-1] = t[j]);
   for (*iter=1;;++(*iter)) {    }
     fp=(*fret);  }
     ibig=0;  
     del=0.0;  /********************** nrerror ********************/
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);  
     for (i=1;i<=n;i++)  void nrerror(char error_text[])
       printf(" %d %.12f",i, p[i]);  {
     printf("\n");    fprintf(stderr,"ERREUR ...\n");
     for (i=1;i<=n;i++) {    fprintf(stderr,"%s\n",error_text);
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    exit(EXIT_FAILURE);
       fptt=(*fret);  }
 #ifdef DEBUG  /*********************** vector *******************/
       printf("fret=%lf \n",*fret);  double *vector(int nl, int nh)
 #endif  {
       printf("%d",i);fflush(stdout);    double *v;
       linmin(p,xit,n,fret,func);    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
       if (fabs(fptt-(*fret)) > del) {    if (!v) nrerror("allocation failure in vector");
         del=fabs(fptt-(*fret));    return v-nl+NR_END;
         ibig=i;  }
       }  
 #ifdef DEBUG  /************************ free vector ******************/
       printf("%d %.12e",i,(*fret));  void free_vector(double*v, int nl, int nh)
       for (j=1;j<=n;j++) {  {
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);    free((FREE_ARG)(v+nl-NR_END));
         printf(" x(%d)=%.12e",j,xit[j]);  }
       }  
       for(j=1;j<=n;j++)  /************************ivector *******************************/
         printf(" p=%.12e",p[j]);  int *ivector(long nl,long nh)
       printf("\n");  {
 #endif    int *v;
     }    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {    if (!v) nrerror("allocation failure in ivector");
 #ifdef DEBUG    return v-nl+NR_END;
       int k[2],l;  }
       k[0]=1;  
       k[1]=-1;  /******************free ivector **************************/
       printf("Max: %.12e",(*func)(p));  void free_ivector(int *v, long nl, long nh)
       for (j=1;j<=n;j++)  {
         printf(" %.12e",p[j]);    free((FREE_ARG)(v+nl-NR_END));
       printf("\n");  }
       for(l=0;l<=1;l++) {  
         for (j=1;j<=n;j++) {  /************************lvector *******************************/
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];  long *lvector(long nl,long nh)
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  {
         }    long *v;
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       }    if (!v) nrerror("allocation failure in ivector");
 #endif    return v-nl+NR_END;
   }
   
       free_vector(xit,1,n);  /******************free lvector **************************/
       free_vector(xits,1,n);  void free_lvector(long *v, long nl, long 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.");  /******************* imatrix *******************************/
     for (j=1;j<=n;j++) {  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       ptt[j]=2.0*p[j]-pt[j];       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       xit[j]=p[j]-pt[j];  { 
       pt[j]=p[j];    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     }    int **m; 
     fptt=(*func)(ptt);    
     if (fptt < fp) {    /* allocate pointers to rows */ 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       if (t < 0.0) {    if (!m) nrerror("allocation failure 1 in matrix()"); 
         linmin(p,xit,n,fret,func);    m += NR_END; 
         for (j=1;j<=n;j++) {    m -= nrl; 
           xi[j][ibig]=xi[j][n];    
           xi[j][n]=xit[j];    
         }    /* allocate rows and set pointers to them */ 
 #ifdef DEBUG    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
         for(j=1;j<=n;j++)    m[nrl] += NR_END; 
           printf(" %.12e",xit[j]);    m[nrl] -= ncl; 
         printf("\n");    
 #endif    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       }    
     }    /* return pointer to array of pointers to rows */ 
   }    return m; 
 }  } 
   
 /**** Prevalence limit ****************/  /****************** free_imatrix *************************/
   void free_imatrix(m,nrl,nrh,ncl,nch)
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)        int **m;
 {        long nch,ncl,nrh,nrl; 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit       /* free an int matrix allocated by imatrix() */ 
      matrix by transitions matrix until convergence is reached */  { 
     free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
   int i, ii,j,k;    free((FREE_ARG) (m+nrl-NR_END)); 
   double min, max, maxmin, maxmax,sumnew=0.;  } 
   double **matprod2();  
   double **out, cov[NCOVMAX], **pmij();  /******************* matrix *******************************/
   double **newm;  double **matrix(long nrl, long nrh, long ncl, long nch)
   double agefin, delaymax=50 ; /* Max number of years to converge */  {
     long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   for (ii=1;ii<=nlstate+ndeath;ii++)    double **m;
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     }    if (!m) nrerror("allocation failure 1 in matrix()");
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */    m += NR_END;
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    m -= nrl;
     newm=savm;  
     /* Covariates have to be included here again */    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     cov[1]=1.;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     cov[2]=agefin;    m[nrl] += NR_END;
     if (cptcovn>0){    m[nrl] -= ncl;
       for (k=1; k<=cptcovn;k++) {cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];/*printf("Tcode[ij]=%d nbcode=%d\n",Tcode[ij],nbcode[k][Tcode[ij]]);*/}  
     }    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);    return m;
     /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
     savm=oldm;     */
     oldm=newm;  }
     maxmax=0.;  
     for(j=1;j<=nlstate;j++){  /*************************free matrix ************************/
       min=1.;  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
       max=0.;  {
       for(i=1; i<=nlstate; i++) {    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         sumnew=0;    free((FREE_ARG)(m+nrl-NR_END));
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  }
         prlim[i][j]= newm[i][j]/(1-sumnew);  
         max=FMAX(max,prlim[i][j]);  /******************* ma3x *******************************/
         min=FMIN(min,prlim[i][j]);  double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       }  {
       maxmin=max-min;    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       maxmax=FMAX(maxmax,maxmin);    double ***m;
     }  
     if(maxmax < ftolpl){    m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
       return prlim;    if (!m) nrerror("allocation failure 1 in matrix()");
     }    m += NR_END;
   }    m -= nrl;
 }  
     m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
 /*************** transition probabilities **********/    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    m[nrl] -= ncl;
 {  
   double s1, s2;    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   /*double t34;*/  
   int i,j,j1, nc, ii, jj;    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
     if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
     for(i=1; i<= nlstate; i++){    m[nrl][ncl] += NR_END;
     for(j=1; j<i;j++){    m[nrl][ncl] -= nll;
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    for (j=ncl+1; j<=nch; j++) 
         /*s2 += param[i][j][nc]*cov[nc];*/      m[nrl][j]=m[nrl][j-1]+nlay;
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    for (i=nrl+1; i<=nrh; i++) {
       }      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       ps[i][j]=s2;      for (j=ncl+1; j<=nch; j++) 
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/        m[i][j]=m[i][j-1]+nlay;
     }    }
     for(j=i+1; j<=nlstate+ndeath;j++){    return m; 
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    */
       }  }
       ps[i][j]=s2;  
     }  /*************************free ma3x ************************/
   }  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
   for(i=1; i<= nlstate; i++){  {
      s1=0;    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
     for(j=1; j<i; j++)    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       s1+=exp(ps[i][j]);    free((FREE_ARG)(m+nrl-NR_END));
     for(j=i+1; j<=nlstate+ndeath; j++)  }
       s1+=exp(ps[i][j]);  
     ps[i][i]=1./(s1+1.);  /*************** function subdirf ***********/
     for(j=1; j<i; j++)  char *subdirf(char fileres[])
       ps[i][j]= exp(ps[i][j])*ps[i][i];  {
     for(j=i+1; j<=nlstate+ndeath; j++)    /* Caution optionfilefiname is hidden */
       ps[i][j]= exp(ps[i][j])*ps[i][i];    strcpy(tmpout,optionfilefiname);
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */    strcat(tmpout,"/"); /* Add to the right */
   } /* end i */    strcat(tmpout,fileres);
     return tmpout;
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){  }
     for(jj=1; jj<= nlstate+ndeath; jj++){  
       ps[ii][jj]=0;  /*************** function subdirf2 ***********/
       ps[ii][ii]=1;  char *subdirf2(char fileres[], char *preop)
     }  {
   }    
     /* Caution optionfilefiname is hidden */
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    strcpy(tmpout,optionfilefiname);
     for(jj=1; jj<= nlstate+ndeath; jj++){    strcat(tmpout,"/");
      printf("%lf ",ps[ii][jj]);    strcat(tmpout,preop);
    }    strcat(tmpout,fileres);
     printf("\n ");    return tmpout;
     }  }
     printf("\n ");printf("%lf ",cov[2]);*/  
 /*  /*************** function subdirf3 ***********/
   for(i=1; i<= npar; i++) printf("%f ",x[i]);  char *subdirf3(char fileres[], char *preop, char *preop2)
   goto end;*/  {
     return ps;    
 }    /* Caution optionfilefiname is hidden */
     strcpy(tmpout,optionfilefiname);
 /**************** Product of 2 matrices ******************/    strcat(tmpout,"/");
     strcat(tmpout,preop);
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    strcat(tmpout,preop2);
 {    strcat(tmpout,fileres);
   /* Computes the matric product of in(1,nrh-nrl+1)(1,nch-ncl+1) times    return tmpout;
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  }
   /* in, b, out are matrice of pointers which should have been initialized  
      before: only the contents of out is modified. The function returns  /***************** f1dim *************************/
      a pointer to pointers identical to out */  extern int ncom; 
   long i, j, k;  extern double *pcom,*xicom;
   for(i=nrl; i<= nrh; i++)  extern double (*nrfunc)(double []); 
     for(k=ncolol; k<=ncoloh; k++)   
       for(j=ncl,out[i][k]=0.; j<=nch; j++)  double f1dim(double x) 
         out[i][k] +=in[i][j]*b[j][k];  { 
     int j; 
   return out;    double f;
 }    double *xt; 
    
     xt=vector(1,ncom); 
 /************* Higher Matrix Product ***************/    for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
     f=(*nrfunc)(xt); 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )    free_vector(xt,1,ncom); 
 {    return f; 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month  } 
      duration (i.e. until  
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  /*****************brent *************************/
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
      (typically every 2 years instead of every month which is too big).  { 
      Model is determined by parameters x and covariates have to be    int iter; 
      included manually here.    double a,b,d,etemp;
     double fu,fv,fw,fx;
      */    double ftemp;
     double p,q,r,tol1,tol2,u,v,w,x,xm; 
   int i, j, d, h, k;    double e=0.0; 
   double **out, cov[NCOVMAX];   
   double **newm;    a=(ax < cx ? ax : cx); 
     b=(ax > cx ? ax : cx); 
   /* Hstepm could be zero and should return the unit matrix */    x=w=v=bx; 
   for (i=1;i<=nlstate+ndeath;i++)    fw=fv=fx=(*f)(x); 
     for (j=1;j<=nlstate+ndeath;j++){    for (iter=1;iter<=ITMAX;iter++) { 
       oldm[i][j]=(i==j ? 1.0 : 0.0);      xm=0.5*(a+b); 
       po[i][j][0]=(i==j ? 1.0 : 0.0);      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
     }      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */      printf(".");fflush(stdout);
   for(h=1; h <=nhstepm; h++){      fprintf(ficlog,".");fflush(ficlog);
     for(d=1; d <=hstepm; d++){  #ifdef DEBUG
       newm=savm;      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);
       /* Covariates have to be included here again */      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);
       cov[1]=1.;      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;  #endif
       if (cptcovn>0){      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][k]];        *xmin=x; 
     }        return fx; 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      } 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/      ftemp=fu;
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,      if (fabs(e) > tol1) { 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));        r=(x-w)*(fx-fv); 
       savm=oldm;        q=(x-v)*(fx-fw); 
       oldm=newm;        p=(x-v)*q-(x-w)*r; 
     }        q=2.0*(q-r); 
     for(i=1; i<=nlstate+ndeath; i++)        if (q > 0.0) p = -p; 
       for(j=1;j<=nlstate+ndeath;j++) {        q=fabs(q); 
         po[i][j][h]=newm[i][j];        etemp=e; 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);        e=d; 
          */        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
       }          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   } /* end h */        else { 
   return po;          d=p/q; 
 }          u=x+d; 
           if (u-a < tol2 || b-u < tol2) 
             d=SIGN(tol1,xm-x); 
 /*************** log-likelihood *************/        } 
 double func( double *x)      } else { 
 {        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   int i, ii, j, k, mi, d;      } 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   double **out;      fu=(*f)(u); 
   double sw; /* Sum of weights */      if (fu <= fx) { 
   double lli; /* Individual log likelihood */        if (u >= x) a=x; else b=x; 
   long ipmx;        SHFT(v,w,x,u) 
   /*extern weight */          SHFT(fv,fw,fx,fu) 
   /* We are differentiating ll according to initial status */          } else { 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/            if (u < x) a=u; else b=u; 
   /*for(i=1;i<imx;i++)            if (fu <= fw || w == x) { 
 printf(" %d\n",s[4][i]);              v=w; 
   */              w=u; 
               fv=fw; 
   for(k=1; k<=nlstate; k++) ll[k]=0.;              fw=fu; 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){            } else if (fu <= fv || v == x || v == w) { 
        for(mi=1; mi<= wav[i]-1; mi++){              v=u; 
       for (ii=1;ii<=nlstate+ndeath;ii++)              fv=fu; 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);            } 
             for(d=0; d<dh[mi][i]; d++){          } 
         newm=savm;    } 
           cov[1]=1.;    nrerror("Too many iterations in brent"); 
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;    *xmin=x; 
           if (cptcovn>0){    return fx; 
             for (k=1; k<=cptcovn;k++) cov[2+k]=covar[1+k-1][i];  } 
             }  
           out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,  /****************** mnbrak ***********************/
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  
           savm=oldm;  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
           oldm=newm;              double (*func)(double)) 
   { 
     double ulim,u,r,q, dum;
       } /* end mult */    double fu; 
       
