Diff for /imach/src/imach.c between versions 1.46 and 1.118

version 1.46, 2002/05/30 17:44:35 version 1.118, 2006/03/14 18:20:07
Line 1 Line 1
 /* $Id$  /* $Id$
    Interpolated Markov Chain    $State$
     $Log$
   Short summary of the programme:    Revision 1.118  2006/03/14 18:20:07  brouard
      (Module): varevsij Comments added explaining the second
   This program computes Healthy Life Expectancies from    table of variances if popbased=1 .
   cross-longitudinal data. Cross-longitudinal data consist in: -1- a    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   first survey ("cross") where individuals from different ages are    (Module): Function pstamp added
   interviewed on their health status or degree of disability (in the    (Module): Version 0.98d
   case of a health survey which is our main interest) -2- at least a  
   second wave of interviews ("longitudinal") which measure each change    Revision 1.117  2006/03/14 17:16:22  brouard
   (if any) in individual health status.  Health expectancies are    (Module): varevsij Comments added explaining the second
   computed from the time spent in each health state according to a    table of variances if popbased=1 .
   model. More health states you consider, more time is necessary to reach the    (Module): Covariances of eij, ekl added, graphs fixed, new html link.
   Maximum Likelihood of the parameters involved in the model.  The    (Module): Function pstamp added
   simplest model is the multinomial logistic model where pij is the    (Module): Version 0.98d
   probability to be observed in state j at the second wave  
   conditional to be observed in state i at the first wave. Therefore    Revision 1.116  2006/03/06 10:29:27  brouard
   the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where    (Module): Variance-covariance wrong links and
   'age' is age and 'sex' is a covariate. If you want to have a more    varian-covariance of ej. is needed (Saito).
   complex model than "constant and age", you should modify the program  
   where the markup *Covariates have to be included here again* invites    Revision 1.115  2006/02/27 12:17:45  brouard
   you to do it.  More covariates you add, slower the    (Module): One freematrix added in mlikeli! 0.98c
   convergence.  
     Revision 1.114  2006/02/26 12:57:58  brouard
   The advantage of this computer programme, compared to a simple    (Module): Some improvements in processing parameter
   multinomial logistic model, is clear when the delay between waves is not    filename with strsep.
   identical for each individual. Also, if a individual missed an  
   intermediate interview, the information is lost, but taken into    Revision 1.113  2006/02/24 14:20:24  brouard
   account using an interpolation or extrapolation.      (Module): Memory leaks checks with valgrind and:
     datafile was not closed, some imatrix were not freed and on matrix
   hPijx is the probability to be observed in state i at age x+h    allocation too.
   conditional to the observed state i at age x. The delay 'h' can be  
   split into an exact number (nh*stepm) of unobserved intermediate    Revision 1.112  2006/01/30 09:55:26  brouard
   states. This elementary transition (by month or quarter trimester,    (Module): Back to gnuplot.exe instead of wgnuplot.exe
   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    (Module): Lots of cleaning and bugs added (Gompertz)
   hPijx.    (Module): Comments can be added in data file. Missing date values
     can be a simple dot '.'.
   Also this programme outputs the covariance matrix of the parameters but also  
   of the life expectancies. It also computes the prevalence limits.    Revision 1.110  2006/01/25 00:51:50  brouard
      (Module): Lots of cleaning and bugs added (Gompertz)
   Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).  
            Institut national d'études démographiques, Paris.    Revision 1.109  2006/01/24 19:37:15  brouard
   This software have been partly granted by Euro-REVES, a concerted action    (Module): Comments (lines starting with a #) are allowed in data.
   from the European Union.  
   It is copyrighted identically to a GNU software product, ie programme and    Revision 1.108  2006/01/19 18:05:42  lievre
   software can be distributed freely for non commercial use. Latest version    Gnuplot problem appeared...
   can be accessed at http://euroreves.ined.fr/imach .    To be fixed
   **********************************************************************/  
      Revision 1.107  2006/01/19 16:20:37  brouard
 #include <math.h>    Test existence of gnuplot in imach path
 #include <stdio.h>  
 #include <stdlib.h>    Revision 1.106  2006/01/19 13:24:36  brouard
 #include <unistd.h>    Some cleaning and links added in html output
   
 #define MAXLINE 256    Revision 1.105  2006/01/05 20:23:19  lievre
 #define GNUPLOTPROGRAM "gnuplot"    *** empty log message ***
 /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/  
 #define FILENAMELENGTH 80    Revision 1.104  2005/09/30 16:11:43  lievre
 /*#define DEBUG*/    (Module): sump fixed, loop imx fixed, and simplifications.
 #define windows    (Module): If the status is missing at the last wave but we know
 #define GLOCK_ERROR_NOPATH              -1      /* empty path */    that the person is alive, then we can code his/her status as -2
 #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */    (instead of missing=-1 in earlier versions) and his/her
     contributions to the likelihood is 1 - Prob of dying from last
 #define MAXPARM 30 /* Maximum number of parameters for the optimization */    health status (= 1-p13= p11+p12 in the easiest case of somebody in
 #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */    the healthy state at last known wave). Version is 0.98
   
 #define NINTERVMAX 8    Revision 1.103  2005/09/30 15:54:49  lievre
 #define NLSTATEMAX 8 /* Maximum number of live states (for func) */    (Module): sump fixed, loop imx fixed, and simplifications.
 #define NDEATHMAX 8 /* Maximum number of dead states (for func) */  
 #define NCOVMAX 8 /* Maximum number of covariates */    Revision 1.102  2004/09/15 17:31:30  brouard
 #define MAXN 20000    Add the possibility to read data file including tab characters.
 #define YEARM 12. /* Number of months per year */  
 #define AGESUP 130    Revision 1.101  2004/09/15 10:38:38  brouard
 #define AGEBASE 40    Fix on curr_time
   
     Revision 1.100  2004/07/12 18:29:06  brouard
 int erreur; /* Error number */    Add version for Mac OS X. Just define UNIX in Makefile
 int nvar;  
 int cptcovn, cptcovage=0, cptcoveff=0,cptcov;    Revision 1.99  2004/06/05 08:57:40  brouard
 int npar=NPARMAX;    *** empty log message ***
 int nlstate=2; /* Number of live states */  
 int ndeath=1; /* Number of dead states */    Revision 1.98  2004/05/16 15:05:56  brouard
 int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */    New version 0.97 . First attempt to estimate force of mortality
 int popbased=0;    directly from the data i.e. without the need of knowing the health
     state at each age, but using a Gompertz model: log u =a + b*age .
 int *wav; /* Number of waves for this individuual 0 is possible */    This is the basic analysis of mortality and should be done before any
 int maxwav; /* Maxim number of waves */    other analysis, in order to test if the mortality estimated from the
 int jmin, jmax; /* min, max spacing between 2 waves */    cross-longitudinal survey is different from the mortality estimated
 int mle, weightopt;    from other sources like vital statistic data.
 int **mw; /* mw[mi][i] is number of the mi wave for this individual */  
 int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */    The same imach parameter file can be used but the option for mle should be -3.
 double jmean; /* Mean space between 2 waves */  
 double **oldm, **newm, **savm; /* Working pointers to matrices */    Agnès, who wrote this part of the code, tried to keep most of the
 double **oldms, **newms, **savms; /* Fixed working pointers to matrices */    former routines in order to include the new code within the former code.
 FILE *fic,*ficpar, *ficparo,*ficres,  *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;  
 FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;    The output is very simple: only an estimate of the intercept and of
 FILE *ficreseij;    the slope with 95% confident intervals.
   char filerese[FILENAMELENGTH];  
  FILE  *ficresvij;    Current limitations:
   char fileresv[FILENAMELENGTH];    A) Even if you enter covariates, i.e. with the
  FILE  *ficresvpl;    model= V1+V2 equation for example, the programm does only estimate a unique global model without covariates.
   char fileresvpl[FILENAMELENGTH];    B) There is no computation of Life Expectancy nor Life Table.
   
 #define NR_END 1    Revision 1.97  2004/02/20 13:25:42  lievre
 #define FREE_ARG char*    Version 0.96d. Population forecasting command line is (temporarily)
 #define FTOL 1.0e-10    suppressed.
   
 #define NRANSI    Revision 1.96  2003/07/15 15:38:55  brouard
 #define ITMAX 200    * imach.c (Repository): Errors in subdirf, 2, 3 while printing tmpout is
     rewritten within the same printf. Workaround: many printfs.
 #define TOL 2.0e-4  
     Revision 1.95  2003/07/08 07:54:34  brouard
 #define CGOLD 0.3819660    * imach.c (Repository):
 #define ZEPS 1.0e-10    (Repository): Using imachwizard code to output a more meaningful covariance
 #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d);    matrix (cov(a12,c31) instead of numbers.
   
 #define GOLD 1.618034    Revision 1.94  2003/06/27 13:00:02  brouard
 #define GLIMIT 100.0    Just cleaning
 #define TINY 1.0e-20  
     Revision 1.93  2003/06/25 16:33:55  brouard
 static double maxarg1,maxarg2;    (Module): On windows (cygwin) function asctime_r doesn't
 #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))    exist so I changed back to asctime which exists.
 #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))    (Module): Version 0.96b
    
 #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))    Revision 1.92  2003/06/25 16:30:45  brouard
 #define rint(a) floor(a+0.5)    (Module): On windows (cygwin) function asctime_r doesn't
     exist so I changed back to asctime which exists.
 static double sqrarg;  
 #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)    Revision 1.91  2003/06/25 15:30:29  brouard
 #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}    * imach.c (Repository): Duplicated warning errors corrected.
     (Repository): Elapsed time after each iteration is now output. It
 int imx;    helps to forecast when convergence will be reached. Elapsed time
 int stepm;    is stamped in powell.  We created a new html file for the graphs
 /* Stepm, step in month: minimum step interpolation*/    concerning matrix of covariance. It has extension -cov.htm.
   
 int estepm;    Revision 1.90  2003/06/24 12:34:15  brouard
 /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/    (Module): Some bugs corrected for windows. Also, when
     mle=-1 a template is output in file "or"mypar.txt with the design
 int m,nb;    of the covariance matrix to be input.
 int *num, firstpass=0, lastpass=4,*cod, *ncodemax, *Tage;  
 double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;    Revision 1.89  2003/06/24 12:30:52  brouard
 double **pmmij, ***probs, ***mobaverage;    (Module): Some bugs corrected for windows. Also, when
 double dateintmean=0;    mle=-1 a template is output in file "or"mypar.txt with the design
     of the covariance matrix to be input.
 double *weight;  
 int **s; /* Status */    Revision 1.88  2003/06/23 17:54:56  brouard
 double *agedc, **covar, idx;    * 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.
 int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;  
     Revision 1.87  2003/06/18 12:26:01  brouard
 double ftol=FTOL; /* Tolerance for computing Max Likelihood */    Version 0.96
 double ftolhess; /* Tolerance for computing hessian */  
     Revision 1.86  2003/06/17 20:04:08  brouard
 /**************** split *************************/    (Module): Change position of html and gnuplot routines and added
 static  int split( char *path, char *dirc, char *name, char *ext, char *finame )    routine fileappend.
 {  
    char *s;                             /* pointer */    Revision 1.85  2003/06/17 13:12:43  brouard
    int  l1, l2;                         /* length counters */    * imach.c (Repository): Check when date of death was earlier that
     current date of interview. It may happen when the death was just
    l1 = strlen( path );                 /* length of path */    prior to the death. In this case, dh was negative and likelihood
    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );    was wrong (infinity). We still send an "Error" but patch by
 #ifdef windows    assuming that the date of death was just one stepm after the
    s = strrchr( path, '\\' );           /* find last / */    interview.
 #else    (Repository): Because some people have very long ID (first column)
    s = strrchr( path, '/' );            /* find last / */    we changed int to long in num[] and we added a new lvector for
 #endif    memory allocation. But we also truncated to 8 characters (left
    if ( s == NULL ) {                   /* no directory, so use current */    truncation)
 #if     defined(__bsd__)                /* get current working directory */    (Repository): No more line truncation errors.
       extern char       *getwd( );  
     Revision 1.84  2003/06/13 21:44:43  brouard
       if ( getwd( dirc ) == NULL ) {    * imach.c (Repository): Replace "freqsummary" at a correct
 #else    place. It differs from routine "prevalence" which may be called
       extern char       *getcwd( );    many times. Probs is memory consuming and must be used with
     parcimony.
       if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {    Version 0.95a3 (should output exactly the same maximization than 0.8a2)
 #endif  
          return( GLOCK_ERROR_GETCWD );    Revision 1.83  2003/06/10 13:39:11  lievre
       }    *** empty log message ***
       strcpy( name, path );             /* we've got it */  
    } else {                             /* strip direcotry from path */    Revision 1.82  2003/06/05 15:57:20  brouard
       s++;                              /* after this, the filename */    Add log in  imach.c and  fullversion number is now printed.
       l2 = strlen( s );                 /* length of filename */  
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );  */
       strcpy( name, s );                /* save file name */  /*
       strncpy( dirc, path, l1 - l2 );   /* now the directory */     Interpolated Markov Chain
       dirc[l1-l2] = 0;                  /* add zero */  
    }    Short summary of the programme:
    l1 = strlen( dirc );                 /* length of directory */    
 #ifdef windows    This program computes Healthy Life Expectancies from
    if ( dirc[l1-1] != '\\' ) { dirc[l1] = '\\'; dirc[l1+1] = 0; }    cross-longitudinal data. Cross-longitudinal data consist in: -1- a
 #else    first survey ("cross") where individuals from different ages are
    if ( dirc[l1-1] != '/' ) { dirc[l1] = '/'; dirc[l1+1] = 0; }    interviewed on their health status or degree of disability (in the
 #endif    case of a health survey which is our main interest) -2- at least a
    s = strrchr( name, '.' );            /* find last / */    second wave of interviews ("longitudinal") which measure each change
    s++;    (if any) in individual health status.  Health expectancies are
    strcpy(ext,s);                       /* save extension */    computed from the time spent in each health state according to a
    l1= strlen( name);    model. More health states you consider, more time is necessary to reach the
    l2= strlen( s)+1;    Maximum Likelihood of the parameters involved in the model.  The
    strncpy( finame, name, l1-l2);    simplest model is the multinomial logistic model where pij is the
    finame[l1-l2]= 0;    probability to be observed in state j at the second wave
    return( 0 );                         /* we're done */    conditional to be observed in state i at the first wave. Therefore
 }    the model is: log(pij/pii)= aij + bij*age+ cij*sex + etc , where
     'age' is age and 'sex' is a covariate. If you want to have a more
     complex model than "constant and age", you should modify the program
 /******************************************/    where the markup *Covariates have to be included here again* invites
     you to do it.  More covariates you add, slower the
 void replace(char *s, char*t)    convergence.
 {  
   int i;    The advantage of this computer programme, compared to a simple
   int lg=20;    multinomial logistic model, is clear when the delay between waves is not
   i=0;    identical for each individual. Also, if a individual missed an
   lg=strlen(t);    intermediate interview, the information is lost, but taken into
   for(i=0; i<= lg; i++) {    account using an interpolation or extrapolation.  
     (s[i] = t[i]);  
     if (t[i]== '\\') s[i]='/';    hPijx is the probability to be observed in state i at age x+h
   }    conditional to the observed state i at age x. The delay 'h' can be
 }    split into an exact number (nh*stepm) of unobserved intermediate
     states. This elementary transition (by month, quarter,
 int nbocc(char *s, char occ)    semester or year) is modelled as a multinomial logistic.  The hPx
 {    matrix is simply the matrix product of nh*stepm elementary matrices
   int i,j=0;    and the contribution of each individual to the likelihood is simply
   int lg=20;    hPijx.
   i=0;  
   lg=strlen(s);    Also this programme outputs the covariance matrix of the parameters but also
   for(i=0; i<= lg; i++) {    of the life expectancies. It also computes the period (stable) prevalence. 
   if  (s[i] == occ ) j++;    
   }    Authors: Nicolas Brouard (brouard@ined.fr) and Agnès Lièvre (lievre@ined.fr).
   return j;             Institut national d'études démographiques, Paris.
 }    This software have been partly granted by Euro-REVES, a concerted action
     from the European Union.
 void cutv(char *u,char *v, char*t, char occ)    It is copyrighted identically to a GNU software product, ie programme and
 {    software can be distributed freely for non commercial use. Latest version
   int i,lg,j,p=0;    can be accessed at http://euroreves.ined.fr/imach .
   i=0;  
   for(j=0; j<=strlen(t)-1; j++) {    Help to debug: LD_PRELOAD=/usr/local/lib/libnjamd.so ./imach foo.imach
     if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;    or better on gdb : set env LD_PRELOAD=/usr/local/lib/libnjamd.so
   }    
     **********************************************************************/
   lg=strlen(t);  /*
   for(j=0; j<p; j++) {    main
     (u[j] = t[j]);    read parameterfile
   }    read datafile
      u[p]='\0';    concatwav
     freqsummary
    for(j=0; j<= lg; j++) {    if (mle >= 1)
     if (j>=(p+1))(v[j-p-1] = t[j]);      mlikeli
   }    print results files
 }    if mle==1 
        computes hessian
 /********************** nrerror ********************/    read end of parameter file: agemin, agemax, bage, fage, estepm
         begin-prev-date,...
 void nrerror(char error_text[])    open gnuplot file
 {    open html file
   fprintf(stderr,"ERREUR ...\n");    period (stable) prevalence
   fprintf(stderr,"%s\n",error_text);     for age prevalim()
   exit(1);    h Pij x
 }    variance of p varprob
 /*********************** vector *******************/    forecasting if prevfcast==1 prevforecast call prevalence()
 double *vector(int nl, int nh)    health expectancies
 {    Variance-covariance of DFLE
   double *v;    prevalence()
   v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));     movingaverage()
   if (!v) nrerror("allocation failure in vector");    varevsij() 
   return v-nl+NR_END;    if popbased==1 varevsij(,popbased)
 }    total life expectancies
     Variance of period (stable) prevalence
 /************************ free vector ******************/   end
 void free_vector(double*v, int nl, int nh)  */
 {  
   free((FREE_ARG)(v+nl-NR_END));  
 }  
    
 /************************ivector *******************************/  #include <math.h>
 int *ivector(long nl,long nh)  #include <stdio.h>
 {  #include <stdlib.h>
   int *v;  #include <string.h>
   v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));  #include <unistd.h>
   if (!v) nrerror("allocation failure in ivector");  
   return v-nl+NR_END;  #include <limits.h>
 }  #include <sys/types.h>
   #include <sys/stat.h>
 /******************free ivector **************************/  #include <errno.h>
 void free_ivector(int *v, long nl, long nh)  extern int errno;
 {  
   free((FREE_ARG)(v+nl-NR_END));  /* #include <sys/time.h> */
 }  #include <time.h>
   #include "timeval.h"
 /******************* imatrix *******************************/  
 int **imatrix(long nrl, long nrh, long ncl, long nch)  /* #include <libintl.h> */
      /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */  /* #define _(String) gettext (String) */
 {  
   long i, nrow=nrh-nrl+1,ncol=nch-ncl+1;  #define MAXLINE 256
   int **m;  
    #define GNUPLOTPROGRAM "gnuplot"
   /* allocate pointers to rows */  /*#define GNUPLOTPROGRAM "..\\gp37mgw\\wgnuplot"*/
   m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*)));  #define FILENAMELENGTH 132
   if (!m) nrerror("allocation failure 1 in matrix()");  
   m += NR_END;  #define GLOCK_ERROR_NOPATH              -1      /* empty path */
   m -= nrl;  #define GLOCK_ERROR_GETCWD              -2      /* cannot get cwd */
    
    #define MAXPARM 30 /* Maximum number of parameters for the optimization */
   /* allocate rows and set pointers to them */  #define NPARMAX 64 /* (nlstate+ndeath-1)*nlstate*ncovmodel */
   m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int)));  
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  #define NINTERVMAX 8
   m[nrl] += NR_END;  #define NLSTATEMAX 8 /* Maximum number of live states (for func) */
   m[nrl] -= ncl;  #define NDEATHMAX 8 /* Maximum number of dead states (for func) */
    #define NCOVMAX 8 /* Maximum number of covariates */
   for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol;  #define MAXN 20000
    #define YEARM 12. /* Number of months per year */
   /* return pointer to array of pointers to rows */  #define AGESUP 130
   return m;  #define AGEBASE 40
 }  #define AGEGOMP 10. /* Minimal age for Gompertz adjustment */
   #ifdef UNIX
 /****************** free_imatrix *************************/  #define DIRSEPARATOR '/'
 void free_imatrix(m,nrl,nrh,ncl,nch)  #define CHARSEPARATOR "/"
       int **m;  #define ODIRSEPARATOR '\\'
       long nch,ncl,nrh,nrl;  #else
      /* free an int matrix allocated by imatrix() */  #define DIRSEPARATOR '\\'
 {  #define CHARSEPARATOR "\\"
   free((FREE_ARG) (m[nrl]+ncl-NR_END));  #define ODIRSEPARATOR '/'
   free((FREE_ARG) (m+nrl-NR_END));  #endif
 }  
   /* $Id$ */
 /******************* matrix *******************************/  /* $State$ */
 double **matrix(long nrl, long nrh, long ncl, long nch)  
 {  char version[]="Imach version 0.98d, March 2006, INED-EUROREVES-Institut de longevite ";
   long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;  char fullversion[]="$Revision$ $Date$"; 
   double **m;  char strstart[80];
   char optionfilext[10], optionfilefiname[FILENAMELENGTH];
   m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  int erreur, nberr=0, nbwarn=0; /* Error number, number of errors number of warnings  */
   if (!m) nrerror("allocation failure 1 in matrix()");  int nvar;
   m += NR_END;  int cptcovn=0, cptcovage=0, cptcoveff=0,cptcov;
   m -= nrl;  int npar=NPARMAX;
   int nlstate=2; /* Number of live states */
   m[nrl]=(double *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  int ndeath=1; /* Number of dead states */
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  int ncovmodel, ncovcol;     /* Total number of covariables including constant a12*1 +b12*x ncovmodel=2 */
   m[nrl] += NR_END;  int popbased=0;
   m[nrl] -= ncl;  
   int *wav; /* Number of waves for this individuual 0 is possible */
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  int maxwav; /* Maxim number of waves */
   return m;  int jmin, jmax; /* min, max spacing between 2 waves */
 }  int ijmin, ijmax; /* Individuals having jmin and jmax */ 
   int gipmx, gsw; /* Global variables on the number of contributions 
 /*************************free matrix ************************/                     to the likelihood and the sum of weights (done by funcone)*/
 void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)  int mle, weightopt;
 {  int **mw; /* mw[mi][i] is number of the mi wave for this individual */
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  int **dh; /* dh[mi][i] is number of steps between mi,mi+1 for this individual */
   free((FREE_ARG)(m+nrl-NR_END));  int **bh; /* bh[mi][i] is the bias (+ or -) for this individual if the delay between
 }             * wave mi and wave mi+1 is not an exact multiple of stepm. */
   double jmean; /* Mean space between 2 waves */
 /******************* ma3x *******************************/  double **oldm, **newm, **savm; /* Working pointers to matrices */
 double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)  double **oldms, **newms, **savms; /* Fixed working pointers to matrices */
 {  FILE *fic,*ficpar, *ficparo,*ficres, *ficresp, *ficrespl, *ficrespij, *ficrest,*ficresf,*ficrespop;
   long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;  FILE *ficlog, *ficrespow;
   double ***m;  int globpr; /* Global variable for printing or not */
   double fretone; /* Only one call to likelihood */
   m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));  long ipmx; /* Number of contributions */
   if (!m) nrerror("allocation failure 1 in matrix()");  double sw; /* Sum of weights */
   m += NR_END;  char filerespow[FILENAMELENGTH];
   m -= nrl;  char fileresilk[FILENAMELENGTH]; /* File of individual contributions to the likelihood */
   FILE *ficresilk;
   m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));  FILE *ficgp,*ficresprob,*ficpop, *ficresprobcov, *ficresprobcor;
   if (!m[nrl]) nrerror("allocation failure 2 in matrix()");  FILE *ficresprobmorprev;
   m[nrl] += NR_END;  FILE *fichtm, *fichtmcov; /* Html File */
   m[nrl] -= ncl;  FILE *ficreseij;
   char filerese[FILENAMELENGTH];
   for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;  FILE *ficresstdeij;
   char fileresstde[FILENAMELENGTH];
   m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));  FILE *ficrescveij;
   if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");  char filerescve[FILENAMELENGTH];
   m[nrl][ncl] += NR_END;  FILE  *ficresvij;
   m[nrl][ncl] -= nll;  char fileresv[FILENAMELENGTH];
   for (j=ncl+1; j<=nch; j++)  FILE  *ficresvpl;
     m[nrl][j]=m[nrl][j-1]+nlay;  char fileresvpl[FILENAMELENGTH];
    char title[MAXLINE];
   for (i=nrl+1; i<=nrh; i++) {  char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];
     m[i][ncl]=m[i-1l][ncl]+ncol*nlay;  char plotcmd[FILENAMELENGTH], pplotcmd[FILENAMELENGTH];
     for (j=ncl+1; j<=nch; j++)  char tmpout[FILENAMELENGTH],  tmpout2[FILENAMELENGTH]; 
       m[i][j]=m[i][j-1]+nlay;  char command[FILENAMELENGTH];
   }  int  outcmd=0;
   return m;  
 }  char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];
   
 /*************************free ma3x ************************/  char filelog[FILENAMELENGTH]; /* Log file */
 void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)  char filerest[FILENAMELENGTH];
 {  char fileregp[FILENAMELENGTH];
   free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));  char popfile[FILENAMELENGTH];
   free((FREE_ARG)(m[nrl]+ncl-NR_END));  
   free((FREE_ARG)(m+nrl-NR_END));  char optionfilegnuplot[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilehtmcov[FILENAMELENGTH] ;
 }  
   struct timeval start_time, end_time, curr_time, last_time, forecast_time;
 /***************** f1dim *************************/  struct timezone tzp;
 extern int ncom;  extern int gettimeofday();
 extern double *pcom,*xicom;  struct tm tmg, tm, tmf, *gmtime(), *localtime();
 extern double (*nrfunc)(double []);  long time_value;
    extern long time();
 double f1dim(double x)  char strcurr[80], strfor[80];
 {  
   int j;  char *endptr;
   double f;  long lval;
   double *xt;  
    #define NR_END 1
   xt=vector(1,ncom);  #define FREE_ARG char*
   for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j];  #define FTOL 1.0e-10
   f=(*nrfunc)(xt);  
   free_vector(xt,1,ncom);  #define NRANSI 
   return f;  #define ITMAX 200 
 }  
   #define TOL 2.0e-4 
 /*****************brent *************************/  
 double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin)  #define CGOLD 0.3819660 
 {  #define ZEPS 1.0e-10 
   int iter;  #define SHFT(a,b,c,d) (a)=(b);(b)=(c);(c)=(d); 
   double a,b,d,etemp;  
   double fu,fv,fw,fx;  #define GOLD 1.618034 
   double ftemp;  #define GLIMIT 100.0 
   double p,q,r,tol1,tol2,u,v,w,x,xm;  #define TINY 1.0e-20 
   double e=0.0;  
    static double maxarg1,maxarg2;
   a=(ax < cx ? ax : cx);  #define FMAX(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)>(maxarg2)? (maxarg1):(maxarg2))
   b=(ax > cx ? ax : cx);  #define FMIN(a,b) (maxarg1=(a),maxarg2=(b),(maxarg1)<(maxarg2)? (maxarg1):(maxarg2))
   x=w=v=bx;    
   fw=fv=fx=(*f)(x);  #define SIGN(a,b) ((b)>0.0 ? fabs(a) : -fabs(a))
   for (iter=1;iter<=ITMAX;iter++) {  #define rint(a) floor(a+0.5)
     xm=0.5*(a+b);  
     tol2=2.0*(tol1=tol*fabs(x)+ZEPS);  static double sqrarg;
     /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/  #define SQR(a) ((sqrarg=(a)) == 0.0 ? 0.0 :sqrarg*sqrarg)
     printf(".");fflush(stdout);  #define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;} 
 #ifdef DEBUG  int agegomp= AGEGOMP;
     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)))) { */  int imx; 
 #endif  int stepm=1;
     if (fabs(x-xm) <= (tol2-0.5*(b-a))){  /* Stepm, step in month: minimum step interpolation*/
       *xmin=x;  
       return fx;  int estepm;
     }  /* Estepm, step in month to interpolate survival function in order to approximate Life Expectancy*/
     ftemp=fu;  
     if (fabs(e) > tol1) {  int m,nb;
       r=(x-w)*(fx-fv);  long *num;
       q=(x-v)*(fx-fw);  int firstpass=0, lastpass=4,*cod, *ncodemax, *Tage,*cens;
       p=(x-v)*q-(x-w)*r;  double **agev,*moisnais, *annais, *moisdc, *andc,**mint, **anint;
       q=2.0*(q-r);  double **pmmij, ***probs;
       if (q > 0.0) p = -p;  double *ageexmed,*agecens;
       q=fabs(q);  double dateintmean=0;
       etemp=e;  
       e=d;  double *weight;
       if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x))  int **s; /* Status */
         d=CGOLD*(e=(x >= xm ? a-x : b-x));  double *agedc, **covar, idx;
       else {  int **nbcode, *Tcode, *Tvar, **codtab, **Tvard, *Tprod, cptcovprod, *Tvaraff;
         d=p/q;  double *lsurv, *lpop, *tpop;
         u=x+d;  
         if (u-a < tol2 || b-u < tol2)  double ftol=FTOL; /* Tolerance for computing Max Likelihood */
           d=SIGN(tol1,xm-x);  double ftolhess; /* Tolerance for computing hessian */
       }  
     } else {  /**************** split *************************/
       d=CGOLD*(e=(x >= xm ? a-x : b-x));  static  int split( char *path, char *dirc, char *name, char *ext, char *finame )
     }  {
     u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d));    /* From a file name with (full) path (either Unix or Windows) we extract the directory (dirc)
     fu=(*f)(u);       the name of the file (name), its extension only (ext) and its first part of the name (finame)
     if (fu <= fx) {    */ 
       if (u >= x) a=x; else b=x;    char  *ss;                            /* pointer */
       SHFT(v,w,x,u)    int   l1, l2;                         /* length counters */
         SHFT(fv,fw,fx,fu)  
         } else {    l1 = strlen(path );                   /* length of path */
           if (u < x) a=u; else b=u;    if ( l1 == 0 ) return( GLOCK_ERROR_NOPATH );
           if (fu <= fw || w == x) {    ss= strrchr( path, DIRSEPARATOR );            /* find last / */
             v=w;    if ( ss == NULL ) {                   /* no directory, so determine current directory */
             w=u;      strcpy( name, path );               /* we got the fullname name because no directory */
             fv=fw;      /*if(strrchr(path, ODIRSEPARATOR )==NULL)
             fw=fu;        printf("Warning you should use %s as a separator\n",DIRSEPARATOR);*/
           } else if (fu <= fv || v == x || v == w) {      /* get current working directory */
             v=u;      /*    extern  char* getcwd ( char *buf , int len);*/
             fv=fu;      if ( getcwd( dirc, FILENAME_MAX ) == NULL ) {
           }        return( GLOCK_ERROR_GETCWD );
         }      }
   }      /* got dirc from getcwd*/
   nrerror("Too many iterations in brent");      printf(" DIRC = %s \n",dirc);
   *xmin=x;    } else {                              /* strip direcotry from path */
   return fx;      ss++;                               /* after this, the filename */
 }      l2 = strlen( ss );                  /* length of filename */
       if ( l2 == 0 ) return( GLOCK_ERROR_NOPATH );
 /****************** mnbrak ***********************/      strcpy( name, ss );         /* save file name */
       strncpy( dirc, path, l1 - l2 );     /* now the directory */
 void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc,      dirc[l1-l2] = 0;                    /* add zero */
             double (*func)(double))      printf(" DIRC2 = %s \n",dirc);
 {    }
   double ulim,u,r,q, dum;    /* We add a separator at the end of dirc if not exists */
   double fu;    l1 = strlen( dirc );                  /* length of directory */
      if( dirc[l1-1] != DIRSEPARATOR ){
   *fa=(*func)(*ax);      dirc[l1] =  DIRSEPARATOR;
   *fb=(*func)(*bx);      dirc[l1+1] = 0; 
   if (*fb > *fa) {      printf(" DIRC3 = %s \n",dirc);
     SHFT(dum,*ax,*bx,dum)    }
       SHFT(dum,*fb,*fa,dum)    ss = strrchr( name, '.' );            /* find last / */
       }    if (ss >0){
   *cx=(*bx)+GOLD*(*bx-*ax);      ss++;
   *fc=(*func)(*cx);      strcpy(ext,ss);                     /* save extension */
   while (*fb > *fc) {      l1= strlen( name);
     r=(*bx-*ax)*(*fb-*fc);      l2= strlen(ss)+1;
     q=(*bx-*cx)*(*fb-*fa);      strncpy( finame, name, l1-l2);
     u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/      finame[l1-l2]= 0;
       (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r));    }
     ulim=(*bx)+GLIMIT*(*cx-*bx);  
     if ((*bx-u)*(u-*cx) > 0.0) {    return( 0 );                          /* we're done */
       fu=(*func)(u);  }
     } else if ((*cx-u)*(u-ulim) > 0.0) {  
       fu=(*func)(u);  
       if (fu < *fc) {  /******************************************/
         SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx))  
           SHFT(*fb,*fc,fu,(*func)(u))  void replace_back_to_slash(char *s, char*t)
           }  {
     } else if ((u-ulim)*(ulim-*cx) >= 0.0) {    int i;
       u=ulim;    int lg=0;
       fu=(*func)(u);    i=0;
     } else {    lg=strlen(t);
       u=(*cx)+GOLD*(*cx-*bx);    for(i=0; i<= lg; i++) {
       fu=(*func)(u);      (s[i] = t[i]);
     }      if (t[i]== '\\') s[i]='/';
     SHFT(*ax,*bx,*cx,u)    }
       SHFT(*fa,*fb,*fc,fu)  }
       }  
 }  int nbocc(char *s, char occ)
   {
 /*************** linmin ************************/    int i,j=0;
     int lg=20;
 int ncom;    i=0;
 double *pcom,*xicom;    lg=strlen(s);
 double (*nrfunc)(double []);    for(i=0; i<= lg; i++) {
      if  (s[i] == occ ) j++;
 void linmin(double p[], double xi[], int n, double *fret,double (*func)(double []))    }
 {    return j;
   double brent(double ax, double bx, double cx,  }
                double (*f)(double), double tol, double *xmin);  
   double f1dim(double x);  void cutv(char *u,char *v, char*t, char occ)
   void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb,  {
               double *fc, double (*func)(double));    /* cuts string t into u and v where u ends before first occurence of char 'occ' 
   int j;       and v starts after first occurence of char 'occ' : ex cutv(u,v,"abcdef2ghi2j",'2')
   double xx,xmin,bx,ax;       gives u="abcedf" and v="ghi2j" */
   double fx,fb,fa;    int i,lg,j,p=0;
      i=0;
   ncom=n;    for(j=0; j<=strlen(t)-1; j++) {
   pcom=vector(1,n);      if((t[j]!= occ) && (t[j+1]== occ)) p=j+1;
   xicom=vector(1,n);    }
   nrfunc=func;  
   for (j=1;j<=n;j++) {    lg=strlen(t);
     pcom[j]=p[j];    for(j=0; j<p; j++) {
     xicom[j]=xi[j];      (u[j] = t[j]);
   }    }
   ax=0.0;       u[p]='\0';
   xx=1.0;  
   mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim);     for(j=0; j<= lg; j++) {
   *fret=brent(ax,xx,bx,f1dim,TOL,&xmin);      if (j>=(p+1))(v[j-p-1] = t[j]);
 #ifdef DEBUG    }
   printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);  }
 #endif  
   for (j=1;j<=n;j++) {  /********************** nrerror ********************/
     xi[j] *= xmin;  
     p[j] += xi[j];  void nrerror(char error_text[])
   }  {
   free_vector(xicom,1,n);    fprintf(stderr,"ERREUR ...\n");
   free_vector(pcom,1,n);    fprintf(stderr,"%s\n",error_text);
 }    exit(EXIT_FAILURE);
   }
 /*************** powell ************************/  /*********************** vector *******************/
 void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret,  double *vector(int nl, int nh)
             double (*func)(double []))  {
 {    double *v;
   void linmin(double p[], double xi[], int n, double *fret,    v=(double *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(double)));
               double (*func)(double []));    if (!v) nrerror("allocation failure in vector");
   int i,ibig,j;    return v-nl+NR_END;
   double del,t,*pt,*ptt,*xit;  }
   double fp,fptt;  
   double *xits;  /************************ free vector ******************/
   pt=vector(1,n);  void free_vector(double*v, int nl, int nh)
   ptt=vector(1,n);  {
   xit=vector(1,n);    free((FREE_ARG)(v+nl-NR_END));
   xits=vector(1,n);  }
   *fret=(*func)(p);  
   for (j=1;j<=n;j++) pt[j]=p[j];  /************************ivector *******************************/
   for (*iter=1;;++(*iter)) {  int *ivector(long nl,long nh)
     fp=(*fret);  {
     ibig=0;    int *v;
     del=0.0;    v=(int *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(int)));
     printf("\nPowell iter=%d -2*LL=%.12f",*iter,*fret);    if (!v) nrerror("allocation failure in ivector");
     for (i=1;i<=n;i++)    return v-nl+NR_END;
       printf(" %d %.12f",i, p[i]);  }
     printf("\n");  
     for (i=1;i<=n;i++) {  /******************free ivector **************************/
       for (j=1;j<=n;j++) xit[j]=xi[j][i];  void free_ivector(int *v, long nl, long nh)
       fptt=(*fret);  {
 #ifdef DEBUG    free((FREE_ARG)(v+nl-NR_END));
       printf("fret=%lf \n",*fret);  }
 #endif  
       printf("%d",i);fflush(stdout);  /************************lvector *******************************/
       linmin(p,xit,n,fret,func);  long *lvector(long nl,long nh)
       if (fabs(fptt-(*fret)) > del) {  {
         del=fabs(fptt-(*fret));    long *v;
         ibig=i;    v=(long *) malloc((size_t)((nh-nl+1+NR_END)*sizeof(long)));
       }    if (!v) nrerror("allocation failure in ivector");
 #ifdef DEBUG    return v-nl+NR_END;
       printf("%d %.12e",i,(*fret));  }
       for (j=1;j<=n;j++) {  
         xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);  /******************free lvector **************************/
         printf(" x(%d)=%.12e",j,xit[j]);  void free_lvector(long *v, long nl, long nh)
       }  {
       for(j=1;j<=n;j++)    free((FREE_ARG)(v+nl-NR_END));
         printf(" p=%.12e",p[j]);  }
       printf("\n");  
 #endif  /******************* imatrix *******************************/
     }  int **imatrix(long nrl, long nrh, long ncl, long nch) 
     if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {       /* allocate a int matrix with subscript range m[nrl..nrh][ncl..nch] */ 
 #ifdef DEBUG  { 
       int k[2],l;    long i, nrow=nrh-nrl+1,ncol=nch-ncl+1; 
       k[0]=1;    int **m; 
       k[1]=-1;    
       printf("Max: %.12e",(*func)(p));    /* allocate pointers to rows */ 
       for (j=1;j<=n;j++)    m=(int **) malloc((size_t)((nrow+NR_END)*sizeof(int*))); 
         printf(" %.12e",p[j]);    if (!m) nrerror("allocation failure 1 in matrix()"); 
       printf("\n");    m += NR_END; 
       for(l=0;l<=1;l++) {    m -= nrl; 
         for (j=1;j<=n;j++) {    
           ptt[j]=p[j]+(p[j]-pt[j])*k[l];    
           printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);    /* allocate rows and set pointers to them */ 
         }    m[nrl]=(int *) malloc((size_t)((nrow*ncol+NR_END)*sizeof(int))); 
         printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));    if (!m[nrl]) nrerror("allocation failure 2 in matrix()"); 
       }    m[nrl] += NR_END; 
 #endif    m[nrl] -= ncl; 
     
