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version 1.19, 2002/02/20 17:19:10 version 1.117, 2006/03/14 17:16:22
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      /* $Id$
 /*********************** Imach **************************************            $State$
   This program computes Healthy Life Expectancies from cross-longitudinal    $Log$
   data. Cross-longitudinal consist in a first survey ("cross") where    Revision 1.117  2006/03/14 17:16:22  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 1.116  2006/03/06 10:29:27  brouard
   The simplest model is the multinomial logistic model where pij is    (Module): Variance-covariance wrong links and
   the probabibility to be observed in state j at the second wave conditional    varian-covariance of ej. is needed (Saito).
   to be observed in state i at the first wave. Therefore the model is:  
   log(pij/pii)= aij + bij*age+ cij*sex + etc , where 'age' is age and 'sex'    Revision 1.115  2006/02/27 12:17:45  brouard
   is a covariate. If you want to have a more complex model than "constant and    (Module): One freematrix added in mlikeli! 0.98c
   age", you should modify the program where the markup  
     *Covariates have to be included here again* invites you to do it.    Revision 1.114  2006/02/26 12:57:58  brouard
   More covariates you add, less is the speed of the convergence.    (Module): Some improvements in processing parameter
     filename with strsep.
   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 1.113  2006/02/24 14:20:24  brouard
   individual missed an interview, the information is not rounded or lost, but    (Module): Memory leaks checks with valgrind and:
   taken into account using an interpolation or extrapolation.    datafile was not closed, some imatrix were not freed and on matrix
   hPijx is the probability to be    allocation too.
   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    Revision 1.112  2006/01/30 09:55:26  brouard
   unobserved intermediate  states. This elementary transition (by month or    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   quarter trimester, semester or year) is model as a multinomial logistic.  
   The hPx matrix is simply the matrix product of nh*stepm elementary matrices    Revision 1.111  2006/01/25 20:38:18  brouard
   and the contribution of each individual to the likelihood is simply hPijx.    (Module): Lots of cleaning and bugs added (Gompertz)
     (Module): Comments can be added in data file. Missing date values
   Also this programme outputs the covariance matrix of the parameters but also    can be a simple dot '.'.
   of the life expectancies. It also computes the prevalence limits.  
      Revision 1.110  2006/01/25 00:51:50  brouard
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).    (Module): Lots of cleaning and bugs added (Gompertz)
            Institut national d'études démographiques, Paris.  
   This software have been partly granted by Euro-REVES, a concerted action    Revision 1.109  2006/01/24 19:37:15  brouard
   from the European Union.    (Module): Comments (lines starting with a #) are allowed in data.
   It is copyrighted identically to a GNU software product, ie programme and  
   software can be distributed freely for non commercial use. Latest version    Revision 1.108  2006/01/19 18:05:42  lievre
   can be accessed at http://euroreves.ined.fr/imach .    Gnuplot problem appeared...
   **********************************************************************/    To be fixed
    
 #include <math.h>    Revision 1.107  2006/01/19 16:20:37  brouard
 #include <stdio.h>    Test existence of gnuplot in imach path
 #include <stdlib.h>  
 #include <unistd.h>    Revision 1.106  2006/01/19 13:24:36  brouard
     Some cleaning and links added in html output
 #define MAXLINE 256  
 #define FILENAMELENGTH 80    Revision 1.105  2006/01/05 20:23:19  lievre
 /*#define DEBUG*/    *** empty log message ***
 #define windows  
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    Revision 1.104  2005/09/30 16:11:43  lievre
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    (Module): sump fixed, loop imx fixed, and simplifications.
     (Module): If the status is missing at the last wave but we know
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    that the person is alive, then we can code his/her status as -2
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    (instead of missing=-1 in earlier versions) and his/her
     contributions to the likelihood is 1 - Prob of dying from last
 #define NINTERVMAX 8    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    the healthy state at last known wave). Version is 0.98
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    Revision 1.103  2005/09/30 15:54:49  lievre
 #define MAXN 20000    (Module): sump fixed, loop imx fixed, and simplifications.
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Revision 1.102  2004/09/15 17:31:30  brouard
 #define AGEBASE 40    Add the possibility to read data file including tab characters.
   
     Revision 1.101  2004/09/15 10:38:38  brouard
 int nvar;    Fix on curr_time
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;  
 int npar=NPARMAX;    Revision 1.100  2004/07/12 18:29:06  brouard
 int nlstate=2; /* Number of live states */    Add version for Mac OS X. Just define UNIX in Makefile
 int ndeath=1; /* Number of dead states */  
 int ncovmodel, ncov;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    Revision 1.99  2004/06/05 08:57:40  brouard
 int popbased=0;    *** empty log message ***
   
 int *wav; /* Number of waves for this individuual 0 is possible */    Revision 1.98  2004/05/16 15:05:56  brouard
 int maxwav; /* Maxim number of waves */    New version 0.97 . First attempt to estimate force of mortality
 int jmin, jmax; /* min, max spacing between 2 waves */    directly from the data i.e. without the need of knowing the health
 int mle, weightopt;    state at each age, but using a Gompertz model: log u =a + b*age .
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */    This is the basic analysis of mortality and should be done before any
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    other analysis, in order to test if the mortality estimated from the
 double jmean; /* Mean space between 2 waves */    cross-longitudinal survey is different from the mortality estimated
 double **oldm, **newm, **savm; /* Working pointers to matrices */    from other sources like vital statistic data.
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */  
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf;    The same imach parameter file can be used but the option for mle should be -3.
 FILE *ficgp, *fichtm,*ficresprob,*ficpop;  
 FILE *ficreseij;    Agnès, who wrote this part of the code, tried to keep most of the
   char filerese[FILENAMELENGTH];    former routines in order to include the new code within the former code.
  FILE  *ficresvij;  
   char fileresv[FILENAMELENGTH];    The output is very simple: only an estimate of the intercept and of
  FILE  *ficresvpl;    the slope with 95% confident intervals.
   char fileresvpl[FILENAMELENGTH];  
     Current limitations:
 #define NR_END 1    A) Even if you enter covariates, i.e. with the
 #define FREE_ARG char*    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
 #define FTOL 1.0e-10    B) There is no computation of Life Expectancy nor Life Table.
   
 #define NRANSI    Revision 1.97  2004/02/20 13:25:42  lievre
 #define ITMAX 200    Version 0.96d. Population forecasting command line is (temporarily)
     suppressed.
 #define TOL 2.0e-4  
     Revision 1.96  2003/07/15 15:38:55  brouard
 #define CGOLD 0.3819660    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
 #define ZEPS 1.0e-10    rewritten within the same printf. Workaround: many printfs.
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);  
     Revision 1.95  2003/07/08 07:54:34  brouard
 #define GOLD 1.618034    * imach.c (Repository):
 #define GLIMIT 100.0    (Repository): Using imachwizard code to output a more meaningful covariance
 #define TINY 1.0e-20    matrix (cov(a12,c31) instead of numbers.
   
 static double maxarg1,maxarg2;    Revision 1.94  2003/06/27 13:00:02  brouard
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    Just cleaning
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))  
      Revision 1.93  2003/06/25 16:33:55  brouard
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    (Module): On windows (cygwin) function asctime_r doesn't
 #define rint(a) floor(a+0.5)    exist so I changed back to asctime which exists.
     (Module): Version 0.96b
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Revision 1.92  2003/06/25 16:30:45  brouard
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
 int imx;  
 int stepm;    Revision 1.91  2003/06/25 15:30:29  brouard
 /* Stepm, step in month: minimum step interpolation*/    * imach.c (Repository): Duplicated warning errors corrected.
     (Repository): Elapsed time after each iteration is now output. It
 int m,nb;    helps to forecast when convergence will be reached. Elapsed time
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;    is stamped in powell.  We created a new html file for the graphs
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    concerning matrix of covariance. It has extension -cov.htm.
 double **pmmij, ***probs, ***mobaverage;  
 double dateintmean=0;    Revision 1.90  2003/06/24 12:34:15  brouard
     (Module): Some bugs corrected for windows. Also, when
 double *weight;    mle=-1 a template is output in file "or"mypar.txt with the design
 int **s; /* Status */    of the covariance matrix to be input.
 double *agedc, **covar, idx;  
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;    Revision 1.89  2003/06/24 12:30:52  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.
   
 /**************** split *************************/    Revision 1.88  2003/06/23 17:54:56  brouard
 static  int split( char *path, char *dirc, char *name )    * 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.
 {  
    char *s;                             /* pointer */    Revision 1.87  2003/06/18 12:26:01  brouard
    int  l1, l2;                         /* length counters */    Version 0.96
   
    l1 = strlen( path );                 /* length of path */    Revision 1.86  2003/06/17 20:04:08  brouard
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    (Module): Change position of html and gnuplot routines and added
    s = strrchr( path, '\\' );           /* find last / */    routine fileappend.
    if ( s == NULL ) {                   /* no directory, so use current */  
 #if     defined(__bsd__)                /* get current working directory */    Revision 1.85  2003/06/17 13:12:43  brouard
       extern char       *getwd( );    * imach.c (Repository): Check when date of death was earlier that
     current date of interview. It may happen when the death was just
       if ( getwd( dirc ) == NULL ) {    prior to the death. In this case, dh was negative and likelihood
 #else    was wrong (infinity). We still send an "Error" but patch by
       extern char       *getcwd( );    assuming that the date of death was just one stepm after the
     interview.
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    (Repository): Because some people have very long ID (first column)
 #endif    we changed int to long in num[] and we added a new lvector for
          return( GLOCK_ERROR_GETCWD );    memory allocation. But we also truncated to 8 characters (left
       }    truncation)
       strcpy( name, path );             /* we've got it */    (Repository): No more line truncation errors.
    } else {                             /* strip direcotry from path */  
       s++;                              /* after this, the filename */    Revision 1.84  2003/06/13 21:44:43  brouard
       l2 = strlen( s );                 /* length of filename */    * imach.c (Repository): Replace "freqsummary" at a correct
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );    place. It differs from routine "prevalence" which may be called
       strcpy( name, s );                /* save file name */    many times. Probs is memory consuming and must be used with
       strncpy( dirc, path, l1 - l2 );   /* now the directory */    parcimony.
       dirc[l1-l2] = 0;                  /* add zero */    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
    }  
    l1 = strlen( dirc );                 /* length of directory */    Revision 1.83  2003/06/10 13:39:11  lievre
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    *** empty log message ***
    return( 0 );                         /* we're done */  
 }    Revision 1.82  2003/06/05 15:57:20  brouard
     Add log in  imach.c and  fullversion number is now printed.
   
 /******************************************/  */
   /*
 void replace(char *s, char*t)     Interpolated Markov Chain
 {  
   int i;    Short summary of the programme:
   int lg=20;    
   i=0;    This program computes Healthy Life Expectancies from
   lg=strlen(t);    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
   for(i=0; i<= lg; i++) {    first survey ("cross") where individuals from different ages are
     (s[i] = t[i]);    interviewed on their health status or degree of disability (in the
     if (t[i]== '\\') s[i]='/';    case of a health survey which is our main interest) -2- at least a
   }    second wave of interviews ("longitudinal") which measure each change
 }    (if any) in individual health status.  Health expectancies are
     computed from the time spent in each health state according to a
 int nbocc(char *s, char occ)    model. More health states you consider, more time is necessary to reach the
 {    Maximum Likelihood of the parameters involved in the model.  The
   int i,j=0;    simplest model is the multinomial logistic model where pij is the
   int lg=20;    probability to be observed in state j at the second wave
   i=0;    conditional to be observed in state i at the first wave. Therefore
   lg=strlen(s);    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
   for(i=0; i<= lg; i++) {    'age' is age and 'sex' is a covariate. If you want to have a more
   if  (s[i] == occ ) j++;    complex model than "constant and age", you should modify the program
   }    where the markup *Covariates have to be included here again* invites
   return j;    you to do it.  More covariates you add, slower the
 }    convergence.
   
 void cutv(char *u,char *v, char*t, char occ)    The advantage of this computer programme, compared to a simple
 {    multinomial logistic model, is clear when the delay between waves is not
   int i,lg,j,p=0;    identical for each individual. Also, if a individual missed an
   i=0;    intermediate interview, the information is lost, but taken into
   for(j=0; j<=strlen(t)-1; j++) {    account using an interpolation or extrapolation.  
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;  
   }    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
   lg=strlen(t);    split into an exact number (nh*stepm) of unobserved intermediate
   for(j=0; j<p; j++) {    states. This elementary transition (by month, quarter,
     (u[j] = t[j]);    semester or year) is modelled as a multinomial logistic.  The hPx
   }    matrix is simply the matrix product of nh*stepm elementary matrices
      u[p]='\0';    and the contribution of each individual to the likelihood is simply
     hPijx.
    for(j=0; j<= lg; j++) {  
     if (j>=(p+1))(v[j-p-1] = t[j]);    Also this programme outputs the covariance matrix of the parameters but also
   }    of the life expectancies. It also computes the period (stable) prevalence. 
 }    
     Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
 /********************** nrerror ********************/             Institut national d'études démographiques, Paris.
     This software have been partly granted by Euro-REVES, a concerted action
 void nrerror(char error_text[])    from the European Union.
 {    It is copyrighted identically to a GNU software product, ie programme and
   fprintf(stderr,"ERREUR ...\n");    software can be distributed freely for non commercial use. Latest version
   fprintf(stderr,"%s\n",error_text);    can be accessed at http://euroreves.ined.fr/imach .
   exit(1);  
 }    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
 /*********************** vector *******************/    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
 double *vector(int nl, int nh)    
 {    **********************************************************************/
   double *v;  /*
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));    main
   if (!v) nrerror("allocation failure in vector");    read parameterfile
   return v-nl+NR_END;    read datafile
 }    concatwav
     freqsummary
 /************************ free vector ******************/    if (mle >= 1)
 void free_vector(double*v, int nl, int nh)      mlikeli
 {    print results files
   free((FREE_ARG)(v+nl-NR_END));    if mle==1 
 }       computes hessian
     read end of parameter file: agemin, agemax, bage, fage, estepm
 /************************ivector *******************************/        begin-prev-date,...
 int *ivector(long nl,long nh)    open gnuplot file
 {    open html file
   int *v;    period (stable) prevalence
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));     for age prevalim()
   if (!v) nrerror("allocation failure in ivector");    h Pij x
   return v-nl+NR_END;    variance of p varprob
 }    forecasting if prevfcast==1 prevforecast call prevalence()
     health expectancies
 /******************free ivector **************************/    Variance-covariance of DFLE
 void free_ivector(int *v, long nl, long nh)    prevalence()
 {     movingaverage()
   free((FREE_ARG)(v+nl-NR_END));    varevsij() 
 }    if popbased==1 varevsij(,popbased)
     total life expectancies
 /******************* imatrix *******************************/    Variance of period (stable) prevalence
 int **imatrix(long nrl, long nrh, long ncl, long nch)   end
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  */
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  
   int **m;  
     
   /* allocate pointers to rows */  #include <math.h>
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  #include <stdio.h>
   if (!m) nrerror("allocation failure 1 in matrix()");  #include <stdlib.h>
   m += NR_END;  #include <string.h>
   m -= nrl;  #include <unistd.h>
    
    #include <limits.h>
   /* allocate rows and set pointers to them */  #include <sys/types.h>
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  #include <sys/stat.h>
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #include <errno.h>
   m[nrl] += NR_END;  extern int errno;
   m[nrl] -= ncl;  
    /* #include <sys/time.h> */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  #include <time.h>
    #include "timeval.h"
   /* return pointer to array of pointers to rows */  
   return m;  /* #include <libintl.h> */
 }  /* #define _(String) gettext (String) */
   