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    *fa=(*func)(*ax); 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    *fb=(*func)(*bx); 
       ipmx +=1;    if (*fb > *fa) { 
       sw += weight[i];      SHFT(dum,*ax,*bx,dum) 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        SHFT(dum,*fb,*fa,dum) 
     } /* end of wave */        } 
   } /* end of individual */    *cx=(*bx)+GOLD*(*bx-*ax); 
     *fc=(*func)(*cx); 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    while (*fb > *fc) { 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      r=(*bx-*ax)*(*fb-*fc); 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      q=(*bx-*cx)*(*fb-*fa); 
   return -l;      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
 }        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
       ulim=(*bx)+GLIMIT*(*cx-*bx); 
       if ((*bx-u)*(u-*cx) > 0.0) { 
 /*********** Maximum Likelihood Estimation ***************/        fu=(*func)(u); 
       } else if ((*cx-u)*(u-ulim) > 0.0) { 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))        fu=(*func)(u); 
 {        if (fu < *fc) { 
   int i,j, iter;          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   double **xi,*delti;            SHFT(*fb,*fc,fu,(*func)(u)) 
   double fret;            } 
   xi=matrix(1,npar,1,npar);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   for (i=1;i<=npar;i++)        u=ulim; 
     for (j=1;j<=npar;j++)        fu=(*func)(u); 
       xi[i][j]=(i==j ? 1.0 : 0.0);      } else { 
   printf("Powell\n");        u=(*cx)+GOLD*(*cx-*bx); 
   powell(p,xi,npar,ftol,&iter,&fret,func);        fu=(*func)(u); 
       } 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));      SHFT(*ax,*bx,*cx,u) 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));        SHFT(*fa,*fb,*fc,fu) 
         } 
 }  } 
   
 /**** Computes Hessian and covariance matrix ***/  /*************** linmin ************************/
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))  
 {  int ncom; 
   double  **a,**y,*x,pd;  double *pcom,*xicom;
   double **hess;  double (*nrfunc)(double []); 
   int i, j,jk;   
   int *indx;  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
   { 
   double hessii(double p[], double delta, int theta, double delti[]);    double brent(double ax, double bx, double cx, 
   double hessij(double p[], double delti[], int i, int j);                 double (*f)(double), double tol, double *xmin); 
   void lubksb(double **a, int npar, int *indx, double b[]) ;    double f1dim(double x); 
   void ludcmp(double **a, int npar, int *indx, double *d) ;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                 double *fc, double (*func)(double)); 
     int j; 
   hess=matrix(1,npar,1,npar);    double xx,xmin,bx,ax; 
     double fx,fb,fa;
   printf("\nCalculation of the hessian matrix. Wait...\n");   
   for (i=1;i<=npar;i++){    ncom=n; 
     printf("%d",i);fflush(stdout);    pcom=vector(1,n); 
     hess[i][i]=hessii(p,ftolhess,i,delti);    xicom=vector(1,n); 
     /*printf(" %f ",p[i]);*/    nrfunc=func; 
   }    for (j=1;j<=n;j++) { 
       pcom[j]=p[j]; 
   for (i=1;i<=npar;i++) {      xicom[j]=xi[j]; 
     for (j=1;j<=npar;j++)  {    } 
       if (j>i) {    ax=0.0; 
         printf(".%d%d",i,j);fflush(stdout);    xx=1.0; 
         hess[i][j]=hessij(p,delti,i,j);    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
         hess[j][i]=hess[i][j];    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
       }  #ifdef DEBUG
     }    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   }    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   printf("\n");  #endif
     for (j=1;j<=n;j++) { 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");      xi[j] *= xmin; 
        p[j] += xi[j]; 
   a=matrix(1,npar,1,npar);    } 
   y=matrix(1,npar,1,npar);    free_vector(xicom,1,n); 
   x=vector(1,npar);    free_vector(pcom,1,n); 
   indx=ivector(1,npar);  } 
   for (i=1;i<=npar;i++)  
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];  char *asc_diff_time(long time_sec, char ascdiff[])
   ludcmp(a,npar,indx,&pd);  {
     long sec_left, days, hours, minutes;
   for (j=1;j<=npar;j++) {    days = (time_sec) / (60*60*24);
     for (i=1;i<=npar;i++) x[i]=0;    sec_left = (time_sec) % (60*60*24);
     x[j]=1;    hours = (sec_left) / (60*60) ;
     lubksb(a,npar,indx,x);    sec_left = (sec_left) %(60*60);
     for (i=1;i<=npar;i++){    minutes = (sec_left) /60;
       matcov[i][j]=x[i];    sec_left = (sec_left) % (60);
     }    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   }    return ascdiff;
   }
   printf("\n#Hessian matrix#\n");  
   for (i=1;i<=npar;i++) {  /*************** powell ************************/
     for (j=1;j<=npar;j++) {  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       printf("%.3e ",hess[i][j]);              double (*func)(double [])) 
     }  { 
     printf("\n");    void linmin(double p[], double xi[], int n, double *fret, 
   }                double (*func)(double [])); 
     int i,ibig,j; 
   /* Recompute Inverse */    double del,t,*pt,*ptt,*xit;
   for (i=1;i<=npar;i++)    double fp,fptt;
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];    double *xits;
   ludcmp(a,npar,indx,&pd);    int niterf, itmp;
   
   /*  printf("\n#Hessian matrix recomputed#\n");    pt=vector(1,n); 
     ptt=vector(1,n); 
   for (j=1;j<=npar;j++) {    xit=vector(1,n); 
     for (i=1;i<=npar;i++) x[i]=0;    xits=vector(1,n); 
     x[j]=1;    *fret=(*func)(p); 
     lubksb(a,npar,indx,x);    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for (i=1;i<=npar;i++){    for (*iter=1;;++(*iter)) { 
       y[i][j]=x[i];      fp=(*fret); 
       printf("%.3e ",y[i][j]);      ibig=0; 
     }      del=0.0; 
     printf("\n");      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);
   free_matrix(a,1,npar,1,npar);      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
   free_matrix(y,1,npar,1,npar);      */
   free_vector(x,1,npar);     for (i=1;i<=n;i++) {
   free_ivector(indx,1,npar);        printf(" %d %.12f",i, p[i]);
   free_matrix(hess,1,npar,1,npar);        fprintf(ficlog," %d %.12lf",i, p[i]);
         fprintf(ficrespow," %.12lf", p[i]);
       }
 }      printf("\n");
       fprintf(ficlog,"\n");
 /*************** hessian matrix ****************/      fprintf(ficrespow,"\n");fflush(ficrespow);
 double hessii( double x[], double delta, int theta, double delti[])      if(*iter <=3){
 {        tm = *localtime(&curr_time.tv_sec);
   int i;        strcpy(strcurr,asctime(&tm));
   int l=1, lmax=20;  /*       asctime_r(&tm,strcurr); */
   double k1,k2;        forecast_time=curr_time; 
   double p2[NPARMAX+1];        itmp = strlen(strcurr);
   double res;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;          strcurr[itmp-1]='\0';
   double fx;        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   int k=0,kmax=10;        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   double l1;        for(niterf=10;niterf<=30;niterf+=10){
           forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
   fx=func(x);          tmf = *localtime(&forecast_time.tv_sec);
   for (i=1;i<=npar;i++) p2[i]=x[i];  /*      asctime_r(&tmf,strfor); */
   for(l=0 ; l <=lmax; l++){          strcpy(strfor,asctime(&tmf));
     l1=pow(10,l);          itmp = strlen(strfor);
     delts=delt;          if(strfor[itmp-1]=='\n')
     for(k=1 ; k <kmax; k=k+1){          strfor[itmp-1]='\0';
       delt = delta*(l1*k);          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);
       p2[theta]=x[theta] +delt;          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);
       k1=func(p2)-fx;        }
       p2[theta]=x[theta]-delt;      }
       k2=func(p2)-fx;      for (i=1;i<=n;i++) { 
       /*res= (k1-2.0*fx+k2)/delt/delt; */        for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */        fptt=(*fret); 
        #ifdef DEBUG
 #ifdef DEBUG        printf("fret=%lf \n",*fret);
       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,"fret=%lf \n",*fret);
 #endif  #endif
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */        printf("%d",i);fflush(stdout);
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){        fprintf(ficlog,"%d",i);fflush(ficlog);
         k=kmax;        linmin(p,xit,n,fret,func); 
       }        if (fabs(fptt-(*fret)) > del) { 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          del=fabs(fptt-(*fret)); 
         k=kmax; l=lmax*10.;          ibig=i; 
       }        } 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){  #ifdef DEBUG
         delts=delt;        printf("%d %.12e",i,(*fret));
       }        fprintf(ficlog,"%d %.12e",i,(*fret));
     }        for (j=1;j<=n;j++) {
   }          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   delti[theta]=delts;          printf(" x(%d)=%.12e",j,xit[j]);
   return res;          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
          }
 }        for(j=1;j<=n;j++) {
           printf(" p=%.12e",p[j]);
 double hessij( double x[], double delti[], int thetai,int thetaj)          fprintf(ficlog," p=%.12e",p[j]);
 {        }
   int i;        printf("\n");
   int l=1, l1, lmax=20;        fprintf(ficlog,"\n");
   double k1,k2,k3,k4,res,fx;  #endif
   double p2[NPARMAX+1];      } 
   int k;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   #ifdef DEBUG
   fx=func(x);        int k[2],l;
   for (k=1; k<=2; k++) {        k[0]=1;
     for (i=1;i<=npar;i++) p2[i]=x[i];        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));
     k1=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;        }
     k2=func(p2)-fx;        printf("\n");
          fprintf(ficlog,"\n");
     p2[thetai]=x[thetai]-delti[thetai]/k;        for(l=0;l<=1;l++) {
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          for (j=1;j<=n;j++) {
     k3=func(p2)-fx;            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]);
     p2[thetai]=x[thetai]-delti[thetai]/k;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          }
     k4=func(p2)-fx;          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 #ifdef DEBUG        }
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);  #endif
 #endif  
   }  
   return res;        free_vector(xit,1,n); 
 }        free_vector(xits,1,n); 
         free_vector(ptt,1,n); 
 /************** Inverse of matrix **************/        free_vector(pt,1,n); 
 void ludcmp(double **a, int n, int *indx, double *d)        return; 
 {      } 
   int i,imax,j,k;      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
   double big,dum,sum,temp;      for (j=1;j<=n;j++) { 
   double *vv;        ptt[j]=2.0*p[j]-pt[j]; 
          xit[j]=p[j]-pt[j]; 
   vv=vector(1,n);        pt[j]=p[j]; 
   *d=1.0;      } 
   for (i=1;i<=n;i++) {      fptt=(*func)(ptt); 
     big=0.0;      if (fptt < fp) { 
     for (j=1;j<=n;j++)        t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
       if ((temp=fabs(a[i][j])) > big) big=temp;        if (t < 0.0) { 
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          linmin(p,xit,n,fret,func); 
     vv[i]=1.0/big;          for (j=1;j<=n;j++) { 
   }            xi[j][ibig]=xi[j][n]; 
   for (j=1;j<=n;j++) {            xi[j][n]=xit[j]; 
     for (i=1;i<j;i++) {          }
       sum=a[i][j];  #ifdef DEBUG
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
       a[i][j]=sum;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     }          for(j=1;j<=n;j++){
     big=0.0;            printf(" %.12e",xit[j]);
     for (i=j;i<=n;i++) {            fprintf(ficlog," %.12e",xit[j]);
       sum=a[i][j];          }
       for (k=1;k<j;k++)          printf("\n");
         sum -= a[i][k]*a[k][j];          fprintf(ficlog,"\n");
       a[i][j]=sum;  #endif
       if ( (dum=vv[i]*fabs(sum)) >= big) {        }
         big=dum;      } 
         imax=i;    } 
       }  } 
     }  
     if (j != imax) {  /**** Prevalence limit (stable or period prevalence)  ****************/
       for (k=1;k<=n;k++) {  
         dum=a[imax][k];  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
         a[imax][k]=a[j][k];  {
         a[j][k]=dum;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
       }       matrix by transitions matrix until convergence is reached */
       *d = -(*d);  
       vv[imax]=vv[j];    int i, ii,j,k;
     }    double min, max, maxmin, maxmax,sumnew=0.;
     indx[j]=imax;    double **matprod2();
     if (a[j][j] == 0.0) a[j][j]=TINY;    double **out, cov[NCOVMAX], **pmij();
     if (j != n) {    double **newm;
       dum=1.0/(a[j][j]);    double agefin, delaymax=50 ; /* Max number of years to converge */
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  
     }    for (ii=1;ii<=nlstate+ndeath;ii++)
   }      for (j=1;j<=nlstate+ndeath;j++){
   free_vector(vv,1,n);  /* Doesn't work */        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 ;      }
 }  
      cov[1]=1.;
 void lubksb(double **a, int n, int *indx, double b[])   
 {   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   int i,ii=0,ip,j;    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   double sum;      newm=savm;
        /* Covariates have to be included here again */
   for (i=1;i<=n;i++) {       cov[2]=agefin;
     ip=indx[i];    
     sum=b[ip];        for (k=1; k<=cptcovn;k++) {
     b[ip]=b[i];          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     if (ii)          /*      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 (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        }
     else if (sum) ii=i;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     b[i]=sum;        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]]];
   for (i=n;i>=1;i--) {  
     sum=b[i];        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     b[i]=sum/a[i][i];        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
   }      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
 }  
       savm=oldm;
 /************ Frequencies ********************/      oldm=newm;
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax)      maxmax=0.;
 {  /* Some frequencies */      for(j=1;j<=nlstate;j++){
          min=1.;
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;        max=0.;
   double ***freq; /* Frequencies */        for(i=1; i<=nlstate; i++) {
   double *pp;          sumnew=0;
   double pos;          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   FILE *ficresp;          prlim[i][j]= newm[i][j]/(1-sumnew);
   char fileresp[FILENAMELENGTH];          max=FMAX(max,prlim[i][j]);
           min=FMIN(min,prlim[i][j]);
   pp=vector(1,nlstate);        }
         maxmin=max-min;
   strcpy(fileresp,"p");        maxmax=FMAX(maxmax,maxmin);
   strcat(fileresp,fileres);      }
   if((ficresp=fopen(fileresp,"w"))==NULL) {      if(maxmax < ftolpl){
     printf("Problem with prevalence resultfile: %s\n", fileresp);        return prlim;
     exit(0);      }
   }    }
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);  }
   j1=0;  
   /*************** transition probabilities ***************/ 
   j=cptcovn;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   {
   for(k1=1; k1<=j;k1++){    double s1, s2;
    for(i1=1; i1<=ncodemax[k1];i1++){    /*double t34;*/
        j1++;    int i,j,j1, nc, ii, jj;
   