     for(i=nrl+1;i<=nrh;i++) m[i]=m[i-1]+ncol; 
       free_vector(xit,1,n);    
       free_vector(xits,1,n);    /* return pointer to array of pointers to rows */ 
       free_vector(ptt,1,n);    return m; 
       free_vector(pt,1,n);  } 
       return;  
     }  /****************** free_imatrix *************************/
     if (*iter == ITMAX) nrerror("powell exceeding maximum iterations.");  void free_imatrix(m,nrl,nrh,ncl,nch)
     for (j=1;j<=n;j++) {        int **m;
       ptt[j]=2.0*p[j]-pt[j];        long nch,ncl,nrh,nrl; 
       xit[j]=p[j]-pt[j];       /* free an int matrix allocated by imatrix() */ 
       pt[j]=p[j];  { 
     }    free((FREE_ARG) (m[nrl]+ncl-NR_END)); 
     fptt=(*func)(ptt);    free((FREE_ARG) (m+nrl-NR_END)); 
     if (fptt < fp) {  } 
       t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt);  
       if (t < 0.0) {  /******************* matrix *******************************/
         linmin(p,xit,n,fret,func);  double **matrix(long nrl, long nrh, long ncl, long nch)
         for (j=1;j<=n;j++) {  {
           xi[j][ibig]=xi[j][n];    long i, nrow=nrh-nrl+1, ncol=nch-ncl+1;
           xi[j][n]=xit[j];    double **m;
         }  
 #ifdef DEBUG    m=(double **) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
         printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);    if (!m) nrerror("allocation failure 1 in matrix()");
         for(j=1;j<=n;j++)    m += NR_END;
           printf(" %.12e",xit[j]);    m -= nrl;
         printf("\n");  
 #endif    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;
   }    m[nrl] -= ncl;
 }  
     for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
 /**** Prevalence limit ****************/    return m;
     /* print *(*(m+1)+70) or print m[1][70]; print m+1 or print &(m[1]) 
 double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)     */
 {  }
   /* Computes the prevalence limit in each live state at age x by left multiplying the unit  
      matrix by transitions matrix until convergence is reached */  /*************************free matrix ************************/
   void free_matrix(double **m, long nrl, long nrh, long ncl, long nch)
   int i, ii,j,k;  {
   double min, max, maxmin, maxmax,sumnew=0.;    free((FREE_ARG)(m[nrl]+ncl-NR_END));
   double **matprod2();    free((FREE_ARG)(m+nrl-NR_END));
   double **out, cov[NCOVMAX], **pmij();  }
   double **newm;  
   double agefin, delaymax=50 ; /* Max number of years to converge */  /******************* ma3x *******************************/
   double ***ma3x(long nrl, long nrh, long ncl, long nch, long nll, long nlh)
   for (ii=1;ii<=nlstate+ndeath;ii++)  {
     for (j=1;j<=nlstate+ndeath;j++){    long i, j, nrow=nrh-nrl+1, ncol=nch-ncl+1, nlay=nlh-nll+1;
       oldm[ii][j]=(ii==j ? 1.0 : 0.0);    double ***m;
     }  
     m=(double ***) malloc((size_t)((nrow+NR_END)*sizeof(double*)));
    cov[1]=1.;    if (!m) nrerror("allocation failure 1 in matrix()");
      m += NR_END;
  /* Even if hstepm = 1, at least one multiplication by the unit matrix */    m -= nrl;
   for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){  
     newm=savm;    m[nrl]=(double **) malloc((size_t)((nrow*ncol+NR_END)*sizeof(double)));
     /* Covariates have to be included here again */    if (!m[nrl]) nrerror("allocation failure 2 in matrix()");
      cov[2]=agefin;    m[nrl] += NR_END;
      m[nrl] -= ncl;
       for (k=1; k<=cptcovn;k++) {  
         cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];    for (i=nrl+1; i<=nrh; i++) m[i]=m[i-1]+ncol;
         /*      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]]);*/  
       }    m[nrl][ncl]=(double *) malloc((size_t)((nrow*ncol*nlay+NR_END)*sizeof(double)));
       for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    if (!m[nrl][ncl]) nrerror("allocation failure 3 in matrix()");
       for (k=1; k<=cptcovprod;k++)    m[nrl][ncl] += NR_END;
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    m[nrl][ncl] -= nll;
     for (j=ncl+1; j<=nch; j++) 
       /*printf("ij=%d cptcovprod=%d tvar=%d ", ij, cptcovprod, Tvar[1]);*/      m[nrl][j]=m[nrl][j-1]+nlay;
       /*printf("ij=%d cov[3]=%lf cov[4]=%lf \n",ij, cov[3],cov[4]);*/    
       /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/    for (i=nrl+1; i<=nrh; i++) {
     out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);      m[i][ncl]=m[i-1l][ncl]+ncol*nlay;
       for (j=ncl+1; j<=nch; j++) 
     savm=oldm;        m[i][j]=m[i][j-1]+nlay;
     oldm=newm;    }
     maxmax=0.;    return m; 
     for(j=1;j<=nlstate;j++){    /*  gdb: p *(m+1) <=> p m[1] and p (m+1) <=> p (m+1) <=> p &(m[1])
       min=1.;             &(m[i][j][k]) <=> *((*(m+i) + j)+k)
       max=0.;    */
       for(i=1; i<=nlstate; i++) {  }
         sumnew=0;  
         for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];  /*************************free ma3x ************************/
         prlim[i][j]= newm[i][j]/(1-sumnew);  void free_ma3x(double ***m, long nrl, long nrh, long ncl, long nch,long nll, long nlh)
         max=FMAX(max,prlim[i][j]);  {
         min=FMIN(min,prlim[i][j]);    free((FREE_ARG)(m[nrl][ncl]+ nll-NR_END));
       }    free((FREE_ARG)(m[nrl]+ncl-NR_END));
       maxmin=max-min;    free((FREE_ARG)(m+nrl-NR_END));
       maxmax=FMAX(maxmax,maxmin);  }
     }  
     if(maxmax < ftolpl){  /*************** function subdirf ***********/
       return prlim;  char *subdirf(char fileres[])
     }  {
   }    /* Caution optionfilefiname is hidden */
 }    strcpy(tmpout,optionfilefiname);
     strcat(tmpout,"/"); /* Add to the right */
 /*************** transition probabilities ***************/    strcat(tmpout,fileres);
     return tmpout;
 double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )  }
 {  
   double s1, s2;  /*************** function subdirf2 ***********/
   /*double t34;*/  char *subdirf2(char fileres[], char *preop)
   int i,j,j1, nc, ii, jj;  {
     
     for(i=1; i<= nlstate; i++){    /* Caution optionfilefiname is hidden */
     for(j=1; j<i;j++){    strcpy(tmpout,optionfilefiname);
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    strcat(tmpout,"/");
         /*s2 += param[i][j][nc]*cov[nc];*/    strcat(tmpout,preop);
         s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    strcat(tmpout,fileres);
         /*printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2);*/    return tmpout;
       }  }
       ps[i][j]=s2;  
       /*printf("s1=%.17e, s2=%.17e\n",s1,s2);*/  /*************** function subdirf3 ***********/
     }  char *subdirf3(char fileres[], char *preop, char *preop2)
     for(j=i+1; j<=nlstate+ndeath;j++){  {
       for (nc=1, s2=0.;nc <=ncovmodel; nc++){    
         s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];    /* Caution optionfilefiname is hidden */
         /*printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2);*/    strcpy(tmpout,optionfilefiname);
       }    strcat(tmpout,"/");
       ps[i][j]=s2;    strcat(tmpout,preop);
     }    strcat(tmpout,preop2);
   }    strcat(tmpout,fileres);
     /*ps[3][2]=1;*/    return tmpout;
   }
   for(i=1; i<= nlstate; i++){  
      s1=0;  /***************** f1dim *************************/
     for(j=1; j<i; j++)  extern int ncom; 
       s1+=exp(ps[i][j]);  extern double *pcom,*xicom;
     for(j=i+1; j<=nlstate+ndeath; j++)  extern double (*nrfunc)(double []); 
       s1+=exp(ps[i][j]);   
     ps[i][i]=1./(s1+1.);  double f1dim(double x) 
     for(j=1; j<i; j++)  { 
       ps[i][j]= exp(ps[i][j])*ps[i][i];    int j; 
     for(j=i+1; j<=nlstate+ndeath; j++)    double f;
       ps[i][j]= exp(ps[i][j])*ps[i][i];    double *xt; 
     /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */   
   } /* end i */    xt=vector(1,ncom); 
     for (j=1;j<=ncom;j++) xt[j]=pcom[j]+x*xicom[j]; 
   for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){    f=(*nrfunc)(xt); 
     for(jj=1; jj<= nlstate+ndeath; jj++){    free_vector(xt,1,ncom); 
       ps[ii][jj]=0;    return f; 
       ps[ii][ii]=1;  } 
     }  
   }  /*****************brent *************************/
   double brent(double ax, double bx, double cx, double (*f)(double), double tol,  double *xmin) 
   { 
   /*   for(ii=1; ii<= nlstate+ndeath; ii++){    int iter; 
     for(jj=1; jj<= nlstate+ndeath; jj++){    double a,b,d,etemp;
      printf("%lf ",ps[ii][jj]);    double fu,fv,fw,fx;
    }    double ftemp;
     printf("\n ");    double p,q,r,tol1,tol2,u,v,w,x,xm; 
     }    double e=0.0; 
     printf("\n ");printf("%lf ",cov[2]);*/   
 /*    a=(ax < cx ? ax : cx); 
   for(i=1; i<= npar; i++) printf("%f ",x[i]);    b=(ax > cx ? ax : cx); 
   goto end;*/    x=w=v=bx; 
     return ps;    fw=fv=fx=(*f)(x); 
 }    for (iter=1;iter<=ITMAX;iter++) { 
       xm=0.5*(a+b); 
 /**************** Product of 2 matrices ******************/      tol2=2.0*(tol1=tol*fabs(x)+ZEPS); 
       /*          if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret)))*/
 double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)      printf(".");fflush(stdout);
 {      fprintf(ficlog,".");fflush(ficlog);
   /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times  #ifdef DEBUG
      b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */      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);
   /* in, b, out are matrice of pointers which should have been initialized      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);
      before: only the contents of out is modified. The function returns      /*          if ((fabs(x-xm) <= (tol2-0.5*(b-a)))||(2.0*fabs(fu-ftemp) <= ftol*1.e-2*(fabs(fu)+fabs(ftemp)))) { */
      a pointer to pointers identical to out */  #endif
   long i, j, k;      if (fabs(x-xm) <= (tol2-0.5*(b-a))){ 
   for(i=nrl; i<= nrh; i++)        *xmin=x; 
     for(k=ncolol; k<=ncoloh; k++)        return fx; 
       for(j=ncl,out[i][k]=0.; j<=nch; j++)      } 
         out[i][k] +=in[i][j]*b[j][k];      ftemp=fu;
       if (fabs(e) > tol1) { 
   return out;        r=(x-w)*(fx-fv); 
 }        q=(x-v)*(fx-fw); 
         p=(x-v)*q-(x-w)*r; 
         q=2.0*(q-r); 
 /************* Higher Matrix Product ***************/        if (q > 0.0) p = -p; 
         q=fabs(q); 
 double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )        etemp=e; 
 {        e=d; 
   /* Computes the transition matrix starting at age 'age' over 'nhstepm*hstepm*stepm' month        if (fabs(p) >= fabs(0.5*q*etemp) || p <= q*(a-x) || p >= q*(b-x)) 
      duration (i.e. until          d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
      age (in years)  age+nhstepm*stepm/12) by multiplying nhstepm*hstepm matrices.        else { 
      Output is stored in matrix po[i][j][h] for h every 'hstepm' step          d=p/q; 
      (typically every 2 years instead of every month which is too big).          u=x+d; 
      Model is determined by parameters x and covariates have to be          if (u-a < tol2 || b-u < tol2) 
      included manually here.            d=SIGN(tol1,xm-x); 
         } 
      */      } else { 
         d=CGOLD*(e=(x >= xm ? a-x : b-x)); 
   int i, j, d, h, k;      } 
   double **out, cov[NCOVMAX];      u=(fabs(d) >= tol1 ? x+d : x+SIGN(tol1,d)); 
   double **newm;      fu=(*f)(u); 
       if (fu <= fx) { 
   /* Hstepm could be zero and should return the unit matrix */        if (u >= x) a=x; else b=x; 
   for (i=1;i<=nlstate+ndeath;i++)        SHFT(v,w,x,u) 
     for (j=1;j<=nlstate+ndeath;j++){          SHFT(fv,fw,fx,fu) 
       oldm[i][j]=(i==j ? 1.0 : 0.0);          } else { 
       po[i][j][0]=(i==j ? 1.0 : 0.0);            if (u < x) a=u; else b=u; 
     }            if (fu <= fw || w == x) { 
   /* Even if hstepm = 1, at least one multiplication by the unit matrix */              v=w; 
   for(h=1; h <=nhstepm; h++){              w=u; 
     for(d=1; d <=hstepm; d++){              fv=fw; 
       newm=savm;              fw=fu; 
       /* Covariates have to be included here again */            } else if (fu <= fv || v == x || v == w) { 
       cov[1]=1.;              v=u; 
       cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;              fv=fu; 
       for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];            } 
       for (k=1; k<=cptcovage;k++)          } 
         cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];    } 
       for (k=1; k<=cptcovprod;k++)    nrerror("Too many iterations in brent"); 
         cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];    *xmin=x; 
     return fx; 
   } 
       /*printf("hxi cptcov=%d cptcode=%d\n",cptcov,cptcode);*/  
       /*printf("h=%d d=%d age=%f cov=%f\n",h,d,age,cov[2]);*/  /****************** mnbrak ***********************/
       out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath,  
                    pmij(pmmij,cov,ncovmodel,x,nlstate));  void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, double *fc, 
       savm=oldm;              double (*func)(double)) 
       oldm=newm;  { 
     }    double ulim,u,r,q, dum;
     for(i=1; i<=nlstate+ndeath; i++)    double fu; 
       for(j=1;j<=nlstate+ndeath;j++) {   
         po[i][j][h]=newm[i][j];    *fa=(*func)(*ax); 
         /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);    *fb=(*func)(*bx); 
          */    if (*fb > *fa) { 
       }      SHFT(dum,*ax,*bx,dum) 
   } /* end h */        SHFT(dum,*fb,*fa,dum) 
   return po;        } 
 }    *cx=(*bx)+GOLD*(*bx-*ax); 
     *fc=(*func)(*cx); 
     while (*fb > *fc) { 
 /*************** log-likelihood *************/      r=(*bx-*ax)*(*fb-*fc); 
 double func( double *x)      q=(*bx-*cx)*(*fb-*fa); 
 {      u=(*bx)-((*bx-*cx)*q-(*bx-*ax)*r)/ 
   int i, ii, j, k, mi, d, kk;        (2.0*SIGN(FMAX(fabs(q-r),TINY),q-r)); 
   double l, ll[NLSTATEMAX], cov[NCOVMAX];      ulim=(*bx)+GLIMIT*(*cx-*bx); 
   double **out;      if ((*bx-u)*(u-*cx) > 0.0) { 
   double sw; /* Sum of weights */        fu=(*func)(u); 
   double lli; /* Individual log likelihood */      } else if ((*cx-u)*(u-ulim) > 0.0) { 
   long ipmx;        fu=(*func)(u); 
   /*extern weight */        if (fu < *fc) { 
   /* We are differentiating ll according to initial status */          SHFT(*bx,*cx,u,*cx+GOLD*(*cx-*bx)) 
   /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/            SHFT(*fb,*fc,fu,(*func)(u)) 
   /*for(i=1;i<imx;i++)            } 
     printf(" %d\n",s[4][i]);      } else if ((u-ulim)*(ulim-*cx) >= 0.0) { 
   */        u=ulim; 
   cov[1]=1.;        fu=(*func)(u); 
       } else { 
   for(k=1; k<=nlstate; k++) ll[k]=0.;        u=(*cx)+GOLD*(*cx-*bx); 
   for (i=1,ipmx=0, sw=0.; i<=imx; i++){        fu=(*func)(u); 
     for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];      } 
     for(mi=1; mi<= wav[i]-1; mi++){      SHFT(*ax,*bx,*cx,u) 
       for (ii=1;ii<=nlstate+ndeath;ii++)        SHFT(*fa,*fb,*fc,fu) 
         for (j=1;j<=nlstate+ndeath;j++) oldm[ii][j]=(ii==j ? 1.0 : 0.0);        } 
       for(d=0; d<dh[mi][i]; d++){  } 
         newm=savm;  
         cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;  /*************** linmin ************************/
         for (kk=1; kk<=cptcovage;kk++) {  
           cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];  int ncom; 
         }  double *pcom,*xicom;
          double (*nrfunc)(double []); 
         out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,   
                      1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));  void linmin(double p[], double xi[], int n, double *fret,double (*func)(double [])) 
         savm=oldm;  { 
         oldm=newm;    double brent(double ax, double bx, double cx, 
                         double (*f)(double), double tol, double *xmin); 
            double f1dim(double x); 
       } /* end mult */    void mnbrak(double *ax, double *bx, double *cx, double *fa, double *fb, 
                      double *fc, double (*func)(double)); 
       lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);    int j; 
       /* printf(" %f ",out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/    double xx,xmin,bx,ax; 
       ipmx +=1;    double fx,fb,fa;
       sw += weight[i];   
       ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;    ncom=n; 
     } /* end of wave */    pcom=vector(1,n); 
   } /* end of individual */    xicom=vector(1,n); 
     nrfunc=func; 
   for(k=1,l=0.; k<=nlstate; k++) l += ll[k];    for (j=1;j<=n;j++) { 
   /* printf("l1=%f l2=%f ",ll[1],ll[2]); */      pcom[j]=p[j]; 
   l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */      xicom[j]=xi[j]; 
   return -l;    } 
 }    ax=0.0; 
     xx=1.0; 
     mnbrak(&ax,&xx,&bx,&fa,&fx,&fb,f1dim); 
 /*********** Maximum Likelihood Estimation ***************/    *fret=brent(ax,xx,bx,f1dim,TOL,&xmin); 
   #ifdef DEBUG
 void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))    printf("retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
 {    fprintf(ficlog,"retour brent fret=%.12e xmin=%.12e\n",*fret,xmin);
   int i,j, iter;  #endif
   double **xi,*delti;    for (j=1;j<=n;j++) { 
   double fret;      xi[j] *= xmin; 
   xi=matrix(1,npar,1,npar);      p[j] += xi[j]; 
   for (i=1;i<=npar;i++)    } 
     for (j=1;j<=npar;j++)    free_vector(xicom,1,n); 
       xi[i][j]=(i==j ? 1.0 : 0.0);    free_vector(pcom,1,n); 
   printf("Powell\n");  } 
   powell(p,xi,npar,ftol,&iter,&fret,func);  
   char *asc_diff_time(long time_sec, char ascdiff[])
    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));  {
   fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));    long sec_left, days, hours, minutes;
     days = (time_sec) / (60*60*24);
 }    sec_left = (time_sec) % (60*60*24);
     hours = (sec_left) / (60*60) ;
 /**** Computes Hessian and covariance matrix ***/    sec_left = (sec_left) %(60*60);
 void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))    minutes = (sec_left) /60;
 {    sec_left = (sec_left) % (60);
   double  **a,**y,*x,pd;    sprintf(ascdiff,"%d day(s) %d hour(s) %d minute(s) %d second(s)",days, hours, minutes, sec_left);  
   double **hess;    return ascdiff;
   int i, j,jk;  }
   int *indx;  
   /*************** powell ************************/
   double hessii(double p[], double delta, int theta, double delti[]);  void powell(double p[], double **xi, int n, double ftol, int *iter, double *fret, 
   double hessij(double p[], double delti[], int i, int j);              double (*func)(double [])) 
   void lubksb(double **a, int npar, int *indx, double b[]) ;  { 
   void ludcmp(double **a, int npar, int *indx, double *d) ;    void linmin(double p[], double xi[], int n, double *fret, 
                 double (*func)(double [])); 
   hess=matrix(1,npar,1,npar);    int i,ibig,j; 
     double del,t,*pt,*ptt,*xit;
   printf("\nCalculation of the hessian matrix. Wait...\n");    double fp,fptt;
   for (i=1;i<=npar;i++){    double *xits;
     printf("%d",i);fflush(stdout);    int niterf, itmp;
     hess[i][i]=hessii(p,ftolhess,i,delti);  
     /*printf(" %f ",p[i]);*/    pt=vector(1,n); 
     /*printf(" %lf ",hess[i][i]);*/    ptt=vector(1,n); 
   }    xit=vector(1,n); 
      xits=vector(1,n); 
   for (i=1;i<=npar;i++) {    *fret=(*func)(p); 
     for (j=1;j<=npar;j++)  {    for (j=1;j<=n;j++) pt[j]=p[j]; 
       if (j>i) {    for (*iter=1;;++(*iter)) { 
         printf(".%d%d",i,j);fflush(stdout);      fp=(*fret); 
         hess[i][j]=hessij(p,delti,i,j);      ibig=0; 
         hess[j][i]=hess[i][j];          del=0.0; 
         /*printf(" %lf ",hess[i][j]);*/      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");      fprintf(ficrespow,"%d %.12f %ld",*iter,*fret,curr_time.tv_sec-start_time.tv_sec);
       */
   printf("\nInverting the hessian to get the covariance matrix. Wait...\n");     for (i=1;i<=n;i++) {
          printf(" %d %.12f",i, p[i]);
   a=matrix(1,npar,1,npar);        fprintf(ficlog," %d %.12lf",i, p[i]);
   y=matrix(1,npar,1,npar);        fprintf(ficrespow," %.12lf", p[i]);
   x=vector(1,npar);      }
   indx=ivector(1,npar);      printf("\n");
   for (i=1;i<=npar;i++)      fprintf(ficlog,"\n");
     for (j=1;j<=npar;j++) a[i][j]=hess[i][j];      fprintf(ficrespow,"\n");fflush(ficrespow);
   ludcmp(a,npar,indx,&pd);      if(*iter <=3){
         tm = *localtime(&curr_time.tv_sec);
   for (j=1;j<=npar;j++) {        strcpy(strcurr,asctime(&tm));
     for (i=1;i<=npar;i++) x[i]=0;  /*       asctime_r(&tm,strcurr); */
     x[j]=1;        forecast_time=curr_time; 
     lubksb(a,npar,indx,x);        itmp = strlen(strcurr);
     for (i=1;i<=npar;i++){        if(strcurr[itmp-1]=='\n')  /* Windows outputs with a new line */
       matcov[i][j]=x[i];          strcurr[itmp-1]='\0';
     }        printf("\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
   }        fprintf(ficlog,"\nConsidering the time needed for this last iteration #%d: %ld seconds,\n",*iter,curr_time.tv_sec-last_time.tv_sec);
         for(niterf=10;niterf<=30;niterf+=10){
   printf("\n#Hessian matrix#\n");          forecast_time.tv_sec=curr_time.tv_sec+(niterf-*iter)*(curr_time.tv_sec-last_time.tv_sec);
   for (i=1;i<=npar;i++) {          tmf = *localtime(&forecast_time.tv_sec);
     for (j=1;j<=npar;j++) {  /*      asctime_r(&tmf,strfor); */
       printf("%.3e ",hess[i][j]);          strcpy(strfor,asctime(&tmf));
     }          itmp = strlen(strfor);
     printf("\n");          if(strfor[itmp-1]=='\n')
   }          strfor[itmp-1]='\0';
           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);
   /* Recompute Inverse */          fprintf(ficlog,"   - if your program needs %d iterations to converge, convergence will be \n   reached in %s i.e.\n   on %s (current time is %s);\n",niterf, asc_diff_time(forecast_time.tv_sec-curr_time.tv_sec,tmpout),strfor,strcurr);
   for (i=1;i<=npar;i++)        }
     for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];      }
   ludcmp(a,npar,indx,&pd);      for (i=1;i<=n;i++) { 
         for (j=1;j<=n;j++) xit[j]=xi[j][i]; 
   /*  printf("\n#Hessian matrix recomputed#\n");        fptt=(*fret); 
   #ifdef DEBUG
   for (j=1;j<=npar;j++) {        printf("fret=%lf \n",*fret);
     for (i=1;i<=npar;i++) x[i]=0;        fprintf(ficlog,"fret=%lf \n",*fret);
     x[j]=1;  #endif
     lubksb(a,npar,indx,x);        printf("%d",i);fflush(stdout);
     for (i=1;i<=npar;i++){        fprintf(ficlog,"%d",i);fflush(ficlog);
       y[i][j]=x[i];        linmin(p,xit,n,fret,func); 
       printf("%.3e ",y[i][j]);        if (fabs(fptt-(*fret)) > del) { 
     }          del=fabs(fptt-(*fret)); 
     printf("\n");          ibig=i; 
   }        } 
   */  #ifdef DEBUG
         printf("%d %.12e",i,(*fret));
   free_matrix(a,1,npar,1,npar);        fprintf(ficlog,"%d %.12e",i,(*fret));
   free_matrix(y,1,npar,1,npar);        for (j=1;j<=n;j++) {
   free_vector(x,1,npar);          xits[j]=FMAX(fabs(p[j]-pt[j]),1.e-5);
   free_ivector(indx,1,npar);          printf(" x(%d)=%.12e",j,xit[j]);
   free_matrix(hess,1,npar,1,npar);          fprintf(ficlog," x(%d)=%.12e",j,xit[j]);
         }
         for(j=1;j<=n;j++) {
 }          printf(" p=%.12e",p[j]);
           fprintf(ficlog," p=%.12e",p[j]);
 /*************** hessian matrix ****************/        }
 double hessii( double x[], double delta, int theta, double delti[])        printf("\n");
 {        fprintf(ficlog,"\n");
   int i;  #endif
   int l=1, lmax=20;      } 
   double k1,k2;      if (2.0*fabs(fp-(*fret)) <= ftol*(fabs(fp)+fabs(*fret))) {
   double p2[NPARMAX+1];  #ifdef DEBUG
   double res;        int k[2],l;
   double delt, delts, nkhi=10.,nkhif=1., khi=1.e-4;        k[0]=1;
   double fx;        k[1]=-1;
   int k=0,kmax=10;        printf("Max: %.12e",(*func)(p));
   double l1;        fprintf(ficlog,"Max: %.12e",(*func)(p));
         for (j=1;j<=n;j++) {
   fx=func(x);          printf(" %.12e",p[j]);
   for (i=1;i<=npar;i++) p2[i]=x[i];          fprintf(ficlog," %.12e",p[j]);
   for(l=0 ; l <=lmax; l++){        }
     l1=pow(10,l);        printf("\n");
     delts=delt;        fprintf(ficlog,"\n");
     for(k=1 ; k <kmax; k=k+1){        for(l=0;l<=1;l++) {
       delt = delta*(l1*k);          for (j=1;j<=n;j++) {
       p2[theta]=x[theta] +delt;            ptt[j]=p[j]+(p[j]-pt[j])*k[l];
       k1=func(p2)-fx;            printf("l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       p2[theta]=x[theta]-delt;            fprintf(ficlog,"l=%d j=%d ptt=%.12e, xits=%.12e, p=%.12e, xit=%.12e", l,j,ptt[j],xits[j],p[j],xit[j]);
       k2=func(p2)-fx;          }
       /*res= (k1-2.0*fx+k2)/delt/delt; */          printf("func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
       res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */          fprintf(ficlog,"func(ptt)=%.12e, deriv=%.12e\n",(*func)(ptt),(ptt[j]-p[j])/((*func)(ptt)-(*func)(p)));
              }
 #ifdef DEBUG  #endif
       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);  
 #endif  
       /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */        free_vector(xit,1,n); 
       if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){        free_vector(xits,1,n); 
         k=kmax;        free_vector(ptt,1,n); 
       }        free_vector(pt,1,n); 
       else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */        return; 
         k=kmax; l=lmax*10.;      } 
       }      if (*iter == ITMAX) nrerror("powell exceeding maximum iterations."); 
       else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){      for (j=1;j<=n;j++) { 
         delts=delt;        ptt[j]=2.0*p[j]-pt[j]; 
       }        xit[j]=p[j]-pt[j]; 
     }        pt[j]=p[j]; 
   }      } 
   delti[theta]=delts;      fptt=(*func)(ptt); 
   return res;      if (fptt < fp) { 
          t=2.0*(fp-2.0*(*fret)+fptt)*SQR(fp-(*fret)-del)-del*SQR(fp-fptt); 
 }        if (t < 0.0) { 
           linmin(p,xit,n,fret,func); 
 double hessij( double x[], double delti[], int thetai,int thetaj)          for (j=1;j<=n;j++) { 
 {            xi[j][ibig]=xi[j][n]; 
   int i;            xi[j][n]=xit[j]; 
   int l=1, l1, lmax=20;          }
   double k1,k2,k3,k4,res,fx;  #ifdef DEBUG
   double p2[NPARMAX+1];          printf("Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
   int k;          fprintf(ficlog,"Direction changed  last moved %d in place of ibig=%d, new last is the average:\n",n,ibig);
           for(j=1;j<=n;j++){
   fx=func(x);            printf(" %.12e",xit[j]);
   for (k=1; k<=2; k++) {            fprintf(ficlog," %.12e",xit[j]);
     for (i=1;i<=npar;i++) p2[i]=x[i];          }
     p2[thetai]=x[thetai]+delti[thetai]/k;          printf("\n");
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;          fprintf(ficlog,"\n");
     k1=func(p2)-fx;  #endif
          }
     p2[thetai]=x[thetai]+delti[thetai]/k;      } 
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;    } 
     k2=func(p2)-fx;  } 
    
     p2[thetai]=x[thetai]-delti[thetai]/k;  /**** Prevalence limit (stable or period prevalence)  ****************/
     p2[thetaj]=x[thetaj]+delti[thetaj]/k;  
     k3=func(p2)-fx;  double **prevalim(double **prlim, int nlstate, double x[], double age, double **oldm, double **savm, double ftolpl, int ij)
    {
     p2[thetai]=x[thetai]-delti[thetai]/k;    /* Computes the prevalence limit in each live state at age x by left multiplying the unit
     p2[thetaj]=x[thetaj]-delti[thetaj]/k;       matrix by transitions matrix until convergence is reached */
     k4=func(p2)-fx;  
     res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */    int i, ii,j,k;
 #ifdef DEBUG    double min, max, maxmin, maxmax,sumnew=0.;
     printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);    double **matprod2();
 #endif    double **out, cov[NCOVMAX], **pmij();
   }    double **newm;
   return res;    double agefin, delaymax=50 ; /* Max number of years to converge */
 }  
     for (ii=1;ii<=nlstate+ndeath;ii++)
 /************** Inverse of matrix **************/      for (j=1;j<=nlstate+ndeath;j++){
 void ludcmp(double **a, int n, int *indx, double *d)        oldm[ii][j]=(ii==j ? 1.0 : 0.0);
 {      }
   int i,imax,j,k;  
   double big,dum,sum,temp;     cov[1]=1.;
   double *vv;   
     /* Even if hstepm = 1, at least one multiplication by the unit matrix */
   vv=vector(1,n);    for(agefin=age-stepm/YEARM; agefin>=age-delaymax; agefin=agefin-stepm/YEARM){
   *d=1.0;      newm=savm;
   for (i=1;i<=n;i++) {      /* Covariates have to be included here again */
     big=0.0;       cov[2]=agefin;
     for (j=1;j<=n;j++)    
       if ((temp=fabs(a[i][j])) > big) big=temp;        for (k=1; k<=cptcovn;k++) {
     if (big == 0.0) nrerror("Singular matrix in routine ludcmp");          cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
     vv[i]=1.0/big;          /*      printf("ij=%d k=%d Tvar[k]=%d nbcode=%d cov=%lf codtab[ij][Tvar[k]]=%d \n",ij,k, Tvar[k],nbcode[Tvar[k]][codtab[ij][Tvar[k]]],cov[2+k], codtab[ij][Tvar[k]]);*/
   }        }
   for (j=1;j<=n;j++) {        for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
     for (i=1;i<j;i++) {        for (k=1; k<=cptcovprod;k++)
       sum=a[i][j];          cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       for (k=1;k<i;k++) sum -= a[i][k]*a[k][j];  
       a[i][j]=sum;        /*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]);*/
     big=0.0;        /*printf("ij=%d cov[3]=%lf \n",ij, cov[3]);*/
     for (i=j;i<=n;i++) {      out=matprod2(newm, pmij(pmmij,cov,ncovmodel,x,nlstate),1,nlstate+ndeath,1,nlstate+ndeath,1,nlstate+ndeath, oldm);
       sum=a[i][j];  
       for (k=1;k<j;k++)      savm=oldm;
         sum -= a[i][k]*a[k][j];      oldm=newm;
       a[i][j]=sum;      maxmax=0.;
       if ( (dum=vv[i]*fabs(sum)) >= big) {      for(j=1;j<=nlstate;j++){
         big=dum;        min=1.;
         imax=i;        max=0.;
       }        for(i=1; i<=nlstate; i++) {
     }          sumnew=0;
     if (j != imax) {          for(k=1; k<=ndeath; k++) sumnew+=newm[i][nlstate+k];
       for (k=1;k<=n;k++) {          prlim[i][j]= newm[i][j]/(1-sumnew);
         dum=a[imax][k];          max=FMAX(max,prlim[i][j]);
         a[imax][k]=a[j][k];          min=FMIN(min,prlim[i][j]);
         a[j][k]=dum;        }
       }        maxmin=max-min;
       *d = -(*d);        maxmax=FMAX(maxmax,maxmin);
       vv[imax]=vv[j];      }
     }      if(maxmax < ftolpl){
     indx[j]=imax;        return prlim;
     if (a[j][j] == 0.0) a[j][j]=TINY;      }
     if (j != n) {    }
       dum=1.0/(a[j][j]);  }
       for (i=j+1;i<=n;i++) a[i][j] *= dum;  
     }  /*************** transition probabilities ***************/ 
   }  
   free_vector(vv,1,n);  /* Doesn't work */  double **pmij(double **ps, double *cov, int ncovmodel, double *x, int nlstate )
 ;  {
 }    double s1, s2;
     /*double t34;*/
 void lubksb(double **a, int n, int *indx, double b[])    int i,j,j1, nc, ii, jj;
 {  
   int i,ii=0,ip,j;      for(i=1; i<= nlstate; i++){
   double sum;        for(j=1; j<i;j++){
            for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   for (i=1;i<=n;i++) {            /*s2 += param[i][j][nc]*cov[nc];*/
     ip=indx[i];            s2 += x[(i-1)*nlstate*ncovmodel+(j-1)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     sum=b[ip];  /*       printf("Int j<i s1=%.17e, s2=%.17e\n",s1,s2); */
     b[ip]=b[i];          }
     if (ii)          ps[i][j]=s2;
       for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j];  /*      printf("s1=%.17e, s2=%.17e\n",s1,s2); */
     else if (sum) ii=i;        }
     b[i]=sum;        for(j=i+1; j<=nlstate+ndeath;j++){
   }          for (nc=1, s2=0.;nc <=ncovmodel; nc++){
   for (i=n;i>=1;i--) {            s2 += x[(i-1)*nlstate*ncovmodel+(j-2)*ncovmodel+nc+(i-1)*(ndeath-1)*ncovmodel]*cov[nc];
     sum=b[i];  /*        printf("Int j>i s1=%.17e, s2=%.17e %lx %lx\n",s1,s2,s1,s2); */
     for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j];          }
     b[i]=sum/a[i][i];          ps[i][j]=s2;
   }        }
 }      }
       /*ps[3][2]=1;*/
 /************ Frequencies ********************/      
 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,double jprev1, double mprev1,double anprev1,double jprev2, double mprev2,double anprev2)      for(i=1; i<= nlstate; i++){
 {  /* Some frequencies */        s1=0;
          for(j=1; j<i; j++)
   int i, m, jk, k1,i1, j1, bool, z1,z2,j;          s1+=exp(ps[i][j]);
   double ***freq; /* Frequencies */        for(j=i+1; j<=nlstate+ndeath; j++)
   double *pp;          s1+=exp(ps[i][j]);
   double pos, k2, dateintsum=0,k2cpt=0;        ps[i][i]=1./(s1+1.);
   FILE *ficresp;        for(j=1; j<i; j++)
   char fileresp[FILENAMELENGTH];          ps[i][j]= exp(ps[i][j])*ps[i][i];
          for(j=i+1; j<=nlstate+ndeath; j++)
   pp=vector(1,nlstate);          ps[i][j]= exp(ps[i][j])*ps[i][i];
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);        /* ps[i][nlstate+1]=1.-s1- ps[i][i];*/ /* Sum should be 1 */
   strcpy(fileresp,"p");      } /* end i */
   strcat(fileresp,fileres);      
   if((ficresp=fopen(fileresp,"w"))==NULL) {      for(ii=nlstate+1; ii<= nlstate+ndeath; ii++){
     printf("Problem with prevalence resultfile: %s\n", fileresp);        for(jj=1; jj<= nlstate+ndeath; jj++){
     exit(0);          ps[ii][jj]=0;
   }          ps[ii][ii]=1;
   freq= ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);        }
   j1=0;      }
        
   j=cptcoveff;  
   if (cptcovn<1) {j=1;ncodemax[1]=1;}  /*        for(ii=1; ii<= nlstate+ndeath; ii++){ */
    /*       for(jj=1; jj<= nlstate+ndeath; jj++){ */
   for(k1=1; k1<=j;k1++){  /*         printf("ddd %lf ",ps[ii][jj]); */
     for(i1=1; i1<=ncodemax[k1];i1++){  /*       } */
       j1++;  /*       printf("\n "); */
       /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);  /*        } */
         scanf("%d", i);*/  /*        printf("\n ");printf("%lf ",cov[2]); */
       for (i=-1; i<=nlstate+ndeath; i++)           /*
         for (jk=-1; jk<=nlstate+ndeath; jk++)          for(i=1; i<= npar; i++) printf("%f ",x[i]);
           for(m=agemin; m <= agemax+3; m++)        goto end;*/
             freq[i][jk][m]=0;      return ps;
        }
       dateintsum=0;  
       k2cpt=0;  /**************** Product of 2 matrices ******************/
       for (i=1; i<=imx; i++) {  
         bool=1;  double **matprod2(double **out, double **in,long nrl, long nrh, long ncl, long nch, long ncolol, long ncoloh, double **b)
         if  (cptcovn>0) {  {
           for (z1=1; z1<=cptcoveff; z1++)    /* Computes the matrix product of in(1,nrh-nrl+1)(1,nch-ncl+1) times
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])       b(1,nch-ncl+1)(1,ncoloh-ncolol+1) into out(...) */
               bool=0;    /* in, b, out are matrice of pointers which should have been initialized 
         }       before: only the contents of out is modified. The function returns
         if (bool==1) {       a pointer to pointers identical to out */
           for(m=firstpass; m<=lastpass; m++){    long i, j, k;
             k2=anint[m][i]+(mint[m][i]/12.);    for(i=nrl; i<= nrh; i++)
             if ((k2>=dateprev1) && (k2<=dateprev2)) {      for(k=ncolol; k<=ncoloh; k++)
               if(agev[m][i]==0) agev[m][i]=agemax+1;        for(j=ncl,out[i][k]=0.; j<=nch; j++)
               if(agev[m][i]==1) agev[m][i]=agemax+2;          out[i][k] +=in[i][j]*b[j][k];
               if (m<lastpass) {  
                 freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];    return out;
                 freq[s[m][i]][s[m+1][i]][(int) agemax+3] += weight[i];  }
               }  
                
               if ((agev[m][i]>1) && (agev[m][i]< (agemax+3))) {  /************* Higher Matrix Product ***************/
                 dateintsum=dateintsum+k2;  
                 k2cpt++;  double ***hpxij(double ***po, int nhstepm, double age, int hstepm, double *x, int nlstate, int stepm, double **oldm, double **savm, int ij )
               }  {
             }    /* Computes the transition matrix starting at age 'age' over 
           }       'nhstepm*hstepm*stepm' months (i.e. until
         }       age (in years)  age+nhstepm*hstepm*stepm/12) by multiplying 
       }       nhstepm*hstepm matrices. 
               Output is stored in matrix po[i][j][h] for h every 'hstepm' step 
       fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);       (typically every 2 years instead of every month which is too big 
        for the memory).
       if  (cptcovn>0) {       Model is determined by parameters x and covariates have to be 
         fprintf(ficresp, "\n#********** Variable ");       included manually here. 
         for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);  
         fprintf(ficresp, "**********\n#");       */
       }  
       for(i=1; i<=nlstate;i++)    int i, j, d, h, k;
         fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);    double **out, cov[NCOVMAX];
       fprintf(ficresp, "\n");    double **newm;
        
       for(i=(int)agemin; i <= (int)agemax+3; i++){    /* Hstepm could be zero and should return the unit matrix */
         if(i==(int)agemax+3)    for (i=1;i<=nlstate+ndeath;i++)
           printf("Total");      for (j=1;j<=nlstate+ndeath;j++){
         else        oldm[i][j]=(i==j ? 1.0 : 0.0);
           printf("Age %d", i);        po[i][j][0]=(i==j ? 1.0 : 0.0);
         for(jk=1; jk <=nlstate ; jk++){      }
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)    /* Even if hstepm = 1, at least one multiplication by the unit matrix */
             pp[jk] += freq[jk][m][i];    for(h=1; h <=nhstepm; h++){
         }      for(d=1; d <=hstepm; d++){
         for(jk=1; jk <=nlstate ; jk++){        newm=savm;
           for(m=-1, pos=0; m <=0 ; m++)        /* Covariates have to be included here again */
             pos += freq[jk][m][i];        cov[1]=1.;
           if(pp[jk]>=1.e-10)        cov[2]=age+((h-1)*hstepm + (d-1))*stepm/YEARM;
             printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);        for (k=1; k<=cptcovn;k++) cov[2+k]=nbcode[Tvar[k]][codtab[ij][Tvar[k]]];
           else        for (k=1; k<=cptcovage;k++)
             printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);          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]]];
         for(jk=1; jk <=nlstate ; jk++){  
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)  
             pp[jk] += freq[jk][m][i];        /*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, 
         for(jk=1,pos=0; jk <=nlstate ; jk++)                     pmij(pmmij,cov,ncovmodel,x,nlstate));
           pos += pp[jk];        savm=oldm;
         for(jk=1; jk <=nlstate ; jk++){        oldm=newm;
           if(pos>=1.e-5)      }
             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);          po[i][j][h]=newm[i][j];
           if( i <= (int) agemax){          /*printf("i=%d j=%d h=%d po[i][j][h]=%f ",i,j,h,po[i][j][h]);
             if(pos>=1.e-5){           */
               fprintf(ficresp," %d %.5f %.0f %.0f",i,pp[jk]/pos, pp[jk],pos);        }
               probs[i][jk][j1]= pp[jk]/pos;    } /* end 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]);*/    return po;
             }  }
             else  
               fprintf(ficresp," %d NaNq %.0f %.0f",i,pp[jk],pos);  
           }  /*************** log-likelihood *************/
         }  double func( double *x)
          {
         for(jk=-1; jk <=nlstate+ndeath; jk++)    int i, ii, j, k, mi, d, kk;
           for(m=-1; m <=nlstate+ndeath; m++)    double l, ll[NLSTATEMAX], cov[NCOVMAX];
             if(freq[jk][m][i] !=0 ) printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);    double **out;
         if(i <= (int) agemax)    double sw; /* Sum of weights */
           fprintf(ficresp,"\n");    double lli; /* Individual log likelihood */
         printf("\n");    int s1, s2;
       }    double bbh, survp;
     }    long ipmx;
   }    /*extern weight */
   dateintmean=dateintsum/k2cpt;    /* We are differentiating ll according to initial status */
      /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
   fclose(ficresp);    /*for(i=1;i<imx;i++) 
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);      printf(" %d\n",s[4][i]);
   free_vector(pp,1,nlstate);    */
      cov[1]=1.;
   /* End of Freq */  
 }    for(k=1; k<=nlstate; k++) ll[k]=0.;
   