 /****************** free_imatrix *************************/  #define MAXLINE 256
 void free_imatrix(m,nrl,nrh,ncl,nch)  
       int **m;  #define GNUPLOTPROGRAM "gnuplot"
       long nch,ncl,nrh,nrl;  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
      /* free an int matrix allocated by imatrix() */  #define FILENAMELENGTH 132
 {  
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   free((FREE_ARG) (m+nrl-NR_END));  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
 }  
   #define MAXPARM 30 /* Maximum number of parameters for the optimization */
 /******************* matrix *******************************/  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
 double **matrix(long nrl, long nrh, long ncl, long nch)  
 {  #define NINTERVMAX 8
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   double **m;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
   #define NCOVMAX 8 /* Maximum number of covariates */
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  #define MAXN 20000
   if (!m) nrerror("allocation failure 1 in matrix()");  #define YEARM 12. /* Number of months per year */
   m += NR_END;  #define AGESUP 130
   m -= nrl;  #define AGEBASE 40
   #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  #ifdef UNIX
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define DIRSEPARATOR '/'
   m[nrl] += NR_END;  #define CHARSEPARATOR "/"
   m[nrl] -= ncl;  #define ODIRSEPARATOR '\\'
   #else
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  #define DIRSEPARATOR '\\'
   return m;  #define CHARSEPARATOR "\\"
 }  #define ODIRSEPARATOR '/'
   #endif
 /*************************free matrix ************************/  
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  /* $Id$ */
 {  /* $State$ */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));  char version[]="Imach version 0.98d, March 2006, INED-EUROREVES-Institut de longevite ";
 }  char fullversion[]="$Revision$ $Date$"; 
   char strstart[80];
 /******************* ma3x *******************************/  char optionfilext[10], optionfilefiname[FILENAMELENGTH];
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
 {  int nvar;
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   double ***m;  int npar=NPARMAX;
   int nlstate=2; /* Number of live states */
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  int ndeath=1; /* Number of dead states */
   if (!m) nrerror("allocation failure 1 in matrix()");  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   m += NR_END;  int popbased=0;
   m -= nrl;  
   int *wav; /* Number of waves for this individuual 0 is possible */
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  int maxwav; /* Maxim number of waves */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int jmin, jmax; /* min, max spacing between 2 waves */
   m[nrl] += NR_END;  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
   m[nrl] -= ncl;  int gipmx, gsw; /* Global variables on the number of contributions 
                      to the likelihood and the sum of weights (done by funcone)*/
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  int mle, weightopt;
   int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
   m[nrl][ncl] += NR_END;             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   m[nrl][ncl] -= nll;  double jmean; /* Mean space between 2 waves */
   for (j=ncl+1; j<=nch; j++)  double **oldm, **newm, **savm; /* Working pointers to matrices */
     m[nrl][j]=m[nrl][j-1]+nlay;  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
    FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   for (i=nrl+1; i<=nrh; i++) {  FILE *ficlog, *ficrespow;
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  int globpr; /* Global variable for printing or not */
     for (j=ncl+1; j<=nch; j++)  double fretone; /* Only one call to likelihood */
       m[i][j]=m[i][j-1]+nlay;  long ipmx; /* Number of contributions */
   }  double sw; /* Sum of weights */
   return m;  char filerespow[FILENAMELENGTH];
 }  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   FILE *ficresilk;
 /*************************free ma3x ************************/  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  FILE *ficresprobmorprev;
 {  FILE *fichtm, *fichtmcov; /* Html File */
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  FILE *ficreseij;
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  char filerese[FILENAMELENGTH];
   free((FREE_ARG)(m+nrl-NR_END));  FILE *ficresstdeij;
 }  char fileresstde[FILENAMELENGTH];
   FILE *ficrescveij;
 /***************** f1dim *************************/  char filerescve[FILENAMELENGTH];
 extern int ncom;  FILE  *ficresvij;
 extern double *pcom,*xicom;  char fileresv[FILENAMELENGTH];
 extern double (*nrfunc)(double []);  FILE  *ficresvpl;
    char fileresvpl[FILENAMELENGTH];
 double f1dim(double x)  char title[MAXLINE];
 {  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
   int j;  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
   double f;  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
   double *xt;  char command[FILENAMELENGTH];
    int  outcmd=0;
   xt=vector(1,ncom);  
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   f=(*nrfunc)(xt);  
   free_vector(xt,1,ncom);  char filelog[FILENAMELENGTH]; /* Log file */
   return f;  char filerest[FILENAMELENGTH];
 }  char fileregp[FILENAMELENGTH];
   char popfile[FILENAMELENGTH];
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 {  
   int iter;  struct timeval start_time, end_time, curr_time, last_time, forecast_time;
   double a,b,d,etemp;  struct timezone tzp;
   double fu,fv,fw,fx;  extern int gettimeofday();
   double ftemp;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
   double p,q,r,tol1,tol2,u,v,w,x,xm;  long time_value;
   double e=0.0;  extern long time();
    char strcurr[80], strfor[80];
   a=(ax < cx ? ax : cx);  
   b=(ax > cx ? ax : cx);  char *endptr;
   x=w=v=bx;  long lval;
   fw=fv=fx=(*f)(x);  
   for (iter=1;iter<=ITMAX;iter++) {  #define NR_END 1
     xm=0.5*(a+b);  #define FREE_ARG char*
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  #define FTOL 1.0e-10
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  
     printf(".");fflush(stdout);  #define NRANSI 
 #ifdef DEBUG  #define ITMAX 200 
     printf("br %d,x=%.10e xm=%.10e b=%.10e a=%.10e tol=%.10e tol1=%.10e tol2=%.10e x-xm=%.10e fx=%.12e fu=%.12e,fw=%.12e,ftemp=%.12e,ftol=%.12e\n",iter,x,xm,b,a,tol,tol1,tol2,(x-xm),fx,fu,fw,ftemp,ftol);  
     /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */  #define TOL 2.0e-4 
 #endif  
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  #define CGOLD 0.3819660 
       *xmin=x;  #define ZEPS 1.0e-10 
       return fx;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
     }  
     ftemp=fu;  #define GOLD 1.618034 
     if (fabs(e) > tol1) {  #define GLIMIT 100.0 
       r=(x-w)*(fx-fv);  #define TINY 1.0e-20 
       q=(x-v)*(fx-fw);  
       p=(x-v)*q-(x-w)*r;  static double maxarg1,maxarg2;
       q=2.0*(q-r);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
       if (q > 0.0) p = -p;  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
       q=fabs(q);    
       etemp=e;  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
       e=d;  #define rint(a) floor(a+0.5)
       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));  static double sqrarg;
       else {  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
         d=p/q;  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
         u=x+d;  int agegomp= AGEGOMP;
         if (u-a < tol2 || b-u < tol2)  
           d=SIGN(tol1,xm-x);  int imx; 
       }  int stepm=1;
     } else {  /* Stepm, step in month: minimum step interpolation*/
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  
     }  int estepm;
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
     fu=(*f)(u);  
     if (fu <= fx) {  int m,nb;
       if (u >= x) a=x; else b=x;  long *num;
       SHFT(v,w,x,u)  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
         SHFT(fv,fw,fx,fu)  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
         } else {  double **pmmij, ***probs;
           if (u < x) a=u; else b=u;  double *ageexmed,*agecens;
           if (fu <= fw || w == x) {  double dateintmean=0;
             v=w;  
             w=u;  double *weight;
             fv=fw;  int **s; /* Status */
             fw=fu;  double *agedc, **covar, idx;
           } else if (fu <= fv || v == x || v == w) {  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
             v=u;  double *lsurv, *lpop, *tpop;
             fv=fu;  
           }  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
         }  double ftolhess; /* Tolerance for computing hessian */
   }  
   nrerror("Too many iterations in brent");  /**************** split *************************/
   *xmin=x;  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
   return fx;  {
 }    /* 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)
 /****************** mnbrak ***********************/    */ 
     char  *ss;                            /* pointer */
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,    int   l1, l2;                         /* length counters */
             double (*func)(double))  
 {    l1 = strlen(path );                   /* length of path */
   double ulim,u,r,q, dum;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
   double fu;    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
      if ( ss == NULL ) {                   /* no directory, so determine current directory */
   *fa=(*func)(*ax);      strcpy( name, path );               /* we got the fullname name because no directory */
   *fb=(*func)(*bx);      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
   if (*fb > *fa) {        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
     SHFT(dum,*ax,*bx,dum)      /* get current working directory */
       SHFT(dum,*fb,*fa,dum)      /*    extern  char* getcwd ( char *buf , int len);*/
       }      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
   *cx=(*bx)+GOLD*(*bx-*ax);        return( GLOCK_ERROR_GETCWD );
   *fc=(*func)(*cx);      }
   while (*fb > *fc) {      /* got dirc from getcwd*/
     r=(*bx-*ax)*(*fb-*fc);      printf(" DIRC = %s \n",dirc);
     q=(*bx-*cx)*(*fb-*fa);    } else {                              /* strip direcotry from path */
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/      ss++;                               /* after this, the filename */
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));      l2 = strlen( ss );                  /* length of filename */
     ulim=(*bx)+GLIMIT*(*cx-*bx);      if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
     if ((*bx-u)*(u-*cx) > 0.0) {      strcpy( name, ss );         /* save file name */
       fu=(*func)(u);      strncpy( dirc, path, l1 - l2 );     /* now the directory */
     } else if ((*cx-u)*(u-ulim) > 0.0) {      dirc[l1-l2] = 0;                    /* add zero */
       fu=(*func)(u);      printf(" DIRC2 = %s \n",dirc);
       if (fu < *fc) {    }
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))    /* We add a separator at the end of dirc if not exists */
           SHFT(*fb,*fc,fu,(*func)(u))    l1 = strlen( dirc );                  /* length of directory */
           }    if( dirc[l1-1] != DIRSEPARATOR ){
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {      dirc[l1] =  DIRSEPARATOR;
       u=ulim;      dirc[l1+1] = 0; 
       fu=(*func)(u);      printf(" DIRC3 = %s \n",dirc);
     } else {    }
       u=(*cx)+GOLD*(*cx-*bx);    ss = strrchr( name, '.' );            /* find last / */
       fu=(*func)(u);    if (ss >0){
     }      ss++;
     SHFT(*ax,*bx,*cx,u)      strcpy(ext,ss);                     /* save extension */
       SHFT(*fa,*fb,*fc,fu)      l1= strlen( name);
       }      l2= strlen(ss)+1;
 }      strncpy( finame, name, l1-l2);
       finame[l1-l2]= 0;
 /*************** linmin ************************/    }
   
 int ncom;    return( 0 );                          /* we're done */
 double *pcom,*xicom;  }
 double (*nrfunc)(double []);  
    
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))  /******************************************/
 {  
   double brent(double ax, double bx, double cx,  void replace_back_to_slash(char *s, char*t)
                double (*f)(double), double tol, double *xmin);  {
   double f1dim(double x);    int i;
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,    int lg=0;
               double *fc, double (*func)(double));    i=0;
   int j;    lg=strlen(t);
   double xx,xmin,bx,ax;    for(i=0; i<= lg; i++) {
   double fx,fb,fa;      (s[i] = t[i]);
        if (t[i]== '\\') s[i]='/';
   ncom=n;    }
   pcom=vector(1,n);  }
   xicom=vector(1,n);  
   nrfunc=func;  int nbocc(char *s, char occ)
   for (j=1;j<=n;j++) {  {
     pcom[j]=p[j];    int i,j=0;
     xicom[j]=xi[j];    int lg=20;
   }    i=0;
   ax=0.0;    lg=strlen(s);
   xx=1.0;    for(i=0; i<= lg; i++) {
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);    if  (s[i] == occ ) j++;
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);    }
 #ifdef DEBUG    return j;
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  }
 #endif  
   for (j=1;j<=n;j++) {  void cutv(char *u,char *v, char*t, char occ)
     xi[j] *= xmin;  {
     p[j] += xi[j];    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
   }       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
   free_vector(xicom,1,n);       gives u="abcedf" and v="ghi2j" */
   free_vector(pcom,1,n);    int i,lg,j,p=0;
 }    i=0;
     for(j=0; j<=strlen(t)-1; j++) {
 /*************** powell ************************/      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,    }
             double (*func)(double []))  
 {    lg=strlen(t);
   void linmin(double p[], double xi[], int n, double *fret,    for(j=0; j<p; j++) {
               double (*func)(double []));      (u[j] = t[j]);
   int i,ibig,j;    }
   double del,t,*pt,*ptt,*xit;       u[p]='\0';
   double fp,fptt;  
   double *xits;     for(j=0; j<= lg; j++) {
   pt=vector(1,n);      if (j>=(p+1))(v[j-p-1] = t[j]);
   ptt=vector(1,n);    }
   xit=vector(1,n);  }
   xits=vector(1,n);  
   *fret=(*func)(p);  /********************** nrerror ********************/
   for (j=1;j<=n;j++) pt[j]=p[j];  
   for (*iter=1;;++(*iter)) {  void nrerror(char error_text[])
     fp=(*fret);  {
     ibig=0;    fprintf(stderr,"ERREUR ...\n");
     del=0.0;    fprintf(stderr,"%s\n",error_text);
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    exit(EXIT_FAILURE);
     for (i=1;i<=n;i++)  }
       printf(" %d %.12f",i, p[i]);  /*********************** vector *******************/
     printf("\n");  double *vector(int nl, int nh)
     for (i=1;i<=n;i++) {  {
       for (j=1;j<=n;j++) xit[j]=xi[j][i];    double *v;
       fptt=(*fret);    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
 #ifdef DEBUG    if (!v) nrerror("allocation failure in vector");
       printf("fret=%lf \n",*fret);    return v-nl+NR_END;
 #endif  }
       printf("%d",i);fflush(stdout);  
       linmin(p,xit,n,fret,func);  /************************ free vector ******************/
       if (fabs(fptt-(*fret)) > del) {  void free_vector(double*v, int nl, int nh)
         del=fabs(fptt-(*fret));  {
         ibig=i;    free((FREE_ARG)(v+nl-NR_END));
       }  }
 #ifdef DEBUG  
       printf("%d %.12e",i,(*fret));  /************************ivector *******************************/
       for (j=1;j<=n;j++) {  int *ivector(long nl,long nh)
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  {
         printf(" x(%d)=%.12e",j,xit[j]);    int *v;
       }    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
       for(j=1;j<=n;j++)    if (!v) nrerror("allocation failure in ivector");
         printf(" p=%.12e",p[j]);    return v-nl+NR_END;
       printf("\n");  }
 #endif  
     }  /******************free ivector **************************/
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {  void free_ivector(int *v, long nl, long nh)
 #ifdef DEBUG  {
       int k[2],l;    free((FREE_ARG)(v+nl-NR_END));
       k[0]=1;  }
       k[1]=-1;  
       printf("Max: %.12e",(*func)(p));  /************************lvector *******************************/
       for (j=1;j<=n;j++)  long *lvector(long nl,long nh)
         printf(" %.12e",p[j]);  {
       printf("\n");    long *v;
       for(l=0;l<=1;l++) {    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
         for (j=1;j<=n;j++) {    if (!v) nrerror("allocation failure in ivector");
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    return v-nl+NR_END;
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);  }
         }  
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));  /******************free lvector **************************/
       }  void free_lvector(long *v, long nl, long nh)
 #endif  {
     free((FREE_ARG)(v+nl-NR_END));
   }
       free_vector(xit,1,n);  
       free_vector(xits,1,n);  /******************* imatrix *******************************/
       free_vector(ptt,1,n);  int **imatrix(long nrl, long nrh, long ncl, long nch) 
       free_vector(pt,1,n);       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
       return;  { 
     }    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");    int **m; 
     for (j=1;j<=n;j++) {    
       ptt[j]=2.0*p[j]-pt[j];    /* allocate pointers to rows */ 
       xit[j]=p[j]-pt[j];    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
       pt[j]=p[j];    if (!m) nrerror("allocation failure 1 in matrix()"); 
     }    m += NR_END; 
     fptt=(*func)(ptt);    m -= nrl; 
     if (fptt < fp) {    
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);    
       if (t < 0.0) {    /* allocate rows and set pointers to them */ 
         linmin(p,xit,n,fret,func);    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
         for (j=1;j<=n;j++) {    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
           xi[j][ibig]=xi[j][n];    m[nrl] += NR_END; 
           xi[j][n]=xit[j];    m[nrl] -= ncl; 
         }    
 #ifdef DEBUG    for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    
         for(j=1;j<=n;j++)    /* return pointer to array of pointers to rows */ 
           printf(" %.12e",xit[j]);    return m; 
         printf("\n");  } 
 #endif  
       }  /****************** free_imatrix *************************/
     }  void free_imatrix(m,nrl,nrh,ncl,nch)
   }        int **m;
 }        long nch,ncl,nrh,nrl; 
        /* free an int matrix allocated by imatrix() */ 
 /**** Prevalence limit ****************/  { 
     free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)    free((FREE_ARG) (m+nrl-NR_END)); 
 {  } 
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  
      matrix by transitions matrix until convergence is reached */  /******************* matrix *******************************/
   double **matrix(long nrl, long nrh, long ncl, long nch)
   int i, ii,j,k;  {
   double min, max, maxmin, maxmax,sumnew=0.;    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
   double **matprod2();    double **m;
   double **out, cov[NCOVMAX], **pmij();  
   double **newm;    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
   double agefin, delaymax=50 ; /* Max number of years to converge */    if (!m) nrerror("allocation failure 1 in matrix()");
     m += NR_END;
   for (ii=1;ii<=nlstate+ndeath;ii++)    m -= nrl;
     for (j=1;j<=nlstate+ndeath;j++){  
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     }    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
     m[nrl] += NR_END;
    cov[1]=1.;    m[nrl] -= ncl;
    
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){    return m;
     newm=savm;    /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
     /* Covariates have to be included here again */     */
      cov[2]=agefin;  }
    
       for (k=1; k<=cptcovn;k++) {  /*************************free matrix ************************/
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];  void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
         /*printf("ij=%d Tvar[k]=%d nbcode=%d cov=%lf\n",ij, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k]);*/  {
       }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       for (k=1; k<=cptcovage;k++)    free((FREE_ARG)(m+nrl-NR_END));
         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]]];  /******************* ma3x *******************************/
   double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/  {
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
     double ***m;
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);  
     m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
     savm=oldm;    if (!m) nrerror("allocation failure 1 in matrix()");
     oldm=newm;    m += NR_END;
     maxmax=0.;    m -= nrl;
     for(j=1;j<=nlstate;j++){  
       min=1.;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
       max=0.;    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
       for(i=1; i<=nlstate; i++) {    m[nrl] += NR_END;
         sumnew=0;    m[nrl] -= ncl;
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  
         prlim[i][j]= newm[i][j]/(1-sumnew);    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
         max=FMAX(max,prlim[i][j]);  
         min=FMIN(min,prlim[i][j]);    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       }    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       maxmin=max-min;    m[nrl][ncl] += NR_END;
       maxmax=FMAX(maxmax,maxmin);    m[nrl][ncl] -= nll;
     }    for (j=ncl+1; j<=nch; j++) 
     if(maxmax < ftolpl){      m[nrl][j]=m[nrl][j-1]+nlay;
       return prlim;    
     }    for (i=nrl+1; i<=nrh; i++) {
   }      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
 }      for (j=ncl+1; j<=nch; j++) 
         m[i][j]=m[i][j-1]+nlay;
 /*************** transition probabilities ***************/    }
     return m; 
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
 {             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
   double s1, s2;    */
   /*double t34;*/  }
   int i,j,j1, nc, ii, jj;  
   /*************************free ma3x ************************/
     for(i=1; i<= nlstate; i++){  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
     for(j=1; j<i;j++){  {
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
         /*s2 += param[i][j][nc]*cov[nc];*/    free((FREE_ARG)(m[nrl]+ncl-NR_END));
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    free((FREE_ARG)(m+nrl-NR_END));
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/  }
       }  
       ps[i][j]=s2;  /*************** function subdirf ***********/
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  char *subdirf(char fileres[])
     }  {
     for(j=i+1; j<=nlstate+ndeath;j++){    /* Caution optionfilefiname is hidden */
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    strcpy(tmpout,optionfilefiname);
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    strcat(tmpout,"/"); /* Add to the right */
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    strcat(tmpout,fileres);
       }    return tmpout;
       ps[i][j]=(s2);  }
     }  
   }  /*************** function subdirf2 ***********/
     /*ps[3][2]=1;*/  char *subdirf2(char fileres[], char *preop)
   {
   for(i=1; i<= nlstate; i++){    
      s1=0;    /* Caution optionfilefiname is hidden */
     for(j=1; j<i; j++)    strcpy(tmpout,optionfilefiname);
       s1+=exp(ps[i][j]);    strcat(tmpout,"/");
     for(j=i+1; j<=nlstate+ndeath; j++)    strcat(tmpout,preop);
       s1+=exp(ps[i][j]);    strcat(tmpout,fileres);
     ps[i][i]=1./(s1+1.);    return tmpout;
     for(j=1; j<i; j++)  }
       ps[i][j]= exp(ps[i][j])*ps[i][i];  
     for(j=i+1; j<=nlstate+ndeath; j++)  /*************** function subdirf3 ***********/
       ps[i][j]= exp(ps[i][j])*ps[i][i];  char *subdirf3(char fileres[], char *preop, char *preop2)
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */  {
   } /* end i */    
     /* Caution optionfilefiname is hidden */
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    strcpy(tmpout,optionfilefiname);
     for(jj=1; jj<= nlstate+ndeath; jj++){    strcat(tmpout,"/");
       ps[ii][jj]=0;    strcat(tmpout,preop);
       ps[ii][ii]=1;    strcat(tmpout,preop2);
     }    strcat(tmpout,fileres);
   }    return tmpout;
   }
   