         for (i=-1; i<=nlstate+ndeath; i++)        for(i=1; i<= nlstate; i++){
          for (jk=-1; jk<=nlstate+ndeath; jk++)          for(j=1; j<i;j++){
            for(m=agemin; m <= agemax+3; m++)          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
              freq[i][jk][m]=0;            /*s2 += param[i][j][nc]*cov[nc];*/
                    s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
        for (i=1; i<=imx; i++) {  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
          bool=1;          }
          if  (cptcovn>0) {          ps[i][j]=s2;
            for (z1=1; z1<=cptcovn; z1++)  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
              if (covar[Tvar[z1]][i]!= nbcode[Tvar[z1]][codtab[j1][z1]]) bool=0;        }
          }        for(j=i+1; j<=nlstate+ndeath;j++){
           if (bool==1) {          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
            for(m=firstpass; m<=lastpass-1; m++){            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*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 %lx %lx\n",s1,s2,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];        }
            }      }
          }      /*ps[3][2]=1;*/
        }      
         if  (cptcovn>0) {      for(i=1; i<= nlstate; i++){
          fprintf(ficresp, "\n#Variable");        s1=0;
          for (z1=1; z1<=cptcovn; z1++) fprintf(ficresp, " V%d=%d",Tvar[z1],nbcode[Tvar[z1]][codtab[j1][z1]]);        for(j=1; j<i; j++)
        }          s1+=exp(ps[i][j]);
        fprintf(ficresp, "\n#");        for(j=i+1; j<=nlstate+ndeath; j++)
        for(i=1; i<=nlstate;i++)          s1+=exp(ps[i][j]);
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);        ps[i][i]=1./(s1+1.);
        fprintf(ficresp, "\n");        for(j=1; j<i; j++)
                  ps[i][j]= exp(ps[i][j])*ps[i][i];
   for(i=(int)agemin; i <= (int)agemax+3; i++){        for(j=i+1; j<=nlstate+ndeath; j++)
     if(i==(int)agemax+3)          ps[i][j]= exp(ps[i][j])*ps[i][i];
       printf("Total");        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
     else      } /* end i */
       printf("Age %d", i);      
     for(jk=1; jk <=nlstate ; jk++){      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)        for(jj=1; jj<= nlstate+ndeath; jj++){
         pp[jk] += freq[jk][m][i];          ps[ii][jj]=0;
     }          ps[ii][ii]=1;
     for(jk=1; jk <=nlstate ; jk++){        }
       for(m=-1, pos=0; m <=0 ; m++)      }
         pos += freq[jk][m][i];      
       if(pp[jk]>=1.e-10)  
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
       else  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);  /*         printf("ddd %lf ",ps[ii][jj]); */
     }  /*       } */
     for(jk=1; jk <=nlstate ; jk++){  /*       printf("\n "); */
       for(m=1, pp[jk]=0; m <=nlstate+ndeath; m++)  /*        } */
         pp[jk] += freq[jk][m][i];  /*        printf("\n ");printf("%lf ",cov[2]); */
     }         /*
     for(jk=1,pos=0; jk <=nlstate ; jk++)        for(i=1; i<= npar; i++) printf("%f ",x[i]);
       pos += pp[jk];        goto end;*/
     for(jk=1; jk <=nlstate ; jk++){      return ps;
       if(pos>=1.e-5)  }
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);  
       else  /**************** Product of 2 matrices ******************/
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);  
       if( i <= (int) agemax){  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
         if(pos>=1.e-5)  {
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
       else       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);    /* 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 */
     for(jk=-1; jk <=nlstate+ndeath; jk++)    long i, j, k;
       for(m=-1; m <=nlstate+ndeath; m++)    for(i=nrl; i<= nrh; i++)
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);      for(k=ncolol; k<=ncoloh; k++)
     if(i <= (int) agemax)        for(j=ncl,out[i][k]=0.; j<=nch; j++)
       fprintf(ficresp,"\n");          out[i][k] +=in[i][j]*b[j][k];
     printf("\n");  
     }    return out;
     }  }
  }  
    
   fclose(ficresp);  /************* Higher Matrix Product ***************/
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);  
   free_vector(pp,1,nlstate);  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
   {
 }  /* End of Freq */    /* Computes the transition matrix starting at age 'age' over 
        'nhstepm*hstepm*stepm' months (i.e. until
 /************* Waves Concatenation ***************/       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
        nhstepm*hstepm matrices. 
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
 {       (typically every 2 years instead of every month which is too big 
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.       for the memory).
      Death is a valid wave (if date is known).       Model is determined by parameters x and covariates have to be 
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i       included manually here. 
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]  
      and mw[mi+1][i]. dh depends on stepm.       */
      */  
     int i, j, d, h, k;
   int i, mi, m;    double **out, cov[NCOVMAX];
   int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;    double **newm;
 float sum=0.;  
     /* Hstepm could be zero and should return the unit matrix */
   for(i=1; i<=imx; i++){    for (i=1;i<=nlstate+ndeath;i++)
     mi=0;      for (j=1;j<=nlstate+ndeath;j++){
     m=firstpass;        oldm[i][j]=(i==j ? 1.0 : 0.0);
     while(s[m][i] <= nlstate){        po[i][j][0]=(i==j ? 1.0 : 0.0);
       if(s[m][i]>=1)      }
         mw[++mi][i]=m;    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       if(m >=lastpass)    for(h=1; h <=nhstepm; h++){
         break;      for(d=1; d <=hstepm; d++){
       else        newm=savm;
         m++;        /* Covariates have to be included here again */
     }/* end while */        cov[1]=1.;
     if (s[m][i] > nlstate){        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
       mi++;     /* Death is another wave */        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
       /* if(mi==0)  never been interviewed correctly before death */        for (k=1; k<=cptcovage;k++)
          /* Only death is a correct wave */          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       mw[mi][i]=m;        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]]];
   