 /************ Prevalence ********************/    if(mle==1){
 void prevalence(int agemin, float 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)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
 {  /* Some frequencies */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
          for(mi=1; mi<= wav[i]-1; mi++){
   int i, m, jk, k1, i1, j1, bool, z1,z2,j;          for (ii=1;ii<=nlstate+ndeath;ii++)
   double ***freq; /* Frequencies */            for (j=1;j<=nlstate+ndeath;j++){
   double *pp;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   double pos, k2;              savm[ii][j]=(ii==j ? 1.0 : 0.0);
             }
   pp=vector(1,nlstate);          for(d=0; d<dh[mi][i]; d++){
   probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);            newm=savm;
              cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,agemin,agemax+3);            for (kk=1; kk<=cptcovage;kk++) {
   j1=0;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
              }
   j=cptcoveff;            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
   if (cptcovn<1) {j=1;ncodemax[1]=1;}                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
              savm=oldm;
   for(k1=1; k1<=j;k1++){            oldm=newm;
     for(i1=1; i1<=ncodemax[k1];i1++){          } /* end mult */
       j1++;        
                /*lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]);*/ /* Original formula */
       for (i=-1; i<=nlstate+ndeath; i++)            /* But now since version 0.9 we anticipate for bias at large stepm.
         for (jk=-1; jk<=nlstate+ndeath; jk++)             * If stepm is larger than one month (smallest stepm) and if the exact delay 
           for(m=agemin; m <= agemax+3; m++)           * (in months) between two waves is not a multiple of stepm, we rounded to 
             freq[i][jk][m]=0;           * the nearest (and in case of equal distance, to the lowest) interval but now
                 * we keep into memory the bias bh[mi][i] and also the previous matrix product
       for (i=1; i<=imx; i++) {           * (i.e to dh[mi][i]-1) saved in 'savm'. Then we inter(extra)polate the
         bool=1;           * probability in order to take into account the bias as a fraction of the way
         if  (cptcovn>0) {           * from savm to out if bh is negative or even beyond if bh is positive. bh varies
           for (z1=1; z1<=cptcoveff; z1++)           * -stepm/2 to stepm/2 .
             if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]])           * For stepm=1 the results are the same as for previous versions of Imach.
               bool=0;           * For stepm > 1 the results are less biased than in previous versions. 
         }           */
         if (bool==1) {          s1=s[mw[mi][i]][i];
           for(m=firstpass; m<=lastpass; m++){          s2=s[mw[mi+1][i]][i];
             k2=anint[m][i]+(mint[m][i]/12.);          bbh=(double)bh[mi][i]/(double)stepm; 
             if ((k2>=dateprev1) && (k2<=dateprev2)) {          /* bias bh is positive if real duration
               if(agev[m][i]==0) agev[m][i]=agemax+1;           * is higher than the multiple of stepm and negative otherwise.
               if(agev[m][i]==1) agev[m][i]=agemax+2;           */
               if (m<lastpass) {          /* 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 (calagedate>0)          if( s2 > nlstate){ 
                   freq[s[m][i]][s[m+1][i]][(int)(agev[m][i]+1-((int)calagedate %12)/12.)] += weight[i];            /* i.e. if s2 is a death state and if the date of death is known 
                 else               then the contribution to the likelihood is the probability to 
                   freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];               die between last step unit time and current  step unit time, 
                 freq[s[m][i]][s[m+1][i]][(int)(agemax+3)] += weight[i];               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
       }          and not the date of a change in health state. The former idea was
       for(i=(int)agemin; i <= (int)agemax+3; i++){          to consider that at each interview the state was recorded
         for(jk=1; jk <=nlstate ; jk++){          (healthy, disable or death) and IMaCh was corrected; but when we
           for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)          introduced the exact date of death then we should have modified
             pp[jk] += freq[jk][m][i];          the contribution of an exact death to the likelihood. This new
         }          contribution is smaller and very dependent of the step unit
         for(jk=1; jk <=nlstate ; jk++){          stepm. It is no more the probability to die between last interview
           for(m=-1, pos=0; m <=0 ; m++)          and month of death but the probability to survive from last
             pos += freq[jk][m][i];          interview up to one month before death multiplied by the
         }          probability to die within a month. Thanks to Chris
                  Jackson for correcting this bug.  Former versions increased
         for(jk=1; jk <=nlstate ; jk++){          mortality artificially. The bad side is that we add another loop
           for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)          which slows down the processing. The difference can be up to 10%
             pp[jk] += freq[jk][m][i];          lower mortality.
         }            */
                    lli=log(out[s1][s2] - savm[s1][s2]);
         for(jk=1,pos=0; jk <=nlstate ; jk++) pos += pp[jk];  
          
         for(jk=1; jk <=nlstate ; jk++){              } else if  (s2==-2) {
           if( i <= (int) agemax){            for (j=1,survp=0. ; j<=nlstate; j++) 
             if(pos>=1.e-5){              survp += out[s1][j];
               probs[i][jk][j1]= pp[jk]/pos;            lli= survp;
             }          }
           }          
         }          else if  (s2==-4) {
                    for (j=3,survp=0. ; j<=nlstate; j++) 
       }              survp += out[s1][j];
     }            lli= survp;
   }          }
           
            else if  (s2==-5) {
   free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath,(int) agemin,(int) agemax+3);            for (j=1,survp=0. ; j<=2; j++) 
   free_vector(pp,1,nlstate);              survp += out[s1][j];
              lli= survp;
 }  /* End of Freq */          }
   
 /************* Waves Concatenation ***************/  
           else{
 void  concatwav(int wav[], int **dh, int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)            lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
 {            /*  lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2]));*/ /* linear interpolation */
   /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.          } 
      Death is a valid wave (if date is known).          /*lli=(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]);*/
      mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i          /*if(lli ==000.0)*/
      dh[m][i] of dh[mw[mi][i][i] is the delay between two effective waves m=mw[mi][i]          /*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); */
      and mw[mi+1][i]. dh depends on stepm.          ipmx +=1;
      */          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   int i, mi, m;        } /* end of wave */
   /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;      } /* end of individual */
      double sum=0., jmean=0.;*/    }  else if(mle==2){
       for (i=1,ipmx=0, sw=0.; i<=imx; i++){
   int j, k=0,jk, ju, jl;        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
   double sum=0.;        for(mi=1; mi<= wav[i]-1; mi++){
   jmin=1e+5;          for (ii=1;ii<=nlstate+ndeath;ii++)
   jmax=-1;            for (j=1;j<=nlstate+ndeath;j++){
   jmean=0.;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   for(i=1; i<=imx; i++){              savm[ii][j]=(ii==j ? 1.0 : 0.0);
     mi=0;            }
     m=firstpass;          for(d=0; d<=dh[mi][i]; d++){
     while(s[m][i] <= nlstate){            newm=savm;
       if(s[m][i]>=1)            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
         mw[++mi][i]=m;            for (kk=1; kk<=cptcovage;kk++) {
       if(m >=lastpass)              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
         break;            }
       else            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         m++;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
     }/* end while */            savm=oldm;
     if (s[m][i] > nlstate){            oldm=newm;
       mi++;     /* Death is another wave */          } /* end mult */
       /* if(mi==0)  never been interviewed correctly before death */        
          /* Only death is a correct wave */          s1=s[mw[mi][i]][i];
       mw[mi][i]=m;          s2=s[mw[mi+1][i]][i];
     }          bbh=(double)bh[mi][i]/(double)stepm; 
           lli= (savm[s1][s2]>(double)1.e-8 ?log((1.+bbh)*out[s1][s2]- bbh*(savm[s1][s2])):log((1.+bbh)*out[s1][s2])); /* linear interpolation */
     wav[i]=mi;          ipmx +=1;
     if(mi==0)          sw += weight[i];
       printf("Warning, no any valid information for:%d line=%d\n",num[i],i);          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
   }        } /* end of wave */
       } /* end of individual */
   for(i=1; i<=imx; i++){    }  else if(mle==3){  /* exponential inter-extrapolation */
     for(mi=1; mi<wav[i];mi++){      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
       if (stepm <=0)        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
         dh[mi][i]=1;        for(mi=1; mi<= wav[i]-1; mi++){
       else{          for (ii=1;ii<=nlstate+ndeath;ii++)
         if (s[mw[mi+1][i]][i] > nlstate) {            for (j=1;j<=nlstate+ndeath;j++){
           if (agedc[i] < 2*AGESUP) {              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
           j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
           if(j==0) j=1;  /* Survives at least one month after exam */            }
           k=k+1;          for(d=0; d<dh[mi][i]; d++){
           if (j >= jmax) jmax=j;            newm=savm;
           if (j <= jmin) jmin=j;            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
           sum=sum+j;            for (kk=1; kk<=cptcovage;kk++) {
           /*if (j<0) printf("j=%d num=%d \n",j,i); */              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
           }            }
         }            out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
         else{                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
           j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));            savm=oldm;
           k=k+1;            oldm=newm;
           if (j >= jmax) jmax=j;          } /* end mult */
           else if (j <= jmin)jmin=j;        
           /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */          s1=s[mw[mi][i]][i];
           sum=sum+j;          s2=s[mw[mi+1][i]][i];
         }          bbh=(double)bh[mi][i]/(double)stepm; 
         jk= j/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 */
         jl= j -jk*stepm;          ipmx +=1;
         ju= j -(jk+1)*stepm;          sw += weight[i];
         if(jl <= -ju)          ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
           dh[mi][i]=jk;        } /* end of wave */
         else      } /* end of individual */
           dh[mi][i]=jk+1;    }else if (mle==4){  /* ml=4 no inter-extrapolation */
         if(dh[mi][i]==0)      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
           dh[mi][i]=1; /* At least one step */        for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
       }        for(mi=1; mi<= wav[i]-1; mi++){
     }          for (ii=1;ii<=nlstate+ndeath;ii++)
   }            for (j=1;j<=nlstate+ndeath;j++){
   jmean=sum/k;              oldm[ii][j]=(ii==j ? 1.0 : 0.0);
   printf("Delay (in months) between two waves Min=%d Max=%d Mean=%f\n\n ",jmin, jmax,jmean);              savm[ii][j]=(ii==j ? 1.0 : 0.0);
  }            }
 /*********** Tricode ****************************/          for(d=0; d<dh[mi][i]; d++){
 void tricode(int *Tvar, int **nbcode, int imx)            newm=savm;
 {            cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   int Ndum[20],ij=1, k, j, i;            for (kk=1; kk<=cptcovage;kk++) {
   int cptcode=0;              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
   cptcoveff=0;            }
            
   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;          if( s2 > nlstate){ 
     }            lli=log(out[s1][s2] - savm[s1][s2]);
           }else{
     for (i=0; i<=cptcode; i++) {            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
       if(Ndum[i]!=0) ncodemax[j]++;          }
     }          ipmx +=1;
     ij=1;          sw += weight[i];
           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]); */
     for (i=1; i<=ncodemax[j]; i++) {        } /* end of wave */
       for (k=0; k<=19; k++) {      } /* end of individual */
         if (Ndum[k] != 0) {    }else{  /* ml=5 no inter-extrapolation no jackson =0.8a */
           nbcode[Tvar[j]][ij]=k;      for (i=1,ipmx=0, sw=0.; i<=imx; i++){
                  for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
           ij++;        for(mi=1; mi<= wav[i]-1; mi++){
         }          for (ii=1;ii<=nlstate+ndeath;ii++)
         if (ij > ncodemax[j]) break;            for (j=1;j<=nlstate+ndeath;j++){
       }                oldm[ii][j]=(ii==j ? 1.0 : 0.0);
     }              savm[ii][j]=(ii==j ? 1.0 : 0.0);
   }              }
           for(d=0; d<dh[mi][i]; d++){
  for (k=0; k<19; k++) Ndum[k]=0;            newm=savm;
             cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
  for (i=1; i<=ncovmodel-2; i++) {            for (kk=1; kk<=cptcovage;kk++) {
       ij=Tvar[i];              cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
       Ndum[ij]++;            }
     }          
             out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
  ij=1;                         1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
  for (i=1; i<=10; i++) {            savm=oldm;
    if((Ndum[i]!=0) && (i<=ncovcol)){            oldm=newm;
      Tvaraff[ij]=i;          } /* end mult */
      ij++;        
    }          s1=s[mw[mi][i]][i];
  }          s2=s[mw[mi+1][i]][i];
            lli=log(out[s[mw[mi][i]][i]][s[mw[mi+1][i]][i]]); /* Original formula */
     cptcoveff=ij-1;          ipmx +=1;
 }          sw += weight[i];
           ll[s[mw[mi][i]][i]] += 2*weight[i]*lli;
 /*********** Health Expectancies ****************/          /*printf("i=%6d s1=%1d s2=%1d mi=%1d mw=%1d dh=%3d prob=%10.6f w=%6.4f out=%10.6f sav=%10.6f\n",i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],out[s1][s2],savm[s1][s2]);*/
         } /* end of wave */
 void evsij(char fileres[], double ***eij, double x[], int nlstate, int stepm, int bage, int fage, double **oldm, double **savm, int ij, int estepm,double delti[],double **matcov )      } /* end of individual */
     } /* End of if */
 {    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
   /* Health expectancies */    /* printf("l1=%f l2=%f ",ll[1],ll[2]); */
   int i, j, nhstepm, hstepm, h, nstepm, k, cptj;    l= l*ipmx/sw; /* To get the same order of magnitude as if weight=1 for every body */
   double age, agelim, hf;    return -l;
   double ***p3mat,***varhe;  }
   double **dnewm,**doldm;  
   double *xp;  /*************** log-likelihood *************/
   double **gp, **gm;  double funcone( double *x)
   double ***gradg, ***trgradg;  {
   int theta;    /* Same as likeli but slower because of a lot of printf and if */
     int i, ii, j, k, mi, d, kk;
   varhe=ma3x(1,nlstate*2,1,nlstate*2,(int) bage, (int) fage);    double l, ll[NLSTATEMAX], cov[NCOVMAX];
   xp=vector(1,npar);    double **out;
   dnewm=matrix(1,nlstate*2,1,npar);    double lli; /* Individual log likelihood */
   doldm=matrix(1,nlstate*2,1,nlstate*2);    double llt;
      int s1, s2;
   fprintf(ficreseij,"# Health expectancies\n");    double bbh, survp;
   fprintf(ficreseij,"# Age");    /*extern weight */
   for(i=1; i<=nlstate;i++)    /* We are differentiating ll according to initial status */
     for(j=1; j<=nlstate;j++)    /*  for (i=1;i<=npar;i++) printf("%f ", x[i]);*/
       fprintf(ficreseij," %1d-%1d (SE)",i,j);    /*for(i=1;i<imx;i++) 
   fprintf(ficreseij,"\n");      printf(" %d\n",s[4][i]);
     */
   if(estepm < stepm){    cov[1]=1.;
     printf ("Problem %d lower than %d\n",estepm, stepm);  
   }    for(k=1; k<=nlstate; k++) ll[k]=0.;
   else  hstepm=estepm;    
   /* We compute the life expectancy from trapezoids spaced every estepm months    for (i=1,ipmx=0, sw=0.; i<=imx; i++){
    * This is mainly to measure the difference between two models: for example      for (k=1; k<=cptcovn;k++) cov[2+k]=covar[Tvar[k]][i];
    * if stepm=24 months pijx are given only every 2 years and by summing them      for(mi=1; mi<= wav[i]-1; mi++){
    * we are calculating an estimate of the Life Expectancy assuming a linear        for (ii=1;ii<=nlstate+ndeath;ii++)
    * progression inbetween and thus overestimating or underestimating according          for (j=1;j<=nlstate+ndeath;j++){
    * to the curvature of the survival function. If, for the same date, we            oldm[ii][j]=(ii==j ? 1.0 : 0.0);
    * estimate the model with stepm=1 month, we can keep estepm to 24 months            savm[ii][j]=(ii==j ? 1.0 : 0.0);
    * to compare the new estimate of Life expectancy with the same linear          }
    * hypothesis. A more precise result, taking into account a more precise        for(d=0; d<dh[mi][i]; d++){
    * curvature will be obtained if estepm is as small as stepm. */          newm=savm;
           cov[2]=agev[mw[mi][i]][i]+d*stepm/YEARM;
   /* For example we decided to compute the life expectancy with the smallest unit */          for (kk=1; kk<=cptcovage;kk++) {
   /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm.            cov[Tage[kk]+2]=covar[Tvar[Tage[kk]]][i]*cov[2];
      nhstepm is the number of hstepm from age to agelim          }
      nstepm is the number of stepm from age to agelin.          out=matprod2(newm,oldm,1,nlstate+ndeath,1,nlstate+ndeath,
      Look at hpijx to understand the reason of that which relies in memory size                       1,nlstate+ndeath,pmij(pmmij,cov,ncovmodel,x,nlstate));
      and note for a fixed period like estepm months */          savm=oldm;
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the          oldm=newm;
      survival function given by stepm (the optimization length). Unfortunately it        } /* end mult */
      means that if the survival funtion is printed only each two years of age and if        
      you sum them up and add 1 year (area under the trapezoids) you won't get the same        s1=s[mw[mi][i]][i];
      results. So we changed our mind and took the option of the best precision.        s2=s[mw[mi+1][i]][i];
   */        bbh=(double)bh[mi][i]/(double)stepm; 
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */        /* bias is positive if real duration
          * is higher than the multiple of stepm and negative otherwise.
   agelim=AGESUP;         */
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */        if( s2 > nlstate && (mle <5) ){  /* Jackson */
     /* nhstepm age range expressed in number of stepm */          lli=log(out[s1][s2] - savm[s1][s2]);
     nstepm=(int) rint((agelim-age)*YEARM/stepm);        } else if (mle==1){
     /* Typically if 20 years nstepm = 20*12/6=40 stepm */          lli= log((1.+bbh)*out[s1][s2]- bbh*savm[s1][s2]); /* linear interpolation */
     /* if (stepm >= YEARM) hstepm=1;*/        } else if(mle==2){
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */          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 */
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        } else if(mle==3){  /* exponential inter-extrapolation */
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate*2);          lli= (savm[s1][s2]>(double)1.e-8 ?(1.+bbh)*log(out[s1][s2])- bbh*log(savm[s1][s2]):log((1.+bbh)*out[s1][s2])); /* exponential inter-extrapolation */
     gp=matrix(0,nhstepm,1,nlstate*2);        } else if (mle==4){  /* mle=4 no inter-extrapolation */
     gm=matrix(0,nhstepm,1,nlstate*2);          lli=log(out[s1][s2]); /* Original formula */
         } else{  /* ml>=5 no inter-extrapolation no jackson =0.8a */
     /* Computed by stepm unit matrices, product of hstepm matrices, stored          lli=log(out[s1][s2]); /* Original formula */
        in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */        } /* End of if */
     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;
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */  /*       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){
     /* Computing Variances of health expectancies */          fprintf(ficresilk,"%9d %6d %1d %1d %1d %1d %3d %10.6f %6.4f\
    %10.6f %10.6f %10.6f ", \
      for(theta=1; theta <=npar; theta++){                  num[i],i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],
       for(i=1; i<=npar; i++){                  2*weight[i]*lli,out[s1][s2],savm[s1][s2]);
         xp[i] = x[i] + (i==theta ?delti[theta]:0);          for(k=1,llt=0.,l=0.; k<=nlstate; k++){
       }            llt +=ll[k]*gipmx/gsw;
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);              fprintf(ficresilk," %10.6f",-ll[k]*gipmx/gsw);
            }
       cptj=0;          fprintf(ficresilk," %10.6f\n", -llt);
       for(j=1; j<= nlstate; j++){        }
         for(i=1; i<=nlstate; i++){      } /* end of wave */
           cptj=cptj+1;    } /* end of individual */
           for(h=0, gp[h][cptj]=0.; h<=nhstepm-1; h++){    for(k=1,l=0.; k<=nlstate; k++) l += ll[k];
             gp[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;    /* 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 */
         }    if(globpr==0){ /* First time we count the contributions and weights */
       }      gipmx=ipmx;
            gsw=sw;
          }
       for(i=1; i<=npar; i++)    return -l;
         xp[i] = x[i] - (i==theta ?delti[theta]:0);  }
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);    
        
       cptj=0;  /*************** function likelione ***********/
       for(j=1; j<= nlstate; j++){  void likelione(FILE *ficres,double p[], int npar, int nlstate, int *globpri, long *ipmx, double *sw, double *fretone, double (*funcone)(double []))
         for(i=1;i<=nlstate;i++){  {
           cptj=cptj+1;    /* This routine should help understanding what is done with 
           for(h=0, gm[h][cptj]=0.; h<=nhstepm-1; h++){       the selection of individuals/waves and
             gm[h][cptj] = (p3mat[i][j][h]+p3mat[i][j][h+1])/2.;       to check the exact contribution to the likelihood.
           }       Plotting could be done.
         }     */
       }    int k;
       for(j=1; j<= nlstate*2; j++)  
         for(h=0; h<=nhstepm-1; h++){    if(*globpri !=0){ /* Just counts and sums, no printings */
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];      strcpy(fileresilk,"ilk"); 
         }      strcat(fileresilk,fileres);
      }      if((ficresilk=fopen(fileresilk,"w"))==NULL) {
            printf("Problem with resultfile: %s\n", fileresilk);
 /* End theta */        fprintf(ficlog,"Problem with resultfile: %s\n", fileresilk);
       }
      trgradg =ma3x(0,nhstepm,1,nlstate*2,1,npar);      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 ");
      for(h=0; h<=nhstepm-1; h++)      /*  i,s1,s2,mi,mw[mi][i],dh[mi][i],exp(lli),weight[i],2*weight[i]*lli,out[s1][s2],savm[s1][s2]); */
       for(j=1; j<=nlstate*2;j++)      for(k=1; k<=nlstate; k++) 
         for(theta=1; theta <=npar; theta++)        fprintf(ficresilk," -2*gipw/gsw*weight*ll[%d]++",k);
           trgradg[h][j][theta]=gradg[h][theta][j];      fprintf(ficresilk," -2*gipw/gsw*weight*ll(total)\n");
          }
   
      for(i=1;i<=nlstate*2;i++)    *fretone=(*funcone)(p);
       for(j=1;j<=nlstate*2;j++)    if(*globpri !=0){
         varhe[i][j][(int)age] =0.;      fclose(ficresilk);
       fprintf(fichtm,"\n<br>File of contributions to the likelihood: <a href=\"%s\">%s</a><br>\n",subdirf(fileresilk),subdirf(fileresilk));
      printf("%d|",(int)age);fflush(stdout);      fflush(fichtm); 
      for(h=0;h<=nhstepm-1;h++){    } 
       for(k=0;k<=nhstepm-1;k++){    return;
         matprod2(dnewm,trgradg[h],1,nlstate*2,1,npar,1,npar,matcov);  }
         matprod2(doldm,dnewm,1,nlstate*2,1,npar,1,nlstate*2,gradg[k]);  
         for(i=1;i<=nlstate*2;i++)  
           for(j=1;j<=nlstate*2;j++)  /*********** Maximum Likelihood Estimation ***************/
             varhe[i][j][(int)age] += doldm[i][j]*hf*hf;  
       }  void mlikeli(FILE *ficres,double p[], int npar, int ncovmodel, int nlstate, double ftol, double (*func)(double []))
     }  {
     int i,j, iter;
          double **xi;
     /* Computing expectancies */    double fret;
     for(i=1; i<=nlstate;i++)    double fretone; /* Only one call to likelihood */
       for(j=1; j<=nlstate;j++)    /*  char filerespow[FILENAMELENGTH];*/
         for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){    xi=matrix(1,npar,1,npar);
           eij[i][j][(int)age] += (p3mat[i][j][h]+p3mat[i][j][h+1])/2.0*hf;    for (i=1;i<=npar;i++)
                for (j=1;j<=npar;j++)
 /* 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]);*/        xi[i][j]=(i==j ? 1.0 : 0.0);
     printf("Powell\n");  fprintf(ficlog,"Powell\n");
         }    strcpy(filerespow,"pow"); 
     strcat(filerespow,fileres);
     fprintf(ficreseij,"%3.0f",age );    if((ficrespow=fopen(filerespow,"w"))==NULL) {
     cptj=0;      printf("Problem with resultfile: %s\n", filerespow);
     for(i=1; i<=nlstate;i++)      fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       for(j=1; j<=nlstate;j++){    }
         cptj++;    fprintf(ficrespow,"# Powell\n# iter -2*LL");
         fprintf(ficreseij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[cptj][cptj][(int)age]) );    for (i=1;i<=nlstate;i++)
       }      for(j=1;j<=nlstate+ndeath;j++)
     fprintf(ficreseij,"\n");        if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
        fprintf(ficrespow,"\n");
     free_matrix(gm,0,nhstepm,1,nlstate*2);  
     free_matrix(gp,0,nhstepm,1,nlstate*2);    powell(p,xi,npar,ftol,&iter,&fret,func);
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*2);  
     free_ma3x(trgradg,0,nhstepm,1,nlstate*2,1,npar);    free_matrix(xi,1,npar,1,npar);
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    fclose(ficrespow);
   }    printf("\n#Number of iterations = %d, -2 Log likelihood = %.12f\n",iter,func(p));
   free_vector(xp,1,npar);    fprintf(ficlog,"\n#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   free_matrix(dnewm,1,nlstate*2,1,npar);    fprintf(ficres,"#Number of iterations = %d, -2 Log likelihood = %.12f \n",iter,func(p));
   free_matrix(doldm,1,nlstate*2,1,nlstate*2);  
   free_ma3x(varhe,1,nlstate*2,1,nlstate*2,(int) bage, (int)fage);  }
 }  
   /**** Computes Hessian and covariance matrix ***/
 /************ Variance ******************/  void hesscov(double **matcov, double p[], int npar, double delti[], double ftolhess, double (*func)(double []))
 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 estepm)  {
 {    double  **a,**y,*x,pd;
   /* Variance of health expectancies */    double **hess;
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/    int i, j,jk;
   double **newm;    int *indx;
   double **dnewm,**doldm;  
   int i, j, nhstepm, hstepm, h, nstepm ;    double hessii(double p[], double delta, int theta, double delti[],double (*func)(double []),int npar);
   int k, cptcode;    double hessij(double p[], double delti[], int i, int j,double (*func)(double []),int npar);
   double *xp;    void lubksb(double **a, int npar, int *indx, double b[]) ;
   double **gp, **gm;    void ludcmp(double **a, int npar, int *indx, double *d) ;
   double ***gradg, ***trgradg;    double gompertz(double p[]);
   double ***p3mat;    hess=matrix(1,npar,1,npar);
   double age,agelim, hf;  
   int theta;    printf("\nCalculation of the hessian matrix. Wait...\n");
     fprintf(ficlog,"\nCalculation of the hessian matrix. Wait...\n");
   fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are the stable prevalence in health states i\n");    for (i=1;i<=npar;i++){
   fprintf(ficresvij,"# Age");      printf("%d",i);fflush(stdout);
   for(i=1; i<=nlstate;i++)      fprintf(ficlog,"%d",i);fflush(ficlog);
     for(j=1; j<=nlstate;j++)     
       fprintf(ficresvij," Cov(e%1d, e%1d)",i,j);       hess[i][i]=hessii(p,ftolhess,i,delti,func,npar);
   fprintf(ficresvij,"\n");      
       /*  printf(" %f ",p[i]);
   xp=vector(1,npar);          printf(" %lf %lf %lf",hess[i][i],ftolhess,delti[i]);*/
   dnewm=matrix(1,nlstate,1,npar);    }
   doldm=matrix(1,nlstate,1,nlstate);    
      for (i=1;i<=npar;i++) {
   if(estepm < stepm){      for (j=1;j<=npar;j++)  {
     printf ("Problem %d lower than %d\n",estepm, stepm);        if (j>i) { 
   }          printf(".%d%d",i,j);fflush(stdout);
   else  hstepm=estepm;            fprintf(ficlog,".%d%d",i,j);fflush(ficlog);
   /* For example we decided to compute the life expectancy with the smallest unit */          hess[i][j]=hessij(p,delti,i,j,func,npar);
   /* 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          hess[j][i]=hess[i][j];    
      nstepm is the number of stepm from age to agelin.          /*printf(" %lf ",hess[i][j]);*/
      Look at hpijx to understand the reason of that which relies in memory size        }
      and note for a fixed period like k years */      }
   /* We decided (b) to get a life expectancy respecting the most precise curvature of the    }
      survival function given by stepm (the optimization length). Unfortunately it    printf("\n");
      means that if the survival funtion is printed only each two years of age and if    fprintf(ficlog,"\n");
      you sum them up and add 1 year (area under the trapezoids) you won't get the same  
      results. So we changed our mind and took the option of the best precision.    printf("\nInverting the hessian to get the covariance matrix. Wait...\n");
   */    fprintf(ficlog,"\nInverting the hessian to get the covariance matrix. Wait...\n");
   hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */    
   agelim = AGESUP;    a=matrix(1,npar,1,npar);
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    y=matrix(1,npar,1,npar);
     nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */    x=vector(1,npar);
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */    indx=ivector(1,npar);
     p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    for (i=1;i<=npar;i++)
     gradg=ma3x(0,nhstepm,1,npar,1,nlstate);      for (j=1;j<=npar;j++) a[i][j]=hess[i][j];
     gp=matrix(0,nhstepm,1,nlstate);    ludcmp(a,npar,indx,&pd);
     gm=matrix(0,nhstepm,1,nlstate);  
     for (j=1;j<=npar;j++) {
     for(theta=1; theta <=npar; theta++){      for (i=1;i<=npar;i++) x[i]=0;
       for(i=1; i<=npar; i++){ /* Computes gradient */      x[j]=1;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      lubksb(a,npar,indx,x);
       }      for (i=1;i<=npar;i++){ 
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);          matcov[i][j]=x[i];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      }
     }
       if (popbased==1) {  
         for(i=1; i<=nlstate;i++)    printf("\n#Hessian matrix#\n");
           prlim[i][i]=probs[(int)age][i][ij];    fprintf(ficlog,"\n#Hessian matrix#\n");
       }    for (i=1;i<=npar;i++) { 
        for (j=1;j<=npar;j++) { 
       for(j=1; j<= nlstate; j++){        printf("%.3e ",hess[i][j]);
         for(h=0; h<=nhstepm; h++){        fprintf(ficlog,"%.3e ",hess[i][j]);
           for(i=1, gp[h][j]=0.;i<=nlstate;i++)      }
             gp[h][j] += prlim[i][i]*p3mat[i][j][h];      printf("\n");
         }      fprintf(ficlog,"\n");
       }    }
      
       for(i=1; i<=npar; i++) /* Computes gradient */    /* Recompute Inverse */
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    for (i=1;i<=npar;i++)
       hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);        for (j=1;j<=npar;j++) a[i][j]=matcov[i][j];
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    ludcmp(a,npar,indx,&pd);
    
       if (popbased==1) {    /*  printf("\n#Hessian matrix recomputed#\n");
         for(i=1; i<=nlstate;i++)  
           prlim[i][i]=probs[(int)age][i][ij];    for (j=1;j<=npar;j++) {
       }      for (i=1;i<=npar;i++) x[i]=0;
       x[j]=1;
       for(j=1; j<= nlstate; j++){      lubksb(a,npar,indx,x);
         for(h=0; h<=nhstepm; h++){      for (i=1;i<=npar;i++){ 
           for(i=1, gm[h][j]=0.;i<=nlstate;i++)        y[i][j]=x[i];
             gm[h][j] += prlim[i][i]*p3mat[i][j][h];        printf("%.3e ",y[i][j]);
         }        fprintf(ficlog,"%.3e ",y[i][j]);
       }      }
       printf("\n");
       for(j=1; j<= nlstate; j++)      fprintf(ficlog,"\n");
         for(h=0; h<=nhstepm; h++){    }
           gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];    */
         }  
     } /* End theta */    free_matrix(a,1,npar,1,npar);
     free_matrix(y,1,npar,1,npar);
     trgradg =ma3x(0,nhstepm,1,nlstate,1,npar);    free_vector(x,1,npar);
     free_ivector(indx,1,npar);
     for(h=0; h<=nhstepm; h++)    free_matrix(hess,1,npar,1,npar);
       for(j=1; j<=nlstate;j++)  
         for(theta=1; theta <=npar; theta++)  
           trgradg[h][j][theta]=gradg[h][theta][j];  }
   
     hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */  /*************** hessian matrix ****************/
     for(i=1;i<=nlstate;i++)  double hessii(double x[], double delta, int theta, double delti[], double (*func)(double []), int npar)
       for(j=1;j<=nlstate;j++)  {
         vareij[i][j][(int)age] =0.;    int i;
     int l=1, lmax=20;
     for(h=0;h<=nhstepm;h++){    double k1,k2;
       for(k=0;k<=nhstepm;k++){    double p2[NPARMAX+1];
         matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);    double res;
         matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);    double delt=0.0001, delts, nkhi=10.,nkhif=1., khi=1.e-4;
         for(i=1;i<=nlstate;i++)    double fx;
           for(j=1;j<=nlstate;j++)    int k=0,kmax=10;
             vareij[i][j][(int)age] += doldm[i][j]*hf*hf;    double l1;
       }  
     }    fx=func(x);
     for (i=1;i<=npar;i++) p2[i]=x[i];
     fprintf(ficresvij,"%.0f ",age );    for(l=0 ; l <=lmax; l++){
     for(i=1; i<=nlstate;i++)      l1=pow(10,l);
       for(j=1; j<=nlstate;j++){      delts=delt;
         fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);      for(k=1 ; k <kmax; k=k+1){
       }        delt = delta*(l1*k);
     fprintf(ficresvij,"\n");        p2[theta]=x[theta] +delt;
     free_matrix(gp,0,nhstepm,1,nlstate);        k1=func(p2)-fx;
     free_matrix(gm,0,nhstepm,1,nlstate);        p2[theta]=x[theta]-delt;
     free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);        k2=func(p2)-fx;
     free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);        /*res= (k1-2.0*fx+k2)/delt/delt; */
     free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        res= (k1+k2)/delt/delt/2.; /* Divided by because L and not 2*L */
   } /* End age */        
    #ifdef DEBUG
   free_vector(xp,1,npar);        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);
   free_matrix(doldm,1,nlstate,1,npar);        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);
   free_matrix(dnewm,1,nlstate,1,nlstate);  #endif
         /*if(fabs(k1-2.0*fx+k2) <1.e-13){ */
 }        if((k1 <khi/nkhi/2.) || (k2 <khi/nkhi/2.)){
           k=kmax;
 /************ Variance of prevlim ******************/        }
 void varprevlim(char fileres[], double **varpl, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij)        else if((k1 >khi/nkhif) || (k2 >khi/nkhif)){ /* Keeps lastvalue before 3.84/2 KHI2 5% 1d.f. */
 {          k=kmax; l=lmax*10.;
   /* Variance of prevalence limit */        }
   /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/        else if((k1 >khi/nkhi) || (k2 >khi/nkhi)){ 
   double **newm;          delts=delt;
   double **dnewm,**doldm;        }
   int i, j, nhstepm, hstepm;      }
   int k, cptcode;    }
   double *xp;    delti[theta]=delts;
   double *gp, *gm;    return res; 
   double **gradg, **trgradg;    
   double age,agelim;  }
   int theta;  
      double hessij( double x[], double delti[], int thetai,int thetaj,double (*func)(double []),int npar)
   fprintf(ficresvpl,"# Standard deviation of prevalence's limit\n");  {
   fprintf(ficresvpl,"# Age");    int i;
   for(i=1; i<=nlstate;i++)    int l=1, l1, lmax=20;
       fprintf(ficresvpl," %1d-%1d",i,i);    double k1,k2,k3,k4,res,fx;
   fprintf(ficresvpl,"\n");    double p2[NPARMAX+1];
     int k;
   xp=vector(1,npar);  
   dnewm=matrix(1,nlstate,1,npar);    fx=func(x);
   doldm=matrix(1,nlstate,1,nlstate);    for (k=1; k<=2; k++) {
        for (i=1;i<=npar;i++) p2[i]=x[i];
   hstepm=1*YEARM; /* Every year of age */      p2[thetai]=x[thetai]+delti[thetai]/k;
   hstepm=hstepm/stepm; /* Typically in stepm units, if j= 2 years, = 2/6 months = 4 */      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
   agelim = AGESUP;      k1=func(p2)-fx;
   for (age=bage; age<=fage; age ++){ /* If stepm=6 months */    
     nhstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */      p2[thetai]=x[thetai]+delti[thetai]/k;
     if (stepm >= YEARM) hstepm=1;      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
     nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */      k2=func(p2)-fx;
     gradg=matrix(1,npar,1,nlstate);    
     gp=vector(1,nlstate);      p2[thetai]=x[thetai]-delti[thetai]/k;
     gm=vector(1,nlstate);      p2[thetaj]=x[thetaj]+delti[thetaj]/k;
       k3=func(p2)-fx;
     for(theta=1; theta <=npar; theta++){    
       for(i=1; i<=npar; i++){ /* Computes gradient */      p2[thetai]=x[thetai]-delti[thetai]/k;
         xp[i] = x[i] + (i==theta ?delti[theta]:0);      p2[thetaj]=x[thetaj]-delti[thetaj]/k;
       }      k4=func(p2)-fx;
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);      res=(k1-k2-k3+k4)/4.0/delti[thetai]*k/delti[thetaj]*k/2.; /* Because of L not 2*L */
       for(i=1;i<=nlstate;i++)  #ifdef DEBUG
         gp[i] = prlim[i][i];      printf("%d %d k=%d, k1=%.12e k2=%.12e k3=%.12e k4=%.12e delti/k=%.12e deltj/k=%.12e, xi-de/k=%.12e xj-de/k=%.12e  res=%.12e k1234=%.12e,k1-2=%.12e,k3-4=%.12e\n",thetai,thetaj,k,k1,k2,k3,k4,delti[thetai]/k,delti[thetaj]/k,x[thetai]-delti[thetai]/k,x[thetaj]-delti[thetaj]/k, res,k1-k2-k3+k4,k1-k2,k3-k4);
          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);
       for(i=1; i<=npar; i++) /* Computes gradient */  #endif
         xp[i] = x[i] - (i==theta ?delti[theta]:0);    }
       prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);    return res;
       for(i=1;i<=nlstate;i++)  }
         gm[i] = prlim[i][i];  
   /************** Inverse of matrix **************/
       for(i=1;i<=nlstate;i++)  void ludcmp(double **a, int n, int *indx, double *d) 
         gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];  { 
     } /* End theta */    int i,imax,j,k; 
     double big,dum,sum,temp; 
     trgradg =matrix(1,nlstate,1,npar);    double *vv; 
    
     for(j=1; j<=nlstate;j++)    vv=vector(1,n); 
       for(theta=1; theta <=npar; theta++)    *d=1.0; 
         trgradg[j][theta]=gradg[theta][j];    for (i=1;i<=n;i++) { 
       big=0.0; 
     for(i=1;i<=nlstate;i++)      for (j=1;j<=n;j++) 
       varpl[i][(int)age] =0.;        if ((temp=fabs(a[i][j])) > big) big=temp; 
     matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);      if (big == 0.0) nrerror("Singular matrix in routine ludcmp"); 
     matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);      vv[i]=1.0/big; 
     for(i=1;i<=nlstate;i++)    } 
       varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */    for (j=1;j<=n;j++) { 
       for (i=1;i<j;i++) { 
     fprintf(ficresvpl,"%.0f ",age );        sum=a[i][j]; 
     for(i=1; i<=nlstate;i++)        for (k=1;k<i;k++) sum -= a[i][k]*a[k][j]; 
       fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));        a[i][j]=sum; 
     fprintf(ficresvpl,"\n");      } 
     free_vector(gp,1,nlstate);      big=0.0; 
     free_vector(gm,1,nlstate);      for (i=j;i<=n;i++) { 
     free_matrix(gradg,1,npar,1,nlstate);        sum=a[i][j]; 
     free_matrix(trgradg,1,nlstate,1,npar);        for (k=1;k<j;k++) 
   } /* End age */          sum -= a[i][k]*a[k][j]; 
         a[i][j]=sum; 
   free_vector(xp,1,npar);        if ( (dum=vv[i]*fabs(sum)) >= big) { 
   free_matrix(doldm,1,nlstate,1,npar);          big=dum; 
   free_matrix(dnewm,1,nlstate,1,nlstate);          imax=i; 
         } 
 }      } 
       if (j != imax) { 
 /************ Variance of one-step probabilities  ******************/        for (k=1;k<=n;k++) { 
 void varprob(char fileres[], double **matcov, double x[], double delti[], int nlstate, double bage, double fage, int ij, int *Tvar, int **nbcode, int *ncodemax)          dum=a[imax][k]; 
 {          a[imax][k]=a[j][k]; 
   int i, j, i1, k1, j1, z1;          a[j][k]=dum; 
   int k=0,l, cptcode;        } 
   double **dnewm,**doldm;        *d = -(*d); 
   double *xp;        vv[imax]=vv[j]; 
   double *gp, *gm;      } 
   double **gradg, **trgradg;      indx[j]=imax; 
   double age,agelim, cov[NCOVMAX];      if (a[j][j] == 0.0) a[j][j]=TINY; 
   int theta;      if (j != n) { 
   char fileresprob[FILENAMELENGTH];        dum=1.0/(a[j][j]); 
   char fileresprobcov[FILENAMELENGTH];        for (i=j+1;i<=n;i++) a[i][j] *= dum; 
   char fileresprobcor[FILENAMELENGTH];      } 
     } 
   strcpy(fileresprob,"prob");    free_vector(vv,1,n);  /* Doesn't work */
   strcat(fileresprob,fileres);  ;
   if((ficresprob=fopen(fileresprob,"w"))==NULL) {  } 
     printf("Problem with resultfile: %s\n", fileresprob);  
   }  void lubksb(double **a, int n, int *indx, double b[]) 
   strcpy(fileresprobcov,"probcov");  { 
   strcat(fileresprobcov,fileres);    int i,ii=0,ip,j; 
   if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {    double sum; 
     printf("Problem with resultfile: %s\n", fileresprobcov);   
   }    for (i=1;i<=n;i++) { 
   strcpy(fileresprobcor,"probcor");      ip=indx[i]; 
   strcat(fileresprobcor,fileres);      sum=b[ip]; 
   if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {      b[ip]=b[i]; 
     printf("Problem with resultfile: %s\n", fileresprobcor);      if (ii) 
   }        for (j=ii;j<=i-1;j++) sum -= a[i][j]*b[j]; 
   printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);      else if (sum) ii=i; 
   printf("Computing matrix of variance covariance of one-step probabilities: result on file '%s' \n",fileresprobcov);      b[i]=sum; 
   printf("and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);    } 
      for (i=n;i>=1;i--) { 
   fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");      sum=b[i]; 
   fprintf(ficresprob,"# Age");      for (j=i+1;j<=n;j++) sum -= a[i][j]*b[j]; 
   fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");      b[i]=sum/a[i][i]; 
   fprintf(ficresprobcov,"# Age");    } 
   fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");  } 
   fprintf(ficresprobcov,"# Age");  
   for(i=1; i<=nlstate;i++)  void pstamp(FILE *fichier)
     for(j=1; j<=(nlstate+ndeath);j++){  {
       fprintf(ficresprob," p%1d-%1d (SE)",i,j);    fprintf(fichier,"# %s.%s\n#%s\n#%s\n# %s", optionfilefiname,optionfilext,version,fullversion,strstart);
       fprintf(ficresprobcov," p%1d-%1d ",i,j);  }
       fprintf(ficresprobcor," p%1d-%1d ",i,j);  
     }    /************ Frequencies ********************/
   fprintf(ficresprob,"\n");  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[])
   fprintf(ficresprobcov,"\n");  {  /* Some frequencies */
   fprintf(ficresprobcor,"\n");    
   xp=vector(1,npar);    int i, m, jk, k1,i1, j1, bool, z1,z2,j;
   dnewm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);    int first;
   doldm=matrix(1,(nlstate+ndeath)*(nlstate+ndeath),1,(nlstate+ndeath)*(nlstate+ndeath));    double ***freq; /* Frequencies */
      double *pp, **prop;
   cov[1]=1;    double pos,posprop, k2, dateintsum=0,k2cpt=0;
   j=cptcoveff;    char fileresp[FILENAMELENGTH];
   if (cptcovn<1) {j=1;ncodemax[1]=1;}    
   j1=0;    pp=vector(1,nlstate);
   for(k1=1; k1<=1;k1++){    prop=matrix(1,nlstate,iagemin,iagemax+3);
     for(i1=1; i1<=ncodemax[k1];i1++){    strcpy(fileresp,"p");
     j1++;    strcat(fileresp,fileres);
     if((ficresp=fopen(fileresp,"w"))==NULL) {
     if  (cptcovn>0) {      printf("Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficresprob, "\n#********** Variable ");      fprintf(ficlog,"Problem with prevalence resultfile: %s\n", fileresp);
       fprintf(ficresprobcov, "\n#********** Variable ");      exit(0);
       fprintf(ficresprobcor, "\n#********** Variable ");    }
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    freq= ma3x(-5,nlstate+ndeath,-5,nlstate+ndeath,iagemin,iagemax+3);
       fprintf(ficresprob, "**********\n#");    j1=0;
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    
       fprintf(ficresprobcov, "**********\n#");    j=cptcoveff;
       for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);    if (cptcovn<1) {j=1;ncodemax[1]=1;}
       fprintf(ficresprobcor, "**********\n#");  
     }    first=1;
      