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){  /***************** f1dim *************************/
     for(jj=1; jj<= nlstate+ndeath; jj++){  extern int ncom; 
      printf("%lf ",ps[ii][jj]);  extern double *pcom,*xicom;
    }  extern double (*nrfunc)(double []); 
     printf("\n ");   
     }  double f1dim(double x) 
     printf("\n ");printf("%lf ",cov[2]);*/  { 
 /*    int j; 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    double f;
   goto end;*/    double *xt; 
     return ps;   
 }    xt=vector(1,ncom); 
     for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
 /**************** Product of 2 matrices ******************/    f=(*nrfunc)(xt); 
     free_vector(xt,1,ncom); 
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)    return f; 
 {  } 
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */  /*****************brent *************************/
   /* in, b, out are matrice of pointers which should have been initialized  double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
      before: only the contents of out is modified. The function returns  { 
      a pointer to pointers identical to out */    int iter; 
   long i, j, k;    double a,b,d,etemp;
   for(i=nrl; i<= nrh; i++)    double fu,fv,fw,fx;
     for(k=ncolol; k<=ncoloh; k++)    double ftemp;
       for(j=ncl,out[i][k]=0.; j<=nch; j++)    double p,q,r,tol1,tol2,u,v,w,x,xm; 
         out[i][k] +=in[i][j]*b[j][k];    double e=0.0; 
    
   return out;    a=(ax < cx ? ax : cx); 
 }    b=(ax > cx ? ax : cx); 
     x=w=v=bx; 
     fw=fv=fx=(*f)(x); 
 /************* Higher Matrix Product ***************/    for (iter=1;iter<=ITMAX;iter++) { 
       xm=0.5*(a+b); 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
 {      /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month      printf(".");fflush(stdout);
      duration (i.e. until      fprintf(ficlog,".");fflush(ficlog);
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.  #ifdef DEBUG
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step      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);
      (typically every 2 years instead of every month which is too big).      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);
      Model is determined by parameters x and covariates have to be      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
      included manually here.  #endif
       if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
      */        *xmin=x; 
         return fx; 
   int i, j, d, h, k;      } 
   double **out, cov[NCOVMAX];      ftemp=fu;
   double **newm;      if (fabs(e) > tol1) { 
         r=(x-w)*(fx-fv); 
   /* Hstepm could be zero and should return the unit matrix */        q=(x-v)*(fx-fw); 
   for (i=1;i<=nlstate+ndeath;i++)        p=(x-v)*q-(x-w)*r; 
     for (j=1;j<=nlstate+ndeath;j++){        q=2.0*(q-r); 
       oldm[i][j]=(i==j ? 1.0 : 0.0);        if (q > 0.0) p = -p; 
       po[i][j][0]=(i==j ? 1.0 : 0.0);        q=fabs(q); 
     }        etemp=e; 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */        e=d; 
   for(h=1; h <=nhstepm; h++){        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
     for(d=1; d <=hstepm; d++){          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
       newm=savm;        else { 
       /* Covariates have to be included here again */          d=p/q; 
       cov[1]=1.;          u=x+d; 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;          if (u-a < tol2 || b-u < tol2) 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];            d=SIGN(tol1,xm-x); 
       for (k=1; k<=cptcovage;k++)        } 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];      } else { 
       for (k=1; k<=cptcovprod;k++)        d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];      } 
       u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
       fu=(*f)(u); 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/      if (fu <= fx) { 
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/        if (u >= x) a=x; else b=x; 
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,        SHFT(v,w,x,u) 
                    pmij(pmmij,cov,ncovmodel,x,nlstate));          SHFT(fv,fw,fx,fu) 
       savm=oldm;          } else { 
       oldm=newm;            if (u < x) a=u; else b=u; 
     }            if (fu <= fw || w == x) { 
     for(i=1; i<=nlstate+ndeath; i++)              v=w; 
       for(j=1;j<=nlstate+ndeath;j++) {              w=u; 
         po[i][j][h]=newm[i][j];              fv=fw; 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);              fw=fu; 
          */            } else if (fu <= fv || v == x || v == w) { 
       }              v=u; 
   } /* end h */              fv=fu; 
   return po;            } 
 }          } 
     } 
     nrerror("Too many iterations in brent"); 
 /*************** log-likelihood *************/    *xmin=x; 
 double func( double *x)    return fx; 
 {  } 
   int i, ii, j, k, mi, d, kk;  
   double l, ll[NLSTATEMAX], cov[NCOVMAX];  /****************** mnbrak ***********************/
   double **out;  
   double sw; /* Sum of weights */  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
   double lli; /* Individual log likelihood */              double (*func)(double)) 
   long ipmx;  { 
   /*extern weight */    double ulim,u,r,q, dum;
   /* We are differentiating ll according to initial status */    double fu; 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/   
   /*for(i=1;i<imx;i++)    *fa=(*func)(*ax); 
     printf(" %d\n",s[4][i]);    *fb=(*func)(*bx); 
   */    if (*fb > *fa) { 
   cov[1]=1.;      SHFT(dum,*ax,*bx,dum) 
         SHFT(dum,*fb,*fa,dum) 
   for(k=1; k<=nlstate; k++) ll[k]=0.;        } 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){    *cx=(*bx)+GOLD*(*bx-*ax); 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];    *fc=(*func)(*cx); 
     for(mi=1; mi<= wav[i]-1; mi++){    while (*fb > *fc) { 
       for (ii=1;ii<=nlstate+ndeath;ii++)      r=(*bx-*ax)*(*fb-*fc); 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);      q=(*bx-*cx)*(*fb-*fa); 
       for(d=0; d<dh[mi][i]; d++){      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
         newm=savm;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;      ulim=(*bx)+GLIMIT*(*cx-*bx); 
         for (kk=1; kk<=cptcovage;kk++) {      if ((*bx-u)*(u-*cx) > 0.0) { 
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];        fu=(*func)(u); 
         }      } else if ((*cx-u)*(u-ulim) > 0.0) { 
                fu=(*func)(u); 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,        if (fu < *fc) { 
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
         savm=oldm;            SHFT(*fb,*fc,fu,(*func)(u)) 
         oldm=newm;            } 
              } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
                u=ulim; 
       } /* end mult */        fu=(*func)(u); 
            } else { 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);        u=(*cx)+GOLD*(*cx-*bx); 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/        fu=(*func)(u); 
       ipmx +=1;      } 
       sw += weight[i];      SHFT(*ax,*bx,*cx,u) 
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;        SHFT(*fa,*fb,*fc,fu) 
     } /* end of wave */        } 
   } /* end of individual */  } 
   
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];  /*************** linmin ************************/
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */  
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */  int ncom; 
   return -l;  double *pcom,*xicom;
 }  double (*nrfunc)(double []); 
    
   void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
 /*********** Maximum Likelihood Estimation ***************/  { 
     double brent(double ax, double bx, double cx, 
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))                 double (*f)(double), double tol, double *xmin); 
 {    double f1dim(double x); 
   int i,j, iter;    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
   double **xi,*delti;                double *fc, double (*func)(double)); 
   double fret;    int j; 
   xi=matrix(1,npar,1,npar);    double xx,xmin,bx,ax; 
   for (i=1;i<=npar;i++)    double fx,fb,fa;
     for (j=1;j<=npar;j++)   
       xi[i][j]=(i==j ? 1.0 : 0.0);    ncom=n; 
   printf("Powell\n");    pcom=vector(1,n); 
   powell(p,xi,npar,ftol,&iter,&fret,func);    xicom=vector(1,n); 
     nrfunc=func; 
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));    for (j=1;j<=n;j++) { 
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f ",iter,func(p));      pcom[j]=p[j]; 
       xicom[j]=xi[j]; 
 }    } 
     ax=0.0; 
 /**** Computes Hessian and covariance matrix ***/    xx=1.0; 
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
 {    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   double  **a,**y,*x,pd;  #ifdef DEBUG
   double **hess;    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   int i, j,jk;    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   int *indx;  #endif
     for (j=1;j<=n;j++) { 
   double hessii(double p[], double delta, int theta, double delti[]);      xi[j] *= xmin; 
   double hessij(double p[], double delti[], int i, int j);      p[j] += xi[j]; 
   void lubksb(double **a, int npar, int *indx, double b[]) ;    } 
   void ludcmp(double **a, int npar, int *indx, double *d) ;    free_vector(xicom,1,n); 
     free_vector(pcom,1,n); 
   hess=matrix(1,npar,1,npar);  } 
   
   printf("\nCalculation of the hessian matrix. Wait...\n");  char *asc_diff_time(long time_sec, char ascdiff[])
   for (i=1;i<=npar;i++){  {
     printf("%d",i);fflush(stdout);    long sec_left, days, hours, minutes;
     hess[i][i]=hessii(p,ftolhess,i,delti);    days = (time_sec) / (60*60*24);
     /*printf(" %f ",p[i]);*/    sec_left = (time_sec) % (60*60*24);
     /*printf(" %lf ",hess[i][i]);*/    hours = (sec_left) / (60*60) ;
   }    sec_left = (sec_left) %(60*60);
      minutes = (sec_left) /60;
   for (i=1;i<=npar;i++) {    sec_left = (sec_left) % (60);
     for (j=1;j<=npar;j++)  {    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
       if (j>i) {    return ascdiff;
         printf(".%d%d",i,j);fflush(stdout);  }
         hess[i][j]=hessij(p,delti,i,j);  
         hess[j][i]=hess[i][j];      /*************** powell ************************/
         /*printf(" %lf ",hess[i][j]);*/  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
       }              double (*func)(double [])) 
     }  { 
   }    void linmin(double p[], double xi[], int n, double *fret, 
   printf("\n");                double (*func)(double [])); 
     int i,ibig,j; 
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");    double del,t,*pt,*ptt,*xit;
      double fp,fptt;
   a=matrix(1,npar,1,npar);    double *xits;
   y=matrix(1,npar,1,npar);    int niterf, itmp;
   x=vector(1,npar);  
   indx=ivector(1,npar);    pt=vector(1,n); 
   for (i=1;i<=npar;i++)    ptt=vector(1,n); 
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];    xit=vector(1,n); 
   ludcmp(a,npar,indx,&pd);    xits=vector(1,n); 
     *fret=(*func)(p); 
   for (j=1;j<=npar;j++) {    for (j=1;j<=n;j++) pt[j]=p[j]; 
     for (i=1;i<=npar;i++) x[i]=0;    for (*iter=1;;++(*iter)) { 
     x[j]=1;      fp=(*fret); 
     lubksb(a,npar,indx,x);      ibig=0; 
     for (i=1;i<=npar;i++){      del=0.0; 
       matcov[i][j]=x[i];      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);
   printf("\n#Hessian matrix#\n");      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
   for (i=1;i<=npar;i++) {      */
     for (j=1;j<=npar;j++) {     for (i=1;i<=n;i++) {
       printf("%.3e ",hess[i][j]);        printf(" %d %.12f",i, p[i]);
     }        fprintf(ficlog," %d %.12lf",i, p[i]);
     printf("\n");        fprintf(ficrespow," %.12lf", p[i]);
   }      }
       printf("\n");
   /* Recompute Inverse */      fprintf(ficlog,"\n");
   for (i=1;i<=npar;i++)      fprintf(ficrespow,"\n");fflush(ficrespow);
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];      if(*iter <=3){
   ludcmp(a,npar,indx,&pd);        tm = *localtime(&curr_time.tv_sec);
         strcpy(strcurr,asctime(&tm));
   /*  printf("\n#Hessian matrix recomputed#\n");  /*       asctime_r(&tm,strcurr); */
         forecast_time=curr_time; 
   for (j=1;j<=npar;j++) {        itmp = strlen(strcurr);
     for (i=1;i<=npar;i++) x[i]=0;        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
     x[j]=1;          strcurr[itmp-1]='\0';
     lubksb(a,npar,indx,x);        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
     for (i=1;i<=npar;i++){        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
       y[i][j]=x[i];        for(niterf=10;niterf<=30;niterf+=10){
       printf("%.3e ",y[i][j]);          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
     }          tmf = *localtime(&forecast_time.tv_sec);
     printf("\n");  /*      asctime_r(&tmf,strfor); */
   }          strcpy(strfor,asctime(&tmf));
   */          itmp = strlen(strfor);
           if(strfor[itmp-1]=='\n')
   free_matrix(a,1,npar,1,npar);          strfor[itmp-1]='\0';
   free_matrix(y,1,npar,1,npar);          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);
   free_vector(x,1,npar);          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);
   free_ivector(indx,1,npar);        }
   free_matrix(hess,1,npar,1,npar);      }
       for (i=1;i<=n;i++) { 
         for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
 }        fptt=(*fret); 
   #ifdef DEBUG
 /*************** hessian matrix ****************/        printf("fret=%lf \n",*fret);
 double hessii( double x[], double delta, int theta, double delti[])        fprintf(ficlog,"fret=%lf \n",*fret);
 {  #endif
   int i;        printf("%d",i);fflush(stdout);
   int l=1, lmax=20;        fprintf(ficlog,"%d",i);fflush(ficlog);
   double k1,k2;        linmin(p,xit,n,fret,func); 
   double p2[NPARMAX+1];        if (fabs(fptt-(*fret)) > del) { 
   double res;          del=fabs(fptt-(*fret)); 
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;          ibig=i; 
   double fx;        } 
   int k=0,kmax=10;  #ifdef DEBUG
   double l1;        printf("%d %.12e",i,(*fret));
         fprintf(ficlog,"%d %.12e",i,(*fret));
   fx=func(x);        for (j=1;j<=n;j++) {
   for (i=1;i<=npar;i++) p2[i]=x[i];          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   for(l=0 ; l <=lmax; l++){          printf(" x(%d)=%.12e",j,xit[j]);
     l1=pow(10,l);          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
     delts=delt;        }
     for(k=1 ; k <kmax; k=k+1){        for(j=1;j<=n;j++) {
       delt = delta*(l1*k);          printf(" p=%.12e",p[j]);
       p2[theta]=x[theta] +delt;          fprintf(ficlog," p=%.12e",p[j]);
       k1=func(p2)-fx;        }
       p2[theta]=x[theta]-delt;        printf("\n");
       k2=func(p2)-fx;        fprintf(ficlog,"\n");
       /*res= (k1-2.0*fx+k2)/delt/delt; */  #endif
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */      } 
            if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
 #ifdef DEBUG  #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);        int k[2],l;
 #endif        k[0]=1;
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */        k[1]=-1;
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){        printf("Max: %.12e",(*func)(p));
         k=kmax;        fprintf(ficlog,"Max: %.12e",(*func)(p));
       }        for (j=1;j<=n;j++) {
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */          printf(" %.12e",p[j]);
         k=kmax; l=lmax*10.;          fprintf(ficlog," %.12e",p[j]);
       }        }
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){        printf("\n");
         delts=delt;        fprintf(ficlog,"\n");
       }        for(l=0;l<=1;l++) {
     }          for (j=1;j<=n;j++) {
   }            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
   delti[theta]=delts;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
   return res;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
            }
 }          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
           fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
 double hessij( double x[], double delti[], int thetai,int thetaj)        }
 {  #endif
   int i;  
   int l=1, l1, lmax=20;  
   double k1,k2,k3,k4,res,fx;        free_vector(xit,1,n); 
   double p2[NPARMAX+1];        free_vector(xits,1,n); 
   int k;        free_vector(ptt,1,n); 
         free_vector(pt,1,n); 
   fx=func(x);        return; 
   for (k=1; k<=2; k++) {      } 
     for (i=1;i<=npar;i++) p2[i]=x[i];      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
     p2[thetai]=x[thetai]+delti[thetai]/k;      for (j=1;j<=n;j++) { 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;        ptt[j]=2.0*p[j]-pt[j]; 
     k1=func(p2)-fx;        xit[j]=p[j]-pt[j]; 
          pt[j]=p[j]; 
     p2[thetai]=x[thetai]+delti[thetai]/k;      } 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;      fptt=(*func)(ptt); 
     k2=func(p2)-fx;      if (fptt < fp) { 
          t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
     p2[thetai]=x[thetai]-delti[thetai]/k;        if (t < 0.0) { 
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          linmin(p,xit,n,fret,func); 
     k3=func(p2)-fx;          for (j=1;j<=n;j++) { 
              xi[j][ibig]=xi[j][n]; 
     p2[thetai]=x[thetai]-delti[thetai]/k;            xi[j][n]=xit[j]; 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;          }
     k4=func(p2)-fx;  #ifdef DEBUG
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
 #ifdef DEBUG          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);          for(j=1;j<=n;j++){
 #endif            printf(" %.12e",xit[j]);
   }            fprintf(ficlog," %.12e",xit[j]);
   return res;          }
 }          printf("\n");
           fprintf(ficlog,"\n");
 /************** Inverse of matrix **************/  #endif
 void ludcmp(double **a, int n, int *indx, double *d)        }
 {      } 
   int i,imax,j,k;    } 
   double big,dum,sum,temp;  } 
   double *vv;  
    /**** Prevalence limit (stable or period prevalence)  ****************/
   vv=vector(1,n);  
   *d=1.0;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
   for (i=1;i<=n;i++) {  {
     big=0.0;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     for (j=1;j<=n;j++)       matrix by transitions matrix until convergence is reached */
       if ((temp=fabs(a[i][j])) > big) big=temp;  
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");    int i, ii,j,k;
     vv[i]=1.0/big;    double min, max, maxmin, maxmax,sumnew=0.;
   }    double **matprod2();
   for (j=1;j<=n;j++) {    double **out, cov[NCOVMAX], **pmij();
     for (i=1;i<j;i++) {    double **newm;
       sum=a[i][j];    double agefin, delaymax=50 ; /* Max number of years to converge */
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;    for (ii=1;ii<=nlstate+ndeath;ii++)
     }      for (j=1;j<=nlstate+ndeath;j++){
     big=0.0;        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for (i=j;i<=n;i++) {      }
       sum=a[i][j];  
       for (k=1;k<j;k++)     cov[1]=1.;
         sum -= a[i][k]*a[k][j];   
       a[i][j]=sum;   /* Even if hstepm = 1, at least one multiplication by the unit matrix */
       if ( (dum=vv[i]*fabs(sum)) >= big) {    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
         big=dum;      newm=savm;
         imax=i;      /* Covariates have to be included here again */
       }       cov[2]=agefin;
     }    
     if (j != imax) {        for (k=1; k<=cptcovn;k++) {
       for (k=1;k<=n;k++) {          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
         dum=a[imax][k];          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
         a[imax][k]=a[j][k];        }
         a[j][k]=dum;        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       }        for (k=1; k<=cptcovprod;k++)
       *d = -(*d);          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       vv[imax]=vv[j];  
     }        /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/
     indx[j]=imax;        /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/
     if (a[j][j] == 0.0) a[j][j]=TINY;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     if (j != n) {      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
       dum=1.0/(a[j][j]);  
       for (i=j+1;i<=n;i++) a[i][j] *= dum;      savm=oldm;
     }      oldm=newm;
   }      maxmax=0.;
   free_vector(vv,1,n);  /* Doesn't work */      for(j=1;j<=nlstate;j++){
 ;        min=1.;
 }        max=0.;
         for(i=1; i<=nlstate; i++) {
 void lubksb(double **a, int n, int *indx, double b[])          sumnew=0;
 {          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
   int i,ii=0,ip,j;          prlim[i][j]= newm[i][j]/(1-sumnew);
   double sum;          max=FMAX(max,prlim[i][j]);
            min=FMIN(min,prlim[i][j]);
   for (i=1;i<=n;i++) {        }
     ip=indx[i];        maxmin=max-min;
     sum=b[ip];        maxmax=FMAX(maxmax,maxmin);
     b[ip]=b[i];      }
     if (ii)      if(maxmax < ftolpl){
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];        return prlim;
     else if (sum) ii=i;      }
     b[i]=sum;    }
   }  }
   for (i=n;i>=1;i--) {  
     sum=b[i];  /*************** transition probabilities ***************/ 
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];  
     b[i]=sum/a[i][i];  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
   }  {
 }    double s1, s2;
     /*double t34;*/
 /************ Frequencies ********************/    int i,j,j1, nc, ii, jj;
 void  freqsummary(char fileres[], int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2)  
 {  /* Some frequencies */      for(i=1; i<= nlstate; i++){
          for(j=1; j<i;j++){
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   double ***freq; /* Frequencies */            /*s2 += param[i][j][nc]*cov[nc];*/
   double *pp;            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   double pos, k2, dateintsum=0,k2cpt=0;  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
   FILE *ficresp;          }
   char fileresp[FILENAMELENGTH];          ps[i][j]=s2;
   /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
   pp=vector(1,nlstate);        }
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        for(j=i+1; j<=nlstate+ndeath;j++){
   strcpy(fileresp,"p");          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   strcat(fileresp,fileres);            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
   if((ficresp=fopen(fileresp,"w"))==NULL) {  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
     printf("Problem with prevalence resultfile: %s\n", fileresp);          }
     exit(0);          ps[i][j]=s2;
   }        }
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);      }
   j1=0;      /*ps[3][2]=1;*/
       
   j=cptcoveff;      for(i=1; i<= nlstate; i++){
   if (cptcovn<1) {j=1;ncodemax[1]=1;}        s1=0;
         for(j=1; j<i; j++)
   for(k1=1; k1<=j;k1++){          s1+=exp(ps[i][j]);
    for(i1=1; i1<=ncodemax[k1];i1++){        for(j=i+1; j<=nlstate+ndeath; j++)
        j1++;          s1+=exp(ps[i][j]);
        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);        ps[i][i]=1./(s1+1.);
          scanf("%d", i);*/        for(j=1; j<i; j++)
         for (i=-1; i<=nlstate+ndeath; i++)            ps[i][j]= exp(ps[i][j])*ps[i][i];
          for (jk=-1; jk<=nlstate+ndeath; jk++)          for(j=i+1; j<=nlstate+ndeath; j++)
            for(m=agemin; m <= agemax+3; m++)          ps[i][j]= exp(ps[i][j])*ps[i][i];
              freq[i][jk][m]=0;        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
       } /* end i */
         dateintsum=0;      
         k2cpt=0;      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
        for (i=1; i<=imx; i++) {        for(jj=1; jj<= nlstate+ndeath; jj++){
          bool=1;          ps[ii][jj]=0;
          if  (cptcovn>0) {          ps[ii][ii]=1;
            for (z1=1; z1<=cptcoveff; z1++)        }
              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])      }
                bool=0;      
          }  
          if (bool==1) {  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
            for(m=firstpass; m<=lastpass; m++){  /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
              k2=anint[m][i]+(mint[m][i]/12.);  /*         printf("ddd %lf ",ps[ii][jj]); */
              if ((k2>=dateprev1) && (k2<=dateprev2)) {  /*       } */
                if(agev[m][i]==0) agev[m][i]=agemax+1;  /*       printf("\n "); */
                if(agev[m][i]==1) agev[m][i]=agemax+2;  /*        } */
                freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];  /*        printf("\n ");printf("%lf ",cov[2]); */
                freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];         /*
                if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {        for(i=1; i<= npar; i++) printf("%f ",x[i]);
                  dateintsum=dateintsum+k2;        goto end;*/
                  k2cpt++;      return ps;
                }  }
   