     wav[i]=mi;  
     if(mi==0)        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);        /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/
   }        out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, 
                      pmij(pmmij,cov,ncovmodel,x,nlstate));
   for(i=1; i<=imx; i++){        savm=oldm;
     for(mi=1; mi<wav[i];mi++){        oldm=newm;
       if (stepm <=0)      }
         dh[mi][i]=1;      for(i=1; i<=nlstate+ndeath; i++)
       else{        for(j=1;j<=nlstate+ndeath;j++) {
         if (s[mw[mi+1][i]][i] > nlstate) {          po[i][j][h]=newm[i][j];
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
           if(j=0) j=1;  /* Survives at least one month after exam */           */
         }        }
         else{    } /* end h */
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));    return po;
           k=k+1;  }
           if (j >= jmax) jmax=j;  
           else if (j <= jmin)jmin=j;  
           sum=sum+j;  /*************** log-likelihood *************/
         }  double func( double *x)
         jk= j/stepm;  {
         jl= j -jk*stepm;    int i, ii, j, k, mi, d, kk;
         ju= j -(jk+1)*stepm;    double l, ll[NLSTATEMAX], cov[NCOVMAX];
         if(jl <= -ju)    double **out;
           dh[mi][i]=jk;    double sw; /* Sum of weights */
         else    double lli; /* Individual log likelihood */
           dh[mi][i]=jk+1;    int s1, s2;
         if(dh[mi][i]==0)    double bbh, survp;
           dh[mi][i]=1; /* At least one step */    long ipmx;
       }    /*extern weight */
     }    /* We are differentiating ll according to initial status */
   }    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,sum/k);    /*for(i=1;i<imx;i++) 
 }      printf(" %d\n",s[4][i]);
 /*********** Tricode ****************************/    */
 void tricode(int *Tvar, int **nbcode, int imx)    cov[1]=1.;
 {  
   int Ndum[80],ij, k, j, i;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   int cptcode=0;  
   for (k=0; k<79; k++) Ndum[k]=0;    if(mle==1){
   for (k=1; k<=7; k++) ncodemax[k]=0;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
          for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   for (j=1; j<=cptcovn; j++) {        for(mi=1; mi<= wav[i]-1; mi++){
     for (i=1; i<=imx; i++) {          for (ii=1;ii<=nlstate+ndeath;ii++)
       ij=(int)(covar[Tvar[j]][i]);            for (j=1;j<=nlstate+ndeath;j++){
       Ndum[ij]++;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
       if (ij > cptcode) cptcode=ij;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     }            }
     /*printf("cptcode=%d cptcovn=%d ",cptcode,cptcovn);*/          for(d=0; d<dh[mi][i]; d++){
     for (i=0; i<=cptcode; i++) {            newm=savm;
       if(Ndum[i]!=0) ncodemax[j]++;            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];
     ij=1;            }
     for (i=1; i<=ncodemax[j]; i++) {            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       for (k=0; k<=79; k++) {                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
         if (Ndum[k] != 0) {            savm=oldm;
           nbcode[Tvar[j]][ij]=k;            oldm=newm;
           ij++;          } /* end mult */
         }        
         if (ij > ncodemax[j]) break;          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       }            /* But now since version 0.9 we anticipate for bias at large stepm.
     }           * If stepm is larger than one month (smallest stepm) and if the exact delay 
   }             * (in months) between two waves is not a multiple of stepm, we rounded to 
            * the nearest (and in case of equal distance, to the lowest) interval but now
   }           * we keep into memory the bias bh[mi][i] and also the previous matrix product
            * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
 /*********** Health Expectancies ****************/           * probability in order to take into account the bias as a fraction of the way
            * from savm to out if bh is negative or even beyond if bh is positive. bh varies
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)           * -stepm/2 to stepm/2 .
 {           * For stepm=1 the results are the same as for previous versions of Imach.
   /* Health expectancies */           * For stepm > 1 the results are less biased than in previous versions. 
   int i, j, nhstepm, hstepm, h;           */
   double age, agelim,hf;          s1=s[mw[mi][i]][i];
   double ***p3mat;          s2=s[mw[mi+1][i]][i];
            bbh=(double)bh[mi][i]/(double)stepm; 
   fprintf(ficreseij,"# Health expectancies\n");          /* bias bh is positive if real duration
   fprintf(ficreseij,"# Age");           * is higher than the multiple of stepm and negative otherwise.
   for(i=1; i<=nlstate;i++)           */
     for(j=1; j<=nlstate;j++)          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
       fprintf(ficreseij," %1d-%1d",i,j);          if( s2 > nlstate){ 
   fprintf(ficreseij,"\n");            /* 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 
   hstepm=1*YEARM; /*  Every j years of age (in month) */               die between last step unit time and current  step unit time, 
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */               which is also equal to probability to die before dh 
                minus probability to die before dh-stepm . 
   agelim=AGESUP;               In version up to 0.92 likelihood was computed
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          as if date of death was unknown. Death was treated as any other
     /* nhstepm age range expressed in number of stepm */          health state: the date of the interview describes the actual state
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);          and not the date of a change in health state. The former idea was
     /* Typically if 20 years = 20*12/6=40 stepm */          to consider that at each interview the state was recorded
     if (stepm >= YEARM) hstepm=1;          (healthy, disable or death) and IMaCh was corrected; but when we
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */          introduced the exact date of death then we should have modified
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          the contribution of an exact death to the likelihood. This new
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          contribution is smaller and very dependent of the step unit
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          stepm. It is no more the probability to die between last interview
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            and month of death but the probability to survive from last
           interview up to one month before death multiplied by the
           probability to die within a month. Thanks to Chris
     for(i=1; i<=nlstate;i++)          Jackson for correcting this bug.  Former versions increased
       for(j=1; j<=nlstate;j++)          mortality artificially. The bad side is that we add another loop
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){          which slows down the processing. The difference can be up to 10%
           eij[i][j][(int)age] +=p3mat[i][j][h];          lower mortality.
         }            */
                lli=log(out[s1][s2] - savm[s1][s2]);
     hf=1;  
     if (stepm >= YEARM) hf=stepm/YEARM;  
     fprintf(ficreseij,"%.0f",age );          } else if  (s2==-2) {
     for(i=1; i<=nlstate;i++)            for (j=1,survp=0. ; j<=nlstate; j++) 
       for(j=1; j<=nlstate;j++){              survp += out[s1][j];
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);            lli= survp;
       }          }
     fprintf(ficreseij,"\n");          
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          else if  (s2==-4) {
   }            for (j=3,survp=0. ; j<=nlstate; j++) 
 }              survp += out[s1][j];
             lli= survp;
 /************ Variance ******************/          }
 void varevsij(char fileres[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)          
 {          else if  (s2==-5) {
   /* Variance of health expectancies */            for (j=1,survp=0. ; j<=2; j++) 
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/              survp += out[s1][j];
   double **newm;            lli= survp;
   double **dnewm,**doldm;          }
   int i, j, nhstepm, hstepm, h;  
   int k, cptcode;  
    double *xp;          else{
   double **gp, **gm;            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   double ***gradg, ***trgradg;            /*  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 */
   double ***p3mat;          } 
   double age,agelim;          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
   int theta;          /*if(lli ==000.0)*/
           /*printf("bbh= %f lli=%f savm=%f out=%f %d\n",bbh,lli,savm[s1][s2], out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]],i); */
    fprintf(ficresvij,"# Covariances of life expectancies\n");          ipmx +=1;
   fprintf(ficresvij,"# Age");          sw += weight[i];
   for(i=1; i<=nlstate;i++)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(j=1; j<=nlstate;j++)        } /* end of wave */
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);      } /* end of individual */
   fprintf(ficresvij,"\n");    }  else if(mle==2){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   xp=vector(1,npar);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   dnewm=matrix(1,nlstate,1,npar);        for(mi=1; mi<= wav[i]-1; mi++){
   doldm=matrix(1,nlstate,1,nlstate);          for (ii=1;ii<=nlstate+ndeath;ii++)
              for (j=1;j<=nlstate+ndeath;j++){
   hstepm=1*YEARM; /* Every year of age */              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   agelim = AGESUP;            }
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          for(d=0; d<=dh[mi][i]; d++){
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */            newm=savm;
     if (stepm >= YEARM) hstepm=1;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */            for (kk=1; kk<=cptcovage;kk++) {
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);            }
     gp=matrix(0,nhstepm,1,nlstate);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     gm=matrix(0,nhstepm,1,nlstate);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
     for(theta=1; theta <=npar; theta++){            oldm=newm;
       for(i=1; i<=npar; i++){ /* Computes gradient */          } /* end mult */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        
       }          s1=s[mw[mi][i]][i];
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);            s2=s[mw[mi+1][i]][i];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          bbh=(double)bh[mi][i]/(double)stepm; 
       for(j=1; j<= nlstate; j++){          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
         for(h=0; h<=nhstepm; h++){          ipmx +=1;
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)          sw += weight[i];
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         }        } /* end of wave */
       }      } /* end of individual */
        }  else if(mle==3){  /* exponential inter-extrapolation */
       for(i=1; i<=npar; i++) /* Computes gradient */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         xp[i] = x[i] - (i==theta ?delti[theta]:0);        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          for(mi=1; mi<= wav[i]-1; mi++){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          for (ii=1;ii<=nlstate+ndeath;ii++)
       for(j=1; j<= nlstate; j++){            for (j=1;j<=nlstate+ndeath;j++){
         for(h=0; h<=nhstepm; h++){              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];            }
         }          for(d=0; d<dh[mi][i]; d++){
       }            newm=savm;
       for(j=1; j<= nlstate; j++)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         for(h=0; h<=nhstepm; h++){            for (kk=1; kk<=cptcovage;kk++) {
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         }            }
     } /* End theta */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                          1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);            savm=oldm;
             oldm=newm;
     for(h=0; h<=nhstepm; h++)          } /* end mult */
       for(j=1; j<=nlstate;j++)        
         for(theta=1; theta <=npar; theta++)          s1=s[mw[mi][i]][i];
           trgradg[h][j][theta]=gradg[h][theta][j];          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
     for(i=1;i<=nlstate;i++)          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
       for(j=1;j<=nlstate;j++)          ipmx +=1;
         vareij[i][j][(int)age] =0.;          sw += weight[i];
     for(h=0;h<=nhstepm;h++){          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
       for(k=0;k<=nhstepm;k++){        } /* end of wave */
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      } /* end of individual */
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    }else if (mle==4){  /* ml=4 no inter-extrapolation */
         for(i=1;i<=nlstate;i++)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           for(j=1;j<=nlstate;j++)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
             vareij[i][j][(int)age] += doldm[i][j];        for(mi=1; mi<= wav[i]-1; mi++){
       }          for (ii=1;ii<=nlstate+ndeath;ii++)
     }            for (j=1;j<=nlstate+ndeath;j++){
     h=1;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     if (stepm >= YEARM) h=stepm/YEARM;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     fprintf(ficresvij,"%.0f ",age );            }
     for(i=1; i<=nlstate;i++)          for(d=0; d<dh[mi][i]; d++){
       for(j=1; j<=nlstate;j++){            newm=savm;
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
       }            for (kk=1; kk<=cptcovage;kk++) {
     fprintf(ficresvij,"\n");              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
     free_matrix(gp,0,nhstepm,1,nlstate);            }
     free_matrix(gm,0,nhstepm,1,nlstate);          
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            savm=oldm;
   } /* End age */            oldm=newm;
            } /* end mult */
   free_vector(xp,1,npar);        
   free_matrix(doldm,1,nlstate,1,npar);          s1=s[mw[mi][i]][i];
   free_matrix(dnewm,1,nlstate,1,nlstate);          s2=s[mw[mi+1][i]][i];
           if( s2 > nlstate){ 
 }            lli=log(out[s1][s2] - savm[s1][s2]);
           }else{
 /************ Variance of prevlim ******************/            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
 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)          }
 {          ipmx +=1;
   /* Variance of prevalence limit */          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;  /*      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 **dnewm,**doldm;        } /* end of wave */
   int i, j, nhstepm, hstepm;      } /* end of individual */
   int k, cptcode;    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   double *xp;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double *gp, *gm;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double **gradg, **trgradg;        for(mi=1; mi<= wav[i]-1; mi++){
   double age,agelim;          for (ii=1;ii<=nlstate+ndeath;ii++)
   int theta;            for (j=1;j<=nlstate+ndeath;j++){
                  oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   fprintf(ficresvpl,"# Age");            }
   for(i=1; i<=nlstate;i++)          for(d=0; d<dh[mi][i]; d++){
       fprintf(ficresvpl," %1d-%1d",i,i);            newm=savm;
   fprintf(ficresvpl,"\n");            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
   xp=vector(1,npar);              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   dnewm=matrix(1,nlstate,1,npar);            }
   doldm=matrix(1,nlstate,1,nlstate);          
              out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   hstepm=1*YEARM; /* Every year of age */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */            savm=oldm;
   agelim = AGESUP;            oldm=newm;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          } /* end mult */
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        
     if (stepm >= YEARM) hstepm=1;          s1=s[mw[mi][i]][i];
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */          s2=s[mw[mi+1][i]][i];
     gradg=matrix(1,npar,1,nlstate);          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     gp=vector(1,nlstate);          ipmx +=1;
     gm=vector(1,nlstate);          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(theta=1; theta <=npar; theta++){          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
       for(i=1; i<=npar; i++){ /* Computes gradient */        } /* end of wave */
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      } /* end of individual */
       }    } /* End of if */
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
       for(i=1;i<=nlstate;i++)    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
         gp[i] = prlim[i][i];    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
        return -l;
       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);  /*************** log-likelihood *************/
       for(i=1;i<=nlstate;i++)  double funcone( double *x)
         gm[i] = prlim[i][i];  {
     /* Same as likeli but slower because of a lot of printf and if */
       for(i=1;i<=nlstate;i++)    int i, ii, j, k, mi, d, kk;
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];    double l, ll[NLSTATEMAX], cov[NCOVMAX];
     } /* End theta */    double **out;
     double lli; /* Individual log likelihood */
     trgradg =matrix(1,nlstate,1,npar);    double llt;
     int s1, s2;
     for(j=1; j<=nlstate;j++)    double bbh, survp;
       for(theta=1; theta <=npar; theta++)    /*extern weight */
         trgradg[j][theta]=gradg[theta][j];    /* We are differentiating ll according to initial status */
     /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
     for(i=1;i<=nlstate;i++)    /*for(i=1;i<imx;i++) 
       varpl[i][(int)age] =0.;      printf(" %d\n",s[4][i]);
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);    */
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);    cov[1]=1.;
     for(i=1;i<=nlstate;i++)  
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
     fprintf(ficresvpl,"%.0f ",age );    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for(i=1; i<=nlstate;i++)      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));      for(mi=1; mi<= wav[i]-1; mi++){
     fprintf(ficresvpl,"\n");        for (ii=1;ii<=nlstate+ndeath;ii++)
     free_vector(gp,1,nlstate);          for (j=1;j<=nlstate+ndeath;j++){
     free_vector(gm,1,nlstate);            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     free_matrix(gradg,1,npar,1,nlstate);            savm[ii][j]=(ii==j ? 1.0 : 0.0);
     free_matrix(trgradg,1,nlstate,1,npar);          }
   } /* End age */        for(d=0; d<dh[mi][i]; d++){
           newm=savm;
   free_vector(xp,1,npar);          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   free_matrix(doldm,1,nlstate,1,npar);          for (kk=1; kk<=cptcovage;kk++) {
   free_matrix(dnewm,1,nlstate,1,nlstate);            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           }
 }          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
                        1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           savm=oldm;
           oldm=newm;
 /***********************************************/        } /* end mult */
 /**************** Main Program *****************/        
 /***********************************************/        s1=s[mw[mi][i]][i];
         s2=s[mw[mi+1][i]][i];
 /*int main(int argc, char *argv[])*/        bbh=(double)bh[mi][i]/(double)stepm; 
 int main()        /* bias is positive if real duration
 {         * is higher than the multiple of stepm and negative otherwise.
          */
   int i,j, k, n=MAXN,iter,m,size,cptcode, aaa, cptcod;        if( s2 > nlstate && (mle <5) ){  /* Jackson */
   double agedeb, agefin,hf;          lli=log(out[s1][s2] - savm[s1][s2]);
   double agemin=1.e20, agemax=-1.e20;        } else if (mle==1){
           lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
   double fret;        } else if(mle==2){
   double **xi,tmp,delta;          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 */
         } else if(mle==3){  /* exponential inter-extrapolation */
   double dum; /* Dummy variable */          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 */
   double ***p3mat;        } else if (mle==4){  /* mle=4 no inter-extrapolation */
   int *indx;          lli=log(out[s1][s2]); /* Original formula */
   char line[MAXLINE], linepar[MAXLINE];        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
   char title[MAXLINE];          lli=log(out[s1][s2]); /* Original formula */
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];        } /* End of if */
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH];        ipmx +=1;
   char filerest[FILENAMELENGTH];        sw += weight[i];
   char fileregp[FILENAMELENGTH];        ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];  /*       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]); */
   int firstobs=1, lastobs=10;        if(globpr){
   int sdeb, sfin; /* Status at beginning and end */          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
   int c,  h , cpt,l;   %10.6f %10.6f %10.6f ", \
   int ju,jl, mi;                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize;                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
              llt +=ll[k]*gipmx/gsw;
   int hstepm, nhstepm;            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
   double bage, fage, age, agelim, agebase;          }
   double ftolpl=FTOL;          fprintf(ficresilk," %10.6f\n", -llt);
   double **prlim;        }
   double *severity;      } /* end of wave */
   double ***param; /* Matrix of parameters */    } /* end of individual */
   double  *p;    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   double **matcov; /* Matrix of covariance */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   double ***delti3; /* Scale */    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   double *delti; /* Scale */    if(globpr==0){ /* First time we count the contributions and weights */
   double ***eij, ***vareij;      gipmx=ipmx;
   double **varpl; /* Variances of prevalence limits by age */      gsw=sw;
   double *epj, vepp;    }
   char version[80]="Imach version 62c, May 1999, INED-EUROREVES ";    return -l;
   char *alph[]={"a","a","b","c","d","e"}, str[4];  }
   