       for (age=bage; age<=fage; age ++){    for(k1=1; k1<=j;k1++){
         cov[2]=age;      for(i1=1; i1<=ncodemax[k1];i1++){
         for (k=1; k<=cptcovn;k++) {        j1++;
           cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];        /*printf("cptcoveff=%d Tvaraff=%d", cptcoveff,Tvaraff[1]);
         }          scanf("%d", i);*/
         for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];        for (i=-5; i<=nlstate+ndeath; i++)  
         for (k=1; k<=cptcovprod;k++)          for (jk=-5; jk<=nlstate+ndeath; jk++)  
           cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];            for(m=iagemin; m <= iagemax+3; m++)
                      freq[i][jk][m]=0;
         gradg=matrix(1,npar,1,9);  
         trgradg=matrix(1,9,1,npar);      for (i=1; i<=nlstate; i++)  
         gp=vector(1,(nlstate+ndeath)*(nlstate+ndeath));        for(m=iagemin; m <= iagemax+3; m++)
         gm=vector(1,(nlstate+ndeath)*(nlstate+ndeath));          prop[i][m]=0;
            
         for(theta=1; theta <=npar; theta++){        dateintsum=0;
           for(i=1; i<=npar; i++)        k2cpt=0;
             xp[i] = x[i] + (i==theta ?delti[theta]:0);        for (i=1; i<=imx; i++) {
                    bool=1;
           pmij(pmmij,cov,ncovmodel,xp,nlstate);          if  (cptcovn>0) {
                      for (z1=1; z1<=cptcoveff; z1++) 
           k=0;              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
           for(i=1; i<= (nlstate+ndeath); i++){                bool=0;
             for(j=1; j<=(nlstate+ndeath);j++){          }
               k=k+1;          if (bool==1){
               gp[k]=pmmij[i][j];            for(m=firstpass; m<=lastpass; m++){
             }              k2=anint[m][i]+(mint[m][i]/12.);
           }              /*if ((k2>=dateprev1) && (k2<=dateprev2)) {*/
                          if(agev[m][i]==0) agev[m][i]=iagemax+1;
           for(i=1; i<=npar; i++)                if(agev[m][i]==1) agev[m][i]=iagemax+2;
             xp[i] = x[i] - (i==theta ?delti[theta]:0);                if (s[m][i]>0 && s[m][i]<=nlstate) prop[s[m][i]][(int)agev[m][i]] += weight[i];
                    if (m<lastpass) {
           pmij(pmmij,cov,ncovmodel,xp,nlstate);                  freq[s[m][i]][s[m+1][i]][(int)agev[m][i]] += weight[i];
           k=0;                  freq[s[m][i]][s[m+1][i]][iagemax+3] += weight[i];
           for(i=1; i<=(nlstate+ndeath); i++){                }
             for(j=1; j<=(nlstate+ndeath);j++){                
               k=k+1;                if ((agev[m][i]>1) && (agev[m][i]< (iagemax+3))) {
               gm[k]=pmmij[i][j];                  dateintsum=dateintsum+k2;
             }                  k2cpt++;
           }                }
                      /*}*/
           for(i=1; i<= (nlstate+ndeath)*(nlstate+ndeath); i++)            }
             gradg[theta][i]=(gp[i]-gm[i])/2./delti[theta];            }
         }        }
          
         for(j=1; j<=(nlstate+ndeath)*(nlstate+ndeath);j++)        /*      fprintf(ficresp, "#Count between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
           for(theta=1; theta <=npar; theta++)        pstamp(ficresp);
             trgradg[j][theta]=gradg[theta][j];        if  (cptcovn>0) {
                  fprintf(ficresp, "\n#********** Variable "); 
         matprod2(dnewm,trgradg,1,9,1,npar,1,npar,matcov);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresp, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
         matprod2(doldm,dnewm,1,9,1,npar,1,9,gradg);          fprintf(ficresp, "**********\n#");
                }
         pmij(pmmij,cov,ncovmodel,x,nlstate);        for(i=1; i<=nlstate;i++) 
                  fprintf(ficresp, " Age Prev(%d) N(%d) N",i,i);
         k=0;        fprintf(ficresp, "\n");
         for(i=1; i<=(nlstate+ndeath); i++){        
           for(j=1; j<=(nlstate+ndeath);j++){        for(i=iagemin; i <= iagemax+3; i++){
             k=k+1;          if(i==iagemax+3){
             gm[k]=pmmij[i][j];            fprintf(ficlog,"Total");
           }          }else{
         }            if(first==1){
                    first=0;
         /*printf("\n%d ",(int)age);              printf("See log file for details...\n");
      for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++){            }
        printf("%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));            fprintf(ficlog,"Age %d", i);
      }*/          }
           for(jk=1; jk <=nlstate ; jk++){
         fprintf(ficresprob,"\n%d ",(int)age);            for(m=-1, pp[jk]=0; m <=nlstate+ndeath ; m++)
         fprintf(ficresprobcov,"\n%d ",(int)age);              pp[jk] += freq[jk][m][i]; 
         fprintf(ficresprobcor,"\n%d ",(int)age);          }
           for(jk=1; jk <=nlstate ; jk++){
         for (i=1; i<=(nlstate+ndeath)*(nlstate+ndeath-1);i++)            for(m=-1, pos=0; m <=0 ; m++)
           fprintf(ficresprob,"%12.3e (%12.3e) ",gm[i],sqrt(doldm[i][j]));              pos += freq[jk][m][i];
         for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){            if(pp[jk]>=1.e-10){
           fprintf(ficresprobcov,"%12.3e ",gm[i]);              if(first==1){
           fprintf(ficresprobcor,"%12.3e ",gm[i]);              printf(" %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         }              }
         i=0;              fprintf(ficlog," %d.=%.0f loss[%d]=%.1f%%",jk,pp[jk],jk,100*pos/pp[jk]);
         for (k=1; k<=(nlstate);k++){            }else{
           for (l=1; l<=(nlstate+ndeath);l++){              if(first==1)
             i=i++;                printf(" %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);              fprintf(ficlog," %d.=%.0f loss[%d]=NaNQ%%",jk,pp[jk],jk);
             fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);            }
             for (j=1; j<=i;j++){          }
               fprintf(ficresprobcov," %12.3e",doldm[i][j]);  
               fprintf(ficresprobcor," %12.3e",doldm[i][j]/sqrt(doldm[i][i])/sqrt(doldm[j][j]));          for(jk=1; jk <=nlstate ; jk++){
             }            for(m=0, pp[jk]=0; m <=nlstate+ndeath; m++)
           }              pp[jk] += freq[jk][m][i];
         }          }       
       }          for(jk=1,pos=0,posprop=0; jk <=nlstate ; jk++){
     }            pos += pp[jk];
     free_vector(gp,1,(nlstate+ndeath)*(nlstate+ndeath));            posprop += prop[jk][i];
     free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));          }
     free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);          for(jk=1; jk <=nlstate ; jk++){
     free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);            if(pos>=1.e-5){
   }              if(first==1)
   free_vector(xp,1,npar);                printf(" %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   fclose(ficresprob);              fprintf(ficlog," %d.=%.0f prev[%d]=%.1f%%",jk,pp[jk],jk,100*pp[jk]/pos);
   fclose(ficresprobcov);            }else{
   fclose(ficresprobcor);              if(first==1)
 }                printf(" %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
               fprintf(ficlog," %d.=%.0f prev[%d]=NaNQ%%",jk,pp[jk],jk);
             }
 /******************* Printing html file ***********/            if( i <= iagemax){
 void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \              if(pos>=1.e-5){
                   int lastpass, int stepm, int weightopt, char model[],\                fprintf(ficresp," %d %.5f %.0f %.0f",i,prop[jk][i]/posprop, prop[jk][i],posprop);
                   int imx,int jmin, int jmax, double jmeanint,char optionfile[], \                /*probs[i][jk][j1]= pp[jk]/pos;*/
                   char optionfilehtm[],char rfileres[], char optionfilegnuplot[],\                /*printf("\ni=%d jk=%d j1=%d %.5f %.0f %.0f %f",i,jk,j1,pp[jk]/pos, pp[jk],pos,probs[i][jk][j1]);*/
                   char version[], int popforecast, int estepm ,\              }
                   double jprev1, double mprev1,double anprev1, \              else
                   double jprev2, double mprev2,double anprev2){                fprintf(ficresp," %d NaNq %.0f %.0f",i,prop[jk][i],posprop);
   int jj1, k1, i1, cpt;            }
   FILE *fichtm;          }
   /*char optionfilehtm[FILENAMELENGTH];*/          
           for(jk=-1; jk <=nlstate+ndeath; jk++)
   strcpy(optionfilehtm,optionfile);            for(m=-1; m <=nlstate+ndeath; m++)
   strcat(optionfilehtm,".htm");              if(freq[jk][m][i] !=0 ) {
   if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {              if(first==1)
     printf("Problem with %s \n",optionfilehtm), exit(0);                printf(" %d%d=%.0f",jk,m,freq[jk][m][i]);
   }                fprintf(ficlog," %d%d=%.0f",jk,m,freq[jk][m][i]);
               }
   fprintf(fichtm,"<body> <font size=\"2\">%s </font> <hr size=\"2\" color=\"#EC5E5E\"> \n          if(i <= iagemax)
 Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n            fprintf(ficresp,"\n");
 \n          if(first==1)
 Total number of observations=%d <br>\n            printf("Others in log...\n");
 Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n          fprintf(ficlog,"\n");
 <hr  size=\"2\" color=\"#EC5E5E\">        }
  <ul><li>Parameter files<br>\n      }
  - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n    }
  - Gnuplot file name: <a href=\"%s\">%s</a><br></ul>\n",version,title,datafile,firstpass,lastpass,stepm, weightopt,model,imx,jmin,jmax,jmean,fileres,fileres,optionfilegnuplot,optionfilegnuplot);    dateintmean=dateintsum/k2cpt; 
    
    fprintf(fichtm,"<ul><li>Result files (first order: no variance)<br>\n    fclose(ficresp);
  - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"p%s\">p%s</a> <br>\n    free_ma3x(freq,-5,nlstate+ndeath,-5,nlstate+ndeath, iagemin, iagemax+3);
  - Estimated transition probabilities over %d (stepm) months: <a href=\"pij%s\">pij%s</a><br>\n    free_vector(pp,1,nlstate);
  - Stable prevalence in each health state: <a href=\"pl%s\">pl%s</a> <br>\n    free_matrix(prop,1,nlstate,iagemin, iagemax+3);
  - Life expectancies by age and initial health status (estepm=%2d months):    /* End of Freq */
    <a href=\"e%s\">e%s</a> <br>\n</li>", \  }
   jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,fileres,fileres,stepm,fileres,fileres,fileres,fileres,estepm,fileres,fileres);  
   /************ Prevalence ********************/
  fprintf(fichtm,"\n<li> Result files (second order: variances)<br>\n  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)
  - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n  {  
  - Variance of one-step probabilities: <a href=\"prob%s\">prob%s</a> <br>\n    /* Compute observed prevalence between dateprev1 and dateprev2 by counting the number of people
  - Variance-covariance of one-step probabilities: <a href=\"probcov%s\">probcov%s</a> <br>\n       in each health status at the date of interview (if between dateprev1 and dateprev2).
  - Correlation matrix of one-step probabilities: <a href=\"probcor%s\">probcor%s</a> <br>\n       We still use firstpass and lastpass as another selection.
  - Variances and covariances of life expectancies by age and initial health status (estepm=%d months): <a href=\"v%s\">v%s</a><br>\n    */
  - Health expectancies with their variances (no covariance): <a href=\"t%s\">t%s</a> <br>\n   
  - Standard deviation of stable prevalences: <a href=\"vpl%s\">vpl%s</a> <br>\n",rfileres,rfileres,fileres,fileres,fileres,fileres,fileres,fileres, estepm, fileres,fileres,fileres,fileres,fileres,fileres);    int i, m, jk, k1, i1, j1, bool, z1,z2,j;
     double ***freq; /* Frequencies */
  if(popforecast==1) fprintf(fichtm,"\n    double *pp, **prop;
  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n    double pos,posprop; 
  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n    double  y2; /* in fractional years */
         <br>",fileres,fileres,fileres,fileres);    int iagemin, iagemax;
  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);    iagemin= (int) agemin;
 fprintf(fichtm," <li>Graphs</li><p>");    iagemax= (int) agemax;
     /*pp=vector(1,nlstate);*/
  m=cptcoveff;    prop=matrix(1,nlstate,iagemin,iagemax+3); 
  if (cptcovn < 1) {m=1;ncodemax[1]=1;}    /*  freq=ma3x(-1,nlstate+ndeath,-1,nlstate+ndeath,iagemin,iagemax+3);*/
     j1=0;
  jj1=0;    
  for(k1=1; k1<=m;k1++){    j=cptcoveff;
    for(i1=1; i1<=ncodemax[k1];i1++){    if (cptcovn<1) {j=1;ncodemax[1]=1;}
      jj1++;    
      if (cptcovn > 0) {    for(k1=1; k1<=j;k1++){
        fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");      for(i1=1; i1<=ncodemax[k1];i1++){
        for (cpt=1; cpt<=cptcoveff;cpt++)        j1++;
          fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);        
        fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");        for (i=1; i<=nlstate; i++)  
      }          for(m=iagemin; m <= iagemax+3; m++)
      /* Pij */            prop[i][m]=0.0;
      fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months before: pe%s%d1.png<br>       
 <img src=\"pe%s%d1.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);            for (i=1; i<=imx; i++) { /* Each individual */
      /* Quasi-incidences */          bool=1;
      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: pe%s%d2.png<br>          if  (cptcovn>0) {
 <img src=\"pe%s%d2.png\">",stepm,strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);            for (z1=1; z1<=cptcoveff; z1++) 
        /* Stable prevalence in each health state */              if (covar[Tvaraff[z1]][i]!= nbcode[Tvaraff[z1]][codtab[j1][z1]]) 
        for(cpt=1; cpt<nlstate;cpt++){                bool=0;
          fprintf(fichtm,"<br>- Stable prevalence in each health state : p%s%d%d.png<br>          } 
 <img src=\"p%s%d%d.png\">",strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);          if (bool==1) { 
        }            for(m=firstpass; m<=lastpass; m++){/* Other selection (we can limit to certain interviews*/
     for(cpt=1; cpt<=nlstate;cpt++) {              y2=anint[m][i]+(mint[m][i]/12.); /* Fractional date in year */
        fprintf(fichtm,"<br>- Observed and stationary prevalence (with confident              if ((y2>=dateprev1) && (y2<=dateprev2)) { /* Here is the main selection (fractional years) */
 interval) in state (%d): v%s%d%d.png <br>                if(agev[m][i]==0) agev[m][i]=iagemax+1;
 <img src=\"v%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);                  if(agev[m][i]==1) agev[m][i]=iagemax+2;
      }                if((int)agev[m][i] <iagemin || (int)agev[m][i] >iagemax+3) printf("Error on individual =%d agev[m][i]=%f m=%d\n",i, agev[m][i],m); 
      for(cpt=1; cpt<=nlstate;cpt++) {                if (s[m][i]>0 && s[m][i]<=nlstate) { 
         fprintf(fichtm,"\n<br>- Health life expectancies by age and initial health state (%d): exp%s%d%d.png <br>                  /*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]]);*/
 <img src=\"exp%s%d%d.png\">",cpt,strtok(optionfile, "."),cpt,jj1,strtok(optionfile, "."),cpt,jj1);                  prop[s[m][i]][(int)agev[m][i]] += weight[i];
      }                  prop[s[m][i]][iagemax+3] += weight[i]; 
      fprintf(fichtm,"\n<br>- Total life expectancy by age and                } 
 health expectancies in states (1) and (2): e%s%d.png<br>              }
 <img src=\"e%s%d.png\">",strtok(optionfile, "."),jj1,strtok(optionfile, "."),jj1);            } /* end selection of waves */
 fprintf(fichtm,"\n</body>");          }
    }        }
  }        for(i=iagemin; i <= iagemax+3; i++){  
 fclose(fichtm);          
 }          for(jk=1,posprop=0; jk <=nlstate ; jk++) { 
             posprop += prop[jk][i]; 
 /******************* Gnuplot file **************/          } 
 void printinggnuplot(char fileres[],char optionfilefiname[],char optionfile[],char optionfilegnuplot[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){  
           for(jk=1; jk <=nlstate ; jk++){     
   int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;            if( i <=  iagemax){ 
   int ng;              if(posprop>=1.e-5){ 
   strcpy(optionfilegnuplot,optionfilefiname);                probs[i][jk][j1]= prop[jk][i]/posprop;
   strcat(optionfilegnuplot,".gp");              } 
   if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {            } 
     printf("Problem with file %s",optionfilegnuplot);          }/* end jk */ 
   }        }/* end i */ 
       } /* end i1 */
 #ifdef windows    } /* end k1 */
     fprintf(ficgp,"cd \"%s\" \n",pathc);    
 #endif    /*  free_ma3x(freq,-1,nlstate+ndeath,-1,nlstate+ndeath, iagemin, iagemax+3);*/
 m=pow(2,cptcoveff);    /*free_vector(pp,1,nlstate);*/
      free_matrix(prop,1,nlstate, iagemin,iagemax+3);
  /* 1eme*/  }  /* End of prevalence */
   for (cpt=1; cpt<= nlstate ; cpt ++) {  
    for (k1=1; k1<= m ; k1 ++) {  /************* Waves Concatenation ***************/
   
 #ifdef windows  void  concatwav(int wav[], int **dh, int **bh,  int **mw, int **s, double *agedc, double **agev, int  firstpass, int lastpass, int imx, int nlstate, int stepm)
      fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);  {
      fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"vpl%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,fileres,k1-1,k1-1);    /* Concatenates waves: wav[i] is the number of effective (useful waves) of individual i.
 #endif       Death is a valid wave (if date is known).
 #ifdef unix       mw[mi][i] is the mi (mi=1 to wav[i])  effective wave of individual i
 fprintf(ficgp,"\nset out \"v%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);       dh[m][i] or dh[mw[mi][i]][i] is the delay between two effective waves m=mw[mi][i]
 fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nplot [%.f:%.f] \"vpl%s\" u 1:2 \"\%%lf",ageminpar,fage,fileres);       and mw[mi+1][i]. dh depends on stepm.
 #endif       */
   
 for (i=1; i<= nlstate ; i ++) {    int i, mi, m;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    /* int j, k=0,jk, ju, jl,jmin=1e+5, jmax=-1;
   else fprintf(ficgp," \%%*lf (\%%*lf)");       double sum=0., jmean=0.;*/
 }    int first;
     fprintf(ficgp,"\" t\"Stationary prevalence\" w l 0,\"vpl%s\" every :::%d::%d u 1:($2+2*$3) \"\%%lf",fileres,k1-1,k1-1);    int j, k=0,jk, ju, jl;
     for (i=1; i<= nlstate ; i ++) {    double sum=0.;
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");    first=0;
   else fprintf(ficgp," \%%*lf (\%%*lf)");    jmin=1e+5;
 }    jmax=-1;
   fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"vpl%s\" every :::%d::%d u 1:($2-2*$3) \"\%%lf",fileres,k1-1,k1-1);    jmean=0.;
      for (i=1; i<= nlstate ; i ++) {    for(i=1; i<=imx; i++){
   if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");      mi=0;
   else fprintf(ficgp," \%%*lf (\%%*lf)");      m=firstpass;
 }        while(s[m][i] <= nlstate){
      fprintf(ficgp,"\" t\"\" w l 1,\"p%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",fileres,k1-1,k1-1,2+4*(cpt-1));        if(s[m][i]>=1 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5)
 #ifdef unix          mw[++mi][i]=m;
 fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\n");        if(m >=lastpass)
 #endif          break;
    }        else
   }          m++;
   /*2 eme*/      }/* end while */
       if (s[m][i] > nlstate){
   for (k1=1; k1<= m ; k1 ++) {        mi++;     /* Death is another wave */
     fprintf(ficgp,"\nset out \"e%s%d.png\" \n",strtok(optionfile, "."),k1);        /* if(mi==0)  never been interviewed correctly before death */
     fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);           /* Only death is a correct wave */
            mw[mi][i]=m;
     for (i=1; i<= nlstate+1 ; i ++) {      }
       k=2*i;  
       fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:2 \"\%%lf",fileres,k1-1,k1-1);      wav[i]=mi;
       for (j=1; j<= nlstate+1 ; j ++) {      if(mi==0){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        nbwarn++;
   else fprintf(ficgp," \%%*lf (\%%*lf)");        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);
       if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");          first=1;
       else fprintf(ficgp,"\" t\"LE in state (%d)\" w l ,",i-1);        }
     fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2-$3*2) \"\%%lf",fileres,k1-1,k1-1);        if(first==1){
       for (j=1; j<= nlstate+1 ; j ++) {          fprintf(ficlog,"Warning! No valid information for individual %ld line=%d (skipped)\n",num[i],i);
         if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        }
         else fprintf(ficgp," \%%*lf (\%%*lf)");      } /* end mi==0 */
 }      } /* End individuals */
       fprintf(ficgp,"\" t\"\" w l 0,");  
      fprintf(ficgp,"\"t%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",fileres,k1-1,k1-1);    for(i=1; i<=imx; i++){
       for (j=1; j<= nlstate+1 ; j ++) {      for(mi=1; mi<wav[i];mi++){
   if (j==i) fprintf(ficgp," \%%lf (\%%lf)");        if (stepm <=0)
   else fprintf(ficgp," \%%*lf (\%%*lf)");          dh[mi][i]=1;
 }          else{
       if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");          if (s[mw[mi+1][i]][i] > nlstate) { /* A death */
       else fprintf(ficgp,"\" t\"\" w l 0,");            if (agedc[i] < 2*AGESUP) {
     }              j= rint(agedc[i]*12-agev[mw[mi][i]][i]*12); 
   }              if(j==0) j=1;  /* Survives at least one month after exam */
                else if(j<0){
   /*3eme*/                nberr++;
                 printf("Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
   for (k1=1; k1<= m ; k1 ++) {                j=1; /* Temporary Dangerous patch */
     for (cpt=1; cpt<= nlstate ; cpt ++) {                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);
       k=2+nlstate*(2*cpt-2);                fprintf(ficlog,"Error! Negative delay (%d to death) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       fprintf(ficgp,"\nset out \"exp%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);                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);
       fprintf(ficgp,"set ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"e%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,fileres,k1-1,k1-1,k,cpt);              }
       /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);              k=k+1;
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");              if (j >= jmax){
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);                jmax=j;
 fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);                ijmax=i;
  for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");              }
 fprintf(ficgp,"\" t \"e%d1\" w l",cpt);              if (j <= jmin){
                 jmin=j;
 */                ijmin=i;
       for (i=1; i< nlstate ; i ++) {              }
         fprintf(ficgp," ,\"e%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",fileres,k1-1,k1-1,k+2*i,cpt,i+1);              sum=sum+j;
               /*if (j<0) printf("j=%d num=%d \n",j,i);*/
       }              /*    printf("%d %d %d %d\n", s[mw[mi][i]][i] ,s[mw[mi+1][i]][i],j,i);*/
     }            }
   }          }
            else{
   /* CV preval stat */            j= rint( (agev[mw[mi+1][i]][i]*12 - agev[mw[mi][i]][i]*12));
     for (k1=1; k1<= m ; k1 ++) {  /*        if (j<0) printf("%d %lf %lf %d %d %d\n", i,agev[mw[mi+1][i]][i], agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]); */
     for (cpt=1; cpt<nlstate ; cpt ++) {  
       k=3;            k=k+1;
       fprintf(ficgp,"\nset out \"p%s%d%d.png\" \n",strtok(optionfile, "."),cpt,k1);            if (j >= jmax) {
       fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] \"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,fileres,k1,k+cpt+1,k+1);              jmax=j;
               ijmax=i;
       for (i=1; i< nlstate ; i ++)            }
         fprintf(ficgp,"+$%d",k+i+1);            else if (j <= jmin){
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);              jmin=j;
                    ijmin=i;
       l=3+(nlstate+ndeath)*cpt;            }
       fprintf(ficgp,",\"pij%s\" u ($1==%d ? ($3):1/0):($%d/($%d",fileres,k1,l+cpt+1,l+1);            /*        if (j<10) printf("j=%d jmin=%d num=%d ",j,jmin,i); */
       for (i=1; i< nlstate ; i ++) {            /*printf("%d %lf %d %d %d\n", i,agev[mw[mi][i]][i],j,s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);*/
         l=3+(nlstate+ndeath)*cpt;            if(j<0){
         fprintf(ficgp,"+$%d",l+i+1);              nberr++;
       }              printf("Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
       fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);                fprintf(ficlog,"Error! Negative delay (%d) between waves %d and %d of individual %ld at line %d who is aged %.1f with statuses from %d to %d\n ",j,mw[mi][i],mw[mi+1][i],num[i], i,agev[mw[mi][i]][i],s[mw[mi][i]][i] ,s[mw[mi+1][i]][i]);
     }            }
   }              sum=sum+j;
            }
   /* proba elementaires */          jk= j/stepm;
    for(i=1,jk=1; i <=nlstate; i++){          jl= j -jk*stepm;
     for(k=1; k <=(nlstate+ndeath); k++){          ju= j -(jk+1)*stepm;
       if (k != i) {          if(mle <=1){ /* only if we use a the linear-interpoloation pseudo-likelihood */
         for(j=1; j <=ncovmodel; j++){            if(jl==0){
                      dh[mi][i]=jk;
           fprintf(ficgp,"p%d=%f ",jk,p[jk]);              bh[mi][i]=0;
           jk++;            }else{ /* We want a negative bias in order to only have interpolation ie
           fprintf(ficgp,"\n");                    * at the price of an extra matrix product in likelihood */
         }              dh[mi][i]=jk+1;
       }              bh[mi][i]=ju;
     }            }
    }          }else{
             if(jl <= -ju){
    for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/              dh[mi][i]=jk;
      for(jk=1; jk <=m; jk++) {              bh[mi][i]=jl;       /* bias is positive if real duration
        fprintf(ficgp,"\nset out \"pe%s%d%d.png\" \n",strtok(optionfile, "."),jk,ng);                                   * is higher than the multiple of stepm and negative otherwise.
        if (ng==2)                                   */
          fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");            }
        else            else{
          fprintf(ficgp,"\nset title \"Probability\"\n");              dh[mi][i]=jk+1;
        fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);              bh[mi][i]=ju;
        i=1;            }
        for(k2=1; k2<=nlstate; k2++) {            if(dh[mi][i]==0){
          k3=i;              dh[mi][i]=1; /* At least one step */
          for(k=1; k<=(nlstate+ndeath); k++) {              bh[mi][i]=ju; /* At least one step */
            if (k != k2){              /*  printf(" bh=%d ju=%d jl=%d dh=%d jk=%d stepm=%d %d\n",bh[mi][i],ju,jl,dh[mi][i],jk,stepm,i);*/
              if(ng==2)            }
                fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);          } /* end if mle */
              else        }
                fprintf(ficgp," exp(p%d+p%d*x",i,i+1);      } /* end wave */
              ij=1;    }
              for(j=3; j <=ncovmodel; j++) {    jmean=sum/k;
                if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    printf("Delay (in months) between two waves Min=%d (for indiviudal %ld) Max=%d (%ld) Mean=%f\n\n ",jmin, num[ijmin], jmax, num[ijmax], jmean);
                  fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);    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);
                  ij++;   }
                }  
                else  /*********** Tricode ****************************/
                  fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);  void tricode(int *Tvar, int **nbcode, int imx)
              }  {
              fprintf(ficgp,")/(1");    
                  int Ndum[20],ij=1, k, j, i, maxncov=19;
              for(k1=1; k1 <=nlstate; k1++){      int cptcode=0;
                fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);    cptcoveff=0; 
                ij=1;   
                for(j=3; j <=ncovmodel; j++){    for (k=0; k<maxncov; k++) Ndum[k]=0;
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {    for (k=1; k<=7; k++) ncodemax[k]=0;
                    fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);  
                    ij++;    for (j=1; j<=(cptcovn+2*cptcovprod); j++) {
                  }      for (i=1; i<=imx; i++) { /*reads the data file to get the maximum 
                  else                                 modality*/ 
                    fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);        ij=(int)(covar[Tvar[j]][i]); /* ij is the modality of this individual*/
                }        Ndum[ij]++; /*store the modality */
                fprintf(ficgp,")");        /*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 
              fprintf(ficgp,") t \"p%d%d\" ", k2,k);                                         Tvar[j]. If V=sex and male is 0 and 
              if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");                                         female is 1, then  cptcode=1.*/
              i=i+ncovmodel;      }
            }  
          }      for (i=0; i<=cptcode; i++) {
        }        if(Ndum[i]!=0) ncodemax[j]++; /* Nomber of modalities of the j th covariates. In fact ncodemax[j]=2 (dichotom. variables) but it can be more */
      }      }
    }  
    fclose(ficgp);      ij=1; 
 }  /* end gnuplot */      for (i=1; i<=ncodemax[j]; i++) {
         for (k=0; k<= maxncov; k++) {
           if (Ndum[k] != 0) {
 /*************** Moving average **************/            nbcode[Tvar[j]][ij]=k; 
 void movingaverage(double agedeb, double fage,double ageminpar, double ***mobaverage){            /* 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; */
             
   int i, cpt, cptcod;            ij++;
     for (agedeb=ageminpar; agedeb<=fage; agedeb++)          }
       for (i=1; i<=nlstate;i++)          if (ij > ncodemax[j]) break; 
         for (cptcod=1;cptcod<=ncodemax[cptcov];cptcod++)        }  
           mobaverage[(int)agedeb][i][cptcod]=0.;      } 
        }  
     for (agedeb=ageminpar+4; agedeb<=fage; agedeb++){  
       for (i=1; i<=nlstate;i++){   for (k=0; k< maxncov; k++) Ndum[k]=0;
         for (cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){  
           for (cpt=0;cpt<=4;cpt++){   for (i=1; i<=ncovmodel-2; i++) { 
             mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]+probs[(int)agedeb-cpt][i][cptcod];     /* Listing of all covariables in statement model to see if some covariates appear twice. For example, V1 appears twice in V1+V1*V2.*/
           }     ij=Tvar[i];
           mobaverage[(int)agedeb-2][i][cptcod]=mobaverage[(int)agedeb-2][i][cptcod]/5;     Ndum[ij]++;
         }   }
       }  
     }   ij=1;
       for (i=1; i<= maxncov; i++) {
 }     if((Ndum[i]!=0) && (i<=ncovcol)){
        Tvaraff[ij]=i; /*For printing */
        ij++;
 /************** Forecasting ******************/     }
 prevforecast(char fileres[], double anproj1,double mproj1,double jproj1,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anproj2,double p[], int i2){   }
     
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;   cptcoveff=ij-1; /*Number of simple covariates*/
   int *popage;  }
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  
   double *popeffectif,*popcount;  /*********** Health Expectancies ****************/
   double ***p3mat;  
   char fileresf[FILENAMELENGTH];  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[] )
   
  agelim=AGESUP;  {
 calagedate=(anproj1+mproj1/12.+jproj1/365.-dateintmean)*YEARM;    /* Health expectancies, no variances */
     int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    double age, agelim, hf;
      double ***p3mat;
      double eip;
   strcpy(fileresf,"f");  
   strcat(fileresf,fileres);    pstamp(ficreseij);
   if((ficresf=fopen(fileresf,"w"))==NULL) {    fprintf(ficreseij,"# (a) Life expectancies by health status at initial age and (b) health expectancies by health status at initial age\n");
     printf("Problem with forecast resultfile: %s\n", fileresf);    fprintf(ficreseij,"# Age");
   }    for(i=1; i<=nlstate;i++){
   printf("Computing forecasting: result on file '%s' \n", fileresf);      for(j=1; j<=nlstate;j++){
         fprintf(ficreseij," e%1d%1d ",i,j);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;      }
       fprintf(ficreseij," e%1d. ",i);
   if (mobilav==1) {    }
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    fprintf(ficreseij,"\n");
     movingaverage(agedeb, fage, ageminpar, mobaverage);  
   }    
     if(estepm < stepm){
   stepsize=(int) (stepm+YEARM-1)/YEARM;      printf ("Problem %d lower than %d\n",estepm, stepm);
   if (stepm<=12) stepsize=1;    }
      else  hstepm=estepm;   
   agelim=AGESUP;    /* We compute the life expectancy from trapezoids spaced every estepm months
       * This is mainly to measure the difference between two models: for example
   hstepm=1;     * if stepm=24 months pijx are given only every 2 years and by summing them
   hstepm=hstepm/stepm;     * we are calculating an estimate of the Life Expectancy assuming a linear 
   yp1=modf(dateintmean,&yp);     * progression in between and thus overestimating or underestimating according
   anprojmean=yp;     * to the curvature of the survival function. If, for the same date, we 
   yp2=modf((yp1*12),&yp);     * estimate the model with stepm=1 month, we can keep estepm to 24 months
   mprojmean=yp;     * to compare the new estimate of Life expectancy with the same linear 
   yp1=modf((yp2*30.5),&yp);     * hypothesis. A more precise result, taking into account a more precise
   jprojmean=yp;     * curvature will be obtained if estepm is as small as stepm. */
   if(jprojmean==0) jprojmean=1;  
   if(mprojmean==0) jprojmean=1;    /* For example we decided to compute the life expectancy with the smallest unit */
      /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
   fprintf(ficresf,"# Estimated date of observed prevalence: %.lf/%.lf/%.lf ",jprojmean,mprojmean,anprojmean);       nhstepm is the number of hstepm from age to agelim 
         nstepm is the number of stepm from age to agelin. 
   for(cptcov=1;cptcov<=i2;cptcov++){       Look at hpijx to understand the reason of that which relies in memory size
     for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){       and note for a fixed period like estepm months */
       k=k+1;    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       fprintf(ficresf,"\n#******");       survival function given by stepm (the optimization length). Unfortunately it
       for(j=1;j<=cptcoveff;j++) {       means that if the survival funtion is printed only each two years of age and if
         fprintf(ficresf," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);       you sum them up and add 1 year (area under the trapezoids) you won't get the same 
       }       results. So we changed our mind and took the option of the best precision.
       fprintf(ficresf,"******\n");    */
       fprintf(ficresf,"# StartingAge FinalAge");    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficresf," P.%d",j);  
          agelim=AGESUP;
          /* nhstepm age range expressed in number of stepm */
       for (cpt=0; cpt<=(anproj2-anproj1);cpt++) {    nstepm=(int) rint((agelim-age)*YEARM/stepm); 
         fprintf(ficresf,"\n");    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
         fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+cpt);      /* if (stepm >= YEARM) hstepm=1;*/
     nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){    p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);  
           nhstepm = nhstepm/hstepm;    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
                /* Computed by stepm unit matrices, product of hstepm matrices, stored
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
           oldm=oldms;savm=savms;  
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);        hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
           
           for (h=0; h<=nhstepm; h++){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
             if (h==(int) (calagedate+YEARM*cpt)) {  
               fprintf(ficresf,"\n %.f %.f ",anproj1+cpt,agedeb+h*hstepm/YEARM*stepm);      /* Computing  Variances of health expectancies */
             }      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
             for(j=1; j<=nlstate+ndeath;j++) {         decrease memory allocation */
               kk1=0.;kk2=0;       printf("%d|",(int)age);fflush(stdout);
               for(i=1; i<=nlstate;i++) {                     fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
                 if (mobilav==1)      /* Computing expectancies */
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];      for(i=1; i<=nlstate;i++)
                 else {        for(j=1; j<=nlstate;j++)
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];          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;
                            
               }  /* 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]);*/
               if (h==(int)(calagedate+12*cpt)){  
                 fprintf(ficresf," %.3f", kk1);          }
                          