              }  /**************** Product of 2 matrices ******************/
            }  
          }  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
        }  {
         if  (cptcovn>0) {    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
          fprintf(ficresp, "\n#********** Variable ");       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    /* in, b, out are matrice of pointers which should have been initialized 
        fprintf(ficresp, "**********\n#");       before: only the contents of out is modified. The function returns
         }       a pointer to pointers identical to out */
        for(i=1; i<=nlstate;i++)    long i, j, k;
          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    for(i=nrl; i<= nrh; i++)
        fprintf(ficresp, "\n");      for(k=ncolol; k<=ncoloh; k++)
                for(j=ncl,out[i][k]=0.; j<=nch; j++)
   for(i=(int)agemin; i <= (int)agemax+3; i++){          out[i][k] +=in[i][j]*b[j][k];
     if(i==(int)agemax+3)  
       printf("Total");    return out;
     else  }
       printf("Age %d", i);  
     for(jk=1; jk <=nlstate ; jk++){  
       for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)  /************* Higher Matrix Product ***************/
         pp[jk] += freq[jk][m][i];  
     }  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
     for(jk=1; jk <=nlstate ; jk++){  {
       for(m=-1, pos=0; m <=0 ; m++)    /* Computes the transition matrix starting at age 'age' over 
         pos += freq[jk][m][i];       'nhstepm*hstepm*stepm' months (i.e. until
       if(pp[jk]>=1.e-10)       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
         printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);       nhstepm*hstepm matrices. 
       else       Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
         printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);       (typically every 2 years instead of every month which is too big 
     }       for the memory).
        Model is determined by parameters x and covariates have to be 
      for(jk=1; jk <=nlstate ; jk++){       included manually here. 
       for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  
         pp[jk] += freq[jk][m][i];       */
      }  
     int i, j, d, h, k;
     for(jk=1,pos=0; jk <=nlstate ; jk++)    double **out, cov[NCOVMAX];
       pos += pp[jk];    double **newm;
     for(jk=1; jk <=nlstate ; jk++){  
       if(pos>=1.e-5)    /* Hstepm could be zero and should return the unit matrix */
         printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);    for (i=1;i<=nlstate+ndeath;i++)
       else      for (j=1;j<=nlstate+ndeath;j++){
         printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);        oldm[i][j]=(i==j ? 1.0 : 0.0);
       if( i <= (int) agemax){        po[i][j][0]=(i==j ? 1.0 : 0.0);
         if(pos>=1.e-5){      }
           fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
           probs[i][jk][j1]= pp[jk]/pos;    for(h=1; h <=nhstepm; h++){
           /*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(d=1; d <=hstepm; d++){
         }        newm=savm;
       else        /* Covariates have to be included here again */
           fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);        cov[1]=1.;
       }        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
     }        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     for(jk=-1; jk <=nlstate+ndeath; jk++)        for (k=1; k<=cptcovage;k++)
       for(m=-1; m <=nlstate+ndeath; m++)          cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
         if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);        for (k=1; k<=cptcovprod;k++)
     if(i <= (int) agemax)          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       fprintf(ficresp,"\n");  
     printf("\n");  
     }        /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/
     }        /*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, 
   dateintmean=dateintsum/k2cpt;                     pmij(pmmij,cov,ncovmodel,x,nlstate));
          savm=oldm;
   fclose(ficresp);        oldm=newm;
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      }
   free_vector(pp,1,nlstate);      for(i=1; i<=nlstate+ndeath; i++)
         for(j=1;j<=nlstate+ndeath;j++) {
   /* End of Freq */          po[i][j][h]=newm[i][j];
 }          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
            */
 /************ Prevalence ********************/        }
 void prevalence(int agemin, int agemax, int **s, double **agev, int nlstate, int imx, int *Tvar, int **nbcode, int *ncodemax,double **mint,double **anint, double dateprev1,double dateprev2, double calagedate)    } /* end h */
 {  /* Some frequencies */    return po;
    }
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;  
   double ***freq; /* Frequencies */  
   double *pp;  /*************** log-likelihood *************/
   double pos, k2;  double func( double *x)
   {
   pp=vector(1,nlstate);    int i, ii, j, k, mi, d, kk;
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);    double l, ll[NLSTATEMAX], cov[NCOVMAX];
      double **out;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);    double sw; /* Sum of weights */
   j1=0;    double lli; /* Individual log likelihood */
      int s1, s2;
   j=cptcoveff;    double bbh, survp;
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    long ipmx;
      /*extern weight */
  for(k1=1; k1<=j;k1++){    /* We are differentiating ll according to initial status */
     for(i1=1; i1<=ncodemax[k1];i1++){    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       j1++;    /*for(i=1;i<imx;i++) 
        printf(" %d\n",s[4][i]);
       for (i=-1; i<=nlstate+ndeath; i++)      */
         for (jk=-1; jk<=nlstate+ndeath; jk++)      cov[1]=1.;
           for(m=agemin; m <= agemax+3; m++)  
             freq[i][jk][m]=0;    for(k=1; k<=nlstate; k++) ll[k]=0.;
        
       for (i=1; i<=imx; i++) {    if(mle==1){
         bool=1;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         if  (cptcovn>0) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           for (z1=1; z1<=cptcoveff; z1++)        for(mi=1; mi<= wav[i]-1; mi++){
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])          for (ii=1;ii<=nlstate+ndeath;ii++)
               bool=0;            for (j=1;j<=nlstate+ndeath;j++){
         }              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         if (bool==1) {              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           for(m=firstpass; m<=lastpass; m++){            }
             k2=anint[m][i]+(mint[m][i]/12.);          for(d=0; d<dh[mi][i]; d++){
             if ((k2>=dateprev1) && (k2<=dateprev2)) {            newm=savm;
               if(agev[m][i]==0) agev[m][i]=agemax+1;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
               if(agev[m][i]==1) agev[m][i]=agemax+2;            for (kk=1; kk<=cptcovage;kk++) {
               freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-1/12.)] += weight[i];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
               freq[s[m][i]][s[m+1][i]][(int)(agemax+3+1)] += weight[i];              }
             }            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 */
         for(i=(int)agemin; i <= (int)agemax+3; i++){        
           for(jk=1; jk <=nlstate ; jk++){          /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
             for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          /* But now since version 0.9 we anticipate for bias at large stepm.
               pp[jk] += freq[jk][m][i];           * 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 
           for(jk=1; jk <=nlstate ; jk++){           * the nearest (and in case of equal distance, to the lowest) interval but now
             for(m=-1, pos=0; m <=0 ; m++)           * we keep into memory the bias bh[mi][i] and also the previous matrix product
             pos += freq[jk][m][i];           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
         }           * probability in order to take into account the bias as a fraction of the way
                   * from savm to out if bh is negative or even beyond if bh is positive. bh varies
          for(jk=1; jk <=nlstate ; jk++){           * -stepm/2 to stepm/2 .
            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)           * For stepm=1 the results are the same as for previous versions of Imach.
              pp[jk] += freq[jk][m][i];           * For stepm > 1 the results are less biased than in previous versions. 
          }           */
                    s1=s[mw[mi][i]][i];
          for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];          s2=s[mw[mi+1][i]][i];
           bbh=(double)bh[mi][i]/(double)stepm; 
          for(jk=1; jk <=nlstate ; jk++){                    /* bias bh is positive if real duration
            if( i <= (int) agemax){           * is higher than the multiple of stepm and negative otherwise.
              if(pos>=1.e-5){           */
                probs[i][jk][j1]= pp[jk]/pos;          /* lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2]));*/
              }          if( s2 > nlstate){ 
            }            /* i.e. if s2 is a death state and if the date of death is known 
          }               then the contribution to the likelihood is the probability to 
                         die between last step unit time and current  step unit time, 
         }               which is also equal to probability to die before dh 
     }               minus probability to die before dh-stepm . 
   }               In version up to 0.92 likelihood was computed
            as if date of death was unknown. Death was treated as any other
            health state: the date of the interview describes the actual state
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);          and not the date of a change in health state. The former idea was
   free_vector(pp,1,nlstate);          to consider that at each interview the state was recorded
            (healthy, disable or death) and IMaCh was corrected; but when we
 }  /* End of Freq */          introduced the exact date of death then we should have modified
           the contribution of an exact death to the likelihood. This new
 /************* Waves Concatenation ***************/          contribution is smaller and very dependent of the step unit
           stepm. It is no more the probability to die between last interview
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)          and month of death but the probability to survive from last
 {          interview up to one month before death multiplied by the
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.          probability to die within a month. Thanks to Chris
      Death is a valid wave (if date is known).          Jackson for correcting this bug.  Former versions increased
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          mortality artificially. The bad side is that we add another loop
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          which slows down the processing. The difference can be up to 10%
      and mw[mi+1][i]. dh depends on stepm.          lower mortality.
      */            */
             lli=log(out[s1][s2] - savm[s1][s2]);
   int i, mi, m;  
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;  
      double sum=0., jmean=0.;*/          } else if  (s2==-2) {
             for (j=1,survp=0. ; j<=nlstate; j++) 
   int j, k=0,jk, ju, jl;              survp += out[s1][j];
   double sum=0.;            lli= survp;
   jmin=1e+5;          }
   jmax=-1;          
   jmean=0.;          else if  (s2==-4) {
   for(i=1; i<=imx; i++){            for (j=3,survp=0. ; j<=nlstate; j++) 
     mi=0;              survp += out[s1][j];
     m=firstpass;            lli= survp;
     while(s[m][i] <= nlstate){          }
       if(s[m][i]>=1)          
         mw[++mi][i]=m;          else if  (s2==-5) {
       if(m >=lastpass)            for (j=1,survp=0. ; j<=2; j++) 
         break;              survp += out[s1][j];
       else            lli= survp;
         m++;          }
     }/* end while */  
     if (s[m][i] > nlstate){  
       mi++;     /* Death is another wave */          else{
       /* if(mi==0)  never been interviewed correctly before death */            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
          /* Only death is a correct wave */            /*  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 */
       mw[mi][i]=m;          } 
     }          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
           /*if(lli ==000.0)*/
     wav[i]=mi;          /*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); */
     if(mi==0)          ipmx +=1;
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          sw += weight[i];
   }          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         } /* end of wave */
   for(i=1; i<=imx; i++){      } /* end of individual */
     for(mi=1; mi<wav[i];mi++){    }  else if(mle==2){
       if (stepm <=0)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
         dh[mi][i]=1;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       else{        for(mi=1; mi<= wav[i]-1; mi++){
         if (s[mw[mi+1][i]][i] > nlstate) {          for (ii=1;ii<=nlstate+ndeath;ii++)
           if (agedc[i] < 2*AGESUP) {            for (j=1;j<=nlstate+ndeath;j++){
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           if(j==0) j=1;  /* Survives at least one month after exam */              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           k=k+1;            }
           if (j >= jmax) jmax=j;          for(d=0; d<=dh[mi][i]; d++){
           if (j <= jmin) jmin=j;            newm=savm;
           sum=sum+j;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           /* if (j<10) printf("j=%d num=%d ",j,i); */            for (kk=1; kk<=cptcovage;kk++) {
           }              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         }            }
         else{            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           k=k+1;            savm=oldm;
           if (j >= jmax) jmax=j;            oldm=newm;
           else if (j <= jmin)jmin=j;          } /* end mult */
           /*   if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */        
           sum=sum+j;          s1=s[mw[mi][i]][i];
         }          s2=s[mw[mi+1][i]][i];
         jk= j/stepm;          bbh=(double)bh[mi][i]/(double)stepm; 
         jl= j -jk*stepm;          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
         ju= j -(jk+1)*stepm;          ipmx +=1;
         if(jl <= -ju)          sw += weight[i];
           dh[mi][i]=jk;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
         else        } /* end of wave */
           dh[mi][i]=jk+1;      } /* end of individual */
         if(dh[mi][i]==0)    }  else if(mle==3){  /* exponential inter-extrapolation */
           dh[mi][i]=1; /* At least one step */      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       }        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
     }        for(mi=1; mi<= wav[i]-1; mi++){
   }          for (ii=1;ii<=nlstate+ndeath;ii++)
   jmean=sum/k;            for (j=1;j<=nlstate+ndeath;j++){
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
  }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
 /*********** Tricode ****************************/            }
 void tricode(int *Tvar, int **nbcode, int imx)          for(d=0; d<dh[mi][i]; d++){
 {            newm=savm;
   int Ndum[20],ij=1, k, j, i;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   int cptcode=0;            for (kk=1; kk<=cptcovage;kk++) {
   cptcoveff=0;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
              }
   for (k=0; k<19; k++) Ndum[k]=0;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   for (k=1; k<=7; k++) ncodemax[k]=0;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
             savm=oldm;
   for (j=1; j<=(cptcovn+2*cptcovprod); j++) {            oldm=newm;
     for (i=1; i<=imx; i++) {          } /* end mult */
       ij=(int)(covar[Tvar[j]][i]);        
       Ndum[ij]++;          s1=s[mw[mi][i]][i];
       /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/          s2=s[mw[mi+1][i]][i];
       if (ij > cptcode) cptcode=ij;          bbh=(double)bh[mi][i]/(double)stepm; 
     }          lli= (savm[s1][s2]>1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
           ipmx +=1;
     for (i=0; i<=cptcode; i++) {          sw += weight[i];
       if(Ndum[i]!=0) ncodemax[j]++;          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     }        } /* end of wave */
     ij=1;      } /* end of individual */
     }else if (mle==4){  /* ml=4 no inter-extrapolation */
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
     for (i=1; i<=ncodemax[j]; i++) {        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for (k=0; k<=19; k++) {        for(mi=1; mi<= wav[i]-1; mi++){
         if (Ndum[k] != 0) {          for (ii=1;ii<=nlstate+ndeath;ii++)
           nbcode[Tvar[j]][ij]=k;            for (j=1;j<=nlstate+ndeath;j++){
           ij++;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
         }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
         if (ij > ncodemax[j]) break;            }
       }            for(d=0; d<dh[mi][i]; d++){
     }            newm=savm;
   }              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
             for (kk=1; kk<=cptcovage;kk++) {
  for (k=0; k<19; k++) Ndum[k]=0;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
  for (i=1; i<=ncovmodel-2; i++) {          
       ij=Tvar[i];            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
       Ndum[ij]++;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     }            savm=oldm;
             oldm=newm;
  ij=1;          } /* end mult */
  for (i=1; i<=10; i++) {        
    if((Ndum[i]!=0) && (i<=ncov)){          s1=s[mw[mi][i]][i];
      Tvaraff[ij]=i;          s2=s[mw[mi+1][i]][i];
      ij++;          if( s2 > nlstate){ 
    }            lli=log(out[s1][s2] - savm[s1][s2]);
  }          }else{
              lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     cptcoveff=ij-1;          }
 }          ipmx +=1;
           sw += weight[i];
 /*********** Health Expectancies ****************/          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   /*      printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]); */
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij)        } /* end of wave */
 {      } /* end of individual */
   /* Health expectancies */    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
   int i, j, nhstepm, hstepm, h;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   double age, agelim,hf;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double ***p3mat;        for(mi=1; mi<= wav[i]-1; mi++){
            for (ii=1;ii<=nlstate+ndeath;ii++)
   fprintf(ficreseij,"# Health expectancies\n");            for (j=1;j<=nlstate+ndeath;j++){
   fprintf(ficreseij,"# Age");              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   for(i=1; i<=nlstate;i++)              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(j=1; j<=nlstate;j++)            }
       fprintf(ficreseij," %1d-%1d",i,j);          for(d=0; d<dh[mi][i]; d++){
   fprintf(ficreseij,"\n");            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   hstepm=1*YEARM; /*  Every j years of age (in month) */            for (kk=1; kk<=cptcovage;kk++) {
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
             }
   agelim=AGESUP;          
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
     /* nhstepm age range expressed in number of stepm */                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     nhstepm=(int) rint((agelim-age)*YEARM/stepm);            savm=oldm;
     /* Typically if 20 years = 20*12/6=40 stepm */            oldm=newm;
     if (stepm >= YEARM) hstepm=1;          } /* end mult */
     nhstepm = nhstepm/hstepm;/* Expressed in hstepm, typically 40/4=10 */        
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          s1=s[mw[mi][i]][i];
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          s2=s[mw[mi+1][i]][i];
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */          lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, ij);            ipmx +=1;
           sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
     for(i=1; i<=nlstate;i++)          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
       for(j=1; j<=nlstate;j++)        } /* end of wave */
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm; h++){      } /* end of individual */
           eij[i][j][(int)age] +=p3mat[i][j][h];    } /* End of if */
         }    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
        /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
     hf=1;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
     if (stepm >= YEARM) hf=stepm/YEARM;    return -l;
     fprintf(ficreseij,"%.0f",age );  }
     for(i=1; i<=nlstate;i++)  
       for(j=1; j<=nlstate;j++){  /*************** log-likelihood *************/
         fprintf(ficreseij," %.4f", hf*eij[i][j][(int)age]);  double funcone( double *x)
       }  {
     fprintf(ficreseij,"\n");    /* Same as likeli but slower because of a lot of printf and if */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    int i, ii, j, k, mi, d, kk;
   }    double l, ll[NLSTATEMAX], cov[NCOVMAX];
 }    double **out;
     double lli; /* Individual log likelihood */
 /************ Variance ******************/    double llt;
 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)    int s1, s2;
 {    double bbh, survp;
   /* Variance of health expectancies */    /*extern weight */
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    /* We are differentiating ll according to initial status */
   double **newm;    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   double **dnewm,**doldm;    /*for(i=1;i<imx;i++) 
   int i, j, nhstepm, hstepm, h;      printf(" %d\n",s[4][i]);
   int k, cptcode;    */
   double *xp;    cov[1]=1.;
   double **gp, **gm;  
   double ***gradg, ***trgradg;    for(k=1; k<=nlstate; k++) ll[k]=0.;
   double ***p3mat;  
   double age,agelim;    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int theta;      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       for(mi=1; mi<= wav[i]-1; mi++){
    fprintf(ficresvij,"# Covariances of life expectancies\n");        for (ii=1;ii<=nlstate+ndeath;ii++)
   fprintf(ficresvij,"# Age");          for (j=1;j<=nlstate+ndeath;j++){
   for(i=1; i<=nlstate;i++)            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     for(j=1; j<=nlstate;j++)            savm[ii][j]=(ii==j ? 1.0 : 0.0);
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);          }
   fprintf(ficresvij,"\n");        for(d=0; d<dh[mi][i]; d++){
           newm=savm;
   xp=vector(1,npar);          cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   dnewm=matrix(1,nlstate,1,npar);          for (kk=1; kk<=cptcovage;kk++) {
   doldm=matrix(1,nlstate,1,nlstate);            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
            }
   hstepm=1*YEARM; /* Every year of age */          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
   agelim = AGESUP;          savm=oldm;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */          oldm=newm;
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */        } /* end mult */
     if (stepm >= YEARM) hstepm=1;        
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */        s1=s[mw[mi][i]][i];
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        s2=s[mw[mi+1][i]][i];
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);        bbh=(double)bh[mi][i]/(double)stepm; 
     gp=matrix(0,nhstepm,1,nlstate);        /* bias is positive if real duration
     gm=matrix(0,nhstepm,1,nlstate);         * is higher than the multiple of stepm and negative otherwise.
          */
     for(theta=1; theta <=npar; theta++){        if( s2 > nlstate && (mle <5) ){  /* Jackson */
       for(i=1; i<=npar; i++){ /* Computes gradient */          lli=log(out[s1][s2] - savm[s1][s2]);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);        } else if (mle==1){
       }          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          } else if(mle==2){
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
         } else if(mle==3){  /* exponential inter-extrapolation */
       if (popbased==1) {          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 */
         for(i=1; i<=nlstate;i++)        } else if (mle==4){  /* mle=4 no inter-extrapolation */
           prlim[i][i]=probs[(int)age][i][ij];          lli=log(out[s1][s2]); /* Original formula */
       }        } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
                lli=log(out[s1][s2]); /* Original formula */
       for(j=1; j<= nlstate; j++){        } /* End of if */
         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;
         }  /*       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]); */
       }        if(globpr){
              fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
       for(i=1; i<=npar; i++) /* Computes gradient */   %10.6f %10.6f %10.6f ", \
         xp[i] = x[i] - (i==theta ?delti[theta]:0);                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);                    2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
             llt +=ll[k]*gipmx/gsw;
       if (popbased==1) {            fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
         for(i=1; i<=nlstate;i++)          }
           prlim[i][i]=probs[(int)age][i][ij];          fprintf(ficresilk," %10.6f\n", -llt);
       }        }
       } /* end of wave */
       for(j=1; j<= nlstate; j++){    } /* end of individual */
         for(h=0; h<=nhstepm; h++){    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
         }    if(globpr==0){ /* First time we count the contributions and weights */
       }      gipmx=ipmx;
       gsw=sw;
       for(j=1; j<= nlstate; j++)    }
         for(h=0; h<=nhstepm; h++){    return -l;
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];  }
         }  
     } /* End theta */  
   /*************** function likelione ***********/
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
   {
     for(h=0; h<=nhstepm; h++)    /* This routine should help understanding what is done with 
       for(j=1; j<=nlstate;j++)       the selection of individuals/waves and
         for(theta=1; theta <=npar; theta++)       to check the exact contribution to the likelihood.
           trgradg[h][j][theta]=gradg[h][theta][j];       Plotting could be done.
      */
     for(i=1;i<=nlstate;i++)    int k;
       for(j=1;j<=nlstate;j++)  
         vareij[i][j][(int)age] =0.;    if(*globpri !=0){ /* Just counts and sums, no printings */
     for(h=0;h<=nhstepm;h++){      strcpy(fileresilk,"ilk"); 
       for(k=0;k<=nhstepm;k++){      strcat(fileresilk,fileres);
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);        printf("Problem with resultfile: %s\n", fileresilk);
         for(i=1;i<=nlstate;i++)        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
           for(j=1;j<=nlstate;j++)      }
             vareij[i][j][(int)age] += doldm[i][j];      fprintf(ficresilk, "#individual(line's_record) s1 s2 wave# effective_wave# number_of_matrices_product pij weight -2ln(pij)*weight 0pij_x 0pij_(x-stepm) cumulating_loglikeli_by_health_state(reweighted=-2ll*weightXnumber_of_contribs/sum_of_weights) and_total\n");
       }      fprintf(ficresilk, "#num_i i s1 s2 mi mw dh likeli weight 2wlli out sav ");
     }      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
     h=1;      for(k=1; k<=nlstate; k++) 
     if (stepm >= YEARM) h=stepm/YEARM;        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
     fprintf(ficresvij,"%.0f ",age );      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
     for(i=1; i<=nlstate;i++)    }
       for(j=1; j<=nlstate;j++){  
         fprintf(ficresvij," %.4f", h*vareij[i][j][(int)age]);    *fretone=(*funcone)(p);
       }    if(*globpri !=0){
     fprintf(ficresvij,"\n");      fclose(ficresilk);
     free_matrix(gp,0,nhstepm,1,nlstate);      fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
     free_matrix(gm,0,nhstepm,1,nlstate);      fflush(fichtm); 
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);    } 
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);    return;
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  }
   } /* End age */  
    