   char z[1]="c", occ;  
 #include <sys/time.h>  /*************** function likelione ***********/
 #include <time.h>  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];  {
   /* long total_usecs;    /* This routine should help understanding what is done with 
   struct timeval start_time, end_time;       the selection of individuals/waves and
         to check the exact contribution to the likelihood.
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */       Plotting could be done.
      */
     int k;
   printf("\nIMACH, Version 0.64a");  
   printf("\nEnter the parameter file name: ");    if(*globpri !=0){ /* Just counts and sums, no printings */
       strcpy(fileresilk,"ilk"); 
 #ifdef windows      strcat(fileresilk,fileres);
   scanf("%s",pathtot);      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
   getcwd(pathcd, size);        printf("Problem with resultfile: %s\n", fileresilk);
   /*cygwin_split_path(pathtot,path,optionfile);        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/      }
   /* cutv(path,optionfile,pathtot,'\\');*/      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 ");
 split(pathtot, path,optionfile);      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
   chdir(path);      for(k=1; k<=nlstate; k++) 
   replace(pathc,path);        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
 #endif      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
 #ifdef unix    }
   scanf("%s",optionfile);  
 #endif    *fretone=(*funcone)(p);
     if(*globpri !=0){
 /*-------- arguments in the command line --------*/      fclose(ficresilk);
       fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
   strcpy(fileres,"r");      fflush(fichtm); 
   strcat(fileres, optionfile);    } 
     return;
   /*---------arguments file --------*/  }
   
   if((ficpar=fopen(optionfile,"r"))==NULL)    {  
     printf("Problem with optionfile %s\n",optionfile);  /*********** Maximum Likelihood Estimation ***************/
     goto end;  
   }  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   {
   strcpy(filereso,"o");    int i,j, iter;
   strcat(filereso,fileres);    double **xi;
   if((ficparo=fopen(filereso,"w"))==NULL) {    double fret;
     printf("Problem with Output resultfile: %s\n", filereso);goto end;    double fretone; /* Only one call to likelihood */
   }    /*  char filerespow[FILENAMELENGTH];*/
     xi=matrix(1,npar,1,npar);
   /* Reads comments: lines beginning with '#' */    for (i=1;i<=npar;i++)
   while((c=getc(ficpar))=='#' && c!= EOF){      for (j=1;j<=npar;j++)
     ungetc(c,ficpar);        xi[i][j]=(i==j ? 1.0 : 0.0);
     fgets(line, MAXLINE, ficpar);    printf("Powell\n");  fprintf(ficlog,"Powell\n");
     puts(line);    strcpy(filerespow,"pow"); 
     fputs(line,ficparo);    strcat(filerespow,fileres);
   }    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   ungetc(c,ficpar);      printf("Problem with resultfile: %s\n", filerespow);
       fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncov, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    }
   printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncov, nlstate,ndeath, maxwav, mle, weightopt,model);    fprintf(ficrespow,"# Powell\n# iter -2*LL");
   fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncov=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncov,nlstate,ndeath,maxwav, mle, weightopt,model);    for (i=1;i<=nlstate;i++)
       for(j=1;j<=nlstate+ndeath;j++)
   covar=matrix(1,NCOVMAX,1,n);            if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
   if (strlen(model)<=1) cptcovn=0;    fprintf(ficrespow,"\n");
   else {  
     j=0;    powell(p,xi,npar,ftol,&iter,&fret,func);
     j=nbocc(model,'+');  
     cptcovn=j+1;    free_matrix(xi,1,npar,1,npar);
   }    fclose(ficrespow);
     printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   ncovmodel=2+cptcovn;    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
    
   /* Read guess parameters */  }
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){  /**** Computes Hessian and covariance matrix ***/
     ungetc(c,ficpar);  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     fgets(line, MAXLINE, ficpar);  {
     puts(line);    double  **a,**y,*x,pd;
     fputs(line,ficparo);    double **hess;
   }    int i, j,jk;
   ungetc(c,ficpar);    int *indx;
    
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
     for(i=1; i <=nlstate; i++)    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
     for(j=1; j <=nlstate+ndeath-1; j++){    void lubksb(double **a, int npar, int *indx, double b[]) ;
       fscanf(ficpar,"%1d%1d",&i1,&j1);    void ludcmp(double **a, int npar, int *indx, double *d) ;
       fprintf(ficparo,"%1d%1d",i1,j1);    double gompertz(double p[]);
       printf("%1d%1d",i,j);    hess=matrix(1,npar,1,npar);
       for(k=1; k<=ncovmodel;k++){  
         fscanf(ficpar," %lf",&param[i][j][k]);    printf("\nCalculation of the hessian matrix. Wait...\n");
         printf(" %lf",param[i][j][k]);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
         fprintf(ficparo," %lf",param[i][j][k]);    for (i=1;i<=npar;i++){
       }      printf("%d",i);fflush(stdout);
       fscanf(ficpar,"\n");      fprintf(ficlog,"%d",i);fflush(ficlog);
       printf("\n");     
       fprintf(ficparo,"\n");       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     }      
        /*  printf(" %f ",p[i]);
   npar= (nlstate+ndeath-1)*nlstate*ncovmodel;          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   p=param[1][1];    }
      
   /* Reads comments: lines beginning with '#' */    for (i=1;i<=npar;i++) {
   while((c=getc(ficpar))=='#' && c!= EOF){      for (j=1;j<=npar;j++)  {
     ungetc(c,ficpar);        if (j>i) { 
     fgets(line, MAXLINE, ficpar);          printf(".%d%d",i,j);fflush(stdout);
     puts(line);          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     fputs(line,ficparo);          hess[i][j]=hessij(p,delti,i,j,func,npar);
   }          
   ungetc(c,ficpar);          hess[j][i]=hess[i][j];    
           /*printf(" %lf ",hess[i][j]);*/
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);        }
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */      }
   for(i=1; i <=nlstate; i++){    }
     for(j=1; j <=nlstate+ndeath-1; j++){    printf("\n");
       fscanf(ficpar,"%1d%1d",&i1,&j1);    fprintf(ficlog,"\n");
       printf("%1d%1d",i,j);  
       fprintf(ficparo,"%1d%1d",i1,j1);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
       for(k=1; k<=ncovmodel;k++){    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
         fscanf(ficpar,"%le",&delti3[i][j][k]);    
         printf(" %le",delti3[i][j][k]);    a=matrix(1,npar,1,npar);
         fprintf(ficparo," %le",delti3[i][j][k]);    y=matrix(1,npar,1,npar);
       }    x=vector(1,npar);
       fscanf(ficpar,"\n");    indx=ivector(1,npar);
       printf("\n");    for (i=1;i<=npar;i++)
       fprintf(ficparo,"\n");      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     }    ludcmp(a,npar,indx,&pd);
   }  
   delti=delti3[1][1];    for (j=1;j<=npar;j++) {
        for (i=1;i<=npar;i++) x[i]=0;
   /* Reads comments: lines beginning with '#' */      x[j]=1;
   while((c=getc(ficpar))=='#' && c!= EOF){      lubksb(a,npar,indx,x);
     ungetc(c,ficpar);      for (i=1;i<=npar;i++){ 
     fgets(line, MAXLINE, ficpar);        matcov[i][j]=x[i];
     puts(line);      }
     fputs(line,ficparo);    }
   }  
   ungetc(c,ficpar);    printf("\n#Hessian matrix#\n");
      fprintf(ficlog,"\n#Hessian matrix#\n");
   matcov=matrix(1,npar,1,npar);    for (i=1;i<=npar;i++) { 
   for(i=1; i <=npar; i++){      for (j=1;j<=npar;j++) { 
     fscanf(ficpar,"%s",&str);        printf("%.3e ",hess[i][j]);
     printf("%s",str);        fprintf(ficlog,"%.3e ",hess[i][j]);
     fprintf(ficparo,"%s",str);      }
     for(j=1; j <=i; j++){      printf("\n");
       fscanf(ficpar," %le",&matcov[i][j]);      fprintf(ficlog,"\n");
       printf(" %.5le",matcov[i][j]);    }
       fprintf(ficparo," %.5le",matcov[i][j]);  
     }    /* Recompute Inverse */
     fscanf(ficpar,"\n");    for (i=1;i<=npar;i++)
     printf("\n");      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
     fprintf(ficparo,"\n");    ludcmp(a,npar,indx,&pd);
   }  
   for(i=1; i <=npar; i++)    /*  printf("\n#Hessian matrix recomputed#\n");
     for(j=i+1;j<=npar;j++)  
       matcov[i][j]=matcov[j][i];    for (j=1;j<=npar;j++) {
          for (i=1;i<=npar;i++) x[i]=0;
   printf("\n");      x[j]=1;
       lubksb(a,npar,indx,x);
       for (i=1;i<=npar;i++){ 
    if(mle==1){        y[i][j]=x[i];
     /*-------- data file ----------*/        printf("%.3e ",y[i][j]);
     if((ficres =fopen(fileres,"w"))==NULL) {        fprintf(ficlog,"%.3e ",y[i][j]);
       printf("Problem with resultfile: %s\n", fileres);goto end;      }
     }      printf("\n");
     fprintf(ficres,"#%s\n",version);      fprintf(ficlog,"\n");
        }
     if((fic=fopen(datafile,"r"))==NULL)    {    */
       printf("Problem with datafile: %s\n", datafile);goto end;  
     }    free_matrix(a,1,npar,1,npar);
     free_matrix(y,1,npar,1,npar);
     n= lastobs;    free_vector(x,1,npar);
     severity = vector(1,maxwav);    free_ivector(indx,1,npar);
     outcome=imatrix(1,maxwav+1,1,n);    free_matrix(hess,1,npar,1,npar);
     num=ivector(1,n);  
     moisnais=vector(1,n);  
     annais=vector(1,n);  }
     moisdc=vector(1,n);  
     andc=vector(1,n);  /*************** hessian matrix ****************/
     agedc=vector(1,n);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
     cod=ivector(1,n);  {
     weight=vector(1,n);    int i;
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */    int l=1, lmax=20;
     mint=matrix(1,maxwav,1,n);    double k1,k2;
     anint=matrix(1,maxwav,1,n);    double p2[NPARMAX+1];
     s=imatrix(1,maxwav+1,1,n);    double res;
     adl=imatrix(1,maxwav+1,1,n);        double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
     tab=ivector(1,NCOVMAX);    double fx;
     ncodemax=ivector(1,8);    int k=0,kmax=10;
     double l1;
     i=1;  
     while (fgets(line, MAXLINE, fic) != NULL)    {    fx=func(x);
       if ((i >= firstobs) && (i <=lastobs)) {    for (i=1;i<=npar;i++) p2[i]=x[i];
            for(l=0 ; l <=lmax; l++){
         for (j=maxwav;j>=1;j--){      l1=pow(10,l);
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);      delts=delt;
           strcpy(line,stra);      for(k=1 ; k <kmax; k=k+1){
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        delt = delta*(l1*k);
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);        p2[theta]=x[theta] +delt;
         }        k1=func(p2)-fx;
                p2[theta]=x[theta]-delt;
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);        k2=func(p2)-fx;
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);        /*res= (k1-2.0*fx+k2)/delt/delt; */
         res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);        
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);  #ifdef DEBUG
         printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
         cutv(stra, strb,line,' '); weight[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);
         for (j=ncov;j>=1;j--){  #endif
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
         }        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
         num[i]=atol(stra);          k=kmax;
         }
         /*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]));*/        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
           k=kmax; l=lmax*10.;
         i=i+1;        }
       }        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
     }          delts=delt;
         }
     /*scanf("%d",i);*/      }
   imx=i-1; /* Number of individuals */    }
     delti[theta]=delts;
   /* Calculation of the number of parameter from char model*/    return res; 
   Tvar=ivector(1,8);        
      }
   if (strlen(model) >1){  
     j=0;  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
     j=nbocc(model,'+');  {
     cptcovn=j+1;    int i;
        int l=1, l1, lmax=20;
     strcpy(modelsav,model);    double k1,k2,k3,k4,res,fx;
     if (j==0) {    double p2[NPARMAX+1];
       cutv(stra,strb,modelsav,'V'); Tvar[1]=atoi(strb);    int k;
     }  
     else {    fx=func(x);
       for(i=j; i>=1;i--){    for (k=1; k<=2; k++) {
         cutv(stra,strb,modelsav,'+');      for (i=1;i<=npar;i++) p2[i]=x[i];
         if (strchr(strb,'*')) {      p2[thetai]=x[thetai]+delti[thetai]/k;
           cutv(strd,strc,strb,'*');      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
           cutv(strb,stre,strc,'V');Tvar[i+1]=ncov+1;      k1=func(p2)-fx;
           cutv(strb,strc,strd,'V');    
           for (k=1; k<=lastobs;k++)      p2[thetai]=x[thetai]+delti[thetai]/k;
             covar[ncov+1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
         }      k2=func(p2)-fx;
         else {cutv(strd,strc,strb,'V');    
         Tvar[i+1]=atoi(strc);      p2[thetai]=x[thetai]-delti[thetai]/k;
         }      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
         strcpy(modelsav,stra);        k3=func(p2)-fx;
       }    
       cutv(strd,strc,stra,'V');      p2[thetai]=x[thetai]-delti[thetai]/k;
       Tvar[1]=atoi(strc);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     }      k4=func(p2)-fx;
   }      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   /*printf("tvar=%d ",Tvar[1]);  #ifdef DEBUG
   scanf("%d ",i);*/      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);
     fclose(fic);      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);
   #endif
     if (weightopt != 1) { /* Maximisation without weights*/    }
       for(i=1;i<=n;i++) weight[i]=1.0;    return res;
     }  }
     /*-calculation of age at interview from date of interview and age at death -*/  
     agev=matrix(1,maxwav,1,imx);  /************** Inverse of matrix **************/
      void ludcmp(double **a, int n, int *indx, double *d) 
     for (i=1; i<=imx; i++)  {  { 
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);    int i,imax,j,k; 
       for(m=1; (m<= maxwav); m++){    double big,dum,sum,temp; 
         if(s[m][i] >0){    double *vv; 
           if (s[m][i] == nlstate+1) {   
             if(agedc[i]>0)    vv=vector(1,n); 
               if(moisdc[i]!=99 && andc[i]!=9999)    *d=1.0; 
               agev[m][i]=agedc[i];    for (i=1;i<=n;i++) { 
             else{      big=0.0; 
               printf("Warning negative age at death: %d line:%d\n",num[i],i);      for (j=1;j<=n;j++) 
               agev[m][i]=-1;        if ((temp=fabs(a[i][j])) > big) big=temp; 
             }      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
           }      vv[i]=1.0/big; 
           else if(s[m][i] !=9){ /* Should no more exist */    } 
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);    for (j=1;j<=n;j++) { 
             if(mint[m][i]==99 || anint[m][i]==9999)      for (i=1;i<j;i++) { 
               agev[m][i]=1;        sum=a[i][j]; 
             else if(agev[m][i] <agemin){        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
               agemin=agev[m][i];        a[i][j]=sum; 
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/      } 
             }      big=0.0; 
             else if(agev[m][i] >agemax){      for (i=j;i<=n;i++) { 
               agemax=agev[m][i];        sum=a[i][j]; 
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/        for (k=1;k<j;k++) 
             }          sum -= a[i][k]*a[k][j]; 
             /*agev[m][i]=anint[m][i]-annais[i];*/        a[i][j]=sum; 
             /*   agev[m][i] = age[i]+2*m;*/        if ( (dum=vv[i]*fabs(sum)) >= big) { 
           }          big=dum; 
           else { /* =9 */          imax=i; 
             agev[m][i]=1;        } 
             s[m][i]=-1;      } 
           }      if (j != imax) { 
         }        for (k=1;k<=n;k++) { 
         else /*= 0 Unknown */          dum=a[imax][k]; 
           agev[m][i]=1;          a[imax][k]=a[j][k]; 
       }          a[j][k]=dum; 
            } 
     }        *d = -(*d); 
     for (i=1; i<=imx; i++)  {        vv[imax]=vv[j]; 
       for(m=1; (m<= maxwav); m++){      } 
         if (s[m][i] > (nlstate+ndeath)) {      indx[j]=imax; 
           printf("Error: Wrong value in nlstate or ndeath\n");        if (a[j][j] == 0.0) a[j][j]=TINY; 
           goto end;      if (j != n) { 
         }        dum=1.0/(a[j][j]); 
       }        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
     }      } 
     } 
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);    free_vector(vv,1,n);  /* Doesn't work */
   ;
     free_vector(severity,1,maxwav);  } 
     free_imatrix(outcome,1,maxwav+1,1,n);  
     free_vector(moisnais,1,n);  void lubksb(double **a, int n, int *indx, double b[]) 
     free_vector(annais,1,n);  { 
     free_matrix(mint,1,maxwav,1,n);    int i,ii=0,ip,j; 
     free_matrix(anint,1,maxwav,1,n);    double sum; 
     free_vector(moisdc,1,n);   
     free_vector(andc,1,n);    for (i=1;i<=n;i++) { 
       ip=indx[i]; 
          sum=b[ip]; 
     wav=ivector(1,imx);      b[ip]=b[i]; 
     dh=imatrix(1,lastpass-firstpass+1,1,imx);      if (ii) 
     mw=imatrix(1,lastpass-firstpass+1,1,imx);        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
          else if (sum) ii=i; 
     /* Concatenates waves */      b[i]=sum; 
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    } 
     for (i=n;i>=1;i--) { 
       sum=b[i]; 
 Tcode=ivector(1,100);      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
    nbcode=imatrix(1,nvar,1,8);        b[i]=sum/a[i][i]; 
    ncodemax[1]=1;    } 
    if (cptcovn > 0) tricode(Tvar,nbcode,imx);  } 
    