               }      fprintf(ficreseij,"%3.0f",age );
             }      for(i=1; i<=nlstate;i++){
           }        eip=0;
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(j=1; j<=nlstate;j++){
         }          eip +=eij[i][j][(int)age];
       }          fprintf(ficreseij,"%9.4f", eij[i][j][(int)age] );
     }        }
   }        fprintf(ficreseij,"%9.4f", eip );
              }
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);      fprintf(ficreseij,"\n");
   
   fclose(ficresf);    }
 }    free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
 /************** Forecasting ******************/    printf("\n");
 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){    fprintf(ficlog,"\n");
    
   int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;  }
   int *popage;  
   double calagedate, agelim, kk1, kk2, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;  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[] )
   double *popeffectif,*popcount;  
   double ***p3mat,***tabpop,***tabpopprev;  {
   char filerespop[FILENAMELENGTH];    /* Covariances of health expectancies eij and of total life expectancies according
      to initial status i, ei. .
   tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    */
   tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    int i, j, nhstepm, hstepm, h, nstepm, k, cptj, cptj2, i2, j2, ij, ji;
   agelim=AGESUP;    double age, agelim, hf;
   calagedate=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;    double ***p3matp, ***p3matm, ***varhe;
      double **dnewm,**doldm;
   prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);    double *xp, *xm;
      double **gp, **gm;
      double ***gradg, ***trgradg;
   strcpy(filerespop,"pop");    int theta;
   strcat(filerespop,fileres);  
   if((ficrespop=fopen(filerespop,"w"))==NULL) {    double eip, vip;
     printf("Problem with forecast resultfile: %s\n", filerespop);  
   }    varhe=ma3x(1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int) fage);
   printf("Computing forecasting: result on file '%s' \n", filerespop);    xp=vector(1,npar);
     xm=vector(1,npar);
   if (cptcoveff==0) ncodemax[cptcoveff]=1;    dnewm=matrix(1,nlstate*nlstate,1,npar);
     doldm=matrix(1,nlstate*nlstate,1,nlstate*nlstate);
   if (mobilav==1) {    
     mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);    pstamp(ficresstdeij);
     movingaverage(agedeb, fage, ageminpar, mobaverage);    fprintf(ficresstdeij,"# Health expectancies with standard errors\n");
   }    fprintf(ficresstdeij,"# Age");
     for(i=1; i<=nlstate;i++){
   stepsize=(int) (stepm+YEARM-1)/YEARM;      for(j=1; j<=nlstate;j++)
   if (stepm<=12) stepsize=1;        fprintf(ficresstdeij," e%1d%1d (SE)",i,j);
        fprintf(ficresstdeij," e%1d. ",i);
   agelim=AGESUP;    }
      fprintf(ficresstdeij,"\n");
   hstepm=1;  
   hstepm=hstepm/stepm;    pstamp(ficrescveij);
      fprintf(ficrescveij,"# Subdiagonal matrix of covariances of health expectancies by age: cov(eij,ekl)\n");
   if (popforecast==1) {    fprintf(ficrescveij,"# Age");
     if((ficpop=fopen(popfile,"r"))==NULL) {    for(i=1; i<=nlstate;i++)
       printf("Problem with population file : %s\n",popfile);exit(0);      for(j=1; j<=nlstate;j++){
     }        cptj= (j-1)*nlstate+i;
     popage=ivector(0,AGESUP);        for(i2=1; i2<=nlstate;i2++)
     popeffectif=vector(0,AGESUP);          for(j2=1; j2<=nlstate;j2++){
     popcount=vector(0,AGESUP);            cptj2= (j2-1)*nlstate+i2;
                if(cptj2 <= cptj)
     i=1;                fprintf(ficrescveij,"  %1d%1d,%1d%1d",i,j,i2,j2);
     while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;          }
          }
     imx=i;    fprintf(ficrescveij,"\n");
     for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];    
   }    if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
   for(cptcov=1;cptcov<=i2;cptcov++){    }
    for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){    else  hstepm=estepm;   
       k=k+1;    /* We compute the life expectancy from trapezoids spaced every estepm months
       fprintf(ficrespop,"\n#******");     * This is mainly to measure the difference between two models: for example
       for(j=1;j<=cptcoveff;j++) {     * if stepm=24 months pijx are given only every 2 years and by summing them
         fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);     * we are calculating an estimate of the Life Expectancy assuming a linear 
       }     * progression in between and thus overestimating or underestimating according
       fprintf(ficrespop,"******\n");     * to the curvature of the survival function. If, for the same date, we 
       fprintf(ficrespop,"# Age");     * estimate the model with stepm=1 month, we can keep estepm to 24 months
       for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);     * to compare the new estimate of Life expectancy with the same linear 
       if (popforecast==1)  fprintf(ficrespop," [Population]");     * hypothesis. A more precise result, taking into account a more precise
           * curvature will be obtained if estepm is as small as stepm. */
       for (cpt=0; cpt<=0;cpt++) {  
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);      /* For example we decided to compute the life expectancy with the smallest unit */
            /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){       nhstepm is the number of hstepm from age to agelim 
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);       nstepm is the number of stepm from age to agelin. 
           nhstepm = nhstepm/hstepm;       Look at hpijx to understand the reason of that which relies in memory size
                 and note for a fixed period like estepm months */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
           oldm=oldms;savm=savms;       survival function given by stepm (the optimization length). Unfortunately it
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);         means that if the survival funtion is printed only each two years of age and if
               you sum them up and add 1 year (area under the trapezoids) you won't get the same 
           for (h=0; h<=nhstepm; h++){       results. So we changed our mind and took the option of the best precision.
             if (h==(int) (calagedate+YEARM*cpt)) {    */
               fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
             }  
             for(j=1; j<=nlstate+ndeath;j++) {    /* If stepm=6 months */
               kk1=0.;kk2=0;    /* nhstepm age range expressed in number of stepm */
               for(i=1; i<=nlstate;i++) {                  agelim=AGESUP;
                 if (mobilav==1)    nstepm=(int) rint((agelim-age)*YEARM/stepm); 
                   kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];    /* Typically if 20 years nstepm = 20*12/6=40 stepm */ 
                 else {    /* if (stepm >= YEARM) hstepm=1;*/
                   kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];    nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
                 }    
               }    p3matp=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
               if (h==(int)(calagedate+12*cpt)){    p3matm=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
                 tabpop[(int)(agedeb)][j][cptcod]=kk1;    gradg=ma3x(0,nhstepm,1,npar,1,nlstate*nlstate);
                   /*fprintf(ficrespop," %.3f", kk1);    trgradg =ma3x(0,nhstepm,1,nlstate*nlstate,1,npar);
                     if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/    gp=matrix(0,nhstepm,1,nlstate*nlstate);
               }    gm=matrix(0,nhstepm,1,nlstate*nlstate);
             }  
             for(i=1; i<=nlstate;i++){    for (age=bage; age<=fage; age ++){ 
               kk1=0.;  
                 for(j=1; j<=nlstate;j++){      /* Computed by stepm unit matrices, product of hstepm matrices, stored
                   kk1= kk1+tabpop[(int)(agedeb)][j][cptcod];         in an array of nhstepm length: nhstepm=10, hstepm=4, stepm=6 months */
                 }   
                   tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedate+12*cpt)*hstepm/YEARM*stepm-1)];      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
             }  
       /* Computing  Variances of health expectancies */
             if (h==(int)(calagedate+12*cpt)) for(j=1; j<=nlstate;j++)      /* Gradient is computed with plus gp and minus gm. Code is duplicated in order to
               fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);         decrease memory allocation */
           }      for(theta=1; theta <=npar; theta++){
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);        for(i=1; i<=npar; i++){ 
         }          xp[i] = x[i] + (i==theta ?delti[theta]:0);
       }          xm[i] = x[i] - (i==theta ?delti[theta]:0);
          }
   /******/        hpxij(p3matp,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, cij);  
         hpxij(p3matm,nhstepm,age,hstepm,xm,nlstate,stepm,oldm,savm, cij);  
       for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) {    
         fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);          for(j=1; j<= nlstate; j++){
         for (agedeb=(fage-((int)calagedate %12/12.)); agedeb>=(ageminpar-((int)calagedate %12)/12.); agedeb--){          for(i=1; i<=nlstate; i++){
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm);            for(h=0; h<=nhstepm-1; h++){
           nhstepm = nhstepm/hstepm;              gp[h][(j-1)*nlstate + i] = (p3matp[i][j][h]+p3matp[i][j][h+1])/2.;
                        gm[h][(j-1)*nlstate + i] = (p3matm[i][j][h]+p3matm[i][j][h+1])/2.;
           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) (calagedate+YEARM*cpt)) {        for(ij=1; ij<= nlstate*nlstate; ij++)
               fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);          for(h=0; h<=nhstepm-1; h++){
             }            gradg[h][theta][ij]= (gp[h][ij]-gm[h][ij])/2./delti[theta];
             for(j=1; j<=nlstate+ndeath;j++) {          }
               kk1=0.;kk2=0;      }/* End theta */
               for(i=1; i<=nlstate;i++) {                    
                 kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];          
               }      for(h=0; h<=nhstepm-1; h++)
               if (h==(int)(calagedate+12*cpt)) fprintf(ficresf," %15.2f", kk1);        for(j=1; j<=nlstate*nlstate;j++)
             }          for(theta=1; theta <=npar; theta++)
           }            trgradg[h][j][theta]=gradg[h][theta][j];
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);      
         }  
       }       for(ij=1;ij<=nlstate*nlstate;ij++)
    }        for(ji=1;ji<=nlstate*nlstate;ji++)
   }          varhe[ij][ji][(int)age] =0.;
    
   if (mobilav==1) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);       printf("%d|",(int)age);fflush(stdout);
        fprintf(ficlog,"%d|",(int)age);fflush(ficlog);
   if (popforecast==1) {       for(h=0;h<=nhstepm-1;h++){
     free_ivector(popage,0,AGESUP);        for(k=0;k<=nhstepm-1;k++){
     free_vector(popeffectif,0,AGESUP);          matprod2(dnewm,trgradg[h],1,nlstate*nlstate,1,npar,1,npar,matcov);
     free_vector(popcount,0,AGESUP);          matprod2(doldm,dnewm,1,nlstate*nlstate,1,npar,1,nlstate*nlstate,gradg[k]);
   }          for(ij=1;ij<=nlstate*nlstate;ij++)
   free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);            for(ji=1;ji<=nlstate*nlstate;ji++)
   free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);              varhe[ij][ji][(int)age] += doldm[ij][ji]*hf*hf;
   fclose(ficrespop);        }
 }      }
       /* Computing expectancies */
 /***********************************************/      hpxij(p3matm,nhstepm,age,hstepm,x,nlstate,stepm,oldm, savm, cij);  
 /**************** Main Program *****************/      for(i=1; i<=nlstate;i++)
 /***********************************************/        for(j=1; j<=nlstate;j++)
           for (h=0, eij[i][j][(int)age]=0; h<=nhstepm-1; h++){
 int main(int argc, char *argv[])            eij[i][j][(int)age] += (p3matm[i][j][h]+p3matm[i][j][h+1])/2.0*hf;
 {            
             /* if((int)age==70)printf("i=%2d,j=%2d,h=%2d,age=%3d,%9.4f,%9.4f,%9.4f\n",i,j,h,(int)age,p3mat[i][j][h],hf,eij[i][j][(int)age]);*/
   int i,j, k, n=MAXN,iter,m,size,cptcode, cptcod;  
   double agedeb, agefin,hf;          }
   double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;  
       fprintf(ficresstdeij,"%3.0f",age );
   double fret;      for(i=1; i<=nlstate;i++){
   double **xi,tmp,delta;        eip=0.;
         vip=0.;
   double dum; /* Dummy variable */        for(j=1; j<=nlstate;j++){
   double ***p3mat;          eip += eij[i][j][(int)age];
   int *indx;          for(k=1; k<=nlstate;k++) /* Sum on j and k of cov(eij,eik) */
   char line[MAXLINE], linepar[MAXLINE];            vip += varhe[(j-1)*nlstate+i][(k-1)*nlstate+i][(int)age];
   char title[MAXLINE];          fprintf(ficresstdeij," %9.4f (%.4f)", eij[i][j][(int)age], sqrt(varhe[(j-1)*nlstate+i][(j-1)*nlstate+i][(int)age]) );
   char optionfile[FILENAMELENGTH], datafile[FILENAMELENGTH],  filerespl[FILENAMELENGTH];        }
   char optionfilext[10], optionfilefiname[FILENAMELENGTH], optionfilehtm[FILENAMELENGTH], optionfilegnuplot[FILENAMELENGTH], plotcmd[FILENAMELENGTH];        fprintf(ficresstdeij," %9.4f (%.4f)", eip, sqrt(vip));
        }
   char fileres[FILENAMELENGTH], filerespij[FILENAMELENGTH], filereso[FILENAMELENGTH], rfileres[FILENAMELENGTH];      fprintf(ficresstdeij,"\n");
   
   char filerest[FILENAMELENGTH];      fprintf(ficrescveij,"%3.0f",age );
   char fileregp[FILENAMELENGTH];      for(i=1; i<=nlstate;i++)
   char popfile[FILENAMELENGTH];        for(j=1; j<=nlstate;j++){
   char path[80],pathc[80],pathcd[80],pathtot[80],model[20];          cptj= (j-1)*nlstate+i;
   int firstobs=1, lastobs=10;          for(i2=1; i2<=nlstate;i2++)
   int sdeb, sfin; /* Status at beginning and end */            for(j2=1; j2<=nlstate;j2++){
   int c,  h , cpt,l;              cptj2= (j2-1)*nlstate+i2;
   int ju,jl, mi;              if(cptj2 <= cptj)
   int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;                fprintf(ficrescveij," %.4f", varhe[cptj][cptj2][(int)age]);
   int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,**adl,*tab;            }
   int mobilav=0,popforecast=0;        }
   int hstepm, nhstepm;      fprintf(ficrescveij,"\n");
   double jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,jpyram, mpyram,anpyram,jpyram1, mpyram1,anpyram1, calagedate;     
     }
   double bage, fage, age, agelim, agebase;    free_matrix(gm,0,nhstepm,1,nlstate*nlstate);
   double ftolpl=FTOL;    free_matrix(gp,0,nhstepm,1,nlstate*nlstate);
   double **prlim;    free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate*nlstate);
   double *severity;    free_ma3x(trgradg,0,nhstepm,1,nlstate*nlstate,1,npar);
   double ***param; /* Matrix of parameters */    free_ma3x(p3matm,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   double  *p;    free_ma3x(p3matp,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
   double **matcov; /* Matrix of covariance */    printf("\n");
   double ***delti3; /* Scale */    fprintf(ficlog,"\n");
   double *delti; /* Scale */  
   double ***eij, ***vareij;    free_vector(xm,1,npar);
   double **varpl; /* Variances of prevalence limits by age */    free_vector(xp,1,npar);
   double *epj, vepp;    free_matrix(dnewm,1,nlstate*nlstate,1,npar);
   double kk1, kk2;    free_matrix(doldm,1,nlstate*nlstate,1,nlstate*nlstate);
   double dateprev1, dateprev2,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2;    free_ma3x(varhe,1,nlstate*nlstate,1,nlstate*nlstate,(int) bage, (int)fage);
    }
   
   char version[80]="Imach version 0.8g, May 2002, INED-EUROREVES ";  /************ Variance ******************/
   char *alph[]={"a","a","b","c","d","e"}, str[4];  void varevsij(char optionfilefiname[], double ***vareij, double **matcov, double x[], double delti[], int nlstate, int stepm, double bage, double fage, double **oldm, double **savm, double **prlim, double ftolpl, int ij, int estepm, int cptcov, int cptcod, int popbased, int mobilav, char strstart[])
   {
     /* Variance of health expectancies */
   char z[1]="c", occ;    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double ** savm,double ftolpl);*/
 #include <sys/time.h>    /* double **newm;*/
 #include <time.h>    double **dnewm,**doldm;
   char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];    double **dnewmp,**doldmp;
      int i, j, nhstepm, hstepm, h, nstepm ;
   /* long total_usecs;    int k, cptcode;
   struct timeval start_time, end_time;    double *xp;
      double **gp, **gm;  /* for var eij */
   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */    double ***gradg, ***trgradg; /*for var eij */
   getcwd(pathcd, size);    double **gradgp, **trgradgp; /* for var p point j */
     double *gpp, *gmp; /* for var p point j */
   printf("\n%s",version);    double **varppt; /* for var p point j nlstate to nlstate+ndeath */
   if(argc <=1){    double ***p3mat;
     printf("\nEnter the parameter file name: ");    double age,agelim, hf;
     scanf("%s",pathtot);    double ***mobaverage;
   }    int theta;
   else{    char digit[4];
     strcpy(pathtot,argv[1]);    char digitp[25];
   }  
   /*if(getcwd(pathcd, 80)!= NULL)printf ("Error pathcd\n");*/    char fileresprobmorprev[FILENAMELENGTH];
   /*cygwin_split_path(pathtot,path,optionfile);  
     printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/    if(popbased==1){
   /* cutv(path,optionfile,pathtot,'\\');*/      if(mobilav!=0)
         strcpy(digitp,"-populbased-mobilav-");
   split(pathtot,path,optionfile,optionfilext,optionfilefiname);      else strcpy(digitp,"-populbased-nomobil-");
    printf("pathtot=%s, path=%s, optionfile=%s optionfilext=%s optionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);    }
   chdir(path);    else 
   replace(pathc,path);      strcpy(digitp,"-stablbased-");
   
 /*-------- arguments in the command line --------*/    if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   strcpy(fileres,"r");      if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
   strcat(fileres, optionfilefiname);        fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
   strcat(fileres,".txt");    /* Other files have txt extension */        printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
   /*---------arguments file --------*/    }
   
   if((ficpar=fopen(optionfile,"r"))==NULL)    {    strcpy(fileresprobmorprev,"prmorprev"); 
     printf("Problem with optionfile %s\n",optionfile);    sprintf(digit,"%-d",ij);
     goto end;    /*printf("DIGIT=%s, ij=%d ijr=%-d|\n",digit, ij,ij);*/
   }    strcat(fileresprobmorprev,digit); /* Tvar to be done */
     strcat(fileresprobmorprev,digitp); /* Popbased or not, mobilav or not */
   strcpy(filereso,"o");    strcat(fileresprobmorprev,fileres);
   strcat(filereso,fileres);    if((ficresprobmorprev=fopen(fileresprobmorprev,"w"))==NULL) {
   if((ficparo=fopen(filereso,"w"))==NULL) {      printf("Problem with resultfile: %s\n", fileresprobmorprev);
     printf("Problem with Output resultfile: %s\n", filereso);goto end;      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobmorprev);
   }    }
     printf("Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
   /* Reads comments: lines beginning with '#' */   
   while((c=getc(ficpar))=='#' && c!= EOF){    fprintf(ficlog,"Computing total mortality p.j=w1*p1j+w2*p2j+..: result on file '%s' \n",fileresprobmorprev);
     ungetc(c,ficpar);    pstamp(ficresprobmorprev);
     fgets(line, MAXLINE, ficpar);    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);
     puts(line);    fprintf(ficresprobmorprev,"# Age cov=%-d",ij);
     fputs(line,ficparo);    for(j=nlstate+1; j<=(nlstate+ndeath);j++){
   }      fprintf(ficresprobmorprev," p.%-d SE",j);
   ungetc(c,ficpar);      for(i=1; i<=nlstate;i++)
         fprintf(ficresprobmorprev," w%1d p%-d%-d",i,i,j);
   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\nmodel=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);    }  
   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(ficresprobmorprev,"\n");
   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(ficgp,"\n# Routine varevsij");
 while((c=getc(ficpar))=='#' && c!= EOF){    /* fprintf(fichtm, "#Local time at start: %s", strstart);*/
     ungetc(c,ficpar);    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");
     fgets(line, MAXLINE, ficpar);    fprintf(fichtm,"\n<br>%s  <br>\n",digitp);
     puts(line);  /*   } */
     fputs(line,ficparo);    varppt = matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
   }    pstamp(ficresvij);
   ungetc(c,ficpar);    fprintf(ficresvij,"# Variance and covariance of health expectancies e.j \n#  (weighted average of eij where weights are ");
      if(popbased==1)
          fprintf(ficresvij,"the age specific prevalence observed in the population i.e cross-sectionally\n in each health state (popbased=1)");
   covar=matrix(0,NCOVMAX,1,n);    else
   cptcovn=0;      fprintf(ficresvij,"the age specific period (stable) prevalences in each health state \n");
   if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;    fprintf(ficresvij,"# Age");
     for(i=1; i<=nlstate;i++)
   ncovmodel=2+cptcovn;      for(j=1; j<=nlstate;j++)
   nvar=ncovmodel-1; /* Suppressing age as a basic covariate */        fprintf(ficresvij," Cov(e.%1d, e.%1d)",i,j);
      fprintf(ficresvij,"\n");
   /* Read guess parameters */  
   /* Reads comments: lines beginning with '#' */    xp=vector(1,npar);
   while((c=getc(ficpar))=='#' && c!= EOF){    dnewm=matrix(1,nlstate,1,npar);
     ungetc(c,ficpar);    doldm=matrix(1,nlstate,1,nlstate);
     fgets(line, MAXLINE, ficpar);    dnewmp= matrix(nlstate+1,nlstate+ndeath,1,npar);
     puts(line);    doldmp= matrix(nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
     fputs(line,ficparo);  
   }    gradgp=matrix(1,npar,nlstate+1,nlstate+ndeath);
   ungetc(c,ficpar);    gpp=vector(nlstate+1,nlstate+ndeath);
      gmp=vector(nlstate+1,nlstate+ndeath);
   param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);    trgradgp =matrix(nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
     for(i=1; i <=nlstate; i++)    
     for(j=1; j <=nlstate+ndeath-1; j++){    if(estepm < stepm){
       fscanf(ficpar,"%1d%1d",&i1,&j1);      printf ("Problem %d lower than %d\n",estepm, stepm);
       fprintf(ficparo,"%1d%1d",i1,j1);    }
       printf("%1d%1d",i,j);    else  hstepm=estepm;   
       for(k=1; k<=ncovmodel;k++){    /* For example we decided to compute the life expectancy with the smallest unit */
         fscanf(ficpar," %lf",&param[i][j][k]);    /* hstepm beeing the number of stepms, if hstepm=1 the length of hstepm is stepm. 
         printf(" %lf",param[i][j][k]);       nhstepm is the number of hstepm from age to agelim 
         fprintf(ficparo," %lf",param[i][j][k]);       nstepm is the number of stepm from age to agelin. 
       }       Look at hpijx to understand the reason of that which relies in memory size
       fscanf(ficpar,"\n");       and note for a fixed period like k years */
       printf("\n");    /* We decided (b) to get a life expectancy respecting the most precise curvature of the
       fprintf(ficparo,"\n");       survival function given by stepm (the optimization length). Unfortunately it
     }       means that if the survival funtion is printed every two years of age and if
         you sum them up and add 1 year (area under the trapezoids) you won't get the same 
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel;       results. So we changed our mind and took the option of the best precision.
     */
   p=param[1][1];    hstepm=hstepm/stepm; /* Typically in stepm units, if stepm=6 & estepm=24 , = 24/6 months = 4 */ 
      agelim = AGESUP;
   /* Reads comments: lines beginning with '#' */    for (age=bage; age<=fage; age ++){ /* If stepm=6 months */
   while((c=getc(ficpar))=='#' && c!= EOF){      nstepm=(int) rint((agelim-age)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
     ungetc(c,ficpar);      nhstepm = nstepm/hstepm;/* Expressed in hstepm, typically nhstepm=40/4=10 */
     fgets(line, MAXLINE, ficpar);      p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
     puts(line);      gradg=ma3x(0,nhstepm,1,npar,1,nlstate);
     fputs(line,ficparo);      gp=matrix(0,nhstepm,1,nlstate);
   }      gm=matrix(0,nhstepm,1,nlstate);
   ungetc(c,ficpar);  
   
   delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);      for(theta=1; theta <=npar; theta++){
   delti=vector(1,npar); /* Scale of each paramater (output from hesscov) */        for(i=1; i<=npar; i++){ /* Computes gradient x + delta*/
   for(i=1; i <=nlstate; i++){          xp[i] = x[i] + (i==theta ?delti[theta]:0);
     for(j=1; j <=nlstate+ndeath-1; j++){        }
       fscanf(ficpar,"%1d%1d",&i1,&j1);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       printf("%1d%1d",i,j);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
       fprintf(ficparo,"%1d%1d",i1,j1);  
       for(k=1; k<=ncovmodel;k++){        if (popbased==1) {
         fscanf(ficpar,"%le",&delti3[i][j][k]);          if(mobilav ==0){
         printf(" %le",delti3[i][j][k]);            for(i=1; i<=nlstate;i++)
         fprintf(ficparo," %le",delti3[i][j][k]);              prlim[i][i]=probs[(int)age][i][ij];
       }          }else{ /* mobilav */ 
       fscanf(ficpar,"\n");            for(i=1; i<=nlstate;i++)
       printf("\n");              prlim[i][i]=mobaverage[(int)age][i][ij];
       fprintf(ficparo,"\n");          }
     }        }
   }    
   delti=delti3[1][1];        for(j=1; j<= nlstate; j++){
            for(h=0; h<=nhstepm; h++){
   /* Reads comments: lines beginning with '#' */            for(i=1, gp[h][j]=0.;i<=nlstate;i++)
   while((c=getc(ficpar))=='#' && c!= EOF){              gp[h][j] += prlim[i][i]*p3mat[i][j][h];
     ungetc(c,ficpar);          }
     fgets(line, MAXLINE, ficpar);        }
     puts(line);        /* This for computing probability of death (h=1 means
     fputs(line,ficparo);           computed over hstepm matrices product = hstepm*stepm months) 
   }           as a weighted average of prlim.
   ungetc(c,ficpar);        */
          for(j=nlstate+1;j<=nlstate+ndeath;j++){
   matcov=matrix(1,npar,1,npar);          for(i=1,gpp[j]=0.; i<= nlstate; i++)
   for(i=1; i <=npar; i++){            gpp[j] += prlim[i][i]*p3mat[i][j][1];
     fscanf(ficpar,"%s",&str);        }    
     printf("%s",str);        /* end probability of death */
     fprintf(ficparo,"%s",str);  
     for(j=1; j <=i; j++){        for(i=1; i<=npar; i++) /* Computes gradient x - delta */
       fscanf(ficpar," %le",&matcov[i][j]);          xp[i] = x[i] - (i==theta ?delti[theta]:0);
       printf(" %.5le",matcov[i][j]);        hpxij(p3mat,nhstepm,age,hstepm,xp,nlstate,stepm,oldm,savm, ij);  
       fprintf(ficparo," %.5le",matcov[i][j]);        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
     }   
     fscanf(ficpar,"\n");        if (popbased==1) {
     printf("\n");          if(mobilav ==0){
     fprintf(ficparo,"\n");            for(i=1; i<=nlstate;i++)
   }              prlim[i][i]=probs[(int)age][i][ij];
   for(i=1; i <=npar; i++)          }else{ /* mobilav */ 
     for(j=i+1;j<=npar;j++)            for(i=1; i<=nlstate;i++)
       matcov[i][j]=matcov[j][i];              prlim[i][i]=mobaverage[(int)age][i][ij];
              }
   printf("\n");        }
   
         for(j=1; j<= nlstate; j++){
     /*-------- Rewriting paramater file ----------*/          for(h=0; h<=nhstepm; h++){
      strcpy(rfileres,"r");    /* "Rparameterfile */            for(i=1, gm[h][j]=0.;i<=nlstate;i++)
      strcat(rfileres,optionfilefiname);    /* Parameter file first name*/              gm[h][j] += prlim[i][i]*p3mat[i][j][h];
      strcat(rfileres,".");    /* */          }
      strcat(rfileres,optionfilext);    /* Other files have txt extension */        }
     if((ficres =fopen(rfileres,"w"))==NULL) {        /* This for computing probability of death (h=1 means
       printf("Problem writing new parameter file: %s\n", fileres);goto end;           computed over hstepm matrices product = hstepm*stepm months) 
     }           as a weighted average of prlim.
     fprintf(ficres,"#%s\n",version);        */
            for(j=nlstate+1;j<=nlstate+ndeath;j++){
     /*-------- data file ----------*/          for(i=1,gmp[j]=0.; i<= nlstate; i++)
     if((fic=fopen(datafile,"r"))==NULL)    {           gmp[j] += prlim[i][i]*p3mat[i][j][1];
       printf("Problem with datafile: %s\n", datafile);goto end;        }    
     }        /* end probability of death */
   
     n= lastobs;        for(j=1; j<= nlstate; j++) /* vareij */
     severity = vector(1,maxwav);          for(h=0; h<=nhstepm; h++){
     outcome=imatrix(1,maxwav+1,1,n);            gradg[h][theta][j]= (gp[h][j]-gm[h][j])/2./delti[theta];
     num=ivector(1,n);          }
     moisnais=vector(1,n);  
     annais=vector(1,n);        for(j=nlstate+1; j<= nlstate+ndeath; j++){ /* var mu */
     moisdc=vector(1,n);          gradgp[theta][j]= (gpp[j]-gmp[j])/2./delti[theta];
     andc=vector(1,n);        }
     agedc=vector(1,n);  
     cod=ivector(1,n);      } /* End theta */
     weight=vector(1,n);  
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */      trgradg =ma3x(0,nhstepm,1,nlstate,1,npar); /* veij */
     mint=matrix(1,maxwav,1,n);  
     anint=matrix(1,maxwav,1,n);      for(h=0; h<=nhstepm; h++) /* veij */
     s=imatrix(1,maxwav+1,1,n);        for(j=1; j<=nlstate;j++)
     adl=imatrix(1,maxwav+1,1,n);              for(theta=1; theta <=npar; theta++)
     tab=ivector(1,NCOVMAX);            trgradg[h][j][theta]=gradg[h][theta][j];
     ncodemax=ivector(1,8);  
       for(j=nlstate+1; j<=nlstate+ndeath;j++) /* mu */
     i=1;        for(theta=1; theta <=npar; theta++)
     while (fgets(line, MAXLINE, fic) != NULL)    {          trgradgp[j][theta]=gradgp[theta][j];
       if ((i >= firstobs) && (i <=lastobs)) {    
          
         for (j=maxwav;j>=1;j--){      hf=hstepm*stepm/YEARM;  /* Duration of hstepm expressed in year unit. */
           cutv(stra, strb,line,' '); s[j][i]=atoi(strb);      for(i=1;i<=nlstate;i++)
           strcpy(line,stra);        for(j=1;j<=nlstate;j++)
           cutv(stra, strb,line,'/'); anint[j][i]=(double)(atoi(strb)); strcpy(line,stra);          vareij[i][j][(int)age] =0.;
           cutv(stra, strb,line,' '); mint[j][i]=(double)(atoi(strb)); strcpy(line,stra);  
         }      for(h=0;h<=nhstepm;h++){
                for(k=0;k<=nhstepm;k++){
         cutv(stra, strb,line,'/'); andc[i]=(double)(atoi(strb)); strcpy(line,stra);          matprod2(dnewm,trgradg[h],1,nlstate,1,npar,1,npar,matcov);
         cutv(stra, strb,line,' '); moisdc[i]=(double)(atoi(strb)); strcpy(line,stra);          matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg[k]);
           for(i=1;i<=nlstate;i++)
         cutv(stra, strb,line,'/'); annais[i]=(double)(atoi(strb)); strcpy(line,stra);            for(j=1;j<=nlstate;j++)
         cutv(stra, strb,line,' '); moisnais[i]=(double)(atoi(strb)); strcpy(line,stra);              vareij[i][j][(int)age] += doldm[i][j]*hf*hf;
         }
         cutv(stra, strb,line,' '); weight[i]=(double)(atoi(strb)); strcpy(line,stra);      }
         for (j=ncovcol;j>=1;j--){    
           cutv(stra, strb,line,' '); covar[j][i]=(double)(atoi(strb)); strcpy(line,stra);      /* pptj */
         }      matprod2(dnewmp,trgradgp,nlstate+1,nlstate+ndeath,1,npar,1,npar,matcov);
         num[i]=atol(stra);      matprod2(doldmp,dnewmp,nlstate+1,nlstate+ndeath,1,npar,nlstate+1,nlstate+ndeath,gradgp);
              for(j=nlstate+1;j<=nlstate+ndeath;j++)
         /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){        for(i=nlstate+1;i<=nlstate+ndeath;i++)
           printf("%d %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/          varppt[j][i]=doldmp[j][i];
       /* end ppptj */
         i=i+1;      /*  x centered again */
       }      hpxij(p3mat,nhstepm,age,hstepm,x,nlstate,stepm,oldm,savm, ij);  
     }      prevalim(prlim,nlstate,x,age,oldm,savm,ftolpl,ij);
     /* printf("ii=%d", ij);   
        scanf("%d",i);*/      if (popbased==1) {
   imx=i-1; /* Number of individuals */        if(mobilav ==0){
           for(i=1; i<=nlstate;i++)
   /* for (i=1; i<=imx; i++){            prlim[i][i]=probs[(int)age][i][ij];
     if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;        }else{ /* mobilav */ 
     if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;          for(i=1; i<=nlstate;i++)
     if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;            prlim[i][i]=mobaverage[(int)age][i][ij];
     }*/        }
    /*  for (i=1; i<=imx; i++){      }
      if (s[4][i]==9)  s[4][i]=-1;               
      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]));}*/      /* This for computing probability of death (h=1 means
           computed over hstepm (estepm) matrices product = hstepm*stepm months) 
           as a weighted average of prlim.
   /* Calculation of the number of parameter from char model*/      */
   Tvar=ivector(1,15);      for(j=nlstate+1;j<=nlstate+ndeath;j++){
   Tprod=ivector(1,15);        for(i=1,gmp[j]=0.;i<= nlstate; i++) 
   Tvaraff=ivector(1,15);          gmp[j] += prlim[i][i]*p3mat[i][j][1]; 
   Tvard=imatrix(1,15,1,2);      }    
   Tage=ivector(1,15);            /* end probability of death */
      
   if (strlen(model) >1){      fprintf(ficresprobmorprev,"%3d %d ",(int) age, ij);
     j=0, j1=0, k1=1, k2=1;      for(j=nlstate+1; j<=(nlstate+ndeath);j++){
     j=nbocc(model,'+');        fprintf(ficresprobmorprev," %11.3e %11.3e",gmp[j], sqrt(varppt[j][j]));
     j1=nbocc(model,'*');        for(i=1; i<=nlstate;i++){
     cptcovn=j+1;          fprintf(ficresprobmorprev," %11.3e %11.3e ",prlim[i][i],p3mat[i][j][1]);
     cptcovprod=j1;        }
          } 
     strcpy(modelsav,model);      fprintf(ficresprobmorprev,"\n");
     if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){  
       printf("Error. Non available option model=%s ",model);      fprintf(ficresvij,"%.0f ",age );
       goto end;      for(i=1; i<=nlstate;i++)
     }        for(j=1; j<=nlstate;j++){
              fprintf(ficresvij," %.4f", vareij[i][j][(int)age]);
     for(i=(j+1); i>=1;i--){        }
       cutv(stra,strb,modelsav,'+');      fprintf(ficresvij,"\n");
       if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav);      free_matrix(gp,0,nhstepm,1,nlstate);
       /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/      free_matrix(gm,0,nhstepm,1,nlstate);
       /*scanf("%d",i);*/      free_ma3x(gradg,0,nhstepm,1,npar,1,nlstate);
       if (strchr(strb,'*')) {      free_ma3x(trgradg,0,nhstepm,1,nlstate,1,npar);
         cutv(strd,strc,strb,'*');      free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
         if (strcmp(strc,"age")==0) {    } /* End age */
           cptcovprod--;    free_vector(gpp,nlstate+1,nlstate+ndeath);
           cutv(strb,stre,strd,'V');    free_vector(gmp,nlstate+1,nlstate+ndeath);
           Tvar[i]=atoi(stre);    free_matrix(gradgp,1,npar,nlstate+1,nlstate+ndeath);
           cptcovage++;    free_matrix(trgradgp,nlstate+1,nlstate+ndeath,1,npar); /* mu or p point j*/
             Tage[cptcovage]=i;    fprintf(ficgp,"\nset noparametric;set nolabel; set ter png small;set size 0.65, 0.65");
             /*printf("stre=%s ", stre);*/    /* for(j=nlstate+1; j<= nlstate+ndeath; j++){ *//* Only the first actually */
         }    fprintf(ficgp,"\n set log y; set nolog x;set xlabel \"Age\"; set ylabel \"Force of mortality (year-1)\";");
         else if (strcmp(strd,"age")==0) {  /*   fprintf(ficgp,"\n plot \"%s\"  u 1:($3*%6.3f) not w l 1 ",fileresprobmorprev,YEARM/estepm); */
           cptcovprod--;  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)*%6.3f) t \"95\%% interval\" w l 2 ",fileresprobmorprev,YEARM/estepm); */
           cutv(strb,stre,strc,'V');  /*   fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)*%6.3f) not w l 2 ",fileresprobmorprev,YEARM/estepm); */
           Tvar[i]=atoi(stre);    fprintf(ficgp,"\n plot \"%s\"  u 1:($3) not w l 1 ",subdirf(fileresprobmorprev));
           cptcovage++;    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3+1.96*$4)) t \"95\%% interval\" w l 2 ",subdirf(fileresprobmorprev));
           Tage[cptcovage]=i;    fprintf(ficgp,"\n replot \"%s\"  u 1:(($3-1.96*$4)) not w l 2 ",subdirf(fileresprobmorprev));
         }    fprintf(fichtm,"\n<br> File (multiple files are possible if covariates are present): <A href=\"%s\">%s</a>\n",subdirf(fileresprobmorprev),subdirf(fileresprobmorprev));
         else {    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);
           cutv(strb,stre,strc,'V');    /*  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);
           Tvar[i]=ncovcol+k1;  */
           cutv(strb,strc,strd,'V');  /*   fprintf(ficgp,"\nset out \"varmuptjgr%s%s%s.png\";replot;",digitp,optionfilefiname,digit); */
           Tprod[k1]=i;    fprintf(ficgp,"\nset out \"%s%s.png\";replot;\n",subdirf3(optionfilefiname,"varmuptjgr",digitp),digit);
           Tvard[k1][1]=atoi(strc);  
           Tvard[k1][2]=atoi(stre);    free_vector(xp,1,npar);
           Tvar[cptcovn+k2]=Tvard[k1][1];    free_matrix(doldm,1,nlstate,1,nlstate);
           Tvar[cptcovn+k2+1]=Tvard[k1][2];    free_matrix(dnewm,1,nlstate,1,npar);
           for (k=1; k<=lastobs;k++)    free_matrix(doldmp,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
             covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];    free_matrix(dnewmp,nlstate+1,nlstate+ndeath,1,npar);
           k1++;    free_matrix(varppt,nlstate+1,nlstate+ndeath,nlstate+1,nlstate+ndeath);
           k2=k2+2;    if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         }    fclose(ficresprobmorprev);
       }    fflush(ficgp);
       else {    fflush(fichtm); 
         /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/  }  /* end varevsij */
        /*  scanf("%d",i);*/  
       cutv(strd,strc,strb,'V');  /************ Variance of prevlim ******************/
       Tvar[i]=atoi(strc);  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[])
       }  {
       strcpy(modelsav,stra);      /* Variance of prevalence limit */
       /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);    /*  double **prevalim(double **prlim, int nlstate, double *xp, double age, double **oldm, double **savm,double ftolpl);*/
         scanf("%d",i);*/    double **newm;
     }    double **dnewm,**doldm;
 }    int i, j, nhstepm, hstepm;
      int k, cptcode;
   /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);    double *xp;
   printf("cptcovprod=%d ", cptcovprod);    double *gp, *gm;
   scanf("%d ",i);*/    double **gradg, **trgradg;
     fclose(fic);    double age,agelim;
     int theta;
     /*  if(mle==1){*/    
     if (weightopt != 1) { /* Maximisation without weights*/    pstamp(ficresvpl);
       for(i=1;i<=n;i++) weight[i]=1.0;    fprintf(ficresvpl,"# Standard deviation of period (stable) prevalences \n");
     }    fprintf(ficresvpl,"# Age");
     /*-calculation of age at interview from date of interview and age at death -*/    for(i=1; i<=nlstate;i++)
     agev=matrix(1,maxwav,1,imx);        fprintf(ficresvpl," %1d-%1d",i,i);
     fprintf(ficresvpl,"\n");
     for (i=1; i<=imx; i++) {  
       for(m=2; (m<= maxwav); m++) {    xp=vector(1,npar);
        if ((mint[m][i]== 99) && (s[m][i] <= nlstate)){    dnewm=matrix(1,nlstate,1,npar);
          anint[m][i]=9999;    doldm=matrix(1,nlstate,1,nlstate);
          s[m][i]=-1;    
        }    hstepm=1*YEARM; /* Every year of age */
      if(moisdc[i]==99 && andc[i]==9999 & s[m][i]>nlstate) s[m][i]=-1;    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 */ 
     for (i=1; i<=imx; i++)  {      if (stepm >= YEARM) hstepm=1;
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);      nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
       for(m=1; (m<= maxwav); m++){      gradg=matrix(1,npar,1,nlstate);
         if(s[m][i] >0){      gp=vector(1,nlstate);
           if (s[m][i] >= nlstate+1) {      gm=vector(1,nlstate);
             if(agedc[i]>0)  
               if(moisdc[i]!=99 && andc[i]!=9999)      for(theta=1; theta <=npar; theta++){
                 agev[m][i]=agedc[i];        for(i=1; i<=npar; i++){ /* Computes gradient */
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/          xp[i] = x[i] + (i==theta ?delti[theta]:0);
            else {        }
               if (andc[i]!=9999){        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
               printf("Warning negative age at death: %d line:%d\n",num[i],i);        for(i=1;i<=nlstate;i++)
               agev[m][i]=-1;          gp[i] = prlim[i][i];
               }      
             }        for(i=1; i<=npar; i++) /* Computes gradient */
           }          xp[i] = x[i] - (i==theta ?delti[theta]:0);
           else if(s[m][i] !=9){ /* Should no more exist */        prevalim(prlim,nlstate,xp,age,oldm,savm,ftolpl,ij);
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);        for(i=1;i<=nlstate;i++)
             if(mint[m][i]==99 || anint[m][i]==9999)          gm[i] = prlim[i][i];
               agev[m][i]=1;  
             else if(agev[m][i] <agemin){        for(i=1;i<=nlstate;i++)
               agemin=agev[m][i];          gradg[theta][i]= (gp[i]-gm[i])/2./delti[theta];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/      } /* End theta */
             }  
             else if(agev[m][i] >agemax){      trgradg =matrix(1,nlstate,1,npar);
               agemax=agev[m][i];  
              /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/      for(j=1; j<=nlstate;j++)
             }        for(theta=1; theta <=npar; theta++)
             /*agev[m][i]=anint[m][i]-annais[i];*/          trgradg[j][theta]=gradg[theta][j];
             /*   agev[m][i] = age[i]+2*m;*/  
           }      for(i=1;i<=nlstate;i++)
           else { /* =9 */        varpl[i][(int)age] =0.;
             agev[m][i]=1;      matprod2(dnewm,trgradg,1,nlstate,1,npar,1,npar,matcov);
             s[m][i]=-1;      matprod2(doldm,dnewm,1,nlstate,1,npar,1,nlstate,gradg);
           }      for(i=1;i<=nlstate;i++)
         }        varpl[i][(int)age] = doldm[i][i]; /* Covariances are useless */
         else /*= 0 Unknown */  
           agev[m][i]=1;      fprintf(ficresvpl,"%.0f ",age );
       }      for(i=1; i<=nlstate;i++)
            fprintf(ficresvpl," %.5f (%.5f)",prlim[i][i],sqrt(varpl[i][(int)age]));
     }      fprintf(ficresvpl,"\n");
     for (i=1; i<=imx; i++)  {      free_vector(gp,1,nlstate);
       for(m=1; (m<= maxwav); m++){      free_vector(gm,1,nlstate);
         if (s[m][i] > (nlstate+ndeath)) {      free_matrix(gradg,1,npar,1,nlstate);
           printf("Error: Wrong value in nlstate or ndeath\n");        free_matrix(trgradg,1,nlstate,1,npar);
           goto end;    } /* End age */
         }  
       }    free_vector(xp,1,npar);
     }    free_matrix(doldm,1,nlstate,1,npar);
     free_matrix(dnewm,1,nlstate,1,nlstate);
 printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);  
   }
     free_vector(severity,1,maxwav);  
     free_imatrix(outcome,1,maxwav+1,1,n);  /************ Variance of one-step probabilities  ******************/
     free_vector(moisnais,1,n);  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[])
     free_vector(annais,1,n);  {
     /* free_matrix(mint,1,maxwav,1,n);    int i, j=0,  i1, k1, l1, t, tj;
        free_matrix(anint,1,maxwav,1,n);*/    int k2, l2, j1,  z1;
     free_vector(moisdc,1,n);    int k=0,l, cptcode;
     free_vector(andc,1,n);    int first=1, first1;
     double cv12, mu1, mu2, lc1, lc2, v12, v21, v11, v22,v1,v2, c12, tnalp;
        double **dnewm,**doldm;
     wav=ivector(1,imx);    double *xp;
     dh=imatrix(1,lastpass-firstpass+1,1,imx);    double *gp, *gm;
     mw=imatrix(1,lastpass-firstpass+1,1,imx);    double **gradg, **trgradg;
        double **mu;
     /* Concatenates waves */    double age,agelim, cov[NCOVMAX];
       concatwav(wav, dh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);    double std=2.0; /* Number of standard deviation wide of confidence ellipsoids */
     int theta;
     char fileresprob[FILENAMELENGTH];
       Tcode=ivector(1,100);    char fileresprobcov[FILENAMELENGTH];
       nbcode=imatrix(0,NCOVMAX,0,NCOVMAX);    char fileresprobcor[FILENAMELENGTH];
       ncodemax[1]=1;  
       if (cptcovn > 0) tricode(Tvar,nbcode,imx);    double ***varpij;
        