   free_vector(xp,1,npar);  /*********** Maximum Likelihood Estimation ***************/
   free_matrix(doldm,1,nlstate,1,npar);  
   free_matrix(dnewm,1,nlstate,1,nlstate);  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
   {
 }    int i,j, iter;
     double **xi;
 /************ Variance of prevlim ******************/    double fret;
 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)    double fretone; /* Only one call to likelihood */
 {    /*  char filerespow[FILENAMELENGTH];*/
   /* Variance of prevalence limit */    xi=matrix(1,npar,1,npar);
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    for (i=1;i<=npar;i++)
   double **newm;      for (j=1;j<=npar;j++)
   double **dnewm,**doldm;        xi[i][j]=(i==j ? 1.0 : 0.0);
   int i, j, nhstepm, hstepm;    printf("Powell\n");  fprintf(ficlog,"Powell\n");
   int k, cptcode;    strcpy(filerespow,"pow"); 
   double *xp;    strcat(filerespow,fileres);
   double *gp, *gm;    if((ficrespow=fopen(filerespow,"w"))==NULL) {
   double **gradg, **trgradg;      printf("Problem with resultfile: %s\n", filerespow);
   double age,agelim;      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
   int theta;    }
        fprintf(ficrespow,"# Powell\n# iter -2*LL");
   fprintf(ficresvpl,"# Standard deviation of prevalences limit\n");    for (i=1;i<=nlstate;i++)
   fprintf(ficresvpl,"# Age");      for(j=1;j<=nlstate+ndeath;j++)
   for(i=1; i<=nlstate;i++)        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       fprintf(ficresvpl," %1d-%1d",i,i);    fprintf(ficrespow,"\n");
   fprintf(ficresvpl,"\n");  
     powell(p,xi,npar,ftol,&iter,&fret,func);
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);    free_matrix(xi,1,npar,1,npar);
   doldm=matrix(1,nlstate,1,nlstate);    fclose(ficrespow);
      printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   hstepm=1*YEARM; /* Every year of age */    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   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;  /**** Computes Hessian and covariance matrix ***/
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
     gradg=matrix(1,npar,1,nlstate);  {
     gp=vector(1,nlstate);    double  **a,**y,*x,pd;
     gm=vector(1,nlstate);    double **hess;
     int i, j,jk;
     for(theta=1; theta <=npar; theta++){    int *indx;
       for(i=1; i<=npar; i++){ /* Computes gradient */  
         xp[i] = x[i] + (i==theta ?delti[theta]:0);    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
       }    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    void lubksb(double **a, int npar, int *indx, double b[]) ;
       for(i=1;i<=nlstate;i++)    void ludcmp(double **a, int npar, int *indx, double *d) ;
         gp[i] = prlim[i][i];    double gompertz(double p[]);
        hess=matrix(1,npar,1,npar);
       for(i=1; i<=npar; i++) /* Computes gradient */  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    printf("\nCalculation of the hessian matrix. Wait...\n");
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
       for(i=1;i<=nlstate;i++)    for (i=1;i<=npar;i++){
         gm[i] = prlim[i][i];      printf("%d",i);fflush(stdout);
       fprintf(ficlog,"%d",i);fflush(ficlog);
       for(i=1;i<=nlstate;i++)     
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
     } /* End theta */      
       /*  printf(" %f ",p[i]);
     trgradg =matrix(1,nlstate,1,npar);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
     }
     for(j=1; j<=nlstate;j++)    
       for(theta=1; theta <=npar; theta++)    for (i=1;i<=npar;i++) {
         trgradg[j][theta]=gradg[theta][j];      for (j=1;j<=npar;j++)  {
         if (j>i) { 
     for(i=1;i<=nlstate;i++)          printf(".%d%d",i,j);fflush(stdout);
       varpl[i][(int)age] =0.;          fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);          hess[i][j]=hessij(p,delti,i,j,func,npar);
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);          
     for(i=1;i<=nlstate;i++)          hess[j][i]=hess[i][j];    
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */          /*printf(" %lf ",hess[i][j]);*/
         }
     fprintf(ficresvpl,"%.0f ",age );      }
     for(i=1; i<=nlstate;i++)    }
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));    printf("\n");
     fprintf(ficresvpl,"\n");    fprintf(ficlog,"\n");
     free_vector(gp,1,nlstate);  
     free_vector(gm,1,nlstate);    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
     free_matrix(gradg,1,npar,1,nlstate);    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
     free_matrix(trgradg,1,nlstate,1,npar);    
   } /* End age */    a=matrix(1,npar,1,npar);
     y=matrix(1,npar,1,npar);
   free_vector(xp,1,npar);    x=vector(1,npar);
   free_matrix(doldm,1,nlstate,1,npar);    indx=ivector(1,npar);
   free_matrix(dnewm,1,nlstate,1,nlstate);    for (i=1;i<=npar;i++)
       for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
 }    ludcmp(a,npar,indx,&pd);
   
 /************ Variance of one-step probabilities  ******************/    for (j=1;j<=npar;j++) {
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij)      for (i=1;i<=npar;i++) x[i]=0;
 {      x[j]=1;
   int i, j;      lubksb(a,npar,indx,x);
   int k=0, cptcode;      for (i=1;i<=npar;i++){ 
   double **dnewm,**doldm;        matcov[i][j]=x[i];
   double *xp;      }
   double *gp, *gm;    }
   double **gradg, **trgradg;  
   double age,agelim, cov[NCOVMAX];    printf("\n#Hessian matrix#\n");
   int theta;    fprintf(ficlog,"\n#Hessian matrix#\n");
   char fileresprob[FILENAMELENGTH];    for (i=1;i<=npar;i++) { 
       for (j=1;j<=npar;j++) { 
   strcpy(fileresprob,"prob");        printf("%.3e ",hess[i][j]);
   strcat(fileresprob,fileres);        fprintf(ficlog,"%.3e ",hess[i][j]);
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {      }
     printf("Problem with resultfile: %s\n", fileresprob);      printf("\n");
   }      fprintf(ficlog,"\n");
   printf("Computing variance of one-step probabilities: result on file '%s' \n",fileresprob);    }
    
     /* Recompute Inverse */
   xp=vector(1,npar);    for (i=1;i<=npar;i++)
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);      for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    ludcmp(a,npar,indx,&pd);
    
   cov[1]=1;    /*  printf("\n#Hessian matrix recomputed#\n");
   for (age=bage; age<=fage; age ++){  
     cov[2]=age;    for (j=1;j<=npar;j++) {
     gradg=matrix(1,npar,1,9);      for (i=1;i<=npar;i++) x[i]=0;
     trgradg=matrix(1,9,1,npar);      x[j]=1;
     gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      lubksb(a,npar,indx,x);
     gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));      for (i=1;i<=npar;i++){ 
            y[i][j]=x[i];
     for(theta=1; theta <=npar; theta++){        printf("%.3e ",y[i][j]);
       for(i=1; i<=npar; i++)        fprintf(ficlog,"%.3e ",y[i][j]);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      }
            printf("\n");
       pmij(pmmij,cov,ncovmodel,xp,nlstate);      fprintf(ficlog,"\n");
        }
       k=0;    */
       for(i=1; i<= (nlstate+ndeath); i++){  
         for(j=1; j<=(nlstate+ndeath);j++){    free_matrix(a,1,npar,1,npar);
            k=k+1;    free_matrix(y,1,npar,1,npar);
           gp[k]=pmmij[i][j];    free_vector(x,1,npar);
         }    free_ivector(indx,1,npar);
       }    free_matrix(hess,1,npar,1,npar);
   
       for(i=1; i<=npar; i++)  
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  }
      
   /*************** hessian matrix ****************/
       pmij(pmmij,cov,ncovmodel,xp,nlstate);  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
       k=0;  {
       for(i=1; i<=(nlstate+ndeath); i++){    int i;
         for(j=1; j<=(nlstate+ndeath);j++){    int l=1, lmax=20;
           k=k+1;    double k1,k2;
           gm[k]=pmmij[i][j];    double p2[NPARMAX+1];
         }    double res;
       }    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
          double fx;
        for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)    int k=0,kmax=10;
            gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];      double l1;
     }  
     fx=func(x);
      for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)    for (i=1;i<=npar;i++) p2[i]=x[i];
       for(theta=1; theta <=npar; theta++)    for(l=0 ; l <=lmax; l++){
       trgradg[j][theta]=gradg[theta][j];      l1=pow(10,l);
        delts=delt;
      matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);      for(k=1 ; k <kmax; k=k+1){
      matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);        delt = delta*(l1*k);
         p2[theta]=x[theta] +delt;
      pmij(pmmij,cov,ncovmodel,x,nlstate);        k1=func(p2)-fx;
         p2[theta]=x[theta]-delt;
      k=0;        k2=func(p2)-fx;
      for(i=1; i<=(nlstate+ndeath); i++){        /*res= (k1-2.0*fx+k2)/delt/delt; */
        for(j=1; j<=(nlstate+ndeath);j++){        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
          k=k+1;        
          gm[k]=pmmij[i][j];  #ifdef DEBUG
         }        printf("%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
      }        fprintf(ficlog,"%d %d k1=%.12e k2=%.12e xk1=%.12e xk2=%.12e delt=%.12e res=%.12e l=%d k=%d,fx=%.12e\n",theta,theta,k1,k2,x[theta]+delt,x[theta]-delt,delt,res, l, k,fx);
        #endif
      /*printf("\n%d ",(int)age);        /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
                  k=kmax;
         }
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
      }*/          k=kmax; l=lmax*10.;
         }
   fprintf(ficresprob,"\n%d ",(int)age);        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
           delts=delt;
   for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){        }
     if (i== 2) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);      }
 if (i== 4) fprintf(ficresprob,"%.3e %.3e ",gm[i],doldm[i][i]);    }
   }    delti[theta]=delts;
     return res; 
     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);  double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
 }  {
  free_vector(xp,1,npar);    int i;
 fclose(ficresprob);    int l=1, l1, lmax=20;
  exit(0);    double k1,k2,k3,k4,res,fx;
 }    double p2[NPARMAX+1];
     int k;
 /***********************************************/  
 /**************** Main Program *****************/    fx=func(x);
 /***********************************************/    for (k=1; k<=2; k++) {
       for (i=1;i<=npar;i++) p2[i]=x[i];
 /*int main(int argc, char *argv[])*/      p2[thetai]=x[thetai]+delti[thetai]/k;
 int main()      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
 {      k1=func(p2)-fx;
     
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;      p2[thetai]=x[thetai]+delti[thetai]/k;
   double agedeb, agefin,hf;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   double agemin=1.e20, agemax=-1.e20;      k2=func(p2)-fx;
     
   double fret;      p2[thetai]=x[thetai]-delti[thetai]/k;
   double **xi,tmp,delta;      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k3=func(p2)-fx;
   double dum; /* Dummy variable */    
   double ***p3mat;      p2[thetai]=x[thetai]-delti[thetai]/k;
   int *indx;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
   char line[MAXLINE], linepar[MAXLINE];      k4=func(p2)-fx;
   char title[MAXLINE];      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH];  #ifdef DEBUG
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], fileresf[FILENAMELENGTH];      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);
   char filerest[FILENAMELENGTH];      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);
   char fileregp[FILENAMELENGTH];  #endif
   char popfile[FILENAMELENGTH];    }
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];    return res;
   int firstobs=1, lastobs=10;  }
   int sdeb, sfin; /* Status at beginning and end */  
   int c,  h , cpt,l;  /************** Inverse of matrix **************/
   int ju,jl, mi;  void ludcmp(double **a, int n, int *indx, double *d) 
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;  { 
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;    int i,imax,j,k; 
   int mobilav=0,popforecast=0;    double big,dum,sum,temp; 
   int hstepm, nhstepm;    double *vv; 
   int *popage;/*boolprev=0 if date and zero if wave*/   
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2;    vv=vector(1,n); 
     *d=1.0; 
   double bage, fage, age, agelim, agebase;    for (i=1;i<=n;i++) { 
   double ftolpl=FTOL;      big=0.0; 
   double **prlim;      for (j=1;j<=n;j++) 
   double *severity;        if ((temp=fabs(a[i][j])) > big) big=temp; 
   double ***param; /* Matrix of parameters */      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
   double  *p;      vv[i]=1.0/big; 
   double **matcov; /* Matrix of covariance */    } 
   double ***delti3; /* Scale */    for (j=1;j<=n;j++) { 
   double *delti; /* Scale */      for (i=1;i<j;i++) { 
   double ***eij, ***vareij;        sum=a[i][j]; 
   double **varpl; /* Variances of prevalence limits by age */        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
   double *epj, vepp;        a[i][j]=sum; 
   double kk1, kk2;      } 
   double *popeffectif,*popcount;      big=0.0; 
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,jprojmean,mprojmean,anprojmean, calagedate;      for (i=j;i<=n;i++) { 
   double yp,yp1,yp2;        sum=a[i][j]; 
         for (k=1;k<j;k++) 
   char version[80]="Imach version 64b, May 2001, INED-EUROREVES ";          sum -= a[i][k]*a[k][j]; 
   char *alph[]={"a","a","b","c","d","e"}, str[4];        a[i][j]=sum; 
         if ( (dum=vv[i]*fabs(sum)) >= big) { 
           big=dum; 
   char z[1]="c", occ;          imax=i; 
 #include <sys/time.h>        } 
 #include <time.h>      } 
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];      if (j != imax) { 
          for (k=1;k<=n;k++) { 
   /* long total_usecs;          dum=a[imax][k]; 
   struct timeval start_time, end_time;          a[imax][k]=a[j][k]; 
            a[j][k]=dum; 
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */        } 
         *d = -(*d); 
         vv[imax]=vv[j]; 
   printf("\nIMACH, Version 0.7");      } 
   printf("\nEnter the parameter file name: ");      indx[j]=imax; 
       if (a[j][j] == 0.0) a[j][j]=TINY; 
 #ifdef windows      if (j != n) { 
   scanf("%s",pathtot);        dum=1.0/(a[j][j]); 
   getcwd(pathcd, size);        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   /*cygwin_split_path(pathtot,path,optionfile);      } 
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    } 
   /* cutv(path,optionfile,pathtot,'\\');*/    free_vector(vv,1,n);  /* Doesn't work */
   ;
 split(pathtot, path,optionfile);  } 
   chdir(path);  
   replace(pathc,path);  void lubksb(double **a, int n, int *indx, double b[]) 
 #endif  { 
 #ifdef unix    int i,ii=0,ip,j; 
   scanf("%s",optionfile);    double sum; 
 #endif   
     for (i=1;i<=n;i++) { 
 /*-------- arguments in the command line --------*/      ip=indx[i]; 
       sum=b[ip]; 
   strcpy(fileres,"r");      b[ip]=b[i]; 
   strcat(fileres, optionfile);      if (ii) 
         for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   /*---------arguments file --------*/      else if (sum) ii=i; 
       b[i]=sum; 
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    } 
     printf("Problem with optionfile %s\n",optionfile);    for (i=n;i>=1;i--) { 
     goto end;      sum=b[i]; 
   }      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
       b[i]=sum/a[i][i]; 
   strcpy(filereso,"o");    } 
   strcat(filereso,fileres);  } 
   if((ficparo=fopen(filereso,"w"))==NULL) {  
     printf("Problem with Output resultfile: %s\n", filereso);goto end;  void pstamp(FILE *fichier)
   }  {
     fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
   /* Reads comments: lines beginning with '#' */  }
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);  /************ Frequencies ********************/
     fgets(line, MAXLINE, ficpar);  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[])
     puts(line);  {  /* Some frequencies */
     fputs(line,ficparo);    
   }    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   ungetc(c,ficpar);    int first;
     double ***freq; /* Frequencies */
   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);    double *pp, **prop;
   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);    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   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);    char fileresp[FILENAMELENGTH];
 while((c=getc(ficpar))=='#' && c!= EOF){    
     ungetc(c,ficpar);    pp=vector(1,nlstate);
     fgets(line, MAXLINE, ficpar);    prop=matrix(1,nlstate,iagemin,iagemax+3);
     puts(line);    strcpy(fileresp,"p");
     fputs(line,ficparo);    strcat(fileresp,fileres);
   }    if((ficresp=fopen(fileresp,"w"))==NULL) {
   ungetc(c,ficpar);      printf("Problem with prevalence resultfile: %s\n", fileresp);
        fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
          exit(0);
   covar=matrix(0,NCOVMAX,1,n);    }
   cptcovn=0;    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    j1=0;
     
   ncovmodel=2+cptcovn;    j=cptcoveff;
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */    if (cptcovn<1) {j=1;ncodemax[1]=1;}
    