    codtab=imatrix(1,100,1,10);  void pstamp(FILE *fichier)
    h=0;  {
    m=pow(2,cptcovn);    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
    }
    for(k=1;k<=cptcovn; k++){  
      for(i=1; i <=(m/pow(2,k));i++){  /************ Frequencies ********************/
        for(j=1; j <= ncodemax[k]; j++){  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[])
          for(cpt=1; cpt <=(m/pow(2,cptcovn+1-k)); cpt++){  {  /* Some frequencies */
            h++;    
            if (h>m) h=1;codtab[h][k]=j;    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
          }    int first;
        }    double ***freq; /* Frequencies */
      }    double *pp, **prop;
    }    double pos,posprop, k2, dateintsum=0,k2cpt=0;
     char fileresp[FILENAMELENGTH];
    /*for(i=1; i <=m ;i++){    
      for(k=1; k <=cptcovn; k++){    pp=vector(1,nlstate);
        printf("i=%d k=%d %d ",i,k,codtab[i][k]);    prop=matrix(1,nlstate,iagemin,iagemax+3);
      }    strcpy(fileresp,"p");
      printf("\n");    strcat(fileresp,fileres);
    }*/    if((ficresp=fopen(fileresp,"w"))==NULL) {
    /*scanf("%d",i);*/      printf("Problem with prevalence resultfile: %s\n", fileresp);
          fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
    /* Calculates basic frequencies. Computes observed prevalence at single age      exit(0);
        and prints on file fileres'p'. */    }
   freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
     j1=0;
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    j=cptcoveff;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */    first=1;
      
     /* For Powell, parameters are in a vector p[] starting at p[1]    for(k1=1; k1<=j;k1++){
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */      for(i1=1; i1<=ncodemax[k1];i1++){
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */        j1++;
            /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);          scanf("%d", i);*/
         for (i=-5; i<=nlstate+ndeath; i++)  
              for (jk=-5; jk<=nlstate+ndeath; jk++)  
     /*--------- results files --------------*/            for(m=iagemin; m <= iagemax+3; m++)
     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);              freq[i][jk][m]=0;
      
    jk=1;      for (i=1; i<=nlstate; i++)  
    fprintf(ficres,"# Parameters\n");        for(m=iagemin; m <= iagemax+3; m++)
    printf("# Parameters\n");          prop[i][m]=0;
    for(i=1,jk=1; i <=nlstate; i++){        
      for(k=1; k <=(nlstate+ndeath); k++){        dateintsum=0;
        if (k != i)        k2cpt=0;
          {        for (i=1; i<=imx; i++) {
            printf("%d%d ",i,k);          bool=1;
            fprintf(ficres,"%1d%1d ",i,k);          if  (cptcovn>0) {
            for(j=1; j <=ncovmodel; j++){            for (z1=1; z1<=cptcoveff; z1++) 
              printf("%f ",p[jk]);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
              fprintf(ficres,"%f ",p[jk]);                bool=0;
              jk++;          }
            }          if (bool==1){
            printf("\n");            for(m=firstpass; m<=lastpass; m++){
            fprintf(ficres,"\n");              k2=anint[m][i]+(mint[m][i]/12.);
          }              /*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;
                 if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     /* Computing hessian and covariance matrix */                if (m<lastpass) {
     ftolhess=ftol; /* Usually correct */                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     hesscov(matcov, p, npar, delti, ftolhess, func);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
     fprintf(ficres,"# Scales\n");                }
     printf("# Scales\n");                
      for(i=1,jk=1; i <=nlstate; i++){                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
       for(j=1; j <=nlstate+ndeath; j++){                  dateintsum=dateintsum+k2;
         if (j!=i) {                  k2cpt++;
           fprintf(ficres,"%1d%1d",i,j);                }
           printf("%1d%1d",i,j);                /*}*/
           for(k=1; k<=ncovmodel;k++){            }
             printf(" %.5e",delti[jk]);          }
             fprintf(ficres," %.5e",delti[jk]);        }
             jk++;         
           }        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
           printf("\n");        pstamp(ficresp);
           fprintf(ficres,"\n");        if  (cptcovn>0) {
         }          fprintf(ficresp, "\n#********** Variable "); 
       }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       }          fprintf(ficresp, "**********\n#");
            }
     k=1;        for(i=1; i<=nlstate;i++) 
     fprintf(ficres,"# Covariance\n");          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
     printf("# Covariance\n");        fprintf(ficresp, "\n");
     for(i=1;i<=npar;i++){        
       /*  if (k>nlstate) k=1;        for(i=iagemin; i <= iagemax+3; i++){
       i1=(i-1)/(ncovmodel*nlstate)+1;          if(i==iagemax+3){
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);            fprintf(ficlog,"Total");
       printf("%s%d%d",alph[k],i1,tab[i]);*/          }else{
       fprintf(ficres,"%3d",i);            if(first==1){
       printf("%3d",i);              first=0;
       for(j=1; j<=i;j++){              printf("See log file for details...\n");
         fprintf(ficres," %.5e",matcov[i][j]);            }
         printf(" %.5e",matcov[i][j]);            fprintf(ficlog,"Age %d", i);
       }          }
       fprintf(ficres,"\n");          for(jk=1; jk <=nlstate ; jk++){
       printf("\n");            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
       k++;              pp[jk] += freq[jk][m][i]; 
     }          }
              for(jk=1; jk <=nlstate ; jk++){
     while((c=getc(ficpar))=='#' && c!= EOF){            for(m=-1, pos=0; m <=0 ; m++)
       ungetc(c,ficpar);              pos += freq[jk][m][i];
       fgets(line, MAXLINE, ficpar);            if(pp[jk]>=1.e-10){
       puts(line);              if(first==1){
       fputs(line,ficparo);              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     }              }
     ungetc(c,ficpar);              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
              }else{
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);              if(first==1)
                    printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     if (fage <= 2) {              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       bage = agemin;            }
       fage = agemax;          }
     }  
           for(jk=1; jk <=nlstate ; jk++){
     fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);              pp[jk] += freq[jk][m][i];
 /*------------ gnuplot -------------*/          }       
 chdir(pathcd);          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
   if((ficgp=fopen("graph.plt","w"))==NULL) {            pos += pp[jk];
     printf("Problem with file graph.gp");goto end;            posprop += prop[jk][i];
   }          }
 #ifdef windows          for(jk=1; jk <=nlstate ; jk++){
   fprintf(ficgp,"cd \"%s\" \n",pathc);            if(pos>=1.e-5){
 #endif              if(first==1)
 m=pow(2,cptcovn);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
                fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
  /* 1eme*/            }else{
   for (cpt=1; cpt<= nlstate ; cpt ++) {              if(first==1)
    for (k1=1; k1<= m ; k1 ++) {                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
 #ifdef windows            }
     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( i <= iagemax){
 #endif              if(pos>=1.e-5){
 #ifdef unix                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);                /*probs[i][jk][j1]= pp[jk]/pos;*/
 #endif                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
               }
 for (i=1; i<= nlstate ; i ++) {              else
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   else fprintf(ficgp," \%%*lf (\%%*lf)");            }
 }          }
     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(jk=-1; jk <=nlstate+ndeath; jk++)
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");            for(m=-1; m <=nlstate+ndeath; m++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");              if(freq[jk][m][i] !=0 ) {
 }              if(first==1)
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
      for (i=1; i<= nlstate ; i ++) {                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");              }
   else fprintf(ficgp," \%%*lf (\%%*lf)");          if(i <= iagemax)
 }              fprintf(ficresp,"\n");
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));          if(first==1)
 #ifdef unix            printf("Others in log...\n");
 fprintf(ficgp,"\nset ter gif small size 400,300");          fprintf(ficlog,"\n");
 #endif        }
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      }
    }    }
   }    dateintmean=dateintsum/k2cpt; 
   /*2 eme*/   
     fclose(ficresp);
   for (k1=1; k1<= m ; k1 ++) {    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);    free_vector(pp,1,nlstate);
        free_matrix(prop,1,nlstate,iagemin, iagemax+3);
     for (i=1; i<= nlstate+1 ; i ++) {    /* End of Freq */
       k=2*i;  }
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);  
       for (j=1; j<= nlstate+1 ; j ++) {  /************ Prevalence ********************/
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  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)
   else fprintf(ficgp," \%%*lf (\%%*lf)");  {  
 }      /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");       in each health status at the date of interview (if between dateprev1 and dateprev2).
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);       We still use firstpass and lastpass as another selection.
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    */
       for (j=1; j<= nlstate+1 ; j ++) {   
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
         else fprintf(ficgp," \%%*lf (\%%*lf)");    double ***freq; /* Frequencies */
 }      double *pp, **prop;
       fprintf(ficgp,"\" t\"\" w l 0,");    double pos,posprop; 
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    double  y2; /* in fractional years */
       for (j=1; j<= nlstate+1 ; j ++) {    int iagemin, iagemax;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");    iagemin= (int) agemin;
 }      iagemax= (int) agemax;
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    /*pp=vector(1,nlstate);*/
       else fprintf(ficgp,"\" t\"\" w l 0,");    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     }    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    j1=0;
   }    
      j=cptcoveff;
   /*3eme*/    if (cptcovn<1) {j=1;ncodemax[1]=1;}
     