    codtab=imatrix(1,100,1,10);    strcpy(fileresprob,"prob"); 
    h=0;    strcat(fileresprob,fileres);
    m=pow(2,cptcoveff);    if((ficresprob=fopen(fileresprob,"w"))==NULL) {
        printf("Problem with resultfile: %s\n", fileresprob);
    for(k=1;k<=cptcoveff; k++){      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprob);
      for(i=1; i <=(m/pow(2,k));i++){    }
        for(j=1; j <= ncodemax[k]; j++){    strcpy(fileresprobcov,"probcov"); 
          for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){    strcat(fileresprobcov,fileres);
            h++;    if((ficresprobcov=fopen(fileresprobcov,"w"))==NULL) {
            if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;      printf("Problem with resultfile: %s\n", fileresprobcov);
            /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcov);
          }    }
        }    strcpy(fileresprobcor,"probcor"); 
      }    strcat(fileresprobcor,fileres);
    }    if((ficresprobcor=fopen(fileresprobcor,"w"))==NULL) {
    /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]);      printf("Problem with resultfile: %s\n", fileresprobcor);
       codtab[1][2]=1;codtab[2][2]=2; */      fprintf(ficlog,"Problem with resultfile: %s\n", fileresprobcor);
    /* for(i=1; i <=m ;i++){    }
       for(k=1; k <=cptcovn; k++){    printf("Computing standard deviation of one-step probabilities: result on file '%s' \n",fileresprob);
       printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);    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);
       printf("\n");    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);
       scanf("%d",i);*/    fprintf(ficlog,"and correlation matrix of one-step probabilities: result on file '%s' \n",fileresprobcor);
        pstamp(ficresprob);
    /* Calculates basic frequencies. Computes observed prevalence at single age    fprintf(ficresprob,"#One-step probabilities and stand. devi in ()\n");
        and prints on file fileres'p'. */    fprintf(ficresprob,"# Age");
     pstamp(ficresprobcov);
        fprintf(ficresprobcov,"#One-step probabilities and covariance matrix\n");
        fprintf(ficresprobcov,"# Age");
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    pstamp(ficresprobcor);
     oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficresprobcor,"#One-step probabilities and correlation matrix\n");
     newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */    fprintf(ficresprobcor,"# Age");
     savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */  
     oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */  
          for(i=1; i<=nlstate;i++)
     /* For Powell, parameters are in a vector p[] starting at p[1]      for(j=1; j<=(nlstate+ndeath);j++){
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */        fprintf(ficresprob," p%1d-%1d (SE)",i,j);
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */        fprintf(ficresprobcov," p%1d-%1d ",i,j);
         fprintf(ficresprobcor," p%1d-%1d ",i,j);
     if(mle==1){      }  
     mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);   /* fprintf(ficresprob,"\n");
     }    fprintf(ficresprobcov,"\n");
        fprintf(ficresprobcor,"\n");
     /*--------- 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);   xp=vector(1,npar);
      dnewm=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     doldm=matrix(1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
    jk=1;    mu=matrix(1,(nlstate)*(nlstate+ndeath), (int) bage, (int)fage);
    fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    varpij=ma3x(1,nlstate*(nlstate+ndeath),1,nlstate*(nlstate+ndeath),(int) bage, (int) fage);
    printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");    first=1;
    for(i=1,jk=1; i <=nlstate; i++){    fprintf(ficgp,"\n# Routine varprob");
      for(k=1; k <=(nlstate+ndeath); k++){    fprintf(fichtm,"\n<li><h4> Computing and drawing one step probabilities with their confidence intervals</h4></li>\n");
        if (k != i)    fprintf(fichtm,"\n");
          {  
            printf("%d%d ",i,k);    fprintf(fichtm,"\n<li><h4> <a href=\"%s\">Matrix of variance-covariance of pairs of step probabilities (drawings)</a></h4></li>\n",optionfilehtmcov);
            fprintf(ficres,"%1d%1d ",i,k);    fprintf(fichtmcov,"\n<h4>Matrix of variance-covariance of pairs of step probabilities</h4>\n\
            for(j=1; j <=ncovmodel; j++){    file %s<br>\n",optionfilehtmcov);
              printf("%f ",p[jk]);    fprintf(fichtmcov,"\nEllipsoids of confidence centered on point (p<inf>ij</inf>, p<inf>kl</inf>) are estimated\
              fprintf(ficres,"%f ",p[jk]);  and drawn. It helps understanding how is the covariance between two incidences.\
              jk++;   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. \
            printf("\n");  It can be understood this way: if pij and pkl where uncorrelated the (2x2) matrix of covariance \
            fprintf(ficres,"\n");  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>\
  if(mle==1){  To be simple, these graphs help to understand the significativity of each parameter in relation to a second other one.<br> \n");
     /* Computing hessian and covariance matrix */  
     ftolhess=ftol; /* Usually correct */    cov[1]=1;
     hesscov(matcov, p, npar, delti, ftolhess, func);    tj=cptcoveff;
  }    if (cptcovn<1) {tj=1;ncodemax[1]=1;}
     fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");    j1=0;
     printf("# Scales (for hessian or gradient estimation)\n");    for(t=1; t<=tj;t++){
      for(i=1,jk=1; i <=nlstate; i++){      for(i1=1; i1<=ncodemax[t];i1++){ 
       for(j=1; j <=nlstate+ndeath; j++){        j1++;
         if (j!=i) {        if  (cptcovn>0) {
           fprintf(ficres,"%1d%1d",i,j);          fprintf(ficresprob, "\n#********** Variable "); 
           printf("%1d%1d",i,j);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprob, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
           for(k=1; k<=ncovmodel;k++){          fprintf(ficresprob, "**********\n#\n");
             printf(" %.5e",delti[jk]);          fprintf(ficresprobcov, "\n#********** Variable "); 
             fprintf(ficres," %.5e",delti[jk]);          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcov, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
             jk++;          fprintf(ficresprobcov, "**********\n#\n");
           }          
           printf("\n");          fprintf(ficgp, "\n#********** Variable "); 
           fprintf(ficres,"\n");          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 "); 
     k=1;          for (z1=1; z1<=cptcoveff; z1++) fprintf(fichtm, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
     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");          fprintf(fichtmcov, "**********\n<hr size=\"2\" color=\"#EC5E5E\">");
     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");          
     for(i=1;i<=npar;i++){          fprintf(ficresprobcor, "\n#********** Variable ");    
       /*  if (k>nlstate) k=1;          for (z1=1; z1<=cptcoveff; z1++) fprintf(ficresprobcor, "V%d=%d ",Tvaraff[z1],nbcode[Tvaraff[z1]][codtab[j1][z1]]);
       i1=(i-1)/(ncovmodel*nlstate)+1;          fprintf(ficresprobcor, "**********\n#");    
       fprintf(ficres,"%s%d%d",alph[k],i1,tab[i]);        }
       printf("%s%d%d",alph[k],i1,tab[i]);*/        
       fprintf(ficres,"%3d",i);        for (age=bage; age<=fage; age ++){ 
       printf("%3d",i);          cov[2]=age;
       for(j=1; j<=i;j++){          for (k=1; k<=cptcovn;k++) {
         fprintf(ficres," %.5e",matcov[i][j]);            cov[2+k]=nbcode[Tvar[k]][codtab[j1][Tvar[k]]];
         printf(" %.5e",matcov[i][j]);          }
       }          for (k=1; k<=cptcovage;k++) cov[2+Tage[k]]=cov[2+Tage[k]]*cov[2];
       fprintf(ficres,"\n");          for (k=1; k<=cptcovprod;k++)
       printf("\n");            cov[2+Tprod[k]]=nbcode[Tvard[k][1]][codtab[ij][Tvard[k][1]]]*nbcode[Tvard[k][2]][codtab[ij][Tvard[k][2]]];
       k++;          
     }          gradg=matrix(1,npar,1,(nlstate)*(nlstate+ndeath));
              trgradg=matrix(1,(nlstate)*(nlstate+ndeath),1,npar);
     while((c=getc(ficpar))=='#' && c!= EOF){          gp=vector(1,(nlstate)*(nlstate+ndeath));
       ungetc(c,ficpar);          gm=vector(1,(nlstate)*(nlstate+ndeath));
       fgets(line, MAXLINE, ficpar);      
       puts(line);          for(theta=1; theta <=npar; theta++){
       fputs(line,ficparo);            for(i=1; i<=npar; i++)
     }              xp[i] = x[i] + (i==theta ?delti[theta]:(double)0);
     ungetc(c,ficpar);            
     estepm=0;            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     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;            k=0;
     if (fage <= 2) {            for(i=1; i<= (nlstate); i++){
       bage = ageminpar;              for(j=1; j<=(nlstate+ndeath);j++){
       fage = agemaxpar;                k=k+1;
     }                gp[k]=pmmij[i][j];
                  }
     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);            for(i=1; i<=npar; i++)
                xp[i] = x[i] - (i==theta ?delti[theta]:(double)0);
     while((c=getc(ficpar))=='#' && c!= EOF){      
     ungetc(c,ficpar);            pmij(pmmij,cov,ncovmodel,xp,nlstate);
     fgets(line, MAXLINE, ficpar);            k=0;
     puts(line);            for(i=1; i<=(nlstate); i++){
     fputs(line,ficparo);              for(j=1; j<=(nlstate+ndeath);j++){
   }                k=k+1;
   ungetc(c,ficpar);                gm[k]=pmmij[i][j];
                }
   fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2);            }
   fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);       
  fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);            for(i=1; i<= (nlstate)*(nlstate+ndeath); i++) 
                    gradg[theta][i]=(gp[i]-gm[i])/(double)2./delti[theta];  
   while((c=getc(ficpar))=='#' && c!= EOF){          }
     ungetc(c,ficpar);  
     fgets(line, MAXLINE, ficpar);          for(j=1; j<=(nlstate)*(nlstate+ndeath);j++)
     puts(line);            for(theta=1; theta <=npar; theta++)
     fputs(line,ficparo);              trgradg[j][theta]=gradg[theta][j];
   }          
   ungetc(c,ficpar);          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));
    dateprev1=anprev1+mprev1/12.+jprev1/365.;          free_vector(gm,1,(nlstate+ndeath)*(nlstate+ndeath));
    dateprev2=anprev2+mprev2/12.+jprev2/365.;          free_matrix(trgradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
           free_matrix(gradg,1,(nlstate+ndeath)*(nlstate+ndeath),1,npar);
   fscanf(ficpar,"pop_based=%d\n",&popbased);  
   fprintf(ficparo,"pop_based=%d\n",popbased);            pmij(pmmij,cov,ncovmodel,x,nlstate);
   fprintf(ficres,"pop_based=%d\n",popbased);            
            k=0;
   while((c=getc(ficpar))=='#' && c!= EOF){          for(i=1; i<=(nlstate); i++){
     ungetc(c,ficpar);            for(j=1; j<=(nlstate+ndeath);j++){
     fgets(line, MAXLINE, ficpar);              k=k+1;
     puts(line);              mu[k][(int) age]=pmmij[i][j];
     fputs(line,ficparo);            }
   }          }
   ungetc(c,ficpar);          for(i=1;i<=(nlstate)*(nlstate+ndeath);i++)
             for(j=1;j<=(nlstate)*(nlstate+ndeath);j++)
   fscanf(ficpar,"starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mov_average=%d\n",&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilav);              varpij[i][j][(int)age] = doldm[i][j];
 fprintf(ficparo,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);  
 fprintf(ficres,"starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mov_average=%d\n",jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilav);          /*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]));
 while((c=getc(ficpar))=='#' && c!= EOF){            fprintf(ficlog,"%e [%e ;%e] ",gm[i],gm[i]-2*sqrt(doldm[i][i]),gm[i]+2*sqrt(doldm[i][i]));
     ungetc(c,ficpar);            }*/
     fgets(line, MAXLINE, ficpar);  
     puts(line);          fprintf(ficresprob,"\n%d ",(int)age);
     fputs(line,ficparo);          fprintf(ficresprobcov,"\n%d ",(int)age);
   }          fprintf(ficresprobcor,"\n%d ",(int)age);
   ungetc(c,ficpar);  
           for (i=1; i<=(nlstate)*(nlstate+ndeath);i++)
   fscanf(ficpar,"popforecast=%d popfile=%s popfiledate=%lf/%lf/%lf last-popfiledate=%lf/%lf/%lf\n",&popforecast,popfile,&jpyram,&mpyram,&anpyram,&jpyram1,&mpyram1,&anpyram1);            fprintf(ficresprob,"%11.3e (%11.3e) ",mu[i][(int) age],sqrt(varpij[i][i][(int)age]));
   fprintf(ficparo,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);          for (i=1; i<=(nlstate)*(nlstate+ndeath);i++){
   fprintf(ficres,"popforecast=%d popfile=%s popfiledate=%.lf/%.lf/%.lf last-popfiledate=%.lf/%.lf/%.lf\n",popforecast,popfile,jpyram,mpyram,anpyram,jpyram1,mpyram1,anpyram1);            fprintf(ficresprobcov,"%11.3e ",mu[i][(int) age]);
             fprintf(ficresprobcor,"%11.3e ",mu[i][(int) age]);
  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);          }
           i=0;
 /*------------ gnuplot -------------*/          for (k=1; k<=(nlstate);k++){
  printinggnuplot(fileres,optionfilefiname,optionfile,optionfilegnuplot, ageminpar,agemaxpar,fage, pathc,p);            for (l=1; l<=(nlstate+ndeath);l++){ 
                i=i++;
 /*------------ free_vector  -------------*/              fprintf(ficresprobcov,"\n%d %d-%d",(int)age,k,l);
  chdir(path);              fprintf(ficresprobcor,"\n%d %d-%d",(int)age,k,l);
                for (j=1; j<=i;j++){
  free_ivector(wav,1,imx);                fprintf(ficresprobcov," %11.3e",varpij[i][j][(int)age]);
  free_imatrix(dh,1,lastpass-firstpass+1,1,imx);                fprintf(ficresprobcor," %11.3e",varpij[i][j][(int) age]/sqrt(varpij[i][i][(int) age])/sqrt(varpij[j][j][(int)age]));
  free_imatrix(mw,1,lastpass-firstpass+1,1,imx);                }
  free_ivector(num,1,n);            }
  free_vector(agedc,1,n);          }/* end of loop for state */
  /*free_matrix(covar,1,NCOVMAX,1,n);*/        } /* end of loop for age */
  fclose(ficparo);  
  fclose(ficres);        /* Confidence intervalle of pij  */
         /*
 /*--------- index.htm --------*/          fprintf(ficgp,"\nset noparametric;unset label");
           fprintf(ficgp,"\nset log y;unset log x; set xlabel \"Age\";set ylabel \"probability (year-1)\"");
  printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,model,imx,jmin,jmax,jmean,optionfile,optionfilehtm,rfileres,optionfilegnuplot,version,popforecast,estepm,jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);          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);
   /*--------------- Prevalence limit --------------*/          fprintf(ficgp,"\nset out \"pijgr%s.png\"",optionfilefiname);
            fprintf(ficgp,"\nplot \"%s\" every :::%d::%d u 1:2 \"\%%lf",k1,k2,xfilevarprob);
   strcpy(filerespl,"pl");        */
   strcat(filerespl,fileres);  
   if((ficrespl=fopen(filerespl,"w"))==NULL) {        /* Drawing ellipsoids of confidence of two variables p(k1-l1,k2-l2)*/
     printf("Problem with Prev limit resultfile: %s\n", filerespl);goto end;        first1=1;
   }        for (k2=1; k2<=(nlstate);k2++){
   printf("Computing prevalence limit: result on file '%s' \n", filerespl);          for (l2=1; l2<=(nlstate+ndeath);l2++){ 
   fprintf(ficrespl,"#Prevalence limit\n");            if(l2==k2) continue;
   fprintf(ficrespl,"#Age ");            j=(k2-1)*(nlstate+ndeath)+l2;
   for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);            for (k1=1; k1<=(nlstate);k1++){
   fprintf(ficrespl,"\n");              for (l1=1; l1<=(nlstate+ndeath);l1++){ 
                  if(l1==k1) continue;
   prlim=matrix(1,nlstate,1,nlstate);                i=(k1-1)*(nlstate+ndeath)+l1;
   pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                if(i<=j) continue;
   oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                for (age=bage; age<=fage; age ++){ 
   newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                  if ((int)age %5==0){
   savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */                    v1=varpij[i][i][(int)age]/stepm*YEARM/stepm*YEARM;
   oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */                    v2=varpij[j][j][(int)age]/stepm*YEARM/stepm*YEARM;
   k=0;                    cv12=varpij[i][j][(int)age]/stepm*YEARM/stepm*YEARM;
   agebase=ageminpar;                    mu1=mu[i][(int) age]/stepm*YEARM ;
   agelim=agemaxpar;                    mu2=mu[j][(int) age]/stepm*YEARM;
   ftolpl=1.e-10;                    c12=cv12/sqrt(v1*v2);
   i1=cptcoveff;                    /* Computing eigen value of matrix of covariance */
   if (cptcovn < 1){i1=1;}                    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.;
   for(cptcov=1;cptcov<=i1;cptcov++){                    /* Eigen vectors */
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                    v11=(1./sqrt(1+(v1-lc1)*(v1-lc1)/cv12/cv12));
         k=k+1;                    /*v21=sqrt(1.-v11*v11); *//* error */
         /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/                    v21=(lc1-v1)/cv12*v11;
         fprintf(ficrespl,"\n#******");                    v12=-v21;
         for(j=1;j<=cptcoveff;j++)                    v22=v11;
           fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    tnalp=v21/v11;
         fprintf(ficrespl,"******\n");                    if(first1==1){
                              first1=0;
         for (age=agebase; age<=agelim; age++){                      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);
           prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);                    }
           fprintf(ficrespl,"%.0f",age );                    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);
           for(i=1; i<=nlstate;i++)                    /*printf(fignu*/
           fprintf(ficrespl," %.5f", prlim[i][i]);                    /* mu1+ v11*lc1*cost + v12*lc2*sin(t) */
           fprintf(ficrespl,"\n");                    /* mu2+ v21*lc1*cost + v22*lc2*sin(t) */
         }                    if(first==1){
       }                      first=0;
     }                      fprintf(ficgp,"\nset parametric;unset label");
   fclose(ficrespl);                      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");
   /*------------- h Pij x at various ages ------------*/                      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\">\
   strcpy(filerespij,"pij");  strcat(filerespij,fileres);  %s%d%1d%1d-%1d%1d.png</A>, ",k1,l1,k2,l2,\
   if((ficrespij=fopen(filerespij,"w"))==NULL) {                              subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2,\
     printf("Problem with Pij resultfile: %s\n", filerespij);goto end;                              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);
   printf("Computing pij: result on file '%s' \n", filerespij);                      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);
   stepsize=(int) (stepm+YEARM-1)/YEARM;                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
   /*if (stepm<=24) stepsize=2;*/                      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",\
   agelim=AGESUP;                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
   hstepm=stepsize*YEARM; /* Every year of age */                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
   hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */                    }else{
                        first=0;
   k=0;                      fprintf(fichtmcov," %d (%.3f),",(int) age, c12);
   for(cptcov=1;cptcov<=i1;cptcov++){                      fprintf(ficgp,"\n# Age %d, p%1d%1d - p%1d%1d",(int) age, k1,l1,k2,l2);
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){                      fprintf(ficgp,"\nset label \"%d\" at %11.3e,%11.3e center",(int) age, mu1,mu2);
       k=k+1;                      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",\
         fprintf(ficrespij,"\n#****** ");                              mu1,std,v11,sqrt(lc1),v12,sqrt(lc2),\
         for(j=1;j<=cptcoveff;j++)                              mu2,std,v21,sqrt(lc1),v22,sqrt(lc2));
           fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);                    }/* if first */
         fprintf(ficrespij,"******\n");                  } /* age mod 5 */
                        } /* end loop age */
         for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */                fprintf(ficgp,"\nset out \"%s%d%1d%1d-%1d%1d.png\";replot;",subdirf2(optionfilefiname,"varpijgr"), j1,k1,l1,k2,l2);
           nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */                first=1;
           nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */              } /*l12 */
           p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);            } /* k12 */
           oldm=oldms;savm=savms;          } /*l1 */
           hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);          }/* k1 */
           fprintf(ficrespij,"# Age");      } /* loop covariates */
           for(i=1; i<=nlstate;i++)    }
             for(j=1; j<=nlstate+ndeath;j++)    free_ma3x(varpij,1,nlstate,1,nlstate+ndeath,(int) bage, (int)fage);
               fprintf(ficrespij," %1d-%1d",i,j);    free_matrix(mu,1,(nlstate+ndeath)*(nlstate+ndeath),(int) bage, (int)fage);
           fprintf(ficrespij,"\n");    free_matrix(doldm,1,(nlstate)*(nlstate+ndeath),1,(nlstate)*(nlstate+ndeath));
            for (h=0; h<=nhstepm; h++){    free_matrix(dnewm,1,(nlstate)*(nlstate+ndeath),1,npar);
             fprintf(ficrespij,"%d %.0f %.0f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );    free_vector(xp,1,npar);
             for(i=1; i<=nlstate;i++)    fclose(ficresprob);
               for(j=1; j<=nlstate+ndeath;j++)    fclose(ficresprobcov);
                 fprintf(ficrespij," %.5f", p3mat[i][j][h]);    fclose(ficresprobcor);
             fprintf(ficrespij,"\n");    fflush(ficgp);
              }    fflush(fichtmcov);
           free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);  }
           fprintf(ficrespij,"\n");  
         }  
     }  /******************* Printing html file ***********/
   }  void printinghtml(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
   varprob(fileres, matcov, p, delti, nlstate, (int) bage, (int) fage,k,Tvar,nbcode, ncodemax);                    int imx,int jmin, int jmax, double jmeanint,char rfileres[],\
                     int popforecast, int estepm ,\
   fclose(ficrespij);                    double jprev1, double mprev1,double anprev1, \
                     double jprev2, double mprev2,double anprev2){
     int jj1, k1, i1, cpt;
   /*---------- Forecasting ------------------*/  
   if((stepm == 1) && (strcmp(model,".")==0)){     fprintf(fichtm,"<ul><li><a href='#firstorder'>Result files (first order: no variance)</a>\n \
     prevforecast(fileres, anproj1,mproj1,jproj1, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anproj2,p, i1);     <li><a href='#secondorder'>Result files (second order (variance)</a>\n \
     if (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);  </ul>");
   }     fprintf(fichtm,"<ul><li><h4><a name='firstorder'>Result files (first order: no variance)</a></h4>\n \
   else{   - Observed prevalence in each state (during the period defined between %.lf/%.lf/%.lf and %.lf/%.lf/%.lf): <a href=\"%s\">%s</a> <br>\n ",
     erreur=108;             jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,subdirf2(fileres,"p"),subdirf2(fileres,"p"));
     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(fichtm,"\
   }   - Estimated transition probabilities over %d (stepm) months: <a href=\"%s\">%s</a><br>\n ",
               stepm,subdirf2(fileres,"pij"),subdirf2(fileres,"pij"));
      fprintf(fichtm,"\
   /*---------- Health expectancies and variances ------------*/   - Period (stable) prevalence in each health state: <a href=\"%s\">%s</a> <br>\n",
              subdirf2(fileres,"pl"),subdirf2(fileres,"pl"));
   strcpy(filerest,"t");     fprintf(fichtm,"\
   strcat(filerest,fileres);   - (a) Life expectancies by health status at initial age, (b) health expectancies by health status at initial age:  ei., eij (estepm=%2d months): \
   if((ficrest=fopen(filerest,"w"))==NULL) {     <a href=\"%s\">%s</a> <br>\n</li>",
     printf("Problem with total LE resultfile: %s\n", filerest);goto end;             estepm,subdirf2(fileres,"e"),subdirf2(fileres,"e"));
   }  
   printf("Computing Total LEs with variances: file '%s' \n", filerest);  
   fprintf(fichtm," \n<ul><li><b>Graphs</b></li><p>");
   
   strcpy(filerese,"e");   m=cptcoveff;
   strcat(filerese,fileres);   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   if((ficreseij=fopen(filerese,"w"))==NULL) {  
     printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);   jj1=0;
   }   for(k1=1; k1<=m;k1++){
   printf("Computing Health Expectancies: result on file '%s' \n", filerese);     for(i1=1; i1<=ncodemax[k1];i1++){
        jj1++;
  strcpy(fileresv,"v");       if (cptcovn > 0) {
   strcat(fileresv,fileres);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   if((ficresvij=fopen(fileresv,"w"))==NULL) {         for (cpt=1; cpt<=cptcoveff;cpt++) 
     printf("Problem with variance resultfile: %s\n", fileresv);exit(0);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
   }         fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);       }
   calagedate=-1;       /* Pij */
 prevalence(ageminpar, agemax, s, agev, nlstate, imx,Tvar,nbcode, ncodemax,mint,anint,dateprev1,dateprev2, calagedate);       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);     
   k=0;       /* Quasi-incidences */
   for(cptcov=1;cptcov<=i1;cptcov++){       fprintf(fichtm,"<br>- Pij or Conditional probabilities to be observed in state j being in state i %d (stepm) months\
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){   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> \
       k=k+1;  <img src=\"%s%d2.png\">",stepm,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1,subdirf2(optionfilefiname,"pe"),jj1); 
       fprintf(ficrest,"\n#****** ");         /* Period (stable) prevalence in each health state */
       for(j=1;j<=cptcoveff;j++)         for(cpt=1; cpt<nlstate;cpt++){
         fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);           fprintf(fichtm,"<br>- Period (stable) prevalence in each health state : <a href=\"%s%d%d.png\">%s%d%d.png</a><br> \
       fprintf(ficrest,"******\n");  <img src=\"%s%d%d.png\">",subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1,subdirf2(optionfilefiname,"p"),cpt,jj1);
          }
       fprintf(ficreseij,"\n#****** ");       for(cpt=1; cpt<=nlstate;cpt++) {
       for(j=1;j<=cptcoveff;j++)          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> \
         fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1,subdirf2(optionfilefiname,"exp"),cpt,jj1);
       fprintf(ficreseij,"******\n");       }
      } /* end i1 */
       fprintf(ficresvij,"\n#****** ");   }/* End k1 */
       for(j=1;j<=cptcoveff;j++)   fprintf(fichtm,"</ul>");
         fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  
       fprintf(ficresvij,"******\n");  
    fprintf(fichtm,"\
       eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);  \n<br><li><h4> <a name='secondorder'>Result files (second order: variances)</a></h4>\n\
       oldm=oldms;savm=savms;   - Parameter file with estimated parameters and covariance matrix: <a href=\"%s\">%s</a> <br>\n", rfileres,rfileres);
       evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov);    
     fprintf(fichtm," - Variance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
       vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);           subdirf2(fileres,"prob"),subdirf2(fileres,"prob"));
       oldm=oldms;savm=savms;   fprintf(fichtm,"\
        varevsij(fileres, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm);   - Variance-covariance of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
               subdirf2(fileres,"probcov"),subdirf2(fileres,"probcov"));
   
     fprintf(fichtm,"\
       fprintf(ficrest,"#Total LEs with variances: e.. (std) ");   - Correlation matrix of one-step probabilities: <a href=\"%s\">%s</a> <br>\n",
       for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);           subdirf2(fileres,"probcor"),subdirf2(fileres,"probcor"));
       fprintf(ficrest,"\n");   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): \
       epj=vector(1,nlstate+1);     <a href=\"%s\">%s</a> <br>\n</li>",
       for(age=bage; age <=fage ;age++){             estepm,subdirf2(fileres,"cve"),subdirf2(fileres,"cve"));
         prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);   fprintf(fichtm,"\
         if (popbased==1) {   - (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): \
           for(i=1; i<=nlstate;i++)     <a href=\"%s\">%s</a> <br>\n</li>",
             prlim[i][i]=probs[(int)age][i][k];             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",
         fprintf(ficrest," %4.0f",age);           estepm, subdirf2(fileres,"v"),subdirf2(fileres,"v"));
         for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){   fprintf(fichtm,"\
           for(i=1, epj[j]=0.;i <=nlstate;i++) {   - 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",
             epj[j] += prlim[i][i]*eij[i][j][(int)age];           subdirf2(fileres,"t"),subdirf2(fileres,"t"));
             /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/   fprintf(fichtm,"\
           }   - Standard deviation of period (stable) prevalences: <a href=\"%s\">%s</a> <br>\n",\
           epj[nlstate+1] +=epj[j];           subdirf2(fileres,"vpl"),subdirf2(fileres,"vpl"));
         }  
   /*  if(popforecast==1) fprintf(fichtm,"\n */
         for(i=1, vepp=0.;i <=nlstate;i++)  /*  - Prevalences forecasting: <a href=\"f%s\">f%s</a> <br>\n */
           for(j=1;j <=nlstate;j++)  /*  - Population forecasting (if popforecast=1): <a href=\"pop%s\">pop%s</a> <br>\n */
             vepp += vareij[i][j][(int)age];  /*      <br>",fileres,fileres,fileres,fileres); */
         fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));  /*  else  */
         for(j=1;j <=nlstate;j++){  /*    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); */
           fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));   fflush(fichtm);
         }   fprintf(fichtm," <ul><li><b>Graphs</b></li><p>");
         fprintf(ficrest,"\n");  
       }   m=cptcoveff;
     }   if (cptcovn < 1) {m=1;ncodemax[1]=1;}
   }  
 free_matrix(mint,1,maxwav,1,n);   jj1=0;
     free_matrix(anint,1,maxwav,1,n); free_imatrix(s,1,maxwav+1,1,n);   for(k1=1; k1<=m;k1++){
     free_vector(weight,1,n);     for(i1=1; i1<=ncodemax[k1];i1++){
   fclose(ficreseij);       jj1++;
   fclose(ficresvij);       if (cptcovn > 0) {
   fclose(ficrest);         fprintf(fichtm,"<hr  size=\"2\" color=\"#EC5E5E\">************ Results for covariates");
   fclose(ficpar);         for (cpt=1; cpt<=cptcoveff;cpt++) 
   free_vector(epj,1,nlstate+1);           fprintf(fichtm," V%d=%d ",Tvaraff[cpt],nbcode[Tvaraff[cpt]][codtab[jj1][cpt]]);
           fprintf(fichtm," ************\n<hr size=\"2\" color=\"#EC5E5E\">");
   /*------- Variance limit prevalence------*/         }
        for(cpt=1; cpt<=nlstate;cpt++) {
   strcpy(fileresvpl,"vpl");         fprintf(fichtm,"<br>- Observed (cross-sectional) and period (incidence based) \
   strcat(fileresvpl,fileres);  prevalence (with 95%% confidence interval) in state (%d): %s%d%d.png <br>\
   if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {  <img src=\"%s%d%d.png\">",cpt,subdirf2(optionfilefiname,"v"),cpt,jj1,subdirf2(optionfilefiname,"v"),cpt,jj1);  
     printf("Problem with variance prev lim resultfile: %s\n", fileresvpl);       }
     exit(0);       fprintf(fichtm,"\n<br>- Total life expectancy by age and \
   }  health expectancies in states (1) and (2): %s%d.png<br>\
   printf("Computing Variance-covariance of Prevalence limit: file '%s' \n", fileresvpl);  <img src=\"%s%d.png\">",subdirf2(optionfilefiname,"e"),jj1,subdirf2(optionfilefiname,"e"),jj1);
      } /* end i1 */
   k=0;   }/* End k1 */
   for(cptcov=1;cptcov<=i1;cptcov++){   fprintf(fichtm,"</ul>");
     for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){   fflush(fichtm);
       k=k+1;  }
       fprintf(ficresvpl,"\n#****** ");  
       for(j=1;j<=cptcoveff;j++)  /******************* Gnuplot file **************/
         fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);  void printinggnuplot(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
       fprintf(ficresvpl,"******\n");  
          char dirfileres[132],optfileres[132];
       varpl=matrix(1,nlstate,(int) bage, (int) fage);    int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
       oldm=oldms;savm=savms;    int ng;
      varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k);  /*   if((ficgp=fopen(optionfilegnuplot,"a"))==NULL) { */
     }  /*     printf("Problem with file %s",optionfilegnuplot); */
  }  /*     fprintf(ficlog,"Problem with file %s",optionfilegnuplot); */
   /*   } */
   fclose(ficresvpl);  
     /*#ifdef windows */
   /*---------- End : free ----------------*/    fprintf(ficgp,"cd \"%s\" \n",pathc);
   free_matrix(varpl,1,nlstate,(int) bage, (int)fage);      /*#endif */
      m=pow(2,cptcoveff);
   free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);  
   free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);    strcpy(dirfileres,optionfilefiname);
      strcpy(optfileres,"vpl");
     /* 1eme*/
   free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);    for (cpt=1; cpt<= nlstate ; cpt ++) {
   free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);     for (k1=1; k1<= m ; k1 ++) {
   free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);       fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"v"),cpt,k1);
   free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);       fprintf(ficgp,"\n#set out \"v%s%d%d.png\" \n",optionfilefiname,cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \n\
   free_matrix(matcov,1,npar,1,npar);  set ylabel \"Probability\" \n\
   free_vector(delti,1,npar);  set ter png small\n\
   free_matrix(agev,1,maxwav,1,imx);  set size 0.65,0.65\n\
   free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);  plot [%.f:%.f] \"%s\" every :::%d::%d u 1:2 \"\%%lf",ageminpar,fage,subdirf2(fileres,"vpl"),k1-1,k1-1);
   
   if(erreur >0)       for (i=1; i<= nlstate ; i ++) {
     printf("End of Imach with error or warning %d\n",erreur);         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   else   printf("End of Imach\n");         else fprintf(ficgp," \%%*lf (\%%*lf)");
   /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */       }
         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);
   /* printf("Total time was %d Sec. %d uSec.\n", end_time.tv_sec -start_time.tv_sec, end_time.tv_usec -start_time.tv_usec);*/       for (i=1; i<= nlstate ; i ++) {
   /*printf("Total time was %d uSec.\n", total_usecs);*/         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   /*------ End -----------*/         else fprintf(ficgp," \%%*lf (\%%*lf)");
        } 
        fprintf(ficgp,"\" t\"95\%% CI\" w l 1,\"%s\" every :::%d::%d u 1:($2-1.96*$3) \"\%%lf",subdirf2(fileres,"vpl"),k1-1,k1-1); 
  end:       for (i=1; i<= nlstate ; i ++) {
 #ifdef windows         if (i==cpt) fprintf(ficgp," \%%lf (\%%lf)");
   /* chdir(pathcd);*/         else fprintf(ficgp," \%%*lf (\%%*lf)");
 #endif       }  
  /*system("wgnuplot graph.plt");*/       fprintf(ficgp,"\" t\"\" w l 1,\"%s\" every :::%d::%d u 1:($%d) t\"Observed prevalence \" w l 2",subdirf2(fileres,"p"),k1-1,k1-1,2+4*(cpt-1));
  /*system("../gp37mgw/wgnuplot graph.plt");*/     }
  /*system("cd ../gp37mgw");*/    }
  /* system("..\\gp37mgw\\wgnuplot graph.plt");*/    /*2 eme*/
  strcpy(plotcmd,GNUPLOTPROGRAM);    
  strcat(plotcmd," ");    for (k1=1; k1<= m ; k1 ++) { 
  strcat(plotcmd,optionfilegnuplot);      fprintf(ficgp,"\nset out \"%s%d.png\" \n",subdirf2(optionfilefiname,"e"),k1);
  system(plotcmd);      fprintf(ficgp,"set ylabel \"Years\" \nset ter png small\nset size 0.65,0.65\nplot [%.f:%.f] ",ageminpar,fage);
       
 #ifdef windows      for (i=1; i<= nlstate+1 ; i ++) {
   while (z[0] != 'q') {        k=2*i;
     /* chdir(path); */        fprintf(ficgp,"\"%s\" every :::%d::%d u 1:2 \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
     printf("\nType e to edit output files, g to graph again, c to start again, and q for exiting: ");        for (j=1; j<= nlstate+1 ; j ++) {
     scanf("%s",z);          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
     if (z[0] == 'c') system("./imach");          else fprintf(ficgp," \%%*lf (\%%*lf)");
     else if (z[0] == 'e') system(optionfilehtm);        }   
     else if (z[0] == 'g') system(plotcmd);        if (i== 1) fprintf(ficgp,"\" t\"TLE\" w l ,");
     else if (z[0] == 'q') exit(0);        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);
 #endif        for (j=1; j<= nlstate+1 ; j ++) {
 }          if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         fprintf(ficgp,"\" t\"\" w l 0,");
         fprintf(ficgp,"\"%s\" every :::%d::%d u 1:($2+$3*2) \"\%%lf",subdirf2(fileres,"t"),k1-1,k1-1);
         for (j=1; j<= nlstate+1 ; j ++) {
           if (j==i) fprintf(ficgp," \%%lf (\%%lf)");
           else fprintf(ficgp," \%%*lf (\%%*lf)");
         }   
         if (i== (nlstate+1)) fprintf(ficgp,"\" t\"\" w l 0");
         else fprintf(ficgp,"\" t\"\" w l 0,");
       }
     }
     
     /*3eme*/
     
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<= nlstate ; cpt ++) {
         /*       k=2+nlstate*(2*cpt-2); */
         k=2+(nlstate+1)*(cpt-1);
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"exp"),cpt,k1);
         fprintf(ficgp,"set ter png small\n\
   set size 0.65,0.65\n\
   plot [%.f:%.f] \"%s\" every :::%d::%d u 1:%d t \"e%d1\" w l",ageminpar,fage,subdirf2(fileres,"e"),k1-1,k1-1,k,cpt);
         /*fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d-2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           fprintf(ficgp,",\"e%s\" every :::%d::%d u 1:($%d+2*$%d) \"\%%lf ",fileres,k1-1,k1-1,k,k+1);
           for (i=1; i<= nlstate*2 ; i ++) fprintf(ficgp,"\%%lf (\%%lf) ");
           fprintf(ficgp,"\" t \"e%d1\" w l",cpt);
           
         */
         for (i=1; i< nlstate ; i ++) {
           fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+i,cpt,i+1);
           /*      fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d%d\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+2*i,cpt,i+1);*/
           
         } 
         fprintf(ficgp," ,\"%s\" every :::%d::%d u 1:%d t \"e%d.\" w l",subdirf2(fileres,"e"),k1-1,k1-1,k+nlstate,cpt);
       }
     }
     
     /* CV preval stable (period) */
     for (k1=1; k1<= m ; k1 ++) { 
       for (cpt=1; cpt<=nlstate ; cpt ++) {
         k=3;
         fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"p"),cpt,k1);
         fprintf(ficgp,"set xlabel \"Age\" \nset ylabel \"Probability\" \n\
   set ter png small\nset size 0.65,0.65\n\
   unset log y\n\
   plot [%.f:%.f] \"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",ageminpar,agemaxpar,subdirf2(fileres,"pij"),k1,k+cpt+1,k+1);
         
         for (i=1; i< nlstate ; i ++)
           fprintf(ficgp,"+$%d",k+i+1);
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l",cpt,cpt+1);
         
         l=3+(nlstate+ndeath)*cpt;
         fprintf(ficgp,",\"%s\" u ($1==%d ? ($3):1/0):($%d/($%d",subdirf2(fileres,"pij"),k1,l+cpt+1,l+1);
         for (i=1; i< nlstate ; i ++) {
           l=3+(nlstate+ndeath)*cpt;
           fprintf(ficgp,"+$%d",l+i+1);
         }
         fprintf(ficgp,")) t\"prev(%d,%d)\" w l\n",cpt+1,cpt+1);   
       } 
     }  
     
     /* proba elementaires */
     for(i=1,jk=1; i <=nlstate; i++){
       for(k=1; k <=(nlstate+ndeath); k++){
         if (k != i) {
           for(j=1; j <=ncovmodel; j++){
             fprintf(ficgp,"p%d=%f ",jk,p[jk]);
             jk++; 
             fprintf(ficgp,"\n");
           }
         }
       }
      }
   
      for(ng=1; ng<=2;ng++){ /* Number of graphics: first is probabilities second is incidence per year*/
        for(jk=1; jk <=m; jk++) {
          fprintf(ficgp,"\nset out \"%s%d%d.png\" \n",subdirf2(optionfilefiname,"pe"),jk,ng); 
          if (ng==2)
            fprintf(ficgp,"\nset ylabel \"Quasi-incidence per year\"\n");
          else
            fprintf(ficgp,"\nset title \"Probability\"\n");
          fprintf(ficgp,"\nset ter png small\nset size 0.65,0.65\nset log y\nplot  [%.f:%.f] ",ageminpar,agemaxpar);
          i=1;
          for(k2=1; k2<=nlstate; k2++) {
            k3=i;
            for(k=1; k<=(nlstate+ndeath); k++) {
              if (k != k2){
                if(ng==2)
                  fprintf(ficgp," %f*exp(p%d+p%d*x",YEARM/stepm,i,i+1);
                else
                  fprintf(ficgp," exp(p%d+p%d*x",i,i+1);
                ij=1;
                for(j=3; j <=ncovmodel; j++) {
                  if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                    fprintf(ficgp,"+p%d*%d*x",i+j-1,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                    ij++;
                  }
                  else
                    fprintf(ficgp,"+p%d*%d",i+j-1,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                }
                fprintf(ficgp,")/(1");
                
                for(k1=1; k1 <=nlstate; k1++){   
                  fprintf(ficgp,"+exp(p%d+p%d*x",k3+(k1-1)*ncovmodel,k3+(k1-1)*ncovmodel+1);
                  ij=1;
                  for(j=3; j <=ncovmodel; j++){
                    if(((j-2)==Tage[ij]) &&(ij <=cptcovage)) {
                      fprintf(ficgp,"+p%d*%d*x",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][Tvar[j-2]]]);
                      ij++;
                    }
                    else
                      fprintf(ficgp,"+p%d*%d",k3+(k1-1)*ncovmodel+1+j-2,nbcode[Tvar[j-2]][codtab[jk][j-2]]);
                  }
                  fprintf(ficgp,")");
                }
                fprintf(ficgp,") t \"p%d%d\" ", k2,k);
                if ((k+k2)!= (nlstate*2+ndeath)) fprintf(ficgp,",");
                i=i+ncovmodel;
              }
            } /* end k */
          } /* end k2 */
        } /* end jk */
      } /* end ng */
      fflush(ficgp); 
   }  /* end gnuplot */
   
   
   /*************** Moving average **************/
   int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav){
   
     int i, cpt, cptcod;
     int modcovmax =1;
     int mobilavrange, mob;
     double age;
   
     modcovmax=2*cptcoveff;/* Max number of modalities. We suppose 
                              a covariate has 2 modalities */
     if (cptcovn<1) modcovmax=1; /* At least 1 pass */
   
     if(mobilav==1||mobilav ==3 ||mobilav==5 ||mobilav== 7){
       if(mobilav==1) mobilavrange=5; /* default */
       else mobilavrange=mobilav;
       for (age=bage; age<=fage; age++)
         for (i=1; i<=nlstate;i++)
           for (cptcod=1;cptcod<=modcovmax;cptcod++)
             mobaverage[(int)age][i][cptcod]=probs[(int)age][i][cptcod];
       /* We keep the original values on the extreme ages bage, fage and for 
          fage+1 and bage-1 we use a 3 terms moving average; for fage+2 bage+2
          we use a 5 terms etc. until the borders are no more concerned. 
       */ 
       for (mob=3;mob <=mobilavrange;mob=mob+2){
         for (age=bage+(mob-1)/2; age<=fage-(mob-1)/2; age++){
           for (i=1; i<=nlstate;i++){
             for (cptcod=1;cptcod<=modcovmax;cptcod++){
               mobaverage[(int)age][i][cptcod] =probs[(int)age][i][cptcod];
                 for (cpt=1;cpt<=(mob-1)/2;cpt++){
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age-cpt][i][cptcod];
                   mobaverage[(int)age][i][cptcod] +=probs[(int)age+cpt][i][cptcod];
                 }
               mobaverage[(int)age][i][cptcod]=mobaverage[(int)age][i][cptcod]/mob;
             }
           }
         }/* end age */
       }/* end mob */
     }else return -1;
     return 0;
   }/* End movingaverage */
   