   /* Read guess parameters */    first=1;
   /* Reads comments: lines beginning with '#' */  
   while((c=getc(ficpar))=='#' && c!= EOF){    for(k1=1; k1<=j;k1++){
     ungetc(c,ficpar);      for(i1=1; i1<=ncodemax[k1];i1++){
     fgets(line, MAXLINE, ficpar);        j1++;
     puts(line);        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
     fputs(line,ficparo);          scanf("%d", i);*/
   }        for (i=-5; i<=nlstate+ndeath; i++)  
   ungetc(c,ficpar);          for (jk=-5; jk<=nlstate+ndeath; jk++)  
              for(m=iagemin; m <= iagemax+3; m++)
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);              freq[i][jk][m]=0;
     for(i=1; i <=nlstate; i++)  
     for(j=1; j <=nlstate+ndeath-1; j++){      for (i=1; i<=nlstate; i++)  
       fscanf(ficpar,"%1d%1d",&i1,&j1);        for(m=iagemin; m <= iagemax+3; m++)
       fprintf(ficparo,"%1d%1d",i1,j1);          prop[i][m]=0;
       printf("%1d%1d",i,j);        
       for(k=1; k<=ncovmodel;k++){        dateintsum=0;
         fscanf(ficpar," %lf",&param[i][j][k]);        k2cpt=0;
         printf(" %lf",param[i][j][k]);        for (i=1; i<=imx; i++) {
         fprintf(ficparo," %lf",param[i][j][k]);          bool=1;
       }          if  (cptcovn>0) {
       fscanf(ficpar,"\n");            for (z1=1; z1<=cptcoveff; z1++) 
       printf("\n");              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       fprintf(ficparo,"\n");                bool=0;
     }          }
            if (bool==1){
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;            for(m=firstpass; m<=lastpass; m++){
               k2=anint[m][i]+(mint[m][i]/12.);
   p=param[1][1];              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                  if(agev[m][i]==0) agev[m][i]=iagemax+1;
   /* Reads comments: lines beginning with '#' */                if(agev[m][i]==1) agev[m][i]=iagemax+2;
   while((c=getc(ficpar))=='#' && c!= EOF){                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
     ungetc(c,ficpar);                if (m<lastpass) {
     fgets(line, MAXLINE, ficpar);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
     puts(line);                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
     fputs(line,ficparo);                }
   }                
   ungetc(c,ficpar);                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
                   dateintsum=dateintsum+k2;
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);                  k2cpt++;
   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++){            }
       fscanf(ficpar,"%1d%1d",&i1,&j1);          }
       printf("%1d%1d",i,j);        }
       fprintf(ficparo,"%1d%1d",i1,j1);         
       for(k=1; k<=ncovmodel;k++){        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
         fscanf(ficpar,"%le",&delti3[i][j][k]);        pstamp(ficresp);
         printf(" %le",delti3[i][j][k]);        if  (cptcovn>0) {
         fprintf(ficparo," %le",delti3[i][j][k]);          fprintf(ficresp, "\n#********** Variable "); 
       }          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       fscanf(ficpar,"\n");          fprintf(ficresp, "**********\n#");
       printf("\n");        }
       fprintf(ficparo,"\n");        for(i=1; i<=nlstate;i++) 
     }          fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
   }        fprintf(ficresp, "\n");
   delti=delti3[1][1];        
          for(i=iagemin; i <= iagemax+3; i++){
   /* Reads comments: lines beginning with '#' */          if(i==iagemax+3){
   while((c=getc(ficpar))=='#' && c!= EOF){            fprintf(ficlog,"Total");
     ungetc(c,ficpar);          }else{
     fgets(line, MAXLINE, ficpar);            if(first==1){
     puts(line);              first=0;
     fputs(line,ficparo);              printf("See log file for details...\n");
   }            }
   ungetc(c,ficpar);            fprintf(ficlog,"Age %d", i);
            }
   matcov=matrix(1,npar,1,npar);          for(jk=1; jk <=nlstate ; jk++){
   for(i=1; i <=npar; i++){            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
     fscanf(ficpar,"%s",&str);              pp[jk] += freq[jk][m][i]; 
     printf("%s",str);          }
     fprintf(ficparo,"%s",str);          for(jk=1; jk <=nlstate ; jk++){
     for(j=1; j <=i; j++){            for(m=-1, pos=0; m <=0 ; m++)
       fscanf(ficpar," %le",&matcov[i][j]);              pos += freq[jk][m][i];
       printf(" %.5le",matcov[i][j]);            if(pp[jk]>=1.e-10){
       fprintf(ficparo," %.5le",matcov[i][j]);              if(first==1){
     }              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     fscanf(ficpar,"\n");              }
     printf("\n");              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
     fprintf(ficparo,"\n");            }else{
   }              if(first==1)
   for(i=1; i <=npar; i++)                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
     for(j=i+1;j<=npar;j++)              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
       matcov[i][j]=matcov[j][i];            }
              }
   printf("\n");  
           for(jk=1; jk <=nlstate ; jk++){
             for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
     /*-------- data file ----------*/              pp[jk] += freq[jk][m][i];
     if((ficres =fopen(fileres,"w"))==NULL) {          }       
       printf("Problem with resultfile: %s\n", fileres);goto end;          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
     }            pos += pp[jk];
     fprintf(ficres,"#%s\n",version);            posprop += prop[jk][i];
              }
     if((fic=fopen(datafile,"r"))==NULL)    {          for(jk=1; jk <=nlstate ; jk++){
       printf("Problem with datafile: %s\n", datafile);goto end;            if(pos>=1.e-5){
     }              if(first==1)
                 printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     n= lastobs;              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
     severity = vector(1,maxwav);            }else{
     outcome=imatrix(1,maxwav+1,1,n);              if(first==1)
     num=ivector(1,n);                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     moisnais=vector(1,n);              fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
     annais=vector(1,n);            }
     moisdc=vector(1,n);            if( i <= iagemax){
     andc=vector(1,n);              if(pos>=1.e-5){
     agedc=vector(1,n);                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
     cod=ivector(1,n);                /*probs[i][jk][j1]= pp[jk]/pos;*/
     weight=vector(1,n);                /*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<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */              }
     mint=matrix(1,maxwav,1,n);              else
     anint=matrix(1,maxwav,1,n);                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
     s=imatrix(1,maxwav+1,1,n);            }
     adl=imatrix(1,maxwav+1,1,n);              }
     tab=ivector(1,NCOVMAX);          
     ncodemax=ivector(1,8);          for(jk=-1; jk <=nlstate+ndeath; jk++)
             for(m=-1; m <=nlstate+ndeath; m++)
     i=1;              if(freq[jk][m][i] !=0 ) {
     while (fgets(line, MAXLINE, fic) != NULL)    {              if(first==1)
       if ((i >= firstobs) && (i <=lastobs)) {                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
                        fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
         for (j=maxwav;j>=1;j--){              }
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);          if(i <= iagemax)
           strcpy(line,stra);            fprintf(ficresp,"\n");
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          if(first==1)
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);            printf("Others in log...\n");
         }          fprintf(ficlog,"\n");
                }
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);      }
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);    }
     dateintmean=dateintsum/k2cpt; 
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);   
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);    fclose(ficresp);
     free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);    free_vector(pp,1,nlstate);
         for (j=ncov;j>=1;j--){    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);    /* End of Freq */
         }  }
         num[i]=atol(stra);  
          /************ Prevalence ********************/
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){  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)
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/  {  
     /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
         i=i+1;       in each health status at the date of interview (if between dateprev1 and dateprev2).
       }       We still use firstpass and lastpass as another selection.
     }    */
     /* printf("ii=%d", ij);   
        scanf("%d",i);*/    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
   imx=i-1; /* Number of individuals */    double ***freq; /* Frequencies */
     double *pp, **prop;
   /* for (i=1; i<=imx; i++){    double pos,posprop; 
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;    double  y2; /* in fractional years */
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;    int iagemin, iagemax;
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;  
     }    iagemin= (int) agemin;
     iagemax= (int) agemax;
     for (i=1; i<=imx; i++)    /*pp=vector(1,nlstate);*/
     if (covar[1][i]==0) printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));*/    prop=matrix(1,nlstate,iagemin,iagemax+3); 
     /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
   /* Calculation of the number of parameter from char model*/    j1=0;
   Tvar=ivector(1,15);    
   Tprod=ivector(1,15);    j=cptcoveff;
   Tvaraff=ivector(1,15);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
   Tvard=imatrix(1,15,1,2);    
   Tage=ivector(1,15);          for(k1=1; k1<=j;k1++){
          for(i1=1; i1<=ncodemax[k1];i1++){
   if (strlen(model) >1){        j1++;
     j=0, j1=0, k1=1, k2=1;        
     j=nbocc(model,'+');        for (i=1; i<=nlstate; i++)  
     j1=nbocc(model,'*');          for(m=iagemin; m <= iagemax+3; m++)
     cptcovn=j+1;            prop[i][m]=0.0;
     cptcovprod=j1;       
            for (i=1; i<=imx; i++) { /* Each individual */
              bool=1;
     strcpy(modelsav,model);          if  (cptcovn>0) {
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){            for (z1=1; z1<=cptcoveff; z1++) 
       printf("Error. Non available option model=%s ",model);              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
       goto end;                bool=0;
     }          } 
              if (bool==1) { 
     for(i=(j+1); i>=1;i--){            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
       cutv(stra,strb,modelsav,'+');              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/                if(agev[m][i]==0) agev[m][i]=iagemax+1;
       /*scanf("%d",i);*/                if(agev[m][i]==1) agev[m][i]=iagemax+2;
       if (strchr(strb,'*')) {                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); 
         cutv(strd,strc,strb,'*');                if (s[m][i]>0 && s[m][i]<=nlstate) { 
         if (strcmp(strc,"age")==0) {                  /*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]]);*/
           cptcovprod--;                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
           cutv(strb,stre,strd,'V');                  prop[s[m][i]][iagemax+3] += weight[i]; 
           Tvar[i]=atoi(stre);                } 
           cptcovage++;              }
             Tage[cptcovage]=i;            } /* end selection of waves */
             /*printf("stre=%s ", stre);*/          }
         }        }
         else if (strcmp(strd,"age")==0) {        for(i=iagemin; i <= iagemax+3; i++){  
           cptcovprod--;          
           cutv(strb,stre,strc,'V');          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
           Tvar[i]=atoi(stre);            posprop += prop[jk][i]; 
           cptcovage++;          } 
           Tage[cptcovage]=i;  
         }          for(jk=1; jk <=nlstate ; jk++){     
         else {            if( i <=  iagemax){ 
           cutv(strb,stre,strc,'V');              if(posprop>=1.e-5){ 
           Tvar[i]=ncov+k1;                probs[i][jk][j1]= prop[jk][i]/posprop;
           cutv(strb,strc,strd,'V');              } 
           Tprod[k1]=i;            } 
           Tvard[k1][1]=atoi(strc);          }/* end jk */ 
           Tvard[k1][2]=atoi(stre);        }/* end i */ 
           Tvar[cptcovn+k2]=Tvard[k1][1];      } /* end i1 */
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    } /* end k1 */
           for (k=1; k<=lastobs;k++)    
             covar[ncov+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
           k1++;    /*free_vector(pp,1,nlstate);*/
           k2=k2+2;    free_matrix(prop,1,nlstate, iagemin,iagemax+3);
         }  }  /* End of prevalence */
       }  
       else {  /************* Waves Concatenation ***************/
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/  
        /*  scanf("%d",i);*/  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)
       cutv(strd,strc,strb,'V');  {
       Tvar[i]=atoi(strc);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
       }       Death is a valid wave (if date is known).
       strcpy(modelsav,stra);         mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
         scanf("%d",i);*/       and mw[mi+1][i]. dh depends on stepm.
     }       */
 }  
      int i, mi, m;
   /*printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   printf("cptcovprod=%d ", cptcovprod);       double sum=0., jmean=0.;*/
   scanf("%d ",i);*/    int first;
     fclose(fic);    int j, k=0,jk, ju, jl;
     double sum=0.;
     /*  if(mle==1){*/    first=0;
     if (weightopt != 1) { /* Maximisation without weights*/    jmin=1e+5;
       for(i=1;i<=n;i++) weight[i]=1.0;    jmax=-1;
     }    jmean=0.;
     /*-calculation of age at interview from date of interview and age at death -*/    for(i=1; i<=imx; i++){
     agev=matrix(1,maxwav,1,imx);      mi=0;
       m=firstpass;
    for (i=1; i<=imx; i++)      while(s[m][i] <= nlstate){
      for(m=2; (m<= maxwav); m++)        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){          mw[++mi][i]=m;
          anint[m][i]=9999;        if(m >=lastpass)
          s[m][i]=-1;          break;
        }        else
              m++;
     for (i=1; i<=imx; i++)  {      }/* end while */
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      if (s[m][i] > nlstate){
       for(m=1; (m<= maxwav); m++){        mi++;     /* Death is another wave */
         if(s[m][i] >0){        /* if(mi==0)  never been interviewed correctly before death */
           if (s[m][i] == nlstate+1) {           /* Only death is a correct wave */
             if(agedc[i]>0)        mw[mi][i]=m;
               if(moisdc[i]!=99 && andc[i]!=9999)      }
               agev[m][i]=agedc[i];  
             else {      wav[i]=mi;
               if (andc[i]!=9999){      if(mi==0){
               printf("Warning negative age at death: %d line:%d\n",num[i],i);        nbwarn++;
               agev[m][i]=-1;        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;
           }        }
           else if(s[m][i] !=9){ /* Should no more exist */        if(first==1){
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
             if(mint[m][i]==99 || anint[m][i]==9999)        }
               agev[m][i]=1;      } /* end mi==0 */
             else if(agev[m][i] <agemin){    } /* End individuals */
               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);*/    for(i=1; i<=imx; i++){
             }      for(mi=1; mi<wav[i];mi++){
             else if(agev[m][i] >agemax){        if (stepm <=0)
               agemax=agev[m][i];          dh[mi][i]=1;
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/        else{
             }          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
             /*agev[m][i]=anint[m][i]-annais[i];*/            if (agedc[i] < 2*AGESUP) {
             /*   agev[m][i] = age[i]+2*m;*/              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
           }              if(j==0) j=1;  /* Survives at least one month after exam */
           else { /* =9 */              else if(j<0){
             agev[m][i]=1;                nberr++;
             s[m][i]=-1;                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]);
           }                j=1; /* Temporary Dangerous patch */
         }                printf("   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
         else /*= 0 Unknown */                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]);
           agev[m][i]=1;                fprintf(ficlog,"   We assumed that the date of interview was correct (and not the date of death) and postponed the death %d month(s) (one stepm) after the interview. You MUST fix the contradiction between dates.\n",stepm);
       }              }
                  k=k+1;
     }              if (j >= jmax){
     for (i=1; i<=imx; i++)  {                jmax=j;
       for(m=1; (m<= maxwav); m++){                ijmax=i;
         if (s[m][i] > (nlstate+ndeath)) {              }
           printf("Error: Wrong value in nlstate or ndeath\n");                if (j <= jmin){
           goto end;                jmin=j;
         }                ijmin=i;
       }              }
     }              sum=sum+j;
               /*if (j<0) printf("j=%d num=%d \n",j,i);*/
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
             }
     free_vector(severity,1,maxwav);          }
     free_imatrix(outcome,1,maxwav+1,1,n);          else{
     free_vector(moisnais,1,n);            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     free_vector(annais,1,n);  /*        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]); */
     /* free_matrix(mint,1,maxwav,1,n);  
        free_matrix(anint,1,maxwav,1,n);*/            k=k+1;
     free_vector(moisdc,1,n);            if (j >= jmax) {
     free_vector(andc,1,n);              jmax=j;
               ijmax=i;
                }
     wav=ivector(1,imx);            else if (j <= jmin){
     dh=imatrix(1,lastpass-firstpass+1,1,imx);              jmin=j;
     mw=imatrix(1,lastpass-firstpass+1,1,imx);              ijmin=i;
                }
     /* Concatenates waves */            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);            /*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]);*/
             if(j<0){
               nberr++;
       Tcode=ivector(1,100);              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]);
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);              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]);
       ncodemax[1]=1;            }
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);            sum=sum+j;
                }
    codtab=imatrix(1,100,1,10);          jk= j/stepm;
    h=0;          jl= j -jk*stepm;
    m=pow(2,cptcoveff);          ju= j -(jk+1)*stepm;
            if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
    for(k=1;k<=cptcoveff; k++){            if(jl==0){
      for(i=1; i <=(m/pow(2,k));i++){              dh[mi][i]=jk;
        for(j=1; j <= ncodemax[k]; j++){              bh[mi][i]=0;
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){            }else{ /* We want a negative bias in order to only have interpolation ie
            h++;                    * at the price of an extra matrix product in likelihood */
            if (h>m) h=1;codtab[h][k]=j;              dh[mi][i]=jk+1;
          }              bh[mi][i]=ju;
        }            }
      }          }else{
    }            if(jl <= -ju){
                  dh[mi][i]=jk;
    /* Calculates basic frequencies. Computes observed prevalence at single age              bh[mi][i]=jl;       /* bias is positive if real duration
        and prints on file fileres'p'. */                                   * is higher than the multiple of stepm and negative otherwise.
                                    */
                }
                else{
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              dh[mi][i]=jk+1;
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */              bh[mi][i]=ju;
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            }
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */            if(dh[mi][i]==0){
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */              dh[mi][i]=1; /* At least one step */
                    bh[mi][i]=ju; /* At least one step */
     /* For Powell, parameters are in a vector p[] starting at p[1]              /*  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);*/
        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) */          } /* end if mle */
         }
     if(mle==1){      } /* end wave */
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);    }
     }    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);
     /*--------- results files --------------*/    fprintf(ficlog,"Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, ijmin, jmax, ijmax, jmean);
     fprintf(ficres,"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);   }
    