   for (k1=1; k1<= m ; k1 ++) {    for(k1=1; k1<=j;k1++){
     for (cpt=1; cpt<= nlstate ; cpt ++) {      for(i1=1; i1<=ncodemax[k1];i1++){
       k=2+nlstate*(cpt-1);        j1++;
       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);        
       for (i=1; i< nlstate ; i ++) {        for (i=1; i<=nlstate; i++)  
         fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+i,cpt,i+1);          for(m=iagemin; m <= iagemax+3; m++)
       }            prop[i][m]=0.0;
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);       
     }        for (i=1; i<=imx; i++) { /* Each individual */
   }          bool=1;
            if  (cptcovn>0) {
   /* CV preval stat */            for (z1=1; z1<=cptcoveff; z1++) 
   for (k1=1; k1<= m ; k1 ++) {              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
     for (cpt=1; cpt<nlstate ; cpt ++) {                bool=0;
       k=3;          } 
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter gif small size 400,300\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);          if (bool==1) { 
       for (i=1; i< nlstate ; i ++)            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
         fprintf(ficgp,"+$%d",k+i+1);              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
                      if(agev[m][i]==0) agev[m][i]=iagemax+1;
       l=3+(nlstate+ndeath)*cpt;                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
       for (i=1; i< nlstate ; i ++) {                if (s[m][i]>0 && s[m][i]<=nlstate) { 
         l=3+(nlstate+ndeath)*cpt;                  /*if(i>4620) printf(" i=%d m=%d s[m][i]=%d (int)agev[m][i]=%d weight[i]=%f prop=%f\n",i,m,s[m][i],(int)agev[m][m],weight[i],prop[s[m][i]][(int)agev[m][i]]);*/
         fprintf(ficgp,"+$%d",l+i+1);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
       }                  prop[s[m][i]][iagemax+3] += weight[i]; 
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                  } 
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);              }
     }            } /* end selection of waves */
   }          }
         }
   /* proba elementaires */        for(i=iagemin; i <= iagemax+3; i++){  
    for(i=1,jk=1; i <=nlstate; i++){          
     for(k=1; k <=(nlstate+ndeath); k++){          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
       if (k != i) {            posprop += prop[jk][i]; 
         for(j=1; j <=ncovmodel; j++){          } 
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/  
           /*fprintf(ficgp,"%s",alph[1]);*/          for(jk=1; jk <=nlstate ; jk++){     
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);            if( i <=  iagemax){ 
           jk++;              if(posprop>=1.e-5){ 
           fprintf(ficgp,"\n");                probs[i][jk][j1]= prop[jk][i]/posprop;
         }              } 
       }            } 
     }          }/* end jk */ 
     }        }/* end i */ 
       } /* end i1 */
   for(jk=1; jk <=m; jk++) {    } /* end k1 */
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    
    i=1;    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
    for(k2=1; k2<=nlstate; k2++) {    /*free_vector(pp,1,nlstate);*/
      k3=i;    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
      for(k=1; k<=(nlstate+ndeath); k++) {  }  /* End of prevalence */
        if (k != k2){  
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);  /************* Waves Concatenation ***************/
   
         for(j=3; j <=ncovmodel; 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)
           fprintf(ficgp,"+p%d*%d",k2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  {
         fprintf(ficgp,")/(1");    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
        Death is a valid wave (if date is known).
         for(k1=1; k1 <=nlstate+1; k1=k1+2){         mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
             fprintf(ficgp,"+exp(p%d+p%d*x",k1+k3-1,k1+k3);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
        and mw[mi+1][i]. dh depends on stepm.
             for(j=3; j <=ncovmodel; j++)       */
               fprintf(ficgp,"+p%d*%d",k2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  
             fprintf(ficgp,")");    int i, mi, m;
         }    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);       double sum=0., jmean=0.;*/
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");    int first;
     i=i+ncovmodel;    int j, k=0,jk, ju, jl;
        }    double sum=0.;
      }    first=0;
    }    jmin=1e+5;
   fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);    jmax=-1;
    }    jmean=0.;
        for(i=1; i<=imx; i++){
   fclose(ficgp);      mi=0;
          m=firstpass;
 chdir(path);      while(s[m][i] <= nlstate){
     free_matrix(agev,1,maxwav,1,imx);        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
     free_ivector(wav,1,imx);          mw[++mi][i]=m;
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);        if(m >=lastpass)
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);          break;
            else
     free_imatrix(s,1,maxwav+1,1,n);          m++;
          }/* end while */
          if (s[m][i] > nlstate){
     free_ivector(num,1,n);        mi++;     /* Death is another wave */
     free_vector(agedc,1,n);        /* if(mi==0)  never been interviewed correctly before death */
     free_vector(weight,1,n);           /* Only death is a correct wave */
     /*free_matrix(covar,1,NCOVMAX,1,n);*/        mw[mi][i]=m;
     fclose(ficparo);      }
     fclose(ficres);  
    }      wav[i]=mi;
          if(mi==0){
    /*________fin mle=1_________*/        nbwarn++;
            if(first==0){
           printf("Warning! No valid information for individual %ld line=%d (skipped) and may be others, see log file\n",num[i],i);
            first=1;
     /* No more information from the sample is required now */        }
   /* Reads comments: lines beginning with '#' */        if(first==1){
   while((c=getc(ficpar))=='#' && c!= EOF){          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
     ungetc(c,ficpar);        }
     fgets(line, MAXLINE, ficpar);      } /* end mi==0 */
     puts(line);    } /* End individuals */
     fputs(line,ficparo);  
   }    for(i=1; i<=imx; i++){
   ungetc(c,ficpar);      for(mi=1; mi<wav[i];mi++){
          if (stepm <=0)
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);          dh[mi][i]=1;
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);        else{
   fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
 /*--------- index.htm --------*/            if (agedc[i] < 2*AGESUP) {
               j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   if((fichtm=fopen("index.htm","w"))==NULL)    {              if(j==0) j=1;  /* Survives at least one month after exam */
     printf("Problem with index.htm \n");goto end;              else if(j<0){
   }                nberr++;
                 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(fichtm,"<body><ul> Imach, Version 0.64a<hr> <li>Outputs files<br><br>\n                j=1; /* Temporary Dangerous patch */
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>                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]);
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>                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);
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>              }
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>              k=k+1;
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>              if (j >= jmax){
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>                jmax=j;
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>                ijmax=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 (j <= jmin){
  fprintf(fichtm," <li>Graphs</li>\n<p>");                jmin=j;
                 ijmin=i;
  m=cptcovn;              }
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}              sum=sum+j;
               /*if (j<0) printf("j=%d num=%d \n",j,i);*/
  j1=0;              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
  for(k1=1; k1<=m;k1++){            }
    for(i1=1; i1<=ncodemax[k1];i1++){          }
        j1++;          else{
        if (cptcovn > 0) {            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
          fprintf(fichtm,"<hr>************ Results for covariates");  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
          for (cpt=1; cpt<=cptcovn;cpt++)  
            fprintf(fichtm," V%d=%d ",Tvar[cpt],nbcode[Tvar[cpt]][codtab[j1][cpt]]);            k=k+1;
          fprintf(fichtm," ************\n<hr>");            if (j >= jmax) {
        }              jmax=j;
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>              ijmax=i;
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);                }
        for(cpt=1; cpt<nlstate;cpt++){            else if (j <= jmin){
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>              jmin=j;
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);              ijmin=i;
        }            }
     for(cpt=1; cpt<=nlstate;cpt++) {            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident            /*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]);*/
 interval) in state (%d): v%s%d%d.gif <br>            if(j<0){
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);                nberr++;
      }              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]);
      for(cpt=1; cpt<=nlstate;cpt++) {              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(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>            }
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);            sum=sum+j;
      }          }
      fprintf(fichtm,"\n<br>- Total life expectancy by age and          jk= j/stepm;
 health expectancies in states (1) and (2): e%s%d.gif<br>          jl= j -jk*stepm;
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);          ju= j -(jk+1)*stepm;
 fprintf(fichtm,"\n</body>");          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
    }            if(jl==0){
  }              dh[mi][i]=jk;
 fclose(fichtm);              bh[mi][i]=0;
             }else{ /* We want a negative bias in order to only have interpolation ie
   /*--------------- Prevalence limit --------------*/                    * at the price of an extra matrix product in likelihood */
                dh[mi][i]=jk+1;
   strcpy(filerespl,"pl");              bh[mi][i]=ju;
   strcat(filerespl,fileres);            }
   if((ficrespl=fopen(filerespl,"w"))==NULL) {          }else{
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;            if(jl <= -ju){
   }              dh[mi][i]=jk;
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);              bh[mi][i]=jl;       /* bias is positive if real duration
   fprintf(ficrespl,"#Prevalence limit\n");                                   * is higher than the multiple of stepm and negative otherwise.
   fprintf(ficrespl,"#Age ");                                   */
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);            }
   fprintf(ficrespl,"\n");            else{
                dh[mi][i]=jk+1;
   prlim=matrix(1,nlstate,1,nlstate);              bh[mi][i]=ju;
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            }
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            if(dh[mi][i]==0){
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              dh[mi][i]=1; /* At least one step */
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              bh[mi][i]=ju; /* At least one step */
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */              /*  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);*/
   k=0;            }
   agebase=agemin;          } /* end if mle */
   agelim=agemax;        }
   ftolpl=1.e-10;      } /* end wave */
   i1=cptcovn;    }
   if (cptcovn < 1){i1=1;}    jmean=sum/k;
     printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
   for(cptcov=1;cptcov<=i1;cptcov++){    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);
     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]);*/  /*********** Tricode ****************************/
         fprintf(ficrespl,"\n#****** ");  void tricode(int *Tvar, int **nbcode, int imx)
         for(j=1;j<=cptcovn;j++)  {
           fprintf(ficrespl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);    
         fprintf(ficrespl,"******\n");    int Ndum[20],ij=1, k, j, i, maxncov=19;
            int cptcode=0;
         for (age=agebase; age<=agelim; age++){    cptcoveff=0; 
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);   
           fprintf(ficrespl,"%.0f",age );    for (k=0; k<maxncov; k++) Ndum[k]=0;
           for(i=1; i<=nlstate;i++)    for (k=1; k<=7; k++) ncodemax[k]=0;
           fprintf(ficrespl," %.5f", prlim[i][i]);  
           fprintf(ficrespl,"\n");    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
         }      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
       }                                 modality*/ 
     }        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
   fclose(ficrespl);        Ndum[ij]++; /*store the modality */
   /*------------- h Pij x at various ages ------------*/        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
          if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);                                         Tvar[j]. If V=sex and male is 0 and 
   if((ficrespij=fopen(filerespij,"w"))==NULL) {                                         female is 1, then  cptcode=1.*/
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;      }
   }  
   printf("Computing pij: result on file '%s' \n", filerespij);      for (i=0; i<=cptcode; i++) {
          if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
   stepsize=(int) (stepm+YEARM-1)/YEARM;      }
   if (stepm<=24) stepsize=2;  
       ij=1; 
   agelim=AGESUP;      for (i=1; i<=ncodemax[j]; i++) {
   hstepm=stepsize*YEARM; /* Every year of age */        for (k=0; k<= maxncov; k++) {
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */          if (Ndum[k] != 0) {
              nbcode[Tvar[j]][ij]=k; 
   k=0;            /* 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(cptcov=1;cptcov<=i1;cptcov++){            
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){            ij++;
       k=k+1;          }
         fprintf(ficrespij,"\n#****** ");          if (ij > ncodemax[j]) break; 
         for(j=1;j<=cptcovn;j++)        }  
           fprintf(ficrespij,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);      } 
         fprintf(ficrespij,"******\n");    }  
          