   
   /************** Forecasting ******************/
   prevforecast(char fileres[], double anproj1, double mproj1, double jproj1, double ageminpar, double agemax, double dateprev1, double dateprev2, int mobilav, double bage, double fage, int firstpass, int lastpass, double anproj2, double p[], int cptcoveff){
     /* proj1, year, month, day of starting projection 
        agemin, agemax range of age
        dateprev1 dateprev2 range of dates during which prevalence is computed
        anproj2 year of en of projection (same day and month as proj1).
     */
     int yearp, stepsize, hstepm, nhstepm, j, k, c, cptcod, i, h, i1;
     int *popage;
     double agec; /* generic age */
     double agelim, ppij, yp,yp1,yp2,jprojmean,mprojmean,anprojmean;
     double *popeffectif,*popcount;
     double ***p3mat;
     double ***mobaverage;
     char fileresf[FILENAMELENGTH];
   
     agelim=AGESUP;
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
    
     strcpy(fileresf,"f"); 
     strcat(fileresf,fileres);
     if((ficresf=fopen(fileresf,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", fileresf);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", fileresf);
     }
     printf("Computing forecasting: result on file '%s' \n", fileresf);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", fileresf);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     if(estepm < stepm){
       printf ("Problem %d lower than %d\n",estepm, stepm);
     }
     else  hstepm=estepm;   
   
     hstepm=hstepm/stepm; 
     yp1=modf(dateintmean,&yp);/* extracts integral of datemean in yp  and
                                  fractional in yp1 */
     anprojmean=yp;
     yp2=modf((yp1*12),&yp);
     mprojmean=yp;
     yp1=modf((yp2*30.5),&yp);
     jprojmean=yp;
     if(jprojmean==0) jprojmean=1;
     if(mprojmean==0) jprojmean=1;
   
     i1=cptcoveff;
     if (cptcovn < 1){i1=1;}
     
     fprintf(ficresf,"# Mean day of interviews %.lf/%.lf/%.lf (%.2f) between %.2f and %.2f \n",jprojmean,mprojmean,anprojmean,dateintmean,dateprev1,dateprev2); 
     
     fprintf(ficresf,"#****** Routine prevforecast **\n");
   
   /*            if (h==(int)(YEARM*yearp)){ */
     for(cptcov=1, k=0;cptcov<=i1;cptcov++){
       for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficresf,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficresf," V%d=%d, hpijx=probability over h years, hp.jx is weighted by observed prev ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficresf,"******\n");
         fprintf(ficresf,"# Covariate valuofcovar yearproj age");
         for(j=1; j<=nlstate+ndeath;j++){ 
           for(i=1; i<=nlstate;i++)              
             fprintf(ficresf," p%d%d",i,j);
           fprintf(ficresf," p.%d",j);
         }
         for (yearp=0; yearp<=(anproj2-anproj1);yearp +=stepsize) { 
           fprintf(ficresf,"\n");
           fprintf(ficresf,"\n# Forecasting at date %.lf/%.lf/%.lf ",jproj1,mproj1,anproj1+yearp);   
   
           for (agec=fage; agec>=(ageminpar-1); agec--){ 
             nhstepm=(int) rint((agelim-agec)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agec,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h*hstepm/YEARM*stepm ==yearp) {
                 fprintf(ficresf,"\n");
                 for(j=1;j<=cptcoveff;j++) 
                   fprintf(ficresf,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
                 fprintf(ficresf,"%.f %.f ",anproj1+yearp,agec+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 ppij=0.;
                 for(i=1; i<=nlstate;i++) {
                   if (mobilav==1) 
                     ppij=ppij+p3mat[i][j][h]*mobaverage[(int)agec][i][cptcod];
                   else {
                     ppij=ppij+p3mat[i][j][h]*probs[(int)(agec)][i][cptcod];
                   }
                   if (h*hstepm/YEARM*stepm== yearp) {
                     fprintf(ficresf," %.3f", p3mat[i][j][h]);
                   }
                 } /* end i */
                 if (h*hstepm/YEARM*stepm==yearp) {
                   fprintf(ficresf," %.3f", ppij);
                 }
               }/* end j */
             } /* end h */
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           } /* end agec */
         } /* end yearp */
       } /* end cptcod */
     } /* end  cptcov */
          
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     fclose(ficresf);
   }
   
   /************** Forecasting *****not tested NB*************/
   populforecast(char fileres[], double anpyram,double mpyram,double jpyram,double ageminpar, double agemax,double dateprev1, double dateprev2, int mobilav, double agedeb, double fage, int popforecast, char popfile[], double anpyram1,double p[], int i2){
     
     int cpt, stepsize, hstepm, nhstepm, j,k,c, cptcod, i,h;
     int *popage;
     double calagedatem, agelim, kk1, kk2;
     double *popeffectif,*popcount;
     double ***p3mat,***tabpop,***tabpopprev;
     double ***mobaverage;
     char filerespop[FILENAMELENGTH];
   
     tabpop= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     tabpopprev= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     agelim=AGESUP;
     calagedatem=(anpyram+mpyram/12.+jpyram/365.-dateintmean)*YEARM;
     
     prevalence(probs, ageminpar, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
     
     
     strcpy(filerespop,"pop"); 
     strcat(filerespop,fileres);
     if((ficrespop=fopen(filerespop,"w"))==NULL) {
       printf("Problem with forecast resultfile: %s\n", filerespop);
       fprintf(ficlog,"Problem with forecast resultfile: %s\n", filerespop);
     }
     printf("Computing forecasting: result on file '%s' \n", filerespop);
     fprintf(ficlog,"Computing forecasting: result on file '%s' \n", filerespop);
   
     if (cptcoveff==0) ncodemax[cptcoveff]=1;
   
     if (mobilav!=0) {
       mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       if (movingaverage(probs, ageminpar, fage, mobaverage,mobilav)!=0){
         fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
         printf(" Error in movingaverage mobilav=%d\n",mobilav);
       }
     }
   
     stepsize=(int) (stepm+YEARM-1)/YEARM;
     if (stepm<=12) stepsize=1;
     
     agelim=AGESUP;
     
     hstepm=1;
     hstepm=hstepm/stepm; 
     
     if (popforecast==1) {
       if((ficpop=fopen(popfile,"r"))==NULL) {
         printf("Problem with population file : %s\n",popfile);exit(0);
         fprintf(ficlog,"Problem with population file : %s\n",popfile);exit(0);
       } 
       popage=ivector(0,AGESUP);
       popeffectif=vector(0,AGESUP);
       popcount=vector(0,AGESUP);
       
       i=1;   
       while ((c=fscanf(ficpop,"%d %lf\n",&popage[i],&popcount[i])) != EOF) i=i+1;
      
       imx=i;
       for (i=1; i<imx;i++) popeffectif[popage[i]]=popcount[i];
     }
   
     for(cptcov=1,k=0;cptcov<=i2;cptcov++){
      for(cptcod=1;cptcod<=ncodemax[cptcoveff];cptcod++){
         k=k+1;
         fprintf(ficrespop,"\n#******");
         for(j=1;j<=cptcoveff;j++) {
           fprintf(ficrespop," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
         }
         fprintf(ficrespop,"******\n");
         fprintf(ficrespop,"# Age");
         for(j=1; j<=nlstate+ndeath;j++) fprintf(ficrespop," P.%d",j);
         if (popforecast==1)  fprintf(ficrespop," [Population]");
         
         for (cpt=0; cpt<=0;cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
           
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficrespop,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   if (mobilav==1) 
                     kk1=kk1+p3mat[i][j][h]*mobaverage[(int)agedeb+1][i][cptcod];
                   else {
                     kk1=kk1+p3mat[i][j][h]*probs[(int)(agedeb+1)][i][cptcod];
                   }
                 }
                 if (h==(int)(calagedatem+12*cpt)){
                   tabpop[(int)(agedeb)][j][cptcod]=kk1;
                     /*fprintf(ficrespop," %.3f", kk1);
                       if (popforecast==1) fprintf(ficrespop," [%.f]", kk1*popeffectif[(int)agedeb+1]);*/
                 }
               }
               for(i=1; i<=nlstate;i++){
                 kk1=0.;
                   for(j=1; j<=nlstate;j++){
                     kk1= kk1+tabpop[(int)(agedeb)][j][cptcod]; 
                   }
                     tabpopprev[(int)(agedeb)][i][cptcod]=tabpop[(int)(agedeb)][i][cptcod]/kk1*popeffectif[(int)(agedeb+(calagedatem+12*cpt)*hstepm/YEARM*stepm-1)];
               }
   
               if (h==(int)(calagedatem+12*cpt)) for(j=1; j<=nlstate;j++) 
                 fprintf(ficrespop," %15.2f",tabpopprev[(int)(agedeb+1)][j][cptcod]);
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
    
     /******/
   
         for (cpt=1; cpt<=(anpyram1-anpyram);cpt++) { 
           fprintf(ficrespop,"\n\n# Forecasting at date %.lf/%.lf/%.lf ",jpyram,mpyram,anpyram+cpt);   
           for (agedeb=(fage-((int)calagedatem %12/12.)); agedeb>=(ageminpar-((int)calagedatem %12)/12.); agedeb--){ 
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); 
             nhstepm = nhstepm/hstepm; 
             
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             for (h=0; h<=nhstepm; h++){
               if (h==(int) (calagedatem+YEARM*cpt)) {
                 fprintf(ficresf,"\n %3.f ",agedeb+h*hstepm/YEARM*stepm);
               } 
               for(j=1; j<=nlstate+ndeath;j++) {
                 kk1=0.;kk2=0;
                 for(i=1; i<=nlstate;i++) {              
                   kk1=kk1+p3mat[i][j][h]*tabpopprev[(int)agedeb+1][i][cptcod];    
                 }
                 if (h==(int)(calagedatem+12*cpt)) fprintf(ficresf," %15.2f", kk1);        
               }
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
           }
         }
      } 
     }
    
     if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     if (popforecast==1) {
       free_ivector(popage,0,AGESUP);
       free_vector(popeffectif,0,AGESUP);
       free_vector(popcount,0,AGESUP);
     }
     free_ma3x(tabpop,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     free_ma3x(tabpopprev,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
     fclose(ficrespop);
   } /* End of popforecast */
   
   int fileappend(FILE *fichier, char *optionfich)
   {
     if((fichier=fopen(optionfich,"a"))==NULL) {
       printf("Problem with file: %s\n", optionfich);
       fprintf(ficlog,"Problem with file: %s\n", optionfich);
       return (0);
     }
     fflush(fichier);
     return (1);
   }
   
   
   /**************** function prwizard **********************/
   void prwizard(int ncovmodel, int nlstate, int ndeath,  char model[], FILE *ficparo)
   {
   
     /* Wizard to print covariance matrix template */
   
     char ca[32], cb[32], cc[32];
     int i,j, k, l, li, lj, lk, ll, jj, npar, itimes;
     int numlinepar;
   
     printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     fprintf(ficparo,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         /*ca[0]= k+'a'-1;ca[1]='\0';*/
         printf("%1d%1d",i,j);
         fprintf(ficparo,"%1d%1d",i,j);
         for(k=1; k<=ncovmodel;k++){
           /*        printf(" %lf",param[i][j][k]); */
           /*        fprintf(ficparo," %lf",param[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Scales (for hessian or gradient estimation)\n");
     fprintf(ficparo,"# Scales (for hessian or gradient estimation)\n");
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/ 
     for(i=1; i <=nlstate; i++){
       jj=0;
       for(j=1; j <=nlstate+ndeath; j++){
         if(j==i) continue;
         jj++;
         fprintf(ficparo,"%1d%1d",i,j);
         printf("%1d%1d",i,j);
         fflush(stdout);
         for(k=1; k<=ncovmodel;k++){
           /*      printf(" %le",delti3[i][j][k]); */
           /*      fprintf(ficparo," %le",delti3[i][j][k]); */
           printf(" 0.");
           fprintf(ficparo," 0.");
         }
         numlinepar++;
         printf("\n");
         fprintf(ficparo,"\n");
       }
     }
     printf("# Covariance matrix\n");
   /* # 121 Var(a12)\n\ */
   /* # 122 Cov(b12,a12) Var(b12)\n\ */
   /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
   /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
   /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
   /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
   /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
   /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
     fflush(stdout);
     fprintf(ficparo,"# Covariance matrix\n");
     /* # 121 Var(a12)\n\ */
     /* # 122 Cov(b12,a12) Var(b12)\n\ */
     /* #   ...\n\ */
     /* # 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n" */
     
     for(itimes=1;itimes<=2;itimes++){
       jj=0;
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if(j==i) continue;
           for(k=1; k<=ncovmodel;k++){
             jj++;
             ca[0]= k+'a'-1;ca[1]='\0';
             if(itimes==1){
               printf("#%1d%1d%d",i,j,k);
               fprintf(ficparo,"#%1d%1d%d",i,j,k);
             }else{
               printf("%1d%1d%d",i,j,k);
               fprintf(ficparo,"%1d%1d%d",i,j,k);
               /*  printf(" %.5le",matcov[i][j]); */
             }
             ll=0;
             for(li=1;li <=nlstate; li++){
               for(lj=1;lj <=nlstate+ndeath; lj++){
                 if(lj==li) continue;
                 for(lk=1;lk<=ncovmodel;lk++){
                   ll++;
                   if(ll<=jj){
                     cb[0]= lk +'a'-1;cb[1]='\0';
                     if(ll<jj){
                       if(itimes==1){
                         printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         fprintf(ficparo," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }else{
                       if(itimes==1){
                         printf(" Var(%s%1d%1d)",ca,i,j);
                         fprintf(ficparo," Var(%s%1d%1d)",ca,i,j);
                       }else{
                         printf(" 0.");
                         fprintf(ficparo," 0.");
                       }
                     }
                   }
                 } /* end lk */
               } /* end lj */
             } /* end li */
             printf("\n");
             fprintf(ficparo,"\n");
             numlinepar++;
           } /* end k*/
         } /*end j */
       } /* end i */
     } /* end itimes */
   
   } /* end of prwizard */
   /******************* Gompertz Likelihood ******************************/
   double gompertz(double x[])
   { 
     double A,B,L=0.0,sump=0.,num=0.;
     int i,n=0; /* n is the size of the sample */
   
     for (i=0;i<=imx-1 ; i++) {
       sump=sump+weight[i];
       /*    sump=sump+1;*/
       num=num+1;
     }
    
    
     /* for (i=0; i<=imx; i++) 
        if (wav[i]>0) printf("i=%d ageex=%lf agecens=%lf agedc=%lf cens=%d %d\n" ,i,ageexmed[i],agecens[i],agedc[i],cens[i],wav[i]);*/
   
     for (i=1;i<=imx ; i++)
       {
         if (cens[i] == 1 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agecens[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)));
         
         if (cens[i] == 0 && wav[i]>1)
           A=-x[1]/(x[2])*(exp(x[2]*(agedc[i]-agegomp))-exp(x[2]*(ageexmed[i]-agegomp)))
                +log(x[1]/YEARM)+x[2]*(agedc[i]-agegomp)+log(YEARM);  
         
         /*if (wav[i] > 1 && agecens[i] > 15) {*/ /* ??? */
         if (wav[i] > 1 ) { /* ??? */
           L=L+A*weight[i];
           /*      printf("\ni=%d A=%f L=%lf x[1]=%lf x[2]=%lf ageex=%lf agecens=%lf cens=%d agedc=%lf weight=%lf\n",i,A,L,x[1],x[2],ageexmed[i]*12,agecens[i]*12,cens[i],agedc[i]*12,weight[i]);*/
         }
       }
   
    /*printf("x1=%2.9f x2=%2.9f x3=%2.9f L=%f\n",x[1],x[2],x[3],L);*/
    
     return -2*L*num/sump;
   }
   
   /******************* Printing html file ***********/
   void printinghtmlmort(char fileres[], char title[], char datafile[], int firstpass, \
                     int lastpass, int stepm, int weightopt, char model[],\
                     int imx,  double p[],double **matcov,double agemortsup){
     int i,k;
   
     fprintf(fichtm,"<ul><li><h4>Result files </h4>\n Force of mortality. Parameters of the Gompertz fit (with confidence interval in brackets):<br>");
     fprintf(fichtm,"  mu(age) =%lf*exp(%lf*(age-%d)) per year<br><br>",p[1],p[2],agegomp);
     for (i=1;i<=2;i++) 
       fprintf(fichtm," p[%d] = %lf [%f ; %f]<br>\n",i,p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
     fprintf(fichtm,"<br><br><img src=\"graphmort.png\">");
     fprintf(fichtm,"</ul>");
   
   fprintf(fichtm,"<ul><li><h4>Life table</h4>\n <br>");
   
    fprintf(fichtm,"\nAge   l<inf>x</inf>     q<inf>x</inf> d(x,x+1)    L<inf>x</inf>     T<inf>x</inf>     e<infx</inf><br>");
   
    for (k=agegomp;k<(agemortsup-2);k++) 
      fprintf(fichtm,"%d %.0lf %lf %.0lf %.0lf %.0lf %lf<br>\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
   
    
     fflush(fichtm);
   }
   
   /******************* Gnuplot file **************/
   void printinggnuplotmort(char fileres[], char optionfilefiname[], double ageminpar, double agemaxpar, double fage , char pathc[], double p[]){
   
     char dirfileres[132],optfileres[132];
     int m,cpt,k1,i,k,j,jk,k2,k3,ij,l;
     int ng;
   
   
     /*#ifdef windows */
     fprintf(ficgp,"cd \"%s\" \n",pathc);
       /*#endif */
   
   
     strcpy(dirfileres,optionfilefiname);
     strcpy(optfileres,"vpl");
     fprintf(ficgp,"set out \"graphmort.png\"\n "); 
     fprintf(ficgp,"set xlabel \"Age\"\n set ylabel \"Force of mortality (per year)\" \n "); 
     fprintf(ficgp, "set ter png small\n set log y\n"); 
     fprintf(ficgp, "set size 0.65,0.65\n");
     fprintf(ficgp,"plot [%d:100] %lf*exp(%lf*(x-%d))",agegomp,p[1],p[2],agegomp);
   
   } 
   
   
   
   
   
   /***********************************************/
   /**************** Main Program *****************/
   /***********************************************/
   
   int main(int argc, char *argv[])
   {
     int movingaverage(double ***probs, double bage,double fage, double ***mobaverage, int mobilav);
     int i,j, k, n=MAXN,iter,m,size=100,cptcode, cptcod;
     int linei, month, year,iout;
     int jj, ll, li, lj, lk, imk;
     int numlinepar=0; /* Current linenumber of parameter file */
     int itimes;
     int NDIM=2;
   
     char ca[32], cb[32], cc[32];
     char dummy[]="                         ";
     /*  FILE *fichtm; *//* Html File */
     /* FILE *ficgp;*/ /*Gnuplot File */
     struct stat info;
     double agedeb, agefin,hf;
     double ageminpar=1.e20,agemin=1.e20, agemaxpar=-1.e20, agemax=-1.e20;
   
     double fret;
     double **xi,tmp,delta;
   
     double dum; /* Dummy variable */
     double ***p3mat;
     double ***mobaverage;
     int *indx;
     char line[MAXLINE], linepar[MAXLINE];
     char path[MAXLINE],pathc[MAXLINE],pathcd[MAXLINE],pathtot[MAXLINE],model[MAXLINE];
     char pathr[MAXLINE], pathimach[MAXLINE]; 
     char **bp, *tok, *val; /* pathtot */
     int firstobs=1, lastobs=10;
     int sdeb, sfin; /* Status at beginning and end */
     int c,  h , cpt,l;
     int ju,jl, mi;
     int i1,j1, k1,k2,k3,jk,aa,bb, stepsize, ij;
     int jnais,jdc,jint4,jint1,jint2,jint3,**outcome,*tab; 
     int mobilavproj=0 , prevfcast=0 ; /* moving average of prev, If prevfcast=1 prevalence projection */
     int mobilav=0,popforecast=0;
     int hstepm, nhstepm;
     int agemortsup;
     float  sumlpop=0.;
     double jprev1=1, mprev1=1,anprev1=2000,jprev2=1, mprev2=1,anprev2=2000;
     double jpyram=1, mpyram=1,anpyram=2000,jpyram1=1, mpyram1=1,anpyram1=2000;
   
     double bage, fage, age, agelim, agebase;
     double ftolpl=FTOL;
     double **prlim;
     double *severity;
     double ***param; /* Matrix of parameters */
     double  *p;
     double **matcov; /* Matrix of covariance */
     double ***delti3; /* Scale */
     double *delti; /* Scale */
     double ***eij, ***vareij;
     double **varpl; /* Variances of prevalence limits by age */
     double *epj, vepp;
     double kk1, kk2;
     double dateprev1, dateprev2,jproj1=1,mproj1=1,anproj1=2000,jproj2=1,mproj2=1,anproj2=2000;
     double **ximort;
     char *alph[]={"a","a","b","c","d","e"}, str[4];
     int *dcwave;
   
     char z[1]="c", occ;
   
     char stra[80], strb[80], strc[80], strd[80],stre[80],modelsav[80];
     char  *strt, strtend[80];
     char *stratrunc;
     int lstra;
   
     long total_usecs;
    
   /*   setlocale (LC_ALL, ""); */
   /*   bindtextdomain (PACKAGE, LOCALEDIR); */
   /*   textdomain (PACKAGE); */
   /*   setlocale (LC_CTYPE, ""); */
   /*   setlocale (LC_MESSAGES, ""); */
   
     /*   gettimeofday(&start_time, (struct timezone*)0); */ /* at first time */
     (void) gettimeofday(&start_time,&tzp);
     curr_time=start_time;
     tm = *localtime(&start_time.tv_sec);
     tmg = *gmtime(&start_time.tv_sec);
     strcpy(strstart,asctime(&tm));
   
   /*  printf("Localtime (at start)=%s",strstart); */
   /*  tp.tv_sec = tp.tv_sec +86400; */
   /*  tm = *localtime(&start_time.tv_sec); */
   /*   tmg.tm_year=tmg.tm_year +dsign*dyear; */
   /*   tmg.tm_mon=tmg.tm_mon +dsign*dmonth; */
   /*   tmg.tm_hour=tmg.tm_hour + 1; */
   /*   tp.tv_sec = mktime(&tmg); */
   /*   strt=asctime(&tmg); */
   /*   printf("Time(after) =%s",strstart);  */
   /*  (void) time (&time_value);
   *  printf("time=%d,t-=%d\n",time_value,time_value-86400);
   *  tm = *localtime(&time_value);
   *  strstart=asctime(&tm);
   *  printf("tim_value=%d,asctime=%s\n",time_value,strstart); 
   */
   
     nberr=0; /* Number of errors and warnings */
     nbwarn=0;
     getcwd(pathcd, size);
   
     printf("\n%s\n%s",version,fullversion);
     if(argc <=1){
       printf("\nEnter the parameter file name: ");
       fgets(pathr,FILENAMELENGTH,stdin);
       i=strlen(pathr);
       if(pathr[i-1]=='\n')
         pathr[i-1]='\0';
      for (tok = pathr; tok != NULL; ){
         printf("Pathr |%s|\n",pathr);
         while ((val = strsep(&tok, "\"" )) != NULL && *val == '\0');
         printf("val= |%s| pathr=%s\n",val,pathr);
         strcpy (pathtot, val);
         if(pathr[0] == '\0') break; /* Un peu sale */
       }
     }
     else{
       strcpy(pathtot,argv[1]);
     }
     /*if(getcwd(pathcd, MAXLINE)!= NULL)printf ("Error pathcd\n");*/
     /*cygwin_split_path(pathtot,path,optionfile);
       printf("pathtot=%s, path=%s, optionfile=%s\n",pathtot,path,optionfile);*/
     /* cutv(path,optionfile,pathtot,'\\');*/
   
     /* Split argv[0], imach program to get pathimach */
     printf("\nargv[0]=%s argv[1]=%s, \n",argv[0],argv[1]);
     split(argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
     printf("\nargv[0]=%s pathimach=%s, \noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",argv[0],pathimach,optionfile,optionfilext,optionfilefiname);
    /*   strcpy(pathimach,argv[0]); */
     /* Split argv[1]=pathtot, parameter file name to get path, optionfile, extension and name */
     split(pathtot,path,optionfile,optionfilext,optionfilefiname);
     printf("\npathtot=%s,\npath=%s,\noptionfile=%s \noptionfilext=%s \noptionfilefiname=%s\n",pathtot,path,optionfile,optionfilext,optionfilefiname);
     chdir(path);
     strcpy(command,"mkdir ");
     strcat(command,optionfilefiname);
     if((outcmd=system(command)) != 0){
       printf("Problem creating directory or it already exists %s%s, err=%d\n",path,optionfilefiname,outcmd);
       /* fprintf(ficlog,"Problem creating directory %s%s\n",path,optionfilefiname); */
       /* fclose(ficlog); */
   /*     exit(1); */
     }
   /*   if((imk=mkdir(optionfilefiname))<0){ */
   /*     perror("mkdir"); */
   /*   } */
   
     /*-------- arguments in the command line --------*/
   
     /* Log file */
     strcat(filelog, optionfilefiname);
     strcat(filelog,".log");    /* */
     if((ficlog=fopen(filelog,"w"))==NULL)    {
       printf("Problem with logfile %s\n",filelog);
       goto end;
     }
     fprintf(ficlog,"Log filename:%s\n",filelog);
     fprintf(ficlog,"\n%s\n%s",version,fullversion);
     fprintf(ficlog,"\nEnter the parameter file name: \n");
     fprintf(ficlog,"pathimach=%s\npathtot=%s\n\
    path=%s \n\
    optionfile=%s\n\
    optionfilext=%s\n\
    optionfilefiname=%s\n",pathimach,pathtot,path,optionfile,optionfilext,optionfilefiname);
   
     printf("Local time (at start):%s",strstart);
     fprintf(ficlog,"Local time (at start): %s",strstart);
     fflush(ficlog);
   /*   (void) gettimeofday(&curr_time,&tzp); */
   /*   printf("Elapsed time %d\n", asc_diff_time(curr_time.tv_sec-start_time.tv_sec,tmpout)); */
   
     /* */
     strcpy(fileres,"r");
     strcat(fileres, optionfilefiname);
     strcat(fileres,".txt");    /* Other files have txt extension */
   
     /*---------arguments file --------*/
   
     if((ficpar=fopen(optionfile,"r"))==NULL)    {
       printf("Problem with optionfile %s\n",optionfile);
       fprintf(ficlog,"Problem with optionfile %s\n",optionfile);
       fflush(ficlog);
       goto end;
     }
   
   
   
     strcpy(filereso,"o");
     strcat(filereso,fileres);
     if((ficparo=fopen(filereso,"w"))==NULL) { /* opened on subdirectory */
       printf("Problem with Output resultfile: %s\n", filereso);
       fprintf(ficlog,"Problem with Output resultfile: %s\n", filereso);
       fflush(ficlog);
       goto end;
     }
   
     /* Reads comments: lines beginning with '#' */
     numlinepar=0;
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
     fscanf(ficpar,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%lf stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d model=%s\n",title, datafile, &lastobs, &firstpass,&lastpass,&ftol, &stepm, &ncovcol, &nlstate,&ndeath, &maxwav, &mle, &weightopt,model);
     numlinepar++;
     printf("title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate,ndeath, maxwav, mle, weightopt,model);
     fprintf(ficparo,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fprintf(ficlog,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle=%d weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol,stepm,ncovcol,nlstate,ndeath,maxwav, mle, weightopt,model);
     fflush(ficlog);
     while((c=getc(ficpar))=='#' && c!= EOF){
       ungetc(c,ficpar);
       fgets(line, MAXLINE, ficpar);
       numlinepar++;
       puts(line);
       fputs(line,ficparo);
       fputs(line,ficlog);
     }
     ungetc(c,ficpar);
   
      
     covar=matrix(0,NCOVMAX,1,n); 
     cptcovn=0; /*Number of covariates, i.e. number of '+' in model statement*/
     if (strlen(model)>1) cptcovn=nbocc(model,'+')+1;
   
     ncovmodel=2+cptcovn; /*Number of variables = cptcovn + intercept + age */
     nvar=ncovmodel-1; /* Suppressing age as a basic covariate */
     npar= (nlstate+ndeath-1)*nlstate*ncovmodel; /* Number of parameters*/
   
     delti3= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
     delti=delti3[1][1];
     /*delti=vector(1,npar); *//* Scale of each paramater (output from hesscov)*/
     if(mle==-1){ /* Print a wizard for help writing covariance matrix */
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-1, look at file %s for a template of covariance matrix \n",filereso);
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       fclose (ficparo);
       fclose (ficlog);
       exit(0);
     }
     else if(mle==-3) {
       prwizard(ncovmodel, nlstate, ndeath, model, ficparo);
       printf(" You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       fprintf(ficlog," You choose mle=-3, look at file %s for a template of covariance matrix \n",filereso);
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       matcov=matrix(1,npar,1,npar);
     }
     else{
       /* Read guess parameters */
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
       
       param= ma3x(1,nlstate,1,nlstate+ndeath-1,1,ncovmodel);
       for(i=1; i <=nlstate; i++){
         j=0;
         for(jj=1; jj <=nlstate+ndeath; jj++){
           if(jj==i) continue;
           j++;
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1 != i) && (j1 != j)){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           fprintf(ficparo,"%1d%1d",i1,j1);
           if(mle==1)
             printf("%1d%1d",i,j);
           fprintf(ficlog,"%1d%1d",i,j);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar," %lf",&param[i][j][k]);
             if(mle==1){
               printf(" %lf",param[i][j][k]);
               fprintf(ficlog," %lf",param[i][j][k]);
             }
             else
               fprintf(ficlog," %lf",param[i][j][k]);
             fprintf(ficparo," %lf",param[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           if(mle==1)
             printf("\n");
           fprintf(ficlog,"\n");
           fprintf(ficparo,"\n");
         }
       }  
       fflush(ficlog);
   
       p=param[1][1];
       
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
   
       for(i=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath-1; j++){
           fscanf(ficpar,"%1d%1d",&i1,&j1);
           if ((i1-i)*(j1-j)!=0){
             printf("Error in line parameters number %d, %1d%1d instead of %1d%1d \n",numlinepar, i,j, i1, j1);
             exit(1);
           }
           printf("%1d%1d",i,j);
           fprintf(ficparo,"%1d%1d",i1,j1);
           fprintf(ficlog,"%1d%1d",i1,j1);
           for(k=1; k<=ncovmodel;k++){
             fscanf(ficpar,"%le",&delti3[i][j][k]);
             printf(" %le",delti3[i][j][k]);
             fprintf(ficparo," %le",delti3[i][j][k]);
             fprintf(ficlog," %le",delti3[i][j][k]);
           }
           fscanf(ficpar,"\n");
           numlinepar++;
           printf("\n");
           fprintf(ficparo,"\n");
           fprintf(ficlog,"\n");
         }
       }
       fflush(ficlog);
   
       delti=delti3[1][1];
   
   
       /* free_ma3x(delti3,1,nlstate,1,nlstate+ndeath-1,1,ncovmodel); */ /* Hasn't to to freed here otherwise delti is no more allocated */
     
       /* Reads comments: lines beginning with '#' */
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         numlinepar++;
         puts(line);
         fputs(line,ficparo);
         fputs(line,ficlog);
       }
       ungetc(c,ficpar);
     
       matcov=matrix(1,npar,1,npar);
       for(i=1; i <=npar; i++){
         fscanf(ficpar,"%s",&str);
         if(mle==1)
           printf("%s",str);
         fprintf(ficlog,"%s",str);
         fprintf(ficparo,"%s",str);
         for(j=1; j <=i; j++){
           fscanf(ficpar," %le",&matcov[i][j]);
           if(mle==1){
             printf(" %.5le",matcov[i][j]);
           }
           fprintf(ficlog," %.5le",matcov[i][j]);
           fprintf(ficparo," %.5le",matcov[i][j]);
         }
         fscanf(ficpar,"\n");
         numlinepar++;
         if(mle==1)
           printf("\n");
         fprintf(ficlog,"\n");
         fprintf(ficparo,"\n");
       }
       for(i=1; i <=npar; i++)
         for(j=i+1;j<=npar;j++)
           matcov[i][j]=matcov[j][i];
       
       if(mle==1)
         printf("\n");
       fprintf(ficlog,"\n");
       
       fflush(ficlog);
       
       /*-------- Rewriting parameter file ----------*/
       strcpy(rfileres,"r");    /* "Rparameterfile */
       strcat(rfileres,optionfilefiname);    /* Parameter file first name*/
       strcat(rfileres,".");    /* */
       strcat(rfileres,optionfilext);    /* Other files have txt extension */
       if((ficres =fopen(rfileres,"w"))==NULL) {
         printf("Problem writing new parameter file: %s\n", fileres);goto end;
         fprintf(ficlog,"Problem writing new parameter file: %s\n", fileres);goto end;
       }
       fprintf(ficres,"#%s\n",version);
     }    /* End of mle != -3 */
   
     /*-------- data file ----------*/
     if((fic=fopen(datafile,"r"))==NULL)    {
       printf("Problem while opening datafile: %s\n", datafile);goto end;
       fprintf(ficlog,"Problem while opening datafile: %s\n", datafile);goto end;
     }
   
     n= lastobs;
     severity = vector(1,maxwav);
     outcome=imatrix(1,maxwav+1,1,n);
     num=lvector(1,n);
     moisnais=vector(1,n);
     annais=vector(1,n);
     moisdc=vector(1,n);
     andc=vector(1,n);
     agedc=vector(1,n);
     cod=ivector(1,n);
     weight=vector(1,n);
     for(i=1;i<=n;i++) weight[i]=1.0; /* Equal weights, 1 by default */
     mint=matrix(1,maxwav,1,n);
     anint=matrix(1,maxwav,1,n);
     s=imatrix(1,maxwav+1,1,n);
     tab=ivector(1,NCOVMAX);
     ncodemax=ivector(1,8);
   
     i=1;
     linei=0;
     while ((fgets(line, MAXLINE, fic) != NULL) &&((i >= firstobs) && (i <=lastobs))) {
       linei=linei+1;
       for(j=strlen(line); j>=0;j--){  /* Untabifies line */
         if(line[j] == '\t')
           line[j] = ' ';
       }
       for(j=strlen(line)-1; (line[j]==' ')||(line[j]==10)||(line[j]==13);j--){
         ;
       };
       line[j+1]=0;  /* Trims blanks at end of line */
       if(line[0]=='#'){
         fprintf(ficlog,"Comment line\n%s\n",line);
         printf("Comment line\n%s\n",line);
         continue;
       }
   
       for (j=maxwav;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         /*        if (errno == ERANGE && (lval == LONG_MAX || lval == LONG_MIN))*/
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %d %s for individual %d, '%s'\nShould be a status of wave %d. Setting maxwav=%d might be wrong.  Exiting.\n", strb, linei,i,line,j,maxwav);
           exit(1);
         }
         s[j][i]=lval;
         
         strcpy(line,stra);
         cutv(stra, strb,line,' ');
         if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
         }
         else  if(iout=sscanf(strb,"%s.") != 0){
           month=99;
           year=9999;
         }else{
           printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of interview (mm/yyyy or .) at wave %d.  Exiting.\n",strb, linei,i, line,j);
           exit(1);
         }
         anint[j][i]= (double) year; 
         mint[j][i]= (double)month; 
         strcpy(line,stra);
       } /* ENd Waves */
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.",dummy) != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of death (mm/yyyy or .).  Exiting.\n",strb, linei,i,line);
         exit(1);
       }
       andc[i]=(double) year; 
       moisdc[i]=(double) month; 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       if(iout=sscanf(strb,"%d/%d",&month, &year) != 0){
       }
       else  if(iout=sscanf(strb,"%s.") != 0){
         month=99;
         year=9999;
       }else{
         printf("Error reading data around '%s' at line number %ld %s for individual %d, '%s'\nShould be a date of birth (mm/yyyy or .).  Exiting.\n",strb, linei,i,line,j);
         exit(1);
       }
       annais[i]=(double)(year);
       moisnais[i]=(double)(month); 
       strcpy(line,stra);
       
       cutv(stra, strb,line,' '); 
       errno=0;
       lval=strtol(strb,&endptr,10); 
       if( strb[0]=='\0' || (*endptr != '\0')){
         printf("Error reading data around '%d' at line number %ld %s for individual %d\nShould be a weight.  Exiting.\n",lval, i,line,linei);
         exit(1);
       }
       weight[i]=(double)(lval); 
       strcpy(line,stra);
       
       for (j=ncovcol;j>=1;j--){
         cutv(stra, strb,line,' '); 
         errno=0;
         lval=strtol(strb,&endptr,10); 
         if( strb[0]=='\0' || (*endptr != '\0')){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a covar (meaning 0 for the reference or 1).  Exiting.\n",lval, linei,i, line);
           exit(1);
         }
         if(lval <-1 || lval >1){
           printf("Error reading data around '%d' at line number %ld %s for individual %d, '%s'\nShould be a value of the %d covar (meaning 0 for the reference or 1. IMaCh does not build design variables, do it your self).  Exiting.\n",lval,linei, i,line,j);
           exit(1);
         }
         covar[j][i]=(double)(lval);
         strcpy(line,stra);
       } 
       lstra=strlen(stra);
       
       if(lstra > 9){ /* More than 2**32 or max of what printf can write with %ld */
         stratrunc = &(stra[lstra-9]);
         num[i]=atol(stratrunc);
       }
       else
         num[i]=atol(stra);
       /*if((s[2][i]==2) && (s[3][i]==-1)&&(s[4][i]==9)){
         printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]),weight[i], (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i])); ij=ij+1;}*/
       
       i=i+1;
     } /* End loop reading  data */
     fclose(fic);
     /* printf("ii=%d", ij);
        scanf("%d",i);*/
     imx=i-1; /* Number of individuals */
   
     /* for (i=1; i<=imx; i++){
       if ((s[1][i]==3) && (s[2][i]==2)) s[2][i]=3;
       if ((s[2][i]==3) && (s[3][i]==2)) s[3][i]=3;
       if ((s[3][i]==3) && (s[4][i]==2)) s[4][i]=3;
       }*/
      /*  for (i=1; i<=imx; i++){
        if (s[4][i]==9)  s[4][i]=-1; 
        printf("%ld %.lf %.lf %.lf %.lf/%.lf %.lf/%.lf %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d %.lf/%.lf %d\n",num[i],(covar[1][i]), (covar[2][i]), (weight[i]), (moisnais[i]), (annais[i]), (moisdc[i]), (andc[i]), (mint[1][i]), (anint[1][i]), (s[1][i]),  (mint[2][i]), (anint[2][i]), (s[2][i]),  (mint[3][i]), (anint[3][i]), (s[3][i]),  (mint[4][i]), (anint[4][i]), (s[4][i]));}*/
     
     /* for (i=1; i<=imx; i++) */
    
      /*if ((s[3][i]==3) ||  (s[4][i]==3)) weight[i]=0.08;
        else weight[i]=1;*/
   
     /* Calculation of the number of parameters from char model */
     Tvar=ivector(1,15); /* stores the number n of the covariates in Vm+Vn at 1 and m at 2 */
     Tprod=ivector(1,15); 
     Tvaraff=ivector(1,15); 
     Tvard=imatrix(1,15,1,2);
     Tage=ivector(1,15);      
      
     if (strlen(model) >1){ /* If there is at least 1 covariate */
       j=0, j1=0, k1=1, k2=1;
       j=nbocc(model,'+'); /* j=Number of '+' */
       j1=nbocc(model,'*'); /* j1=Number of '*' */
       cptcovn=j+1; 
       cptcovprod=j1; /*Number of products */
       
       strcpy(modelsav,model); 
       if ((strcmp(model,"age")==0) || (strcmp(model,"age*age")==0)){
         printf("Error. Non available option model=%s ",model);
         fprintf(ficlog,"Error. Non available option model=%s ",model);
         goto end;
       }
       
       /* This loop fills the array Tvar from the string 'model'.*/
   
       for(i=(j+1); i>=1;i--){
         cutv(stra,strb,modelsav,'+'); /* keeps in strb after the last + */ 
         if (nbocc(modelsav,'+')==0) strcpy(strb,modelsav); /* and analyzes it */
         /*      printf("i=%d a=%s b=%s sav=%s\n",i, stra,strb,modelsav);*/
         /*scanf("%d",i);*/
         if (strchr(strb,'*')) {  /* Model includes a product */
           cutv(strd,strc,strb,'*'); /* strd*strc  Vm*Vn (if not *age)*/
           if (strcmp(strc,"age")==0) { /* Vn*age */
             cptcovprod--;
             cutv(strb,stre,strd,'V');
             Tvar[i]=atoi(stre); /* computes n in Vn and stores in Tvar*/
             cptcovage++;
               Tage[cptcovage]=i;
               /*printf("stre=%s ", stre);*/
           }
           else if (strcmp(strd,"age")==0) { /* or age*Vn */
             cptcovprod--;
             cutv(strb,stre,strc,'V');
             Tvar[i]=atoi(stre);
             cptcovage++;
             Tage[cptcovage]=i;
           }
           else {  /* Age is not in the model */
             cutv(strb,stre,strc,'V'); /* strc= Vn, stre is n*/
             Tvar[i]=ncovcol+k1;
             cutv(strb,strc,strd,'V'); /* strd was Vm, strc is m */
             Tprod[k1]=i;
             Tvard[k1][1]=atoi(strc); /* m*/
             Tvard[k1][2]=atoi(stre); /* n */
             Tvar[cptcovn+k2]=Tvard[k1][1];
             Tvar[cptcovn+k2+1]=Tvard[k1][2]; 
             for (k=1; k<=lastobs;k++) 
               covar[ncovcol+k1][k]=covar[atoi(stre)][k]*covar[atoi(strc)][k];
             k1++;
             k2=k2+2;
           }
         }
         else { /* no more sum */
           /*printf("d=%s c=%s b=%s\n", strd,strc,strb);*/
          /*  scanf("%d",i);*/
         cutv(strd,strc,strb,'V');
         Tvar[i]=atoi(strc);
         }
         strcpy(modelsav,stra);  
         /*printf("a=%s b=%s sav=%s\n", stra,strb,modelsav);
           scanf("%d",i);*/
       } /* end of loop + */
     } /* end model */
     
     /*The number n of Vn is stored in Tvar. cptcovage =number of age covariate. Tage gives the position of age. cptcovprod= number of products.
       If model=V1+V1*age then Tvar[1]=1 Tvar[2]=1 cptcovage=1 Tage[1]=2 cptcovprod=0*/
   