   /*********** Tricode ****************************/
    jk=1;  void tricode(int *Tvar, int **nbcode, int imx)
    fprintf(ficres,"# Parameters\n");  {
    printf("# Parameters\n");    
    for(i=1,jk=1; i <=nlstate; i++){    int Ndum[20],ij=1, k, j, i, maxncov=19;
      for(k=1; k <=(nlstate+ndeath); k++){    int cptcode=0;
        if (k != i)    cptcoveff=0; 
          {   
            printf("%d%d ",i,k);    for (k=0; k<maxncov; k++) Ndum[k]=0;
            fprintf(ficres,"%1d%1d ",i,k);    for (k=1; k<=7; k++) ncodemax[k]=0;
            for(j=1; j <=ncovmodel; j++){  
              printf("%f ",p[jk]);    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
              fprintf(ficres,"%f ",p[jk]);      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
              jk++;                                 modality*/ 
            }        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
            printf("\n");        Ndum[ij]++; /*store the modality */
            fprintf(ficres,"\n");        /*printf("i=%d ij=%d Ndum[ij]=%d imx=%d",i,ij,Ndum[ij],imx);*/
          }        if (ij > cptcode) cptcode=ij; /* getting the maximum of covariable 
      }                                         Tvar[j]. If V=sex and male is 0 and 
    }                                         female is 1, then  cptcode=1.*/
  if(mle==1){      }
     /* Computing hessian and covariance matrix */  
     ftolhess=ftol; /* Usually correct */      for (i=0; i<=cptcode; i++) {
     hesscov(matcov, p, npar, delti, ftolhess, func);        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
  }      }
     fprintf(ficres,"# Scales\n");  
     printf("# Scales\n");      ij=1; 
      for(i=1,jk=1; i <=nlstate; i++){      for (i=1; i<=ncodemax[j]; i++) {
       for(j=1; j <=nlstate+ndeath; j++){        for (k=0; k<= maxncov; k++) {
         if (j!=i) {          if (Ndum[k] != 0) {
           fprintf(ficres,"%1d%1d",i,j);            nbcode[Tvar[j]][ij]=k; 
           printf("%1d%1d",i,j);            /* 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(k=1; k<=ncovmodel;k++){            
             printf(" %.5e",delti[jk]);            ij++;
             fprintf(ficres," %.5e",delti[jk]);          }
             jk++;          if (ij > ncodemax[j]) break; 
           }        }  
           printf("\n");      } 
           fprintf(ficres,"\n");    }  
         }  
       }   for (k=0; k< maxncov; k++) Ndum[k]=0;
      }  
       for (i=1; i<=ncovmodel-2; i++) { 
     k=1;     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
     fprintf(ficres,"# Covariance\n");     ij=Tvar[i];
     printf("# Covariance\n");     Ndum[ij]++;
     for(i=1;i<=npar;i++){   }
       /*  if (k>nlstate) k=1;  
       i1=(i-1)/(ncovmodel*nlstate)+1;   ij=1;
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);   for (i=1; i<= maxncov; i++) {
       printf("%s%d%d",alph[k],i1,tab[i]);*/     if((Ndum[i]!=0) && (i<=ncovcol)){
       fprintf(ficres,"%3d",i);       Tvaraff[ij]=i; /*For printing */
       printf("%3d",i);       ij++;
       for(j=1; j<=i;j++){     }
         fprintf(ficres," %.5e",matcov[i][j]);   }
         printf(" %.5e",matcov[i][j]);   
       }   cptcoveff=ij-1; /*Number of simple covariates*/
       fprintf(ficres,"\n");  }
       printf("\n");  
       k++;  /*********** 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[] )
     while((c=getc(ficpar))=='#' && c!= EOF){  
       ungetc(c,ficpar);  {
       fgets(line, MAXLINE, ficpar);    /* Health expectancies, no variances */
       puts(line);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
       fputs(line,ficparo);    double age, agelim, hf;
     }    double ***p3mat;
     ungetc(c,ficpar);    double eip;
    
     fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);    pstamp(ficreseij);
        fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
     if (fage <= 2) {    fprintf(ficreseij,"# Age");
       bage = agemin;    for(i=1; i<=nlstate;i++){
       fage = agemax;      for(j=1; j<=nlstate;j++){
     }        fprintf(ficreseij," e%1d%1d ",i,j);
       }
     fprintf(ficres,"# agemin agemax for life expectancy.\n");      fprintf(ficreseij," e%1d. ",i);
     }
     fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);    fprintf(ficreseij,"\n");
     fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);  
      
     while((c=getc(ficpar))=='#' && c!= EOF){    if(estepm < stepm){
     ungetc(c,ficpar);      printf ("Problem %d lower than %d\n",estepm, stepm);
     fgets(line, MAXLINE, ficpar);    }
     puts(line);    else  hstepm=estepm;   
     fputs(line,ficparo);    /* We compute the life expectancy from trapezoids spaced every estepm months
   }     * This is mainly to measure the difference between two models: for example
   ungetc(c,ficpar);     * 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 
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mob_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);     * progression in between and thus overestimating or underestimating according
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);     * to the curvature of the survival function. If, for the same date, we 
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mob_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);     * 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 
   while((c=getc(ficpar))=='#' && c!= EOF){     * hypothesis. A more precise result, taking into account a more precise
     ungetc(c,ficpar);     * curvature will be obtained if estepm is as small as stepm. */
     fgets(line, MAXLINE, ficpar);  
     puts(line);    /* For example we decided to compute the life expectancy with the smallest unit */
     fputs(line,ficparo);    /* 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 
   ungetc(c,ficpar);       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 */
    dateprev1=anprev1+mprev1/12.+jprev1/365.;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
    dateprev2=anprev2+mprev2/12.+jprev2/365.;       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
   fscanf(ficpar,"pop_based=%d\n",&popbased);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
    fprintf(ficparo,"pop_based=%d\n",popbased);         results. So we changed our mind and took the option of the best precision.
    fprintf(ficres,"pop_based=%d\n",popbased);      */
     hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
   while((c=getc(ficpar))=='#' && c!= EOF){  
     ungetc(c,ficpar);    agelim=AGESUP;
     fgets(line, MAXLINE, ficpar);    /* nhstepm age range expressed in number of stepm */
     puts(line);    nstepm=(int) rint((agelim-age)*YEARM/stepm); 
     fputs(line,ficparo);    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
   }    /* if (stepm >= YEARM) hstepm=1;*/
   ungetc(c,ficpar);    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
   fscanf(ficpar,"popforecast=%d popfile=%s starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf\n",&popforecast,popfile,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2);    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 fprintf(ficparo,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);  
 fprintf(ficres,"popforecast=%d popfile=%s starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf\n",popforecast,popfile,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2);    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
       /* Computed by stepm unit matrices, product of hstepm matrices, stored
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
   
  /*------------ gnuplot -------------*/      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
 chdir(pathcd);   
   if((ficgp=fopen("graph.plt","w"))==NULL) {      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
     printf("Problem with file graph.gp");goto end;  
   }      /* Computing  Variances of health expectancies */
 #ifdef windows      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
   fprintf(ficgp,"cd \"%s\" \n",pathc);         decrease memory allocation */
 #endif       printf("%d|",(int)age);fflush(stdout);
 m=pow(2,cptcoveff);       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
        /* Computing expectancies */
  /* 1eme*/      for(i=1; i<=nlstate;i++)
   for (cpt=1; cpt<= nlstate ; cpt ++) {        for(j=1; j<=nlstate;j++)
    for (k1=1; k1<= m ; k1 ++) {          for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
             eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;
 #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((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]);*/
 #endif  
 #ifdef unix          }
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",agemin,fage,fileres);  
 #endif      fprintf(ficreseij,"%3.0f",age );
       for(i=1; i<=nlstate;i++){
 for (i=1; i<= nlstate ; i ++) {        eip=0;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");        for(j=1; j<=nlstate;j++){
   else fprintf(ficgp," \%%*lf (\%%*lf)");          eip +=eij[i][j][(int)age];
 }          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
     fprintf(ficgp,"\" t\"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 ++) {        fprintf(ficreseij,"%9.4f", eip );
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      }
   else fprintf(ficgp," \%%*lf (\%%*lf)");      fprintf(ficreseij,"\n");
 }  
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    }
      for (i=1; i<= nlstate ; i ++) {    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    printf("\n");
   else fprintf(ficgp," \%%*lf (\%%*lf)");    fprintf(ficlog,"\n");
 }    
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));  }
 #ifdef unix  
 fprintf(ficgp,"\nset ter gif small size 400,300");  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[] )
 #endif  
 fprintf(ficgp,"\nset out \"v%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);  {
    }    /* Covariances of health expectancies eij and of total life expectancies according
   }     to initial status i, ei. .
   /*2 eme*/    */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
   for (k1=1; k1<= m ; k1 ++) {    double age, agelim, hf;
     fprintf(ficgp,"set ylabel \"Years\" \nset ter gif small size 400,300\nplot [%.f:%.f] ",agemin,fage);    double ***p3matp, ***p3matm, ***varhe;
        double **dnewm,**doldm;
     for (i=1; i<= nlstate+1 ; i ++) {    double *xp, *xm;
       k=2*i;    double **gp, **gm;
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);    double ***gradg, ***trgradg;
       for (j=1; j<= nlstate+1 ; j ++) {    int theta;
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");  
   else fprintf(ficgp," \%%*lf (\%%*lf)");    double eip, vip;
 }    
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);    xp=vector(1,npar);
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);    xm=vector(1,npar);
       for (j=1; j<= nlstate+1 ; j ++) {    dnewm=matrix(1,nlstate*nlstate,1,npar);
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");    doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
         else fprintf(ficgp," \%%*lf (\%%*lf)");    
 }      pstamp(ficresstdeij);
       fprintf(ficgp,"\" t\"\" w l 0,");    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    fprintf(ficresstdeij,"# Age");
       for (j=1; j<= nlstate+1 ; j ++) {    for(i=1; i<=nlstate;i++){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");      for(j=1; j<=nlstate;j++)
   else fprintf(ficgp," \%%*lf (\%%*lf)");        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
 }        fprintf(ficresstdeij," e%1d. ",i);
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");    }
       else fprintf(ficgp,"\" t\"\" w l 0,");    fprintf(ficresstdeij,"\n");
     }  
     fprintf(ficgp,"\nset out \"e%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),k1);    pstamp(ficrescveij);
   }    fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
      fprintf(ficrescveij,"# Age");
   /*3eme*/    for(i=1; i<=nlstate;i++)
       for(j=1; j<=nlstate;j++){
   for (k1=1; k1<= m ; k1 ++) {        cptj= (j-1)*nlstate+i;
     for (cpt=1; cpt<= nlstate ; cpt ++) {        for(i2=1; i2<=nlstate;i2++)
       k=2+nlstate*(cpt-1);          for(j2=1; j2<=nlstate;j2++){
       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);            cptj2= (j2-1)*nlstate+i2;
       for (i=1; i< nlstate ; i ++) {            if(cptj2 <= cptj)
         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);              fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
       }          }
       fprintf(ficgp,"\nset out \"exp%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);      }
     }    fprintf(ficrescveij,"\n");
   }    
      if(estepm < stepm){
   /* CV preval stat */      printf ("Problem %d lower than %d\n",estepm, stepm);
   for (k1=1; k1<= m ; k1 ++) {    }
     for (cpt=1; cpt<nlstate ; cpt ++) {    else  hstepm=estepm;   
       k=3;    /* We compute the life expectancy from trapezoids spaced every estepm months
       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/($%d",agemin,agemax,fileres,k1,k+cpt+1,k+1);     * This is mainly to measure the difference between two models: for example
       for (i=1; i< nlstate ; i ++)     * if stepm=24 months pijx are given only every 2 years and by summing them
         fprintf(ficgp,"+$%d",k+i+1);     * we are calculating an estimate of the Life Expectancy assuming a linear 
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);     * progression in between and thus overestimating or underestimating according
           * to the curvature of the survival function. If, for the same date, we 
       l=3+(nlstate+ndeath)*cpt;     * estimate the model with stepm=1 month, we can keep estepm to 24 months
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);     * to compare the new estimate of Life expectancy with the same linear 
       for (i=1; i< nlstate ; i ++) {     * hypothesis. A more precise result, taking into account a more precise
         l=3+(nlstate+ndeath)*cpt;     * curvature will be obtained if estepm is as small as stepm. */
         fprintf(ficgp,"+$%d",l+i+1);  
       }    /* For example we decided to compute the life expectancy with the smallest unit */
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);      /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
       fprintf(ficgp,"set out \"p%s%d%d.gif\" \nreplot\n\n",strtok(optionfile, "."),cpt,k1);       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 */
   /* proba elementaires */    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
    for(i=1,jk=1; i <=nlstate; i++){       survival function given by stepm (the optimization length). Unfortunately it
     for(k=1; k <=(nlstate+ndeath); k++){       means that if the survival funtion is printed only each two years of age and if
       if (k != i) {       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
         for(j=1; j <=ncovmodel; j++){       results. So we changed our mind and took the option of the best precision.
           /*fprintf(ficgp,"%s%1d%1d=%f ",alph[j],i,k,p[jk]);*/    */
           /*fprintf(ficgp,"%s",alph[1]);*/    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);  
           jk++;    /* If stepm=6 months */
           fprintf(ficgp,"\n");    /* 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 */
   for(jk=1; jk <=m; jk++) {    
   fprintf(ficgp,"\nset ter gif small size 400,300\nset log y\nplot  [%.f:%.f] ",agemin,agemax);    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    i=1;    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
    for(k2=1; k2<=nlstate; k2++) {    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
      k3=i;    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
      for(k=1; k<=(nlstate+ndeath); k++) {    gp=matrix(0,nhstepm,1,nlstate*nlstate);
        if (k != k2){    gm=matrix(0,nhstepm,1,nlstate*nlstate);
         fprintf(ficgp," exp(p%d+p%d*x",i,i+1);  
 ij=1;    for (age=bage; age<=fage; age ++){ 
         for(j=3; j <=ncovmodel; j++) {  
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {      /* Computed by stepm unit matrices, product of hstepm matrices, stored
             fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
             ij++;   
           }      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           else  
           fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);      /* Computing  Variances of health expectancies */
         }      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
           fprintf(ficgp,")/(1");         decrease memory allocation */
              for(theta=1; theta <=npar; theta++){
         for(k1=1; k1 <=nlstate; k1++){          for(i=1; i<=npar; i++){ 
           fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);          xp[i] = x[i] + (i==theta ?delti[theta]:0);
 ij=1;          xm[i] = x[i] - (i==theta ?delti[theta]:0);
           for(j=3; j <=ncovmodel; j++){        }
           if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
             fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);        hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
             ij++;    
           }        for(j=1; j<= nlstate; j++){
           else          for(i=1; i<=nlstate; i++){
             fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);            for(h=0; h<=nhstepm-1; h++){
           }              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
           fprintf(ficgp,")");              gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
         }            }
         fprintf(ficgp,") t \"p%d%d\" ", k2,k);          }
         if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");        }
         i=i+ncovmodel;       
        }        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];
    fprintf(ficgp,"\nset out \"pe%s%d.gif\" \nreplot\n\n",strtok(optionfile, "."),jk);          }
   }      }/* End theta */
          
   fclose(ficgp);      
          for(h=0; h<=nhstepm-1; h++)
 chdir(path);        for(j=1; j<=nlstate*nlstate;j++)
              for(theta=1; theta <=npar; theta++)
     free_ivector(wav,1,imx);            trgradg[h][j][theta]=gradg[h][theta][j];
     free_imatrix(dh,1,lastpass-firstpass+1,1,imx);      
     free_imatrix(mw,1,lastpass-firstpass+1,1,imx);    
     free_ivector(num,1,n);       for(ij=1;ij<=nlstate*nlstate;ij++)
     free_vector(agedc,1,n);        for(ji=1;ji<=nlstate*nlstate;ji++)
     /*free_matrix(covar,1,NCOVMAX,1,n);*/          varhe[ij][ji][(int)age] =0.;
     fclose(ficparo);  
     fclose(ficres);       printf("%d|",(int)age);fflush(stdout);
     /*  }*/       fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
           for(h=0;h<=nhstepm-1;h++){
    /*________fin mle=1_________*/        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++)
     /* No more information from the sample is required now */            for(ji=1;ji<=nlstate*nlstate;ji++)
   /* Reads comments: lines beginning with '#' */              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
   while((c=getc(ficpar))=='#' && c!= EOF){        }
     ungetc(c,ficpar);      }
     fgets(line, MAXLINE, ficpar);      /* Computing expectancies */
     puts(line);      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
     fputs(line,ficparo);      for(i=1; i<=nlstate;i++)
   }        for(j=1; j<=nlstate;j++)
   ungetc(c,ficpar);          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;
   fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf\n",&agemin,&agemax, &bage, &fage);            
   printf("agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax, bage, fage);            /* 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(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f\n",agemin,agemax,bage,fage);  
 /*--------- index.htm --------*/          }
   
   strcpy(optionfilehtm,optionfile);      fprintf(ficresstdeij,"%3.0f",age );
   strcat(optionfilehtm,".htm");      for(i=1; i<=nlstate;i++){
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {        eip=0.;
     printf("Problem with %s \n",optionfilehtm);goto end;        vip=0.;
   }        for(j=1; j<=nlstate;j++){
           eip += eij[i][j][(int)age];
  fprintf(fichtm,"<body><ul> <font size=\"6\">Imach, Version 0.7 </font> <hr size=\"2\" color=\"#EC5E5E\">          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
 Titre=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
 Total number of observations=%d <br>          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>        }
 <hr  size=\"2\" color=\"#EC5E5E\">        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
 <li>Outputs files<br><br>\n      }
         - Observed prevalence in each state: <a href=\"p%s\">p%s</a> <br>\n      fprintf(ficresstdeij,"\n");
 - Estimated parameters and the covariance matrix: <a href=\"%s\">%s</a> <br>  
         - Stationary prevalence in each state: <a href=\"pl%s\">pl%s</a> <br>      fprintf(ficrescveij,"%3.0f",age );
         - Transition probabilities: <a href=\"pij%s\">pij%s</a><br>      for(i=1; i<=nlstate;i++)
         - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>        for(j=1; j<=nlstate;j++){
         - Life expectancies by age and initial health status: <a href=\"e%s\">e%s</a> <br>          cptj= (j-1)*nlstate+i;
         - Variances of life expectancies by age and initial health status: <a href=\"v%s\">v%s</a><br>          for(i2=1; i2<=nlstate;i2++)
         - Health expectancies with their variances: <a href=\"t%s\">t%s</a> <br>            for(j2=1; j2<=nlstate;j2++){
         - Standard deviation of stationary prevalences: <a href=\"vpl%s\">vpl%s</a> <br>              cptj2= (j2-1)*nlstate+i2;
         - Prevalences and population forecasting: <a href=\"f%s\">f%s</a> <br>              if(cptj2 <= cptj)
 <br>",title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres,fileres);                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
             }
  fprintf(fichtm," <li>Graphs</li><p>");        }
       fprintf(ficrescveij,"\n");
  m=cptcoveff;     
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    }
     free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
  j1=0;    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
  for(k1=1; k1<=m;k1++){    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
    for(i1=1; i1<=ncodemax[k1];i1++){    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
        j1++;    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
        if (cptcovn > 0) {    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
          fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");    printf("\n");
          for (cpt=1; cpt<=cptcoveff;cpt++)    fprintf(ficlog,"\n");
            fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[j1][cpt]]);  
          fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");    free_vector(xm,1,npar);
        }    free_vector(xp,1,npar);
        fprintf(fichtm,"<br>- Probabilities: pe%s%d.gif<br>    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
 <img src=\"pe%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);        free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
        for(cpt=1; cpt<nlstate;cpt++){    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
          fprintf(fichtm,"<br>- Prevalence of disability : p%s%d%d.gif<br>  }
 <img src=\"p%s%d%d.gif\">",strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);  
        }  /************ Variance ******************/
     for(cpt=1; cpt<=nlstate;cpt++) {  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[])
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident  {
 interval) in state (%d): v%s%d%d.gif <br>    /* Variance of health expectancies */
 <img src=\"v%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);      /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
      }    /* double **newm;*/
      for(cpt=1; cpt<=nlstate;cpt++) {    double **dnewm,**doldm;
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.gif <br>    double **dnewmp,**doldmp;
 <img src=\"exp%s%d%d.gif\">",cpt,strtok(optionfile, "."),cpt,j1,strtok(optionfile, "."),cpt,j1);    int i, j, nhstepm, hstepm, h, nstepm ;
      }    int k, cptcode;
      fprintf(fichtm,"\n<br>- Total life expectancy by age and    double *xp;
 health expectancies in states (1) and (2): e%s%d.gif<br>    double **gp, **gm;  /* for var eij */
 <img src=\"e%s%d.gif\">",strtok(optionfile, "."),j1,strtok(optionfile, "."),j1);    double ***gradg, ***trgradg; /*for var eij */
 fprintf(fichtm,"\n</body>");    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 */
 fclose(fichtm);    double ***p3mat;
     double age,agelim, hf;
   /*--------------- Prevalence limit --------------*/    double ***mobaverage;
      int theta;
   strcpy(filerespl,"pl");    char digit[4];
   strcat(filerespl,fileres);    char digitp[25];
   if((ficrespl=fopen(filerespl,"w"))==NULL) {  
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;    char fileresprobmorprev[FILENAMELENGTH];
   }  
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);    if(popbased==1){
   fprintf(ficrespl,"#Prevalence limit\n");      if(mobilav!=0)
   fprintf(ficrespl,"#Age ");        strcpy(digitp,"-populbased-mobilav-");
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);      else strcpy(digitp,"-populbased-nomobil-");
   fprintf(ficrespl,"\n");    }
      else 
   prlim=matrix(1,nlstate,1,nlstate);      strcpy(digitp,"-stablbased-");
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    if (mobilav!=0) {
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   k=0;        printf(" Error in movingaverage mobilav=%d\n",mobilav);
   agebase=agemin;      }
   agelim=agemax;    }
   ftolpl=1.e-10;  
   i1=cptcoveff;    strcpy(fileresprobmorprev,"prmorprev"); 
   if (cptcovn < 1){i1=1;}    sprintf(digit,"%-d",ij);
     /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   for(cptcov=1;cptcov<=i1;cptcov++){    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
         k=k+1;    strcat(fileresprobmorprev,fileres);
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
         fprintf(ficrespl,"\n#******");      printf("Problem with resultfile: %s\n", fileresprobmorprev);
         for(j=1;j<=cptcoveff;j++)      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    }
         fprintf(ficrespl,"******\n");    printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
           