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */   for (k=0; k< maxncov; k++) Ndum[k]=0;
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */  
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */   for (i=1; i<=ncovmodel-2; i++) { 
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
           oldm=oldms;savm=savms;     ij=Tvar[i];
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);       Ndum[ij]++;
           fprintf(ficrespij,"# Age");   }
           for(i=1; i<=nlstate;i++)  
             for(j=1; j<=nlstate+ndeath;j++)   ij=1;
               fprintf(ficrespij," %1d-%1d",i,j);   for (i=1; i<= maxncov; i++) {
           fprintf(ficrespij,"\n");     if((Ndum[i]!=0) && (i<=ncovcol)){
           for (h=0; h<=nhstepm; h++){       Tvaraff[ij]=i; /*For printing */
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );       ij++;
             for(i=1; i<=nlstate;i++)     }
               for(j=1; j<=nlstate+ndeath;j++)   }
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);   
             fprintf(ficrespij,"\n");   cptcoveff=ij-1; /*Number of simple covariates*/
           }  }
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  
           fprintf(ficrespij,"\n");  /*********** Health Expectancies ****************/
         }  
     }  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[] )
   }  
   {
   fclose(ficrespij);    /* Health expectancies, no variances */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
   /*---------- Health expectancies and variances ------------*/    double age, agelim, hf;
     double ***p3mat;
   strcpy(filerest,"t");    double eip;
   strcat(filerest,fileres);  
   if((ficrest=fopen(filerest,"w"))==NULL) {    pstamp(ficreseij);
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
   }    fprintf(ficreseij,"# Age");
   printf("Computing Total LEs with variances: file '%s' \n", filerest);    for(i=1; i<=nlstate;i++){
       for(j=1; j<=nlstate;j++){
         fprintf(ficreseij," e%1d%1d ",i,j);
   strcpy(filerese,"e");      }
   strcat(filerese,fileres);      fprintf(ficreseij," e%1d. ",i);
   if((ficreseij=fopen(filerese,"w"))==NULL) {    }
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);    fprintf(ficreseij,"\n");
   }  
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);    
     if(estepm < stepm){
  strcpy(fileresv,"v");      printf ("Problem %d lower than %d\n",estepm, stepm);
   strcat(fileresv,fileres);    }
   if((ficresvij=fopen(fileresv,"w"))==NULL) {    else  hstepm=estepm;   
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);    /* We compute the life expectancy from trapezoids spaced every estepm months
   }     * This is mainly to measure the difference between two models: for example
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);     * if stepm=24 months pijx are given only every 2 years and by summing them
      * we are calculating an estimate of the Life Expectancy assuming a linear 
   k=0;     * progression in between and thus overestimating or underestimating according
   for(cptcov=1;cptcov<=i1;cptcov++){     * to the curvature of the survival function. If, for the same date, we 
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){     * estimate the model with stepm=1 month, we can keep estepm to 24 months
       k=k+1;     * to compare the new estimate of Life expectancy with the same linear 
       fprintf(ficrest,"\n#****** ");     * hypothesis. A more precise result, taking into account a more precise
       for(j=1;j<=cptcovn;j++)     * curvature will be obtained if estepm is as small as stepm. */
         fprintf(ficrest,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);  
       fprintf(ficrest,"******\n");    /* 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. 
       fprintf(ficreseij,"\n#****** ");       nhstepm is the number of hstepm from age to agelim 
       for(j=1;j<=cptcovn;j++)       nstepm is the number of stepm from age to agelin. 
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);       Look at hpijx to understand the reason of that which relies in memory size
       fprintf(ficreseij,"******\n");       and note for a fixed period like estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       fprintf(ficresvij,"\n#****** ");       survival function given by stepm (the optimization length). Unfortunately it
       for(j=1;j<=cptcovn;j++)       means that if the survival funtion is printed only each two years of age and if
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       fprintf(ficresvij,"******\n");       results. So we changed our mind and took the option of the best precision.
     */
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       oldm=oldms;savm=savms;  
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);      agelim=AGESUP;
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    /* nhstepm age range expressed in number of stepm */
       oldm=oldms;savm=savms;    nstepm=(int) rint((agelim-age)*YEARM/stepm); 
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
          /* if (stepm >= YEARM) hstepm=1;*/
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
       fprintf(ficrest,"\n");  
            for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       hf=1;      /* Computed by stepm unit matrices, product of hstepm matrices, stored
       if (stepm >= YEARM) hf=stepm/YEARM;         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
       epj=vector(1,nlstate+1);  
       for(age=bage; age <=fage ;age++){      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);   
         fprintf(ficrest," %.0f",age);      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){  
           for(i=1, epj[j]=0.;i <=nlstate;i++) {      /* Computing  Variances of health expectancies */
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
           }         decrease memory allocation */
           epj[nlstate+1] +=epj[j];       printf("%d|",(int)age);fflush(stdout);
         }       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
         for(i=1, vepp=0.;i <=nlstate;i++)      /* Computing expectancies */
           for(j=1;j <=nlstate;j++)      for(i=1; i<=nlstate;i++)
             vepp += vareij[i][j][(int)age];        for(j=1; j<=nlstate;j++)
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
         for(j=1;j <=nlstate;j++){            eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));            
         }  /* 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(ficrest,"\n");  
       }          }
     }  
   }      fprintf(ficreseij,"%3.0f",age );
              for(i=1; i<=nlstate;i++){
  fclose(ficreseij);        eip=0;
  fclose(ficresvij);        for(j=1; j<=nlstate;j++){
   fclose(ficrest);          eip +=eij[i][j][(int)age];
   fclose(ficpar);          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
   free_vector(epj,1,nlstate+1);        }
   /*  scanf("%d ",i); */        fprintf(ficreseij,"%9.4f", eip );
       }
   /*------- Variance limit prevalence------*/        fprintf(ficreseij,"\n");
   
 strcpy(fileresvpl,"vpl");    }
   strcat(fileresvpl,fileres);    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {    printf("\n");
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);    fprintf(ficlog,"\n");
     exit(0);  
   }  }
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);  
   void cvevsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int cij, int estepm,double delti[],double **matcov,char strstart[] )
  k=0;  
  for(cptcov=1;cptcov<=i1;cptcov++){  {
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    /* Covariances of health expectancies eij and of total life expectancies according
      k=k+1;     to initial status i, ei. .
      fprintf(ficresvpl,"\n#****** ");    */
      for(j=1;j<=cptcovn;j++)    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
        fprintf(ficresvpl,"V%d=%d ",Tvar[j],nbcode[Tvar[j]][codtab[k][j]]);    double age, agelim, hf;
      fprintf(ficresvpl,"******\n");    double ***p3matp, ***p3matm, ***varhe;
          double **dnewm,**doldm;
      varpl=matrix(1,nlstate,(int) bage, (int) fage);    double *xp, *xm;
      oldm=oldms;savm=savms;    double **gp, **gm;
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    double ***gradg, ***trgradg;
    }    int theta;
  }  
     double eip, vip;
   fclose(ficresvpl);  
     varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   /*---------- End : free ----------------*/    xp=vector(1,npar);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);    xm=vector(1,npar);
      dnewm=matrix(1,nlstate*nlstate,1,npar);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    
      pstamp(ficresstdeij);
      fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    fprintf(ficresstdeij,"# Age");
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);    for(i=1; i<=nlstate;i++){
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);      for(j=1; j<=nlstate;j++)
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
        fprintf(ficresstdeij," e%1d. ",i);
   free_matrix(matcov,1,npar,1,npar);    }
   free_vector(delti,1,npar);    fprintf(ficresstdeij,"\n");
    
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);    pstamp(ficrescveij);
     fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
   printf("End of Imach\n");    fprintf(ficrescveij,"# Age");
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */    for(i=1; i<=nlstate;i++)
        for(j=1; j<=nlstate;j++){
   /* 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);*/        cptj= (j-1)*nlstate+i;
   /*printf("Total time was %d uSec.\n", total_usecs);*/        for(i2=1; i2<=nlstate;i2++)
   /*------ End -----------*/          for(j2=1; j2<=nlstate;j2++){
             cptj2= (j2-1)*nlstate+i2;
  end:            if(cptj2 <= cptj)
 #ifdef windows              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
  chdir(pathcd);          }
 #endif      }
  system("wgnuplot graph.plt");    fprintf(ficrescveij,"\n");
     
 #ifdef windows    if(estepm < stepm){
   while (z[0] != 'q') {      printf ("Problem %d lower than %d\n",estepm, stepm);
     chdir(pathcd);    }
     printf("\nType e to edit output files, c to start again, and q for exiting: ");    else  hstepm=estepm;   
     scanf("%s",z);    /* We compute the life expectancy from trapezoids spaced every estepm months
     if (z[0] == 'c') system("./imach");     * This is mainly to measure the difference between two models: for example
     else if (z[0] == 'e') {     * if stepm=24 months pijx are given only every 2 years and by summing them
       chdir(path);     * we are calculating an estimate of the Life Expectancy assuming a linear 
       system("index.htm");     * progression in between and thus overestimating or underestimating according
     }     * to the curvature of the survival function. If, for the same date, we 
     else if (z[0] == 'q') exit(0);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   }     * to compare the new estimate of Life expectancy with the same linear 
 #endif     * hypothesis. A more precise result, taking into account a more precise
 }     * curvature will be obtained if estepm is as small as stepm. */
   
     /* 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 estepm months */
     /* We decided (b) to get a life expectancy respecting the most precise curvature of the
        survival function given by stepm (the optimization length). Unfortunately it
        means that if the survival funtion is printed only each two years of age and if
        you sum them up and add 1 year (area under the trapezoids) you won't get the same 
        results. So we changed our mind and took the option of the best precision.
     */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   
     /* If stepm=6 months */
     /* nhstepm age range expressed in number of stepm */
     agelim=AGESUP;
     nstepm=(int) rint((agelim-age)*YEARM/stepm); 
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
     /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     
     p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
     trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
     gp=matrix(0,nhstepm,1,nlstate*nlstate);
     gm=matrix(0,nhstepm,1,nlstate*nlstate);
   
     for (age=bage; age<=fage; age ++){ 
   
       /* Computed by stepm unit matrices, product of hstepm matrices, stored
          in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
    
       hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
   
       /* Computing  Variances of health expectancies */
       /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
          decrease memory allocation */
       for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ 
           xp[i] = x[i] + (i==theta ?delti[theta]:0);
           xm[i] = x[i] - (i==theta ?delti[theta]:0);
         }
         hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
         hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
     
         for(j=1; j<= nlstate; j++){
           for(i=1; i<=nlstate; i++){
             for(h=0; h<=nhstepm-1; h++){
               gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
               gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
             }
           }
         }
        
         for(ij=1; ij<= nlstate*nlstate; ij++)
           for(h=0; h<=nhstepm-1; h++){
             gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
           }
       }/* End theta */
       
       
       for(h=0; h<=nhstepm-1; h++)
         for(j=1; j<=nlstate*nlstate;j++)
           for(theta=1; theta <=npar; theta++)
             trgradg[h][j][theta]=gradg[h][theta][j];
       
   
        for(ij=1;ij<=nlstate*nlstate;ij++)
         for(ji=1;ji<=nlstate*nlstate;ji++)
           varhe[ij][ji][(int)age] =0.;
   
        printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        for(h=0;h<=nhstepm-1;h++){
         for(k=0;k<=nhstepm-1;k++){
           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]);
           for(ij=1;ij<=nlstate*nlstate;ij++)
             for(ji=1;ji<=nlstate*nlstate;ji++)
               varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
         }
       }
       /* Computing expectancies */
       hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
       for(i=1; i<=nlstate;i++)
         for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
             
             /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   
           }
   
       fprintf(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 (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; /* Un peu sale */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem 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;
       lval=strtol(strb,&endptr,10); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight.  Exiting.\n",lval, i,line,linei);
         exit(1);
       }
       weight[i]=(double)(lval); 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);
           exit(1);
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self).  Exiting.\n",lval,linei, i,line,j);
           exit(1);
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       } 
       lstra=strlen(stra);
       
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
     fclose(fic);
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
     /* for (i=1; i<=imx; i++) */
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameters from char model */
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - 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,path); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
     
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (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 -----------*/
   
     chdir(path);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   
Removed from v.1.5  
changed lines
  Added in v.1.118

FreeBSD-CVSweb <freebsd-cvsweb@FreeBSD.org>