     /* printf("tvar1=%d tvar2=%d tvar3=%d cptcovage=%d Tage=%d",Tvar[1],Tvar[2],Tvar[3],cptcovage,Tage[1]);
     printf("cptcovprod=%d ", cptcovprod);
     fprintf(ficlog,"cptcovprod=%d ", cptcovprod);
   
     scanf("%d ",i);*/
   
       /*  if(mle==1){*/
     if (weightopt != 1) { /* Maximisation without weights*/
       for(i=1;i<=n;i++) weight[i]=1.0;
     }
       /*-calculation of age at interview from date of interview and age at death -*/
     agev=matrix(1,maxwav,1,imx);
   
     for (i=1; i<=imx; i++) {
       for(m=2; (m<= maxwav); m++) {
         if (((int)mint[m][i]== 99) && (s[m][i] <= nlstate)){
           anint[m][i]=9999;
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]==9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           fprintf(ficlog,"Error! Date of death (month %2d and year %4d) of individual %ld on line %d was unknown, you must set an arbitrary year of death or he/she is skipped and results are biased\n",(int)moisdc[i],(int)andc[i],num[i],i);
           s[m][i]=-1;
         }
         if((int)moisdc[i]==99 && (int)andc[i]!=9999 && s[m][i]>nlstate){
           nberr++;
           printf("Error! Month of death of individual %ld on line %d was unknown %2d, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,(int)moisdc[i]); 
           fprintf(ficlog,"Error! Month of death of individual %ld on line %d was unknown %f, you should set it otherwise the information on the death is skipped and results are biased.\n",num[i],i,moisdc[i]); 
           s[m][i]=-1; /* We prefer to skip it (and to skip it in version 0.8a1 too */
         }
       }
     }
   
     for (i=1; i<=imx; i++)  {
       agedc[i]=(moisdc[i]/12.+andc[i])-(moisnais[i]/12.+annais[i]);
       for(m=firstpass; (m<= lastpass); m++){
         if(s[m][i] >0 || s[m][i]==-2 || s[m][i]==-4 || s[m][i]==-5){
           if (s[m][i] >= nlstate+1) {
             if(agedc[i]>0)
               if((int)moisdc[i]!=99 && (int)andc[i]!=9999)
                 agev[m][i]=agedc[i];
             /*if(moisdc[i]==99 && andc[i]==9999) s[m][i]=-1;*/
               else {
                 if ((int)andc[i]!=9999){
                   nbwarn++;
                   printf("Warning negative age at death: %ld line:%d\n",num[i],i);
                   fprintf(ficlog,"Warning negative age at death: %ld line:%d\n",num[i],i);
                   agev[m][i]=-1;
                 }
               }
           }
           else if(s[m][i] !=9){ /* Standard case, age in fractional
                                    years but with the precision of a month */
             agev[m][i]=(mint[m][i]/12.+1./24.+anint[m][i])-(moisnais[i]/12.+1./24.+annais[i]);
             if((int)mint[m][i]==99 || (int)anint[m][i]==9999)
               agev[m][i]=1;
             else if(agev[m][i] <agemin){ 
               agemin=agev[m][i];
               /*printf(" Min anint[%d][%d]=%.2f annais[%d]=%.2f, agemin=%.2f\n",m,i,anint[m][i], i,annais[i], agemin);*/
             }
             else if(agev[m][i] >agemax){
               agemax=agev[m][i];
               /* printf(" anint[%d][%d]=%.0f annais[%d]=%.0f, agemax=%.0f\n",m,i,anint[m][i], i,annais[i], agemax);*/
             }
             /*agev[m][i]=anint[m][i]-annais[i];*/
             /*     agev[m][i] = age[i]+2*m;*/
           }
           else { /* =9 */
             agev[m][i]=1;
             s[m][i]=-1;
           }
         }
         else /*= 0 Unknown */
           agev[m][i]=1;
       }
       
     }
     for (i=1; i<=imx; i++)  {
       for(m=firstpass; (m<=lastpass); m++){
         if (s[m][i] > (nlstate+ndeath)) {
           nberr++;
           printf("Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           fprintf(ficlog,"Error: on wave %d of individual %d status %d > (nlstate+ndeath)=(%d+%d)=%d\n",m,i,s[m][i],nlstate, ndeath, nlstate+ndeath);     
           goto end;
         }
       }
     }
   
     /*for (i=1; i<=imx; i++){
     for (m=firstpass; (m<lastpass); m++){
        printf("%ld %d %.lf %d %d\n", num[i],(covar[1][i]),agev[m][i],s[m][i],s[m+1][i]);
   }
   
   }*/
   
   
     printf("Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax);
     fprintf(ficlog,"Total number of individuals= %d, Agemin = %.2f, Agemax= %.2f\n\n", imx, agemin, agemax); 
   
     agegomp=(int)agemin;
     free_vector(severity,1,maxwav);
     free_imatrix(outcome,1,maxwav+1,1,n);
     free_vector(moisnais,1,n);
     free_vector(annais,1,n);
     /* free_matrix(mint,1,maxwav,1,n);
        free_matrix(anint,1,maxwav,1,n);*/
     free_vector(moisdc,1,n);
     free_vector(andc,1,n);
   
      
     wav=ivector(1,imx);
     dh=imatrix(1,lastpass-firstpass+1,1,imx);
     bh=imatrix(1,lastpass-firstpass+1,1,imx);
     mw=imatrix(1,lastpass-firstpass+1,1,imx);
      
     /* Concatenates waves */
     concatwav(wav, dh, bh, mw, s, agedc, agev,  firstpass, lastpass, imx, nlstate, stepm);
   
     /* Routine tricode is to calculate cptcoveff (real number of unique covariates) and to associate covariable number and modality */
   
     Tcode=ivector(1,100);
     nbcode=imatrix(0,NCOVMAX,0,NCOVMAX); 
     ncodemax[1]=1;
     if (cptcovn > 0) tricode(Tvar,nbcode,imx);
         
     codtab=imatrix(1,100,1,10); /* Cross tabulation to get the order of 
                                    the estimations*/
     h=0;
     m=pow(2,cptcoveff);
    
     for(k=1;k<=cptcoveff; k++){
       for(i=1; i <=(m/pow(2,k));i++){
         for(j=1; j <= ncodemax[k]; j++){
           for(cpt=1; cpt <=(m/pow(2,cptcoveff+1-k)); cpt++){
             h++;
             if (h>m) h=1;codtab[h][k]=j;codtab[h][Tvar[k]]=j;
             /*  printf("h=%d k=%d j=%d codtab[h][k]=%d tvar[k]=%d \n",h, k,j,codtab[h][k],Tvar[k]);*/
           } 
         }
       }
     } 
     /* printf("codtab[1][2]=%d codtab[2][2]=%d",codtab[1][2],codtab[2][2]); 
        codtab[1][2]=1;codtab[2][2]=2; */
     /* for(i=1; i <=m ;i++){ 
        for(k=1; k <=cptcovn; k++){
        printf("i=%d k=%d %d %d ",i,k,codtab[i][k], cptcoveff);
        }
        printf("\n");
        }
        scanf("%d",i);*/
       
     /*------------ gnuplot -------------*/
     strcpy(optionfilegnuplot,optionfilefiname);
     if(mle==-3)
       strcat(optionfilegnuplot,"-mort");
     strcat(optionfilegnuplot,".gp");
   
     if((ficgp=fopen(optionfilegnuplot,"w"))==NULL) {
       printf("Problem with file %s",optionfilegnuplot);
     }
     else{
       fprintf(ficgp,"\n# %s\n", version); 
       fprintf(ficgp,"# %s\n", optionfilegnuplot); 
       fprintf(ficgp,"set missing 'NaNq'\n");
     }
     /*  fclose(ficgp);*/
     /*--------- index.htm --------*/
   
     strcpy(optionfilehtm,optionfilefiname); /* Main html file */
     if(mle==-3)
       strcat(optionfilehtm,"-mort");
     strcat(optionfilehtm,".htm");
     if((fichtm=fopen(optionfilehtm,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtm), exit(0);
     }
   
     strcpy(optionfilehtmcov,optionfilefiname); /* Only for matrix of covariance */
     strcat(optionfilehtmcov,"-cov.htm");
     if((fichtmcov=fopen(optionfilehtmcov,"w"))==NULL)    {
       printf("Problem with %s \n",optionfilehtmcov), exit(0);
     }
     else{
     fprintf(fichtmcov,"<body>\n<title>IMaCh Cov %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model);
     }
   
     fprintf(fichtm,"<body>\n<title>IMaCh %s</title>\n <font size=\"2\">%s <br> %s</font> \
   <hr size=\"2\" color=\"#EC5E5E\"> \n\
   Title=%s <br>Datafile=%s Firstpass=%d Lastpass=%d Stepm=%d Weight=%d Model=%s<br>\n\
   \n\
   <hr  size=\"2\" color=\"#EC5E5E\">\
    <ul><li><h4>Parameter files</h4>\n\
    - Parameter file: <a href=\"%s.%s\">%s.%s</a><br>\n\
    - Copy of the parameter file: <a href=\"o%s\">o%s</a><br>\n\
    - Log file of the run: <a href=\"%s\">%s</a><br>\n\
    - Gnuplot file name: <a href=\"%s\">%s</a><br>\n\
    - Date and time at start: %s</ul>\n",\
             fileres,version,fullversion,title,datafile,firstpass,lastpass,stepm, weightopt, model,\
             optionfilefiname,optionfilext,optionfilefiname,optionfilext,\
             fileres,fileres,\
             filelog,filelog,optionfilegnuplot,optionfilegnuplot,strstart);
     fflush(fichtm);
   
     strcpy(pathr,path);
     strcat(pathr,optionfilefiname);
     chdir(optionfilefiname); /* Move to directory named optionfile */
     
     /* Calculates basic frequencies. Computes observed prevalence at single age
        and prints on file fileres'p'. */
     freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint,strstart);
   
     fprintf(fichtm,"\n");
     fprintf(fichtm,"<br>Total number of observations=%d <br>\n\
   Youngest age at first (selected) pass %.2f, oldest age %.2f<br>\n\
   Interval (in months) between two waves: Min=%d Max=%d Mean=%.2lf<br>\n",\
             imx,agemin,agemax,jmin,jmax,jmean);
     pmmij= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       newms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       savms= matrix(1,nlstate+ndeath,1,nlstate+ndeath); /* creation */
       oldm=oldms; newm=newms; savm=savms; /* Keeps fixed addresses to free */
       
      
     /* For Powell, parameters are in a vector p[] starting at p[1]
        so we point p on param[1][1] so that p[1] maps on param[1][1][1] */
     p=param[1][1]; /* *(*(*(param +1)+1)+0) */
   
     globpr=0; /* To get the number ipmx of contributions and the sum of weights*/
   
     if (mle==-3){
       ximort=matrix(1,NDIM,1,NDIM);
       cens=ivector(1,n);
       ageexmed=vector(1,n);
       agecens=vector(1,n);
       dcwave=ivector(1,n);
    
       for (i=1; i<=imx; i++){
         dcwave[i]=-1;
         for (m=firstpass; m<=lastpass; m++)
           if (s[m][i]>nlstate) {
             dcwave[i]=m;
             /*    printf("i=%d j=%d s=%d dcwave=%d\n",i,j, s[j][i],dcwave[i]);*/
             break;
           }
       }
   
       for (i=1; i<=imx; i++) {
         if (wav[i]>0){
           ageexmed[i]=agev[mw[1][i]][i];
           j=wav[i];
           agecens[i]=1.; 
   
           if (ageexmed[i]> 1 && wav[i] > 0){
             agecens[i]=agev[mw[j][i]][i];
             cens[i]= 1;
           }else if (ageexmed[i]< 1) 
             cens[i]= -1;
           if (agedc[i]< AGESUP && agedc[i]>1 && dcwave[i]>firstpass && dcwave[i]<=lastpass)
             cens[i]=0 ;
         }
         else cens[i]=-1;
       }
       
       for (i=1;i<=NDIM;i++) {
         for (j=1;j<=NDIM;j++)
           ximort[i][j]=(i == j ? 1.0 : 0.0);
       }
       
       p[1]=0.0268; p[NDIM]=0.083;
       /*printf("%lf %lf", p[1], p[2]);*/
       
       
       printf("Powell\n");  fprintf(ficlog,"Powell\n");
       strcpy(filerespow,"pow-mort"); 
       strcat(filerespow,fileres);
       if((ficrespow=fopen(filerespow,"w"))==NULL) {
         printf("Problem with resultfile: %s\n", filerespow);
         fprintf(ficlog,"Problem with resultfile: %s\n", filerespow);
       }
       fprintf(ficrespow,"# Powell\n# iter -2*LL");
       /*  for (i=1;i<=nlstate;i++)
           for(j=1;j<=nlstate+ndeath;j++)
           if(j!=i)fprintf(ficrespow," p%1d%1d",i,j);
       */
       fprintf(ficrespow,"\n");
       
       powell(p,ximort,NDIM,ftol,&iter,&fret,gompertz);
       fclose(ficrespow);
       
       hesscov(matcov, p, NDIM, delti, 1e-4, gompertz); 
   
       for(i=1; i <=NDIM; i++)
         for(j=i+1;j<=NDIM;j++)
           matcov[i][j]=matcov[j][i];
       
       printf("\nCovariance matrix\n ");
       for(i=1; i <=NDIM; i++) {
         for(j=1;j<=NDIM;j++){ 
           printf("%f ",matcov[i][j]);
         }
         printf("\n ");
       }
       
       printf("iter=%d MLE=%f Eq=%lf*exp(%lf*(age-%d))\n",iter,-gompertz(p),p[1],p[2],agegomp);
       for (i=1;i<=NDIM;i++) 
         printf("%f [%f ; %f]\n",p[i],p[i]-2*sqrt(matcov[i][i]),p[i]+2*sqrt(matcov[i][i]));
   
       lsurv=vector(1,AGESUP);
       lpop=vector(1,AGESUP);
       tpop=vector(1,AGESUP);
       lsurv[agegomp]=100000;
       
       for (k=agegomp;k<=AGESUP;k++) {
         agemortsup=k;
         if (p[1]*exp(p[2]*(k-agegomp))>1) break;
       }
       
       for (k=agegomp;k<agemortsup;k++)
         lsurv[k+1]=lsurv[k]-lsurv[k]*(p[1]*exp(p[2]*(k-agegomp)));
       
       for (k=agegomp;k<agemortsup;k++){
         lpop[k]=(lsurv[k]+lsurv[k+1])/2.;
         sumlpop=sumlpop+lpop[k];
       }
       
       tpop[agegomp]=sumlpop;
       for (k=agegomp;k<(agemortsup-3);k++){
         /*  tpop[k+1]=2;*/
         tpop[k+1]=tpop[k]-lpop[k];
       }
       
       
       printf("\nAge   lx     qx    dx    Lx     Tx     e(x)\n");
       for (k=agegomp;k<(agemortsup-2);k++) 
         printf("%d %.0lf %lf %.0lf %.0lf %.0lf %lf\n",k,lsurv[k],p[1]*exp(p[2]*(k-agegomp)),(p[1]*exp(p[2]*(k-agegomp)))*lsurv[k],lpop[k],tpop[k],tpop[k]/lsurv[k]);
       
       
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplotmort(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtmlmort(fileres,title,datafile, firstpass, lastpass, \
                        stepm, weightopt,\
                        model,imx,p,matcov,agemortsup);
       
       free_vector(lsurv,1,AGESUP);
       free_vector(lpop,1,AGESUP);
       free_vector(tpop,1,AGESUP);
     } /* Endof if mle==-3 */
     
     else{ /* For mle >=1 */
     
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("First Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       globpr=1; /* to print the contributions */
       likelione(ficres, p, npar, nlstate, &globpr, &ipmx, &sw, &fretone, funcone); /* Prints the contributions to the likelihood */
       printf("Second Likeli=%12.6f ipmx=%ld sw=%12.6f",fretone,ipmx,sw);
       for (k=1; k<=npar;k++)
         printf(" %d %8.5f",k,p[k]);
       printf("\n");
       if(mle>=1){ /* Could be 1 or 2 */
         mlikeli(ficres,p, npar, ncovmodel, nlstate, ftol, func);
       }
       
       /*--------- results files --------------*/
       fprintf(ficres,"title=%s datafile=%s lastobs=%d firstpass=%d lastpass=%d\nftol=%e stepm=%d ncovcol=%d nlstate=%d ndeath=%d maxwav=%d mle= 0 weight=%d\nmodel=%s\n", title, datafile, lastobs, firstpass,lastpass,ftol, stepm, ncovcol, nlstate, ndeath, maxwav, weightopt,model);
       
       
       fprintf(ficres,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       printf("# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       fprintf(ficlog,"# Parameters nlstate*nlstate*ncov a12*1 + b12 * age + ...\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(k=1; k <=(nlstate+ndeath); k++){
           if (k != i) {
             printf("%d%d ",i,k);
             fprintf(ficlog,"%d%d ",i,k);
             fprintf(ficres,"%1d%1d ",i,k);
             for(j=1; j <=ncovmodel; j++){
               printf("%f ",p[jk]);
               fprintf(ficlog,"%f ",p[jk]);
               fprintf(ficres,"%f ",p[jk]);
               jk++; 
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       if(mle!=0){
         /* Computing hessian and covariance matrix */
         ftolhess=ftol; /* Usually correct */
         hesscov(matcov, p, npar, delti, ftolhess, func);
       }
       fprintf(ficres,"# Scales (for hessian or gradient estimation)\n");
       printf("# Scales (for hessian or gradient estimation)\n");
       fprintf(ficlog,"# Scales (for hessian or gradient estimation)\n");
       for(i=1,jk=1; i <=nlstate; i++){
         for(j=1; j <=nlstate+ndeath; j++){
           if (j!=i) {
             fprintf(ficres,"%1d%1d",i,j);
             printf("%1d%1d",i,j);
             fprintf(ficlog,"%1d%1d",i,j);
             for(k=1; k<=ncovmodel;k++){
               printf(" %.5e",delti[jk]);
               fprintf(ficlog," %.5e",delti[jk]);
               fprintf(ficres," %.5e",delti[jk]);
               jk++;
             }
             printf("\n");
             fprintf(ficlog,"\n");
             fprintf(ficres,"\n");
           }
         }
       }
       
       fprintf(ficres,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       if(mle>=1)
         printf("# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       fprintf(ficlog,"# Covariance matrix \n# 121 Var(a12)\n# 122 Cov(b12,a12) Var(b12)\n#   ...\n# 232 Cov(b23,a12)  Cov(b23,b12) ... Var (b23)\n");
       /* # 121 Var(a12)\n\ */
       /* # 122 Cov(b12,a12) Var(b12)\n\ */
       /* # 131 Cov(a13,a12) Cov(a13,b12, Var(a13)\n\ */
       /* # 132 Cov(b13,a12) Cov(b13,b12, Cov(b13,a13) Var(b13)\n\ */
       /* # 212 Cov(a21,a12) Cov(a21,b12, Cov(a21,a13) Cov(a21,b13) Var(a21)\n\ */
       /* # 212 Cov(b21,a12) Cov(b21,b12, Cov(b21,a13) Cov(b21,b13) Cov(b21,a21) Var(b21)\n\ */
       /* # 232 Cov(a23,a12) Cov(a23,b12, Cov(a23,a13) Cov(a23,b13) Cov(a23,a21) Cov(a23,b21) Var(a23)\n\ */
       /* # 232 Cov(b23,a12) Cov(b23,b12) ... Var (b23)\n" */
       
       
       /* Just to have a covariance matrix which will be more understandable
          even is we still don't want to manage dictionary of variables
       */
       for(itimes=1;itimes<=2;itimes++){
         jj=0;
         for(i=1; i <=nlstate; i++){
           for(j=1; j <=nlstate+ndeath; j++){
             if(j==i) continue;
             for(k=1; k<=ncovmodel;k++){
               jj++;
               ca[0]= k+'a'-1;ca[1]='\0';
               if(itimes==1){
                 if(mle>=1)
                   printf("#%1d%1d%d",i,j,k);
                 fprintf(ficlog,"#%1d%1d%d",i,j,k);
                 fprintf(ficres,"#%1d%1d%d",i,j,k);
               }else{
                 if(mle>=1)
                   printf("%1d%1d%d",i,j,k);
                 fprintf(ficlog,"%1d%1d%d",i,j,k);
                 fprintf(ficres,"%1d%1d%d",i,j,k);
               }
               ll=0;
               for(li=1;li <=nlstate; li++){
                 for(lj=1;lj <=nlstate+ndeath; lj++){
                   if(lj==li) continue;
                   for(lk=1;lk<=ncovmodel;lk++){
                     ll++;
                     if(ll<=jj){
                       cb[0]= lk +'a'-1;cb[1]='\0';
                       if(ll<jj){
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficlog," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                           fprintf(ficres," Cov(%s%1d%1d,%s%1d%1d)",ca,i,j,cb, li,lj);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }else{
                         if(itimes==1){
                           if(mle>=1)
                             printf(" Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficlog," Var(%s%1d%1d)",ca,i,j);
                           fprintf(ficres," Var(%s%1d%1d)",ca,i,j);
                         }else{
                           if(mle>=1)
                             printf(" %.5e",matcov[jj][ll]); 
                           fprintf(ficlog," %.5e",matcov[jj][ll]); 
                           fprintf(ficres," %.5e",matcov[jj][ll]); 
                         }
                       }
                     }
                   } /* end lk */
                 } /* end lj */
               } /* end li */
               if(mle>=1)
                 printf("\n");
               fprintf(ficlog,"\n");
               fprintf(ficres,"\n");
               numlinepar++;
             } /* end k*/
           } /*end j */
         } /* end i */
       } /* end itimes */
       
       fflush(ficlog);
       fflush(ficres);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       estepm=0;
       fscanf(ficpar,"agemin=%lf agemax=%lf bage=%lf fage=%lf estepm=%d\n",&ageminpar,&agemaxpar, &bage, &fage, &estepm);
       if (estepm==0 || estepm < stepm) estepm=stepm;
       if (fage <= 2) {
         bage = ageminpar;
         fage = agemaxpar;
       }
       
       fprintf(ficres,"# agemin agemax for life expectancy, bage fage (if mle==0 ie no data nor Max likelihood).\n");
       fprintf(ficres,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       fprintf(ficparo,"agemin=%.0f agemax=%.0f bage=%.0f fage=%.0f estepm=%d\n",ageminpar,agemaxpar,bage,fage, estepm);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"begin-prev-date=%lf/%lf/%lf end-prev-date=%lf/%lf/%lf mov_average=%d\n",&jprev1, &mprev1,&anprev1,&jprev2, &mprev2,&anprev2,&mobilav);
       fprintf(ficparo,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficres,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       printf("begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       fprintf(ficlog,"begin-prev-date=%.lf/%.lf/%.lf end-prev-date=%.lf/%.lf/%.lf mov_average=%d\n",jprev1, mprev1,anprev1,jprev2, mprev2,anprev2,mobilav);
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       
       dateprev1=anprev1+(mprev1-1)/12.+(jprev1-1)/365.;
       dateprev2=anprev2+(mprev2-1)/12.+(jprev2-1)/365.;
       
       fscanf(ficpar,"pop_based=%d\n",&popbased);
       fprintf(ficparo,"pop_based=%d\n",popbased);   
       fprintf(ficres,"pop_based=%d\n",popbased);   
       
       while((c=getc(ficpar))=='#' && c!= EOF){
         ungetc(c,ficpar);
         fgets(line, MAXLINE, ficpar);
         puts(line);
         fputs(line,ficparo);
       }
       ungetc(c,ficpar);
       
       fscanf(ficpar,"prevforecast=%d starting-proj-date=%lf/%lf/%lf final-proj-date=%lf/%lf/%lf mobil_average=%d\n",&prevfcast,&jproj1,&mproj1,&anproj1,&jproj2,&mproj2,&anproj2,&mobilavproj);
       fprintf(ficparo,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       printf("prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficlog,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       fprintf(ficres,"prevforecast=%d starting-proj-date=%.lf/%.lf/%.lf final-proj-date=%.lf/%.lf/%.lf mobil_average=%d\n",prevfcast,jproj1,mproj1,anproj1,jproj2,mproj2,anproj2,mobilavproj);
       /* day and month of proj2 are not used but only year anproj2.*/
       
       
       
       /*  freqsummary(fileres, agemin, agemax, s, agev, nlstate, imx,Tvaraff,nbcode, ncodemax,mint,anint);*/
       /*,dateprev1,dateprev2,jprev1, mprev1,anprev1,jprev2, mprev2,anprev2);*/
       
       replace_back_to_slash(pathc,path); /* Even gnuplot wants a / */
       printinggnuplot(fileres, optionfilefiname,ageminpar,agemaxpar,fage, pathc,p);
       
       printinghtml(fileres,title,datafile, firstpass, lastpass, stepm, weightopt,\
                    model,imx,jmin,jmax,jmean,rfileres,popforecast,estepm,\
                    jprev1,mprev1,anprev1,jprev2,mprev2,anprev2);
         
      /*------------ free_vector  -------------*/
      /*  chdir(path); */
    
       free_ivector(wav,1,imx);
       free_imatrix(dh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(bh,1,lastpass-firstpass+1,1,imx);
       free_imatrix(mw,1,lastpass-firstpass+1,1,imx);   
       free_lvector(num,1,n);
       free_vector(agedc,1,n);
       /*free_matrix(covar,0,NCOVMAX,1,n);*/
       /*free_matrix(covar,1,NCOVMAX,1,n);*/
       fclose(ficparo);
       fclose(ficres);
   
   
       /*--------------- Prevalence limit  (period or stable prevalence) --------------*/
     
       strcpy(filerespl,"pl");
       strcat(filerespl,fileres);
       if((ficrespl=fopen(filerespl,"w"))==NULL) {
         printf("Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
         fprintf(ficlog,"Problem with period (stable) prevalence resultfile: %s\n", filerespl);goto end;
       }
       printf("Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       fprintf(ficlog,"Computing period (stable) prevalence: result on file '%s' \n", filerespl);
       pstamp(ficrespl);
       fprintf(ficrespl,"# Period (stable) prevalence \n");
       fprintf(ficrespl,"#Age ");
       for(i=1; i<=nlstate;i++) fprintf(ficrespl,"%d-%d ",i,i);
       fprintf(ficrespl,"\n");
     
       prlim=matrix(1,nlstate,1,nlstate);
   
       agebase=ageminpar;
       agelim=agemaxpar;
       ftolpl=1.e-10;
       i1=cptcoveff;
       if (cptcovn < 1){i1=1;}
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           /*printf("cptcov=%d cptcod=%d codtab=%d nbcode=%d\n",cptcov, cptcod,Tcode[cptcode],codtab[cptcod][cptcov]);*/
           fprintf(ficrespl,"\n#******");
           printf("\n#******");
           fprintf(ficlog,"\n#******");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficrespl," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             printf(" V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficlog," V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficrespl,"******\n");
           printf("******\n");
           fprintf(ficlog,"******\n");
           
           for (age=agebase; age<=agelim; age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             fprintf(ficrespl,"%.0f ",age );
             for(j=1;j<=cptcoveff;j++)
               fprintf(ficrespl,"%d %d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             for(i=1; i<=nlstate;i++)
               fprintf(ficrespl," %.5f", prlim[i][i]);
             fprintf(ficrespl,"\n");
           }
         }
       }
       fclose(ficrespl);
   
       /*------------- h Pij x at various ages ------------*/
     
       strcpy(filerespij,"pij");  strcat(filerespij,fileres);
       if((ficrespij=fopen(filerespij,"w"))==NULL) {
         printf("Problem with Pij resultfile: %s\n", filerespij);goto end;
         fprintf(ficlog,"Problem with Pij resultfile: %s\n", filerespij);goto end;
       }
       printf("Computing pij: result on file '%s' \n", filerespij);
       fprintf(ficlog,"Computing pij: result on file '%s' \n", filerespij);
     
       stepsize=(int) (stepm+YEARM-1)/YEARM;
       /*if (stepm<=24) stepsize=2;*/
   
       agelim=AGESUP;
       hstepm=stepsize*YEARM; /* Every year of age */
       hstepm=hstepm/stepm; /* Typically 2 years, = 2/6 months = 4 */ 
   
       /* hstepm=1;   aff par mois*/
       pstamp(ficrespij);
       fprintf(ficrespij,"#****** h Pij x Probability to be in state j at age x+h being in i at x ");
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficrespij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrespij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrespij,"******\n");
           
           for (agedeb=fage; agedeb>=bage; agedeb--){ /* If stepm=6 months */
             nhstepm=(int) rint((agelim-agedeb)*YEARM/stepm); /* Typically 20 years = 20*12/6=40 */ 
             nhstepm = nhstepm/hstepm; /* Typically 40/4=10 */
   
             /*      nhstepm=nhstepm*YEARM; aff par mois*/
   
             p3mat=ma3x(1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             oldm=oldms;savm=savms;
             hpxij(p3mat,nhstepm,agedeb,hstepm,p,nlstate,stepm,oldm,savm, k);  
             fprintf(ficrespij,"# Cov Agex agex+h hpijx with i,j=");
             for(i=1; i<=nlstate;i++)
               for(j=1; j<=nlstate+ndeath;j++)
                 fprintf(ficrespij," %1d-%1d",i,j);
             fprintf(ficrespij,"\n");
             for (h=0; h<=nhstepm; h++){
               fprintf(ficrespij,"%d %3.f %3.f",k,agedeb, agedeb+ h*hstepm/YEARM*stepm );
               for(i=1; i<=nlstate;i++)
                 for(j=1; j<=nlstate+ndeath;j++)
                   fprintf(ficrespij," %.5f", p3mat[i][j][h]);
               fprintf(ficrespij,"\n");
             }
             free_ma3x(p3mat,1,nlstate+ndeath,1, nlstate+ndeath, 0,nhstepm);
             fprintf(ficrespij,"\n");
           }
         }
       }
   
       varprob(optionfilefiname, matcov, p, delti, nlstate, bage, fage,k,Tvar,nbcode, ncodemax,strstart);
   
       fclose(ficrespij);
   
       probs= ma3x(1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
       for(i=1;i<=AGESUP;i++)
         for(j=1;j<=NCOVMAX;j++)
           for(k=1;k<=NCOVMAX;k++)
             probs[i][j][k]=0.;
   
       /*---------- Forecasting ------------------*/
       /*if((stepm == 1) && (strcmp(model,".")==0)){*/
       if(prevfcast==1){
         /*    if(stepm ==1){*/
         prevforecast(fileres, anproj1, mproj1, jproj1, agemin, agemax, dateprev1, dateprev2, mobilavproj, bage, fage, firstpass, lastpass, anproj2, p, cptcoveff);
         /* (popforecast==1) populforecast(fileres, anpyram,mpyram,jpyram, agemin,agemax, dateprev1, dateprev2,mobilav, agedeb, fage, popforecast, popfile, anpyram1,p, i1);*/
         /*      }  */
         /*      else{ */
         /*        erreur=108; */
         /*        printf("Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*        fprintf(ficlog,"Warning %d!! You can only forecast the prevalences if the optimization\n  has been performed with stepm = 1 (month) instead of %d or model=. instead of '%s'\n", erreur, stepm, model); */
         /*      } */
       }
     
   
       /*---------- Health expectancies and variances ------------*/
   
       strcpy(filerest,"t");
       strcat(filerest,fileres);
       if((ficrest=fopen(filerest,"w"))==NULL) {
         printf("Problem with total LE resultfile: %s\n", filerest);goto end;
         fprintf(ficlog,"Problem with total LE resultfile: %s\n", filerest);goto end;
       }
       printf("Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
       fprintf(ficlog,"Computing Total Life expectancies with their standard errors: file '%s' \n", filerest); 
   
   
       strcpy(filerese,"e");
       strcat(filerese,fileres);
       if((ficreseij=fopen(filerese,"w"))==NULL) {
         printf("Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
         fprintf(ficlog,"Problem with Health Exp. resultfile: %s\n", filerese); exit(0);
       }
       printf("Computing Health Expectancies: result on file '%s' \n", filerese);
       fprintf(ficlog,"Computing Health Expectancies: result on file '%s' \n", filerese);
   
       strcpy(fileresstde,"stde");
       strcat(fileresstde,fileres);
       if((ficresstdeij=fopen(fileresstde,"w"))==NULL) {
         printf("Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
         fprintf(ficlog,"Problem with Health Exp. and std errors resultfile: %s\n", fileresstde); exit(0);
       }
       printf("Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
       fprintf(ficlog,"Computing Health Expectancies and standard errors: result on file '%s' \n", fileresstde);
   
       strcpy(filerescve,"cve");
       strcat(filerescve,fileres);
       if((ficrescveij=fopen(filerescve,"w"))==NULL) {
         printf("Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
         fprintf(ficlog,"Problem with Covar. Health Exp. resultfile: %s\n", filerescve); exit(0);
       }
       printf("Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
       fprintf(ficlog,"Computing Covar. of Health Expectancies: result on file '%s' \n", filerescve);
   
       strcpy(fileresv,"v");
       strcat(fileresv,fileres);
       if((ficresvij=fopen(fileresv,"w"))==NULL) {
         printf("Problem with variance resultfile: %s\n", fileresv);exit(0);
         fprintf(ficlog,"Problem with variance resultfile: %s\n", fileresv);exit(0);
       }
       printf("Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
       fprintf(ficlog,"Computing Variance-covariance of DFLEs: file '%s' \n", fileresv);
   
       /* Computes prevalence between agemin (i.e minimal age computed) and no more ageminpar */
       prevalence(probs, agemin, agemax, s, agev, nlstate, imx, Tvar, nbcode, ncodemax, mint, anint, dateprev1, dateprev2, firstpass, lastpass);
       /*  printf("ageminpar=%f, agemax=%f, s[lastpass][imx]=%d, agev[lastpass][imx]=%f, nlstate=%d, imx=%d,  mint[lastpass][imx]=%f, anint[lastpass][imx]=%f,dateprev1=%f, dateprev2=%f, firstpass=%d, lastpass=%d\n",\
           ageminpar, agemax, s[lastpass][imx], agev[lastpass][imx], nlstate, imx, mint[lastpass][imx],anint[lastpass][imx], dateprev1, dateprev2, firstpass, lastpass);
       */
   
       if (mobilav!=0) {
         mobaverage= ma3x(1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
         if (movingaverage(probs, bage, fage, mobaverage,mobilav)!=0){
           fprintf(ficlog," Error in movingaverage mobilav=%d\n",mobilav);
           printf(" Error in movingaverage mobilav=%d\n",mobilav);
         }
       }
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1; 
           fprintf(ficrest,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficrest,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficrest,"******\n");
   
           fprintf(ficreseij,"\n#****** ");
           fprintf(ficresstdeij,"\n#****** ");
           fprintf(ficrescveij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) {
             fprintf(ficreseij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficresstdeij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
             fprintf(ficrescveij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           }
           fprintf(ficreseij,"******\n");
           fprintf(ficresstdeij,"******\n");
           fprintf(ficrescveij,"******\n");
   
           fprintf(ficresvij,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvij,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvij,"******\n");
   
           eij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           evsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, strstart);  
           cvevsij(fileres, eij, p, nlstate, stepm, (int) bage, (int)fage, oldm, savm, k, estepm, delti, matcov, strstart);  
    
           vareij=ma3x(1,nlstate,1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,0, mobilav, strstart);
           if(popbased==1){
             varevsij(optionfilefiname, vareij, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k, estepm, cptcov,cptcod,popbased,mobilav, strstart);
           }
   
           pstamp(ficrest);
           fprintf(ficrest,"# Total life expectancy with std error and decomposition into time to be expected in each health state\n# Age ( e.. (std) ");
           for (i=1;i<=nlstate;i++) fprintf(ficrest,"e.%d (std) ",i);
           fprintf(ficrest,"\n");
   
           epj=vector(1,nlstate+1);
           for(age=bage; age <=fage ;age++){
             prevalim(prlim, nlstate, p, age, oldm, savm,ftolpl,k);
             if (popbased==1) {
               if(mobilav ==0){
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=probs[(int)age][i][k];
               }else{ /* mobilav */ 
                 for(i=1; i<=nlstate;i++)
                   prlim[i][i]=mobaverage[(int)age][i][k];
               }
             }
           
             fprintf(ficrest," %4.0f",age);
             for(j=1, epj[nlstate+1]=0.;j <=nlstate;j++){
               for(i=1, epj[j]=0.;i <=nlstate;i++) {
                 epj[j] += prlim[i][i]*eij[i][j][(int)age];
                 /*  printf("%lf %lf ", prlim[i][i] ,eij[i][j][(int)age]);*/
               }
               epj[nlstate+1] +=epj[j];
             }
   
             for(i=1, vepp=0.;i <=nlstate;i++)
               for(j=1;j <=nlstate;j++)
                 vepp += vareij[i][j][(int)age];
             fprintf(ficrest," %7.3f (%7.3f)", epj[nlstate+1],sqrt(vepp));
             for(j=1;j <=nlstate;j++){
               fprintf(ficrest," %7.3f (%7.3f)", epj[j],sqrt(vareij[j][j][(int)age]));
             }
             fprintf(ficrest,"\n");
           }
           free_ma3x(eij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_ma3x(vareij,1,nlstate,1,nlstate,(int) bage, (int)fage);
           free_vector(epj,1,nlstate+1);
         }
       }
       free_vector(weight,1,n);
       free_imatrix(Tvard,1,15,1,2);
       free_imatrix(s,1,maxwav+1,1,n);
       free_matrix(anint,1,maxwav,1,n); 
       free_matrix(mint,1,maxwav,1,n);
       free_ivector(cod,1,n);
       free_ivector(tab,1,NCOVMAX);
       fclose(ficreseij);
       fclose(ficresstdeij);
       fclose(ficrescveij);
       fclose(ficresvij);
       fclose(ficrest);
       fclose(ficpar);
     
       /*------- Variance of period (stable) prevalence------*/   
   
       strcpy(fileresvpl,"vpl");
       strcat(fileresvpl,fileres);
       if((ficresvpl=fopen(fileresvpl,"w"))==NULL) {
         printf("Problem with variance of period (stable) prevalence  resultfile: %s\n", fileresvpl);
         exit(0);
       }
       printf("Computing Variance-covariance of period (stable) prevalence: file '%s' \n", fileresvpl);
   
       for(cptcov=1,k=0;cptcov<=i1;cptcov++){
         for(cptcod=1;cptcod<=ncodemax[cptcov];cptcod++){
           k=k+1;
           fprintf(ficresvpl,"\n#****** ");
           for(j=1;j<=cptcoveff;j++) 
             fprintf(ficresvpl,"V%d=%d ",Tvaraff[j],nbcode[Tvaraff[j]][codtab[k][j]]);
           fprintf(ficresvpl,"******\n");
         
           varpl=matrix(1,nlstate,(int) bage, (int) fage);
           oldm=oldms;savm=savms;
           varprevlim(fileres, varpl, matcov, p, delti, nlstate, stepm, (int) bage, (int) fage, oldm, savm, prlim, ftolpl,k,strstart);
           free_matrix(varpl,1,nlstate,(int) bage, (int)fage);
         }
       }
   
       fclose(ficresvpl);
   
       /*---------- End : free ----------------*/
       if (mobilav!=0) free_ma3x(mobaverage,1, AGESUP,1,NCOVMAX, 1,NCOVMAX);
       free_ma3x(probs,1,AGESUP,1,NCOVMAX, 1,NCOVMAX);
   
     }  /* mle==-3 arrives here for freeing */
     free_matrix(prlim,1,nlstate,1,nlstate);
       free_matrix(pmmij,1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(oldms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(newms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(savms, 1,nlstate+ndeath,1,nlstate+ndeath);
       free_matrix(covar,0,NCOVMAX,1,n);
       free_matrix(matcov,1,npar,1,npar);
       /*free_vector(delti,1,npar);*/
       free_ma3x(delti3,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel); 
       free_matrix(agev,1,maxwav,1,imx);
       free_ma3x(param,1,nlstate,1, nlstate+ndeath-1,1,ncovmodel);
   
       free_ivector(ncodemax,1,8);
       free_ivector(Tvar,1,15);
       free_ivector(Tprod,1,15);
       free_ivector(Tvaraff,1,15);
       free_ivector(Tage,1,15);
       free_ivector(Tcode,1,100);
   
       free_imatrix(nbcode,0,NCOVMAX,0,NCOVMAX);
       free_imatrix(codtab,1,100,1,10);
     fflush(fichtm);
     fflush(ficgp);
     
   
     if((nberr >0) || (nbwarn>0)){
       printf("End of Imach with %d errors and/or %d warnings\n",nberr,nbwarn);
       fprintf(ficlog,"End of Imach with %d errors and/or warnings %d\n",nberr,nbwarn);
     }else{
       printf("End of Imach\n");
       fprintf(ficlog,"End of Imach\n");
     }
     printf("See log file on %s\n",filelog);
     /*  gettimeofday(&end_time, (struct timezone*)0);*/  /* after time */
     (void) gettimeofday(&end_time,&tzp);
     tm = *localtime(&end_time.tv_sec);
     tmg = *gmtime(&end_time.tv_sec);
     strcpy(strtend,asctime(&tm));
     printf("Local time at start %s\nLocal time at end   %s",strstart, strtend); 
     fprintf(ficlog,"Local time at start %s\nLocal time at end   %s\n",strstart, strtend); 
     printf("Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
   
     printf("Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     fprintf(ficlog,"Total time used %s\n", asc_diff_time(end_time.tv_sec -start_time.tv_sec,tmpout));
     fprintf(ficlog,"Total time was %d Sec.\n", end_time.tv_sec -start_time.tv_sec);
     /*  printf("Total time was %d uSec.\n", total_usecs);*/
   /*   if(fileappend(fichtm,optionfilehtm)){ */
     fprintf(fichtm,"<br>Local time at start %s<br>Local time at end   %s<br>",strstart, strtend);
     fclose(fichtm);
     fclose(fichtmcov);
     fclose(ficgp);
     fclose(ficlog);
     /*------ End -----------*/
   
     chdir(path);
     /*strcat(plotcmd,CHARSEPARATOR);*/
     sprintf(plotcmd,"gnuplot");
   #ifndef UNIX
     sprintf(plotcmd,"\"%sgnuplot.exe\"",pathimach);
   #endif
     if(!stat(plotcmd,&info)){
       printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       if(!stat(getenv("GNUPLOTBIN"),&info)){
         printf("Error gnuplot program not found: %s Environment GNUPLOTBIN not set.\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #ifdef UNIX
       strcpy(plotcmd,GNUPLOTPROGRAM);
       if(!stat(plotcmd,&info)){
         printf("Error gnuplot program not found: %s\n",plotcmd);fflush(stdout);
       }else
         strcpy(pplotcmd,plotcmd);
   #endif
     }else
       strcpy(pplotcmd,plotcmd);
     
     sprintf(plotcmd,"%s %s",pplotcmd, optionfilegnuplot);
     printf("Starting graphs with: %s\n",plotcmd);fflush(stdout);
   
     if((outcmd=system(plotcmd)) != 0){
       printf("\n Problem with gnuplot\n");
     }
     printf(" Wait...");
     while (z[0] != 'q') {
       /* chdir(path); */
       printf("\nType e to edit output files, g to graph again and q for exiting: ");
       scanf("%s",z);
   /*     if (z[0] == 'c') system("./imach"); */
       if (z[0] == 'e') {
         printf("Starting browser with: %s",optionfilehtm);fflush(stdout);
         system(optionfilehtm);
       }
       else if (z[0] == 'g') system(plotcmd);
       else if (z[0] == 'q') exit(0);
     }
     end:
     while (z[0] != 'q') {
       printf("\nType  q for exiting: ");
       scanf("%s",z);
     }
   }
   
   
   

Removed from v.1.46  
changed lines
  Added in v.1.118


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