         for (age=agebase; age<=agelim; age++){    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    pstamp(ficresprobmorprev);
           fprintf(ficrespl,"%.0f",age );    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);
           for(i=1; i<=nlstate;i++)    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
           fprintf(ficrespl," %.5f", prlim[i][i]);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
           fprintf(ficrespl,"\n");      fprintf(ficresprobmorprev," p.%-d SE",j);
         }      for(i=1; i<=nlstate;i++)
       }        fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
     }    }  
   fclose(ficrespl);    fprintf(ficresprobmorprev,"\n");
     fprintf(ficgp,"\n# Routine varevsij");
   /*------------- h Pij x at various ages ------------*/    /* 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");
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
   if((ficrespij=fopen(filerespij,"w"))==NULL) {  /*   } */
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   }    pstamp(ficresvij);
   printf("Computing pij: result on file '%s' \n", filerespij);    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
      if(popbased==1)
   stepsize=(int) (stepm+YEARM-1)/YEARM;      fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
   /*if (stepm<=24) stepsize=2;*/    else
       fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
   agelim=AGESUP;    fprintf(ficresvij,"# Age");
   hstepm=stepsize*YEARM; /* Every year of age */    for(i=1; i<=nlstate;i++)
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */      for(j=1; j<=nlstate;j++)
          fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
   k=0;    fprintf(ficresvij,"\n");
   for(cptcov=1;cptcov<=i1;cptcov++){  
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    xp=vector(1,npar);
       k=k+1;    dnewm=matrix(1,nlstate,1,npar);
         fprintf(ficrespij,"\n#****** ");    doldm=matrix(1,nlstate,1,nlstate);
         for(j=1;j<=cptcoveff;j++)    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
         fprintf(ficrespij,"******\n");  
            gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */    gpp=vector(nlstate+1,nlstate+ndeath);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    gmp=vector(nlstate+1,nlstate+ndeath);
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    
           oldm=oldms;savm=savms;    if(estepm < stepm){
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        printf ("Problem %d lower than %d\n",estepm, stepm);
           fprintf(ficrespij,"# Age");    }
           for(i=1; i<=nlstate;i++)    else  hstepm=estepm;   
             for(j=1; j<=nlstate+ndeath;j++)    /* For example we decided to compute the life expectancy with the smallest unit */
               fprintf(ficrespij," %1d-%1d",i,j);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
           fprintf(ficrespij,"\n");       nhstepm is the number of hstepm from age to agelim 
           for (h=0; h<=nhstepm; h++){       nstepm is the number of stepm from age to agelin. 
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );       Look at hpijx to understand the reason of that which relies in memory size
             for(i=1; i<=nlstate;i++)       and note for a fixed period like k years */
               for(j=1; j<=nlstate+ndeath;j++)    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);       survival function given by stepm (the optimization length). Unfortunately it
             fprintf(ficrespij,"\n");       means that if the survival funtion is printed every two years of age and if
           }       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);       results. So we changed our mind and took the option of the best precision.
           fprintf(ficrespij,"\n");    */
         }    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 */ 
   /* varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k);*/      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
       p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   fclose(ficrespij);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
       gp=matrix(0,nhstepm,1,nlstate);
   /*---------- Forecasting ------------------*/      gm=matrix(0,nhstepm,1,nlstate);
   calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;  
   
   prevalence(agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);      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);
   strcpy(fileresf,"f");        }
   strcat(fileresf,fileres);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
   if((ficresf=fopen(fileresf,"w"))==NULL) {        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     printf("Problem with forecast resultfile: %s\n", fileresf);goto end;  
   }        if (popbased==1) {
   printf("Computing forecasting: result on file '%s' \n", fileresf);          if(mobilav ==0){
             for(i=1; i<=nlstate;i++)
   free_matrix(mint,1,maxwav,1,n);              prlim[i][i]=probs[(int)age][i][ij];
   free_matrix(anint,1,maxwav,1,n);          }else{ /* mobilav */ 
   free_matrix(agev,1,maxwav,1,imx);            for(i=1; i<=nlstate;i++)
   /* Mobile average */              prlim[i][i]=mobaverage[(int)age][i][ij];
           }
   if (cptcoveff==0) ncodemax[cptcoveff]=1;        }
     
   if (mobilav==1) {        for(j=1; j<= nlstate; j++){
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);          for(h=0; h<=nhstepm; h++){
     for (agedeb=bage+3; agedeb<=fage-2; agedeb++)            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
       for (i=1; i<=nlstate;i++)              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)          }
           mobaverage[(int)agedeb][i][cptcod]=0.;        }
            /* This for computing probability of death (h=1 means
     for (agedeb=bage+4; agedeb<=fage; agedeb++){           computed over hstepm matrices product = hstepm*stepm months) 
       for (i=1; i<=nlstate;i++){           as a weighted average of prlim.
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){        */
           for (cpt=0;cpt<=4;cpt++){        for(j=nlstate+1;j<=nlstate+ndeath;j++){
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];          for(i=1,gpp[j]=0.; i<= nlstate; i++)
           }            gpp[j] += prlim[i][i]*p3mat[i][j][1];
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;        }    
         }        /* 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);  
   stepsize=(int) (stepm+YEARM-1)/YEARM;        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   if (stepm<=12) stepsize=1;   
         if (popbased==1) {
   agelim=AGESUP;          if(mobilav ==0){
   /*hstepm=stepsize*YEARM; *//* Every year of age */            for(i=1; i<=nlstate;i++)
   hstepm=1;              prlim[i][i]=probs[(int)age][i][ij];
   hstepm=hstepm/stepm; /* Typically 2 years, = 2 years/6 months = 4 */          }else{ /* mobilav */ 
   yp1=modf(dateintmean,&yp);            for(i=1; i<=nlstate;i++)
   anprojmean=yp;              prlim[i][i]=mobaverage[(int)age][i][ij];
   yp2=modf((yp1*12),&yp);          }
   mprojmean=yp;        }
   yp1=modf((yp2*30.5),&yp);  
   jprojmean=yp;        for(j=1; j<= nlstate; j++){
   fprintf(ficresf,"Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);          for(h=0; h<=nhstepm; h++){
             for(i=1, gm[h][j]=0.;i<=nlstate;i++)
   if (popforecast==1) {              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
     if((ficpop=fopen(popfile,"r"))==NULL)    {          }
       printf("Problem with population file : %s\n",popfile);goto end;        }
     }        /* This for computing probability of death (h=1 means
     popage=ivector(0,AGESUP);           computed over hstepm matrices product = hstepm*stepm months) 
     popeffectif=vector(0,AGESUP);           as a weighted average of prlim.
     popcount=vector(0,AGESUP);        */
         for(j=nlstate+1;j<=nlstate+ndeath;j++){
     i=1;            for(i=1,gmp[j]=0.; i<= nlstate; i++)
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF)           gmp[j] += prlim[i][i]*p3mat[i][j][1];
       {        }    
         i=i+1;        /* end probability of death */
       }  
     imx=i;        for(j=1; j<= nlstate; j++) /* vareij */
              for(h=0; h<=nhstepm; h++){
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
   }          }
   
   for(cptcov=1;cptcov<=i1;cptcov++){        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
       k=k+1;        }
       fprintf(ficresf,"\n#******");  
       for(j=1;j<=cptcoveff;j++) {      } /* End theta */
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       }      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
       fprintf(ficresf,"******\n");  
       fprintf(ficresf,"# StartingAge FinalAge");      for(h=0; h<=nhstepm; h++) /* veij */
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);        for(j=1; j<=nlstate;j++)
       if (popforecast==1)  fprintf(ficresf," [Population]");          for(theta=1; theta <=npar; theta++)
              trgradg[h][j][theta]=gradg[h][theta][j];
       for (cpt=0; cpt<=1;cpt++) {  
         fprintf(ficresf,"\n");      for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
   fprintf(ficresf,"\nForecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);          for(theta=1; theta <=npar; theta++)
       for (agedeb=(fage-(1/12.)); agedeb>=(bage-(1/12.)); agedeb--){ /* If stepm=6 months */          trgradgp[j][theta]=gradgp[theta][j];
         nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);    
         nhstepm = nhstepm/hstepm;  
         /*printf("agedeb=%.lf stepm=%d hstepm=%d nhstepm=%d \n",agedeb,stepm,hstepm,nhstepm);*/      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
       for(i=1;i<=nlstate;i++)
         p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(j=1;j<=nlstate;j++)
         oldm=oldms;savm=savms;          vareij[i][j][(int)age] =0.;
         hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);    
                      for(h=0;h<=nhstepm;h++){
         for (h=0; h<=nhstepm; h++){        for(k=0;k<=nhstepm;k++){
           if (h==(int) (calagedate+12*cpt)) {          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
             fprintf(ficresf,"h=%d ", h);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
             fprintf(ficresf,"\n %f %f ",agedeb,agedeb+h*hstepm/YEARM*stepm);          for(i=1;i<=nlstate;i++)
           }            for(j=1;j<=nlstate;j++)
           for(j=1; j<=nlstate+ndeath;j++) {              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
             kk1=0.;kk2=0;        }
             for(i=1; i<=nlstate;i++) {              }
               if (mobilav==1)    
                 kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb][i][cptcod];      /* pptj */
               else {      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
                 kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
                 /*  fprintf(ficresf," p3=%.3f p=%.3f ", p3mat[i][j][h],probs[(int)(agedeb)+1][i][cptcod]);*/      for(j=nlstate+1;j<=nlstate+ndeath;j++)
               }        for(i=nlstate+1;i<=nlstate+ndeath;i++)
           varppt[j][i]=doldmp[j][i];
               if (popforecast==1) kk2=kk1*popeffectif[(int)agedeb];      /* end ppptj */
             }      /*  x centered again */
                hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
             if (h==(int)(calagedate+12*cpt)){      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
               fprintf(ficresf," %.3f", kk1);   
                    if (popbased==1) {
               if (popforecast==1) fprintf(ficresf," [%.f]", kk2);        if(mobilav ==0){
             }          for(i=1; i<=nlstate;i++)
           }            prlim[i][i]=probs[(int)age][i][ij];
         }        }else{ /* mobilav */ 
         free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);          for(i=1; i<=nlstate;i++)
       }            prlim[i][i]=mobaverage[(int)age][i][ij];
       }        }
     }      }
   }               
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      /* This for computing probability of death (h=1 means
   if (popforecast==1) {         computed over hstepm (estepm) matrices product = hstepm*stepm months) 
     free_ivector(popage,0,AGESUP);         as a weighted average of prlim.
     free_vector(popeffectif,0,AGESUP);      */
     free_vector(popcount,0,AGESUP);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
   }        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   free_imatrix(s,1,maxwav+1,1,n);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   free_vector(weight,1,n);      }    
   fclose(ficresf);      /* end probability of death */
   /*---------- Health expectancies and variances ------------*/  
       fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
   strcpy(filerest,"t");      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   strcat(filerest,fileres);        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
   if((ficrest=fopen(filerest,"w"))==NULL) {        for(i=1; i<=nlstate;i++){
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
   }        }
   printf("Computing Total LEs with variances: file '%s' \n", filerest);      } 
       fprintf(ficresprobmorprev,"\n");
   
   strcpy(filerese,"e");      fprintf(ficresvij,"%.0f ",age );
   strcat(filerese,fileres);      for(i=1; i<=nlstate;i++)
   if((ficreseij=fopen(filerese,"w"))==NULL) {        for(j=1; j<=nlstate;j++){
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);          fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
   }        }
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);      fprintf(ficresvij,"\n");
       free_matrix(gp,0,nhstepm,1,nlstate);
  strcpy(fileresv,"v");      free_matrix(gm,0,nhstepm,1,nlstate);
   strcat(fileresv,fileres);      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
   if((ficresvij=fopen(fileresv,"w"))==NULL) {      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   }    } /* End age */
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);    free_vector(gpp,nlstate+1,nlstate+ndeath);
     free_vector(gmp,nlstate+1,nlstate+ndeath);
   k=0;    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
   for(cptcov=1;cptcov<=i1;cptcov++){    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
       k=k+1;    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
       fprintf(ficrest,"\n#****** ");    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
       for(j=1;j<=cptcoveff;j++)  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
       fprintf(ficrest,"******\n");  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
     fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
       fprintf(ficreseij,"\n#****** ");    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
       for(j=1;j<=cptcoveff;j++)    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
         fprintf(ficreseij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
       fprintf(ficreseij,"******\n");    fprintf(fichtm,"\n<br> Probability is computed over estepm=%d months. <br> <img src=\"%s%s.png\"> <br>\n", estepm,subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
     /*  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(ficresvij,"\n#****** ");  */
       for(j=1;j<=cptcoveff;j++)  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
         fprintf(ficresvij,"V%d=%d ",j,nbcode[j][codtab[k][j]]);    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
       fprintf(ficresvij,"******\n");  
     free_vector(xp,1,npar);
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    free_matrix(doldm,1,nlstate,1,nlstate);
       oldm=oldms;savm=savms;    free_matrix(dnewm,1,nlstate,1,npar);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k);      free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
       oldm=oldms;savm=savms;    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
       varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
          fclose(ficresprobmorprev);
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");    fflush(ficgp);
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);    fflush(fichtm); 
       fprintf(ficrest,"\n");  }  /* end varevsij */
          
       hf=1;  /************ Variance of prevlim ******************/
       if (stepm >= YEARM) hf=stepm/YEARM;  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[])
       epj=vector(1,nlstate+1);  {
       for(age=bage; age <=fage ;age++){    /* Variance of prevalence limit */
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
         if (popbased==1) {    double **newm;
           for(i=1; i<=nlstate;i++)    double **dnewm,**doldm;
             prlim[i][i]=probs[(int)age][i][k];    int i, j, nhstepm, hstepm;
         }    int k, cptcode;
            double *xp;
         fprintf(ficrest," %.0f",age);    double *gp, *gm;
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){    double **gradg, **trgradg;
           for(i=1, epj[j]=0.;i <=nlstate;i++) {    double age,agelim;
             epj[j] += prlim[i][i]*hf*eij[i][j][(int)age];    int theta;
           }    
           epj[nlstate+1] +=epj[j];    pstamp(ficresvpl);
         }    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
         for(i=1, vepp=0.;i <=nlstate;i++)    fprintf(ficresvpl,"# Age");
           for(j=1;j <=nlstate;j++)    for(i=1; i<=nlstate;i++)
             vepp += vareij[i][j][(int)age];        fprintf(ficresvpl," %1d-%1d",i,i);
         fprintf(ficrest," %.2f (%.2f)", epj[nlstate+1],hf*sqrt(vepp));    fprintf(ficresvpl,"\n");
         for(j=1;j <=nlstate;j++){  
           fprintf(ficrest," %.2f (%.2f)", epj[j],hf*sqrt(vareij[j][j][(int)age]));    xp=vector(1,npar);
         }    dnewm=matrix(1,nlstate,1,npar);
         fprintf(ficrest,"\n");    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;
  fclose(ficreseij);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
  fclose(ficresvij);      gradg=matrix(1,npar,1,nlstate);
   fclose(ficrest);      gp=vector(1,nlstate);
   fclose(ficpar);      gm=vector(1,nlstate);
   free_vector(epj,1,nlstate+1);  
   /*  scanf("%d ",i); */      for(theta=1; theta <=npar; theta++){
         for(i=1; i<=npar; i++){ /* Computes gradient */
   /*------- Variance limit prevalence------*/            xp[i] = x[i] + (i==theta ?delti[theta]:0);
         }
 strcpy(fileresvpl,"vpl");        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
   strcat(fileresvpl,fileres);        for(i=1;i<=nlstate;i++)
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {          gp[i] = prlim[i][i];
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);      
     exit(0);        for(i=1; i<=npar; i++) /* Computes gradient */
   }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
         for(i=1;i<=nlstate;i++)
  k=0;          gm[i] = prlim[i][i];
  for(cptcov=1;cptcov<=i1;cptcov++){  
    for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){        for(i=1;i<=nlstate;i++)
      k=k+1;          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
      fprintf(ficresvpl,"\n#****** ");      } /* End theta */
      for(j=1;j<=cptcoveff;j++)  
        fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);      trgradg =matrix(1,nlstate,1,npar);
      fprintf(ficresvpl,"******\n");  
            for(j=1; j<=nlstate;j++)
      varpl=matrix(1,nlstate,(int) bage, (int) fage);        for(theta=1; theta <=npar; theta++)
      oldm=oldms;savm=savms;          trgradg[j][theta]=gradg[theta][j];
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  
    }      for(i=1;i<=nlstate;i++)
  }        varpl[i][(int)age] =0.;
       matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
   fclose(ficresvpl);      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
       for(i=1;i<=nlstate;i++)
   /*---------- End : free ----------------*/        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);  
        fprintf(ficresvpl,"%.0f ",age );
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);      for(i=1; i<=nlstate;i++)
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);        fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
        fprintf(ficresvpl,"\n");
        free_vector(gp,1,nlstate);
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);      free_vector(gm,1,nlstate);
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);      free_matrix(gradg,1,npar,1,nlstate);
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);      free_matrix(trgradg,1,nlstate,1,npar);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);    } /* End age */
    
   free_matrix(matcov,1,npar,1,npar);    free_vector(xp,1,npar);
   free_vector(delti,1,npar);    free_matrix(doldm,1,nlstate,1,npar);
      free_matrix(dnewm,1,nlstate,1,nlstate);
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);  
   }
   printf("End of Imach\n");  
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */  /************ 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[])
   /* 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);*/  {
   /*printf("Total time was %d uSec.\n", total_usecs);*/    int i, j=0,  i1, k1, l1, t, tj;
   /*------ End -----------*/    int k2, l2, j1,  z1;
     int k=0,l, cptcode;
     int first=1, first1;
  end:    double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
 #ifdef windows    double **dnewm,**doldm;
  chdir(pathcd);    double *xp;
 #endif    double *gp, *gm;
      double **gradg, **trgradg;
  system("..\\gp37mgw\\wgnuplot graph.plt");    double **mu;
     double age,agelim, cov[NCOVMAX];
 #ifdef windows    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
   while (z[0] != 'q') {    int theta;
     chdir(pathcd);    char fileresprob[FILENAMELENGTH];
     printf("\nType e to edit output files, c to start again, and q for exiting: ");    char fileresprobcov[FILENAMELENGTH];
     scanf("%s",z);    char fileresprobcor[FILENAMELENGTH];
     if (z[0] == 'c') system("./imach");  
     else if (z[0] == 'e') {    double ***varpij;
       chdir(path);  
       system(optionfilehtm);    strcpy(fileresprob,"prob"); 
     }    strcat(fileresprob,fileres);
     else if (z[0] == 'q') exit(0);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
   }      printf("Problem with resultfile: %s\n", fileresprob);
 #endif      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 with datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem with datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
           exit(1);
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           exit(1);
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         exit(1);
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
         exit(1);
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       lval=strtol(strb,&endptr,10); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight.  Exiting.\n",lval, i,line,linei);
         exit(1);
       }
       weight[i]=(double)(lval); 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);
           exit(1);
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self).  Exiting.\n",lval,linei, i,line,j);
           exit(1);
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       } 
       lstra=strlen(stra);
       
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
     fclose(fic);
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
     /* for (i=1; i<=imx; i++) */
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameters from char model */
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - 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 ( 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.1.19  
changed lines
  Added in v.1.117

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